Effects of resource chemistry on the composition and function of stream hyporheic biofilms.

USGS Publications Warehouse

Hall, E.K.; Besemer, K.; Kohl, L.; Preiler, C.; Reidel, K.; Schneider, T.; Wanek, W.; Battin, T.J.

2012-01-01

Fluvial ecosystems process large quantities of dissolved organic matter as it moves from the headwater streams to the sea. In particular, hyporheic sediments are centers of high biogeochemical reactivity due to their elevated residence time and high microbial biomass and activity. However, the interaction between organic matter and microbial dynamics in the hyporheic zone remains poorly understood. We evaluated how variance in resource chemistry affected the microbial community and its associated activity in experimentally grown hyporheic biofilms. To do this we fed beech leaf leachates that differed in chemical composition to a series of bioreactors filled with sediment from a sub-alpine stream. Differences in resource chemistry resulted in differences in diversity and phylogenetic origin of microbial proteins, enzyme activity, and microbial biomass stoichiometry. Specifically, increased lignin, phenolics, and manganese in a single leachate resulted in increased phenoloxidase and peroxidase activity, elevated microbial biomass carbon:nitrogen ratio, and a greater proportion of proteins of Betaproteobacteria origin. We used this model system to attempt to link microbial form (community composition and metaproteome) with function (enzyme activity) in order to better understand the mechanisms that link resource heterogeneity to ecosystem function in stream ecosystems.

Microbial dynamics and enzyme activities in tropical Andosols depending on land use and nutrient inputs

NASA Astrophysics Data System (ADS)

Mganga, Kevin; Razavi, Bahar; Kuzyakov, Yakov

2015-04-01

Microbial decomposition of soil organic matter is mediated by enzymes and is a key source of terrestrial CO2 emissions. Microbial and enzyme activities are necessary to understand soil biochemical functioning and identify changes in soil quality. However, little is known about land use and nutrients availability effects on enzyme activities and microbial processes, especially in tropical soils of Africa. This study was conducted to examine how microbial and enzyme activities differ between different land uses and nutrient availability. As Andosols of Mt. Kilimanjaro are limited by nutrient concentrations, we hypothesize that N and P additions will stimulate enzyme activity. N and P were added to soil samples (0-20 cm) representing common land use types in East Africa: (1) savannah, (2) maize fields, (3) lower montane forest, (4) coffee plantation, (5) grasslands and (6) traditional Chagga homegardens. Total CO2 efflux from soil, microbial biomass and activities of β-glucosidase, cellobiohydrolase, chitinase and phosphatase involved in C, N and P cycling, respectively was monitored for 60 days. Total CO2 production, microbial biomass and enzyme activities varied in the order forest soils > grassland soils > arable soils. Increased β-glucosidase and cellobiohydrolase activities after N addition of grassland soils suggest that microorganisms increased N uptake and utilization to produce C-acquiring enzymes. Low N concentration in all soils inhibited chitinase activity. Depending on land use, N and P addition had an inhibitory or neutral effect on phosphatase activity. We attribute this to the high P retention of Andosols and low impact of N and P on the labile P fractions. Enhanced CO2 production after P addition suggests that increased P availability could stimulate soil organic matter biodegradation in Andosols. In conclusion, land use and nutrients influenced soil enzyme activities and microbial dynamics and demonstrated the decline in soil quality after landuse change. Key words: Andosols, β-glucosidase, Cellobiohydrolase, Chitinase, Phosphatase, Mt. Kilimanjaro

Application of a weak magnetic field to improve microbial fuel cell performance.

PubMed

Tong, Zhong-Hua; Yu, Han-Qing; Li, Wen-Wei; Wang, Yun-Kun; Sun, Min; Liu, Xian-Wei; Sheng, Guo-Ping

2015-12-01

Microbial fuel cells (MFCs) have emerged as a promising technology for wastewater treatment with concomitant energy production but the performance is usually limited by low microbial activities. This has spurred intensive research interest for microbial enhancement. This study demonstrated an interesting stimulation effect of a static magnetic field (MF) on sludge-inoculated MFCs and explored into the mechanisms. The implementation of a 100-mT MF accelerated the reactor startup and led to increased electricity generation. Under the MF exposure, the activation loss of the MFC was decreased, but there was no increased secretion of redox mediators. Thus, the MF effect was mainly due to enhanced bioelectrochemical activities of anodic microorganisms, which are likely attributed to the oxidative stress and magnetohydrodynamic effects under an MF exposure. This work implies that weak MF may be applied as a simple and effective approach to stimulate microbial activities for various bioelectrochemical energy production and decontamination applications.

Effect of gamma irradiation under various atmospheres of packaging on the microbial and physicochemical properties of turmeric powder

NASA Astrophysics Data System (ADS)

Esmaeili, Saeideh; Barzegar, Mohsen; Sahari, Mohammad Ali; Berengi-Ardestani, Samira

2018-07-01

This study investigated the effect of gamma irradiation (0, 5, 10, and 15 kGy) under various atmospheres of packaging (air, N₂, and vacuum) on the microbial load and physicochemical properties of turmeric powder, including antioxidant activities, total phenolic content (TPC), color parameters, and curcuminoid content. The efficiency of irradiation in reducing microbial contamination in the samples was observed even at the lowest dose. By increasing the irradiation dose, the microbial load was not detectable. Irradiation in the presence of oxygen had synergistic effects on the extraction of curcuminoids and TPC, and increased the antioxidant activity of the methanolic extracts: highest activity was observed at 15 kGy. Generally, gamma irradiation up to the dose of 10 kGy under air atmosphere not only ensured microbial safety and desirability of turmeric powder, but also improved the extraction yield of bioactive compounds and, consequently, antioxidant activities of the samples.

Soil microbial diversity and activity linked to crop yield and quality in a dryland organic wheat production system

USDA-ARS?s Scientific Manuscript database

One of the primary goals of organic agriculture is increasing soil quality through the enhancement of soil biological diversity and activity. Greater soil microbial activity and diversity increase soil organic matter turnover and contribute to soil fertility, one of the main challenges associated wi...

Variation in microbial activity in histosols and its relationship to soil moisture.

PubMed

Tate, R L; Terry, R E

1980-08-01

Microbial biomass, dehydrogenase activity, carbon metabolism, and aerobic bacterial populations were examined in cropped and fallow Pahokee muck (a lithic medisaprist) of the Florida Everglades. Dehydrogenase activity was two- to sevenfold greater in soil cropped to St. Augustinegrass (Stenotaphrum secundatum (Walt) Kuntz) compared with uncropped soil, whereas biomass ranged from equivalence in the two soils to a threefold stimulation in the cropped soil. Biomass in soil cropped to sugarcane (Saccharum spp. L) approximated that from the grass field, whereas dehydrogenase activities of the cane soil were nearly equivalent to those of the fallow soil. Microbial biomass, dehydrogenase activity, aerobic bacterial populations, and salicylate oxidation rates all correlated with soil moisture levels. These data indicate that within the moisture ranges detected in the surface soils, increased moisture stimulated microbial activity, whereas within the soil profile where moisture ranges reached saturation, increased moisture inhibited aerobic activities and stimulated anaerobic processes.

Variation in Microbial Activity in Histosols and Its Relationship to Soil Moisture †

PubMed Central

Tate, Robert L.; Terry, Richard E.

1980-01-01

Microbial biomass, dehydrogenase activity, carbon metabolism, and aerobic bacterial populations were examined in cropped and fallow Pahokee muck (a lithic medisaprist) of the Florida Everglades. Dehydrogenase activity was two- to sevenfold greater in soil cropped to St. Augustinegrass (Stenotaphrum secundatum (Walt) Kuntz) compared with uncropped soil, whereas biomass ranged from equivalence in the two soils to a threefold stimulation in the cropped soil. Biomass in soil cropped to sugarcane (Saccharum spp. L) approximated that from the grass field, whereas dehydrogenase activities of the cane soil were nearly equivalent to those of the fallow soil. Microbial biomass, dehydrogenase activity, aerobic bacterial populations, and salicylate oxidation rates all correlated with soil moisture levels. These data indicate that within the moisture ranges detected in the surface soils, increased moisture stimulated microbial activity, whereas within the soil profile where moisture ranges reached saturation, increased moisture inhibited aerobic activities and stimulated anaerobic processes. PMID:16345610

Tracking microbial impact on crop production

USDA-ARS?s Scientific Manuscript database

One of the benefits of no-till systems is that activity of the soil microbial community increases. Producers gain an array of improvements in their production systems due to enhanced microbial functioning. For example, corn yield can increase approximately 25% with the same inputs with more microb...

Effects of heavy metal Cd pollution on microbial activities in soil.

PubMed

Shi, Weilin; Ma, Xiying

2017-12-23

Heavy metal contamination of soil occurs when heavy metals are introduced to soil through human activities, leading to the gradual deterioration of the ecology and environment. Microorganism activity reflects the intensity of various biochemical reactions in soil, and changes in it reflect the level of heavy metal pollution affecting the soil. The effects were studied of heavy metal Cd on the microbial activity of soil at different concentrations by investigating the respiratory intensity, urease activity, and catalase activity in forest soil and garden soil. The results showed that the respiratory intensity, urease and catalase activities in the garden soil were all higher than in the forest soil. Cd has obvious inhibitory effects on microbial activities. The three parameters exhibited a downward trend with increasing concentrations of Cd. Catalase activity increased when the mass concentration of Cd reached 1.0 mg/kg, indicating that low concentrations of Cd can promote the activity of some microorganisms. Respiratory intensity and urease activity also increased when the concentration reached 10.0 mg/kg, showing that respiratory intensity and urease activity have strong response mechanisms to adverse conditions. The effective state of Cd in soil, as well as inhibition of microbial activity, decreased with incubation time.

[Effects of different water and fertilizer supply on cucumber soil nutrient content, enzyme activity, and microbial diversity].

PubMed

Wei, Ze-Xiu; Liang, Yin-Li; Inoue, Mitsuhiro; Zhou, Mao-Juan; Huang, Mao-Lin; Gu, Jian-Feng; Wu, Yan

2009-07-01

With cucumber (Cucumis sativus L.) variety Jinyou 1 as test material, a greenhouse experiment was conducted to study the effects of different water and fertilizer supply on the cucumber soil nutrient content, enzyme activity, and microbial diversity. Three water regimes (50%-60%, 70%-80%, and 90%-100% soil relative moisture content) and two fertilization practices (600 kg N x hm(-2) + 420 kg P2O5 x hm(-2) and 420 kg N x hm(-2) + 294 kg P2O5 x hm(-2)) were designed. The increase of water and fertilizer supply benefited the increase of soil available P content and sucrase activity. Increasing fertilization rate increased soil NH(4+)-N content but decreased soil protease activity, and increasing soil relative moisture content decreased the soil NH(4+)-N content and urease activity. Soil microbial diversity had no significant correlations with soil nutrient contents, but significantly positively correlated with soil urease activity and negatively correlated with soil sucrase activity. Among the treatments, the treatment 70%-80% soil relative moisture content + 600 kg N x hm(-2) and 420 kg P2O5 x hm(-2) had the highest soil nutrient contents, soil urease, sucrase, and phosphatase activities, and soil microbial diversity and evenness, being the best in soil potential productivity.

LABORATORY AND FIELD RESULTS LINKING HIGH BULK CONDUCTIVITIES TO THE MICROBIAL DEGRADATION OF PETROLEUM HYDROCARBONS

EPA Science Inventory

Diesel contaminated layer (i.e. 32-45 cm) was the most geoelectrically conductive and showed the peak microbial activity. Below the saturated zone microbial enhanced mineral weathering increases the ionic concentration of pore fluids, leading to increased bulk electrical conducit...

Altered precipitation regime affects the function and composition of soil microbial communities on multiple time scales.

PubMed

Zeglin, L H; Bottomley, P J; Jumpponen, A; Rice, C W; Arango, M; Lindsley, A; McGowan, A; Mfombep, P; Myrold, D D

2013-10-01

Climate change models predict that future precipitation patterns will entail lower-frequency but larger rainfall events, increasing the duration of dry soil conditions. Resulting shifts in microbial C cycling activity could affect soil C storage. Further, microbial response to rainfall events may be constrained by the physiological or nutrient limitation stress of extended drought periods; thus seasonal or multiannual precipitation regimes may influence microbial activity following soil wet-up. We quantified rainfall-driven dynamics of microbial processes that affect soil C loss and retention, and microbial community composition, in soils from a long-term (14-year) field experiment contrasting "Ambient" and "Altered" (extended intervals between rainfalls) precipitation regimes. We collected soil before, the day following, and five days following 2.5-cm rainfall events during both moist and dry periods (June and September 2011; soil water potential = -0.01 and -0.83 MPa, respectively), and measured microbial respiration, microbial biomass, organic matter decomposition potential (extracellular enzyme activities), and microbial community composition (phospholipid fatty acids). The equivalent rainfall events caused equivalent microbial respiration responses in both treatments. In contrast, microbial biomass was higher and increased after rainfall in the Altered treatment soils only, thus microbial C use efficiency (CUE) was higher in Altered than Ambient treatments (0.70 +/- 0.03 > 0.46 +/- 0.10). CUE was also higher in dry (September) soils. C-acquiring enzyme activities (beta-glucosidase, cellobiohydrolase, and phenol oxidase) increased after rainfall in moist (June), but not dry (September) soils. Both microbial biomass C:N ratios and fungal:bacterial ratios were higher at lower soil water contents, suggesting a functional and/or population-level shift in the microbiota at low soil water contents, and microbial community composition also differed following wet-up and between seasons and treatments. Overall, microbial activity may directly (C respiration) and indirectly (enzyme potential) reduce soil organic matter pools less in drier soils, and soil C sequestration potential (CUE) may be higher in soils with a history of extended dry periods between rainfall events. The implications include that soil C loss may be reduced or compensated for via different mechanisms at varying time scales, and that microbial taxa with better stress tolerance or growth efficiency may be associated with these functional shifts.

Microbial Activity in Organic Soils as Affected by Soil Depth and Crop †

PubMed Central

Tate, Robert L.

1979-01-01

The microbial activity of Pahokee muck, a lithic medisaprist, and the effect of various environmental factors, such as position in the profile and type of plant cover, were examined. Catabolic activity for [7-14C]salicylic acid, [1,4-14C]succinate, and [1,2-14C]acetate remained reasonably constant in surface (0 to 10 cm) soil samples from a fallow (bare) field from late in the wet season (May to September) through January. Late in January, the microbial activity toward all three compounds decreased approximately 50%. The microbial activity of the soil decreased with increasing depth of soil. Salicylate catabolism was the most sensitive to increasing moisture deep in the soil profile. At the end of the wet season, a 90% decrease in activity between the surface and the 60- to 70-cm depth occurred. Catabolism of acetate and succinate decreased approximately 75% in the same samples. Little effect of crop was observed. Variation in the microbial activity, as measured by the catabolism of labeled acetate, salicylate, or succinate, was not significant between a sugarcane (Saccharum officinarum L.) field and a fallow field. The activity with acetate was insignificantly different in a St. Augustine grass [Stenotaphrum secundatum (Walt) Kuntz] field, whereas the catabolism of the remaining substrates was elevated in the grass field. These results indicate that the total carbon evolved from the different levels of the soil profile by the microbial community oxidizing the soil organic matter decreased as the depth of the soil column increased. However, correction of the amount of carbon yielded at each level for the bulk density of that level reveals that the microbial contribution to the soil subsidence is approximately equivalent throughout the soil profile above the water table. PMID:16345393

Microbial activity in organic soils as affected by soil depth and crop.

PubMed

Tate, R L

1979-06-01

The microbial activity of Pahokee muck, a lithic medisaprist, and the effect of various environmental factors, such as position in the profile and type of plant cover, were examined. Catabolic activity for [7-C]salicylic acid, [1,4-C]succinate, and [1,2-C]acetate remained reasonably constant in surface (0 to 10 cm) soil samples from a fallow (bare) field from late in the wet season (May to September) through January. Late in January, the microbial activity toward all three compounds decreased approximately 50%. The microbial activity of the soil decreased with increasing depth of soil. Salicylate catabolism was the most sensitive to increasing moisture deep in the soil profile. At the end of the wet season, a 90% decrease in activity between the surface and the 60- to 70-cm depth occurred. Catabolism of acetate and succinate decreased approximately 75% in the same samples. Little effect of crop was observed. Variation in the microbial activity, as measured by the catabolism of labeled acetate, salicylate, or succinate, was not significant between a sugarcane (Saccharum officinarum L.) field and a fallow field. The activity with acetate was insignificantly different in a St. Augustine grass [Stenotaphrum secundatum (Walt) Kuntz] field, whereas the catabolism of the remaining substrates was elevated in the grass field. These results indicate that the total carbon evolved from the different levels of the soil profile by the microbial community oxidizing the soil organic matter decreased as the depth of the soil column increased. However, correction of the amount of carbon yielded at each level for the bulk density of that level reveals that the microbial contribution to the soil subsidence is approximately equivalent throughout the soil profile above the water table.

Microbial Growth and Carbon Use Efficiency in the Rhizosphere and Root-Free Soil

PubMed Central

Blagodatskaya, Evgenia; Blagodatsky, Sergey; Anderson, Traute-Heidi; Kuzyakov, Yakov

2014-01-01

Plant-microbial interactions alter C and N balance in the rhizosphere and affect the microbial carbon use efficiency (CUE)–the fundamental characteristic of microbial metabolism. Estimation of CUE in microbial hotspots with high dynamics of activity and changes of microbial physiological state from dormancy to activity is a challenge in soil microbiology. We analyzed respiratory activity, microbial DNA content and CUE by manipulation the C and nutrients availability in the soil under Beta vulgaris. All measurements were done in root-free and rhizosphere soil under steady-state conditions and during microbial growth induced by addition of glucose. Microorganisms in the rhizosphere and root-free soil differed in their CUE dynamics due to varying time delays between respiration burst and DNA increase. Constant CUE in an exponentially-growing microbial community in rhizosphere demonstrated the balanced growth. In contrast, the CUE in the root-free soil increased more than three times at the end of exponential growth and was 1.5 times higher than in the rhizosphere. Plants alter the dynamics of microbial CUE by balancing the catabolic and anabolic processes, which were decoupled in the root-free soil. The effects of N and C availability on CUE in rhizosphere and root-free soil are discussed. PMID:24722409

Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank

PubMed Central

Leite, Márcio F. A.; Pan, Yao; Bloem, Jaap; Berge, Hein ten; Kuramae, Eiko E.

2017-01-01

Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates. We considered the microbial soil DNA as the microbial seedbank. High C/N ratio favored fungal presence, while low C/N favored dominance of bacterial populations. Our results suggest that organic amendments shape the soil microbial community structure through a feedback mechanism by which microbial activity responds to changing organic inputs and rearranges composition of the microbial seedbank. We hypothesize that the microbial seedbank composition responds to changing organic inputs according to the resistance and resilience of individual species, while changes in microbial activity may result in increases or decreases in availability of various soil nutrients that affect plant nutrient uptake. PMID:28198425

Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank.

PubMed

Leite, Márcio F A; Pan, Yao; Bloem, Jaap; Berge, Hein Ten; Kuramae, Eiko E

2017-02-15

Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates. We considered the microbial soil DNA as the microbial seedbank. High C/N ratio favored fungal presence, while low C/N favored dominance of bacterial populations. Our results suggest that organic amendments shape the soil microbial community structure through a feedback mechanism by which microbial activity responds to changing organic inputs and rearranges composition of the microbial seedbank. We hypothesize that the microbial seedbank composition responds to changing organic inputs according to the resistance and resilience of individual species, while changes in microbial activity may result in increases or decreases in availability of various soil nutrients that affect plant nutrient uptake.

Native soil organic matter conditions the response of microbial communities to organic inputs with different stability

NASA Astrophysics Data System (ADS)

Yanardaǧ, Ibrahim H.; Zornoza, Raúl; Bastida, Felipe; Büyükkiliç-Yanardaǧ, Asuman; Acosta, Jose A.; García, Carlos; Faz, Ángel; Mermut, Ahmet R.

2017-04-01

The response of soil microbial communities from soils with different soil organic matter (SOM) content to organic inputs with different stability is still poorly understood. Thus, an incubation experiment was designed to study how the addition of pig slurry (PS), its manure (M) and its biochar (BC) affect soil microbial community and activity in three soils differing in SOM content (Regosol, Luvisol and Kastanozem). The evolution of different C and N fractions, microbial biomass C and N, enzyme activities and microbial community structure by the use of phospholipid fatty acid (PLFA) analysis was assessed for 60 days. Results showed that the different amendments had different effect on microbial properties depending on the soil type. The addition of M caused the highest increase in all microbial properties in the three soils, followed by PS. These changes were more intense in the soil with the lowest SOM (Regosol). The addition of M and PS caused changes in the microbial community structure in all soils, which were more related to the presence of available sources of N than to the labile fractions of C. The addition of BC was followed by increases in the proportions of fungi and Gram positive bacteria in the Regosol, while enhanced the proportion of actinobacteria in all soil types, related to increments in pH and soil C recalcitrance. Thus, native SOM determined the response of microbial communities to external inputs with different stability, soils with low SOM being more prone to increase microbial biomass and activity and change microbial community structure.

Effect of magnesium oxide nanoparticles on microbial diversity and removal performance of sequencing batch reactor.

PubMed

Ma, Bingrui; Yu, Naling; Han, Yuetong; Gao, Mengchun; Wang, Sen; Li, Shanshan; Guo, Liang; She, Zonglian; Zhao, Yangguo; Jin, Chunji; Gao, Feng

2018-06-13

The performance, microbial enzymatic activity and microbial community of a sequencing batch reactor (SBR) have been explored under magnesium oxide nanoparticles (MgO NPs) stress. The NH 4 + -N removal efficiency kept relatively stable during the whole operational process. The MgO NPs at 30-60 mg/L slightly restrained the removal of chemical oxygen demand (COD), and the presence of MgO NPs also affected the denitrification and phosphorus removal. The specific oxygen uptake rate, nitrifying and denitrifying rates, phosphorus removal rate, and microbial enzymatic activities distinctly varied with the increase of MgO NPs concentration. The appearance of MgO NPs promoted more reactive oxygen species generation and lactate dehydrogenase leakage from activated sludge, suggesting that MgO NPs had obvious toxicity to activated sludge in the SBR. The protein and polysaccharide contents of extracellular polymeric substances from activated sludge increased with the increase of MgO NPs concentration. The microbial richness and diversity at different MgO NPs concentrations obviously varied at the phylum, class and genus levels due to the biological toxicity of MgO NPs. Copyright © 2018 Elsevier Ltd. All rights reserved.

Effects of biochar amendments on soil microbial biomass and activity.

PubMed

Zhang, H; Voroney, R P; Price, G W

2014-11-01

Environmental benefits reported in the literature of using biochar as a soil amendment are generally increased microbial activity and reduced greenhouse gas (GHG) emissions. This study determined the effects of amendment with biomass feedstocks (spent coffee grounds, wood pellets, and horse bedding compost) and that of biochars (700°C) produced from these feedstocks on soil microbial biomass (C and N) and activity. Soils were amended with these substrates at 0.75% by weight and incubated for up to 175 d under laboratory conditions. Biochar residual effects on soil microbial activity were also studied by amending these soils with either ammonium nitrate (NHNO, 35 mg N kg) or with glucose (864 mg C kg) plus NHNO. Soil microbial biomass C and N, net N mineralization, and CO, NO, and CH emissions were measured. Amendment with biomass feedstocks significantly increased soil microbial biomass and activity, whereas amendment with the biochars had no significant effect. Also, biochar amendment had no significant effect on either net N mineralization or NO and CH emissions from soil. These results indicate that production of biochars at this high temperature eliminated potential substrates. Microbial biomass C in biochar-amended and unamended soils was not significantly different following additions of NHNO or glucose plus NHNO, suggesting that microbial access to otherwise labile C and N was not affected. This study shows that biochars produced at 700°C, regardless of feedstock source, do not enhance soil microbial biomass or activity. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Effects of Jet Fuel Spills on the Microbial Community of Soil †

PubMed Central

Song, Hong-Gyu; Bartha, Richard

1990-01-01

Hydrocarbon residues, microbial numbers, and microbial activity were measured and correlated in loam soil contaminated by jet fuel spills resulting in 50 and 135 mg of hydrocarbon g of soil−1. Contaminated soil was incubated at 27°C either as well-aerated surface soil or as poorly aerated subsurface soil. In the former case, the effects of bioremediation treatment on residues, microbial numbers, and microbial activity were also assessed. Hydrocarbon residues were measured by quantitative gas chromatography. Enumerations included direct counts of metabolically active bacteria, measurement of mycelial length, plate counts of aerobic heterotrophs, and most probable numbers of hydrocarbon degraders. Activity was assessed by fluorescein diacetate (FDA) hydrolysis. Jet fuel disappeared much more rapidly from surface soil than it did from subsurface soil. In surface soil, microbial numbers and mycelial length were increased by 2 to 2.5 orders of magnitude as a result of jet fuel contamination alone and by 3 to 4 orders of magnitude as a result of the combination of jet fuel contamination and bioremediation. FDA hydrolysis was stimulated by jet fuel and bioremediation, but was inhibited by jet fuel alone. The latter was traced to an inhibition of the FDA assay by jet fuel biodegradation products. In subsurface soil, oxygen limitation strongly attenuated microbial responses to jet fuel. An increase in the most probable numbers of hydrocarbon degraders was accompanied by a decline in other aerobic heterotrophs, so that total plate counts changed little. The correlations between hydrocarbon residues, microbial numbers, and microbial activity help in elucidating microbial contributions to jet fuel elimination from soil. PMID:16348138

Elevated CO2 benefits the soil microenvironment in the rhizosphere of Robinia pseudoacacia L. seedlings in Cd- and Pb-contaminated soils.

PubMed

Huang, Shuping; Jia, Xia; Zhao, Yonghua; Bai, Bo; Chang, Yafei

2017-02-01

Soil contamination by heavy metals in combination with elevated atmospheric CO 2 has important effects on the rhizosphere microenvironment by influencing plant growth. Here, we investigated the response of the R. pseudoacacia rhizosphere microenvironment to elevated CO 2 in combination with cadmium (Cd)- and lead (Pb)-contamination. Organic compounds (total soluble sugars, soluble phenolic acids, free amino acids, and organic acids), microbial abundance and activity, and enzyme activity (urease, dehydrogenase, invertase, and β-glucosidase) in rhizosphere soils increased significantly (p < 0.05) under elevated CO 2 relative to ambient CO 2 ; however, l-asparaginase activity decreased. Addionally, elevated CO 2 alone affected soil microbial community in the rhizosphere. Heavy metals alone resulted in an increase in total soluble sugars, free amino acids, and organic acids, a decrease in phenolic acids, microbial populations and biomass, and enzyme activity, and a change in microbial community in rhizosphere soils. Elevated CO 2 led to an increase in organic compounds, microbial populations, biomass, and activity, and enzyme activity (except for l-asparaginase), and changes in microbial community under Cd, Pb, or Cd + Pb treatments relative to ambient CO 2 . In addition, elevated CO 2 significantly (p < 0.05) enhanced the removal ratio of Cd and Pb in rhizosphere soils. Overall, elevated CO 2 benefited the rhizosphere microenvironment of R. pseudoacacia seedlings under heavy metal stress, which suggests that increased atmospheric CO 2 concentrations could have positive effects on soil fertility and rhizosphere microenvironment under heavy metals. Copyright © 2016 Elsevier Ltd. All rights reserved.

Microbial Activity and Silica Degradation in Rice Straw

NASA Astrophysics Data System (ADS)

Kim, Esther Jin-kyung

Abundantly available agricultural residues like rice straw have the potential to be feedstocks for bioethanol production. Developing optimized conditions for rice straw deconstruction is a key step toward utilizing the biomass to its full potential. One challenge associated with conversion of rice straw to bioenergy is its high silica content as high silica erodes machinery. Another obstacle is the availability of enzymes that hydrolyze polymers in rice straw under industrially relevant conditions. Microbial communities that colonize compost may be a source of enzymes for bioconversion of lignocellulose to products because composting systems operate under thermophilic and high solids conditions that have been shown to be commercially relevant. Compost microbial communities enriched on rice straw could provide insight into a more targeted source of enzymes for the breakdown of rice straw polysaccharides and silica. Because rice straw is low in nitrogen it is important to understand the impact of nitrogen concentrations on the production of enzyme activity by the microbial community. This study aims to address this issue by developing a method to measure microbial silica-degrading activity and measure the effect of nitrogen amendment to rice straw on microbial activity and extracted enzyme activity during a high-solids, thermophilic incubation. An assay was developed to measure silica-degrading enzyme or silicase activity. This process included identifying methods of enzyme extraction from rice straw, identifying a model substrate for the assay, and optimizing measurement techniques. Rice straw incubations were conducted with five different levels of nitrogen added to the biomass. Microbial activity was measured by respiration and enzyme activity. A microbial community analysis was performed to understand the shift in community structure with different treatments. With increased levels of nitrogen, respiration and cellulose and hemicellulose degrading activity increased. Silicase activity did not change across nitrogen treatments despite a shift in microbial community with varied nitrogen concentration. Samples treated with different nitrogen concentrations had similar levels of diversity, however the microbial community composition differed with added nitrogen. The results demonstrated that adding nitrogen to rice straw during thermophilic decomposition nurtured a more active microbial community and promoted enzyme secretion thus improving the ability to discover enzymes for rice straw deconstruction. These results can inform future experiments for cultivating a unique, thriving compost-derived microbial community that can successfully decompose rice straw. Understanding the silicase activity of microorganisms may alleviate the challenges associated with silica in various feedstocks.

Elevated atmospheric CO2 increases microbial growth rates and enzymes activity in soil

NASA Astrophysics Data System (ADS)

Blagodatskaya, Evgenia; Blagodatsky, Sergey; Dorodnikov, Maxim; Kuzyakov, Yakov

2010-05-01

Increasing the belowground translocation of assimilated carbon by plants grown under elevated CO2 can cause a shift in the structure and activity of the microbial community responsible for the turnover of organic matter in soil. We investigated the long-term effect of elevated CO2 in the atmosphere on microbial biomass and specific growth rates in root-free and rhizosphere soil. The experiments were conducted under two free air carbon dioxide enrichment (FACE) systems: in Hohenheim and Braunschweig, as well as in the intensively managed forest mesocosm of the Biosphere 2 Laboratory (B2L) in Oracle, AZ. Specific microbial growth rates (μ) were determined using the substrate-induced respiration response after glucose and/or yeast extract addition to the soil. We evaluated the effect of elevated CO2 on b-glucosidase, chitinase, phosphatase, and sulfatase to estimate the potential enzyme activity after soil amendment with glucose and nutrients. For B2L and both FACE systems, up to 58% higher μ were observed under elevated vs. ambient CO2, depending on site, plant species and N fertilization. The μ-values increased linearly with atmospheric CO2 concentration at all three sites. The effect of elevated CO2 on rhizosphere microorganisms was plant dependent and increased for: Brassica napus=Triticum aestivum

[Effects of altitudes on soil microbial biomass and enzyme activity in alpine-gorge regions.

PubMed

Cao, Rui; Wu, Fu Zhong; Yang, Wan Qin; Xu, Zhen Feng; Tani, Bo; Wang, Bin; Li, Jun; Chang, Chen Hui

2016-04-22

In order to understand the variations of soil microbial biomass and soil enzyme activities with the change of altitude, a field incubation was conducted in dry valley, ecotone between dry valley and mountain forest, subalpine coniferous forest, alpine forest and alpine meadow from 1563 m to 3994 m of altitude in the alpine-gorge region of western Sichuan. The microbial biomass carbon and nitrogen, and the activities of invertase, urease and acid phosphorus were measured in both soil organic layer and mineral soil layer. Both the soil microbial biomass and soil enzyme activities showed the similar tendency in soil organic layer. They increased from 2158 m to 3028 m, then decreased to the lowest value at 3593 m, and thereafter increased until 3994 m in the alpine-gorge region. In contrast, the soil microbial biomass and soil enzyme activities in mineral soil layer showed the trends as, the subalpine forest at 3028 m > alpine meadow at 3994 m > montane forest ecotone at 2158 m > alpine forest at 3593 m > dry valley at 1563 m. Regardless of altitudes, soil microbial biomass and soil enzyme activities were significantly higher in soil organic layer than in mineral soil layer. The soil microbial biomass was significantly positively correlated with the activities of the measured soil enzymes. Moreover, both the soil microbial biomass and soil enzyme activities were significantly positively correlated with soil water content, organic carbon, and total nitrogen. The activity of soil invertase was significantly positively correlated with soil phosphorus content, and the soil acid phosphatase was so with soil phosphorus content and soil temperature. In brief, changes in vegetation and other environmental factors resulting from altitude change might have strong effects on soil biochemical properties in the alpine-gorge region.

Decreases in Soil Moisture and Organic Matter Quality Suppress Microbial Decomposition Following a Boreal Forest Fire

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holden, Sandra R.; Berhe, Asmeret A.; Treseder, Kathleen K.

Climate warming is projected to increase the frequency and severity of wildfires in boreal forests, and increased wildfire activity may alter the large soil carbon (C) stocks in boreal forests. Changes in boreal soil C stocks that result from increased wildfire activity will be regulated in part by the response of microbial decomposition to fire, but post-fire changes in microbial decomposition are poorly understood. Here, we investigate the response of microbial decomposition to a boreal forest fire in interior Alaska and test the mechanisms that control post-fire changes in microbial decomposition. We used a reciprocal transplant between a recently burnedmore » boreal forest stand and a late successional boreal forest stand to test how post-fire changes in abiotic conditions, soil organic matter (SOM) composition, and soil microbial communities influence microbial decomposition. We found that SOM decomposing at the burned site lost 30.9% less mass over two years than SOM decomposing at the unburned site, indicating that post-fire changes in abiotic conditions suppress microbial decomposition. Our results suggest that moisture availability is one abiotic factor that constrains microbial decomposition in recently burned forests. In addition, we observed that burned SOM decomposed more slowly than unburned SOM, but the exact nature of SOM changes in the recently burned stand are unclear. Finally, we found no evidence that post-fire changes in soil microbial community composition significantly affect decomposition. Taken together, our study has demonstrated that boreal forest fires can suppress microbial decomposition due to post-fire changes in abiotic factors and the composition of SOM. Models that predict the consequences of increased wildfires for C storage in boreal forests may increase their predictive power by incorporating the observed negative response of microbial decomposition to boreal wildfires.« less

Why does carbon increase in highly weathered soil under no-till upon lime and gypsum use?

PubMed

Inagaki, Thiago Massao; de Moraes Sá, João Carlos; Caires, Eduardo Fávero; Gonçalves, Daniel Ruiz Potma

2017-12-01

Field experiments have been used to explain how soil organic carbon (SOC) dynamics is affected by lime and gypsum applications, however, how SOC storage occurs is still debatable. We hypothesized that although many studies conclude that Ca-based soil amendments such as lime and gypsum may lead to SOC depletion due to the enhancement of microbial activity, the same does not occur under conservation agriculture conditions. Thus, the objective of this study was to elucidate the effects of lime and gypsum applications on soil microbial activity and SOC stocks in a no-till field and in a laboratory incubation study simulating no-till conditions. The field experiment was established in 1998 in a clayey Oxisol in southern Brazil following a completely randomized blocks design with a split-plot arrangement and three replications. Lime and gypsum were surface applied in 1998 and reapplied in 2013. Undisturbed soil samples were collected before the treatments reapplications, and one year after. The incubation experiment was carried out during 16months using these samples adding crop residues on the soil surface to simulate no-till field conditions. Lime and gypsum applications significantly increased the labile SOC stocks, microbial activity and soil fertility attributes in both field and laboratory experiments. Although the microbial activity was increased, no depletion of SOC stocks was observed in both experiments. Positive correlations were observed between microbial activity increase and SOC gains. Labile SOC and Ca 2+ content increase leads to forming complex with mineral soil fractions. Gypsum applications performed a higher influence on labile SOC pools in the field than in the laboratory experiment, which may be related to the presence of active root system in the soil profile. We conclude that incubation experiments using lime and gypsum in undisturbed samples confirm that soil microbial activity increase does not deplete SOC stocks under conservation agriculture. Copyright © 2017 Elsevier B.V. All rights reserved.

[Effects of exogenous glucose and starch on soil carbon metabolism of root zone and root function in potted sweet cherry].

PubMed

Zhou, Wen-jie; Zhang, Peng; Qin, Si-jun; Lyu, De-guo

2015-11-01

One-year-old potted sweet cheery trees were treated with 4 g · kg(-1) exogenous glucose or starch and with non-addition of exogenous carbon as the control for up to 60 days. Soil of root zone was sampled to analyze soil microbial biomass carbon, activities of invertase and amylase and microbial community functional diversity during the 60-day treatment, and roots were sampled for analysis of root respiratory rate, respiratory pathways and root viability after treatment for 30 days. Results showed that the invertase activity and the microbial biomass carbon initially increased and decreased subsequently, with the maxima which were 14.0% and 13.1% higher in the glucose treatment than in the control treatment appeared after 15 and 7 days of treatments, respectively. Soil organic matter content increased first then decreased and finally moderately increased again. Amylase activity was 7.5-fold higher in the starch treatment than in the control treatment after 15-day treatment. Soil microbial biomass carbon was higher in the starch treatment than in the control treatment except after 7-day treatment. Soil organic matter content initially increased and then decreased, but it was still 19.8% higher than in the control after 60-day treatment. BIOLOG results showed that the maximum average well color development (AWCD) value and microbial activity appeared after 15-day treatment in the following order: starch>glucose>control. After 30-day treatment, glucose treatment resulted in a significant increase in the soil microbial utilization of carbohydrates, carboxylic acid, amino acids, phenolic acids and amines, and starch treatment significantly increased the soil microbial utilization of carbohydrates, carboxylic acid, polymers and phenolic acids. After 30-day treatment, the total root respiratory rate and root viability were 21.4%, 19.4% and 65.5%, 37.0% higher in glucose treatment than in the control and starch treatments, respectively. These results indicated exogenous glucose and starch affected soil carbon metabolism and enhanced soil microbial activity, the root respiratory rate and root viability.

Microbial response of an acid forest soil to experimental soil warming

Treesearch

S.S. Arnold; I.J. Fernandez; L.E. Rustad; L.M. Zibilske

1999-01-01

Effects of increased soil temperature on soil microbial biomass and dehydrogenase activity were examined on organic (O) horizon material in a low-elevation spruce-fir ecosystem. Soil temperature was maintained at 5 °C above ambient during the growing season in the experimental plots, and soil temperature, moisture, microbial biomass, and dehydrogenase activity were...

Endophytic fungus Phomopsis liquidambari and different doses of N-fertilizer alter microbial community structure and function in rhizosphere of rice

PubMed Central

Siddikee, Md. Ashaduzzaman; Zereen, Mst Israt; Li, Cai-Feng; Dai, Chuan-Chao

2016-01-01

Microbial community structure and functions of rhizosphere soil of rice were investigated after applying low and high doses of nitrogenous fertilizer and Phomopsis liquidambari. Average well color development, substrate richness, catabolic diversity and soil enzymes activities varied after applying N-fertilizer and P. liquidambari and were greater in P. liquidambari treated soil than only N-fertilization. Multivariate analysis distinctly separated the catabolic and enzymes activity profile which statistically proved alteration of microbial functional diversity. Nitrogen fertilizer altered microbial community structure revealed by the increased content of total PLFAs, specific subgroup marker PLFAs except fungal PLFAs and by the decreased ratio of G+/G−, sat/monunsat, iso/anteiso, F/B except trans/cis while P. liquidambari inoculation enhanced N-fertilization effect except increased fungal PLFA and decreased trans/cis. PCA using identified marker PLFAs revealed definite discrimination among the treatments which further statistically confirmed structural changed of microbial community. Nitrogenase activity representative of N-fixing community decreased in N-fertilizer treatment while P. liquidambari inoculation increased. In short, application of P. liquidambari with low doses of N-fertilizer improved rice growth and reduced N-fertilizer requirement by increasing enzymes activities involved in C, N and P cycling, structural and functional diversity of microbes, nitrogenase activity involved in N2 fixation and accumulation of total-N. PMID:27596935

Citrate and malonate increase microbial activity and alter microbial community composition in uncontaminated and diesel-contaminated soil microcosms

NASA Astrophysics Data System (ADS)

Martin, Belinda C.; George, Suman J.; Price, Charles A.; Shahsavari, Esmaeil; Ball, Andrew S.; Tibbett, Mark; Ryan, Megan H.

2016-09-01

Petroleum hydrocarbons (PHCs) are among the most prevalent sources of environmental contamination. It has been hypothesized that plant root exudation of low molecular weight organic acid anions (carboxylates) may aid degradation of PHCs by stimulating heterotrophic microbial activity. To test their potential implication for bioremediation, we applied two commonly exuded carboxylates (citrate and malonate) to uncontaminated and diesel-contaminated microcosms (10 000 mg kg-1; aged 40 days) and determined their impact on the microbial community and PHC degradation. Every 48 h for 18 days, soil received 5 µmol g-1 of (i) citrate, (ii) malonate, (iii) citrate + malonate or (iv) water. Microbial activity was measured daily as the flux of CO2. After 18 days, changes in the microbial community were assessed by a community-level physiological profile (CLPP) and 16S rRNA bacterial community profiles determined by denaturing gradient gel electrophoresis (DGGE). Saturated PHCs remaining in the soil were assessed by gas chromatography-mass spectrometry (GC-MS). Cumulative soil respiration increased 4- to 6-fold with the addition of carboxylates, while diesel contamination resulted in a small, but similar, increase across all carboxylate treatments. The addition of carboxylates resulted in distinct changes to the microbial community in both contaminated and uncontaminated soils but only a small increase in the biodegradation of saturated PHCs as measured by the n-C17 : pristane biomarker. We conclude that while the addition of citrate and malonate had little direct effect on the biodegradation of saturated hydrocarbons present in diesel, their effect on the microbial community leads us to suggest further studies using a variety of soils and organic acids, and linked to in situ studies of plants, to investigate the role of carboxylates in microbial community dynamics.

Soil C and N availability determine the priming effect: microbial N mining and stoichiometric decomposition theories.

PubMed

Chen, Ruirui; Senbayram, Mehmet; Blagodatsky, Sergey; Myachina, Olga; Dittert, Klaus; Lin, Xiangui; Blagodatskaya, Evgenia; Kuzyakov, Yakov

2014-07-01

The increasing input of anthropogenically derived nitrogen (N) to ecosystems raises a crucial question: how does available N modify the decomposer community and thus affects the mineralization of soil organic matter (SOM). Moreover, N input modifies the priming effect (PE), that is, the effect of fresh organics on the microbial decomposition of SOM. We studied the interactive effects of C and N on SOM mineralization (by natural (13) C labelling adding C4 -sucrose or C4 -maize straw to C3 -soil) in relation to microbial growth kinetics and to the activities of five hydrolytic enzymes. This encompasses the groups of parameters governing two mechanisms of priming effects - microbial N mining and stoichiometric decomposition theories. In sole C treatments, positive PE was accompanied by a decrease in specific microbial growth rates, confirming a greater contribution of K-strategists to the decomposition of native SOM. Sucrose addition with N significantly accelerated mineralization of native SOM, whereas mineral N added with plant residues accelerated decomposition of plant residues. This supports the microbial mining theory in terms of N limitation. Sucrose addition with N was accompanied by accelerated microbial growth, increased activities of β-glucosidase and cellobiohydrolase, and decreased activities of xylanase and leucine amino peptidase. This indicated an increased contribution of r-strategists to the PE and to decomposition of cellulose but the decreased hemicellulolytic and proteolytic activities. Thus, the acceleration of the C cycle was primed by exogenous organic C and was controlled by N. This confirms the stoichiometric decomposition theory. Both K- and r-strategists were beneficial for priming effects, with an increasing contribution of K-selected species under N limitation. Thus, the priming phenomenon described in 'microbial N mining' theory can be ascribed to K-strategists. In contrast, 'stoichiometric decomposition' theory, that is, accelerated OM mineralization due to balanced microbial growth, is explained by domination of r-strategists. © 2013 John Wiley & Sons Ltd.

Soil C and N availability determine the priming effect: microbial N mining and stoichiometric decomposition theories

NASA Astrophysics Data System (ADS)

Chen, Ruirui; Senbayram, Mehmet; Blagodatsky, Sergey; Dittert, Klaus; Lin, Xiangui; Blagodatskaya, Evgenia; Kuzyakov, Yakov

2014-05-01

The increasing input of anthropogenically derived nitrogen (N) to ecosystems raises a crucial question: how does available N modify the decomposer community and thus affects the mineralization of soil organic matter (SOM). Moreover, N input modifies the priming effect (PE), that is, the effect of fresh organics on the microbial decomposition of SOM. We studied the interactive effects of C and N on SOM mineralization (by natural 13C labelling adding C4-sucrose or C4-maize straw to C3-soil) in relation to microbial growth kinetics and to the activities of five hydrolytic enzymes. This encompasses the groups of parameters governing two mechanisms of priming effects - microbial N mining and stoichiometric decomposition theories. In sole C treatments, positive PE was accompanied by a decrease in specific microbial growth rates, confirming a greater contribution of K-strategists to the decomposition of native SOM. Sucrose addition with N significantly accelerated mineralization of native SOM, whereas mineral N added with plant residues accelerated decomposition of plant residues. This supports the microbial mining theory in terms of N limitation. Sucrose addition with N was accompanied by accelerated microbial growth, increased activities of β-glucosidase and cellobiohydrolase, and decreased activities of xylanase and leucine amino peptidase. This indicated an increased contribution of r-strategists to the PE and to decomposition of cellulose but the decreased hemicellulolytic and proteolytic activities. Thus, the acceleration of the C cycle was primed by exogenous organic C and was controlled by N. This confirms the stoichiometric decomposition theory. Both K- and r-strategists were beneficial for priming effects, with an increasing contribution of K-selected species under N limitation. Thus, the priming phenomenon described in 'microbial N mining' theory can be ascribed to K-strategists. In contrast, 'stoichiometric decomposition' theory, that is, accelerated OM mineralization due to balanced microbial growth, is explained by domination of r-strategists.

Soil Microbial Community Structure and Metabolic Activity of Pinus elliottii Plantations across Different Stand Ages in a Subtropical Area.

PubMed

Wu, Zeyan; Haack, Stacey Elizabeth; Lin, Wenxiong; Li, Bailian; Wu, Linkun; Fang, Changxun; Zhang, Zhixing

2015-01-01

Soil microbes play an essential role in the forest ecosystem as an active component. This study examined the hypothesis that soil microbial community structure and metabolic activity would vary with the increasing stand ages in long-term pure plantations of Pinus elliottii. The phospholipid fatty acids (PLFA) combined with community level physiological profiles (CLPP) method was used to assess these characteristics in the rhizospheric soils of P. elliottii. We found that the soil microbial communities were significantly different among different stand ages of P. elliottii plantations. The PLFA analysis indicated that the bacterial biomass was higher than the actinomycic and fungal biomass in all stand ages. However, the bacterial biomass decreased with the increasing stand ages, while the fungal biomass increased. The four maximum biomarker concentrations in rhizospheric soils of P. elliottii for all stand ages were 18:1ω9c, 16:1ω7c, 18:3ω6c (6,9,12) and cy19:0, representing measures of fungal and gram negative bacterial biomass. In addition, CLPP analysis revealed that the utilization rate of amino acids, polymers, phenolic acids, and carbohydrates of soil microbial community gradually decreased with increasing stand ages, though this pattern was not observed for carboxylic acids and amines. Microbial community diversity, as determined by the Simpson index, Shannon-Wiener index, Richness index and McIntosh index, significantly decreased as stand age increased. Overall, both the PLFA and CLPP illustrated that the long-term pure plantation pattern exacerbated the microecological imbalance previously described in the rhizospheric soils of P. elliottii, and markedly decreased the soil microbial community diversity and metabolic activity. Based on the correlation analysis, we concluded that the soil nutrient and C/N ratio most significantly contributed to the variation of soil microbial community structure and metabolic activity in different stand ages of P. elliottii plantations.

Soil Microbial Community Structure and Metabolic Activity of Pinus elliottii Plantations across Different Stand Ages in a Subtropical Area

PubMed Central

Wu, Zeyan; Haack, Stacey Elizabeth; Lin, Wenxiong; Li, Bailian; Wu, Linkun; Fang, Changxun; Zhang, Zhixing

2015-01-01

Soil microbes play an essential role in the forest ecosystem as an active component. This study examined the hypothesis that soil microbial community structure and metabolic activity would vary with the increasing stand ages in long-term pure plantations of Pinus elliottii. The phospholipid fatty acids (PLFA) combined with community level physiological profiles (CLPP) method was used to assess these characteristics in the rhizospheric soils of P. elliottii. We found that the soil microbial communities were significantly different among different stand ages of P. elliottii plantations. The PLFA analysis indicated that the bacterial biomass was higher than the actinomycic and fungal biomass in all stand ages. However, the bacterial biomass decreased with the increasing stand ages, while the fungal biomass increased. The four maximum biomarker concentrations in rhizospheric soils of P. elliottii for all stand ages were 18:1ω9c, 16:1ω7c, 18:3ω6c (6,9,12) and cy19:0, representing measures of fungal and gram negative bacterial biomass. In addition, CLPP analysis revealed that the utilization rate of amino acids, polymers, phenolic acids, and carbohydrates of soil microbial community gradually decreased with increasing stand ages, though this pattern was not observed for carboxylic acids and amines. Microbial community diversity, as determined by the Simpson index, Shannon-Wiener index, Richness index and McIntosh index, significantly decreased as stand age increased. Overall, both the PLFA and CLPP illustrated that the long-term pure plantation pattern exacerbated the microecological imbalance previously described in the rhizospheric soils of P. elliottii, and markedly decreased the soil microbial community diversity and metabolic activity. Based on the correlation analysis, we concluded that the soil nutrient and C/N ratio most significantly contributed to the variation of soil microbial community structure and metabolic activity in different stand ages of P. elliottii plantations. PMID:26267338

Soil microbial communities and enzyme activities in sea-buckthorn (Hippophae rhamnoides) plantation at different ages.

PubMed

Yang, Miao; Yang, Dan; Yu, Xuan

2018-01-01

The aim of this study was to assess the impact of forest age and season on the soil microbial community and enzyme activities in sea-buckthorn plantation system and to determine the relative contributions to soil microbial properties. Soil sampling was carried out in the dry season (April) and wet season (September) in four areas, including: abandoned farmland (NH), an 8-year- old plantation (young plantation, 8Y), a 13-year-old plantation (middle-aged plantation, 13Y), and an 18-year-old plantation (mature plantation, 18Y). The results showed that forest age and season have a significant effect on soil microbial community structure and enzyme activities. The total, bacterial, fungal, Gram-negative (G+), and Gram-positive (G-) PLFAs increased gradually with forest age, with the highest values detected in 18Y. All the detected enzyme activities showed the trend as a consequence of forest age. The microbial PLFAs and soil enzyme activities were higher in the wet season than the dry season. However, there were no significant interactions between forest age and season. A Correlation analysis suggested that soil microbial communities and enzyme activities were significantly and positively correlated with pH, total nitrogen (TN) and available phosphorus (AP). Season had a stronger influence on soil microbial communities than forest age. In general, sea-buckthorn plantations establishment might be a potential tool for maintaining and increasing soil fertility in arid and semi-arid regions.

Soil microbial communities and enzyme activities in sea-buckthorn (Hippophae rhamnoides) plantation at different ages

PubMed Central

Yang, Miao; Yang, Dan

2018-01-01

The aim of this study was to assess the impact of forest age and season on the soil microbial community and enzyme activities in sea-buckthorn plantation system and to determine the relative contributions to soil microbial properties. Soil sampling was carried out in the dry season (April) and wet season (September) in four areas, including: abandoned farmland (NH), an 8-year- old plantation (young plantation, 8Y), a 13-year-old plantation (middle-aged plantation, 13Y), and an 18-year-old plantation (mature plantation, 18Y). The results showed that forest age and season have a significant effect on soil microbial community structure and enzyme activities. The total, bacterial, fungal, Gram-negative (G+), and Gram-positive (G-) PLFAs increased gradually with forest age, with the highest values detected in 18Y. All the detected enzyme activities showed the trend as a consequence of forest age. The microbial PLFAs and soil enzyme activities were higher in the wet season than the dry season. However, there were no significant interactions between forest age and season. A Correlation analysis suggested that soil microbial communities and enzyme activities were significantly and positively correlated with pH, total nitrogen (TN) and available phosphorus (AP). Season had a stronger influence on soil microbial communities than forest age. In general, sea-buckthorn plantations establishment might be a potential tool for maintaining and increasing soil fertility in arid and semi-arid regions. PMID:29324845

Microbial responses to multi-factor climate change: effects on soil enzymes.

PubMed

Steinweg, J Megan; Dukes, Jeffrey S; Paul, Eldor A; Wallenstein, Matthew D

2013-01-01

The activities of extracellular enzymes, the proximate agents of decomposition in soils, are known to depend strongly on temperature, but less is known about how they respond to changes in precipitation patterns, and the interaction of these two components of climate change. Both enzyme production and turnover can be affected by changes in temperature and soil moisture, thus it is difficult to predict how enzyme pool size may respond to altered climate. Soils from the Boston-Area Climate Experiment (BACE), which is located in an old field (on abandoned farmland), were used to examine how climate variables affect enzyme activities and microbial biomass carbon (MBC) in different seasons and in soils exposed to a combination of three levels of precipitation treatments (ambient, 150% of ambient during growing season, and 50% of ambient year-round) and four levels of warming treatments (unwarmed to ~4°C above ambient) over the course of a year. Warming, precipitation and season had very little effect on potential enzyme activity. Most models assume that enzyme dynamics follow microbial biomass, because enzyme production should be directly controlled by the size and activity of microbial biomass. We observed differences among seasons and treatments in mass-specific potential enzyme activity, suggesting that this assumption is invalid. In June 2009, mass-specific potential enzyme activity, using chloroform fumigation-extraction MBC, increased with temperature, peaking under medium warming and then declining under the highest warming. This finding suggests that either enzyme production increased with temperature or turnover rates decreased. Increased maintenance costs associated with warming may have resulted in increased mass-specific enzyme activities due to increased nutrient demand. Our research suggests that allocation of resources to enzyme production could be affected by climate-induced changes in microbial efficiency and maintenance costs.

Microbial enhancement of non-Darcy flow: Theoretical consideration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, Jianxin; Schneider, D.R.

1995-12-31

In the near well-bore region and perforations, petroleum fluids usually flow at high velocities and may exhibit non-Darcy-flow behavior. Microorganisms can increase permeability and porosity by removing paraffin or asphaltene accumulations. They can also reduce interfacial tension by producing biosurfactants. These changes can significantly affect non-Darcy flow behavior. Theoretical analysis shows that microbial activities can enhance production by decreasing the turbulence pressure drop and in some cases increasing the drag force exerted to the oil phase. This implies that the effects of microbial activities on non-Darcy flow are important and should be considered in the evaluation of microbial well stimulationmore » and enhanced oil recovery.« less

Contrasting effects of biochar versus manure on soil microbial communities and enzyme activities in an Aridisol.

PubMed

Elzobair, Khalid A; Stromberger, Mary E; Ippolito, James A; Lentz, Rodrick D

2016-01-01

Biochar can increase microbial activity, alter microbial community structure, and increase soil fertility in arid and semi-arid soils, but at relatively high rates that may be impractical for large-scale field studies. This contrasts with organic amendments such as manure, which can be abundant and inexpensive if locally available, and thus can be applied to fields at greater rates than biochar. In a field study comparing biochar and manure, a fast pyrolysis hardwood biochar (22.4 Mg ha(-1)), dairy manure (42 Mg ha(-1) dry wt), a combination of biochar and manure at the aforementioned rates, or no amendment (control) was applied to an Aridisol (n=3) in fall 2008. Plots were annually cropped to corn (Zea maize L.). Surface soils (0-30 cm) were sampled directly under corn plants in late June 2009 and early August 2012, and assayed for microbial community fatty acid methyl ester (FAME) profiles and six extracellular enzyme activities involved in soil C, N, and P cycling. Arbuscular mycorrhizal (AM) fungal colonization was assayed in corn roots in 2012. Biochar had no effect on microbial biomass, community structure, extracellular enzyme activities, or AM fungi root colonization of corn. In the short-term, manure amendment increased microbial biomass, altered microbial community structure, and significantly reduced the relative concentration of the AM fungal biomass in soil. Manure also reduced the percent root colonization of corn by AM fungi in the longer-term. Thus, biochar and manure had contrasting short-term effects on soil microbial communities, perhaps because of the relatively low application rate of biochar. Copyright © 2015 Elsevier Ltd. All rights reserved.

Structural, spectroscopic and anti-microbial inspection of PEG capped ZnO nanoparticles for biomedical applications

NASA Astrophysics Data System (ADS)

Meshram, J. V.; Koli, V. B.; Kumbhar, S. G.; Borde, L. C.; Phadatare, M. R.; Pawar, S. H.

2018-04-01

Zinc oxide (ZnO) nanoparticles (NPs) have a wide range of biomedical applications. Present study demonstrates the new methodology in sol-gel technology for synthesizing Polyethylene glycol (PEG) capped ZnO NPs and its size effect on anti-microbial activity. The reaction time was increased from 1 h to 5 h for the synthesis of ZnO NPs at 130 °C. The size of PEG capped ZnO NPs is increased from 10 to 84 nm by increasing the reaction upto 5 h. The x-ray diffraction studies and transmission electron microscopy analysis reveals the phase purity and hexagonal wurtzite crystal structure with uniform PEG capping on the surface of ZnO NPs. UV–visible spectroscopy exhibits the peak at 366 nm which is attributed to ZnO NPs. No adverse effect is observed in case of absorbance spectroscopy. Further, Fourier transforms infrared spectroscopy and thermo gravimetric analysis depicts the adsorption of PEG molecules on the ZnO NPs surface. The anti-microbial activities for both Gram-positive (S. aureus) and Gram-negative (E. coli) bacteria were studied by optical density (OD) mesurement. The remarkable anti-microbial activity was observed for PEG capped ZnO NPs synthesized at 1 h reaction time showing higher activity in comparison with that synthesized from 2 h to 5 h reaction time. The microbial growth was found to be inhibited after 10 h OD measurement for both the bacteria. The anti-microbial activity may be attributed to the generation of ROS and H2O2. However, these generated species plays a vital role in inhibition of microbial growth. Hence, PEG capped ZnO NPs has promising biomedical applications.

Influences of Different Halophyte Vegetation on Soil Microbial Community at Temperate Salt Marsh.

PubMed

Chaudhary, Doongar R; Kim, Jinhyun; Kang, Hojeong

2018-04-01

Salt marshes are transitional zone between terrestrial and aquatic ecosystems, occupied mainly by halophytic vegetation which provides numerous ecological services to coastal ecosystem. Halophyte-associated microbial community plays an important role in the adaptation of plants to adverse condition and also affected habitat characteristics. To explore the relationship between halophytes and soil microbial community, we studied the soil enzyme activities, soil microbial community structure, and functional gene abundance in halophytes- (Carex scabrifolia, Phragmites australis, and Suaeda japonica) covered and un-vegetated (mud flat) soils at Suncheon Bay, South Korea. Higher concentrations of total, Gram-positive, Gram-negative, total bacterial, and actinomycetes PLFAs (phospholipid fatty acids) were observed in the soil underneath the halophytes compared with mud flat soil and were highest in Carex soil. Halophyte-covered soils had different microbial community composition due to higher abundance of Gram-negative bacteria than mud flat soil. Similar to PLFA concentrations, the increased activities of β-glucosidase, cellulase, phosphatase, and sulfatase enzymes were observed under halophyte soil compared to mud flat soil and Carex exhibited highest activities. The abundance of archaeal 16S rRNA, fungal ITS, and denitrifying genes (nirK, nirS, and nosZ) were not influenced by the halophytes. Abundance bacterial 16S rRNA and dissimilatory (bi)sulfite (dsrA) genes were highest in Carex-covered soil. The abundance of functional genes involved in methane cycle (mcrA and pmoA) was not affected by the halophytes. However, the ratios of mcrA/pmoA and mcrA/dsrA increased in halophyte-covered soils which indicate higher methanogenesis activities. The finding of the study also suggests that halophytes had increased the microbial and enzyme activities, and played a pivotal role in shaping microbial community structure.

Interactions among roots, mycorrhizas and free-living microbial communities differentially impact soil carbon processes

DOE PAGES

Moore, Jessica A. M.; Jiang, Jiang; Patterson, Courtney M.; ...

2015-10-20

Plant roots, their associated microbial community and free-living soil microbes interact to regulate the movement of carbon from the soil to the atmosphere, one of the most important and least understood fluxes of terrestrial carbon. Our inadequate understanding of how plant-microbial interactions alter soil carbon decomposition may lead to poor model predictions of terrestrial carbon feedbacks to the atmosphere. Roots, mycorrhizal fungi and free-living soil microbes can alter soil carbon decomposition through exudation of carbon into soil. Exudates of simple carbon compounds can increase microbial activity because microbes are typically carbon limited. When both roots and mycorrhizal fungi are presentmore » in the soil, they may additively increase carbon decomposition. However, when mycorrhizas are isolated from roots, they may limit soil carbon decomposition by competing with free-living decomposers for resources. We manipulated the access of roots and mycorrhizal fungi to soil insitu in a temperate mixed deciduous forest. We added 13C-labelled substrate to trace metabolized carbon in respiration and measured carbon-degrading microbial extracellular enzyme activity and soil carbon pools. We used our data in a mechanistic soil carbon decomposition model to simulate and compare the effects of root and mycorrhizal fungal presence on soil carbon dynamics over longer time periods. Contrary to what we predicted, root and mycorrhizal biomass did not interact to additively increase microbial activity and soil carbon degradation. The metabolism of 13C-labelled starch was highest when root biomass was high and mycorrhizal biomass was low. These results suggest that mycorrhizas may negatively interact with the free-living microbial community to influence soil carbon dynamics, a hypothesis supported by our enzyme results. Our steady-state model simulations suggested that root presence increased mineral-associated and particulate organic carbon pools, while mycorrhizal fungal presence had a greater influence on particulate than mineral-associated organic carbon pools.Synthesis. Our results suggest that the activity of enzymes involved in organic matter decomposition was contingent upon root-mycorrhizal-microbial interactions. Using our experimental data in a decomposition simulation model, we show that root-mycorrhizal-microbial interactions may have longer-term legacy effects on soil carbon sequestration. Lastly, our study suggests that roots stimulate microbial activity in the short term, but contribute to soil carbon storage over longer periods of time.« less

Interactions among roots, mycorrhizas and free-living microbial communities differentially impact soil carbon processes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moore, Jessica A. M.; Jiang, Jiang; Patterson, Courtney M.

Plant roots, their associated microbial community and free-living soil microbes interact to regulate the movement of carbon from the soil to the atmosphere, one of the most important and least understood fluxes of terrestrial carbon. Our inadequate understanding of how plant-microbial interactions alter soil carbon decomposition may lead to poor model predictions of terrestrial carbon feedbacks to the atmosphere. Roots, mycorrhizal fungi and free-living soil microbes can alter soil carbon decomposition through exudation of carbon into soil. Exudates of simple carbon compounds can increase microbial activity because microbes are typically carbon limited. When both roots and mycorrhizal fungi are presentmore » in the soil, they may additively increase carbon decomposition. However, when mycorrhizas are isolated from roots, they may limit soil carbon decomposition by competing with free-living decomposers for resources. We manipulated the access of roots and mycorrhizal fungi to soil insitu in a temperate mixed deciduous forest. We added 13C-labelled substrate to trace metabolized carbon in respiration and measured carbon-degrading microbial extracellular enzyme activity and soil carbon pools. We used our data in a mechanistic soil carbon decomposition model to simulate and compare the effects of root and mycorrhizal fungal presence on soil carbon dynamics over longer time periods. Contrary to what we predicted, root and mycorrhizal biomass did not interact to additively increase microbial activity and soil carbon degradation. The metabolism of 13C-labelled starch was highest when root biomass was high and mycorrhizal biomass was low. These results suggest that mycorrhizas may negatively interact with the free-living microbial community to influence soil carbon dynamics, a hypothesis supported by our enzyme results. Our steady-state model simulations suggested that root presence increased mineral-associated and particulate organic carbon pools, while mycorrhizal fungal presence had a greater influence on particulate than mineral-associated organic carbon pools.Synthesis. Our results suggest that the activity of enzymes involved in organic matter decomposition was contingent upon root-mycorrhizal-microbial interactions. Using our experimental data in a decomposition simulation model, we show that root-mycorrhizal-microbial interactions may have longer-term legacy effects on soil carbon sequestration. Lastly, our study suggests that roots stimulate microbial activity in the short term, but contribute to soil carbon storage over longer periods of time.« less

Differential sensitivity of total and active soil microbial communities to drought and forest management.

PubMed

Bastida, Felipe; Torres, Irene F; Andrés-Abellán, Manuela; Baldrian, Petr; López-Mondéjar, Rubén; Větrovský, Tomáš; Richnow, Hans H; Starke, Robert; Ondoño, Sara; García, Carlos; López-Serrano, Francisco R; Jehmlich, Nico

2017-10-01

Climate change will affect semiarid ecosystems through severe droughts that increase the competition for resources in plant and microbial communities. In these habitats, adaptations to climate change may consist of thinning-that reduces competition for resources through a decrease in tree density and the promotion of plant survival. We deciphered the functional and phylogenetic responses of the microbial community to 6 years of drought induced by rainfall exclusion and how forest management affects its resistance to drought, in a semiarid forest ecosystem dominated by Pinus halepensis Mill. A multiOMIC approach was applied to reveal novel, community-based strategies in the face of climate change. The diversity and the composition of the total and active soil microbiome were evaluated by 16S rRNA gene (bacteria) and ITS (fungal) sequencing, and by metaproteomics. The microbial biomass was analyzed by phospholipid fatty acids (PLFAs), and the microbially mediated ecosystem multifunctionality was studied by the integration of soil enzyme activities related to the cycles of C, N, and P. The microbial biomass and ecosystem multifunctionality decreased in drought-plots, as a consequence of the lower soil moisture and poorer plant development, but this decrease was more notable in unthinned plots. The structure and diversity of the total bacterial community was unaffected by drought at phylum and order level, but did so at genus level, and was influenced by seasonality. However, the total fungal community and the active microbial community were more sensitive to drought and were related to ecosystem multifunctionality. Thinning in plots without drought increased the active diversity while the total diversity was not affected. Thinning promoted the resistance of ecosystem multifunctionality to drought through changes in the active microbial community. The integration of total and active microbiome analyses avoids misinterpretations of the links between the soil microbial community and climate change. © 2017 John Wiley & Sons Ltd.

Changes in microbial community characteristics and soil organic matter with nitrogen additions in two tropical forests.

PubMed

Cusack, Daniela F; Silver, Whendee L; Torn, Margaret S; Burton, Sarah D; Firestone, Mary K

2011-03-01

Microbial communities and their associated enzyme activities affect the amount and chemical quality of carbon (C) in soils. Increasing nitrogen (N) deposition, particularly in N-rich tropical forests, is likely to change the composition and behavior of microbial communities and feed back on ecosystem structure and function. This study presents a novel assessment of mechanistic links between microbial responses to N deposition and shifts in soil organic matter (SOM) quality and quantity. We used phospholipid fatty acid (PLFA) analysis and microbial enzyme assays in soils to assess microbial community responses to long-term N additions in two distinct tropical rain forests. We used soil density fractionation and 13C nuclear magnetic resonance (NMR) spectroscopy to measure related changes in SOM pool sizes and chemical quality. Microbial biomass increased in response to N fertilization in both tropical forests and corresponded to declines in pools of low-density SOM. The chemical quality of this soil C pool reflected ecosystem-specific changes in microbial community composition. In the lower-elevation forest, there was an increase in gram-negative bacteria PLFA biomass, and there were significant losses of labile C chemical groups (O-alkyls). In contrast, the upper-elevation tropical forest had an increase in fungal PLFAs with N additions and declines in C groups associated with increased soil C storage (alkyls). The dynamics of microbial enzymatic activities with N addition provided a functional link between changes in microbial community structure and SOM chemistry. Ecosystem-specific changes in microbial community composition are likely to have far-reaching effects on soil carbon storage and cycling. This study indicates that microbial communities in N-rich tropical forests can be sensitive to added N, but we can expect significant variability in how ecosystem structure and function respond to N deposition among tropical forest types.

Biomass of active microorganisms is not limited only by available carbon in the rhizosphere

NASA Astrophysics Data System (ADS)

Gilmullina, Aliia

2017-04-01

Microbial activity is generally limited by carbon (C) availability. The easily available substrate release by roots creates so called "hotspots" in the rhizosphere that drives microbial activity removing C limitation. We simulated a gradient of root exudates by glucose addition at different concentrations to stimulate the activation of microbial biomass (MB). Glucose was added at the rates lower than MB (5, 10, 25 and 50%) and at the rates similar or higher than MB (100, 150, 200, 250, 300 and 400%). During incubation CO2 efflux was measured by conductometry, the size of active MB and specific growth rate were estimated by substrate-induced growth response method. We tested a hypothesis that glucose addition exceeding 100% MB is able to activate major fraction of soil microbial community. Addition of glucose at concentrations higher than 5% decreased specific growth rate, demonstrating the shift of microbial community from r-strategy to K-strategy. The percentage of active MB grew up by the increase of glucose concentration. The treatment with glucose at 100% presented a dramatic shift in the activation of MB up to 14%. Contrary to our hypothesis, further increase in glucose rate caused moderate stimulation of active MB up to 22% of total MB. Furthermore, glucose addition above 200% did not increase the fraction of active biomass indicating glucose oversaturation and possible limitation by other nutrients. The results suggest that despite the fact that C is the most important limitation factor, limitless C supply is not able to activate MB up to 100%. Thus, if the rhizosphere is limited by nutrients, the fraction of active biomass remains at low level despite an excess of available C.

Microbial activity and community diversity in a variable charge soil as affected by cadmium exposure levels and time*

PubMed Central

Shentu, Jia-li; He, Zhen-li; Yang, Xiao-e; Li, Ting-qiang

2008-01-01

Effects of cadmium (Cd) on microbial biomass, activity and community diversity were assessed in a representative variable charge soil (Typic Aquult) using an incubation study. Cadmium was added as Cd(NO3)2 to reach a concentration range of 0~16 mg Cd/kg soil. Soil extractable Cd generally increased with Cd loading rate, but decreased with incubation time. Soil microbial biomass was enhanced at low Cd levels (0.5~1 mg/kg), but was inhibited consistently with increasing Cd rate. The ratio of microbial biomass C/N varied with Cd treatment levels, decreasing at low Cd rate (<0.7 mg/kg available Cd), but increasing progressively with Cd loading. Soil respiration was restrained at low Cd loading (<1 mg/kg), and enhanced at higher Cd levels. Soil microbial metabolic quotient (MMQ) was generally greater at high Cd loading (1~16 mg/kg). However, the MMQ is also affected by other factors. Cd contamination reduces species diversity of soil microbial communities and their ability to metabolize different C substrates. Soils with higher levels of Cd contamination showed decreases in indicator phospholipids fatty acids (PLFAs) for Gram-negative bacteria and actinomycetes, while the indicator PLFAs for Gram-positive bacteria and fungi increased with increasing levels of Cd contamination. PMID:18357628

Heavy metal immobilization and microbial community abundance by vegetable waste and pine cone biochar of agricultural soils.

PubMed

Igalavithana, Avanthi Deshani; Lee, Sung-Eun; Lee, Young Han; Tsang, Daniel C W; Rinklebe, Jörg; Kwon, Eilhann E; Ok, Yong Sik

2017-05-01

In order to determine the efficacy of vegetable waste and pine cone biochar for immobilization of metal/metalloid (lead and arsenic) and abundance of microbial community in different agricultural soils, we applied the biochar produced at two different temperatures to two contaminated soils. Biochar was produced by vegetable waste, pine cone, and their mixture (1:1 ww -1 ) at 200 °C (torrefied biomass) and 500 °C (biochar). Contaminated soils were incubated with 5% (ww -1 ) torrefied biomass or biochar. Sequential extraction, thermodynamic modeling, and scanning electron microscopy equipped with energy-dispersive X-ray spectroscopy were used to evaluate the metal immobilization. Microbial communities were characterized by microbial fatty acid profiles and microbial activity was assessed by dehydrogenase activity. Vegetable waste and the mixture of vegetable waste and pine cone biochar exhibited greater ability for Pb immobilization than pine cone biochar and three torrefied biomass, and vegetable waste biochar was found to be most effective. However, torrefied biomass was most effective in increasing both microbial community and dehydrogenase activity. This study confirms that vegetable waste could be a vital biomass to produce biochar to immobilize Pb, and increase the microbial communities and enzyme activity in soils. Biomass and pyrolytic temperature were not found to be effective in the immobilization of As in this study. Copyright © 2017. Published by Elsevier Ltd.

[Influence of different slope position and profile in Disporopsis pernyi forest land on soil microbial biomass and enzyme activity in southwest Karst mountain of China ].

PubMed

Qin, Hua-Jun; He, Bing-Hui; Zhao, Xuan-chi; Li, Yuan; Mao, Wen-tao; Zeng, Qing-ping

2014-09-01

Soil microbial biomass and enzyme activity are important parameters to evaluate the quality of the soil environment. The goal of this study was to determine the influence of different slope position and section in Disporopsis pernyi forest land on the soil microbial biomass and enzyme activity in southwest Karst Mountain. In this study, we chose the Dip forest land at Yunfo village Chengdong town Liangping country Chongqing Province as the study object, to analyze the influence of three different slope positions [Up Slope(US), Middle Slope(MS), Below Slope(BS)] and two different sections-upper layer(0-15 cm) and bottom layer(15-30 cm) on the soil microbial biomass carbon (SMBC), soil microbial biomass nitrogen (SMBN), microbial carbon entropy (qMBC), microbial nitrogen entropy (qMBN) , catalase(CAT), alkaline phosphatase (ALK), urease(URE), and invertase(INV). The results showed that the same trend (BS > MS > US) was found for SMBC, SMBN, qMBC, qMBN, CAT and INV of upper soil layer, while a different trend (BS > US > MS) was observed for ALK. In addition, another trend (MS > US > BS) was observed for URE. The same trend (BS > MS >US) was observed for SMBN, qMBN, CAT, ALK, URE and INV in bottom layer, but a different trend (MS > BS > US) was observed for SMBC and qMBC. The SMBC, SMBN, CAT, ALK, URE and INV manifested as upper > bottom with reduction of the section, while qMBC and qMBN showed the opposite trend. Correlation analysis indicated that there were significant (P <0.05) or highly significant (P < 0.01) positive correlations among SMBC in different slope position and section, soil enzyme activity and moisture. According to the two equations of regression analysis, SMBC tended to increase with the increasing CAT and ALK, while decreased with the increasing pH. Then SMBN tended to increase with the increasing URE and INV.

Alteration of extracellular enzyme activity and microbial abundance by biochar addition: Implication for carbon sequestration in subtropical mangrove sediment.

PubMed

Luo, Ling; Gu, Ji-Dong

2016-11-01

Biochar has attracted more and more attention due to its essential role in adsorbing pollutants, improving soil fertility, and modifying greenhouse gas emission. However, the influences of biochar on extracellular enzyme activity and microbial abundance are still lack and debatable. Currently, there is no information about the impact of biochar on the function of mangrove ecosystems. Therefore, we explored the effects of biochar on extracellular enzyme activity and microbial abundance in subtropical mangrove sediment, and further estimated the contribution of biochar to C sequestration. In this study, sediments were amended with 0 (control), 0.5, 1.0 and 2.0% of biochar and incubated at 25 °C for 90 days. After incubation, enzyme activities, microbial abundance and the increased percentage of sediment organic C content were determined. Both increase (phenol oxidase and β-glucosidase) and decrease (peroxidase, N-acetyl-glucosaminidase and acid phosphatase) of enzyme activities were observed in biochar treatments, but only peroxidase activity showed statistical significance (at least p < 0.01) compared to the control. Moreover, the activities of all enzymes tested were significantly related to the content of biochar addition (at least p < 0.05). On the other hand, bacterial and fungal abundance in biochar treatments were remarkably lower than control (p < 0.001), and the significantly negative relationship (p < 0.05) between bacterial abundance and the content of biochar was found. Additionally, the increased percentage of organic C gradually increased with biochar addition rate, which provided evidence for applying biochar to mitigate climate change. Given the importance of microorganisms and enzyme activities in sediment organic matter decomposition, the increased C sequestration might be explained by the large decrease of microbial abundance and enzyme activity after biochar intervention. Copyright © 2016 Elsevier Ltd. All rights reserved.

Response of soil microbial activities and microbial community structure to vanadium stress.

PubMed

Xiao, Xi-Yuan; Wang, Ming-Wei; Zhu, Hui-Wen; Guo, Zhao-Hui; Han, Xiao-Qing; Zeng, Peng

2017-08-01

High levels of vanadium (V) have long-term, hazardous impacts on soil ecosystems and biological processes. In the present study, the effects of V on soil enzymatic activities, basal respiration (BR), microbial biomass carbon (MBC), and the microbial community structure were investigated through 12-week greenhouse incubation experiments. The results showed that V content affected soil dehydrogenase activity (DHA), BR, and MBC, while urease activity (UA) was less sensitive to V stress. The average median effective concentration (EC 50 ) thresholds of V were predicted using a log-logistic dose-response model, and they were 362mgV/kg soil for BR and 417mgV/kg soil for DHA. BR and DHA were more sensitive to V addition and could be used as biological indicators for soil V pollution. According to a polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis, the structural diversity of the microbial community decreased for soil V contents ranged between 254 and 1104mg/kg after 1 week of incubation. As the incubation time increased, the diversity of the soil microbial community structure increased for V contents ranged between 354 and 1104mg/kg, indicating that some new V-tolerant bacterial species might have replicated under these conditions. Copyright © 2017 Elsevier Inc. All rights reserved.

Labile and recalcitrant organic matter utilization by river biofilm under increasing water temperature.

PubMed

Ylla, Irene; Romaní, Anna M; Sabater, Sergi

2012-10-01

Microbial biofilms in rivers contribute to the decomposition of the available organic matter which typically shows changes in composition and bioavailability due to their origin, seasonality, and watershed characteristics. In the context of global warming, enhanced biofilm organic matter decomposition would be expected but this effect could be specific when either a labile or a recalcitrant organic matter source would be available. A laboratory experiment was performed to mimic the effect of the predicted increase in river water temperature (+4 °C above an ambient temperature) on the microbial biofilm under differential organic matter sources. The biofilm microbial community responded to higher water temperature by increasing bacterial cell number, respiratory activity (electron transport system) and microbial extracellular enzymes (extracellular enzyme activity). At higher temperature, the phenol oxidase enzyme explained a large fraction of respiratory activity variation suggesting an enhanced microbial use of degradation products from humic substances. The decomposition of hemicellulose (β-xylosidase activity) seemed to be also favored by warmer conditions. However, at ambient temperature, the enzymes highly responsible for respiration activity variation were β-glucosidase and leu-aminopeptidase, suggesting an enhanced microbial use of polysaccharides and peptides degradation products. The addition of labile dissolved organic carbon (DOC; dipeptide plus cellobiose) caused a further augmentation of heterotrophic biomass and respiratory activity. The changes in the fluorescence index and the ratio Abs(250)/total DOC indicated that higher temperature accelerated the rates of DOC degradation. The experiment showed that the more bioavailable organic matter was rapidly cycled irrespective of higher temperature while degradation of recalcitrant substances was enhanced by warming. Thus, pulses of carbon at higher water temperature might have consequences for DOC processing.

Rational design of anti-microbial peptides with enhanced activity and low cytotoxicity based on the structure of the arginine/histidine-rich peptide, chensinin-1.

PubMed

Shang, D; Sun, Y; Wang, C; Ma, L; Li, J; Wang, X

2012-09-01

To understand the structure-activity relationship of chensinin-1, a anti-microbial peptide (AMP) with an unusual structure, and to develop novel AMPs as therapeutic agents. A series of chensinin-1 analogues were designed and synthesized by one to three replacement of glycines with leucines at the hydrophilic face of chensinin-1 or rearrangement of some of the residues in its sequence. Circular dichroism spectroscopy showed that the analogues adopted α-helical-type conformations in 50% trifluoroethanol/water but adopted β-strand-type conformations in 30 mmol l(-1) sodium dodecyl sulphate. The anti-microbial activities of the peptides against Gram-positive bacteria increased 5- to 30-fold, and these increases paralleled the increases in the peptides' hydrophobicities. Their haemolytic activities also increased. Amphipathicities had little influence on the bactericidal activity of chensinin-1. All peptides caused leakage of calcein entrapped in negatively charged liposomes although with different efficiencies. The peptides did not induce leakage of calcein from uncharged liposomes. Peptide adopted an aperiodic structure can improve the anti-microbial potency by increasing peptide hydrophobicity. Its target is bacteria plasma membrane. Chensinin-1 can act as a new lead molecule for the study of AMPs with atypical structures. © 2012 The Authors Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

Tools and perspectives for a unified approach to understanding microbial ecology in the critical zone

NASA Astrophysics Data System (ADS)

Gallery, R. E.; Aronson, E. L.; Fairbanks, D.; Murphy, M. A.; Rich, V. I.; Hart, S. C.

2015-12-01

Microbial communities that control nutrient transformation and storage in ecosystems are themselves influenced by landscape topography and vegetative cover. Globally, disturbances such as fires and insect outbreaks are increasing in frequency and severity with enormous impacts on global carbon cycling. The resiliency of soil microbial communities to these heterogeneous disturbances determines rates of nutrient transformations as well as ecosystem structure and recovery. Natural and anthropogenic disturbances are a common thread throughout Critical Zone Observatories and ecosystems in general. Using the 2013 Thompson Ridge Fire in the Jemez River Basin CZO as a case study, we examine the effect of a wildfire disturbance regime on successional changes in soil microbiota and ecosystem fluxes across a landscape with high topographic variation. We find that, layered over the topographic controls of hotspots of biogeochemical activity, fire alters organic substrate quality, microbial biomass, community structure, and activity. For example, fire increases soil pH, which is commonly found as an explanatory variable describing bacterial community structure. Soil microbes excrete exoenzymes to decompose polymers and acquire nutrients, and these activities can indicate changing microbial function or soil quality. In these mixed conifer forests, we find shifts from carbon to nitrogen-dominated exoenzyme activities in burned forests with alkaline soils, suggesting shifts of microbial taxa and function that correspond with recovering soil microbial biomass. More generally we ask - what combination of tools and perspectives is needed to fully understand soil microbial ecology and biogeochemistry of the critical zone? Results from an NSF Science Across Virtual Institutes (SAVI) CZO Network Biogeochemistry Workshop highlight the importance of incorporating a standard suite of microbial activity and community assays along with soil biogeochemical and flux measurements to enable comparisons across the broader CZO network. These characterizations would provide regional microbial function and biodiversity data in a standardized framework that can be used to enable more effective management and valuation of critical zone services and inform projections under global change scenarios.

Copper immobilization by biochar and microbial community abundance in metal-contaminated soils.

PubMed

Moore, Francisca; González, María-Eugenia; Khan, Naser; Curaqueo, Gustavo; Sanchez-Monedero, Miguel; Rilling, Joaquín; Morales, Esteban; Panichini, Marcelo; Mutis, Ana; Jorquera, Milko; Mejias, Jaime; Hirzel, Juan; Meier, Sebastián

2018-03-01

Biochar (BC) is gaining attention as a soil amendment that can remediate metal polluted soils. The simultaneous effects of BC on copper (Cu) mobility, microbial activities in soil using metallophytes have scarcely been addressed. The objective of this study was to evaluate the effects of biochar BCs on Cu immobilization and over soil microbial communities in a Cu-contaminated soil evaluated over a two-year trial. A Cu-contaminated soil (338mgkg -1 ) was incubated with chicken manure biochar (CMB) or oat hull biochar (OHB) at rates of 1 and 5% w/w. Metallophyte Oenothera picensis was grown over one season (six months). The above process was repeated for 3 more consecutive seasons using the same soils. The BCs increased the soil pH and decreased the Cu exchangeable fraction Cu by 5 and 10 times (for OHB and CMB, respectively) by increasing the Cu bound in organic matter and residual fractions, and its effects were consistent across all seasons evaluated. BCs provided favorable habitat for microorganisms that was evident in increased microbial activity. The DHA activity was increased in all BC treatments, reaching a maximum of 7 and 6 times higher than control soils in CMB and OHB. Similar results were observed in microbial respiration, which increased 53% in OHB and 61% in CMB with respect to control. The BCs produced changes in microbial communities in all seasons evaluated. The fungal and bacterial richness were increased by CMB and OHB treatments; however, no clear effects were observed in the microbial diversity estimators. The physiochemical and microbiological effects produced by BC result in an increase of plant biomass production, which was on average 3 times higher than control treatments. However, despite being a metallophyte, O. picensis did not uptake Cu efficiently. Root and shoot Cu concentrations decreased or changed insignificantly in most BC treatments. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

Microbial succession and stimulation following a test well injection simulating CO2 leakage into shallow Newark Basin aquifers

NASA Astrophysics Data System (ADS)

Dueker, M.; Clauson, K.; Yang, Q.; Umemoto, K.; Seltzer, A. M.; Zakharova, N. V.; Matter, J. M.; Stute, M.; Takahashi, T.; Goldberg, D.; O'Mullan, G. D.

2012-12-01

Despite growing appreciation for the importance of microbes in altering geochemical reactions in the subsurface, the microbial response to geological carbon sequestration injections and the role of microbes in altering metal mobilization following leakage scenarios in shallow aquifers remain poorly constrained. A Newark Basin test well was utilized in field experiments to investigate patterns of microbial succession following injection of CO2 saturated water into isolated aquifer intervals. Additionally, laboratory mesocosm experiments, including microbially-active and inactive (autoclave sterilized) treatments, were used to constrain the microbial role in mineral dissolution, trace metal release, and gas production (e.g. hydrogen and methane). Hydrogen production was detected in both sterilized and unsterilized laboratory mesocosm treatments, indicating abiotic hydrogen production may occur following CO2 leakage, and methane production was detected in unsterilized, microbially active mesocosms. In field experiments, a decrease in pH following injection of CO2 saturated aquifer water was accompanied by mobilization of trace elements (e.g. Fe and Mn), the production of hydrogen gas, and increased bacterial cell concentrations. 16S ribosomal RNA clone libraries, from samples collected before and after the test well injection, were compared in an attempt to link variability in geochemistry to changes in aquifer microbiology. Significant changes in microbial composition, compared to background conditions, were found following the test well injection, including a decrease in Proteobacteria, and an increased presence of Firmicutes, Verrucomicrobia, Acidobacteria and other microbes associated with iron reducing and syntrophic metabolism. The concurrence of increased microbial cell concentration, and rapid microbial community succession, with increased concentrations of hydrogen gas suggests that abiotically produced hydrogen may serve as an ecologically-relevant energy source stimulating changes in aquifer microbial communities immediately following CO2 leakage.

Influence of Pig Slurry on Microbial and Biochemical Characteristics of Soil in Albacete Region, SE Spain

NASA Astrophysics Data System (ADS)

Halil Yanardaǧ, Ibrahim

2013-04-01

Soil quality is very important in terms of agricultural sustainability, ecosystem and terrestrial carbon (C) cycle. In turn, soil microbial and biochemical characteristics are indicative of nutrient cycling and soil organic matter dynamics. We investigated the effects of the pig slurries (raw pig slurry (RPS) and treated pig slurry (TPS) from liquid and solid feeding diets) on microbial and biochemical characteristics of soil under barley cropping system. Application doses of slurries are identified with legal doses of Castilla La Mancha Region, which is 210 kg N ha-1 year-1. Microbial biomass C, soluble C, black C and three soil enzymes (β-Glucosidase, β-galactosidase and Arylesterase enzymes) are studied to determine effect slurry on soil biochemical characteristics, which are very important in terms of C cycle in soil. Black carbon content and β-Glucosidase enzyme activities are increased with all pig slurry applications from liquid and traditional feeding diet, as well as microbial biomass and organic carbon content and β-galactosidase enzyme activities are increased with slurry from liquid feeding diet doses. However, pig slurry application from liquid feeding diet doses have increased yield, quality, length and total biomass content of barley. Bioavailable metal contents are increased with all slurry application and with using high doses of slurry can be caused soil pollution. Pig slurries from liquid feeding diet had positive impacts on microbial and biochemical characteristics in terms of soil quality in comparison to the different feeding diets. PS addition to soil had a very significant stimulating effect on the enzyme activities, microbial biomass, soluble and black C compared with different kind of PS and control plots on Mediterranean soil in barley monoculture. This effect may originate from the organic C, N, P and S compounds added with PS. The highest enzyme activity and microbial biomass were observed on the soil samples from the RPS treatment, whereas, black and soluble C was decreased with PS addition. There may have been a transient positive effect of the RPS treatments on the soil biochemical parameters. However, the effect could not be detected because of less labile C content during the experiment. The beneficial effects of the PS additions were less pronounced in the 0-30 cm. soil layer. In this monoculture barley production system and under these Mediterranean climate conditions, applications of TPS should be avoided, so they were associated with a decline in microbial counts and a leveling of almost all the enzymatic activities and microbial biomass C. Keywords: Pig slurry, Microbial biomass C, soluble C, black C, β-Glucosidase, β-galactosidase and Arylesterase enzyme activities.

Gene expression in the deep biosphere.

PubMed

Orsi, William D; Edgcomb, Virginia P; Christman, Glenn D; Biddle, Jennifer F

2013-07-11

Scientific ocean drilling has revealed a deep biosphere of widespread microbial life in sub-seafloor sediment. Microbial metabolism in the marine subsurface probably has an important role in global biogeochemical cycles, but deep biosphere activities are not well understood. Here we describe and analyse the first sub-seafloor metatranscriptomes from anaerobic Peru Margin sediment up to 159 metres below the sea floor, represented by over 1 billion complementary DNA (cDNA) sequence reads. Anaerobic metabolism of amino acids, carbohydrates and lipids seem to be the dominant metabolic processes, and profiles of dissimilatory sulfite reductase (dsr) transcripts are consistent with pore-water sulphate concentration profiles. Moreover, transcripts involved in cell division increase as a function of microbial cell concentration, indicating that increases in sub-seafloor microbial abundance are a function of cell division across all three domains of life. These data support calculations and models of sub-seafloor microbial metabolism and represent the first holistic picture of deep biosphere activities.

Total RNA concentration as an index of microbial activity and oxygen supply in an oxidation ditch.

PubMed

Kanazawa, Nobuhiro; Urushigawa, Yoshikuni; Yato, Yumio

2005-06-01

Total RNA and chromosomal DNA concentrations at a municipal wastewater treatment plant with an oxidation ditch (OD) were monitored for 1.5 years using commercial extraction kits for DNA and RNA. No parameters correlated with the chromosomal DNA concentration. The total RNA concentration exhibited better correlation than the solids retention time and the mixed liquor suspended solids with the removal rate of total organic carbon, and can be regarded as an index of microbial activity. The total RNA concentration varied with a cycle of one year and increased at lower water temperatures in this OD. When diffusion theory was taken into account, it was found that the oxygen dissolution rate increased at lower temperature, and a small change in the oxygen dissolution rate caused a large variation in microbial activity and also affected nitrification and denitrification. The information was insufficient to clarify the various reaction relationships, but total RNA concentration will likely be useful as an index of microbial activity in actual wastewater treatment reactors.

Transitory microbial habitat in the hyperarid Atacama Desert

PubMed Central

Schulze-Makuch, Dirk; Wagner, Dirk; Mangelsdorf, Kai; Devine, Kevin G.; de Vera, Jean-Pierre; Parro, Victor; Kaupenjohann, Martin; Galy, Albert; Schneider, Beate; Airo, Alessandro; Frösler, Jan; Davila, Alfonso F.; Arens, Felix L.; Cáceres, Luis; Cornejo, Francisco Solís; Carrizo, Daniel; Dartnell, Lewis; DiRuggiero, Jocelyne; Ganzert, Lars; Gessner, Mark O.; Grathwohl, Peter; Guan, Lisa; Heinz, Jacob; Hess, Matthias; Keppler, Frank; Maus, Deborah; McKay, Christopher P.; Meckenstock, Rainer U.; Montgomery, Wren; Oberlin, Elizabeth A.; Probst, Alexander J.; Sáenz, Johan S.; Sattler, Tobias; Schirmack, Janosch; Sephton, Mark A.; Schloter, Michael; Uhl, Jenny; Valenzuela, Bernardita; Vestergaard, Gisle; Wörmer, Lars; Zamorano, Pedro

2018-01-01

Traces of life are nearly ubiquitous on Earth. However, a central unresolved question is whether these traces always indicate an active microbial community or whether, in extreme environments, such as hyperarid deserts, they instead reflect just dormant or dead cells. Although microbial biomass and diversity decrease with increasing aridity in the Atacama Desert, we provide multiple lines of evidence for the presence of an at times metabolically active, microbial community in one of the driest places on Earth. We base this observation on four major lines of evidence: (i) a physico-chemical characterization of the soil habitability after an exceptional rain event, (ii) identified biomolecules indicative of potentially active cells [e.g., presence of ATP, phospholipid fatty acids (PLFAs), metabolites, and enzymatic activity], (iii) measurements of in situ replication rates of genomes of uncultivated bacteria reconstructed from selected samples, and (iv) microbial community patterns specific to soil parameters and depths. We infer that the microbial populations have undergone selection and adaptation in response to their specific soil microenvironment and in particular to the degree of aridity. Collectively, our results highlight that even the hyperarid Atacama Desert can provide a habitable environment for microorganisms that allows them to become metabolically active following an episodic increase in moisture and that once it decreases, so does the activity of the microbiota. These results have implications for the prospect of life on other planets such as Mars, which has transitioned from an earlier wetter environment to today’s extreme hyperaridity. PMID:29483268

Transitory microbial habitat in the hyperarid Atacama Desert.

PubMed

Schulze-Makuch, Dirk; Wagner, Dirk; Kounaves, Samuel P; Mangelsdorf, Kai; Devine, Kevin G; de Vera, Jean-Pierre; Schmitt-Kopplin, Philippe; Grossart, Hans-Peter; Parro, Victor; Kaupenjohann, Martin; Galy, Albert; Schneider, Beate; Airo, Alessandro; Frösler, Jan; Davila, Alfonso F; Arens, Felix L; Cáceres, Luis; Cornejo, Francisco Solís; Carrizo, Daniel; Dartnell, Lewis; DiRuggiero, Jocelyne; Flury, Markus; Ganzert, Lars; Gessner, Mark O; Grathwohl, Peter; Guan, Lisa; Heinz, Jacob; Hess, Matthias; Keppler, Frank; Maus, Deborah; McKay, Christopher P; Meckenstock, Rainer U; Montgomery, Wren; Oberlin, Elizabeth A; Probst, Alexander J; Sáenz, Johan S; Sattler, Tobias; Schirmack, Janosch; Sephton, Mark A; Schloter, Michael; Uhl, Jenny; Valenzuela, Bernardita; Vestergaard, Gisle; Wörmer, Lars; Zamorano, Pedro

2018-03-13

Traces of life are nearly ubiquitous on Earth. However, a central unresolved question is whether these traces always indicate an active microbial community or whether, in extreme environments, such as hyperarid deserts, they instead reflect just dormant or dead cells. Although microbial biomass and diversity decrease with increasing aridity in the Atacama Desert, we provide multiple lines of evidence for the presence of an at times metabolically active, microbial community in one of the driest places on Earth. We base this observation on four major lines of evidence: ( i ) a physico-chemical characterization of the soil habitability after an exceptional rain event, ( ii ) identified biomolecules indicative of potentially active cells [e.g., presence of ATP, phospholipid fatty acids (PLFAs), metabolites, and enzymatic activity], ( iii ) measurements of in situ replication rates of genomes of uncultivated bacteria reconstructed from selected samples, and ( iv ) microbial community patterns specific to soil parameters and depths. We infer that the microbial populations have undergone selection and adaptation in response to their specific soil microenvironment and in particular to the degree of aridity. Collectively, our results highlight that even the hyperarid Atacama Desert can provide a habitable environment for microorganisms that allows them to become metabolically active following an episodic increase in moisture and that once it decreases, so does the activity of the microbiota. These results have implications for the prospect of life on other planets such as Mars, which has transitioned from an earlier wetter environment to today's extreme hyperaridity. Copyright © 2018 the Author(s). Published by PNAS.

Transitory microbial habitat in the hyperarid Atacama Desert

NASA Astrophysics Data System (ADS)

Schulze-Makuch, Dirk; Wagner, Dirk; Kounaves, Samuel P.; Mangelsdorf, Kai; Devine, Kevin G.; de Vera, Jean-Pierre; Schmitt-Kopplin, Philippe; Grossart, Hans-Peter; Parro, Victor; Kaupenjohann, Martin; Galy, Albert; Schneider, Beate; Airo, Alessandro; Frösler, Jan; Davila, Alfonso F.; Arens, Felix L.; Cáceres, Luis; Solís Cornejo, Francisco; Carrizo, Daniel; Dartnell, Lewis; DiRuggiero, Jocelyne; Flury, Markus; Ganzert, Lars; Gessner, Mark O.; Grathwohl, Peter; Guan, Lisa; Heinz, Jacob; Hess, Matthias; Keppler, Frank; Maus, Deborah; McKay, Christopher P.; Meckenstock, Rainer U.; Montgomery, Wren; Oberlin, Elizabeth A.; Probst, Alexander J.; Sáenz, Johan S.; Sattler, Tobias; Schirmack, Janosch; Sephton, Mark A.; Schloter, Michael; Uhl, Jenny; Valenzuela, Bernardita; Vestergaard, Gisle; Wörmer, Lars; Zamorano, Pedro

2018-03-01

Traces of life are nearly ubiquitous on Earth. However, a central unresolved question is whether these traces always indicate an active microbial community or whether, in extreme environments, such as hyperarid deserts, they instead reflect just dormant or dead cells. Although microbial biomass and diversity decrease with increasing aridity in the Atacama Desert, we provide multiple lines of evidence for the presence of an at times metabolically active, microbial community in one of the driest places on Earth. We base this observation on four major lines of evidence: (i) a physico-chemical characterization of the soil habitability after an exceptional rain event, (ii) identified biomolecules indicative of potentially active cells [e.g., presence of ATP, phospholipid fatty acids (PLFAs), metabolites, and enzymatic activity], (iii) measurements of in situ replication rates of genomes of uncultivated bacteria reconstructed from selected samples, and (iv) microbial community patterns specific to soil parameters and depths. We infer that the microbial populations have undergone selection and adaptation in response to their specific soil microenvironment and in particular to the degree of aridity. Collectively, our results highlight that even the hyperarid Atacama Desert can provide a habitable environment for microorganisms that allows them to become metabolically active following an episodic increase in moisture and that once it decreases, so does the activity of the microbiota. These results have implications for the prospect of life on other planets such as Mars, which has transitioned from an earlier wetter environment to today’s extreme hyperaridity.

Deep subsurface microbial processes

USGS Publications Warehouse

Lovley, D.R.; Chapelle, F.H.

1995-01-01

Information on the microbiology of the deep subsurface is necessary in order to understand the factors controlling the rate and extent of the microbially catalyzed redox reactions that influence the geophysical properties of these environments. Furthermore, there is an increasing threat that deep aquifers, an important drinking water resource, may be contaminated by man's activities, and there is a need to predict the extent to which microbial activity may remediate such contamination. Metabolically active microorganisms can be recovered from a diversity of deep subsurface environments. The available evidence suggests that these microorganisms are responsible for catalyzing the oxidation of organic matter coupled to a variety of electron acceptors just as microorganisms do in surface sediments, but at much slower rates. The technical difficulties in aseptically sampling deep subsurface sediments and the fact that microbial processes in laboratory incubations of deep subsurface material often do not mimic in situ processes frequently necessitate that microbial activity in the deep subsurface be inferred through nonmicrobiological analyses of ground water. These approaches include measurements of dissolved H2, which can predict the predominant microbially catalyzed redox reactions in aquifers, as well as geochemical and groundwater flow modeling, which can be used to estimate the rates of microbial processes. Microorganisms recovered from the deep subsurface have the potential to affect the fate of toxic organics and inorganic contaminants in groundwater. Microbial activity also greatly influences 1 the chemistry of many pristine groundwaters and contributes to such phenomena as porosity development in carbonate aquifers, accumulation of undesirably high concentrations of dissolved iron, and production of methane and hydrogen sulfide. Although the last decade has seen a dramatic increase in interest in deep subsurface microbiology, in comparison with the study of other habitats, the study of deep subsurface microbiology is still in its infancy.

Metagenomic approaches to exploit the biotechnological potential of the microbial consortia of marine sponges.

PubMed

Kennedy, Jonathan; Marchesi, Julian R; Dobson, Alan D W

2007-05-01

Natural products isolated from sponges are an important source of new biologically active compounds. However, the development of these compounds into drugs has been held back by the difficulties in achieving a sustainable supply of these often-complex molecules for pre-clinical and clinical development. Increasing evidence implicates microbial symbionts as the source of many of these biologically active compounds, but the vast majority of the sponge microbial community remain uncultured. Metagenomics offers a biotechnological solution to this supply problem. Metagenomes of sponge microbial communities have been shown to contain genes and gene clusters typical for the biosynthesis of biologically active natural products. Heterologous expression approaches have also led to the isolation of secondary metabolism gene clusters from uncultured microbial symbionts of marine invertebrates and from soil metagenomic libraries. Combining a metagenomic approach with heterologous expression holds much promise for the sustainable exploitation of the chemical diversity present in the sponge microbial community.

Short-term parasite-infection alters already the biomass, activity and functional diversity of soil microbial communities

PubMed Central

Li, Jun-Min; Jin, Ze-Xin; Hagedorn, Frank; Li, Mai-He

2014-01-01

Native parasitic plants may be used to infect and control invasive plants. We established microcosms with invasive Mikania micrantha and native Coix lacryma-jobi growing in mixture on native soils, with M. micrantha being infected by parasitic Cuscuta campestris at four intensity levels for seven weeks to estimate the top-down effects of plant parasitism on the biomass and functional diversity of soil microbial communities. Parasitism significantly decreased root biomass and altered soil microbial communities. Soil microbial biomass decreased, but soil respiration increased at the two higher infection levels, indicating a strong stimulation of soil microbial metabolic activity (+180%). Moreover, a Biolog assay showed that the infection resulted in a significant change in the functional diversity indices of soil microbial communities. Pearson correlation analysis indicated that microbial biomass declined significantly with decreasing root biomass, particularly of the invasive M. micrantha. Also, the functional diversity indices of soil microbial communities were positively correlated with soil microbial biomass. Therefore, the negative effects on the biomass, activity and functional diversity of soil microbial community by the seven week long plant parasitism was very likely caused by decreased root biomass and root exudation of the invasive M. micrantha. PMID:25367357

Short-term parasite-infection alters already the biomass, activity and functional diversity of soil microbial communities

NASA Astrophysics Data System (ADS)

Li, Jun-Min; Jin, Ze-Xin; Hagedorn, Frank; Li, Mai-He

2014-11-01

Native parasitic plants may be used to infect and control invasive plants. We established microcosms with invasive Mikania micrantha and native Coix lacryma-jobi growing in mixture on native soils, with M. micrantha being infected by parasitic Cuscuta campestris at four intensity levels for seven weeks to estimate the top-down effects of plant parasitism on the biomass and functional diversity of soil microbial communities. Parasitism significantly decreased root biomass and altered soil microbial communities. Soil microbial biomass decreased, but soil respiration increased at the two higher infection levels, indicating a strong stimulation of soil microbial metabolic activity (+180%). Moreover, a Biolog assay showed that the infection resulted in a significant change in the functional diversity indices of soil microbial communities. Pearson correlation analysis indicated that microbial biomass declined significantly with decreasing root biomass, particularly of the invasive M. micrantha. Also, the functional diversity indices of soil microbial communities were positively correlated with soil microbial biomass. Therefore, the negative effects on the biomass, activity and functional diversity of soil microbial community by the seven week long plant parasitism was very likely caused by decreased root biomass and root exudation of the invasive M. micrantha.

Durability and regeneration of activated carbon air-cathodes in long-term operated microbial fuel cells

NASA Astrophysics Data System (ADS)

Zhang, Enren; Wang, Feng; Yu, Qingling; Scott, Keith; Wang, Xu; Diao, Guowang

2017-08-01

The performance of activated carbon catalyst in air-cathodes in microbial fuel cells was investigated over one year. A maximum power of 1722 mW m-2 was produced within the initial one-month microbial fuel cell operation. The air-cathodes produced a maximum power >1200 mW m-2 within six months, but gradually became a limiting factor for the power output in prolonged microbial fuel cell operation. The maximum power decreased by 55% when microbial fuel cells were operated over one year due to deterioration in activated carbon air-cathodes. While salt/biofilm removal from cathodes experiencing one-year operation increased a limiting performance enhancement in cathodes, a washing-drying-pressing procedure could restore the cathode performance to its original levels, although the performance restoration was temporary. Durable cathodes could be regenerated by re-pressing activated carbon catalyst, recovered from one year deteriorated air-cathodes, with new gas diffusion layer, resulting in ∼1800 mW m-2 of maximum power production. The present study indicated that activated carbon was an effective catalyst in microbial fuel cell cathodes, and could be recovered for reuse in long-term operated microbial fuel cells by simple methods.

Microbial Functional Potential and Community Composition in Permafrost-Affected Soils of the NW Canadian Arctic

PubMed Central

Frank-Fahle, Béatrice A.; Yergeau, Étienne; Greer, Charles W.; Lantuit, Hugues; Wagner, Dirk

2014-01-01

Permafrost-affected soils are among the most obvious ecosystems in which current microbial controls on organic matter decomposition are changing as a result of global warming. Warmer conditions in polygonal tundra will lead to a deepening of the seasonal active layer, provoking changes in microbial processes and possibly resulting in exacerbated carbon degradation under increasing anoxic conditions. To identify current microbial assemblages in carbon rich, water saturated permafrost environments, four polygonal tundra sites were investigated on Herschel Island and the Yukon Coast, Western Canadian Arctic. Ion Torrent sequencing of bacterial and archaeal 16S rRNA amplicons revealed the presence of all major microbial soil groups and indicated a local, vertical heterogeneity of the polygonal tundra soil community with increasing depth. Microbial diversity was found to be highest in the surface layers, decreasing towards the permafrost table. Quantitative PCR analysis of functional genes involved in carbon and nitrogen-cycling revealed a high functional potential in the surface layers, decreasing with increasing active layer depth. We observed that soil properties driving microbial diversity and functional potential varied in each study site. These results highlight the small-scale heterogeneity of geomorphologically comparable sites, greatly restricting generalizations about the fate of permafrost-affected environments in a warming Arctic. PMID:24416279

Repeated application of composted tannery sludge affects differently soil microbial biomass, enzymes activity, and ammonia-oxidizing organisms.

PubMed

Araújo, Ademir Sérgio Ferreira; Lima, Luciano Moura; Santos, Vilma Maria; Schmidt, Radomir

2016-10-01

Repeated application of composted tannery sludge (CTS) changes the soil chemical properties and, consequently, can affect the soil microbial properties. The aim of this study was to evaluate the responses of soil microbial biomass and ammonia-oxidizing organisms to repeated application of CTS. CTS was applied repeatedly during 6 years, and, at the sixth year, the soil microbial biomass, enzymes activity, and ammonia-oxidizing organisms were determined in the soil. The treatments consisted of 0 (without CTS application), 2.5, 5, 10, and 20 t ha(-1) of CTS (dry basis). Soil pH, EC, SOC, total N, and Cr concentration increased with the increase in CTS rate. Soil microbial biomass did not change significantly with the amendment of 2.5 Mg ha(-1), while it decreased at the higher rates. Total and specific enzymes activity responded differently after CTS application. The abundance of bacteria did not change with the 2.5-Mg ha(-1) CTS treatment and decreased after this rate, while the abundance of archaea increased significantly with the 2.5-Mg ha(-1) CTS treatment. Repeated application of different CTS rates for 6 years had different effects on the soil microbial biomass and ammonia-oxidizing organisms as a response to changes in soil chemical properties.

Duckweed diversity decreases heavy metal toxicity by altering the metabolic function of associated microbial communities.

PubMed

Zhao, Zhao; Shi, Huijuan; Liu, Cunqi; Kang, Xianjiang; Chen, Lingci; Liang, Xiaofei; Jin, Lei

2018-07-01

Mono-cultured and mix-cultured duckweed species were investigated with respect to the function of their associated microbial communities in heavy metal contaminated wastewater. Results show that the carbon source utilization patterns of the L. aequinoctialis- and S. polyrhiza-associated microbial communities were different. The relationships between microbial activity, antioxidant enzyme activity (CAT, GSH, and SOD) and growth was positive and significant. The microbial activity of L. aequinoctialis and S. polyrhiza in mixture was higher than in monoculture in low and high heavy metal, respectively, thereby altering the utilization of specific carbon source types and increasing duckweed growth and antioxidant enzyme activity, when compared to the monocultured duckweed. Furthermore, results indicate that duckweed species in mixture are protected from damage through regulation of the associated bacterial communities. Copyright © 2018 Elsevier Ltd. All rights reserved.

Mechanisms for increased soil C storage with increasing temporal and spatial plant diversity in Agroecosystems

NASA Astrophysics Data System (ADS)

Tiemann, L. K.; Grandy, S.; Marin-Spiotta, E.; Atkinson, E. E.

2012-12-01

Generally, there are positive relationships between plant species diversity and net primary production and other key ecosystem functions. However, the effects of aboveground diversity on soil microbial communities and ecosystem processes they mediate, such as soil C sequestration, remain unclear. In this study, we used an 11-y cropping diversity study where increases in diversity have increased crop yields. At the experimental site, temporal diversity is altered using combinations of annual crop rotations, while spatial diversity is altered using cover crop species. We used five treatments ranging in diversity from one to five species consisting of continuous corn with no cover crop or one cover crop and corn-soy-wheat rotations with no cover, one cover or two cover crop species. We collected soils from four replicate plots of each treatment and measured the distribution of mega- (>2 mm), macro- (0.25-2 mm), and micro- (0.053-0.25 mm) aggregates. Within each aggregate size class, we also measured total soil C and N, permanganate oxidizable C (POXC), extracellular enzyme activities (EEA), and microbial community structure with phospholipid fatty acid (PLFA) analysis. We use these data to address the impacts of both rotational and cover crop diversity on soil physical structure, associated microbial community structure and activity and soil C storage. As spatial diversity increased, we found concurrent increases in mega-aggregate abundance as well as increasing soil C in the mega- and micro-aggregates but not macro-aggregates. The proportion of total soil C in each aggregate size class that is relatively labile (POXC) was highest in the micro-aggregates, as was enzyme activity associated with labile C acquisition across all levels of diversity. Enzyme activity associated with more recalcitrant forms of soil C was highest in the mega-aggregate class, also across all diversity levels; however, the ratio of labile to recalcitrant EEA increased with increasing diversity in the mega- and micro-aggregates. In addition, soil N increased with diversity such that microbial C:N EEA simultaneously decreased in mega-aggregates. We also found that cropping diversity has created distinctive soil microbial communities, highlighted by variation in the abundance of gram positive bacteria and Actinomycetes. Further research will help us determine how these changes in community structure with increasing diversity are related to concomitant changes in aggregation and enzyme activities. We suggest that the additional organic matter inputs from cover crops in the high diversity treatments have increased aggregation processes and C pools. While microbial activity has also increased in association with this increased C availability, the activity of recalcitrant and N-acquiring enzymes has declined, suggesting an overall decrease in SOM mineralization with possible increased SOM stabilization. The addition of crop species in rotation (temporal diversity) had minimal influence on any of the measured parameters. We thus conclude that spatial diversity is a more important driver of soil structure and microbial activity, likely due to the high quality organic matter inputs derived from the leguminous cover crops; however, spatial diversity alone did not lead to the same level of C storage potential as mixtures of temporal and spatial diversity.

Microbial ecology of terrestrial Antarctica: Are microbial systems at risk from human activities?

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, G.J.

1996-08-01

Many of the ecological systems found in continental Antarctica are comprised entirely of microbial species. Concerns have arisen that these microbial systems might be at risk either directly through the actions of humans or indirectly through increased competition from introduced species. Although protection of native biota is covered by the Protocol on Environmental Protection to the Antarctic Treaty, strict measures for preventing the introduction on non-native species or for protecting microbial habitats may be impractical. This report summarizes the research conducted to date on microbial ecosystems in continental Antarctica and discusses the need for protecting these ecosystems. The focus ismore » on communities inhabiting soil and rock surfaces in non-coastal areas of continental Antarctica. Although current polices regarding waste management and other operations in Antarctic research stations serve to reduce the introduction on non- native microbial species, importation cannot be eliminated entirely. Increased awareness of microbial habitats by field personnel and protection of certain unique habitats from physical destruction by humans may be necessary. At present, small-scale impacts from human activities are occurring in certain areas both in terms of introduced species and destruction of habitat. On a large scale, however, it is questionable whether the introduction of non-native microbial species to terrestrial Antarctica merits concern.« less

Limited recovery of soil microbial activity after transient exposure to gasoline vapors.

PubMed

Modrzyński, Jakub J; Christensen, Jan H; Mayer, Philipp; Brandt, Kristian K

2016-09-01

During gasoline spills complex mixtures of toxic volatile organic compounds (VOCs) are released to terrestrial environments. Gasoline VOCs exert baseline toxicity (narcosis) and may thus broadly affect soil biota. We assessed the functional resilience (i.e. resistance and recovery of microbial functions) in soil microbial communities transiently exposed to gasoline vapors by passive dosing via headspace for 40 days followed by a recovery phase of 84 days. Chemical exposure was characterized with GC-MS, whereas microbial activity was monitored as soil respiration (CO2 release) and soil bacterial growth ([(3)H]leucine incorporation). Microbial activity was strongly stimulated and inhibited at low and high exposure levels, respectively. Microbial growth efficiency decreased with increasing exposure, but rebounded during the recovery phase for low-dose treatments. Although benzene, toluene, ethylbenzene and xylene (BTEX) concentrations decreased by 83-97% during the recovery phase, microbial activity in high-dose treatments did not recover and numbers of viable bacteria were 3-4 orders of magnitude lower than in control soil. Re-inoculation with active soil microorganisms failed to restore microbial activity indicating residual soil toxicity, which could not be attributed to BTEX, but rather to mixture toxicity of more persistent gasoline constituents or degradation products. Our results indicate a limited potential for functional recovery of soil microbial communities after transient exposure to high, but environmentally relevant, levels of gasoline VOCs which therefore may compromise ecosystem services provided by microorganisms even after extensive soil VOC dissipation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Nitrogen amendments have predictable effects on soil microbial communities and processes

NASA Astrophysics Data System (ADS)

Ramirez, K. S.; Craine, J. M.; Fierer, N.

2011-12-01

Ecosystems worldwide are receiving increasing amounts of reactive nitrogen (N) through anthropogenic activities. While there has been much effort devoted to quantifying aboveground impacts of anthropogenic N effects, less work has focused on identifying belowground impacts. Bacteria play critical roles in ecosystem processes and identifying how anthropogenic N impacts bacterial communities may elucidate how critical microbially-mediated ecosystem functions are altered by N additions. In order to connect changes in soil processes to changes in the microbial community, we need to first determine if the changes are consistent across different soil types and ecosystems. We assessed the patterns of N effects across a variety of ecosystems in two ways. First, utilizing long-term experimental N gradients at Cedar Creek LTER, MN and Kellogg Biological Station LTER, MI, we examined the response of microbial communities to anthropogenic N additions. Using high-throughput pyrosequencing techniques we quantified changes in soil microbial communities across the nitrogen gradients. We observed strong directional shifts in community composition at both sites; N fertilization consistently impacted both the phylogenetic and taxonomic structure of soil bacterial community structure in a predictable manner regardless of ecosystem type. For example, at both sites Acidobacteria experienced significant declines as nitrogen increased, while other groups such as Actinobacteria and Bacteroidetes increased in relative abundance. Our results suggest that bacterial communities across these N fertility gradients are structured by either nitrogen and/or soil carbon availability, rather than by shifts in the plant community or soil pH indirectly associated with the elevated nitrogen inputs. Still, this field-work does not incorporate changes in soil processes (e.g. soil respiration) or microbial activity (e.g. microbial biomass and extracellular enzyme activity), or separate N from C effects. To address these factors, we performed a lab experiment, amending 30 soils collected from across North America with inorganic N. From this year-long incubation we obtained soil respiration, microbial biomass, bacterial community and extracellular enzyme activity measurements. Across all soil types we consistently observed a significant decrease in both soil respiration, approximately 10%, and microbial biomass, approximately 35%. Using high-throughput pyrosequencing we identified seven bacterial groups that responded significantly to the N additions, including those observed in our field survey. Together, this work suggests that increases in soil N shifts the functional capabilities of the microbial community and highlights possibly mechanisms behind the observed changes.

Historical precipitation predictably alters the shape and magnitude of microbial functional response to soil moisture.

PubMed

Averill, Colin; Waring, Bonnie G; Hawkes, Christine V

2016-05-01

Soil moisture constrains the activity of decomposer soil microorganisms, and in turn the rate at which soil carbon returns to the atmosphere. While increases in soil moisture are generally associated with increased microbial activity, historical climate may constrain current microbial responses to moisture. However, it is not known if variation in the shape and magnitude of microbial functional responses to soil moisture can be predicted from historical climate at regional scales. To address this problem, we measured soil enzyme activity at 12 sites across a broad climate gradient spanning 442-887 mm mean annual precipitation. Measurements were made eight times over 21 months to maximize sampling during different moisture conditions. We then fit saturating functions of enzyme activity to soil moisture and extracted half saturation and maximum activity parameter values from model fits. We found that 50% of the variation in maximum activity parameters across sites could be predicted by 30-year mean annual precipitation, an indicator of historical climate, and that the effect is independent of variation in temperature, soil texture, or soil carbon concentration. Based on this finding, we suggest that variation in the shape and magnitude of soil microbial response to soil moisture due to historical climate may be remarkably predictable at regional scales, and this approach may extend to other systems. If historical contingencies on microbial activities prove to be persistent in the face of environmental change, this approach also provides a framework for incorporating historical climate effects into biogeochemical models simulating future global change scenarios. © 2016 John Wiley & Sons Ltd.

Malnutrition in HIV-Infected Children Is an Indicator of Severe Disease with an Impaired Response to Antiretroviral Therapy.

PubMed

Muenchhoff, Maximilian; Healy, Michael; Singh, Ravesh; Roider, Julia; Groll, Andreas; Kindra, Chirjeev; Sibaya, Thobekile; Moonsamy, Angeline; McGregor, Callum; Phan, Michelle Q; Palma, Alejandro; Kloverpris, Henrik; Leslie, Alasdair; Bobat, Raziya; LaRussa, Philip; Ndung'u, Thumbi; Goulder, Philip; Sobieszczyk, Magdalena E; Archary, Mohendran

2018-01-01

This observational study aimed to describe immunopathogenesis and treatment outcomes in children with and without severe acute malnutrition (SAM) and HIV-infection. We studied markers of microbial translocation (16sDNA), intestinal damage (iFABP), monocyte activation (sCD14), T-cell activation (CD38, HLA-DR) and immune exhaustion (PD1) in 32 HIV-infected children with and 41 HIV-infected children without SAM prior to initiation of antiretroviral therapy (ART) and cross-sectionally compared these children to 15 HIV-uninfected children with and 19 HIV-uninfected children without SAM. We then prospectively measured these markers and correlated them to treatment outcomes in the HIV-infected children at 48 weeks following initiation of ART. Plasma levels of 16sDNA, iFABP and sCD14 were measured by quantitative real time PCR, ELISA and Luminex, respectively. T cell phenotype markers were measured by flow cytometry. Multiple regression analysis was performed using generalized linear models (GLMs) and the least absolute shrinkage and selection operator (LASSO) approach for variable selection. Microbial translocation, T cell activation and exhaustion were increased in HIV-uninfected children with SAM compared to HIV-uninfected children without SAM. In HIV-infected children microbial translocation, immune activation, and exhaustion was strongly increased but did not differ by SAM-status. SAM was associated with increased mortality rates early after ART initiation. Malnutrition, age, microbial translocation, monocyte, and CD8 T cell activation were independently associated with decreased rates of CD4% immune recovery after 48 weeks of ART. SAM is associated with increased microbial translocation, immune activation, and immune exhaustion in HIV-uninfected children and with worse prognosis and impaired immune recovery in HIV-infected children on ART.

Carbon mineralization in acidic, xeric forest soils: induction of new activities.

PubMed

Tate, R L

1985-08-01

Carbon mineralization was examined in Lakehurst and Atsion sands collected from the New Jersey Pinelands and in Pahokee muck from the Everglades Agricultural Area. Objectives were (i) to estimate the carbon mineralization capacities of acidic, xeric Pinelands soils in the absence of exogenously supplied carbon substrate (nonamended carbon mineralization rate) and to compare these activities with those of agriculturally developed pahokee muck, and (ii) to measure the capacity for increased carbon mineralization in the soils after carbon amendment. In most cases, nonamended carbon mineralization rates were greater in samples of the acid- and moisture-stressed Pinelands soils than in Pahokee muck collected from a fallow (bare) field. Carbon amendment resulted in augmented catabolic activity in Pahokee muck samples, suggesting that the microbial community was carbon limited in this soil. With many of the substrates, no stimulation of the catabolic rate was detected after amendment of Pinelands soils. This was documented by the observation that amendment of Pahokee muck with an amino acid mixture, glucose, or acetate resulted in a 3.0-, 3.9-, or 10.5-fold stimulation of catabolic activity, respectively, for the added substrate. In contrast, amendment of the Pinelands soils resulted in increased amino acid and acetate catabolic rates in Lakehurst sand and increased acetate metabolism only in Atsion sand. Other activities were unchanged. The increased glucose respiration rates resulted from stimulation of existing microbial activity rather than from microbial proliferation since no change in the microbial growth rate, as estimated by the rate of incorporation of C-labeled acetate into cell membranes, occurred after glucose amendment of the soils. A stimulation of microbial growth rate was recorded with glucose-amended Lakehurst sand collected from the B horizon.

Carbon Mineralization in Acidic, Xeric Forest Soils: Induction of New Activities †

PubMed Central

Tate, Robert L.

1985-01-01

Carbon mineralization was examined in Lakehurst and Atsion sands collected from the New Jersey Pinelands and in Pahokee muck from the Everglades Agricultural Area. Objectives were (i) to estimate the carbon mineralization capacities of acidic, xeric Pinelands soils in the absence of exogenously supplied carbon substrate (nonamended carbon mineralization rate) and to compare these activities with those of agriculturally developed pahokee muck, and (ii) to measure the capacity for increased carbon mineralization in the soils after carbon amendment. In most cases, nonamended carbon mineralization rates were greater in samples of the acid- and moisture-stressed Pinelands soils than in Pahokee muck collected from a fallow (bare) field. Carbon amendment resulted in augmented catabolic activity in Pahokee muck samples, suggesting that the microbial community was carbon limited in this soil. With many of the substrates, no stimulation of the catabolic rate was detected after amendment of Pinelands soils. This was documented by the observation that amendment of Pahokee muck with an amino acid mixture, glucose, or acetate resulted in a 3.0-, 3.9-, or 10.5-fold stimulation of catabolic activity, respectively, for the added substrate. In contrast, amendment of the Pinelands soils resulted in increased amino acid and acetate catabolic rates in Lakehurst sand and increased acetate metabolism only in Atsion sand. Other activities were unchanged. The increased glucose respiration rates resulted from stimulation of existing microbial activity rather than from microbial proliferation since no change in the microbial growth rate, as estimated by the rate of incorporation of 14C-labeled acetate into cell membranes, occurred after glucose amendment of the soils. A stimulation of microbial growth rate was recorded with glucose-amended Lakehurst sand collected from the B horizon. PMID:16346862

Malnutrition in HIV-Infected Children Is an Indicator of Severe Disease with an Impaired Response to Antiretroviral Therapy

PubMed Central

Healy, Michael; Singh, Ravesh; Roider, Julia; Groll, Andreas; Kindra, Chirjeev; Sibaya, Thobekile; Moonsamy, Angeline; McGregor, Callum; Phan, Michelle Q.; Palma, Alejandro; Kloverpris, Henrik; Leslie, Alasdair; Bobat, Raziya; LaRussa, Philip; Ndung'u, Thumbi; Goulder, Philip; Sobieszczyk, Magdalena E.; Archary, Mohendran

2018-01-01

Abstract This observational study aimed to describe immunopathogenesis and treatment outcomes in children with and without severe acute malnutrition (SAM) and HIV-infection. We studied markers of microbial translocation (16sDNA), intestinal damage (iFABP), monocyte activation (sCD14), T-cell activation (CD38, HLA-DR) and immune exhaustion (PD1) in 32 HIV-infected children with and 41 HIV-infected children without SAM prior to initiation of antiretroviral therapy (ART) and cross-sectionally compared these children to 15 HIV-uninfected children with and 19 HIV-uninfected children without SAM. We then prospectively measured these markers and correlated them to treatment outcomes in the HIV-infected children at 48 weeks following initiation of ART. Plasma levels of 16sDNA, iFABP and sCD14 were measured by quantitative real time PCR, ELISA and Luminex, respectively. T cell phenotype markers were measured by flow cytometry. Multiple regression analysis was performed using generalized linear models (GLMs) and the least absolute shrinkage and selection operator (LASSO) approach for variable selection. Microbial translocation, T cell activation and exhaustion were increased in HIV-uninfected children with SAM compared to HIV-uninfected children without SAM. In HIV-infected children microbial translocation, immune activation, and exhaustion was strongly increased but did not differ by SAM-status. SAM was associated with increased mortality rates early after ART initiation. Malnutrition, age, microbial translocation, monocyte, and CD8 T cell activation were independently associated with decreased rates of CD4% immune recovery after 48 weeks of ART. SAM is associated with increased microbial translocation, immune activation, and immune exhaustion in HIV-uninfected children and with worse prognosis and impaired immune recovery in HIV-infected children on ART. PMID:28670966

Linking microbial heterotrophic activity and sediment lithology in oxic, oligotrophic sub-seafloor sediments of the north atlantic ocean.

PubMed

Picard, Aude; Ferdelman, Timothy G

2011-01-01

Microbial heterotrophic activity was investigated in oxic sub-seafloor sediments at North Pond, a sediment pond situated at 23°N on the western flank of the Mid-Atlantic Ridge. The North Pond sediments underlie the oligotrophic North Atlantic Gyre at 4580-m water depth and cover a 7-8 million-year-old basaltic crust aquifer through which seawater flows. Discrete samples for experimentation were obtained from up to ~9 m-long gravity cores taken at 14 stations in the North Pond area. Potential respiration rates were determined in sediment slurries incubated under aerobic conditions with (14)C-acetate. Microbial heterotrophic activity, as defined by oxidation of acetate to CO(2) (with O(2) as electron acceptor), was detected in all 14 stations and all depths sampled. Potential respiration rates were generally low (<0.2 nmol of respired acetate cm(-3) d(-1)) in the sediment, but indicate that microbial heterotrophic activity occurs in deep-sea, oxic, sub-seafloor sediments. Furthermore, discernable differences in activity existed between sites and within given depth profiles. At seven stations, activity was increased by several orders of magnitude at depth (up to ~12 nmol of acetate respired cm(-3) d(-1)). We attempted to correlate the measures of activity with high-resolution color and element stratigraphy. Increased activities at certain depths may be correlated to variations in the sediment geology, i.e., to the presence of dark clay-rich layers, of sandy layers, or within clay-rich horizons presumably overlying basalts. This would suggest that the distribution of microbial heterotrophic activity in deeply buried sediments may be linked to specific lithologies. Nevertheless, high-resolution microbial examination at the level currently enjoyed by sedimentologists will be required to fully explore this link.

Linking Microbial Heterotrophic Activity and Sediment Lithology in Oxic, Oligotrophic Sub-Seafloor Sediments of the North Atlantic Ocean

PubMed Central

Picard, Aude; Ferdelman, Timothy G.

2011-01-01

Microbial heterotrophic activity was investigated in oxic sub-seafloor sediments at North Pond, a sediment pond situated at 23°N on the western flank of the Mid-Atlantic Ridge. The North Pond sediments underlie the oligotrophic North Atlantic Gyre at 4580-m water depth and cover a 7–8 million-year-old basaltic crust aquifer through which seawater flows. Discrete samples for experimentation were obtained from up to ~9 m-long gravity cores taken at 14 stations in the North Pond area. Potential respiration rates were determined in sediment slurries incubated under aerobic conditions with 14C-acetate. Microbial heterotrophic activity, as defined by oxidation of acetate to CO2 (with O2 as electron acceptor), was detected in all 14 stations and all depths sampled. Potential respiration rates were generally low (<0.2 nmol of respired acetate cm−3 d−1) in the sediment, but indicate that microbial heterotrophic activity occurs in deep-sea, oxic, sub-seafloor sediments. Furthermore, discernable differences in activity existed between sites and within given depth profiles. At seven stations, activity was increased by several orders of magnitude at depth (up to ~12 nmol of acetate respired cm−3 d−1). We attempted to correlate the measures of activity with high-resolution color and element stratigraphy. Increased activities at certain depths may be correlated to variations in the sediment geology, i.e., to the presence of dark clay-rich layers, of sandy layers, or within clay-rich horizons presumably overlying basalts. This would suggest that the distribution of microbial heterotrophic activity in deeply buried sediments may be linked to specific lithologies. Nevertheless, high-resolution microbial examination at the level currently enjoyed by sedimentologists will be required to fully explore this link. PMID:22207869

Effects of single-walled carbon nanotubes on soil microorganisms

NASA Astrophysics Data System (ADS)

Jin, L.; Chung, H.; Son, Y.

2011-12-01

Single-walled carbon nanotubes (SWCNTs) are novel materials that have the potential to be used in various commercial fields due to their unique physicochemical properties. As a result of commercial development of nanotechnology, SWCNTs may be discharged to the soil environment with unknown consequences. However, there are as yet no data in the scientific literature that demonstrate the effects of SWCNTs on microbial function in soils. Therefore, we aimed to determine the effects of SWCNTs on soil microbial activity through a 2-week incubation study on urban soils supplemented with different concentrations of SWCNTs ranging from 0 to 1000 μg CNT/g soil. Fluorometric test using fluorogenic substrates were employed for the measurement of several enzyme activities in soil samples. More specifically, we determined the changes in the activities of cellobiohydrolase, β-1,4-glucosidase, β-1,4-xylosidase, β-1,4-N-acetylglucosaminidase, L-leucine aminopeptidase and acid phosphatase which play important roles in the carbon, nitrogen, and phosphorus cycles in response to the addition of SWCNTs. We found that microbial enzyme activities decreased as the concentrations of SWCNT added increased. The lowest enzyme activities were observed under 1000 μg CNT/g soil. The overall pattern shows that enzyme activities decreased slightly in the first 2-3 days and increased in the later stage of the incubation. Our results suggest that relatively high concentrations of SWCNTs can inhibit microbial activities, and this may be due to microbial cell membrane damage caused by SWCNTs. However, further study needs to be conducted to determine the mechanism responsible for inhibitory effect of SWCNTs on soil microbial activity. It can be concluded that changes in the activities of extracellular enzymes can indicate the effect of SWCNTs on soil microorganisms and nutrient cycling.

Changes in microbial populations and enzyme activities during the bioremediation of oil-contaminated soil.

PubMed

Lin, Xin; Li, Xiaojun; Sun, Tieheng; Li, Peijun; Zhou, Qixing; Sun, Lina; Hu, Xiaojun

2009-10-01

In the process of bioremediation in the soil contaminated by different oil concentrations, the changes in the microbial numbers (bacteria and fungi) and the enzyme (catalase (CAT), polyphenol oxidase (PPO) and lipase) activities were evaluated over a 2-year period. The results showed that the microbial numbers after 2-year bioremediation were one to ten times higher than those in the initial. The changes in the bacterial and the fungal populations were different during the bioremediation, and the highest microbial numbers for bacteria and fungi were 5.51 x 10(9) CFU g(-1) dry soil in treatment 3 (10,000 mg kg(-1)) in the initial and 5.54 x 10(5) CFU g(-1) dry soil in treatment 5 (50,000 mg kg(-1)) after the 2-year bioremediation period, respectively. The CAT and PPO activities in the contaminated soil decreased with increasing oil concentration, while the lipase activity increased. The activities of CAT and PPO improved after the bioremediation, but lipase activity was on the contrary. The CAT activity was more sensible to the oil than others, and could be alternative to monitor the bioremediation process.

Microbial activity during a coastal phytoplankton bloom on the Western Antarctic Peninsula in late summer.

PubMed

Alcamán-Arias, María E; Farías, Laura; Verdugo, Josefa; Alarcón-Schumacher, Tomás; Díez, Beatriz

2018-05-01

Phytoplankton biomass during the austral summer is influenced by freezing and melting cycles as well as oceanographic processes that enable nutrient redistribution in the West Antarctic Peninsula (WAP). Microbial functional capabilities, metagenomic and metatranscriptomic activities as well as inorganic 13C- and 15N-assimilation rates were studied in the surface waters of Chile Bay during two contrasting summer periods in 2014. Concentrations of Chlorophyll a (Chla) varied from 0.3 mg m-3 in February to a maximum of 2.5 mg m-3 in March, together with a decrease in nutrients; however, nutrients were never depleted. The microbial community composition remained similar throughout both sampling periods; however, microbial abundance and activity changed with Chla levels. An increased biomass of Bacillariophyta, Haptophyceae and Cryptophyceae was observed along with night-grazing activity of Dinophyceae and ciliates (Alveolates). During high Chla conditions, HCO3- uptake rates during daytime incubations increased 5-fold (>2516 nmol C L-1 d-1), and increased photosynthetic transcript numbers that were mainly associated with cryptophytes; meanwhile night time NO3- (>706 nmol N L-1 d-1) and NH4+ (41.7 nmol N L-1 d-1) uptake rates were 2- and 3-fold higher, respectively, due to activity from Alpha-/Gammaproteobacteria and Bacteroidetes (Flavobacteriia). Due to a projected acceleration in climate change in the WAP, this information is valuable for predicting the composition and functional changes in Antarctic microbial communities.

Microbial Functional Diversity, Biomass and Activity as Affected by Soil Surface Mulching in a Semiarid Farmland

PubMed Central

Shen, Yufang; Chen, Yingying; Li, Shiqing

2016-01-01

Mulching is widely used to increase crop yield in semiarid regions in northwestern China, but little is known about the effect of different mulching systems on the microbial properties of the soil, which play an important role in agroecosystemic functioning and nutrient cycling. Based on a 4-year spring maize (Zea mays L.) field experiment at Changwu Agricultural and Ecological Experimental Station, Shaanxi, we evaluated the responses of soil microbial activity and crop to various management systems. The treatments were NMC (no mulching with inorganic N fertilizer), GMC (gravel mulching with inorganic N fertilizer), FMC (plastic-film mulching with inorganic N fertilizer) and FMO (plastic-film mulching with inorganic N fertilizer and organic manure addition). The results showed that the FMO soil had the highest contents of microbial biomass carbon and nitrogen, dehydrogenase activity, microbial activity and Shannon diversity index. The relative use of carbohydrates and amino acids by microbes was highest in the FMO soil, whereas the relative use of polymers, phenolic compounds and amines was highest in the soil in the NMC soil. Compared with the NMC, an increased but no significant trend of biomass production and nitrogen accumulation was observed under the GMC treatment. The FMC and FMO led a greater increase in biomass production than GMC and NMC. Compare with the NMC treatment, FMC increased grain yield, maize biomass and nitrogen accumulation by 62.2, 62.9 and 86.2%, but no significant difference was found between the FMO and FMC treatments. Some soil biological properties, i.e. microbial biomass carbon, microbial biomass nitrogen, being sensitive to the mulching and organic fertilizer, were significant correlated with yield and nitrogen availability. Film mulching over gravel mulching can serve as an effective measure for crop production and nutrient cycling, and plus organic fertilization additions may thus have improvements in the biological quality of the soil and its sustainability in the rainfall-limited semiarid region. PMID:27414400

Alteration of soil microbial communities and water quality in restored wetlands

USGS Publications Warehouse

Bossio, D.A.; Fleck, J.A.; Scow, K.M.; Fujii, R.

2006-01-01

Land usage is a strong determinant of soil microbial community composition and activity, which in turn determine organic matter decomposition rates and decomposition products in soils. Microbial communities in permanently flooded wetlands, such as those created by wetland restoration on Sacramento-San Joaquin Delta islands in California, function under restricted aeration conditions that result in increasing anaerobiosis with depth. It was hypothesized that the change from agricultural management to permanently flooded wetland would alter microbial community composition, increase the amount and reactivity of dissolved organic carbon (DOC) compounds in Delta waters; and have a predominant impact on microbial communities as compared with the effects of other environmental factors including soil type and agricultural management. Based on phospholipid fatty acid (PLFA) analysis, active microbial communities of the restored wetlands were changed significantly from those of the agricultural fields, and wetland microbial communities varied widely with soil depth. The relative abundance of monounsaturated fatty acids decreased with increasing soil depth in both wetland and agricultural profiles, whereas branched fatty acids were relatively more abundant at all soil depths in wetlands as compared to agricultural fields. Decomposition conditions were linked to DOC quantity and quality using fatty acid functional groups to conclude that restricted aeration conditions found in the wetlands were strongly related to production of reactive carbon compounds. But current vegetation may have had an equally important role in determining DOC quality in restored wetlands. In a larger scale analysis, that included data from wetland and agricultural sites on Delta islands and data from two previous studies from the Sacramento Valley, an aeration gradient was defined as the predominant determinant of active microbial communities across soil types and land usage. ?? 2005 Elsevier Ltd. All rights reserved.

Biochar affects soil organic matter cycling and microbial functions but does not alter microbial community structure in a paddy soil.

PubMed

Tian, Jing; Wang, Jingyuan; Dippold, Michaela; Gao, Yang; Blagodatskaya, Evgenia; Kuzyakov, Yakov

2016-06-15

The application of biochar (BC) in conjunction with mineral fertilizers is one of the most promising management practices recommended to improve soil quality. However, the interactive mechanisms of BC and mineral fertilizer addition affecting microbial communities and functions associated with soil organic matter (SOM) cycling are poorly understood. We investigated the SOM in physical and chemical fractions, microbial community structure (using phospholipid fatty acid analysis, PLFA) and functions (by analyzing enzymes involved in C and N cycling and Biolog) in a 6-year field experiment with BC and NPK amendment. BC application increased total soil C and particulate organic C for 47.4-50.4% and 63.7-74.6%, respectively. The effects of BC on the microbial community and C-cycling enzymes were dependent on fertilization. Addition of BC alone did not change the microbial community compared with the control, but altered the microbial community structure in conjunction with NPK fertilization. SOM fractions accounted for 55% of the variance in the PLFA-related microbial community structure. The particulate organic N explained the largest variation in the microbial community structure. Microbial metabolic activity strongly increased after BC addition, particularly the utilization of amino acids and amines due to an increase in the activity of proteolytic (l-leucine aminopeptidase) enzymes. These results indicate that microorganisms start to mine N from the SOM to compensate for high C:N ratios after BC application, which consequently accelerate cycling of stable N. Concluding, BC in combination with NPK fertilizer application strongly affected microbial community composition and functions, which consequently influenced SOM cycling. Copyright © 2016 Elsevier B.V. All rights reserved.

Microbial activity and community composition during bioremediation of diesel-oil-contaminated soil: effects of hydrocarbon concentration, fertilizers, and incubation time.

PubMed

Margesin, Rosa; Hämmerle, Marion; Tscherko, Dagmar

2007-02-01

We investigated the influence of three factors-diesel oil concentration [2500, 5000, 10,000, 20,000 mg total petroleum hydrocarbons (TPH) kg(-1) soil], biostimulation (unfertilized, inorganic fertilization with NPK nutrients, or oleophilic fertilization with Inipol EAP22), and incubation time-on hydrocarbon removal, enzyme activity (lipase), and microbial community structure [phospholipid fatty acids (PLFA)] in a laboratory soil bioremediation treatment. Fertilization enhanced TPH removal and lipase activity significantly (P < or = 0.001). The higher the initial contamination, the more marked was the effect of fertilization. Differences between the two fertilizers were not significant (P > 0.05). Microbial communities, as assessed by PLFA patterns, were primarily influenced by the TPH content, followed by fertilization, and the interaction of these two factors, whereas incubation time was of minor importance. This was demonstrated by three-factorial analysis of variance and multidimensional scaling analysis. Low TPH content had no significant effect on soil microbial community, independent of the treatment. High TPH content generally resulted in increased PLFA concentrations, whereby a significant increase in microbial biomass with time was only observed with inorganic fertilization, whereas oleophilic fertilization (Inipol EAP22) tended to inhibit microbial activity and to reduce PLFA contents with time. Among bacteria, PLFA indicative of the Gram-negative population were significantly (P < or = 0.05) increased in soil samples containing high amounts of diesel oil and fertilized with NPK after 21-38 days of incubation at 20 degrees C. The Gram-positive population was not significantly influenced by TPH content or biostimulation treatment.

The resistance of the active microbiome as a fundamental compartment of soil quality in the face of climate change

NASA Astrophysics Data System (ADS)

Bastida, Felipe; Andrés, Manuela; Torres, Irene; García, Carlos; Ruiz Navarro, Antonio; Moreno, Francisco R.; López Serrano, Francisco R.

2017-04-01

Arid and semiarid ecosystems will be severely affected by drought derived from climate change. Forest management can promote the adaptations of plant and microbial communities to drought. For instance, thinning reduces competition for resources through a decrease in tree density and the promotion of plant survival. The resistance of soil microbial communities must be strongly related to the soil quality. However, in order to evaluate these properties, the active (and not only the total) microbial community should be carefully assessed. Here, we studied the functional and phylogenetic responses of the microbial community to six years of drought induced by rainfall exclusion and how thinning shapes its resistance to drought, in a semiarid ecosystem dominated by Pinus halepensis Mill. A multiOMIC approach was applied to reveal novel strategies against drought. The diversity and the composition of the total and active soil microbial communities were evaluated by 16S rRNA gene (bacteria) and ITS (fungal) sequencing, and by metaproteomics. The microbial biomass was analyzed by phospholipid fatty acids (PLFAs), and the microbially-mediated ecosystem multifunctionality was studied by the evaluation of enzyme activities related to C, N, and P dynamics. The microbial biomass and ecosystem multifunctionality decreased in plots subjected to drought, but this decrease was greater in unthinned plots. The diversity of the total bacterial and fungal communities were resistant to drought but were shaped by seasonal dynamics. However, the active community was more sensitive to drought and related to multifunctionality. Thinning in plots without drought increased the active diversity while the total diversity was not affected. Thinning promoted the resistance of multifunctionality to drought by changes in the active microbiome. Protein-based phylogeny was a better predictor of the impacts of drought and the adaptations of microbial communities. We highlight that the resistance of the microbial community and the active microbial community are ecological concepts strongly related to the concept of soil quality in the face of climate change.

Recovery of microbial community structure and functioning after wildfire in semi-arid environments: optimising methods for monitoring and assessment

NASA Astrophysics Data System (ADS)

Muñoz-Rojas, Miriam; Martini, Dylan; Erickson, Todd; Merritt, David; Dixon, Kingsley

2015-04-01

Introduction In semi-arid areas such as northern Western Australia, wildfires are a natural part of the environment and many ecosystems in these landscapes have evolved and developed a strong relationship with fire. Soil microbial communities play a crucial role in ecosystem processes by regulating the cycling of nutrients via decomposition, mineralization, and immobilization processes. Thus, the structure (e.g. soil microbial biomass) and functioning (e.g. soil microbial activity) of microbial communities, as well as their changes after ecosystem disturbance, can be useful indicators of soil quality and health recovery. In this research, we assess the impacts of fire on soil microbial communities and their recovery in a biodiverse semi-arid environment of Western Australia (Pilbara region). New methods for determining soil microbial respiration as an indicator of microbial activity and soil health are also tested. Methodology Soil samples were collected from 10 similar ecosystems in the Pilbara with analogous native vegetation, but differing levels of post-fire disturbance (i.e. 3 months, 1 year, 5, 7 and 14 years after wildfire). Soil microbial activity was measured with the Solvita test which determines soil microbial respiration rate based on the measurement of the CO2 burst of a dry soil after it is moistened. Soils were dried and re-wetted and a CO2 probe was inserted before incubation at constant conditions of 25°C during 24 h. Measurements were taken with a digital mini spectrometer. Microbial (bacteria and fungi) biomass and community composition were measured by phospholipid fatty acid analysis (PLFA). Results Immediately after the fire (i.e. 3 months), soil microbial activity and microbial biomass are similar to 14 years 'undisturbed' levels (53.18±3.68 ppm CO2-CO and 14.07±0.65 mg kg-1, respectively). However, after the first year post-fire, with larger plant productivity, microbial biomass and microbial activity increase rapidly, peaking after 5-7 years post fire (70.70±8.94 ppm CO2-CO and 21.67±2.62 mg kg-1, respectively). Microbial activity measured with the Solvita test was significantly correlated (R Pearson > 0.7; P < 0.001) with microbial parameters analysed with PLFA such as microbial biomass, bacteria biomass or mycorrhizhal fungi. This method has proven to be reliable, fast and easy to interpret for assessment of soil microbial activity in the recovery of soil quality during the recovery after fire. Keywords Pilbara region, biodiverse ecosystems, microbial biomass, microbial respiration, Solvita test, CO2 burst.

[Effects of organic fish protein liquid fertilizer on enzyme activities and microbial biomass C and N in a silt soil].

PubMed

Wei, Xiu-Li; Lei, Ping; Shi, Wei-Yong

2010-08-01

By the method of thermostatic culture, this paper studied the effects of different application rates (0.5, 1.5, and 2.5 ml x kg(-1)) of organic fish protein liquid fertilizer on the enzyme activities and microbial biomass C and N in a silt soil, and the relationships between these parameters and soil nutrient contents. Under the application of the liquid fertilizer, soil pH varied in the range of 7.07-7.31, but had no significant difference from the control. With the increasing application rate of the liquid fertilizer, the activities of soil phosphatase, urease, and protease, as well as the soil biomass C and N, all increased significantly, and the increment was 127, 190 and 196%, 39.81, 78.06 and 173.24%, 56.37, 108.29 and 199.98%, 167, 395 and 474%, and 121, 243 and 406%, respectively, compared with the control. The peak time of the soil urease and protease activities and microbial biomass C and N differed with the fertilization treatments. Soil phosphase, urease, and protease activities and microbial biomass C and N were significantly positively correlated with soil nutrient contents, suggesting that applying organic fish protein liquid fertilizer to silt soil could improve soil microbial growth and enzyme activities, and accordingly, promote the decomposition and transformation of soil organic matter and the release of soil available nutrient elements.

The importance of anabolism in microbial control over soil carbon storage

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liang, Chao; Schimel, Joshua P.; Jastrow, Julie D.

Studies of the decomposition, transformation and stabilization of soil organic matter (SOM) have dramatically increased in recent years owing to growing interest in studying the global carbon (C) cycle as it pertains to climate change. While it is readily accepted that the magnitude of the organic C reservoir in soils depends upon microbial involvement, as soil C dynamics are ultimately the consequence of microbial growth and activity, it remains largely unknown how these microorganism-mediated processes lead to soil C stabilization. Here, we define two pathways—ex vivo modification and in vivo turnover—which jointly explain soil C dynamics driven by microbial catabolismmore » and/or anabolism. Accordingly, we use the conceptual framework of the soil ‘microbial carbon pump’ (MCP) to demonstrate how microorganisms are an active player in soil C storage. The MCP couples microbial production of a set of organic compounds to their further stabilization, which we define as the entombing effect. This integration captures the cumulative long-term legacy of microbial assimilation on SOM formation, with mechanisms (whether via physical protection or a lack of activation energy due to chemical composition) that ultimately enable the entombment of microbial-derived C in soils. We propose a need for increased efforts and seek to inspire new studies that utilize the soil MCP as a conceptual guideline for improving mechanistic understandings of the contributions of soil C dynamics to the responses of the terrestrial C cycle under global change.« less

Subsurface Environment Sampler for Improved In Situ Characterization of Subsurface Microbial Communities

NASA Astrophysics Data System (ADS)

Barnhart, E. P.; Ruppert, L. F.; Orem, W. H.; McIntosh, J. C.; Cunningham, A. B.; Fields, M. W.; Hiebert, R.; Hyatt, R.

2016-12-01

There is an increasing threat that deep aquifers, an important drinking water resource, may be contaminated by the extraction and transport of fossil fuels. This threat increases the need for improved groundwater monitoring and the ability to predict the extent to which microbial activity may remediate such contamination. The characterization of subsurface microbial communities could provide an ideal biomonitoring tool for the assessment of subsurface contamination due to prokaryotes environmental ubiquity, rapidity of response to environmental perturbation and the important role they play in hydrocarbon degradation and bioremediation. New DNA sequencing technologies provide the opportunity to cost-effectively identify the vast subsurface microbial ecosystem, but use of this new technology is restricted due to issues with sampling. Prior subsurface microbiology studies have relied on core samples that are expensive to obtain hard to collect aseptically and/or ground water samples that do not reflect in situ microbial densities or activities. The development of down-well incubation of sterile sediment with a Diffusive Microbial Sampler (DMS) has emerged as an alternative method to sample subsurface microbial communities that minimizes cost and contamination issues associated with traditional methods. We have designed a Subsurface Environment Sampler with a DMS module that could enable the anaerobic transport of the in situ microbial community from the field for laboratory bioremediation studies. This sampler could provide an inexpensive and standard method for subsurface microbial sampling which would make this tool useful for Federal, State, private and local agencies interested in monitoring contamination or the effectiveness of bioremediation activities in subsurface aquifers.

Nitrogen Deposition Reduces Decomposition Rates Through Shifts in Microbial Community Composition and Function

NASA Astrophysics Data System (ADS)

Waldrop, M.; Zak, D.; Sinsabaugh, R.

2002-12-01

Atmospheric nitrogen (N) deposition may alter soil biological activity in northern hardwood forests by repressing phenol oxidase enzyme activity and altering microbial community composition, thereby slowing decomposition and increasing the export of phenolic compounds. We tested this hypothesis by adding 13C-labelled cellobiose, vanillin, and catechol to control and N fertilized soils (30 and 80 kg ha-1) collected from three forests; two dominated by Acer Saccharum and one dominated by Quercus Alba and Quercus Velutina. While N deposition increased total microbial respiration, it decreased soil oxidative enzyme activities, resulting in slower degradation rates of all compounds, and larger DOC pools. This effect was larger in the oak forest, where fungi dominate C-cycling processes. DNA and 13C-phospolipid analyses showed that N addition altered the fungal community and reduced the activity of fungal and bacterial populations in soil, potentially explaining reduced soil enzyme activities and incomplete decomposition.

Microbial carbon pump and its significance for carbon sequestration in soils

NASA Astrophysics Data System (ADS)

Liang, Chao

2017-04-01

Studies of the decomposition, transformation and stabilization of soil organic carbon have dramatically increased in recent years due to growing interest in studying the global carbon cycle as it pertains to climate change. While it is readily accepted that the magnitude of the organic carbon reservoir in soils depends upon microbial involvement because soil carbon dynamics are ultimately the consequence of microbial growth and activity, it remains largely unknown how these microbe-mediated processes lead to soil carbon stabilization. Here, two pathways, ex vivo modification and in vivo turnover, were defined to jointly explain soil carbon dynamics driven by microbial catabolism and/or anabolism. Accordingly, a conceptual framework consisting of the raised concept of the soil "microbial carbon pump" (MCP) was demonstrated to describe how microbes act as an active player in soil carbon storage. The hypothesis is that the long-term microbial assimilation process may facilitate the formation of a set of organic compounds that are stabilized (whether via protection by physical interactions or a reduction in activation energy due to chemical composition), ultimately leading to the sequestration of microbial-derived carbon in soils. The need for increased efforts was proposed to seek to inspire new studies that utilize the soil MCP as a conceptual guideline for improving mechanistic understandings of the contributions of soil carbon dynamics to the responses of the terrestrial carbon cycle under global change.

The influences of inoculants from municipal sludge and solid waste on compost stability, maturity and enzyme activities during chicken manure composting.

PubMed

Li, Shuyan; Li, Jijin; Yuan, Jing; Li, Guoxue; Zang, Bing; Li, Yangyang

2017-07-01

The aim of this study was to investigate the influence of inoculants on compost stability, maturity and enzyme activities during composting of chicken manure and cornstalk. Two microbial inoculants (originated from aerobic municipal sludge and municipal solid waste, respectively) were used in composting at the rate of 0.3% of initial raw materials (wet weight). No microbial inoculums were added to the control. The experiment was conducted under aerobic conditions for 53 days. The results show that enzyme activity is an important index to comprehensively evaluate the composting stability and maturity. Microbes originated from sludge works best in terms of composting stability and maturity (C:N ratio decreased from 15.5 to 10, and germination index increased to 109%). Microbial inoculums originated from sludge and municipal solid waste extended the time of thermophilic phase for 11 and 7 days, respectively. Microbial inoculums originated from sludge and MSW significantly increased the average of catalase activity (by 15.0% and 12.1%, respectively), urease activity (by 21.5% and 12.2%, respectively) and cellulase activity (by 32.1% and 26.1%, respectively) during composting.

Mineralogical impact on long-term patterns of soil nitrogen and phosphorus enzyme activities

NASA Astrophysics Data System (ADS)

Mikutta, Robert; Turner, Stephanie; Meyer-Stüve, Sandra; Guggenberger, Georg; Dohrmann, Reiner; Schippers, Axel

2014-05-01

Soil chronosequences provide a unique opportunity to study microbial activity over time in mineralogical diverse soils of different ages. The main objective of this study was to test the effect of mineralogical properties, nutrient and organic matter availability over whole soil pro-files on the abundance and activity of the microbial communities. We focused on microbio-logical processes involved in nitrogen and phosphorus cycling at the 120,000-year Franz Josef soil chronosequence. Microbial abundances (microbial biomass and total cell counts) and enzyme activities (protease, urease, aminopeptidase, and phosphatase) were determined and related to nutrient contents and mineralogical soil properties. Both, microbial abundances and enzyme activities decreased with soil depth at all sites. In the organic layers, microbial biomass and the activities of N-hydrolyzing enzymes showed their maximum at the intermediate-aged sites, corresponding to a high aboveground biomass. In contrast, the phosphatase activity increased with site age. The activities of N-hydrolyzing enzymes were positively correlated with total carbon and nitrogen contents, whereas the phosphatase activity was negatively correlated with the phosphorus content. In the mineral soil, the enzyme activities were generally low, thus reflecting the presence of strongly sorbing minerals. Sub-strate-normalized enzyme activities correlated negatively to clay content as well as poorly crystalline Al and Fe oxyhydroxides, supporting the view that the evolution of reactive sec-ondary mineral phases alters the activity of the microbial communities by constraining sub-strate availability. Our data suggest a strong mineralogical influence on nutrient cycling par-ticularly in subsoil environments.

Carbon stabilization and microbial growth in acidic mine soils after addition of different amendments for soil reclamation

NASA Astrophysics Data System (ADS)

Zornoza, Raúl; Acosta, Jose; Ángeles Muñoz, María; Martínez-Martínez, Silvia; Faz, Ángel; Bååth, Erland

2016-04-01

The extreme soil conditions in metalliferous mine soils have a negative influence on soil biological activity and therefore on soil carbon estabilization. Therefore, amendments are used to increase organic carbon content and activate microbial communities. In order to elucidate some of the factors controlling soil organic carbon stabilization in reclaimed acidic mine soils and its interrelationship with microbial growth and community structure, we performed an incubation experiment with four amendments: pig slurry (PS), pig manure (PM) and biochar (BC), applied with and without marble waste (MW; CaCO3). Results showed that PM and BC (alone or together with MW) contributed to an important increment in recalcitrant organic C, C/N ratio and aggregate stability. Bacterial and fungal growths were highly dependent on pH and labile organic C. PS supported the highest microbial growth; applied alone it stimulated fungal growth, and applied with MW it stimulated bacterial growth. BC promoted the lowest microbial growth, especially for fungi, with no significant increase in fungal biomass. MW+BC increased bacterial growth up to values similar to PM and MW+PM, suggesting that part of the biochar was degraded, at least in short-term mainly by bacteria rather than fungi. PM, MW+PS and MW+PM supported the highest microbial biomass and a similar community structure, related with the presence of high organic C and high pH, with immobilization of metals and increased soil quality. BC contributed to improved soil structure, increased recalcitrant organic C, and decreased metal mobility, with low stimulation of microbial growth.

Plant-soil-microbe interactions regulating soil C storage

NASA Astrophysics Data System (ADS)

Hofmockel, K. S.; Bach, E.; Williams, R.

2016-12-01

Integration across disciplines is required to identify the emergent microbial scale properties that regulate the release or occlusion of plant inputs in soil organic matter. To investigate how micro-scale processes influence soil carbon cycling, we measured microbial community composition and activity within soil aggregates monthly over two growing seasons of a long-term bioenergy field experiment. Using a biologically sensitive sieving technique, soil aggregates were isolated and microbial community activity and composition were measured. This aggregate approach revealed biogeochemical processes regulating C cycling that are not detected using whole soil approaches. Soil aggregation influenced microbe-substrate interactions, where diversified perennial grassland systems supported greater aggregation and reduced severity of aggregate turnover compared to corn systems. Aggregate turnover and concurrent increases in activity resulted in greater microbial biomass and physical protection of soil organic matter in prairie systems, especially fertilized prairies. Fertilized prairie enhanced microbial biomass, enzyme activity, and soil aggregation despite greater root biomass in unfertilized prairie. Independent of ecosystem or sampling date, N-acetyl-glucosaminidase activity and Nitrospirae abundance was greatest in large macroaggregates (>2000 µm), which harbored the highest C:N; cellobiohydrolase activity and Acidobacteria abundance was greatest in microaggregates (<250 µm) which had the lowest C:N. Aggregate fractions differed in microbial community composition (bacteria, archaea, and fungi) and potential enzyme activity, independent of cropping system. Microaggregates harbored significantly greater microbial diversity and richness across all bioenergy cropping systems. Together these results suggest that by mediating access to substrates, soil structure (aggregates) can influence the microbial community composition and extracellular enzyme activity to regulate ecosystem scale decomposition of soil organic matter.

Spartina alterniflora invasion alters soil microbial community composition and microbial respiration following invasion chronosequence in a coastal wetland of China

PubMed Central

Yang, Wen; Jeelani, Nasreen; Leng, Xin; Cheng, Xiaoli; An, Shuqing

2016-01-01

The role of exotic plants in regulating soil microbial community structure and activity following invasion chronosequence remains unclear. We investigated soil microbial community structure and microbial respiration following Spartina alterniflora invasion in a chronosequence of 6-, 10-, 17-, and 20-year-old by comparing with bare flat in a coastal wetland of China. S. alterniflora invasion significantly increased soil moisture and salinity, the concentrations of soil water-soluble organic carbon and microbial biomass carbon (MBC), the quantities of total and various types of phospholipid fatty acids (PLFAs), the fungal:bacterial PLFAs ratio and cumulative microbial respiration compared with bare flat. The highest MBC, gram-negative bacterial and saturated straight-chain PLFAs were found in 10-year-old S. alterniflora soil, while the greatest total PLFAs, bacterial and gram-positive bacterial PLFAs were found in 10- and 17-year-old S. alterniflora soils. The monounsaturated:branched PLFAs ratio declined, and cumulative microbial respiration on a per-unit-PLFAs increased following S. alterniflora invasion in the chronosequence. Our results suggest that S. alterniflora invasion significantly increased the biomass of soil various microbial groups and microbial respiration compared to bare flat soil by increasing soil available substrate, and modifying soil physiochemical properties. Soil microbial community reached the most enriched condition in the 10-year-old S. alterniflora community. PMID:27241173

Effects of Phytoecdysteroids (PEDS) Extracted from Cyanotis arachnoidea on Rumen Fermentation, Enzyme Activity and Microbial Efficiency in a Continuous-Culture System.

PubMed

Li, Deyong; Zhang, Yawei; Cui, Zhenliang; He, Liwen; Chen, Wanbao; Meng, Qingxiang; Ren, Liping

2016-01-01

The objective of this study was to evaluate the effects of supplementation of phytoecdysteroids (PEDS) extracted from Cyanotis arachnoidea on rumen fermentation, enzymes activity and microbial efficiency in a dual flow continuous-culture system. A single-factor experimental design was used with twelve fermenters in 4 groups with 3 replicates each. Fermenters were incubated for a total of 7 days that included first 4 days for adaptation and last 3 days for sampling. PEDS was added at levels of zero (as control), 5, 10, and 15 mg/g of the substrate (DM). The results showed that increasing supplementation levels of PEDS resulted in incremental digestibility of dry matter (DMD) (quadratic, P = 0.001) and organic matter (OMD) (quadratic, P = 0.031), but unchanged digestibility of neutral detergent fiber (NDFD), crude protein (CPD) and acid detergent acid (ADFD). As supplementation levels of PEDS increased, there were decreased response in the concentration of ammonia nitrogen (NH3-N) (linear, P = 0.015) and increased response in molar proportions of butyrate (linear, P = 0.004), but unchanged response in total volatile fatty acid (TVFA) and the molar proportion of acetate and propionate, respectively. Increasing PEDS supplementation levels decreased the ratio of acetate to propionate (linear, P = 0.038), suggesting an alteration of rumen fermentation pattern occurring due to PEDS supplementation in the diet. Supplementation of PEDS significantly increased activities of glutamate dehydrogenase (quadratic, P = 0.001), alanine dehydrogenase (quadratic, P = 0.004), glutamate synthase (linear, P = 0.038), glutamine synthetase (quadratic, P = 0.011), respectively. There were no discernible differences in the activity of carboxymethyl cellulose (CMCase), xylanase and protease regardless of the treatments. The daily production of microbial nitrogen (linear, P = 0.002) and microbial efficiency (MOEEF) (linear, P = 0.001) increased linearly as supplementation levels of PEDS increased. The decreased response of fluid NH3-N and the increased response of MN indicated that PEDS positively increased the synthesis of microbial proteins.

[Effects of Different Altitudes on Soil Microbial PLFA and Enzyme Activity in Two Kinds of Forests].

PubMed

Zeng, Qing-ping; He, Bing-hui; Mao, Qiao-zhi; Wu, Yao-peng; Huang, Qi; Li, Yuan

2015-12-01

The soil microbial community is an important part in soil ecosystem, and it is sensitive to the ecological environment. Phospholipid-derived fatty acids ( PLFA ) analysis was used to examine variations in soil microbial community diversity and its influencing factors. The results showed that: there existed 48 PLFAs that were significant in the soil samples from six altitudes. The PLFAs of six altitudes with the highest contents were i16:0, 10Me17:0, 10Me18:0 TBSA. The citrus forest exhibited richer soil PLFAs distribution both in type and amount than those in masson pine. The microbial activity and functional diversity of masson pine were increased with increasing altitudes, and citrus forest gradually decreased, the PLFA content of different microbial groups in each altitude were significantly different. The richness index, Shannon-Wiener index and Pielou evenness index of masson pine in low elevation were holistically higher than those in high elevation. However, the highest richness index of citrus forest was in low altitude, the highest Shannon-Wiener index and Pielou evenness index were in high altitude. The PLFAs content of different microbial groups were closely correlated to the soil enzyme activities and environmental factors. The PLFAs of bacteria, actinomycetes, G⁻ (Gram- positive), G⁺ (Gram-negative) were positively correlated with Ure(urease) , Ive(invertase) , CAT( catalase activity) and forest type, the PLFAs of fungi was significantly correlated with Ure, Ive, CAT, the PLFAs of bacteria, fungi, actinomycetes, G⁻ , G⁺ were significantly negatively or less correlated with elevation. Ure, Ive, CAT, forest type and elevation are the pivotal factors controlling the soil microbial biomass and activities.

Main factors controlling microbial community structure, growth and activity after reclamation of a tailing pond with aided phytostabilization

NASA Astrophysics Data System (ADS)

Zornoza, Raúl; Acosta, José A.; Martínez-Martínez, Silvia; Faz, Ángel; Bååth, Erland

2015-04-01

Reclamation on bare tailing ponds has the potential to represent soil genesis in Technosols favoring the understanding of the changes of microbial communities and function. In this study we used phytostabilization aided with calcium carbonate and pig slurry/manure to reclaim an acidic bare tailing pond with the aim of investigating the effect of amending and different species on microbial community structure and function. We sampled after two years of amending and planting: unamended tailing soil (UTS), non-rhizospheric amended tailing soil (ATS), rhizospheric soil from four species, and non-rhizospheric native forest soil (NS), which acted as reference. The application of amendments increased pH up to neutrality, organic carbon (Corg), C/N and aggregate stability, while decreased salinity and heavy metals availability. No effect of rhizosphere was observed on physicochemical properties, metals immobilization and microbial community structure and function. To account for confounding effects due to soil organic matter, microbial properties were expressed per Corg. The high increments in pH and Corg have been the main factors driving changes in microbial community structure and function. Bacterial biomass was higher in UTS, without significant differences among the rest of soils. Fungal biomass followed the trend UTS < ATS = rhizospheric soils < NS. Bacterial growth increased and fungal growth decreased with increasing pH, despite the high availability of metals at low pH. Enzyme activities were lower in UTS, being β-glucosidase and β-glucosaminidase activities highly correlated with bacterial growth. Microbial activities were not correlated with the exchangeable fraction of heavy metals, indicating that microbial function is not strongly affected by these metals, likely due to the efficiency of the reclamation procedure to reduce metals toxicity. Changes in microbial community composition were largely explained by changes in pH, heavy metals availability and Corg, with increments in fungal and actinobacterial proportions with soil amending. Acknowledgements R. Zornoza acknowledges the financial support to Fundación Séneca-Agencia de Ciencia y Tecnología de la Región de Murcia (Spain).

Soil temperature and water content drive microbial carbon fixation in grassland of permafrost area on the Tibetan plateau

NASA Astrophysics Data System (ADS)

Kong, W.; Guo, G.; Liu, J.

2014-12-01

Soil microbial communities underpin terrestrial biogeochemical cycles and are greatly influenced by global warming and global-warming-induced dryness. However, the response of soil microbial community function to global change remains largely uncertain, particularly in the ecologically vulnerable Tibetan plateau permafrost area with large carbon storage. With the concept of space for time substitution, we investigated the responses of soil CO2-fixing microbial community and its enzyme activity to climate change along an elevation gradient (4400-5100 m) of alpine grassland on the central Tibetan plateau. The elevation gradient in a south-facing hill slope leads to variation in climate and soil physicochemical parameters. The autotrophic microbial communities were characterized by quantitative PCR (qPCR), terminal restriction fragment length polymorphism analysis (T-RFLP) and cloning/sequencing targeting the CO2-fixing gene (RubisCO). The results demonstrated that the autotrophic microbial community abundance, structure and its enzyme activity were mainly driven by soil temperature and water content. Soil temperature increase and water decrease dramatically reduced the abundance of the outnumbered form IC RubisCO-containing microbes, and significantly changed the structure of form IC, IAB and ID RubisCO-containing microbial community. Structural equation model revealed that the RubisCO enzyme was directly derived from RubisCO-containing microbes and its activity was significantly reduced by soil temperature increase and water content decrease. Thus our results provide a novel positive feedback loop of climate warming and warming-induced dryness by that soil microbial carbon fixing potential will reduce by 3.77%-8.86% with the soil temperature increase of 1.94oC and water content decrease of 60%-70%. This positive feedback could be capable of amplifying the climate change given the significant contribution of soil microbial CO2-fixing up to 4.9% of total soil organic carbon.

Excess labile carbon promotes the expression of virulence factors in coral reef bacterioplankton.

PubMed

Cárdenas, Anny; Neave, Matthew J; Haroon, Mohamed Fauzi; Pogoreutz, Claudia; Rädecker, Nils; Wild, Christian; Gärdes, Astrid; Voolstra, Christian R

2018-01-01

Coastal pollution and algal cover are increasing on many coral reefs, resulting in higher dissolved organic carbon (DOC) concentrations. High DOC concentrations strongly affect microbial activity in reef waters and select for copiotrophic, often potentially virulent microbial populations. High DOC concentrations on coral reefs are also hypothesized to be a determinant for switching microbial lifestyles from commensal to pathogenic, thereby contributing to coral reef degradation, but evidence is missing. In this study, we conducted ex situ incubations to assess gene expression of planktonic microbial populations under elevated concentrations of naturally abundant monosaccharides (glucose, galactose, mannose, and xylose) in algal exudates and sewage inflows. We assembled 27 near-complete (>70%) microbial genomes through metagenomic sequencing and determined associated expression patterns through metatranscriptomic sequencing. Differential gene expression analysis revealed a shift in the central carbohydrate metabolism and the induction of metalloproteases, siderophores, and toxins in Alteromonas, Erythrobacter, Oceanicola, and Alcanivorax populations. Sugar-specific induction of virulence factors suggests a mechanistic link for the switch from a commensal to a pathogenic lifestyle, particularly relevant during increased algal cover and human-derived pollution on coral reefs. Although an explicit test remains to be performed, our data support the hypothesis that increased availability of specific sugars changes net microbial community activity in ways that increase the emergence and abundance of opportunistic pathogens, potentially contributing to coral reef degradation.

Evaluation of a Microbial Sensor as a Tool for Antimicrobial Activity Test of Cosmetic Preservatives.

PubMed

Gomyo, Hideyuki; Ookawa, Masaki; Oshibuchi, Kota; Sugamura, Yuriko; Hosokawa, Masahito; Shionoiri, Nozomi; Maeda, Yoshiaki; Matsunaga, Tadashi; Tanaka, Tsuyoshi

2015-01-01

For high-throughput screening of novel cosmetic preservatives, a rapid and simple assay to evaluate the antimicrobial activities should be developed because the conventional agar dilution method is time-consuming and labor-intensive. To address this issue, we evaluated a microbial sensor as a tool for rapid antimicrobial activity testing. The sensor consists of an oxygen electrode and a filter membrane that holds the test microorganisms, Staphylococcus aureus and Candida albicans. The antimicrobial activity of the tested cosmetic preservative was evaluated by measuring the current increases corresponding to the decreases in oxygen consumption in the microbial respiration. The current increases detected by the sensor showed positive correlation to the concentrations of two commercially used preservatives, chlorphenesin and 2-phenoxyethanol. The same tendency was also observed when a model cosmetic product was used as a preservative solvent, indicating the feasibility in practical use. Furthermore, the microbial sensor and microfluidic flow-cell was assembled to achieve sequential measurements. The sensor system presented in this study could be useful in large-scale screening experiments.

Microbial community related to lysozyme digestion process for boosting waste activated sludge biodegradability.

PubMed

Xin, Xiao-Dong; He, Jun-Guo; Qiu, Wei; Tang, Jian; Liu, Tian-Tian

2015-01-01

Waste activated sludge from a lab-scale sequencing batch reactor was used to investigate the potential relation of microbial community with lysozyme digestion process for sludge solubilization. The results showed the microbial community shifted conspicuously as sludge suffered lysozyme digestion. Soluble protein and polysaccharide kept an increasing trend in solution followed with succession of microbial community. The rise of lysozyme dosage augmented the dissimilarity among communities in various digested sludge. A negative relationship presented between community diversity and lysozyme digestion process under various lysozyme/TS from 0 to 240min (correlation coefficient R(2) exceeded 0.9). Pareto-Lorenz curves demonstrated that microbial community tended to be even with sludge disintegration process by lysozyme. Finally, with diversity (H) decrease and community distribution getting even, the SCOD/TCOD increased steadily in solution which suggested the sludge with high community diversity and uneven population distribution might have tremendous potential for improving their biodegradability by lysozyme digestion. Copyright © 2014 Elsevier Ltd. All rights reserved.

Microbial response to salinity stress in a tropical sandy soil amended with native shrub residues or inorganic fertilizer.

PubMed

Sall, Saïdou Nourou; Ndour, Ndèye Yacine Badiane; Diédhiou-Sall, Siré; Dick, Richard; Chotte, Jean-Luc

2015-09-15

Soil degradation and salinization caused by inappropriate cultivation practices and high levels of saltwater intrusion are having an adverse effect on agriculture in Central Senegal. The residues of Piliostigma reticulatum, a local shrub that coexists with crops, were recently shown to increase particulate organic matter and improve soil quality and may be a promising means of alleviating the effects of salinization. This study compared the effects of inorganic fertilizer and P. reticulatum residues on microbial properties and the ability of soil to withstand salinity stress. We hypothesized that soils amended with P. reticulatum would be less affected by salinity stress than soils amended with inorganic fertilizer and control soil. Salinity stress was applied to soil from a field site that had been cultivated for 5 years under a millet/peanut crop rotation when microbial biomass, phospholipid fatty acid (PLFA) community profile, catabolic diversity, microbial activities were determined. Microbial biomass, nitrification potential and dehydrogenase activity were higher by 20%, 56% and 69% respectively in soil with the organic amendment. With salinity stress, the structure and activities of the microbial community were significantly affected. Although the biomass of actinobacteria community increased with salinity stress, there was a substantial reduction in microbial activity in all soils. The soil organically amended was, however, less affected by salinity stress than the control or inorganic fertilizer treatment. This suggests that amendment using P. reticulatum residues may improve the ability of soils to respond to saline conditions. Copyright © 2015 Elsevier Ltd. All rights reserved.

[Effects of tree species transition on soil microbial community composition and functions in subtropical China].

PubMed

Ding, Guo Chang; Wang, Xiao Hua; Yang, Qi Fan; Lin, Qun Xing; Huang, Zhi Qun

2017-11-01

We employed a comparative study to examine the effects of tree species transition on soil microbial biomass, community composition and enzymes activities under Cunninghamia lanceolata (Lamb.) Hook, Eucalyptus grandis and a N-fixing species, Acacia melanoxylon in subtropical China. Results showed that the effect of tree species on soil microbial community and enzymes activities was significant only in the 0-10 cm soil layer. Reforestation with N-fixing species A. melanoxylon on the C. lanceolata harvest site significantly increased the total phospholipid fatty acid (PLFA), fungal PLFAs, Gram-positive bacterial PLFAs, Gram-negative bacterial PLFAs and actinomycetes biomasses in the 0-10 cm soil layer. The principal component analysis (PCA) showed that the soil microbial community composition in A. melanoxylon soil differed significantly from that in C. lanceolata and E. grandis soils. N-fixing species (A. melanoxylon) significantly enhanced the percent abundance of Gram-positive bacteria, Gram-negative bacteria and actinomycetes. Activities of cellobiohydrolase, N-acetyl-β-d-glucosaminidase and acid phosphatase were significantly higher under A. melanoxylon than under C. lanceolata and E. grandis plantations. Our results suggested that reforestation with N-fixing species, A. melanoxylon on C. lanceolata harvest site could increase soil microbial biomass, enzyme activities and soil organic matter content.

Microbial growth associated with granular activated carbon in a pilot water treatment facility.

PubMed Central

Wilcox, D P; Chang, E; Dickson, K L; Johansson, K R

1983-01-01

The microbial dynamics associated with granular activated carbon (GAC) in a pilot water treatment plant were investigated over a period of 16 months. Microbial populations were monitored in the influent and effluent waters and on the GAC particles by means of total plate counts and ATP assays. Microbial populations between the influent and effluent waters of the GAC columns generally increased, indicating microbial growth. The dominant genera of microorganisms isolated from interstitial waters and GAC particles were Achromobacter, Acinetobacter, Aeromonas, Alcaligenes, Bacillus, Chromobacterium, Corynebacterium, Micrococcus, Microcyclus, Paracoccus, and Pseudomonas. Coliform bacteria were found in small numbers in the effluents from some of the GAC columns in the later months of the study. Oxidation of influent waters with ozone and maintenance of aerobic conditions on the GAC columns failed to appreciably enhance the microbial growth on GAC. PMID:6625567

Microbial Community Functional Change during Vertebrate Carrion Decomposition

PubMed Central

Pechal, Jennifer L.; Crippen, Tawni L.; Tarone, Aaron M.; Lewis, Andrew J.; Tomberlin, Jeffery K.; Benbow, M. Eric

2013-01-01

Microorganisms play a critical role in the decomposition of organic matter, which contributes to energy and nutrient transformation in every ecosystem. Yet, little is known about the functional activity of epinecrotic microbial communities associated with carrion. The objective of this study was to provide a description of the carrion associated microbial community functional activity using differential carbon source use throughout decomposition over seasons, between years and when microbial communities were isolated from eukaryotic colonizers (e.g., necrophagous insects). Additionally, microbial communities were identified at the phyletic level using high throughput sequencing during a single study. We hypothesized that carrion microbial community functional profiles would change over the duration of decomposition, and that this change would depend on season, year and presence of necrophagous insect colonization. Biolog EcoPlates™ were used to measure the variation in epinecrotic microbial community function by the differential use of 29 carbon sources throughout vertebrate carrion decomposition. Pyrosequencing was used to describe the bacterial community composition in one experiment to identify key phyla associated with community functional changes. Overall, microbial functional activity increased throughout decomposition in spring, summer and winter while it decreased in autumn. Additionally, microbial functional activity was higher in 2011 when necrophagous arthropod colonizer effects were tested. There were inconsistent trends in the microbial function of communities isolated from remains colonized by necrophagous insects between 2010 and 2011, suggesting a greater need for a mechanistic understanding of the process. These data indicate that functional analyses can be implemented in carrion studies and will be important in understanding the influence of microbial communities on an essential ecosystem process, carrion decomposition. PMID:24265741

Nonantibiotic interventions to control pathogens and undesired microbial activities in mixed microbial populations residing in the gut of food-producing animals and their excreted wastes

USDA-ARS?s Scientific Manuscript database

The intensification and industrialization of animal agriculture throughout the world has led to considerable increases in animal production efficiencies but has also led to concerns that microbial pathogens, antibiotic residues, and other chemical contaminants could be concentrated in the environmen...

Temperature sensitivity of soil microbial activity modeled by the square root equation as a unifying model to differentiate between direct temperature effects and microbial community adaptation.

PubMed

Bååth, Erland

2018-07-01

Numerous models have been used to express the temperature sensitivity of microbial growth and activity in soil making it difficult to compare results from different habitats. Q10 still is one of the most common ways to express temperature relationships. However, Q10 is not constant with temperature and will differ depending on the temperature interval used for the calculation. The use of the square root (Ratkowsky) relationship between microbial activity (A) and temperature below optimum temperature, √A = a × (T-T min ), is proposed as a simple and adequate model that allow for one descriptor, T min (a theoretical minimum temperature for growth and activity), to estimate correct Q10-values over the entire in situ temperature interval. The square root model can adequately describe both microbial growth and respiration, allowing for an easy determination of T min . Q10 for any temperature interval can then be calculated by Q10 = [(T + 10 - T min )/(T-T min )] 2 , where T is the lowest temperature in the Q10 comparison. T min also describes the temperature adaptation of the microbial community. An envelope of T min covering most natural soil habitats varying between -15°C (cold habitats like Antarctica/Arctic) to 0°C (tropical habitats like rain forests and deserts) is suggested, with an 0.3°C increase in T min per 1°C increase in mean annual temperature. It is shown that the main difference between common temperature relationships used in global models is differences in the assumed temperature adaptation of the soil microbial community. The use of the square root equation will allow for one descriptor, T min , determining the temperature response of soil microorganisms, and at the same time allow for comparing temperature sensitivity of microbial activity between habitats, including future projections. © 2018 John Wiley & Sons Ltd.

Effects of root pruning on the physicochemical properties and microbial activities of poplar rhizosphere soil.

PubMed

Jing, Da-Wei; Liu, Fang-Chun; Wang, Ming-You; Ma, Hai-Lin; Du, Zhen-Yu; Ma, Bing-Yao; Dong, Yu-Feng

2017-01-01

This study aimed to determine the effects of root pruning on the physicochemical characteristics and microbial activities of poplar rhizosphere soil. The root systems of 5-year-old poplar (Populus×euramericana cv. 'Neva') trees were manually pruned at 6, 8, or 10 times diameter at breast height (DBH) from the trunk (severe, moderate, and light, respectively) along both inter-row sides. Moderate root pruning significantly increased the concentrations of amino acids, organic acids, and total sugars in the root exudates and decreased the pH of rhizosphere soil. This treatment also increased the contents of available nitrogen, phosphorus, potassium, and total organic carbon as well as high-, medium-, and low-activity organic carbon in rhizosphere soil. Moreover, moderate pruning increased the contents of microbial biomass carbon and nitrogen, and enhanced basal respiration, in addition to decreasing the metabolic quotients in rhizosphere soil by 8.9%, 5.0%, and 11.4% compared with control, light, and severe root pruning treatments, respectively. Moderate pruning increased the growth rates of DBH, tree height, and volume to the highest levels. Furthermore, these indices were not significantly different between the light root pruning and control groups, but varied significantly between severe and moderate root-pruning treatments. Thus, root pruning, depending on the distance from the trunk, significantly influences the physicochemical properties and microbial activities in poplar rhizosphere soil.

Conservation tillage, optimal water and organic nutrient supply enhance soil microbial activities during wheat (Triticum Aestivum L.) cultivation

PubMed Central

Sharma, Pankaj; Singh, Geeta; Singh, Rana P.

2011-01-01

The field experiments were conducted on sandy loam soil at New Delhi, during 2007 and 2008 to investigate the effect of conservation tillage, irrigation regimes (sub-optimal, optimal and supra-optimal water regimes), and integrated nutrient management (INM) practices on soil biological parameters in wheat cultivation. The conservation tillage soils has shown significant (p<0.05) increase in soil respiration (81.1%), soil microbial biomass carbon (SMBC) (104%) and soil dehydrogenase (DH) (59.2%) compared to the conventional tillage soil. Optimum water supply (3-irrigations) enhanced soil respiration over sub-optimum and supra-optimum irrigations by 13.32% and 79% respectively. Soil dehydrogenase (DH) activity in optimum water regime has also increased by 23.33% and 8.18% respectively over the other two irrigation regimes. Similarly, SMBC has also increased by 12.14% and 27.17% respectively in soil with optimum water supply compared to that of sub-optimum and supra-optimum water regime fields. The maximum increase in soil microbial activities is found when sole organic source (50% Farm Yard Manure+25% biofertilizer+25% Green Manure) has been used in combination with the conservation tillage and the optimum water supply. Study demonstrated that microbial activity could be regulated by tillage, water and nitrogen management in the soil in a sustainable manner. PMID:24031665

Effects of root pruning on the physicochemical properties and microbial activities of poplar rhizosphere soil

PubMed Central

Jing, Da-Wei; Liu, Fang-Chun; Wang, Ming-You; Ma, Hai-Lin; Du, Zhen-Yu; Ma, Bing-Yao; Dong, Yu-Feng

2017-01-01

This study aimed to determine the effects of root pruning on the physicochemical characteristics and microbial activities of poplar rhizosphere soil. The root systems of 5-year-old poplar (Populus×euramericana cv. ‘Neva’) trees were manually pruned at 6, 8, or 10 times diameter at breast height (DBH) from the trunk (severe, moderate, and light, respectively) along both inter-row sides. Moderate root pruning significantly increased the concentrations of amino acids, organic acids, and total sugars in the root exudates and decreased the pH of rhizosphere soil. This treatment also increased the contents of available nitrogen, phosphorus, potassium, and total organic carbon as well as high-, medium-, and low-activity organic carbon in rhizosphere soil. Moreover, moderate pruning increased the contents of microbial biomass carbon and nitrogen, and enhanced basal respiration, in addition to decreasing the metabolic quotients in rhizosphere soil by 8.9%, 5.0%, and 11.4% compared with control, light, and severe root pruning treatments, respectively. Moderate pruning increased the growth rates of DBH, tree height, and volume to the highest levels. Furthermore, these indices were not significantly different between the light root pruning and control groups, but varied significantly between severe and moderate root-pruning treatments. Thus, root pruning, depending on the distance from the trunk, significantly influences the physicochemical properties and microbial activities in poplar rhizosphere soil. PMID:29117215

In vitro study on the effect of doxycycline on the microbial activity of soil determined by redox-potential measuring system.

PubMed

Szakmár, Katalin; Reichart, Olivér; Szatmári, István; Erdősi, Orsolya; Szili, Zsuzsanna; László, Noémi; Székely Körmöczy, Péter; Laczay, Péter

2014-09-01

The potential effect of doxycycline on the microbial activity was investigated in three types of soil. Soil samples were spiked with doxycycline, incubated at 25°C and tested at 0, 2, 4 and 6 days after treatment. The microbiological activity of the soil was characterized by the viable count determined by plate pouring and by the time necessary to reach a defined rate of the redox-potential decrease termed as time to detection (TTD).The viable count of the samples was not changed during the storage. The TTD values, however exhibited a significant increase in the 0.2-1.6 mg/kg doxycycline concentration range compared to the untreated samples indicating concentration-dependent inhibitory effect on microbial activity. The potency of the effect was different in the 3 soil types. To describe the combined effect of the doxycycline concentration and time on the biological activity of one type of soil a mathematical model was constructed and applied.The change of microbial metabolic rate could be measured also without (detectable) change of microbial count when the traditional microbiological methods are not applicable. The applied new redox potential measurement-based method is a simple and useful procedure for the examination of microbial activity of soil and its potential inhibition by antibiotics.

Microbial decomposition is highly sensitive to leaf litter emersion in a permanent temperate stream.

PubMed

Mora-Gómez, Juanita; Duarte, Sofia; Cássio, Fernanda; Pascoal, Cláudia; Romaní, Anna M

2018-04-15

Drought frequency and intensity in some temperate regions are forecasted to increase under the ongoing global change, which might expose permanent streams to intermittence and have severe repercussions on stream communities and ecosystem processes. In this study, we investigated the effect of drought duration on microbial decomposition of Populus nigra leaf litter in a temperate permanent stream (Oliveira, NW Portugal). Specifically, we measured the response of the structural (assemblage composition, bacterial and fungal biomass) and functional (leaf litter decomposition, extracellular enzyme activities (EEA), and fungal sporulation) parameters of fungal and bacterial communities on leaf litter exposed to emersion during different time periods (7, 14 and 21d). Emersion time affected microbial assemblages and litter decomposition, but the response differed among variables. Leaf decomposition rates and the activity of β-glucosidase, cellobiohydrolase and phosphatase were gradually reduced with increasing emersion time, while β-xylosidase reduction was similar when emersion last for 7 or more days, and the phenol oxidase reduction was similar at 14 and 21days of leaf emersion. Microbial biomass and fungal sporulation were reduced after 21days of emersion. The structure of microbial assemblages was affected by the duration of the emersion period. The shifts in fungal assemblages were correlated with a decreased microbial capacity to degrade lignin and hemicellulose in leaf litter exposed to emersion. Additionally, some resilience was observed in leaf litter mass loss, bacterial biomass, some enzyme activities and structure of fungal assemblages. Our study shows that drought can strongly alter structural and functional aspects of microbial decomposers. Therefore, the exposure of leaf litter to increasing emersion periods in temperate streams is expected to affect decomposer communities and overall decomposition of plant material by decelerating carbon cycling in streams. Copyright © 2017 Elsevier B.V. All rights reserved.

Effects of P and C inputs on microbial activities in P limiting bulk and rhizosphere soil

NASA Astrophysics Data System (ADS)

Bilyera, Nataliya

2017-04-01

Keywords: phosphorus, soil ATP, phosphatase, microbial biomass, Cambisol. Phosphorus (P) is the second important nutrient for plants and limiting element in many ecosystems. P is a non-renewable resource, and based on its current rate of use, it has been estimated that the worlds known reserves of P rocks may be depleted within the current century. Soils with high-sorption P capacity require higher P additions, but, do not provide plants with sufficient available P. Therefore, it is necessary to reduce P application rates, but facilitate soil microbiological activity to maintain good P availability for plants. We aimed to study soil adenosine triphosphate (ATP), microbial biomass (MBC) and phosphatase activity as microbial response to contrasting P input in a low P Cambisol in a 5 days incubation experiment. The treatments were i) bulk soil (no C), ii) rhizosphere soil (10 μg C g-1 soil day-1 - root exudates imitation) and iii) glucose addition to soil (50 μg C g-1 soil - for microbial activation). Three rates of P as KH2PO4 were applied at each C treatments: i) no P (P0) - for P severe limitation; ii) 10% P from initial extractable soil P (P10) - low P input; and iii) 50% P from initial extractable soil P (P50) - high P input. We tested the following hypotheses: 1) the better response of MBC and ATP to P is expected to be in the rhizosphere soil, as continuous C input resulted in gradual microbial activation; 2) phosphatase activity will decrease with increasing P rates in all soils. Microbial biomass grew linear (R2=0.99) and simultaneously with incremental P addition in bulk soil. In rhizosphere and C-amended soils, on contrary, the MBC response to P level was represented by quadratic model (y=-0.06x2+2.84x+37.03; R2=0.93). This model shows the highest MBC value at P23, which indicates optimal and the most effective application rate for this soil type. The correlation between soil ATP content and P rates ascended in the order bulk soil (R2=0.34) > C-amended soil (R2=0.51) > rhizosphere soil (R2=0.97). That proves our hypothesis that continuous C input (similar to root exudations) stimulates gradual microorganism activation. The soil ATP content per gram of microbial biomass C increased linearly (y=5.09x + 21.4; R2= 0.99) with increasing P rates in rhizosphere, whereas in bulk and C-amendment soils the effect of P was less pronounced. Phosphatase activity declined (57 and 64%) exponentially with increasing P rates for rhizosphere (R2=0.84) and C-amended (R2=0.98) soils, that complies with our hypothesis. In bulk soil, on contrary, phosphatase activity increased (35%) at P10 and remained constant at P50. P0 was resulted in 5-folds higher phosphatase activity in rhizosphere and C-amended soils compared to bulk soil. This proves the significance of root exudates in facilitation of microbial phosphatase production. Our results show that P (re)cycling can be accelerated in P-deficient soils by C addition and so, excessive P fertilization can be avoided to maintain ecosystem sustainability.

Assessment of some cultural experimental methods to study the effects of antibiotics on microbial activities in a soil: An incubation study

PubMed Central

Molaei, Ali; Haghnia, Gholamhosain; Astaraei, Alireza; Rasouli-Sadaghiani, MirHassan; Teresa Ceccherini, Maria; Datta, Rahul

2017-01-01

Oxytetracycline (OTC) and sulfamethoxazole (SMX) are two of most widely used antibiotics in livestock and poultry industry. After consumption of antibiotics, a major portion of these compounds is excreted through the feces and urine of animals. Land application of antibiotic-treated animal wastes has caused increasing concern about their adverse effects on ecosystem health. In this regard, inconsistent results have been reported regarding the effects of antibiotics on soil microbial activities. This study was conducted based on the completely randomized design to the measure microbial biomass carbon, cumulative respiration and iron (III) reduction bioassays. Concentrations of OTC and SMX including 0, 1, 10, 25, 50, and 100 mg/kg were spiked in triplicate to a sandy loam soil and incubated for 21 days at 25°C. Results showed that the effects of OTC and SMX antibiotics on cumulative respiration and microbial biomass carbon were different. SMX antibiotic significantly affected soil microbial biomass carbon and cumulative respiration at different treatments compared to control with increasing incubation time. OTC antibiotic, on the other hand, negatively affected cumulative respiration compared to control treatment throughout the incubation period. Although OTC antibiotic positively affected microbial biomass carbon at day one of incubation, there was no clear trend in microbial biomass carbon between different treatments of this antibiotic after that time period. Nevertheless, sulfamethoxazole and oxytetracycline antibiotics had similar effects on iron (III) reduction such that they considerably affected iron (III) reduction at 1 and 10 mg/kg, and iron (III) reduction was completely inhibited at concentrations above 10 mg/kg. Hence, according to our results, microbial biomass carbon and cumulative respiration experiments are not able alone to exhibit the effect of antibiotics on soil microbial activity, but combination of these two experiments with iron (III) reduction test could well display the effects of sulfamethoxazole (SMX) and oxytetracycline (OTC) antibiotics on soil biochemical activities. PMID:28683144

Linkages among geophysical facies, microbial composition, biogeochemical rates, and seasonal hydrology in the hyporheic zone

NASA Astrophysics Data System (ADS)

Stegen, J.

2016-12-01

The hyporheic zone is a critical ecosystem transition that links terrestrial, aquatic, and subsurface domains. To understand connections among physical, microbial, and biogeochemical components of the hyporheic zone, we obtained freeze cores along the Columbia River in the Hanford 300 Area and performed geologic, molecular, and microbial assays. Mud and sand content were found to be the primary drivers of microbial community attributes (in particular, of nitrite and carbon oxidizers). Microbial community analysis revealed an abundance of nitrifying Archaea (Thaumarchaea) and an absence of nitrifiying Bacteria. Network analysis revealed significant negative correlations between sand content and some statistical modules of microbial taxa, perhaps indicating the importance of pore water residence time on community composition. A similar set of microbial modules was positively correlated with total organic carbon. One such module that also positively correlated with aerobic metabolic rates was dominated by Thaumarchaea and Nitrospira, suggesting that ammonia oxidation was the dominant aerobic process. We also examined temporal changes in hyporheic microbial structure and activity through repeated sampling of attached and pore water microbes across a spatial gradient. We found that microbial communities remained distinct in river, hyporheic, and inland zones across seasonal variation in hydrologic mixing conditions. One reason was temperature-driven increases in microbial species richness in the hyporheic zone. We show that the relative importance of ecological selection and dispersal varied across environments and across geographic zones. Our results also indicated that while selection imposed short-term constraints on microbial community structure, hyporheic sediment communities did not respond to short-term hydrologic variation. Importantly, we demonstrated that the influence of selective pressures varied with phylogenetic affiliation, which may have been responsible for seasonal increases in Thaumarchaea and aerobic activity. Our results elucidate spatiotemporal shifts in composition and activity of hyporheic microbes across sedimentary and seasonal gradients in pore water environments that correlate with the contribution of Thaumarchaea to aerobic processes.

Functional effects of the bacterial insecticide Bacillus thuringiensis var. kurstaki on aquatic microbial communities.

PubMed

Kreutzweiser, D P; Gringorten, J L; Thomas, D R; Butcher, J T

1996-04-01

Epilithic microbial communities were colonized on leaf disks and exposed to commercial preparations of Bacillus thuringiensis var. kurstaki (Btk) in aquatic microcosms. Responses in terms of microbial respiration, bacterial cell density, protozoan density, and microbial decomposition activity were measured. Test concentrations for treatments with Dipel 64AF and Dipel 8AF in microcosms were the expected environmental concentration (EEC) of 20 IU/ml, 100x the EEC, and 1000x the EEC. Bacterial cell density in the biofilm of leaf disks was significantly increased at concentrations as low as the EEC. There were no concomitant alterations in protozoan density. Microbial respiration was significantly increased, and decomposition activity was significantly decreased, but only at the artificially high concentration of 1000x the EEC. This effect was attributed to the spore-crystal component rather than formulation ingredients. Microbial decomposition of leaf material was also determined in outdoor stream channels treated at concentrations ranging from the EEC to 100x the EEC. Although there tended to be reduced decomposition activity in treated channels, there were no significant differences in mass loss of leaf material between treated and control channels. Various regression, classification, and ordination procedures were applied to the experimental data, and none indicated significant treatment effects. These results from laboratory and controlled field experiments indicate that contamination of watercourses with Btk is unlikely to result in significant adverse effects on microbial community function in terms of detrital decomposition.

[Influences of biochar and nitrogen fertilizer on soil nematode assemblage of upland red soil].

PubMed

Lu, Yan-yan; Wang, Ming-wei; Chen, Xiao-vun; Liu, Man-qiang; Chen, Xiao-min; Cheng, Yan-hong; Huang, Qian-ru; Hu, Feng

2016-01-01

The use of biochar as soil remediation amendment has received more and more concerns, but little attention has been paid to its effect on soil fauna. Based on the field experiment in an upland red soil, we studied the influences of different application rates of biochar (0, 10, 20, 30, 40 t · hm⁻²) and nitrogen fertilizer (60, 90, 120 kg N · hm⁻²) on soil basic properties and nematode assemblages during drought and wet periods. Our results showed that the biochar amendment significantly affect soil moisture and pH regardless of drought or wet period. With the increasing of biochar application, soil pH significantly increased, while soil moisture increased first and then decreased. Soil microbial properties (microbial biomass C, microbial biomass N, microbial biomass C/N, basal respiration) were also significantly affected by the application of biochar and N fertilizer. Low doses of biochar could stimulate the microbial activity, while high doses depressed microbial activity. For example, averaged across different N application rates, biochar amendment at less than 30 t · hm⁻² could increase microbial activity in the drought and wet periods. Besides, the effects of biochar also depended on wet or drought period. When the biochar application rate higher than 30 t · hm⁻², the microbial biomass C was significantly higher in the drought period than the control, but no differences were observed in the wet period. On the contrary, microbial biomass N showed a reverse pattern. Dissolved organic matter and mineral N were affected by biochar and N fertilizer significantly in the drought period, however, in the wet period they were only affected by N fertilizer rather than biochar. There was significant interaction between biochar and N fertilizer on soil nematode abundance and nematode trophic composition independent of sampling period. Combined high doses of both biochar and N fertilization promoted soil nematode abundance. Moreover, the biochar amendment increased the proportion of fungivores especially in the drought period, suggesting the biochar was the preferred fungal energy channel in comparison to soil without biochar addition. In summary, complex patterns occurred not only due to the application rate of biochar as well as their interactions with N fertilization but also due to the drought and wet periods. It is, therefore, necessary to consider different ecological factors when evaluating the effects of biochar in future.

Soil acidity amelioration in a no-till system in west Tennessee USA differs by cover crop type and nitrogen application rate

USDA-ARS?s Scientific Manuscript database

Conservation soil management practices may influence the soil acidity. Surface application of lime may be required in no-till systems to ameliorate soil acidity and to improve crop yields. The application of lime may also increase microbial activity on soil. Specifically, the microbial activity of s...

Changes in substrate availability drive carbon cycle response to chronic warming

DOE PAGES

Pold, Grace; Grandy, A. Stuart; Melillo, Jerry M.; ...

2017-03-22

As earth's climate continues to warm, it is important to understand how the capacity of terrestrial ecosystems to retain carbon (C) will be affected. We combined measurements of microbial activity with the concentration, quality, and physical accessibility of soil carbon to microorganisms to evaluate the mechanisms by which more than two decades of experimental warming has altered the carbon cycle in a Northeast US temperate deciduous forest. We have found that concentrations of soil organic matter were reduced in both the organic and mineral soil horizons. The molecular composition of the carbon was altered in the mineral soil with significantmore » reductions in the relative abundance of polysaccharides and lignin, and an increase in lipids. Mineral-associated organic matter was preferentially depleted by warming in the top 3 cm of mineral soil. We found that potential extracellular enzyme activity per gram of soil at a common temperature was generally unaffected by warming treatment. However, by measuring potential extracellular enzyme activities between 4 and 30 °C, we found that activity per unit microbial biomass at in-situ temperatures was increased by warming. This was associated with a tendency for microbial biomass to decrease with warming. These results indicate that chronic warming has reduced soil organic matter concentrations, selecting for a smaller but more active microbial community increasingly dependent on mineral-associated organic matter.« less

Changes in substrate availability drive carbon cycle response to chronic warming

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pold, Grace; Grandy, A. Stuart; Melillo, Jerry M.

As earth's climate continues to warm, it is important to understand how the capacity of terrestrial ecosystems to retain carbon (C) will be affected. We combined measurements of microbial activity with the concentration, quality, and physical accessibility of soil carbon to microorganisms to evaluate the mechanisms by which more than two decades of experimental warming has altered the carbon cycle in a Northeast US temperate deciduous forest. We have found that concentrations of soil organic matter were reduced in both the organic and mineral soil horizons. The molecular composition of the carbon was altered in the mineral soil with significantmore » reductions in the relative abundance of polysaccharides and lignin, and an increase in lipids. Mineral-associated organic matter was preferentially depleted by warming in the top 3 cm of mineral soil. We found that potential extracellular enzyme activity per gram of soil at a common temperature was generally unaffected by warming treatment. However, by measuring potential extracellular enzyme activities between 4 and 30 °C, we found that activity per unit microbial biomass at in-situ temperatures was increased by warming. This was associated with a tendency for microbial biomass to decrease with warming. These results indicate that chronic warming has reduced soil organic matter concentrations, selecting for a smaller but more active microbial community increasingly dependent on mineral-associated organic matter.« less

Impact of heavy metal on activity of some microbial enzymes in the riverbed sediments: Ecotoxicological implications in the Ganga River (India).

PubMed

Jaiswal, Deepa; Pandey, Jitendra

2018-04-15

We studied the extracellular enzyme activity (EEA) in the riverbed sediment along a 518km gradient of the Ganga River receiving carbon and nutrient load from varied human sources. Also, we tested, together with substrate-driven stimulation, if the heavy metal accumulated in the sediment inhibits enzyme activities. Because pristine values are not available, we considered Dev Prayag, a least polluted site located 624km upstream to main study stretch, as a reference site. There were distinct increases in enzyme activities in the sediment along the study gradient from Dev Prayag, however, between-site differences were in concordance with sediment carbon(C), nitrogen (N) and phosphorus (P). Fluorescein diacetate hydrolysis (FDAase), β-glucosidase (Glu) and protease activities showed positive correlation with C, N and P while alkaline phosphatase was found negatively correlated with P. Enzyme activities were found negatively correlated with heavy metal, although ecological risk index (E R i ) varied with site and metal species. Dynamic fit curves showed significant positive correlation between heavy metal and microbial metabolic quotient (qCO 2 ) indicating a decrease in microbial activity in response to increasing heavy metal concentrations. This study forms the first report linking microbial enzyme activities to regional scale sediment heavy metal accumulation in the Ganga River, suggests that the microbial enzyme activities in the riverbed sediment were well associated with the proportion of C, N and P and appeared to be a sensitive indicator of C, N and P accumulation in the river. Heavy metal accumulated in the sediment inhibits enzyme activities, although C rich sediment showed relatively low toxicity due probably to reduced bioavailability of the metal. The study has relevance from ecotoxicological as well as from biomonitoring perspectives. Copyright © 2017 Elsevier Inc. All rights reserved.

Wastewater-Enhanced Microbial Corrosion of Concrete Sewers.

PubMed

Jiang, Guangming; Zhou, Mi; Chiu, Tsz Ho; Sun, Xiaoyan; Keller, Jurg; Bond, Philip L

2016-08-02

Microbial corrosion of concrete in sewers is known to be caused by hydrogen sulfide, although the role of wastewater in regulating the corrosion processes is poorly understood. Flooding and splashing of wastewater in sewers periodically inoculates the concrete surface in sewer pipes. No study has systematically investigated the impacts of wastewater inoculation on the corrosion of concrete in sewers. This study investigated the development of the microbial community, sulfide uptake activity, and the change of the concrete properties for coupons subjected to periodic wastewater inoculation. The concrete coupons were exposed to different levels of hydrogen sulfide under well-controlled conditions in laboratory-scale corrosion chambers simulating real sewers. It was evident that the periodic inoculation induced higher corrosion losses of the concrete in comparison to noninoculated coupons. Instantaneous measurements such as surface pH did not reflect the cumulative corrosion losses caused by long-term microbial activity. Analysis of the long-term profiles of the sulfide uptake rate using a Gompertz model supported the enhanced corrosion activity and greater corrosion loss. The enhanced corrosion rate was due to the higher sulfide uptake rates induced by wastewater inoculation, although the increasing trend of sulfide uptake rates was slower with wastewater. Increased diversity in the corrosion-layer microbial communities was detected when the corrosion rates were higher. This coincided with the environmental conditions of increased levels of gaseous H2S and the concrete type.

Organic farming enhances soil microbial abundance and activity—A meta-analysis and meta-regression

PubMed Central

Symnaczik, Sarah; Mäder, Paul; De Deyn, Gerlinde; Gattinger, Andreas

2017-01-01

Population growth and climate change challenge our food and farming systems and provide arguments for an increased intensification of agriculture. A promising option is eco-functional intensification through organic farming, an approach based on using and enhancing internal natural resources and processes to secure and improve agricultural productivity, while minimizing negative environmental impacts. In this concept an active soil microbiota plays an important role for various soil based ecosystem services such as nutrient cycling, erosion control and pest and disease regulation. Several studies have reported a positive effect of organic farming on soil health and quality including microbial community traits. However, so far no systematic quantification of whether organic farming systems comprise larger and more active soil microbial communities compared to conventional farming systems was performed on a global scale. Therefore, we conducted a meta-analysis on current literature to quantify possible differences in key indicators for soil microbial abundance and activity in organic and conventional cropping systems. All together we integrated data from 56 mainly peer-reviewed papers into our analysis, including 149 pairwise comparisons originating from different climatic zones and experimental duration ranging from 3 to more than 100 years. Overall, we found that organic systems had 32% to 84% greater microbial biomass carbon, microbial biomass nitrogen, total phospholipid fatty-acids, and dehydrogenase, urease and protease activities than conventional systems. Exclusively the metabolic quotient as an indicator for stresses on microbial communities remained unaffected by the farming systems. Categorical subgroup analysis revealed that crop rotation, the inclusion of legumes in the crop rotation and organic inputs are important farming practices affecting soil microbial community size and activity. Furthermore, we show that differences in microbial size and activity between organic and conventional farming systems vary as a function of land use (arable, orchards, and grassland), plant life cycle (annual and perennial) and climatic zone. In summary, this study shows that overall organic farming enhances total microbial abundance and activity in agricultural soils on a global scale. PMID:28700609

Functional and Structural Succession of Soil Microbial Communities below Decomposing Human Cadavers

PubMed Central

Cobaugh, Kelly L.; Schaeffer, Sean M.; DeBruyn, Jennifer M.

2015-01-01

The ecological succession of microbes during cadaver decomposition has garnered interest in both basic and applied research contexts (e.g. community assembly and dynamics; forensic indicator of time since death). Yet current understanding of microbial ecology during decomposition is almost entirely based on plant litter. We know very little about microbes recycling carcass-derived organic matter despite the unique decomposition processes. Our objective was to quantify the taxonomic and functional succession of microbial populations in soils below decomposing cadavers, testing the hypotheses that a) periods of increased activity during decomposition are associated with particular taxa; and b) human-associated taxa are introduced to soils, but do not persist outside their host. We collected soils from beneath four cadavers throughout decomposition, and analyzed soil chemistry, microbial activity and bacterial community structure. As expected, decomposition resulted in pulses of soil C and nutrients (particularly ammonia) and stimulated microbial activity. There was no change in total bacterial abundances, however we observed distinct changes in both function and community composition. During active decay (7 - 12 days postmortem), respiration and biomass production rates were high: the community was dominated by Proteobacteria (increased from 15.0 to 26.1% relative abundance) and Firmicutes (increased from 1.0 to 29.0%), with reduced Acidobacteria abundances (decreased from 30.4 to 9.8%). Once decay rates slowed (10 - 23 d postmortem), respiration was elevated, but biomass production rates dropped dramatically; this community with low growth efficiency was dominated by Firmicutes (increased to 50.9%) and other anaerobic taxa. Human-associated bacteria, including the obligately anaerobic Bacteroides, were detected at high concentrations in soil throughout decomposition, up to 198 d postmortem. Our results revealed the pattern of functional and compositional succession in soil microbial communities during decomposition of human-derived organic matter, provided insight into decomposition processes, and identified putative predictor populations for time since death estimation. PMID:26067226

The influence of temperature and moisture contents regimes on the aerobic microbial activity of a biosolids composting blend.

PubMed

Liang, C; Das, K C; McClendon, R W

2003-01-01

To understand the relationships between temperature, moisture content, and microbial activity during the composting of biosolids (municipal wastewater treatment sludge), well-controlled incubation experiments were conducted using a 2-factor factorial design with six temperatures (22, 29, 36, 43, 50, and 57 degrees C) and five moisture contents (30, 40, 50, 60, and 70%). The microbial activity was measured as O2 uptake rate (mg g(-1) h(-1)) using a computer controlled respirometer. In this study, moisture content proved to be a dominant factor impacting aerobic microbial activity of the composting blend. Fifty percent moisture content appeared to be the minimal requirement for obtaining activities greater than 1.0 mg g(-1) h(-1). Temperature was also documented to be an important factor for biosolids composting. However, its effect was less influential than moisture content. Particularly, the enhancement of composting activities induced by temperature increment could be realized by increasing moisture content alone.

Mechanistic modeling of microbial interactions at pore to profile scale resolve methane emission dynamics from permafrost soil

NASA Astrophysics Data System (ADS)

Ebrahimi, Ali; Or, Dani

2017-05-01

The sensitivity of polar regions to raising global temperatures is reflected in rapidly changing hydrological processes associated with pronounced seasonal thawing of permafrost soil and increased biological activity. Of particular concern is the potential release of large amounts of soil carbon and stimulation of other soil-borne greenhouse gas emissions such as methane. Soil methanotrophic and methanogenic microbial communities rapidly adjust their activity and spatial organization in response to permafrost thawing and other environmental factors. Soil structural elements such as aggregates and layering affect oxygen and nutrient diffusion processes thereby contributing to methanogenic activity within temporal anoxic niches (hot spots). We developed a mechanistic individual-based model to quantify microbial activity dynamics in soil pore networks considering transport processes and enzymatic activity associated with methane production in soil. The model was upscaled from single aggregates to the soil profile where freezing/thawing provides macroscopic boundary conditions for microbial activity at different soil depths. The model distinguishes microbial activity in aerate bulk soil from aggregates (or submerged profile) for resolving methane production and oxidation rates. Methane transport pathways by diffusion and ebullition of bubbles vary with hydration dynamics. The model links seasonal thermal and hydrologic dynamics with evolution of microbial community composition and function affecting net methane emissions in good agreement with experimental data. The mechanistic model enables systematic evaluation of key controlling factors in thawing permafrost and microbial response (e.g., nutrient availability and enzyme activity) on long-term methane emissions and carbon decomposition rates in the rapidly changing polar regions.

Response of oxidative enzyme activities to nitrogen deposition affects soil concentrations of dissolved organic carbon

USGS Publications Warehouse

Waldrop, M.P.; Zak, D.R.

2006-01-01

Recent evidence suggests that atmospheric nitrate (NO3- ) deposition can alter soil carbon (C) storage by directly affecting the activity of lignin-degrading soil fungi. In a laboratory experiment, we studied the direct influence of increasing soil NO 3- concentration on microbial C cycling in three different ecosystems: black oak-white oak (BOWO), sugar maple-red oak (SMRO), and sugar maple-basswood (SMBW). These ecosystems span a broad range of litter biochemistry and recalcitrance; the BOWO ecosystem contains the highest litter lignin content, SMRO had intermediate lignin content, and SMBW leaf litter has the lowest lignin content. We hypothesized that increasing soil solution NO 3- would reduce lignolytic activity in the BOWO ecosystem, due to a high abundance of white-rot fungi and lignin-rich leaf litter. Due to the low lignin content of litter in the SMBW, we further reasoned that the NO3- repression of lignolytic activity would be less dramatic due to a lower relative abundance of white-rot basidiomycetes; the response in the SMRO ecosystem should be intermediate. We increased soil solution NO3- concentrations in a 73-day laboratory incubation and measured microbial respiration and soil solution dissolved organic carbon (DOC) and phenolics concentrations. At the end of the incubation, we measured the activity of ??-glucosidase, N-acetyl-glucosaminidase, phenol oxidase, and peroxidase, which are extracellular enzymes involved with cellulose and lignin degradation. We quantified the fungal biomass, and we also used fungal ribosomal intergenic spacer analysis (RISA) to gain insight into fungal community composition. In the BOWO ecosystem, increasing NO 3- significantly decreased oxidative enzyme activities (-30% to -54%) and increased DOC (+32% upper limit) and phenolic (+77% upper limit) concentrations. In the SMRO ecosystem, we observed a significant decrease in phenol oxidase activity (-73% lower limit) and an increase in soluble phenolic concentrations (+57% upper limit) in response to increasing NO 3- in soil solution, but there was no significant change in DOC concentration. In contrast to these patterns, increasing soil solution NO3- in the SMBW soil resulted in significantly greater phenol oxidase activity (+700% upper limit) and a trend toward lower DOC production (-52% lower limit). Nitrate concentration had no effect on microbial respiration or ??-glucosidase or N-acetyl-glucosaminidase activities. Fungal abundance and basidiomycete diversity tended to be highest in the BOWO soil and lowest in the SMBW, but neither displayed a consistent response to NO 3- additions. Taken together, our results demonstrate that oxidative enzyme production by microbial communities responds directly to NO3- deposition, controlling extracellular enzyme activity and DOC flux. The regulation of oxidative enzymes by different microbial communities in response to NO3- deposition highlights the fact that the composition and function of soil microbial communities directly control ecosystem-level responses to environmental change. ?? 2006 Springer Science+Business Media, Inc.

Microbial Influences on Trace Metal Cycling in a Meromictic Lake, Fayetteville Green Lake, NY

NASA Astrophysics Data System (ADS)

Zerkle, A. L.; House, C.; Kump, L.

2002-12-01

Microorganisms can exist in aquatic environments at very high cell densities of up to 1011 cells/L, and can accumulate significant quantities of trace metals. Bacteria actively take up bioactive trace metals, including Fe, Zn, Mn, Co, Ni, Cu, and Mo, which function as catalytic centers in metalloproteins and metal-activated enzymes involved in virtually all cellular functions. In addition, bacteria may catalyze the release of trace metals from inorganic substrates by processes such as the reduction of iron and manganese oxides, suggesting that trace metal distributions within a natural environment dominated by microbial processes may be controlled primarily by microbial ecology. Fayetteville Green Lake (FGL), NY, is a permanently stratified meromictic lake that has a well-oxygenated surface water mass (mixolimnion) overlying a relatively stagnant, anoxic deep water mass (monimolimnion). A chemocline separates the water masses at around 20m depth, where oxygen concentrations decrease and sulfate and methane concentrations increase. In addition, previous studies have indicated that trace metals such as V, Cr, Co, Mn, and Fe reach elevated concentrations at the chemocline. Using fluorescent in situ hybridization (FISH) of FGL samples from depths of up to 40m with bacterial and archaeal probes, we have shown that fluctuating redox conditions within the FGL water column correlate with significant variations in the composition and distribution of microbial populations with depth. The mixolimnion is dominated by Eubacteria, with increasing concentrations of Archaea in the lower anoxic zone. Increases in microbial cell densities coincide with increases in trace metals at the chemocline, suggesting microbial activity may be responsible for trace metal release at this boundary. 16S rRNA PCR cloning techniques are currently being used to identify dominant microbial populations at various levels within the FGL water column. Future studies will focus on the potential for these dominant microorganisms to influence trace metal cycling and bioavailability in the FGL water column.

Soil microbial and nutrient responses to 7 years of seasonally altered precipitation in a Chihuahuan Desert grassland.

PubMed

Bell, Colin W; Tissue, David T; Loik, Michael E; Wallenstein, Matthew D; Acosta-Martinez, Veronica; Erickson, Richard A; Zak, John C

2014-05-01

Soil microbial communities in Chihuahuan Desert grasslands generally experience highly variable spatiotemporal rainfall patterns. Changes in precipitation regimes can affect belowground ecosystem processes such as decomposition and nutrient cycling by altering soil microbial community structure and function. The objective of this study was to determine if increased seasonal precipitation frequency and magnitude over a 7-year period would generate a persistent shift in microbial community characteristics and soil nutrient availability. We supplemented natural rainfall with large events (one/winter and three/summer) to simulate increased precipitation based on climate model predictions for this region. We observed a 2-year delay in microbial responses to supplemental precipitation treatments. In years 3-5, higher microbial biomass, arbuscular mycorrhizae abundance, and soil enzyme C and P acquisition activities were observed in the supplemental water plots even during extended drought periods. In years 5-7, available soil P was consistently lower in the watered plots compared to control plots. Shifts in soil P corresponded to higher fungal abundances, microbial C utilization activity, and soil pH. This study demonstrated that 25% shifts in seasonal rainfall can significantly influence soil microbial and nutrient properties, which in turn may have long-term effects on nutrient cycling and plant P uptake in this desert grassland. © 2013 John Wiley & Sons Ltd.

Changes in microbial structure and functional communities at different soil depths during 13C labelled root litter degradation

NASA Astrophysics Data System (ADS)

Sanaullah, Muhammad; Baumann, Karen; Chabbi, Abad; Dignac, Marie-France; Maron, Pierre-Alain; Kuzyakov, Yakov; Rumpel, Cornelia

2014-05-01

Soil organic matter turnover depends on substrate quality and microbial activity in soil but little is known about how addition of freshly added organic material modifies the diversity of soil microbial communities with in a soil profile. We took advantage of a decomposition experiment, which was carried out at different soil depths under field conditions and sampled litterbags with 13C-labelled wheat roots, incubated in subsoil horizons at 30, 60 and 90 cm depth for up to 36 months. The effect of root litter addition on microbial community structure, diversity and activity was studied by determining total microbial biomass, PLFA signatures, molecular tools (DNA genotyping and pyrosequencing of 16S and 18S rDNAs) and extracellular enzyme activities. Automated ribosomal intergenic spacer analysis (ARISA) was also carried out to determine the differences in microbial community structure. We found that with the addition of root litter, total microbial biomass as well as microbial community composition and structure changed at different soil depths and change was significantly higher at top 30cm soil layer. Moreover, in the topsoil, population of both gram-positive and gram-negative bacteria increased with root litter addition over time, while subsoil horizons were relatively dominated by fungal community. Extra-cellular enzyme activities confirmed relatively higher fungal community at subsoil horizons compared with surface soil layer with bacteria dominant microbial population. Bacterial-ARISA profiling illustrated that the addition of root litter enhanced the abundance of Actinobacteria and Proteobacteria, at all three soil depths. These bacteria correspond to copiotrophic attributes, which can preferentially consume of labile soil organic C pools. While disappearance of oligotrophic Acidobacteria confirmed the shifting of microbial communities due to the addition of readily available substrate. We concluded that root litter mixing altered microbial community development which was soil horizon specific and its effects on soil microbial activity may impact on nutrient cycling.

Microbial enhancement of compost extracts based on cattle rumen content compost - characterisation of a system.

PubMed

Shrestha, Karuna; Shrestha, Pramod; Walsh, Kerry B; Harrower, Keith M; Midmore, David J

2011-09-01

Microbially enhanced compost extracts ('compost tea') are being used in commercial agriculture as a source of nutrients and for their perceived benefit to soil microbiology, including plant disease suppression. Rumen content material is a waste of cattle abattoirs, which can be value-added by conversion to compost and 'compost tea'. A system for compost extraction and microbial enhancement was characterised. Molasses amendment increased bacterial count 10-fold, while amendment based on molasses and 'fish and kelp hydrolysate' increased fungal count 10-fold. Compost extract incubated at 1:10 (w/v) dilution showed the highest microbial load, activity and humic/fulvic acid content compared to other dilutions. Aeration increased the extraction efficiency of soluble metabolites, and microbial growth rate, as did extraction of compost without the use of a constraining bag. A protocol of 1:10 dilution and aerated incubation with kelp and molasses amendments is recommended to optimise microbial load and fungal-to-bacterial ratio for this inoculum source. Copyright © 2011 Elsevier Ltd. All rights reserved.

Performance evaluation and microbial community of a sequencing batch biofilm reactor (SBBR) treating mariculture wastewater at different chlortetracycline concentrations.

PubMed

Zheng, Dong; Chang, Qingbo; Gao, Mengchun; She, Zonglian; Jin, Chunji; Guo, Liang; Zhao, Yangguo; Wang, Sen; Wang, Xuejiao

2016-11-01

The effects of chlortetracycline (CTC) on the performance, microbial activity, extracellular polymeric substances (EPS) and microbial community of a sequencing batch biofilm reactor (SBBR) were investigated in treating mariculture wastewater. Low CTC concentration (less than 6 mg/L) had no obvious effect on the SBBR performance, whereas high CTC concentration could inhibit the chemical oxygen demand (COD) and nitrogen removal of the SBBR. The microbial activity of the biofilm in the SBBR decreased with the increase of CTC concentration from 0 to 35 mg/L. The protein (PN) contents were always higher than the PS contents in both loosely bound EPS (LB-EPS) and tightly bound EPS (TB-EPS) at different CTC concentrations. The chemical compositions of LB-EPS and TB-EPS had obvious variations with the increase of CTC concentration from 0 to 35 mg/L. The high-throughput sequencing revealed the effects of CTC on the microbial communities of the biofilm at phylum, class and genus level. The relative abundances of some genera displayed a decreasing tendency with the increase of CTC concentration from 0 to 35 mg/L, such as Nitrospira, Paracoccus, Hyphomicrobium, Azospirillum. However, the relative abundances of the genera Flavobacterium, Aequorivita, Buchnera, Azonexus and Thioalbus increased with the increase of CTC concentration. Copyright © 2016 Elsevier Ltd. All rights reserved.

Elucidating microbial community adaptation to anaerobic co-digestion of fats, oils, and grease and food waste.

PubMed

Amha, Yamrot M; Sinha, Pooja; Lagman, Jewls; Gregori, Matt; Smith, Adam L

2017-10-15

Despite growing interest in co-digestion and demonstrated process improvements (e.g., enhanced stability and biogas production), few studies have evaluated how co-digestion impacts the anaerobic digestion (AD) microbiome. Three sequential bench-scale respirometry experiments were conducted at thermophilic temperature (50 °C) with various combinations of primary sludge (PS); thickened waste activated sludge (TWAS); fats, oils, and grease (FOG); and food waste (FW). Two additional runs were then performed to evaluate microbial inhibition at higher organic fractions of FOG (30-60% volatile solids loading (VSL; v/v)). Co-digestion of PS, TWAS, FOG, and FW resulted in a 26% increase in methane production relative to digestion of PS and TWAS. A substantial lag time was observed in biogas production for vessels with FOG addition that decreased by more than half in later runs, likely due to adaptation of the microbial community. 30% FOG with 10% FW showed the highest increase in methane production, increasing 53% compared to digestion of PS and TWAS. FOG addition above 50% VSL was found to be inhibitory with and without FW addition and resulted in volatile fatty acid (VFA) accumulation. Methane production was linked with high relative activity and abundance of syntrophic fatty-acid oxidizers alongside hydrogenotrophic methanogens, signaling the importance of interspecies interactions in AD. Specifically, relative activity of Syntrophomonas was significantly correlated with methane production. Further, methane production increased over subsequent runs along with methyl coenzyme M reductase (mcrA) gene expression, a functional gene in methanogens, suggesting temporal adaptation of the microbial community to co-digestion substrate mixtures. The study demonstrated the benefits of co-digestion in terms of performance enhancement and enrichment of key active microbial populations. Copyright © 2017 Elsevier Ltd. All rights reserved.

Effect of salinity on nitrogenase activity and composition of the active diazotrophic community in intertidal microbial mats.

PubMed

Severin, Ina; Confurius-Guns, Veronique; Stal, Lucas J

2012-06-01

Microbial mats are often found in intertidal areas experiencing a large range of salinities. This study investigated the effect of changing salinities on nitrogenase activity and on the composition of the active diazotrophic community (nifH transcript libraries) of three types of microbial mats situated along a littoral gradient. All three mat types exhibited highest nitrogenase activity at salinities close to ambient seawater or lower. The response to lower or higher salinity was strongest in mats higher up in the littoral zone. Changes in nitrogenase activity as the result of exposure to different salinities were accompanied by changes in the active diazotrophic community. The two stations higher up in the littoral zone showed nifH expression by Cyanobacteria (Oscillatoriales and Chroococcales) and Proteobacteria (Gammaproteobacteria and Deltaproteobacteria). At these stations, a decrease in the relative contribution of Cyanobacteria to the nifH transcript libraries was observed at increasing salinity coinciding with a decrease in nitrogenase activity. The station at the low water mark showed low cyanobacterial contribution to nifH transcript libraries at all salinities but an increase in deltaproteobacterial nifH transcripts under hypersaline conditions. In conclusion, increased salinities caused decreased nitrogenase activity and were accompanied by a lower proportion of cyanobacterial nifH transcripts.

Changes in microbial community characteristics and soil organic matter with nitrogen additions in two tropical forests

Treesearch

Daniela F. Cusack; Whendee L. Silver; Margaret S. Torn; Sarah D. Burton; Mary K. Firestone

2011-01-01

Microbial communities and their associated enzyme activities affect the amount and chemical quality of carbon (C) in soils. Increasing nitrogen (N) deposition, particularly in N-rich tropical forests, is likely to change the composition and behavior of microbial communities and feed back on ecosystem structure and function. This study presents a novel assessment of...

Influence of heavy metals and PCBs pollution on the enzyme activity and microbial community of paddy soils around an e-waste recycling workshop.

PubMed

Tang, Xianjin; Hashmi, Muhammad Z; Long, Dongyan; Chen, Litao; Khan, Muhammad I; Shen, Chaofeng

2014-03-14

Due to the emerging environmental issues related to e-waste there is concern about the quality of paddy soils near e-waste workshops. The levels of heavy metals and PCBs and their influence on the enzyme activity and microbial community of paddy soils obtained from the immediate vicinity of an e-waste workshop were investigated in the present study. The results indicated that the heavy metal and PCB pollution did not differ significantly with an increase of the sampling point distances (5 to 30 m). The concentration of Cd (2.16 mg·kg-1) and Cu (69.2 mg·kg-1) were higher, and the PCB pollution was also serious, ranging from 4.9 to 21.6 μg·kg-1. The highest enzyme activity was found for urease compared to phosphatase and catalase, and a fluctuating trend in soil enzyme activity was observed in soils from different sampling sites. The microbial analysis revealed that there was no apparent correlation between the microbial community and the pollutants. However, a slight influence for soil microbial communities could be found based on DGGE, the Shannon index and PCA analysis. The present study suggests that the contamination stress of heavy metals and PCBs might have a slight influence on microbial activity in paddy soils. This study provides the baseline data for enzyme activities and microbial communities in paddy soil under the influence of mixed contamination.

Influence of Heavy Metals and PCBs Pollution on the Enzyme Activity and Microbial Community of Paddy Soils around an E-Waste Recycling Workshop

PubMed Central

Tang, Xianjin; Hashmi, Muhammad Z.; Long, Dongyan; Chen, Litao; Khan, Muhammad I.; Shen, Chaofeng

2014-01-01

Due to the emerging environmental issues related to e-waste there is concern about the quality of paddy soils near e-waste workshops. The levels of heavy metals and PCBs and their influence on the enzyme activity and microbial community of paddy soils obtained from the immediate vicinity of an e-waste workshop were investigated in the present study. The results indicated that the heavy metal and PCB pollution did not differ significantly with an increase of the sampling point distances (5 to 30 m). The concentration of Cd (2.16 mg·kg−1) and Cu (69.2 mg·kg−1) were higher, and the PCB pollution was also serious, ranging from 4.9 to 21.6 μg·kg−1. The highest enzyme activity was found for urease compared to phosphatase and catalase, and a fluctuating trend in soil enzyme activity was observed in soils from different sampling sites. The microbial analysis revealed that there was no apparent correlation between the microbial community and the pollutants. However, a slight influence for soil microbial communities could be found based on DGGE, the Shannon index and PCA analysis. The present study suggests that the contamination stress of heavy metals and PCBs might have a slight influence on microbial activity in paddy soils. This study provides the baseline data for enzyme activities and microbial communities in paddy soil under the influence of mixed contamination. PMID:24637907

Humic fractions of forest, pasture and maize crop soils resulting from microbial activity

PubMed Central

Tavares, Rose Luiza Moraes; Nahas, Ely

2014-01-01

Humic substances result from the degradation of biopolymers of organic residues in the soil due to microbial activity. The objective of this study was to evaluate the influence of three different ecosystems: forest, pasture and maize crop on the formation of soil humic substances relating to their biological and chemical attributes. Microbial biomass carbon (MBC), microbial respiratory activity, nitrification potential, total organic carbon, soluble carbon, humic and fulvic acid fractions and the rate and degree of humification were determined. Organic carbon and soluble carbon contents decreased in the order: forest > pasture > maize; humic and fulvic acids decreased in the order forest > pasture=maize. The MBC and respiratory activity were not influenced by the ecosystems; however, the nitrification potential was higher in the forest than in other soils. The rate and degree of humification were higher in maize soil indicating greater humification of organic matter in this system. All attributes studied decreased significantly with increasing soil depth, with the exception of the rate and degree of humification. Significant and positive correlations were found between humic and fulvic acids contents with MBC, microbial respiration and nitrification potential, suggesting the microbial influence on the differential formation of humic substances of the different ecosystems. PMID:25477932

Assessing Coral Reefs on a Pacific-Wide Scale Using the Microbialization Score

PubMed Central

McDole, Tracey; Nulton, James; Barott, Katie L.; Felts, Ben; Hand, Carol; Hatay, Mark; Lee, Hochul; Nadon, Marc O.; Nosrat, Bahador; Salamon, Peter; Bailey, Barbara; Sandin, Stuart A.; Vargas-Angel, Bernardo; Youle, Merry; Zgliczynski, Brian J.; Brainard, Russell E.; Rohwer, Forest

2012-01-01

The majority of the world's coral reefs are in various stages of decline. While a suite of disturbances (overfishing, eutrophication, and global climate change) have been identified, the mechanism(s) of reef system decline remain elusive. Increased microbial and viral loading with higher percentages of opportunistic and specific microbial pathogens have been identified as potentially unifying features of coral reefs in decline. Due to their relative size and high per cell activity, a small change in microbial biomass may signal a large reallocation of available energy in an ecosystem; that is the microbialization of the coral reef. Our hypothesis was that human activities alter the energy budget of the reef system, specifically by altering the allocation of metabolic energy between microbes and macrobes. To determine if this is occurring on a regional scale, we calculated the basal metabolic rates for the fish and microbial communities at 99 sites on twenty-nine coral islands throughout the Pacific Ocean using previously established scaling relationships. From these metabolic rate predictions, we derived a new metric for assessing and comparing reef health called the microbialization score. The microbialization score represents the percentage of the combined fish and microbial predicted metabolic rate that is microbial. Our results demonstrate a strong positive correlation between reef microbialization scores and human impact. In contrast, microbialization scores did not significantly correlate with ocean net primary production, local chla concentrations, or the combined metabolic rate of the fish and microbial communities. These findings support the hypothesis that human activities are shifting energy to the microbes, at the expense of the macrobes. Regardless of oceanographic context, the microbialization score is a powerful metric for assessing the level of human impact a reef system is experiencing. PMID:22970122

Assessing coral reefs on a Pacific-wide scale using the microbialization score.

PubMed

McDole, Tracey; Nulton, James; Barott, Katie L; Felts, Ben; Hand, Carol; Hatay, Mark; Lee, Hochul; Nadon, Marc O; Nosrat, Bahador; Salamon, Peter; Bailey, Barbara; Sandin, Stuart A; Vargas-Angel, Bernardo; Youle, Merry; Zgliczynski, Brian J; Brainard, Russell E; Rohwer, Forest

2012-01-01

The majority of the world's coral reefs are in various stages of decline. While a suite of disturbances (overfishing, eutrophication, and global climate change) have been identified, the mechanism(s) of reef system decline remain elusive. Increased microbial and viral loading with higher percentages of opportunistic and specific microbial pathogens have been identified as potentially unifying features of coral reefs in decline. Due to their relative size and high per cell activity, a small change in microbial biomass may signal a large reallocation of available energy in an ecosystem; that is the microbialization of the coral reef. Our hypothesis was that human activities alter the energy budget of the reef system, specifically by altering the allocation of metabolic energy between microbes and macrobes. To determine if this is occurring on a regional scale, we calculated the basal metabolic rates for the fish and microbial communities at 99 sites on twenty-nine coral islands throughout the Pacific Ocean using previously established scaling relationships. From these metabolic rate predictions, we derived a new metric for assessing and comparing reef health called the microbialization score. The microbialization score represents the percentage of the combined fish and microbial predicted metabolic rate that is microbial. Our results demonstrate a strong positive correlation between reef microbialization scores and human impact. In contrast, microbialization scores did not significantly correlate with ocean net primary production, local chla concentrations, or the combined metabolic rate of the fish and microbial communities. These findings support the hypothesis that human activities are shifting energy to the microbes, at the expense of the macrobes. Regardless of oceanographic context, the microbialization score is a powerful metric for assessing the level of human impact a reef system is experiencing.

Will anticipated future climatic conditions affect belowground C utilization? - Insights into the role of microbial functional groups in a temperate heath/grassland.

NASA Astrophysics Data System (ADS)

Reinsch, Sabine; Michelsen, Anders; Sárossy, Zsuzsa; Egsgaard, Helge; Kappel Schmidt, Inger; Jakobsen, Iver; Ambus, Per

2013-04-01

The global terrestrial soil organic matter stock is the biggest terrestrial carbon pool (1500 Pg C) of which about 4 % is turned over annually. Thus, terrestrial ecosystems have the potential to accelerate or diminish atmospheric climate change effects via belowground carbon processes. We investigated the effect of elevated CO2 (510 ppm), prolonged spring/summer droughts and increased temperature (1 ˚C) on belowground carbon allocation and on the recovery of carbon by the soil microbial community. An in-situ 13C-carbon pulse-labeling experiment was carried out in a temperate heath/grassland (Denmark) in May 2011. Recently assimilated 13C-carbon was traced into roots, soil and microbial biomass 1, 2 and 8 days after pulse-labeling. The importance of the microbial community in C utilization was investigated using 13C enrichment patterns in microbial functional groups on the basis of phospholipid fatty acids (PLFAs) in roots. Gram-negative and gram-positive bacteria were distinguished from the decomposer groups of actinomycetes (belonging to the group of gram-positive bacteria) and saprophytic fungi. Mycorrhizal fungi specific PLFAs were not detected probably due to limited sample size in combination with restricted sensitivity of the used GC-c-IRMS setup. Climate treatments did not affect 13C allocation into roots, soil and microbial biomass carbon and also the total microbial biomass size stayed unchanged as frequently observed. However, climate treatments changed the composition of the microbial community: elevated CO2 significantly reduced the abundance of gram-negative bacteria (17:0cy) but did not affect the abundance of decomposers. Drought favored the bacterial community whereas increased temperatures showed reduced abundance of gram-negative bacteria (19:0cy) and changed the actinomycetes community (10Me16:0, 10Me18:0). However, not only the microbial community composition was affected by the applied climatic conditions, but also the activity of microbial functional groups in their utilization of recently assimilated carbon. Particularly the negative effect of the future treatment combination (CO2×T×D) on actinomycetes activity was surprising. By means of activity patterns of gram-negative bacteria, we observed the fastest carbon turnover rate under elevated CO2, and the slowest under extended drought conditions. A changed soil microbial community in combination with altered activities of different microbial functional groups leads to the conclusion that carbon allocation belowground was different under ambient and future climatic conditions and indicated reduced utilization of soil organic matter in the future due to a change of actinomycetes abundance and activity.

A Disease-Associated Microbial and Metabolomics State in Relatives of Pediatric Inflammatory Bowel Disease Patients.

PubMed

Jacobs, Jonathan P; Goudarzi, Maryam; Singh, Namita; Tong, Maomeng; McHardy, Ian H; Ruegger, Paul; Asadourian, Miro; Moon, Bo-Hyun; Ayson, Allyson; Borneman, James; McGovern, Dermot P B; Fornace, Albert J; Braun, Jonathan; Dubinsky, Marla

2016-11-01

Microbes may increase susceptibility to inflammatory bowel disease (IBD) by producing bioactive metabolites that affect immune activity and epithelial function. We undertook a family based study to identify microbial and metabolic features of IBD that may represent a predisease risk state when found in healthy first-degree relatives. Twenty-one families with pediatric IBD were recruited, comprising 26 Crohn's disease patients in clinical remission, 10 ulcerative colitis patients in clinical remission, and 54 healthy siblings/parents. Fecal samples were collected for 16S ribosomal RNA gene sequencing, untargeted liquid chromatography-mass spectrometry metabolomics, and calprotectin measurement. Individuals were grouped into microbial and metabolomics states using Dirichlet multinomial models. Multivariate models were used to identify microbes and metabolites associated with these states. Individuals were classified into 2 microbial community types. One was associated with IBD but irrespective of disease status, had lower microbial diversity, and characteristic shifts in microbial composition including increased Enterobacteriaceae, consistent with dysbiosis. This microbial community type was associated similarly with IBD and reduced microbial diversity in an independent pediatric cohort. Individuals also clustered bioinformatically into 2 subsets with shared fecal metabolomics signatures. One metabotype was associated with IBD and was characterized by increased bile acids, taurine, and tryptophan. The IBD-associated microbial and metabolomics states were highly correlated, suggesting that they represented an integrated ecosystem. Healthy relatives with the IBD-associated microbial community type had an increased incidence of elevated fecal calprotectin. Healthy first-degree relatives can have dysbiosis associated with an altered intestinal metabolome that may signify a predisease microbial susceptibility state or subclinical inflammation. Longitudinal prospective studies are required to determine whether these individuals have a clinically significant increased risk for developing IBD.

The Functional Potential of Microbial Communities in Hydraulic Fracturing Source Water and Produced Water from Natural Gas Extraction Characterized by Metagenomic Sequencing

PubMed Central

Mohan, Arvind Murali; Bibby, Kyle J.; Lipus, Daniel; Hammack, Richard W.; Gregory, Kelvin B.

2014-01-01

Microbial activity in produced water from hydraulic fracturing operations can lead to undesired environmental impacts and increase gas production costs. However, the metabolic profile of these microbial communities is not well understood. Here, for the first time, we present results from a shotgun metagenome of microbial communities in both hydraulic fracturing source water and wastewater produced by hydraulic fracturing. Taxonomic analyses showed an increase in anaerobic/facultative anaerobic classes related to Clostridia, Gammaproteobacteria, Bacteroidia and Epsilonproteobacteria in produced water as compared to predominantly aerobic Alphaproteobacteria in the fracturing source water. The metabolic profile revealed a relative increase in genes responsible for carbohydrate metabolism, respiration, sporulation and dormancy, iron acquisition and metabolism, stress response and sulfur metabolism in the produced water samples. These results suggest that microbial communities in produced water have an increased genetic ability to handle stress, which has significant implications for produced water management, such as disinfection. PMID:25338024

The functional potential of microbial communities in hydraulic fracturing source water and produced water from natural gas extraction characterized by metagenomic sequencing

DOE PAGES

Mohan, Arvind Murali; Bibby, Kyle J.; Lipus, Daniel; ...

2014-10-22

Microbial activity in produced water from hydraulic fracturing operations can lead to undesired environmental impacts and increase gas production costs. However, the metabolic profile of these microbial communities is not well understood. Here, for the first time, we present results from a shotgun metagenome of microbial communities in both hydraulic fracturing source water and wastewater produced by hydraulic fracturing. Taxonomic analyses showed an increase in anaerobic/facultative anaerobic classes related to Clostridia, Gammaproteobacteria, Bacteroidia and Epsilonproteobacteria in produced water as compared to predominantly aerobic Alphaproteobacteria in the fracturing source water. Thus, the metabolic profile revealed a relative increase in genes responsiblemore » for carbohydrate metabolism, respiration, sporulation and dormancy, iron acquisition and metabolism, stress response and sulfur metabolism in the produced water samples. These results suggest that microbial communities in produced water have an increased genetic ability to handle stress, which has significant implications for produced water management, such as disinfection.« less

The functional potential of microbial communities in hydraulic fracturing source water and produced water from natural gas extraction characterized by metagenomic sequencing.

PubMed

Mohan, Arvind Murali; Bibby, Kyle J; Lipus, Daniel; Hammack, Richard W; Gregory, Kelvin B

2014-01-01

Microbial activity in produced water from hydraulic fracturing operations can lead to undesired environmental impacts and increase gas production costs. However, the metabolic profile of these microbial communities is not well understood. Here, for the first time, we present results from a shotgun metagenome of microbial communities in both hydraulic fracturing source water and wastewater produced by hydraulic fracturing. Taxonomic analyses showed an increase in anaerobic/facultative anaerobic classes related to Clostridia, Gammaproteobacteria, Bacteroidia and Epsilonproteobacteria in produced water as compared to predominantly aerobic Alphaproteobacteria in the fracturing source water. The metabolic profile revealed a relative increase in genes responsible for carbohydrate metabolism, respiration, sporulation and dormancy, iron acquisition and metabolism, stress response and sulfur metabolism in the produced water samples. These results suggest that microbial communities in produced water have an increased genetic ability to handle stress, which has significant implications for produced water management, such as disinfection.

On the Functional Overlap between Complement and Anti-Microbial Peptides.

PubMed

Zimmer, Jana; Hobkirk, James; Mohamed, Fatima; Browning, Michael J; Stover, Cordula M

2014-01-01

Intriguingly, activated complement and anti-microbial peptides share certain functionalities; lytic, phagocytic, and chemo-attractant activities and each may, in addition, exert cell instructive roles. Each has been shown to have distinct LPS detoxifying activity and may play a role in the development of endotoxin tolerance. In search of the origin of complement, a functional homolog of complement C3 involved in opsonization has been identified in horseshoe crabs. Horseshoe crabs possess anti-microbial peptides able to bind to acyl chains or phosphate groups/saccharides of endotoxin, LPS. Complement activity as a whole is detectable in marine invertebrates. These are also a source of anti-microbial peptides with potential pharmaceutical applicability. Investigating the locality for the production of complement pathway proteins and their role in modulating cellular immune responses are emerging fields. The significance of local synthesis of complement components is becoming clearer from in vivo studies of parenchymatous disease involving specifically generated, complement-deficient mouse lines. Complement C3 is a central component of complement activation. Its provision by cells of the myeloid lineage varies. Their effector functions in turn are increased in the presence of anti-microbial peptides. This may point to a potentiating range of activities, which should serve the maintenance of health but may also cause disease. Because of the therapeutic implications, this review will consider closely studies dealing with complement activation and anti-microbial peptide activity in acute inflammation (e.g., dialysis-related peritonitis, appendicitis, and ischemia).

Toxic effect of two kinds of mineral collectors on soil microbial richness and activity: analysis by microcalorimetry, microbial count, and enzyme activity assay.

PubMed

Bararunyeretse, Prudence; Yao, Jun; Dai, Yunrong; Bigawa, Samuel; Guo, Zunwei; Zhu, Mijia

2017-01-01

Flotation reagents are hugely and increasingly used in mining and other industrial and economic activities from which an important part is discharged into the environment. China could be the most affected country by the resulting pollution. However, their ecotoxicological dimension is still less addressed and understood. This study aimed to analyze the toxic effect of sodium isobutyl xanthate (SIBX) and sodium isopropyl xanthate (SIPX) to soil microbial richness and activity and to make a comparison between the two compounds in regard to their effects on soil microbial and enzymes activities. Different methods, including microcalorimetry, viable cell counts, cell density, and catalase and fluorescein diacetate (FDA) hydrololase activities measurement, were applied. The two chemicals exhibited a significant inhibitory effect (P < 0.05 or P < 0.01) to all parameters, SIPX being more adverse than SIBX. As the doses of SIBX and SIPX increased from 5 to 300 μg g -1 soil, their inhibitory ratio ranged from 4.84 to 45.16 % and from 16.13 to 69.68 %, respectively. All parameters fluctuated with the incubation time (10-day period). FDA hydrolysis was more directly affected but was relatively more resilient than catalase activity. Potential changes of those chemicals in the experimental media and complementarity between experimental techniques were justified.

Vertical and horizontal distributions of microbial abundances and enzymatic activities in propylene-glycol-affected soils.

PubMed

Biró, Borbála; Toscano, Giuseppe; Horváth, Nikoletta; Matics, Heléna; Domonkos, Mónika; Scotti, Riccardo; Rao, Maria A; Wejden, Bente; French, Helen K

2014-01-01

The natural microbial activity in the unsaturated soil is vital for protecting groundwater in areas where high loads of biodegradable contaminants are supplied to the surface, which usually is the case for airports using aircraft de-icing fluids (ADF) in the cold season. Horizontal and vertical distributions of microbial abundance were assessed along the western runway of Oslo Airport (Gardermoen, Norway) to monitor the effect of ADF dispersion with special reference to the component with the highest chemical oxygen demand (COD), propylene glycol (PG). Microbial abundance was evaluated by several biondicators: colony-forming units (CFU) of some physiological groups (aerobic and anaerobic heterotrophs and microscopic fungi), most probable numbers (MPN) of PG degraders, selected catabolic enzymatic activities (fluorescein diacetate (FDA) hydrolase, dehydrogenase, and β-glucosidase). High correlations were found between the enzymatic activities and microbial counts in vertical soil profiles. All microbial abundance indicators showed a steep drop in the first meter of soil depth. The vertical distribution of microbial abundance can be correlated by a decreasing exponential function of depth. The horizontal trend of microbial abundance (evaluated as total aerobic CFU, MPN of PG-degraders, and FDA hydrolase activity) assessed in the surface soil at an increasing distance from the runway is correlated negatively with the PG and COD loads, suggesting the relevance of other chemicals in the modulation of microbial growth. The possible role of potassium formate, component of runway de-icers, has been tested in the laboratory by using mixed cultures of Pseudomonas spp., obtained by enrichment with a selective PG medium from soil samples taken at the most contaminated area near the runway. The inhibitory effect of formate on the growth of PG degraders is proven by the reduction of biomass yield on PG in the presence of formate.

Microbial activities and dissolved organic matter dynamics in oil-contaminated surface seawater from the Deepwater Horizon oil spill site.

PubMed

Ziervogel, Kai; McKay, Luke; Rhodes, Benjamin; Osburn, Christopher L; Dickson-Brown, Jennifer; Arnosti, Carol; Teske, Andreas

2012-01-01

The Deepwater Horizon oil spill triggered a complex cascade of microbial responses that reshaped the dynamics of heterotrophic carbon degradation and the turnover of dissolved organic carbon (DOC) in oil contaminated waters. Our results from 21-day laboratory incubations in rotating glass bottles (roller bottles) demonstrate that microbial dynamics and carbon flux in oil-contaminated surface water sampled near the spill site two weeks after the onset of the blowout were greatly affected by activities of microbes associated with macroscopic oil aggregates. Roller bottles with oil-amended water showed rapid formation of oil aggregates that were similar in size and appearance compared to oil aggregates observed in surface waters near the spill site. Oil aggregates that formed in roller bottles were densely colonized by heterotrophic bacteria, exhibiting high rates of enzymatic activity (lipase hydrolysis) indicative of oil degradation. Ambient waters surrounding aggregates also showed enhanced microbial activities not directly associated with primary oil-degradation (β-glucosidase; peptidase), as well as a twofold increase in DOC. Concurrent changes in fluorescence properties of colored dissolved organic matter (CDOM) suggest an increase in oil-derived, aromatic hydrocarbons in the DOC pool. Thus our data indicate that oil aggregates mediate, by two distinct mechanisms, the transfer of hydrocarbons to the deep sea: a microbially-derived flux of oil-derived DOC from sinking oil aggregates into the ambient water column, and rapid sedimentation of the oil aggregates themselves, serving as vehicles for oily particulate matter as well as oil aggregate-associated microbial communities.

Microbial Activities and Dissolved Organic Matter Dynamics in Oil-Contaminated Surface Seawater from the Deepwater Horizon Oil Spill Site

PubMed Central

Ziervogel, Kai; McKay, Luke; Rhodes, Benjamin; Osburn, Christopher L.; Dickson-Brown, Jennifer; Arnosti, Carol; Teske, Andreas

2012-01-01

The Deepwater Horizon oil spill triggered a complex cascade of microbial responses that reshaped the dynamics of heterotrophic carbon degradation and the turnover of dissolved organic carbon (DOC) in oil contaminated waters. Our results from 21-day laboratory incubations in rotating glass bottles (roller bottles) demonstrate that microbial dynamics and carbon flux in oil-contaminated surface water sampled near the spill site two weeks after the onset of the blowout were greatly affected by activities of microbes associated with macroscopic oil aggregates. Roller bottles with oil-amended water showed rapid formation of oil aggregates that were similar in size and appearance compared to oil aggregates observed in surface waters near the spill site. Oil aggregates that formed in roller bottles were densely colonized by heterotrophic bacteria, exhibiting high rates of enzymatic activity (lipase hydrolysis) indicative of oil degradation. Ambient waters surrounding aggregates also showed enhanced microbial activities not directly associated with primary oil-degradation (β-glucosidase; peptidase), as well as a twofold increase in DOC. Concurrent changes in fluorescence properties of colored dissolved organic matter (CDOM) suggest an increase in oil-derived, aromatic hydrocarbons in the DOC pool. Thus our data indicate that oil aggregates mediate, by two distinct mechanisms, the transfer of hydrocarbons to the deep sea: a microbially-derived flux of oil-derived DOC from sinking oil aggregates into the ambient water column, and rapid sedimentation of the oil aggregates themselves, serving as vehicles for oily particulate matter as well as oil aggregate-associated microbial communities. PMID:22509359

[Characterization of the Structure of the Prokaryotic Complex of Antarctic Permafrost by Molecular Genetic Techniques].

PubMed

Manucharova, N A; Trosheva, E V; Kol'tsova, E M; Demkina, E V; Karaevskaya, E V; Rivkina, E M; Mardanov, A V; El'-Registan, G I

2016-01-01

A prokaryotic mesophilic organotrophic community responsible for 10% of the total microbial number determined by epifluorescence microscopy was reactivated in the samples ofAntarctic permafrost retrieved from the environment favoring long-term preservation of microbial communities (7500 years). No culturable forms were obtained without resuscitation procedures (CFU = 0). Proteobacteria, Actinobacteria, and Firmicutes were the dominant microbial groups in the complex. Initiation of the reactivated microbial complex by addition of chitin (0.1% wt/vol) resulted in an increased share of metabolically active biomass (up to 50%) due to the functional domination of chitinolytics caused by the target resource. Thus, sequential application of resuscitation procedures and initiation of a specific physiological group (in this case, chitinolytics) to a permafrost-preserved microbial community made it possible to reveal a prokaryotic complex capable of reversion of metabolic activity (FISH data), to determine its phylogenetic structure by metagenomic anal-ysis, and to isolate a pure culture of the dominant microorganism with high chitinolytic activity.

Mechanistic modeling of thermo-hydrological processes and microbial interactions at pore to profile scales resolve methane emission dynamics from permafrost soil

NASA Astrophysics Data System (ADS)

Ebrahimi, Ali; Or, Dani

2017-04-01

The sensitivity of the Earth's polar regions to raising global temperatures is reflected in rapidly changing hydrological processes with pronounced seasonal thawing of permafrost soil and increased biological activity. Of particular concern is the potential release of large amounts of soil carbon and the stimulation of other soil-borne GHG emissions such as methane. Soil methanotrophic and methanogenic microbial communities rapidly adjust their activity and spatial organization in response to permafrost thawing and a host of other environmental factors. Soil structural elements such as aggregates and layering and hydration status affect oxygen and nutrient diffusion processes thereby contributing to methanogenic activity within temporal anoxic niches (hotspots or hot-layers). We developed a mechanistic individual based model to quantify microbial activity dynamics within soil pore networks considering, hydration, temperature, transport processes and enzymatic activity associated with methane production in soil. The model was the upscaled from single aggregates (or hotspots) to quantifying emissions from soil profiles in which freezing/thawing processes provide macroscopic boundary conditions for microbial activity at different soil depths. The model distinguishes microbial activity in aerate bulk soil from aggregates (or submerged parts of the profile) for resolving methane production and oxidation rates. Methane transport pathways through soil by diffusion and ebullition of bubbles vary with hydration dynamics and affect emission patterns. The model links seasonal thermal and hydrologic dynamics with evolution of microbial community composition and function affecting net methane emissions in good agreement with experimental data. The mechanistic model enables systematic evaluation of key controlling factors in thawing permafrost and microbial response (e.g., nutrient availability, enzyme activity, PH) on long term methane emissions and carbon decomposition rates in the rapidly changing polar regions.

Role of cyclic diguanylate in affecting microbial community shifts at different pH during the operation of simultaneous partial nitrification, anammox and denitrification process.

PubMed

Wang, Chao; Liu, Sitong; Xu, Xiaochen; Guo, Yongzhao; Yang, Fenglin; Wang, Dong

2018-05-08

The intracellular cyclic diguanylate acid (c-di-GMP) has emerged as a prominent second signal molecule that coordinates sessile-motile transition and biofilm formation in many bacteria. Herein, we study the role of c-di-GMP in affecting microbial community shifts at different pH levels during simultaneous partial nitrification, anammox and denitrification process (SNAD) in integrated fixed film activated sludge (IFAS) reactor. The results demonstrated that the contents of c-di-GMP notably decreased in suspended sludge, whereas the contents of c-di-GMP in biofilm had no significant change as pH gradually increased from 7.5 to 8.5. Most of the bacteria (Blastocatella, Brevundimonas) with flagella that have been reported to be regulated by c-di-GMP were present in suspended sludge, and the microbial community structure of suspended sludge had obvious change than biofilm. The increased alkaline pH reduced intracellular c-di-GMP content for increasing the motility of bacteria to be washed out from the reactor, causing the microbial community shifts in suspended sludge. This change would lead to the increase of nitrite-oxidizing bacteria which would inhibit anammox activity. Overall, this study provided more comprehensive information regarding the shifts of microbial community induced by c-di-GMP in SNAD-IFAS reactor. Copyright © 2018. Published by Elsevier B.V.

Energetic differences between bacterioplankton trophic groups and coral reef resistance

PubMed Central

McDole Somera, Tracey; Bailey, Barbara; Barott, Katie; Grasis, Juris; Hatay, Mark; Hilton, Brett J.; Hisakawa, Nao; Nosrat, Bahador; Nulton, James; Silveira, Cynthia B.; Sullivan, Chris; Brainard, Russell E.; Rohwer, Forest

2016-01-01

Coral reefs are among the most productive and diverse marine ecosystems on the Earth. They are also particularly sensitive to changing energetic requirements by different trophic levels. Microbialization specifically refers to the increase in the energetic metabolic demands of microbes relative to macrobes and is significantly correlated with increasing human influence on coral reefs. In this study, metabolic theory of ecology is used to quantify the relative contributions of two broad bacterioplankton groups, autotrophs and heterotrophs, to energy flux on 27 Pacific coral reef ecosystems experiencing human impact to varying degrees. The effective activation energy required for photosynthesis is lower than the average energy of activation for the biochemical reactions of the Krebs cycle, and changes in the proportional abundance of these two groups can greatly affect rates of energy and materials cycling. We show that reef-water communities with a higher proportional abundance of microbial autotrophs expend more metabolic energy per gram of microbial biomass. Increased energy and materials flux through fast energy channels (i.e. water-column associated microbial autotrophs) may dampen the detrimental effects of increased heterotrophic loads (e.g. coral disease) on coral reef systems experiencing anthropogenic disturbance. PMID:27097927

Energetic differences between bacterioplankton trophic groups and coral reef resistance.

PubMed

McDole Somera, Tracey; Bailey, Barbara; Barott, Katie; Grasis, Juris; Hatay, Mark; Hilton, Brett J; Hisakawa, Nao; Nosrat, Bahador; Nulton, James; Silveira, Cynthia B; Sullivan, Chris; Brainard, Russell E; Rohwer, Forest

2016-04-27

Coral reefs are among the most productive and diverse marine ecosystems on the Earth. They are also particularly sensitive to changing energetic requirements by different trophic levels. Microbialization specifically refers to the increase in the energetic metabolic demands of microbes relative to macrobes and is significantly correlated with increasing human influence on coral reefs. In this study, metabolic theory of ecology is used to quantify the relative contributions of two broad bacterioplankton groups, autotrophs and heterotrophs, to energy flux on 27 Pacific coral reef ecosystems experiencing human impact to varying degrees. The effective activation energy required for photosynthesis is lower than the average energy of activation for the biochemical reactions of the Krebs cycle, and changes in the proportional abundance of these two groups can greatly affect rates of energy and materials cycling. We show that reef-water communities with a higher proportional abundance of microbial autotrophs expend more metabolic energy per gram of microbial biomass. Increased energy and materials flux through fast energy channels (i.e. water-column associated microbial autotrophs) may dampen the detrimental effects of increased heterotrophic loads (e.g. coral disease) on coral reef systems experiencing anthropogenic disturbance. © 2016 The Author(s).

Accounting for microbial habitats in modeling soil organic matter dynamics

NASA Astrophysics Data System (ADS)

Chenu, Claire; Garnier, Patricia; Nunan, Naoise; Pot, Valérie; Raynaud, Xavier; Vieublé, Laure; Otten, Wilfred; Falconer, Ruth; Monga, Olivier

2017-04-01

The extreme heterogeneity of soils constituents, architecture and inhabitants at the microscopic scale is increasingly recognized. Microbial communities exist and are active in a complex 3-D physical framework of mineral and organic particles defining pores of various sizes, more or less inter-connected. This results in a frequent spatial disconnection between soil carbon, energy sources and the decomposer organisms and a variety of microhabitats that are more or less suitable for microbial growth and activity. However, current biogeochemical models account for C dynamics at the macroscale (cm, m) and consider time- and spatially averaged relationships between microbial activity and soil characteristics. Different modelling approaches have intended to account for this microscale heterogeneity, based either on considering aggregates as surrogates for microbial habitats, or pores. Innovative modelling approaches are based on an explicit representation of soil structure at the fine scale, i.e. at µm to mm scales: pore architecture and their saturation with water, localization of organic resources and of microorganisms. Three recent models are presented here, that describe the heterotrophic activity of either bacteria or fungi and are based upon different strategies to represent the complex soil pore system (Mosaic, LBios and µFun). These models allow to hierarchize factors of microbial activity in soil's heterogeneous architecture. Present limits of these approaches and challenges are presented, regarding the extensive information required on soils at the microscale and to up-scale microbial functioning from the pore to the core scale.

p-Coumaric Acid Influenced Cucumber Rhizosphere Soil Microbial Communities and the Growth of Fusarium oxysporum f.sp. cucumerinum Owen

PubMed Central

Zhou, Xingang; Wu, Fengzhi

2012-01-01

Background Autotoxicity of cucumber root exudates or decaying residues may be the cause of the soil sickness of cucumber. However, how autotoxins affect soil microbial communities is not yet fully understood. Methodology/Principal Findings The aims of this study were to study the effects of an artificially applied autotoxin of cucumber, p-coumaric acid, on cucumber seedling growth, rhizosphere soil microbial communities, and Fusarium oxysporum f.sp. cucumerinum Owen (a soil-borne pathogen of cucumber) growth. Abundance, structure and composition of rhizosphere bacterial and fungal communities were analyzed with real-time PCR, PCR-denaturing gradient gel electrophoresis (DGGE) and clone library methods. Soil dehydrogenase activity and microbial biomass C (MBC) were determined to indicate the activity and size of the soil microflora. Results showed that p-coumaric acid (0.1–1.0 µmol/g soil) decreased cucumber leaf area, and increased soil dehydrogenase activity, MBC and rhizosphere bacterial and fungal community abundances. p-Coumaric acid also changed the structure and composition of rhizosphere bacterial and fungal communities, with increases in the relative abundances of bacterial taxa Firmicutes, Betaproteobacteria, Gammaproteobacteria and fungal taxa Sordariomycete, Zygomycota, and decreases in the relative abundances of bacterial taxa Bacteroidetes, Deltaproteobacteria, Planctomycetes, Verrucomicrobia and fungal taxon Pezizomycete. In addition, p-coumaric acid increased Fusarium oxysporum population densities in soil. Conclusions/Significance These results indicate that p-coumaric acid may play a role in the autotoxicity of cucumber via influencing soil microbial communities. PMID:23118972

p-Coumaric acid influenced cucumber rhizosphere soil microbial communities and the growth of Fusarium oxysporum f.sp. cucumerinum Owen.

PubMed

Zhou, Xingang; Wu, Fengzhi

2012-01-01

Autotoxicity of cucumber root exudates or decaying residues may be the cause of the soil sickness of cucumber. However, how autotoxins affect soil microbial communities is not yet fully understood. The aims of this study were to study the effects of an artificially applied autotoxin of cucumber, p-coumaric acid, on cucumber seedling growth, rhizosphere soil microbial communities, and Fusarium oxysporum f.sp. cucumerinum Owen (a soil-borne pathogen of cucumber) growth. Abundance, structure and composition of rhizosphere bacterial and fungal communities were analyzed with real-time PCR, PCR-denaturing gradient gel electrophoresis (DGGE) and clone library methods. Soil dehydrogenase activity and microbial biomass C (MBC) were determined to indicate the activity and size of the soil microflora. Results showed that p-coumaric acid (0.1-1.0 µmol/g soil) decreased cucumber leaf area, and increased soil dehydrogenase activity, MBC and rhizosphere bacterial and fungal community abundances. p-Coumaric acid also changed the structure and composition of rhizosphere bacterial and fungal communities, with increases in the relative abundances of bacterial taxa Firmicutes, Betaproteobacteria, Gammaproteobacteria and fungal taxa Sordariomycete, Zygomycota, and decreases in the relative abundances of bacterial taxa Bacteroidetes, Deltaproteobacteria, Planctomycetes, Verrucomicrobia and fungal taxon Pezizomycete. In addition, p-coumaric acid increased Fusarium oxysporum population densities in soil. These results indicate that p-coumaric acid may play a role in the autotoxicity of cucumber via influencing soil microbial communities.

Benthic microbial abundance and activities in an intensively trawled ecosystem (Thermaikos Gulf, Aegean Sea)

NASA Astrophysics Data System (ADS)

Polymenakou, Paraskevi N.; Pusceddu, Antonio; Tselepides, Anastasios; Polychronaki, Thalia; Giannakourou, Antonia; Fiordelmondo, Carla; Hatziyanni, Eleni; Danovaro, Roberto

2005-12-01

Abundance of benthic bacteria, heterotrophic nanoflagellates and ciliates, extracellular enzymatic activities, bacterial C production, C mineralisation and sediment community oxygen consumption rates were measured in the Thermaikos Gulf (Northeastern Mediterranean), before (September 2001), and during intense trawling activities (October 2001 and February 2002). The biochemical composition of sedimentary organic matter has revealed that bottom trawling had an effect on the trophic state of Thermaikos Gulf. Changes on the benthic microbial food web were also recorded, during the three sampling seasons. Even though trawling-induced sediment resuspension did not alter significantly the abundance of the microbial components, with the exception of the most impacted station, it determined changes regarding their relative importance. Thus, the ratios of bacterium to nanoflagellates and ciliate to nanoflagellates abundance increased in the trawled stations, causing a sudden increase in bacterial C production, in comparison to the non-trawled station. Four months later, the effects of trawling on the microbial food web were less evident, masked possibly by the drastic decrease in the water temperature. The results of the present work suggest that bottom trawling induces alteration of the sedimentological variables and can be considered as a factor affecting the function of the microbial food web in marine coastal ecosystems. These alterations cause faster mobilisation of organic C buried in the sediment and increase nutrient concentrations and availability in the system, thus inducing an effect that could lead to coastal eutrophication.

In situ stabilization of cadmium-, lead-, and zinc-contaminated soil using various amendments.

PubMed

Lee, Sang-Hwan; Lee, Jin-Soo; Choi, Youn Jeong; Kim, Jeong-Gyu

2009-11-01

Chemical stabilization is an in situ remediation method that uses inexpensive amendments to reduce contaminant availability in polluted soil. We tested the effects of several amendments (limestone, red-mud, and furnace slag) on the extractability of heavy metals, microbial activities, phytoavailability of soil metals (assessed using lettuce, Lactuca sativa L.), and availability of heavy metals in ingested soil to the human gastrointestinal system (assessed using the physiologically based extraction test). The application of soil amendments significantly decreased the amount of soluble and extractable heavy metals in the soil (p<0.05). The decreased extractable metal content of soil was accompanied by increased microbial activity and decreased plant uptake of heavy metals. Soil microbial activities (soil respiration, urease, and dehydrogenase activity) significantly increased in limestone and red-mud-amended soils. Red-mud was the most effective treatment in decreasing heavy-metal concentrations in lettuce. Compared to non-amended control soil, lettuce uptake of Cd, Pb, and Zn was reduced 86%, 58%, and 73%, respectively, by the addition of red-mud.

[Effects of litter and root exclusion on soil microbial community composition and function of four plantations in subtropical sandy coastal plain area, China].

PubMed

Sang, Chang Peng; Wan, Xiao Hua; Yu, Zai Peng; Wang, Min Huang; Lin, Yu; Huang, Zhi Qun

2017-04-18

We conducted detritus input and removal treatment (DIRT) to examine the effects of shifting above- and belowground carbon (C) inputs on soil microbial biomass, community composition and function in subtropical Pinus elliottii, Eucalyptus urophylla × Eucalyptus grandis, Acacia aulacocarpa and Casuarina equisetifolia coastal sandy plain forests, and the treatments included: root trenching, litter removal and control. Up to September 2015, one year after the experiment began, we collected the 0-10 cm soil samples from each plot. Phospholipid fatty acid (PLFA) analysis was used to characterize the microbial community composition, and micro-hole enzymatic detection technology was utilized to determine the activity of six kinds of soil enzymes. Results showed that changes in microbial biomass induced by the C input manipulations differed among tree species, and mainly affected by litter and root qualily. In E. urophylla × E. grandis stands, root trenching significantly decreased the contents of total PLFAs, Gram-positive bacteria, Gram-negative bacteria, fungi and actinomycetes by 31%, 30%, 32%, 36% and 26%, respectively. Litter removal reduced the contents of Gram-positive bacteria, fungi and actinomycetes by 24%, 27% and 24%, respectively. However, C input manipulations had no significant effect on soil microbial biomassunder other three plantations. According to the effect of C input manipulations on soil microbial community structure, litter and root exclusion decreased fungi abundance and increased actinomycetes abundance. Different treatments under different plantations resulted in various soil enzyme activities. Litter removal significantly decreased the activities of cellobiohydrolase, β-glucosidase, acid phosphatase and N-acetyl-β-d-glucosaminidase of P. elliottii, A. aulacocarpa and C. equisetifolia, root exclusion only decreased and increased the activities of β-glucosidase in P. elliottii and A. aulacocarpa forest soils, respectively. Litter removal also decreased the activities of polyphenol oxidase (PPO) and peroxidase (PER) in P. elliottii and C. equisetifolia forest soils, while root trenching had no significant effect on the activities of PPO and PER under all plantations. The properties of litter and root were the important factors in determining the soil microbial community and enzyme activity, and the change of soil microenvironment, such as temperature and moisture, caused by C input manipulations was also the important driver for the change of soil microbial property.

Nitrogen amendment of green waste impacts microbial community, enzyme secretion and potential for lignocellulose decomposition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Chaowei; Harrold, Duff R.; Claypool, Joshua T.

Microorganisms involved in biomass deconstruction are an important resource for organic waste recycling and enzymes for lignocellulose bioconversion. The goals of this paper were to examine the impact of nitrogen amendment on microbial community restructuring, secretion of xylanases and endoglucanases, and potential for biomass deconstruction. Communities were cultivated aerobically at 55 °C on green waste (GW) amended with varying levels of NH 4Cl. Bacterial and fungal communities were determined using 16S rRNA and ITS region gene sequencing and PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was applied to predict relative abundance of genes involved in lignocellulose hydrolysis.more » Nitrogen amendment significantly increased secretion of xylanases and endoglucanases, and microbial activity; enzyme activities and cumulative respiration were greatest when nitrogen level in GW was between 4.13–4.56 wt% (g/g), but decreased with higher nitrogen levels. The microbial community shifted to one with increasing potential to decompose complex polymers as nitrogen increased with peak potential occurring between 3.79–4.45 wt% (g/g) nitrogen amendment. Finally, the results will aid in informing the management of nitrogen level to foster microbial communities capable of secreting enzymes that hydrolyze recalcitrant polymers in lignocellulose and yield rapid decomposition of green waste.« less

Impact of Organic and Conventional Systems of Coffee Farming on Soil Properties and Culturable Microbial Diversity

PubMed Central

2016-01-01

A study was undertaken with an objective of evaluating the long-term impacts of organic (ORG) and conventional (CON) methods of coffee farming on soil physical, chemical, biological, and microbial diversity. Electrical conductivity and bulk density were found to increase by 34% and 21%, respectively, in CON compared to ORG system, while water holding capacity was found decreased in both the systems. Significant increase in organic carbon was observed in ORG system. Major nutrients, nitrogen and potassium, levels showed inclination in both ORG and CON system, but the trend was much more pronounced in CON system. Phosphorus was found to increase in both ORG and CON system, but its availability was found to be more with CON system. In biological attributes, higher soil respiration and fluorescein diacetate activity were recorded in ORG system compared to CON system. Higher soil urease activity was observed in CON system, while dehydrogenase activity does not show significant differences between ORG and CON systems. ORG system was found to have higher macrofauna (31.4%), microbial population (34%), and microbial diversity indices compared to CON system. From the present study, it is accomplished that coffee soil under long-term ORG system has better soil properties compared to CON system. PMID:27042378

Impact of Organic and Conventional Systems of Coffee Farming on Soil Properties and Culturable Microbial Diversity.

PubMed

Velmourougane, Kulandaivelu

2016-01-01

A study was undertaken with an objective of evaluating the long-term impacts of organic (ORG) and conventional (CON) methods of coffee farming on soil physical, chemical, biological, and microbial diversity. Electrical conductivity and bulk density were found to increase by 34% and 21%, respectively, in CON compared to ORG system, while water holding capacity was found decreased in both the systems. Significant increase in organic carbon was observed in ORG system. Major nutrients, nitrogen and potassium, levels showed inclination in both ORG and CON system, but the trend was much more pronounced in CON system. Phosphorus was found to increase in both ORG and CON system, but its availability was found to be more with CON system. In biological attributes, higher soil respiration and fluorescein diacetate activity were recorded in ORG system compared to CON system. Higher soil urease activity was observed in CON system, while dehydrogenase activity does not show significant differences between ORG and CON systems. ORG system was found to have higher macrofauna (31.4%), microbial population (34%), and microbial diversity indices compared to CON system. From the present study, it is accomplished that coffee soil under long-term ORG system has better soil properties compared to CON system.

Changes in the Size of the Active Microbial Pool Explain Short-Term Soil Respiratory Responses to Temperature and Moisture

PubMed Central

Salazar-Villegas, Alejandro; Blagodatskaya, Evgenia; Dukes, Jeffrey S.

2016-01-01

Heterotrophic respiration contributes a substantial fraction of the carbon flux from soil to atmosphere, and responds strongly to environmental conditions. However, the mechanisms through which short-term changes in environmental conditions affect microbial respiration still remain unclear. Microorganisms cope with adverse environmental conditions by transitioning into and out of dormancy, a state in which they minimize rates of metabolism and respiration. These transitions are poorly characterized in soil and are generally omitted from decomposition models. Most current approaches to model microbial control over soil CO2 production relate responses to total microbial biomass (TMB) and do not differentiate between microorganisms in active and dormant physiological states. Indeed, few data for active microbial biomass (AMB) exist with which to compare model output. Here, we tested the hypothesis that differences in soil microbial respiration rates across various environmental conditions are more closely related to differences in AMB (e.g., due to activation of dormant microorganisms) than in TMB. We measured basal respiration (SBR) of soil incubated for a week at two temperatures (24 and 33°C) and two moisture levels (10 and 20% soil dry weight [SDW]), and then determined TMB, AMB, microbial specific growth rate, and the lag time before microbial growth (tlag) using the Substrate-Induced Growth Response (SIGR) method. As expected, SBR was more strongly correlated with AMB than with TMB. This relationship indicated that each g active biomass C contributed ~0.04 g CO2-C h−1 of SBR. TMB responded very little to short-term changes in temperature and soil moisture and did not explain differences in SBR among the treatments. Maximum specific growth rate did not respond to environmental conditions, suggesting that the dominant microbial populations remained similar. However, warmer temperatures and increased soil moisture both reduced tlag, indicating that favorable abiotic conditions activated soil microorganisms. We conclude that soil respiratory responses to short-term changes in environmental conditions are better explained by changes in AMB than in TMB. These results suggest that decomposition models that explicitly represent microbial carbon pools should take into account the active microbial pool, and researchers should be cautious in comparing modeled microbial pool sizes with measurements of TMB. PMID:27148213

Energy harvesting influences electrochemical performance of microbial fuel cells

NASA Astrophysics Data System (ADS)

Lobo, Fernanda Leite; Wang, Xin; Ren, Zhiyong Jason

2017-07-01

Microbial fuel cells (MFCs) can be effective power sources for remote sensing, wastewater treatment and environmental remediation, but their performance needs significant improvement. This study systematically analyzes how active harvesting using electrical circuits increased MFC system outputs as compared to passive resistors not only in the traditional maximal power point (MPP) but also in other desired operating points such as the maximum current point (MCP) and the maximum voltage point (MVP). Results show that active harvesting in MPP increased power output by 81-375% and active harvesting in MCP increased Coulombic efficiency by 207-805% compared with resisters operated at the same points. The cyclic voltammograms revealed redox potential shifts and supported the performance data. The findings demonstrate that active harvesting is a very effective approach to improve MFC performance across different operating points.

Microbial characteristics of purple paddy soil in response to Pb pollution.

PubMed

Jiang, Qiu-Ju; Zhang, Yue-Qiang; Zhang, La-Mei; Zhou, Xin-Bin; Shi, Xiao-Jun

2014-05-01

The study focused on the change of microbial characteristics affected by Plumbum pollution with purple paddy soil in an incubation experiment. The results showed that low concentration of Plumbum had little effect on most of microbial amounts, biological activity and enzymatic activity. However, denitrifying activity was inhibited severely, and inhibition rate was up to 98%. Medium and high concentration of Plumbum significantly reduced the amounts and activity of all microorganisms and enzymatic activity, which increased with incubation time. Negative correlations were found between Plumbum concentrations and microbial amounts, biological activity and enzymatic activities except fungi and actinomyces. Thus they can be used to indicate the Plumbum pollution levels to some extent. LD(50) of denitrifying bacteria (DB) and ED50 of denitrifying activity were 852mg/kg and 33.5mg/kg. Across all test soil microbes, denitrifying bacteria was most sensitive to Plumbum pollution in purple paddy soil. Value of early warning showed that anaerobic cellulose-decomposing bacteria (ACDB) and actinomyces were also sensitive to Plumbum pollution. We concluded that denitrifying activity, actinomyces, ACDB or DB can be chosen as predictor of Plumbum contamination in purple paddy soil.

Geoelectrical Evidence of Microbial Degradation of Diesel Contaminated Sediments

NASA Astrophysics Data System (ADS)

Werkema, D. D.; Atekwana, E. A.; Rossbach, S.; Sauck, W. A.

2003-12-01

The alteration of physical properties by microbial activity in petroleum contaminated sediments was investigated using geophysical techniques in laboratory column experiments. Microbial population growth was determined by the Most Probable Number technique (MPN), community dynamics were determined by the rDNA intergenic spacer analysis (RISA), microbial mineralization of diesel fuel was assessed using dissolved inorganic carbon (DIC), enhanced mineral dissolution was determined by dissolved calcium, and the vertical geoelectrical profile was measured using DC resistivity (converted to conductivity). The columns simulated a saturation profile and contained sanitized, uniform sand with the following experimental treatments: diesel + microbes, diesel, microbes, and no treatment. After 16 months, two important conclusions were drawn. First, the relative increase in magnitude of the parameters measured was highest in the diesel + microbe column (showing at least 110% increase), lower in the diesel column and lowest (actually showing a decrease) in the column with no treatment. Further, the diesel + microbe column showed the greatest increase in oil degrading microbial populations (135%) compared to the column with no treatment, which showed no changes. Secondly, the depth at which the conductivity reached the maximum occurred within and slightly above the diesel layer (which represents a depth that was originally water wet). It was further observed that the relative change in bulk conductivity below the saturated zone is of a lower magnitude than above (<10%). These results suggest the diesel layer, and the zone slightly above, were the most biologically active. Additionally, the diesel + microbe column showed RISA fragments attributed to microbial succession typically observed in organic contaminant plumes. A simple Archie's Law analysis was used to estimate the pore water conductivities necessary to reproduce the bulk conductivity measured. This analysis shows that relative to the column with only microbes (selected as the control to be most representative of field conditions), the diesel column revealed a 2.3 fold increase and the diesel + microbe column showed a 3 fold increase in pore water conductivity. This increase was located within the diesel layer above the water saturated zone. Within the saturated zone, the no treatment column showed a 0.81 fold increase, the diesel column a 1.28, and the diesel + microbe column 1.45. We conclude from this study that microbial activity and the resultant biogeochemical changes played an important role in modifying the geoelectrical properties of aquifers and sediments rich in organic carbon and mineralized by bacteria by increasing the bulk conductivity. This conductive zone occurred within and immediately above the free-phase petroleum layer. In natural environments with high concentrations of organic compounds available as electron donors, geophysical techniques may potentially be used as indicators of microbial activity. Notice: This is an abstract of a proposed presentation and does not necessarily reflect the United States Environmental Protection Agency (EPA) policy. The actual presentation has not been peer reviewed by EPA. Mention of trade names or commercial products does not constitute endorsement or recommendation for use.

Greenhouse gas emissions from a Cu-contaminated soil remediated by in situ stabilization and phytomanaged by a mixed stand of poplar, willows, and false indigo-bush.

PubMed

Šimek, M; Elhottová, D; Mench, M; Giagnoni, L; Nannipieri, P; Renella, G

2017-11-02

Phytomanagement of trace element-contaminated soils can reduce soil toxicity and restore soil ecological functions, including the soil gas exchange with the atmosphere. We studied the emission rate of the greenhouse gases (GHGs) CO 2 , CH 4 , and N 2 O; the potential CH 4 oxidation; denitrification enzyme activity (DEA), and glucose mineralization of a Cu-contaminated soil amended with dolomitic limestone and compost, alone or in combination, after a 2-year phytomanagement with a mixed stand of Populus nigra, Salix viminalis, S. caprea, and Amorpha fruticosa. Soil microbial biomass and microbial community composition after analysis of the phospholipid fatty acids (PLFA) profile were determined. Phytomanagement significantly reduced Cu availability and soil toxicity, increased soil microbial biomass and glucose mineralization capacity, changed the composition of soil microbial communities, and increased the CO 2 and N 2 O emission rates and DEA. Despite such increases, microbial communities were evolving toward less GHG emission per unit of microbial biomass than in untreated soils. Overall, the aided phytostabilization option would allow methanotrophic populations to establish in the remediated soils due to decreased soil toxicity and increased nutrient availability.

Effects of dietary protein levels and 2-methylbutyrate on ruminal fermentation, nutrient degradability, bacterial populations and urinary purine derivatives in Simmental steers.

PubMed

Wang, C; Liu, Q; Guo, G; Huo, W J; Pei, C X; Zhang, S L; Yang, W Z

2018-06-01

The objective of this study was to evaluate the effects of dietary crude protein (CP) levels and 2-methylbutyrate (MB) supplementation on ruminal fermentation, bacterial populations, microbial enzyme activity and urinary excretion of purine derivatives (PD) in Simmental steers. Eight ruminally cannulated Simmental steers, averaging 18 months of age and 465 ± 8.6 kg of body weight (BW), were used in a replicated 4 × 4 Latin square design by a 2 × 2 factorial arrangement. Low protein (98.5 g CP/kg dry matter [LP] or high protein (128.7 g CP/kg dry matter [HP]) diets were fed with MB supplementation (0 g [MB-] or 16.8 g steer -1  day -1 [MB+]). Steers were fed a total mixed ration with dietary corn straw to concentrate ratio of 50:50 (dry matter [DM] basis). The CP × MB interaction was observed for ruminal total VFA, molar proportions of acetate and propionate, acetate to propionate ratio, ammonia-N, effective degradability of neutral detergent fibre (NDF) and CP, microbial enzyme activity, bacterial populations and total PD excretion (p < .05). Ruminal pH decreased (p < .05), but ruminal total VFA concentration increased (p < .05) with increasing dietary CP level or MB supplementation. Acetate molar proportion increased (p = .043) with MB supplementation, but was not affected by dietary CP level. Propionate molar proportion decreased (p < .05) with increasing dietary CP level or MB supplementation. Consequently, acetate-to-propionate ratio increased (p = .001) with MB supplementation, but was not affected by dietary CP level. Ruminal ammonia-N content increased (p = .034) with increasing dietary CP level, but decreased (p = .012) with MB supplementation. The effective degradability of NDF and CP increased (p < .05) with increasing dietary CP level or MB supplementation. Microbial enzyme activity, bacterial populations and total PD excretion also increased (p < .05) with increasing dietary CP level or MB supplementation. The results indicated that ruminal fermentation, nutrient degradability, microbial enzyme activity, ruminal bacterial populations and microbial protein synthesis improved with increasing dietary CP level or MB supplementation in steers. © 2017 Blackwell Verlag GmbH.

Microbial metabolic networks in a complex electrogenic biofilm recovered from a stimulus-induced metatranscriptomics approach

PubMed Central

Ishii, Shun’ichi; Suzuki, Shino; Tenney, Aaron; Norden-Krichmar, Trina M.; Nealson, Kenneth H.; Bretschger, Orianna

2015-01-01

Microorganisms almost always exist as mixed communities in nature. While the significance of microbial community activities is well appreciated, a thorough understanding about how microbial communities respond to environmental perturbations has not yet been achieved. Here we have used a combination of metagenomic, genome binning, and stimulus-induced metatranscriptomic approaches to estimate the metabolic network and stimuli-induced metabolic switches existing in a complex microbial biofilm that was producing electrical current via extracellular electron transfer (EET) to a solid electrode surface. Two stimuli were employed: to increase EET and to stop EET. An analysis of cell activity marker genes after stimuli exposure revealed that only two strains within eleven binned genomes had strong transcriptional responses to increased EET rates, with one responding positively and the other responding negatively. Potential metabolic switches between eleven dominant members were mainly observed for acetate, hydrogen, and ethanol metabolisms. These results have enabled the estimation of a multi-species metabolic network and the associated short-term responses to EET stimuli that induce changes to metabolic flow and cooperative or competitive microbial interactions. This systematic meta-omics approach represents a next step towards understanding complex microbial roles within a community and how community members respond to specific environmental stimuli. PMID:26443302

Effects of Recurring Droughts on Extracellular Enzyme Activity in Mountain Grassland

NASA Astrophysics Data System (ADS)

Fuchslueger, L.; Bahn, M.; Kienzl, S.; Hofhansl, F.; Schnecker, J.; Richter, A.

2015-12-01

Water availability is a key factor for biogeochemical processes and determines microbial activity and functioning, and thereby organic matter decomposition in soils by affecting the osmotic potential, soil pore connectivity, substrate diffusion and nutrient availability. Low water availability during drought periods therefore directly affects microbial activity. Recurring drought periods likely induce shifts in microbial structure that might be reflected in altered responses of microbial turnover of organic matter by extracellular enzymes. To study this we measured a set of potential extracellular enzyme activity rates (cellobiohydrolase CBH; leucine-amino-peptidase LAP; phosphatase PHOS; phenoloxidase POX), in grassland soils that were exposed to extreme experimental droughts during the growing seasons of up to five subsequent years. During the first drought period after eight weeks of rain exclusion all measured potential enzyme activities were significantly decreased. In parallel, soil extractable organic carbon and nitrogen concentrations increased and microbial community structure, determined by phospholipid fatty acid analysis, changed. In soils that were exposed to two and three drought periods only PHOS decreased. After four years of drought again CBH, PHOS and POX decreased, while LAP was unaffected; after five years of drought PHOS and POX decreased and CBH and LAP remained stable. Thus, our results suggest that recurring extreme drought events can cause different responses of extracellular enzyme activities and that the responses change over time. We will discuss whether and to what degree these changes were related to shifts in microbial community composition. However, independent of whether a solitary or a recurrent drought was imposed, in cases when enzyme activity rates were altered during drought, they quickly recovered after rewetting. Overall, our data suggest that microbial functioning in mountain grassland is sensitive to drought, but highly resilient even after five years of drought.

[Effects of Cunninghamia lanceolata-broadleaved tree species mixed leaf litters on active soil organic matter].

PubMed

Wang, Qing-kui; Wang, Si-long; Yu, Xiao-jun; Zhang, Jian; Liu, Yan-xin

2007-06-01

With incubation test, this paper studied the effects of Cunninghamia lanceolata leaf litter and its mixture with the litters of main broadleaved tree species in subtropical China, such as Alnus cremastogyne, Kalopanax septemlobus and Michelia macclurei on active soil organic matter. The results showed that adding leaf litters into soil could significantly increase soil microbial biomass C and N, respiration rate and dissolved organic C, and mixed leaf litters were more effective than C. lanceolata leaf litter in increasing soil dissolved organic C. By the end of the incubation, the increment of soil microbial biomass C and N, respiration rate, and dissolved organic C in treatments C. lanceolata leaf litter and C. lanceolata-broadleaved tree species mixed leaf litters was 49% and 63%, 35% and 75%, 65% and 100%, and 66% and 108%, respectively, compared with control. The addition of leaf litters had no significant effects on soil microbial quotient and microbial biomass C/N ratio.

Accelerated rates of in situ microbial activity after permafrost collapse estimated from a porewater isotope model

NASA Astrophysics Data System (ADS)

Waldrop, M. P.; Neumann, R. B.; Jones, M.; Manies, K.; Mcfarland, J. W.; Blazewicz, S.; Turetsky, M. R.

2016-12-01

Permafrost thaw is expected to become widespread in interior Alaska over the coming century, resulting in increased CO2 and CH4 fluxes from soils and a positive feedback to global warming. However much of our understanding of the microbial response to thaw is predicated on simple laboratory incubations that preclude the multitude of interactions occurring in soils under field situations. Here, we utilize a time series of 13CO2 and 13CH4 measured in porewater collected from thermokarst bogs of different ages to estimate in-situ reaction rates of microbial respiration, methanogenesis from acetate, methanogenesis from CO2, homoacetogenesis, and methane oxidation from porewater concentrations and 13CO2 and 13CH4. We utilized this modeling technique to test the hypothesis that microbial activities are stimulated soon after permafrost thaw and this effect declines over time. Our field site is a chronosequence of thermokarst bogs at the Alaska Peatland Experiment (APEX) in interior AK where we have observed significant losses of peatland carbon since permafrost collapse over the last half century. Concentrations of dissolved CO2 and CH4 in porewater increased with depth, and were higher in the youngest bog compared to the older bogs. With increasing depth 13CH4 became more depleted while 13CO2 became more enriched. Preliminary modeling results, based upon these porewater gas concentrations and isotope values, indicate that microbial activities are higher in the youngest bogs compared to the older bogs, supporting the hypothesis that accelerated rates of microbial activities in young thermokarst features are responsible for high rates of C losses from these systems. Additionally, model results will be compared to variation in the abundance of methanogens, methane oxidizers, and acetogens as well as process rates measured in lab incubations, providing insights into the mechanisms responsible for these losses.

Microbial C:P stoichiometry is shaped by redox conditions along an elevation gradient in humid tropical rainforests

NASA Astrophysics Data System (ADS)

Lin, Y.; Gross, A.; Silver, W. L.

2017-12-01

Elemental stoichiometry of microorganisms is intimately related to ecosystem carbon and nutrient fluxes and is ultimately controlled by the chemical (plant tissue, soil, redox) and physical (temperature, moisture, aeration) environment. Previous meta-analyses have shown that the C:P ratio of soil microbial biomass exhibits significant variations among and within biomes. Little is known about the underlying causes of this variability. We examined soil microbial C:P ratios along an elevation gradient in the Luquillo Experimental Forest in Puerto Rico. We analyzed soils from mixed forest paired with monodominant palm forest every 100 m from 300 m to 1000 m a.s.l.. Mean annual precipitation increased with increasing elevation, resulting in stronger reducing conditions and accumulation of soil Fe(II) at higher elevations. The mean value and variability of soil microbial C:P ratios generally increased with increasing elevation except at 1000 m. At high elevations (600-900 m), the average value of microbial C:P ratio (108±10:1) was significantly higher than the global average ( 55:1). We also found that soil organic P increased with increasing elevation, suggesting that an inhibition of organic P mineralization, not decreased soil P availability, may cause the high microbial C:P ratio. The soil microbial C:P ratio was positively correlated with soil HCl-extractable Fe(II), suggesting that reducing conditions may be responsible for the elevational changes observed. In a follow-up experiment, soils from mixed forests at four elevation levels (300, 500, 700, and 1000 m) were incubated under aerobic and anaerobic conditions for two weeks. We found that anaerobic incubation consistently increased the soil microbial C:P ratio relative to the aerobic incubation. Overall, our results indicate that redox conditions can shift the elemental composition of microbial biomass. The high microbial C:P ratios induced under anoxic conditions may reflect inhibition of microbial P mineralization and/or immobilization under reducing conditions. These results will help us to better understand the patterns of nutrient cycling and microbial activity across macro-scale environmental gradients.

Landscape topography structures the soil microbiome in arctic polygonal tundra.

PubMed

Taş, Neslihan; Prestat, Emmanuel; Wang, Shi; Wu, Yuxin; Ulrich, Craig; Kneafsey, Timothy; Tringe, Susannah G; Torn, Margaret S; Hubbard, Susan S; Jansson, Janet K

2018-02-22

In the Arctic, environmental factors governing microbial degradation of soil carbon (C) in active layer and permafrost are poorly understood. Here we determined the functional potential of soil microbiomes horizontally and vertically across a cryoperturbed polygonal landscape in Alaska. With comparative metagenomics, genome binning of novel microbes, and gas flux measurements we show that microbial greenhouse gas (GHG) production is strongly correlated to landscape topography. Active layer and permafrost harbor contrasting microbiomes, with increasing amounts of Actinobacteria correlating with decreasing soil C in permafrost. While microbial functions such as fermentation and methanogenesis were dominant in wetter polygons, in drier polygons genes for C mineralization and CH 4 oxidation were abundant. The active layer microbiome was poised to assimilate N and not to release N 2 O, reflecting low N 2 O flux measurements. These results provide mechanistic links of microbial metabolism to GHG fluxes that are needed for the refinement of model predictions.

Climate change-driven treeline advances in the Urals alter soil microbial communities

NASA Astrophysics Data System (ADS)

Djukic, Ika; Moiseev, Pavel; Hagedorn, Frank

2016-04-01

Climatic warming may affect microbial communities and their functions either directly through increased temperatures or indirectly by changes in vegetation. Treelines are temperature-limited vegetation boundaries from tundra to forests. In unmanaged regions of the Ural mountains, there is evidence that the forest-tundra ecotone has shifted upward in response to climate warming during the 20th century. Little is known about the effects of the treeline advances on the microbial structure and function and hence they feedbacks on the belowground carbon and nitrogen cycling In our study, we aimed to estimate how ongoing upward shifts of the treeline ecotone might affect soil biodiversity and its function and hence soil carbon (C) and nitrogen (N) dynamics in the Southern and Polar Ural mountains. Along altitudinal gradients reaching from the tundra to forests, we determined the soil microbial community composition (using Phospholipid Fatty Acids method) and quantified the activity of several extracellular enzymes involved in the C and nutrient cycling. In addition, we measured C pools in biomass and soils and quantified C and N mineralization. The results for the top soils, both in South Urals and in the Polar Ural, indicate a close link between climate change driven vegetation changes and soil microbial communities. The observed changes in microbial structure are induced through the resulting more favorable conditions than due to a shift in litter quality. The activities of chitinase were significantly higher under trees than under herbaceous plants, while activities of cellulase and protease declined with altitude from the tundra to the closed forest. In contrast to enzymatic activities, soil carbon stocks did not change significantly with altitude very likely as a result of a balancing out of increased C inputs from vegetation by an enhanced C output through mineralization with forest expansion. The accelerated organic matter turnover in the forest than in the tundra leads to higher contents of mineral N and net nitrification rates. In turn, the increasing N availability may stimulate plant growth and hence, induce a positive feedback between treeline advances and soil nitrogen cycling through soil microbial communities.

Internal Porosity of Mineral Coating Supports Microbial Activity in Rapid Sand Filters for Groundwater Treatment

PubMed Central

Gülay, Arda; Tatari, Karolina; Musovic, Sanin; Mateiu, Ramona V.; Albrechtsen, Hans-Jørgen

2014-01-01

A mineral coating develops on the filter grain surface when groundwater is treated via rapid sand filtration in drinking water production. The coating changes the physical and chemical properties of the filter material, but little is known about its effect on the activity, colonization, diversity, and abundance of microbiota. This study reveals that a mineral coating can positively affect the colonization and activity of microbial communities in rapid sand filters. To understand this effect, we investigated the abundance, spatial distribution, colonization, and diversity of all and of nitrifying prokaryotes in filter material with various degrees of mineral coating. We also examined the physical and chemical characteristics of the mineral coating. The amount of mineral coating correlated positively with the internal porosity, the packed bulk density, and the biologically available surface area of the filter material. The volumetric NH4+ removal rate also increased with the degree of mineral coating. Consistently, bacterial 16S rRNA and amoA abundances positively correlated with increased mineral coating levels. Microbial colonization could be visualized mainly within the outer periphery (60.6 ± 35.6 μm) of the mineral coating, which had a thickness of up to 600 ± 51 μm. Environmental scanning electron microscopic (E-SEM) observations suggested an extracellular polymeric substance-rich matrix and submicron-sized bacterial cells. Nitrifier diversity profiles were similar irrespective of the degree of mineral coating, as indicated by pyrosequencing analysis. Overall, our results demonstrate that mineral coating positively affects microbial colonization and activity in rapid sand filters, most likely due to increased volumetric cell abundances facilitated by the large surface area of internal mineral porosity accessible for microbial colonization. PMID:25192987

Relative contributions of microbial and infrastructure heat at a crude oil-contaminated site

NASA Astrophysics Data System (ADS)

Warren, Ean; Bekins, Barbara A.

2018-04-01

Biodegradation of contaminants can increase the temperature in the subsurface due to heat generated from exothermic reactions, making temperature observations a potentially low-cost approach for determining microbial activity. For this technique to gain more widespread acceptance, it is necessary to better understand all the factors affecting the measured temperatures. Biodegradation has been occurring at a crude oil-contaminated site near Bemidji, Minnesota for 39 years, creating a quasi-steady-state plume of contaminants and degradation products. A model of subsurface heat generation and transport helps elucidate the contribution of microbial and infrastructure heating to observed temperature increases at this site. We created a steady-state, two-dimensional, heat transport model using previous-published parameter values for physical, chemical and biodegradation properties. Simulated temperature distributions closely match the observed average annual temperatures measured in the contaminated area at the site within less than 0.2 °C in the unsaturated zone and 0.4 °C in the saturated zone. The model results confirm that the observed subsurface heat from microbial activity is due primarily to methane oxidation in the unsaturated zone resulting in a 3.6 °C increase in average annual temperature. Another important source of subsurface heat is from the active, crude-oil pipelines crossing the site. The pipelines impact temperatures for a distance of 200 m and contribute half the heat. Model results show that not accounting for the heat from the pipelines leads to overestimating the degradation rates by a factor of 1.7, demonstrating the importance of identifying and quantifying all heat sources. The model results also highlighted a zone where previously unknown microbial activity is occurring at the site.

Relative contributions of microbial and infrastructure heat at a crude oil-contaminated site.

PubMed

Warren, Ean; Bekins, Barbara A

2018-04-01

Biodegradation of contaminants can increase the temperature in the subsurface due to heat generated from exothermic reactions, making temperature observations a potentially low-cost approach for determining microbial activity. For this technique to gain more widespread acceptance, it is necessary to better understand all the factors affecting the measured temperatures. Biodegradation has been occurring at a crude oil-contaminated site near Bemidji, Minnesota for 39 years, creating a quasi-steady-state plume of contaminants and degradation products. A model of subsurface heat generation and transport helps elucidate the contribution of microbial and infrastructure heating to observed temperature increases at this site. We created a steady-state, two-dimensional, heat transport model using previous-published parameter values for physical, chemical and biodegradation properties. Simulated temperature distributions closely match the observed average annual temperatures measured in the contaminated area at the site within less than 0.2 °C in the unsaturated zone and 0.4 °C in the saturated zone. The model results confirm that the observed subsurface heat from microbial activity is due primarily to methane oxidation in the unsaturated zone resulting in a 3.6 °C increase in average annual temperature. Another important source of subsurface heat is from the active, crude-oil pipelines crossing the site. The pipelines impact temperatures for a distance of 200 m and contribute half the heat. Model results show that not accounting for the heat from the pipelines leads to overestimating the degradation rates by a factor of 1.7, demonstrating the importance of identifying and quantifying all heat sources. The model results also highlighted a zone where previously unknown microbial activity is occurring at the site. Published by Elsevier B.V.

Quorum sensing and microbial drug resistance.

PubMed

Chen, Yu-fan; Liu, Shi-yin; Liang, Zhi-bin; Lv, Ming-fa; Zhou, Jia-nuan; Zhang, Lian-hui

2016-10-20

Microbial drug resistance has become a serious problem of global concern, and the evolution and regulatory mechanisms of microbial drug resistance has become a hotspot of research in recent years. Recent studies showed that certain microbial resistance mechanisms are regulated by quorum sensing system. Quorum sensing is a ubiquitous cell-cell communication system in the microbial world, which associates with cell density. High-density microbial cells produce sufficient amount of small signal molecules, activating a range of downstream cellular processes including virulence and drug resistance mechanisms, which increases bacterial drug tolerance and causes infections on host organisms. In this review, the general mechanisms of microbial drug resistance and quorum-sensing systems are summarized with a focus on the association of quorum sensing and chemical signaling systems with microbial drug resistance mechanisms, including biofilm formation and drug efflux pump. The potential use of quorum quenching as a new strategy to control microbial resistance is also discussed.

Colloidal Nanomolybdenum Influence upon the Antioxidative Reaction of Chickpea Plants ( Cicer arietinum L.)

NASA Astrophysics Data System (ADS)

Taran, Nataliya; Batsmanova, Ludmila; Kosyk, Oksana; Smirnov, Oleksandr; Kovalenko, Mariia; Honchar, Liubov; Okanenko, Alexander

2016-10-01

The use of colloidal solutions of metals as micronutrients enhances plant resistance to unfavorable environmental conditions and ensures high yields of food crops. The purpose of the study was a comparative evaluation of presowing treatment with nanomolybdenum and microbiological preparation impact upon the development of adaptive responses in chickpea plants. Oxidative processes did not develop in all variants of the experiment but in variants treated with microbial preparation, and joint action of microbial and nanopreparations even declined, as evidenced by the reduction of thiobarbituric acid reactive substances in photosynthetic tissues by 15 %. The activity of superoxide dismutase increased (by 15 %) in variant "nanomolybdenum" and joint action "microbial + nanomolybdenum," but it decreased by 20 % in variants with microbial preparation treatment. The same dependence was observed in changes of catalase activity. Antioxidant status factor, which takes into account the ratio of antioxidant to pro-oxidant, was the highest in variants with joint action of microbial preparation and nanomolybdenum (0.7), the lowest in variants with microbial treatment only (0.1). Thus, the results show that the action of nanoparticles of molybdenum activated antioxidant enzymes and decreased oxidative processes, thus promoting adaptation of plants.

Chemical manipulation of soil biota in a fescue meadow

DOE Office of Scientific and Technical Information (OSTI.GOV)

Malone, C. R.; Reichle, D. E.

Formalin, phorate, and sodium chlorate were used in field enclosures to create artificial habitats in a fescue meadow containing (1) reduced number of earthworms, (2) reduced numbers of earthworms and soil arthropods, and (3) reduction of total soil fauna and rate of microbial decomposition. Under these conditions, confined fescue litter initially decomposed more rapidly where arthropods or earthworms were suppressed than in controls with full complements of soil animals. After one year, reduction in numbers of soil animals had no net effect on litter decomposition, with faunal activity apparently having been compensated for by increased microbial activity. Where animals andmore » microbial activity were reduced, rate of litter loss was depressed initially but recovered after 10 months as the effects of chemical suppression of microbial populations subsided. Contrary to the effects on annual loss of litter, elimination of all or portions of the soil fauna depressed rates of loss of confined and buried roots, reflecting the role of animals in fragmenting roots before their decomposition by microorganisms. Habitat manipulations had pronounced effects on the mobility of 134Cs, and loss of the radionuclide from labelled litter was retarded despite an accelerated rate of decomposition. This effect apparently was associated with proliferation of microorganisms on litter and microbial immobilization of the radionuclide. Immobilization of 134Cs occurred following chemical perturbations, but only after an initial period of rapid loss resulting from increased microbial activity. Distribution of 134Cs in soil beneath tagged litter bags reflected the role of animals in element redistribution within soil. Finally, restricted vertical mobility of the nuclide occurred except where chemical application killed vegetation within the experimental enclosures.« less

Microbial community structure and activity in trace element-contaminated soils phytomanaged by Gentle Remediation Options (GRO).

PubMed

Touceda-González, M; Prieto-Fernández, Á; Renella, G; Giagnoni, L; Sessitsch, A; Brader, G; Kumpiene, J; Dimitriou, I; Eriksson, J; Friesl-Hanl, W; Galazka, R; Janssen, J; Mench, M; Müller, I; Neu, S; Puschenreiter, M; Siebielec, G; Vangronsveld, J; Kidd, P S

2017-12-01

Gentle remediation options (GRO) are based on the combined use of plants, associated microorganisms and soil amendments, which can potentially restore soil functions and quality. We studied the effects of three GRO (aided-phytostabilisation, in situ stabilisation and phytoexclusion, and aided-phytoextraction) on the soil microbial biomass and respiration, the activities of hydrolase enzymes involved in the biogeochemical cycles of C, N, P, and S, and bacterial community structure of trace element contaminated soils (TECS) from six field trials across Europe. Community structure was studied using denaturing gradient gel electrophoresis (DGGE) fingerprinting of Bacteria, α- and β-Proteobacteria, Actinobacteria and Streptomycetaceae, and sequencing of DGGE bands characteristic of specific treatments. The number of copies of genes involved in ammonia oxidation and denitrification were determined by qPCR. Phytomanagement increased soil microbial biomass at three sites and respiration at the Biogeco site (France). Enzyme activities were consistently higher in treated soils compared to untreated soils at the Biogeco site. At this site, microbial biomass increased from 696 to 2352 mg ATP kg -1 soil, respiration increased from 7.4 to 40.1 mg C-CO 2 kg -1 soil d -1 , and enzyme activities were 2-11-fold higher in treated soils compared to untreated soil. Phytomanagement induced shifts in the bacterial community structure at both, the total community and functional group levels, and generally increased the number of copies of genes involved in the N cycle (nirK, nirS, nosZ, and amoA). The influence of the main soil physico-chemical properties and trace element availability were assessed and eventual site-specific effects elucidated. Overall, our results demonstrate that phytomanagement of TECS influences soil biological activity in the long term. Copyright © 2017 Elsevier Ltd. All rights reserved.

[Effects of different application rates of calcium cyanamide on soil microbial biomass and enzyme activity in cucumber continuous cropping].

PubMed

Zhang, Xue-peng; Ning, Tang-yuan; Yang, Yan; Sun, Tao; Zhang, Shu-min; Wang, Bin

2015-10-01

A 2-year field experiment was conducted to study the effects of CaCN2 combined with cucumber straw retention on soil microbial biomass carbon (SMBC) , soil microbial biomass nitrogen (SMBN) and soil enzyme activities under cucumber continuous cropping system. Four treatments were used in this study as follows: CK (null CaCN2), CaCN2-90 (1350 kg CaCN2 . hm-2) CaCN2-60 (900 kg CaCN2 . hm-2), CaCN2-30 (450 kg CaCN2 . hm-2). The results indicated that, compared with the other treatments, CaCN2-90 treatment significantly decreased SMBC in 0-10 cm soil layer at seedling stage, but increased SMBC in 0-20 cm soil layer after early-fruit stage. Compared with CK, CaCN2 increased SMBC in 0-20 cm soil layer at late-fruit stage, and increased SMBN in 0-10 cm soil layer at mid- and late-fruit stages, however there was no significant trend among CaCN2 treatments in the first year (2012), while in the second year (2013) SMBN increased with the increasing CaCN2 amount after mid-fruit stage. CaCN2 increased straw decaying and nutrients releasing, and also increased soil organic matter. Furthermore, the CaCN2-90 could accelerate straw decomposition. Compared with CK, CaCN2 effectively increased soil urease, catalase and polyphenol oxidase activity. The soil urease activity increased while the polyphenol oxidase activity decreased with the increase of CaCN2, and CaCN2-60 could significantly improve catalase activity. Soil organic matter, urease activity and catalase activity had significant positive correlations with SMBC and SMBN. However, polyphenol oxidase activity was negatively correlated to SMBC and SMBN. Our findings indicated that CaCN2 application at 900 kg . hm-2 combined with cucumber straw retention could effectively improve soil environment, alleviating the soil obstacles under the cucumber continuous cropping system.

Fire Effects on Microbial Enzyme Activities in Larch Forests of the Siberian Arctic

NASA Astrophysics Data System (ADS)

Ludwig, S.; Alexander, H. D.; Bulygina, E. B.; Mann, P. J.; Natali, S.

2012-12-01

Arctic forest ecosystems are warming at an accelerated rate relative to lower latitudes, with global implications for C cycling within these regions. As climate continues to warm and dry, wildfire frequency and severity are predicted to increase, creating a positive feedback to climate warming. Increased fire activity will also influence the microenvironment experienced by soil microbes in disturbed soils. Because soil microbes regulate carbon (C) and nitrogen (N) cycling between terrestrial ecosystems and the atmosphere, it is important to understand microbial response to fires, particularly in the understudied larch forests in the Siberian Arctic. In this project, we created experimental burn plots in a mature larch forest in the Kolyma River watershed of Northeastern Siberia. Plots were burned at several treatments: control (no burn), low, moderate, and severe. After, 1 and 8 d post-fire, we measured soil organic layer depth, soil organic matter (SOM) content, soil moisture, and CO2 flux from the plots. Additionally, we leached soils and measured dissolved organic carbon (DOC), total dissolved nitrogen (TDN), NH4, NO3, soluble reactive phosphorus (SRP), and chromophoric dissolved organic matter (CDOM). Furthermore, we measured extracellular activity of four enzymes involved in soil C and nutrient cycling (leucine aminopeptidase (LAP), β-glucosidase, phosphatase, and phenol oxidase). One day post-fire, LAP activity was similarly low in all treatments, but by 8 d post-fire, LAP activity was lower in burned plots compared to control plots, likely due to increased nitrogen content with increasing burn severity. Phosphatase activity decreased with burn severity 1 d post-fire, but after 8 d, moderate and severe burn plots exhibited increased phosphatase activity. Coupled with trends in LAP activity, this suggests a switch in nutrient limitation from N to phosphorus that is more pronounced with burn severity. β-glucosidase activity similarly decreased with burn severity 1 d post-fire, but by 8 d post-fire activity was the same in all treatments, indicating complete recovery of the microbial population. Phenol oxidase activity was low in all treatments 1 d post-fire, but by 8 d post-fire, severe plots had substantially increased phenol oxidase activity, likely due to microbial efforts to mitigate phenolic compound toxicity following severe fires. Both DOC and the slope ratio of CDOM absorbance increased with burn severity 1 d post-fire, indicating higher extractability of lighter molecular weight C from severe burns. These results imply that black C created from fires remains as a stable C pool while more labile C is mobilized with increasing burn severity. Our results suggest that the immediate effects of fire severity on microbial communities have the potential to change both nutrient use and the form and concentration of C being processed and mobilized from larch forest ecosystems. These findings highlight the importance of changing fire regimes on soil dynamics with implications for forest re-growth, soil-atmospheric feedbacks, and terrestrial inputs to aquatic ecosystems.

Temperature Sensitivity as a Microbial Trait Using Parameters from Macromolecular Rate Theory

PubMed Central

Alster, Charlotte J.; Baas, Peter; Wallenstein, Matthew D.; Johnson, Nels G.; von Fischer, Joseph C.

2016-01-01

The activity of soil microbial extracellular enzymes is strongly controlled by temperature, yet the degree to which temperature sensitivity varies by microbe and enzyme type is unclear. Such information would allow soil microbial enzymes to be incorporated in a traits-based framework to improve prediction of ecosystem response to global change. If temperature sensitivity varies for specific soil enzymes, then determining the underlying causes of variation in temperature sensitivity of these enzymes will provide fundamental insights for predicting nutrient dynamics belowground. In this study, we characterized how both microbial taxonomic variation as well as substrate type affects temperature sensitivity. We measured β-glucosidase, leucine aminopeptidase, and phosphatase activities at six temperatures: 4, 11, 25, 35, 45, and 60°C, for seven different soil microbial isolates. To calculate temperature sensitivity, we employed two models, Arrhenius, which predicts an exponential increase in reaction rate with temperature, and Macromolecular Rate Theory (MMRT), which predicts rate to peak and then decline as temperature increases. We found MMRT provided a more accurate fit and allowed for more nuanced interpretation of temperature sensitivity in all of the enzyme × isolate combinations tested. Our results revealed that both the enzyme type and soil isolate type explain variation in parameters associated with temperature sensitivity. Because we found temperature sensitivity to be an inherent and variable property of an enzyme, we argue that it can be incorporated as a microbial functional trait, but only when using the MMRT definition of temperature sensitivity. We show that the Arrhenius metrics of temperature sensitivity are overly sensitive to test conditions, with activation energy changing depending on the temperature range it was calculated within. Thus, we propose the use of the MMRT definition of temperature sensitivity for accurate interpretation of temperature sensitivity of soil microbial enzymes. PMID:27909429

Nutrient gradients in a granular activated carbon biofilter drives bacterial community organization and dynamics.

PubMed

Boon, Nico; Pycke, Benny F G; Marzorati, Massimo; Hammes, Frederik

2011-12-01

The quality of drinking water is ensured by hygienic barriers and filtration steps, such as ozonation and granular activated carbon (GAC) filtration. Apart from adsorption, GAC filtration involves microbial processes that remove biodegradable organic carbon from the ozonated ground or surface water and ensures biological stability of the treated water. In this study, microbial community dynamics in were monitored during the start-up and maturation of an undisturbed pilot-scale GAC filter at 4 depths (10, 45, 80 and 115 cm) over a period of 6 months. New ecological tools, based on 16S rRNA gene-DGGE, were correlated to filter performance and microbial activity and showed that the microbial gradients developing in the filter was of importance. At 10 cm from the top, receiving the freshly ozonated water with the highest concentration of nutrients, the microbial community dynamics were minimal and the species richness remained low. However, the GAC samples at 80-115 cm showed a 2-3 times higher species richness than the 10-45 cm samples. The highest biomass densities were observed at 45-80 cm, which corresponded with maximum removal of dissolved and assimilable organic carbon. Furthermore, the start-up period was clearly distinguishable using the Lorenz analysis, as after 80 days, the microbial community shifted to an apparent steady-state condition with increased evenness. This study showed that GAC biofilter performance is not necessarily correlated to biomass concentration, but rather that an elevated functionality can be the result of increased microbial community richness, evenness and dynamics. Copyright © 2011 Elsevier Ltd. All rights reserved.

Peatland Microbial Communities and Decomposition Processes in the James Bay Lowlands, Canada

PubMed Central

Preston, Michael D.; Smemo, Kurt A.; McLaughlin, James W.; Basiliko, Nathan

2012-01-01

Northern peatlands are a large repository of atmospheric carbon due to an imbalance between primary production by plants and microbial decomposition. The James Bay Lowlands (JBL) of northern Ontario are a large peatland-complex but remain relatively unstudied. Climate change models predict the region will experience warmer and drier conditions, potentially altering plant community composition, and shifting the region from a long-term carbon sink to a source. We collected a peat core from two geographically separated (ca. 200 km) ombrotrophic peatlands (Victor and Kinoje Bogs) and one minerotrophic peatland (Victor Fen) located near Victor Bog within the JBL. We characterized (i) archaeal, bacterial, and fungal community structure with terminal restriction fragment length polymorphism of ribosomal DNA, (ii) estimated microbial activity using community level physiological profiling and extracellular enzymes activities, and (iii) the aeration and temperature dependence of carbon mineralization at three depths (0–10, 50–60, and 100–110 cm) from each site. Similar dominant microbial taxa were observed at all three peatlands despite differences in nutrient content and substrate quality. In contrast, we observed differences in basal respiration, enzyme activity, and the magnitude of substrate utilization, which were all generally higher at Victor Fen and similar between the two bogs. However, there was no preferential mineralization of carbon substrates between the bogs and fens. Microbial community composition did not correlate with measures of microbial activity but pH was a strong predictor of activity across all sites and depths. Increased peat temperature and aeration stimulated CO2 production but this did not correlate with a change in enzyme activities. Potential microbial activity in the JBL appears to be influenced by the quality of the peat substrate and the presence of microbial inhibitors, which suggests the existing peat substrate will have a large influence on future JBL carbon dynamics. PMID:22393328

Quantifying microbial activity in deep subsurface sediments using a tritium based hydrognease enzyme assay

NASA Astrophysics Data System (ADS)

Adhikari, R.; Nickel, J.; Kallmeyer, J.

2012-12-01

Microbial life is widespread in Earth's subsurface and estimated to represent a significant fraction of Earth's total living biomass. However, very little is known about subsurface microbial activity and its fundamental role in biogeochemical cycles of carbon and other biologically important elements. Hydrogen is one of the most important elements in subsurface anaerobic microbial metabolism. Heterotrophic and chemoautotrophic microorganisms use hydrogen in their metabolic pathways. They either consume or produce protons for ATP synthesis. Hydrogenase (H2ase) is a ubiquitous intracellular enzyme that catalyzes the interconversion of molecular hydrogen and/or water into protons and electrons. The protons are used for the synthesis of ATP, thereby coupling energy generating metabolic processes to electron acceptors such as CO2 or sulfate. H2ase enzyme targets a key metabolic compound in cellular metabolism therefore the assay can be used as a measure for total microbial activity without the need to identify any specific metabolic process. Using the highly sensitive tritium assay we measured H2ase enzyme activity in the organic-rich sediments of Lake Van, a saline, alkaline lake in eastern Turkey, in marine sediments of the Barents Sea and in deep subseafloor sediments from the Nankai Trough. H2ase activity could be quantified at all depths of all sites but the activity distribution varied widely with depth and between sites. At the Lake Van sites H2ase activity ranged from ca. 20 mmol H2 cm-3d-1 close to the sediment-water interface to 0.5 mmol H2 cm-3d-1 at a depth of 0.8 m. In samples from the Barents Sea H2ase activity ranged between 0.1 to 2.5 mmol H2 cm-3d-1 down to a depth of 1.60 m. At all sites the sulfate reduction rate profile followed the upper part of the H2ase activity profile until sulfate reduction reached the minimum detection limit (ca. 10 pmol cm-3d-1). H2ase activity could still be quantified after the decline of sulfate reduction, indicating that other microbial processes are becoming quantitatively more important. Similarly, H2ase activity could be quantified at greater depths (ca. 400 mbsf) in Nankai Trough sediments. Nankai Trough is one of the world's most geologically active accretionary wedges, where the Philippine Plate is subducting under the southwest of Japan. Due to the transient faulting, huge amounts of energy are liberated that enhance chemical transformations of organic and inorganic matter. An increase in H2ase activity could be observed at greater depth, which suggests that microbial activity is stimulated by the fault activity. Current techniques for the quantification of microbial activity in deep sediments have already reached their physical and technical limits and-in many cases- are still not sensitive enough to quantify extremely low rates of microbial activity. Additional to the quantification of specific processes, estimates of total microbial activity will provide valuable information on energy flux and microbial metabolism in the subsurface biosphere and other low-energy environments as well as help identifying hotspots of microbial activity. The tritium H2ase assay has a potential to become a valuable tool to measure total subsurface microbial activity.

Effect of elevated CO2 on degradation of azoxystrobin and soil microbial activity in rice soil.

PubMed

Manna, Suman; Singh, Neera; Singh, V P

2013-04-01

An experiment was conducted in open-top chambers (OTC) to study the effect of elevated CO2 (580 ± 20 μmol mol(-1)) on azoxystrobin degradation and soil microbial activities. Results indicated that elevated CO2 did not have any significant effect on the persistence of azoxystrobin in rice-planted soil. The half-life values for the azoxystrobin in rice soils were 20.3 days in control (rice grown at ambient CO2 outdoors), 19.3 days in rice grown under ambient CO2 atmosphere in OTC, and 17.5 days in rice grown under elevated CO2 atmosphere in OTC. Azoxystrobin acid was recovered as the only metabolite of azoxystrobin, but it did not accumulate in the soil/water and was further metabolized. Elevated CO2 enhanced soil microbial biomass (MBC) and alkaline phosphatase activity of soil. Compared with rice grown at ambient CO2 (both outdoors and in OTC), the soil MBC at elevated CO2 increased by twofold. Elevated CO2 did not affect dehydrogenase, fluorescein diacetate, and acid phosphatase activity. Azoxystrobin application to soils, both ambient and elevated CO2, inhibited alkaline phosphates activity, while no effect was observed on other enzymes. Slight increase (1.8-2 °C) in temperature inside OTC did not affect microbial parameters, as similar activities were recorded in rice grown outdoors and in OTC at ambient CO2. Higher MBC in soil at elevated CO2 could be attributed to increased carbon availability in the rhizosphere via plant metabolism and root secretion; however, it did not significantly increase azoxystrobin degradation, suggesting that pesticide degradation was not the result of soil MBC alone. Study suggested that increased CO2 levels following global warming might not adversely affect azoxystrobin degradation. However, global warming is a continuous and cumulative process, therefore, long-term studies are necessary to get more realistic assessment of global warming on fate of pesticide.

Metagenomic analysis of the soil microbial N-cycling community in response to increased N deposition in the alpine PNW

NASA Astrophysics Data System (ADS)

Simpson, A.; Zabowski, D.

2016-12-01

The effects of nitrogen (N) deposition, caused by increasing agricultural activity and increased fossil fuel usage in populated areas, is of great concern to managers of formerly pristine, N-limited environments such as the alpine. Increasingly available mineral N can cause changes in the soil microbial community, including downshifting naturally N-fixing microbial populations, and increasing nitrification (and soil acidification) with concomitant increases in nitrous oxide release. As part of a larger study to determine critical N loads for PNW alpine ecosystems, we used inorganic N fertilization to mimic increasing levels of N deposition at alpine sites at Mount Rainier, North Cascades, and Olympic National Parks. After 3 years of N application, we isolated DNA from soil samples taken from the rooting zones of two different species categories - lupine spp. and heather (evergreen shrub) spp. Amplicon-based libraries for genes for nitrogenase and ammonia monooxygenase were sequenced for each level of fertilization. We will present changes in diversity and size of the N-fixing and nitrifying microbial communities by increasing N application, site, and plant community.

Hydraulic redistribution affects modeled carbon cycling via soil microbial activity and suppressed fire.

PubMed

Fu, Congsheng; Wang, Guiling; Bible, Kenneth; Goulden, Michael L; Saleska, Scott R; Scott, Russell L; Cardon, Zoe G

2018-04-13

Hydraulic redistribution (HR) of water from moist to drier soils, through plant roots, occurs world-wide in seasonally dry ecosystems. Although the influence of HR on landscape hydrology and plant water use has been amply demonstrated, HR's effects on microbe-controlled processes sensitive to soil moisture, including carbon and nutrient cycling at ecosystem scales, remain difficult to observe in the field and have not been integrated into a predictive framework. We incorporated a representation of HR into the Community Land Model (CLM4.5) and found the new model improved predictions of water, energy, and system-scale carbon fluxes observed by eddy covariance at four seasonally dry yet ecologically diverse temperate and tropical AmeriFlux sites. Modeled plant productivity and microbial activities were differentially stimulated by upward HR, resulting at times in increased plant demand outstripping increased nutrient supply. Modeled plant productivity and microbial activities were diminished by downward HR. Overall, inclusion of HR tended to increase modeled annual ecosystem uptake of CO 2 (or reduce annual CO 2 release to the atmosphere). Moreover, engagement of CLM4.5's ground-truthed fire module indicated that though HR increased modeled fuel load at all four sites, upward HR also moistened surface soil and hydrated vegetation sufficiently to limit the modeled spread of dry season fire and concomitant very large CO 2 emissions to the atmosphere. Historically, fire has been a dominant ecological force in many seasonally dry ecosystems, and intensification of soil drought and altered precipitation regimes are expected for seasonally dry ecosystems in the future. HR may play an increasingly important role mitigating development of extreme soil water potential gradients and associated limitations on plant and soil microbial activities, and may inhibit the spread of fire in seasonally dry ecosystems. © 2018 John Wiley & Sons Ltd.

Metaproteogenomic Profiling of Microbial Communities Colonizing Actively Venting Hydrothermal Chimneys

PubMed Central

Pjevac, Petra; Meier, Dimitri V.; Markert, Stephanie; Hentschker, Christian; Schweder, Thomas; Becher, Dörte; Gruber-Vodicka, Harald R.; Richter, Michael; Bach, Wolfgang; Amann, Rudolf; Meyerdierks, Anke

2018-01-01

At hydrothermal vent sites, chimneys consisting of sulfides, sulfates, and oxides are formed upon contact of reduced hydrothermal fluids with oxygenated seawater. The walls and surfaces of these chimneys are an important habitat for vent-associated microorganisms. We used community proteogenomics to investigate and compare the composition, metabolic potential and relative in situ protein abundance of microbial communities colonizing two actively venting hydrothermal chimneys from the Manus Basin back-arc spreading center (Papua New Guinea). We identified overlaps in the in situ functional profiles of both chimneys, despite differences in microbial community composition and venting regime. Carbon fixation on both chimneys seems to have been primarily mediated through the reverse tricarboxylic acid cycle and fueled by sulfur-oxidation, while the abundant metabolic potential for hydrogen oxidation and carbon fixation via the Calvin–Benson–Bassham cycle was hardly utilized. Notably, the highly diverse microbial community colonizing the analyzed black smoker chimney had a highly redundant metabolic potential. In contrast, the considerably less diverse community colonizing the diffusely venting chimney displayed a higher metabolic versatility. An increased diversity on the phylogenetic level is thus not directly linked to an increased metabolic diversity in microbial communities that colonize hydrothermal chimneys. PMID:29696004

Altered soil microbial community at elevated CO2 leads to loss of soil carbon

PubMed Central

Carney, Karen M.; Hungate, Bruce A.; Drake, Bert G.; Megonigal, J. Patrick

2007-01-01

Increased carbon storage in ecosystems due to elevated CO2 may help stabilize atmospheric CO2 concentrations and slow global warming. Many field studies have found that elevated CO2 leads to higher carbon assimilation by plants, and others suggest that this can lead to higher carbon storage in soils, the largest and most stable terrestrial carbon pool. Here we show that 6 years of experimental CO2 doubling reduced soil carbon in a scrub-oak ecosystem despite higher plant growth, offsetting ≈52% of the additional carbon that had accumulated at elevated CO2 in aboveground and coarse root biomass. The decline in soil carbon was driven by changes in soil microbial composition and activity. Soils exposed to elevated CO2 had higher relative abundances of fungi and higher activities of a soil carbon-degrading enzyme, which led to more rapid rates of soil organic matter degradation than soils exposed to ambient CO2. The isotopic composition of microbial fatty acids confirmed that elevated CO2 increased microbial utilization of soil organic matter. These results show how elevated CO2, by altering soil microbial communities, can cause a potential carbon sink to become a carbon source. PMID:17360374

Stoichiometry of microbial carbon use efficiency in soils

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sinsabaugh, Robert L.; Turner, Benjamin L.; Talbot, Jennifer M.

The carbon use efficiency (CUE) of microbial communities partitions the flow of C from primary producers to the atmosphere, decomposer food webs, and soil C stores. CUE, usually defined as the ratio of growth to assimilation, is a critical parameter in ecosystem models, but is seldom measured directly in soils because of the methodological difficulty of measuring in situ rates of microbial growth and respiration. Alternatively, CUE can be estimated indirectly from the elemental stoichiometry of organic matter and microbial biomass, and the ratios of C to nutrient-acquiring ecoenzymatic activities. In this paper, we used this approach to estimate andmore » compare microbial CUE in >2000 soils from a broad range of ecosystems. Mean CUE based on C:N stoichiometry was 0.269 ± 0.110 (mean ± SD). A parallel calculation based on C:P stoichiometry yielded a mean CUE estimate of 0.252 ± 0.125. The mean values and frequency distributions were similar to those from aquatic ecosystems, also calculated from stoichiometric models, and to those calculated from direct measurements of bacterial and fungal growth and respiration. CUE was directly related to microbial biomass C with a scaling exponent of 0.304 (95% CI 0.237–0.371) and inversely related to microbial biomass P with a scaling exponent of -0.234 (95% CI -0.289 to -0.179). Relative to CUE, biomass specific turnover time increased with a scaling exponent of 0.509 (95% CI 0.467–0.551). CUE increased weakly with mean annual temperature. CUE declined with increasing soil pH reaching a minimum at pH 7.0, then increased again as soil pH approached 9.0, a pattern consistent with pH trends in the ratio of fungal : bacteria abundance and growth. Structural equation models that related geographic variables to CUE component variables showed the strongest connections for paths linking latitude and pH to β-glucosidase activity and soil C:N:P ratios. Finally, the integration of stoichiometric and metabolic models provides a quantitative description of the functional organization of soil microbial communities that can improve the representation of CUE in microbial process and ecosystem simulation models.« less

Acacia Changes Microbial Indicators and Increases C and N in Soil Organic Fractions in Intercropped Eucalyptus Plantations.

PubMed

Pereira, Arthur P A; Zagatto, Maurício R G; Brandani, Carolina B; Mescolotti, Denise de Lourdes; Cotta, Simone R; Gonçalves, José L M; Cardoso, Elke J B N

2018-01-01

Intercropping forest plantations of Eucalyptus with nitrogen-fixing trees can increase soil N inputs and stimulate soil organic matter (OM) cycling. However, microbial indicators and their correlation in specific fractions of soil OM are unclear in the tropical sandy soils. Here, we examined the microbial indicators associated with C and N in the soil resulting from pure and intercropped Eucalyptus grandis and Acacia mangium plantations. We hypothesized that introduction of A. mangium in a Eucalyptus plantation promotes changes in microbial indicators and increases C and N concentrations on labile fractions of the soil OM, when compared to pure eucalyptus plantations. We determined the microbial and enzymatic activity, and the potential for C degradation by the soil microbial community. Additionally, we evaluated soil OM fractions and litter parameters. Soil (0-20 cm) and litter samples were collected at 27 and 39 months after planting from the following treatments: pure E. grandis (E) and A. mangium (A) plantations, pure E. grandis plantations with N fertilizer (E+N) and an E. grandis , and A. mangium intercropped plantations (E+A). The results showed that intercropped plantations (E+A) increase 3, 45, and 70% microbial biomass C as compared to A, E+N, and E, at 27 months after planting. The metabolic quotient ( q CO 2 ) showed a tendency toward stressful values in pure E. grandis plantations and a strong correlation with dehydrogenase activity. A and E+A treatments also exhibited the highest organic fractions (OF) and C and N contents. A canonical redundancy analysis revealed positive correlations between microbial indicators of soil and litter attributes, and a strong effect of C and N variables in differentiating A and E+A from E and E+N treatments. The results suggested that a significant role of A. mangium enhance the dynamics of soil microbial indicators which help in the accumulation of C and N in soil OF in intercropped E. grandis plantations. Our results are mostly relevant to plantations in sandy soil areas with low levels of OM, suggesting and efficient method for improving nutrient availability in the soil and optimizing eucalyptus growth and development.

The interaction between abiotic photodegradation and microbial decomposition under ultraviolet radiation.

PubMed

Wang, Jing; Liu, Lingli; Wang, Xin; Chen, Yiwei

2015-05-01

Elevated ultraviolet (UV) radiation has been demonstrated to stimulate litter decomposition. Despite years of research, it is still not fully understood whether the acceleration in litter degradation is primarily attributed to abiotic photodegradation or the combined effects of abiotic photodegradation and microbial decomposition. In this study, we used meta-analysis to synthesize photodegradation studies and compared the effects of UV radiation on litter decomposition between abiotic and biotic conditions. We also conducted a microcosm experiment to assess the effects of UV radiation on litter biodegradability and microbial activity. Overall, our meta-analysis found that under abiotic photodegradation, UV radiation reduced the remaining litter mass by 1.44% (95% CI: 0.85% to 2.08%), did not affect the remaining lignin and increased the dissolved organic carbon (DOC) concentration by 14.01% (1.49-23.67%). Under combined abiotic photodegradation and microbial decomposition, UV radiation reduced the remaining litter mass and lignin by 1.60% (0.04-3.58%) and 16.07% (9.27-24.23%), respectively, but did not alter DOC concentration. UV radiation had no significant impact on soil microbial biomass carbon (MBC), but it reduced microbial respiration by 44.91% (2.26-78.62%) and altered the composition of the microbial community. In addition, UV radiation reduced nitrogen (N) immobilization by 19.44% (4.77-37.92%). Our microcosm experiment further indicated that DOC concentration and the amount of respired C in UV-treated litter increased with UV exposure time, suggesting that longer UV exposure resulted in greater biodegradability. Overall, our study suggested that UV exposure could increase litter biodegradability by increasing the microbial accessibility of lignin, as well as the labile carbon supply to microbes. However, the remaining litter mass was not different between the abiotic and biotic conditions, most likely because the positive effect of UV radiation on litter biodegradability was offset by its negative effect on microbial activity. Our results also suggested that UV radiation could alter the N cycle during decomposition, primarily by inhibiting N immobilization. © 2014 John Wiley & Sons Ltd.

Stoichiometry of microbial carbon use efficiency in soils

DOE PAGES

Sinsabaugh, Robert L.; Turner, Benjamin L.; Talbot, Jennifer M.; ...

2016-03-23

The carbon use efficiency (CUE) of microbial communities partitions the flow of C from primary producers to the atmosphere, decomposer food webs, and soil C stores. CUE, usually defined as the ratio of growth to assimilation, is a critical parameter in ecosystem models, but is seldom measured directly in soils because of the methodological difficulty of measuring in situ rates of microbial growth and respiration. Alternatively, CUE can be estimated indirectly from the elemental stoichiometry of organic matter and microbial biomass, and the ratios of C to nutrient-acquiring ecoenzymatic activities. In this paper, we used this approach to estimate andmore » compare microbial CUE in >2000 soils from a broad range of ecosystems. Mean CUE based on C:N stoichiometry was 0.269 ± 0.110 (mean ± SD). A parallel calculation based on C:P stoichiometry yielded a mean CUE estimate of 0.252 ± 0.125. The mean values and frequency distributions were similar to those from aquatic ecosystems, also calculated from stoichiometric models, and to those calculated from direct measurements of bacterial and fungal growth and respiration. CUE was directly related to microbial biomass C with a scaling exponent of 0.304 (95% CI 0.237–0.371) and inversely related to microbial biomass P with a scaling exponent of -0.234 (95% CI -0.289 to -0.179). Relative to CUE, biomass specific turnover time increased with a scaling exponent of 0.509 (95% CI 0.467–0.551). CUE increased weakly with mean annual temperature. CUE declined with increasing soil pH reaching a minimum at pH 7.0, then increased again as soil pH approached 9.0, a pattern consistent with pH trends in the ratio of fungal : bacteria abundance and growth. Structural equation models that related geographic variables to CUE component variables showed the strongest connections for paths linking latitude and pH to β-glucosidase activity and soil C:N:P ratios. Finally, the integration of stoichiometric and metabolic models provides a quantitative description of the functional organization of soil microbial communities that can improve the representation of CUE in microbial process and ecosystem simulation models.« less

Acacia Changes Microbial Indicators and Increases C and N in Soil Organic Fractions in Intercropped Eucalyptus Plantations

PubMed Central

Pereira, Arthur P. A.; Zagatto, Maurício R. G.; Brandani, Carolina B.; Mescolotti, Denise de Lourdes; Cotta, Simone R.; Gonçalves, José L. M.; Cardoso, Elke J. B. N.

2018-01-01

Intercropping forest plantations of Eucalyptus with nitrogen-fixing trees can increase soil N inputs and stimulate soil organic matter (OM) cycling. However, microbial indicators and their correlation in specific fractions of soil OM are unclear in the tropical sandy soils. Here, we examined the microbial indicators associated with C and N in the soil resulting from pure and intercropped Eucalyptus grandis and Acacia mangium plantations. We hypothesized that introduction of A. mangium in a Eucalyptus plantation promotes changes in microbial indicators and increases C and N concentrations on labile fractions of the soil OM, when compared to pure eucalyptus plantations. We determined the microbial and enzymatic activity, and the potential for C degradation by the soil microbial community. Additionally, we evaluated soil OM fractions and litter parameters. Soil (0–20 cm) and litter samples were collected at 27 and 39 months after planting from the following treatments: pure E. grandis (E) and A. mangium (A) plantations, pure E. grandis plantations with N fertilizer (E+N) and an E. grandis, and A. mangium intercropped plantations (E+A). The results showed that intercropped plantations (E+A) increase 3, 45, and 70% microbial biomass C as compared to A, E+N, and E, at 27 months after planting. The metabolic quotient (qCO2) showed a tendency toward stressful values in pure E. grandis plantations and a strong correlation with dehydrogenase activity. A and E+A treatments also exhibited the highest organic fractions (OF) and C and N contents. A canonical redundancy analysis revealed positive correlations between microbial indicators of soil and litter attributes, and a strong effect of C and N variables in differentiating A and E+A from E and E+N treatments. The results suggested that a significant role of A. mangium enhance the dynamics of soil microbial indicators which help in the accumulation of C and N in soil OF in intercropped E. grandis plantations. Our results are mostly relevant to plantations in sandy soil areas with low levels of OM, suggesting and efficient method for improving nutrient availability in the soil and optimizing eucalyptus growth and development. PMID:29670606

Microbial hotspots and hot moments in soil

NASA Astrophysics Data System (ADS)

Kuzyakov, Yakov; Blagodatskaya, Evgenia

2015-04-01

Soils are the most heterogeneous parts of the biosphere, with an extremely high differentiation of properties and processes within nano- to macroscales. The spatial and temporal heterogeneity of input of labile organics by plants creates microbial hotspots over short periods of time - the hot moments. We define microbial hotspots as small soil volumes with much faster process rates and much more intensive interactions compared to the average soil conditions. Such hotspots are found in the rhizosphere, detritusphere, biopores (including drilosphere) and on aggregate surfaces, but hotspots are frequently of mixed origin. Hot moments are short-term events or sequences of events inducing accelerated process rates as compared to the averaged rates. Thus, hotspots and hot moments are defined by dynamic characteristics, i.e. by process rates. For this hotspot concept we extensively reviewed and examined the localization and size of hotspots, spatial distribution and visualization approaches, transport of labile C to and from hotspots, lifetime and process intensities, with a special focus on process rates and microbial activities. The fraction of active microorganisms in hotspots is 2-20 times higher than in the bulk soil, and their specific activities (i.e. respiration, microbial growth, mineralization potential, enzyme activities, RNA/DNA ratio) may also be much higher. The duration of hot moments in the rhizosphere is limited and is controlled by the length of the input of labile organics. It can last a few hours up to a few days. In the detritusphere, however, the duration of hot moments is regulated by the output - by decomposition rates of litter - and lasts for weeks and months. Hot moments induce succession in microbial communities and intense intra- and interspecific competition affecting C use efficiency, microbial growth and turnover. The faster turnover and lower C use efficiency in hotspots counterbalances the high C inputs, leading to the absence of strong increases in C stocks. Consequently, the intensification of fluxes is much stronger than the increase of pools. Maintenance of stoichiometric ratios by accelerated microbial growth in hotspots requires additional nutrients (e.g. N and P), causing their microbial mining from soil organic matter, i.e. priming effects. Consequently, priming effects are localized in microbial hotspots and are consequences of hot moments. Finally, we estimated the contribution of the hotspots to the whole soil profile and suggested that, irrespective of their volume, the hotspots are mainly responsible for the ecologically relevant processes in soil.

Effects of replacing dietary starch with neutral detergent-soluble fibre on ruminal fermentation, microbial synthesis and populations of ruminal cellulolytic bacteria using the rumen simulation technique (RUSITEC).

PubMed

Zhao, X H; Liu, C J; Liu, Y; Li, C Y; Yao, J H

2013-12-01

A rumen simulation technique (RUSITEC) apparatus with eight 800 ml fermenters was used to investigate the effects of replacing dietary starch with neutral detergent-soluble fibre (NDSF) by inclusion of sugar beet pulp in diets on ruminal fermentation, microbial synthesis and populations of ruminal cellulolytic bacteria. Experimental diets contained 12.7, 16.4, 20.1 or 23.8% NDSF substituted for starch on a dry matter basis. The experiment was conducted over two independent 15-day incubation periods with the last 8 days used for data collection. There was a tendency that 16.4% NDSF in the diet increased the apparent disappearance of organic matter (OM) and neutral detergent fibre (NDF). Increasing dietary NDSF level increased carboxymethylcellulase and xylanase activity in the solid fraction and apparent disappearance of acid detergent fibre (ADF) but reduced the 16S rDNA copy numbers of Ruminococcus albus in both liquid and solid fractions and R. flavefaciens in the solid fraction. The apparent disappearance of dietary nitrogen (N) was reduced by 29.6% with increased dietary NDSF. Substituting NDSF for starch appeared to increase the ratios of acetate/propionate and methane/volatile fatty acids (VFA) (mol/mol). Replacing dietary starch with NDSF reduced the daily production of ammonia-N and increased the growth of the solid-associated microbial pellets (SAM). Total microbial N flow and efficiency of microbial synthesis (EMS), expressed as g microbial N/kg OM fermented, tended to increase with increased dietary NDSF, but the numerical increase did not continue as dietary NDSF exceeded 20.1% of diet DM. Results suggested that substituting NDSF for starch up to 16.4% of diet DM increased digestion of nutrients (except for N) and microbial synthesis, and further increases (from 16.4% to 23.8%) in dietary NDSF did not repress microbial synthesis but did significantly reduce digestion of dietary N. © 2012 Blackwell Verlag GmbH.

Effects of antimicrobial treatment on fiberglass-acrylic filters.

PubMed

Cecchini, C; Verdenelli, M C; Orpianesi, C; Dadea, G M; Cresci, A

2004-01-01

The aims of the present study were to: (i) analyse a group of antimicrobial agents and to select the most active against test microbial strains; (ii) test the effect of the antimicrobial treatment on air filters in order to reduce microbial colonization. Different kinds of antimicrobial agents were analysed to assess their compatibility with the production process of air filter media. The minimal inhibitory concentration for each antimicrobial agent was determined against a defined list of microbial strains, and an antimicrobial activity assay of filter prototypes was developed to determine the most active agent among the compatible antimicrobials. Then, the most active was chosen and added directly to the filter during the production process. The microbial colonization of treated and untreated filter media was assessed at different working times for different incubation times by stereomicroscope and scanning electron microscope analysis. Some of the antimicrobial agents analysed were more active against microbial test strains and compatible with the production process of the filter media. Filter sections analysis of treated filter media showed a significantly lower microbial colonization than those untreated, a reduction of species both in density and varieties and of the presence of bacteria and fungal hyphae with reproductive structures. This study demonstrated the ability of antimicrobial treatments to inhibit the growth of micro-organisms in filter media and subsequently to increase indoor air quality (IAQ), highlighting the value of adding antimicrobials to filter media. To make a contribution to solving the problem of microbial contamination of air filters, by demonstrating the efficacy of incorporating antimicrobial agents in the filter media to improve IAQ and health.

Soil microbial communities and enzyme activities under various poultry litter application rates.

PubMed

Acosta-Martínez, V; Harmel, R Daren

2006-01-01

The potential excessive nutrient and/or microbial loading from mismanaged land application of organic fertilizers is forcing changes in animal waste management. Currently, it is not clear to what extent different rates of poultry litter impact soil microbial communities, which control nutrient availability, organic matter quality and quantity, and soil degradation potential. From 2002 to 2004, we investigated the microbial community and several enzyme activities in a Vertisol soil (fine, smectitic, thermic, Udic Haplustert) at 0 to 15 cm as affected by different rates of poultry litter application to pasture (0, 6.7, and 13.4 Mg ha(-1)) and cultivated sites (0, 4.5, 6.7, 9.0, 11.2, and 13.4 Mg ha(-1)) in Texas, USA. No differences in soil pH (average: 7.9), total N (pasture: 2.01-3.53, cultivated: 1.09-1.98 g kg(-1) soil) or organic C (pasture average: 25-26.7, cultivated average: 13.9-16.1 g kg(-1) soil) were observed following the first four years of litter application. Microbial biomass carbon (MBC) and nitrogen (MBN) increased at litter rates greater than 6.7 Mg ha(-1) (pasture: MBC = >863, MBN = >88 mg kg(-1) soil) compared to sites with no applied litter (MBC = 722, MBN = 69 mg kg(-1) soil). Enzyme activities of C (beta-glucosidase, alpha-galactosidase, beta-glucosaminidase) or N cycling (beta-glucosaminidase) were increased at litter rates greater than 6.7 Mg ha(-1). Enzyme activities of P (alkaline phosphatase) and S (arylsulfatase) mineralization showed the same response in pasture, but they were only increased at the highest (9.0, 11.2, and 13.4 Mg ha(-1)) litter application rates in cultivated sites. According to fatty acid methyl ester (FAME) analysis, the pasture soils experienced shifts to higher bacterial populations at litter rates of 6.7 Mg ha(-1), and shifts to higher fungal populations at the highest litter application rates in cultivated sites. While rates greater than 6.7 Mg ha(-1) provided rapid enhancement of the soil microbial populations and enzymatic activities, they result in P application in excess of crop needs. Thus, studies will continue to investigate whether litter application at rates below 6.7 Mg ha(-1), previously recommended to maintain water quality, will result in similar improved soil microbial and biochemical functioning with continued annual litter application.

Soil Microbial Activity Responses to Fire in a Semi-arid Savannah Ecosystem Pre- and Post-Monsoon Season

NASA Astrophysics Data System (ADS)

Jimenez, J. R.; Raub, H. D.; Jong, E. L.; Muscarella, C. R.; Smith, W. K.; Gallery, R. E.

2017-12-01

Extracellular enzyme activities (EEA) of soil microorganisms can act as important proxies for nutrient limitation and turnover in soil and provide insight into the biochemical requirements of microbes in terrestrial ecosystems. In semi-arid ecosystems, microbial activity is influenced by topography, disturbances such as fire, and seasonality from monsoon rains. Previous studies from forest ecosystems show that microbial communities shift to similar compositions after severe fires despite different initial conditions. In semi-arid ecosystems with high spatial heterogeniety, we ask does fire lead to patch intensification or patch homogenization and how do monsoon rains influence the successional trajectories of microbial responses? We analyzed microbial activity and soil biogeochemistry throughout the monsoon season in paired burned and unburned sites in the Santa Rita Experimental Range, AZ. Surface soil (5cm) from bare-ground patches, bole, canopy drip line, and nearby grass patches for 5 mesquite trees per site allowed tests of spatiotemporal responses to fire and monsoon rain. Microbial activity was low during the pre-monsoon season and did not differ between the burned and unburned sites. We found greater activity near mesquite trees that reflects soil water and nutrient availability. Fire increased soil alkalinity, though soils near mesquite trees were less affected. Soil water content was significantly higher in the burned sites post-monsoon, potentially reflecting greater hydrophobicity of burned soils. Considering the effects of fire in these semi-arid ecosystems is especially important in the context of the projected changing climate regime in this region. Assessing microbial community recovery pre-, during, and post-monsoon is important for testing predictions about whether successional pathways post-fire lead to recovery or novel trajectories of communities and ecosystem function.

Data-Driven Microbial Modeling for Soil Carbon Decomposition and Stabilization

NASA Astrophysics Data System (ADS)

Luo, Yiqi; Chen, Ji; Chen, Yizhao; Feng, Wenting

2017-04-01

Microorganisms have long been known to catalyze almost all the soil organic carbon (SOC) transformation processes (e.g., decomposition, stabilization, and mineralization). Representing microbial processes in Earth system models (ESMs) has the potential to improve projections of SOC dynamics. We have recently examined (1) relationships of microbial functions with environmental factors and (2) microbial regulations of decomposition and other key soil processes. According to three lines of evidence, we have developed a data-driven enzyme (DENZY) model to simulate soil microbial decomposition and stabilization. First, our meta-analysis of 64 published field studies showed that field experimental warming significantly increased soil microbial communities abundance, which is negatively correlated with the mean annual temperature. The negative correlation indicates that warming had stronger effects in colder than warmer regions. Second, we found that the SOC decomposition, especially the transfer between labile SOC and protected SOC, is nonlinearly regulated by soil texture parameters, such as sand and silt contents. Third, we conducted a global analysis of the C-degrading enzyme activities, soil respiration, and SOC content under N addition. Our results show that N addition has contrasting effects on cellulase (hydrolytic C-degrading enzymes) and ligninase (oxidative C-degrading enzymes) activities. N-enhanced cellulase activity contributes to the minor stimulation of soil respiration whereas N-induced repression on ligninase activity drives soil C sequestration. Our analysis links the microbial extracellular C-degrading enzymes to the SOC dynamics at ecosystem scales across scores of experimental sites around the world. It offers direct evidence that N-induced changes in microbial community and physiology play fundamental roles in controlling the soil C cycle. Built upon those three lines of empirical evidence, the DENZY model includes two enzyme pools and explicitly characterizes two classes of extracellular enzyme activities: one that degrades organic molecules containing both C and N (e.g., chitin or protein) and another that degrades only C (e.g., cellulose). The DENZY model assumes that the microbes allocate resources to different enzyme pools so as to exactly satisfy microbial CN ratio stoichiometry in response to changes in climate conditions and soil attributes. The DENZY model can simulate differential effects of nitrogen fertilization on the two groups of enzymes and thus soil respiration and SOC dynamics. We will select field experimental sites to test the DENZY model. With increasing amounts of available observations and data synthesis, this DENZY model will be better parameterized and have a potential to reveal how responses of microbial enzymes to environmental changes regulate soil carbon decomposition and stabilization.

Unravelling the active microbial community in a thermophilic anaerobic digester-microbial electrolysis cell coupled system under different conditions.

PubMed

Cerrillo, Míriam; Viñas, Marc; Bonmatí, August

2017-03-01

Thermophilic anaerobic digestion (AD) of pig slurry coupled to a microbial electrolysis cell (MEC) with a recirculation loop was studied at lab-scale as a strategy to increase AD stability when submitted to organic and nitrogen overloads. The system performance was studied, with the recirculation loop both connected and disconnected, in terms of AD methane production, chemical oxygen demand removal (COD) and volatile fatty acid (VFA) concentrations. Furthermore, the microbial population was quantitatively and qualitatively assessed through DNA and RNA-based qPCR and high throughput sequencing (MiSeq), respectively to identify the RNA-based active microbial populations from the total DNA-based microbial community composition both in the AD and MEC reactors under different operational conditions. Suppression of the recirculation loop reduced the AD COD removal efficiency (from 40% to 22%) and the methane production (from 0.32 to 0.03 m 3  m -3  d -1 ). Restoring the recirculation loop led to a methane production of 0.55 m 3  m -3  d -1 concomitant with maximum MEC COD and ammonium removal efficiencies of 29% and 34%, respectively. Regarding microbial analysis, the composition of the AD and MEC anode populations differed from really active microorganisms. Desulfuromonadaceae was revealed as the most active family in the MEC (18%-19% of the RNA relative abundance), while hydrogenotrophic methanogens (Methanobacteriaceae) dominated the AD biomass. Copyright © 2016 Elsevier Ltd. All rights reserved.

Season mediates herbivore effects on litter and soil microbial abundance and activity in a semi-arid woodland

DOE Office of Scientific and Technical Information (OSTI.GOV)

Classen, Aimee T; Overby, Stephen; Hart, Stephen C

2007-01-01

Herbivores can directly impact ecosystem function by altering litter quality entering an ecosystem or indirectly by affecting a shift in the microbial community that mediate nutrient processes. We examine herbivore susceptibility and resistance effects on litter microarthropod and soil microbial communities to test the general hypothesis that herbivore driven changes in litter inputs will feedback to the microbial community. Our study population consisted of individual trees that are susceptible or resistant to the stem-boring moth (Dioryctria albovittella) and trees that herbivores have been manually removed since 1982. Moth herbivory increased pi on litter nitrogen concentrations (16%) and canopy precipitation infiltrationmore » (28%), both significant factors influencing litter and soil microbial populations. Our research resulted in three major conclusions: 1) In spite of an increase in litter quality, herbivory does not change litter microarthropod abundance or species richness. 2) Herbivore susceptibility alters bulk soil microbial communities, but not soil properties. 3) Season has a strong influence on microbial communities, and their response to herbivore inputs, in this semi-arid ecosystem.« less

Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate

PubMed Central

De Filippis, Francesca; Genovese, Alessandro; Ferranti, Pasquale; Gilbert, Jack A.; Ercolini, Danilo

2016-01-01

Traditional cheeses harbour complex microbial consortia that play an important role in shaping typical sensorial properties. However, the microbial metabolism is considered difficult to control. Microbial community succession and the related gene expression were analysed during ripening of a traditional Italian cheese, identifying parameters that could be modified to accelerate ripening. Afterwards, we modulated ripening conditions and observed consistent changes in microbial community structure and function. We provide concrete evidence of the essential contribution of non-starter lactic acid bacteria in ripening-related activities. An increase in the ripening temperature promoted the expression of genes related to proteolysis, lipolysis and amino acid/lipid catabolism and significantly increases the cheese maturation rate. Moreover, temperature-promoted microbial metabolisms were consistent with the metabolomic profiles of proteins and volatile organic compounds in the cheese. The results clearly indicate how processing-driven microbiome responses can be modulated in order to optimize production efficiency and product quality. PMID:26911915

Soil bacterial and fungal diversity differently correlated with soil biochemistry in alpine grassland ecosystems in response to environmental changes.

PubMed

Zhang, Yong; Dong, Shikui; Gao, Qingzhu; Liu, Shiliang; Ganjurjav, Hasbagan; Wang, Xuexia; Su, Xukun; Wu, Xiaoyu

2017-03-06

To understand effects of soil microbes on soil biochemistry in alpine grassland ecosystems under environmental changes, we explored relationships between soil microbial diversity and soil total nitrogen, organic carbon, available nitrogen and phosphorus, soil microbial biomass and soil enzyme activities in alpine meadow, alpine steppe and cultivated grassland on the Qinghai-Tibetan plateau under three-year warming, enhanced precipitation and yak overgrazing. Soil total nitrogen, organic carbon and NH 4 -N were little affected by overgrazing, warming or enhanced precipitation in three types of alpine grasslands. Soil microbial biomass carbon and phosphorus along with the sucrase and phosphatase activities were generally stable under different treatments. Soil NO 3 -N, available phosphorus, urease activity and microbial biomass nitrogen were increased by overgrazing in the cultivated grassland. Soil bacterial diversity was positively correlated with, while soil fungal diversity negatively with soil microbial biomass and enzyme activities. Soil bacterial diversity was negatively correlated with, while soil fungal diversity positively with soil available nutrients. Our findings indicated soil bacteria and fungi played different roles in affecting soil nutrients and microbiological activities that might provide an important implication to understand why soil biochemistry was generally stable under environmental changes in alpine grassland ecosystems.

Soil bacterial and fungal diversity differently correlated with soil biochemistry in alpine grassland ecosystems in response to environmental changes

NASA Astrophysics Data System (ADS)

Zhang, Yong; Dong, Shikui; Gao, Qingzhu; Liu, Shiliang; Ganjurjav, Hasbagan; Wang, Xuexia; Su, Xukun; Wu, Xiaoyu

2017-03-01

To understand effects of soil microbes on soil biochemistry in alpine grassland ecosystems under environmental changes, we explored relationships between soil microbial diversity and soil total nitrogen, organic carbon, available nitrogen and phosphorus, soil microbial biomass and soil enzyme activities in alpine meadow, alpine steppe and cultivated grassland on the Qinghai-Tibetan plateau under three-year warming, enhanced precipitation and yak overgrazing. Soil total nitrogen, organic carbon and NH4-N were little affected by overgrazing, warming or enhanced precipitation in three types of alpine grasslands. Soil microbial biomass carbon and phosphorus along with the sucrase and phosphatase activities were generally stable under different treatments. Soil NO3-N, available phosphorus, urease activity and microbial biomass nitrogen were increased by overgrazing in the cultivated grassland. Soil bacterial diversity was positively correlated with, while soil fungal diversity negatively with soil microbial biomass and enzyme activities. Soil bacterial diversity was negatively correlated with, while soil fungal diversity positively with soil available nutrients. Our findings indicated soil bacteria and fungi played different roles in affecting soil nutrients and microbiological activities that might provide an important implication to understand why soil biochemistry was generally stable under environmental changes in alpine grassland ecosystems.

Soil bacterial and fungal diversity differently correlated with soil biochemistry in alpine grassland ecosystems in response to environmental changes

PubMed Central

Zhang, Yong; Dong, Shikui; Gao, Qingzhu; Liu, Shiliang; Ganjurjav, Hasbagan; Wang, Xuexia; Su, Xukun; Wu, Xiaoyu

2017-01-01

To understand effects of soil microbes on soil biochemistry in alpine grassland ecosystems under environmental changes, we explored relationships between soil microbial diversity and soil total nitrogen, organic carbon, available nitrogen and phosphorus, soil microbial biomass and soil enzyme activities in alpine meadow, alpine steppe and cultivated grassland on the Qinghai-Tibetan plateau under three-year warming, enhanced precipitation and yak overgrazing. Soil total nitrogen, organic carbon and NH4-N were little affected by overgrazing, warming or enhanced precipitation in three types of alpine grasslands. Soil microbial biomass carbon and phosphorus along with the sucrase and phosphatase activities were generally stable under different treatments. Soil NO3-N, available phosphorus, urease activity and microbial biomass nitrogen were increased by overgrazing in the cultivated grassland. Soil bacterial diversity was positively correlated with, while soil fungal diversity negatively with soil microbial biomass and enzyme activities. Soil bacterial diversity was negatively correlated with, while soil fungal diversity positively with soil available nutrients. Our findings indicated soil bacteria and fungi played different roles in affecting soil nutrients and microbiological activities that might provide an important implication to understand why soil biochemistry was generally stable under environmental changes in alpine grassland ecosystems. PMID:28262753

Response of sediment microbial community structure in a freshwater reservoir to manipulations in oxygen availability.

PubMed

Bryant, Lee D; Little, John C; Bürgmann, Helmut

2012-04-01

Hypolimnetic oxygenation systems (HOx) are being increasingly used in freshwater reservoirs to elevate dissolved oxygen levels in the hypolimnion and suppress sediment-water fluxes of soluble metals (e.g. Fe and Mn) which are often microbially mediated. We assessed changes in sediment microbial community structure and corresponding biogeochemical cycling on a reservoir-wide scale as a function of HOx operations. Sediment microbial biomass as quantified by DNA concentration was increased in regions most influenced by the HOx. Following an initial decrease in biomass in the upper sediment while oxygen concentrations were low, biomass typically increased at all depths as the 4-month-long oxygenation season progressed. A distinct shift in microbial community structure was only observed at the end of the season in the upper sediment near the HOx. While this shift was correlated to HOx-enhanced oxygen availability, increased TOC levels and precipitation of Fe- and Mn-oxides, abiotic controls on Fe and Mn cycling, and/or the adaptability of many bacteria to variations in prevailing electron acceptors may explain the delayed response and the comparatively limited changes at other locations. While the sediment microbial community proved remarkably resistant to relatively short-term changes in HOx operations, HOx-induced variation in microbial structure, biomass, and activity was observed after a full season of oxygenation. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Tillage system affects microbiological properties of soil

NASA Astrophysics Data System (ADS)

Delgado, A.; de Santiago, A.; Avilés, M.; Perea, F.

2012-04-01

Soil tillage significantly affects organic carbon accumulation, microbial biomass, and subsequently enzymatic activity in surface soil. Microbial activity in soil is a crucial parameter contributing to soil functioning, and thus a basic quality factor for soil. Since enzymes remain soil after excretion by living or disintegrating cells, shifts in their activities reflect long-term fluctuations in microbial biomass. In order to study the effects of no-till on biochemical and microbiological properties in comparison to conventional tillage in a representative soil from South Spain, an experiment was conducted since 1982 on the experimental farm of the Institute of Agriculture and Fisheries Research of Andalusia (IFAPA) in Carmona, SW Spain (37o24'07''N, 5o35'10''W). The soil at the experimental site was a very fine, montomorillonitic, thermic Chromic Haploxerert (Soil Survey Staff, 2010). A randomized complete block design involving three replications and the following two tillage treatments was performed: (i) Conventional tillage, which involved mouldboard plowing to a depth of 50 cm in the summer (once every three years), followed by field cultivation to a depth of 15 cm before sowing; crop residues being burnt, (ii) No tillage, which involved controlling weeds before sowing by spraying glyphosate and sowing directly into the crop residue from the previous year by using a planter with double-disk openers. For all tillage treatments, the crop rotation (annual crops) consisted of winter wheat, sunflower, and legumes (pea, chickpea, or faba bean, depending on the year), which were grown under rainfed conditions. Enzymatic activities (ß-glucosidase, dehydrogenase, aryl-sulphatase, acid phosphatase, and urease), soil microbial biomass by total viable cells number by acridine orange direct count, the density of cultivable groups of bacteria and fungi by dilution plating on semi-selective media, the physiological profiles of the microbial communities by BiologR, and the Shannon (H') and Gini (1-G) diversity index of microbial communities were determined in soil samples (0-10 cm depth) taken in autumn 2009. All the enzymatic activities and the biomass estimated by viable cell counting were significantly higher under no-till than under conventional tillage. However, only fluorescents pseudomonas population was increased under no-till, meanwhile oligotrophic bacteria and actinomycetes populations were higher with conventional tillage than with no-till. Overall, there was a higher use all the group of carbon sources used in the BiologR test with conventional tillage than with no-till, by except amines and phenols which showed non-significant differences. This reveals different physiological profiles in the microbial communities under both tillage systems. The Gini diversity was significantly lower with no-till than with conventional tillage. It can be concluded that no-till increases microbial biomass in soil and subsequently enzymatic activities likely ascribed to an increased organic matter content. Under low availability of hydrocarbon sources in soil due to conventional tillage, which promotes a decrease in the organic matter content of the soil, populations of oligotrophods and the diversity of microbial communities are increased. Under these conditions, there must not be dominant carbon sources promoting the selection of microorganisms with a given physiological profile. The reduced hydrocarbon availability and the higher diversity contribute to explain the increased use of carbon sources used in Biolog with conventional tillage than with no-till.

Long-Term Application of Bioorganic Fertilizers Improved Soil Biochemical Properties and Microbial Communities of an Apple Orchard Soil

PubMed Central

Wang, Lei; Yang, Fang; E, Yaoyao; Yuan, Jun; Raza, Waseem; Huang, Qiwei; Shen, Qirong

2016-01-01

Soil biochemical properties and microbial communities are usually considered as important indicators of soil health because of their association with plant nutrition. In this study, we investigated the impact of long-term application of bioorganic fertilizer (BOF) on soil biochemical properties and microbial communities in the apple orchard soil of the Loess Plateau. The experiment included three treatments: (1) control without fertilization (CK); (2) chemical fertilizer application (CF); and (3) bioorganic fertilizer application (BOF). The high throughput sequencing was used to examine the bacterial and fungal communities in apple orchard soil. The results showed that the BOF treatment significantly increased the apple yield during the experimental time (2009–2015). The application of BOF significantly increased the activities of catalase and invertase compared to those in CK and CF treatments. The high throughput sequencing data showed that the application of BOF changed the microbial community composition of all soil depths considered (0–20 cm, 20–40 cm, and 40–60 cm), e.g., the relative abundance of bio-control bacteria (Xanthomonadales, Lysobacter, Pseudomonas, and Bacillus), Proteobacteria, Bacteroidetes, Ohtaekwangia, Ilyonectria, and Lecanicillium was increased while that of Acidobacteria, Chloroflexi, Gp4, Gp6 and Sphaerobacter was decreased. The increase in apple yield after the application of BOF might be due to increase in organic matter, total nitrogen and catalase and invertase activities of soil and change in the bacterial community composition by enriching Bacillus, Pseudomonas, Lysobacter, and Ohtaekwangia. These results further enhance the understanding on how BOFs alter soil microbial community composition to stimulate soil productivity. PMID:27965631

Long-Term Application of Bioorganic Fertilizers Improved Soil Biochemical Properties and Microbial Communities of an Apple Orchard Soil.

PubMed

Wang, Lei; Yang, Fang; E, Yaoyao; Yuan, Jun; Raza, Waseem; Huang, Qiwei; Shen, Qirong

2016-01-01

Soil biochemical properties and microbial communities are usually considered as important indicators of soil health because of their association with plant nutrition. In this study, we investigated the impact of long-term application of bioorganic fertilizer (BOF) on soil biochemical properties and microbial communities in the apple orchard soil of the Loess Plateau. The experiment included three treatments: (1) control without fertilization (CK); (2) chemical fertilizer application (CF); and (3) bioorganic fertilizer application (BOF). The high throughput sequencing was used to examine the bacterial and fungal communities in apple orchard soil. The results showed that the BOF treatment significantly increased the apple yield during the experimental time (2009-2015). The application of BOF significantly increased the activities of catalase and invertase compared to those in CK and CF treatments. The high throughput sequencing data showed that the application of BOF changed the microbial community composition of all soil depths considered (0-20 cm, 20-40 cm, and 40-60 cm), e.g., the relative abundance of bio-control bacteria ( Xanthomonadales, Lysobacter, Pseudomonas , and Bacillus ), Proteobacteria, Bacteroidetes, Ohtaekwangia, Ilyonectria , and Lecanicillium was increased while that of Acidobacteria, Chloroflexi, Gp4, Gp6 and Sphaerobacter was decreased. The increase in apple yield after the application of BOF might be due to increase in organic matter, total nitrogen and catalase and invertase activities of soil and change in the bacterial community composition by enriching Bacillus, Pseudomonas, Lysobacter , and Ohtaekwangia . These results further enhance the understanding on how BOFs alter soil microbial community composition to stimulate soil productivity.

Spatio-temporal reproducibility of the microbial food web structure associated with the change in temperature: Long-term observations in the Adriatic Sea

NASA Astrophysics Data System (ADS)

Šolić, Mladen; Grbec, Branka; Matić, Frano; Šantić, Danijela; Šestanović, Stefanija; Ninčević Gladan, Živana; Bojanić, Natalia; Ordulj, Marin; Jozić, Slaven; Vrdoljak, Ana

2018-02-01

Global and atmospheric climate change is altering the thermal conditions in the Adriatic Sea and, consequently, the marine ecosystem. Along the eastern Adriatic coast sea surface temperature (SST) increased by an average of 1.03 °C during the period from 1979 to 2015, while in the recent period, starting from 2008, a strong upward almost linear trend of 0.013 °C/month was noted. Being mainly oligotrophic, the middle Adriatic Sea is characterized by the important role played by the microbial food web in the production and transfer of biomass and energy towards higher trophic levels. It is very important to understand the effect of warming on microbial communities, since small temperature increases in surface seawater can greatly modify the microbial role in the global carbon cycle. In this study, the Self-Organizing Map (SOM) procedure was used to analyse the time series of a number of microbial parameters at two stations with different trophic status in the central Adriatic Sea. The results show that responses of the microbial food web (MFW) structure to temperature changes are reproducible in time. Furthermore, qualitatively similar changes in the structure of the MFW occurred regardless of the trophic status. The rise in temperature was associated with: (1) the increasing importance of microbial heterotrophic activities (increase bacterial growth and bacterial predator abundance, particularly heterotrophic nanoflagellates) and (2) the increasing importance of autotrophic picoplankton (APP) in the MFW.

Seasonal and interannual dynamics of soil microbial biomass and available nitrogen in an alpine meadow in the eastern part of Qinghai-Tibet Plateau, China

NASA Astrophysics Data System (ADS)

Xu, Bo; Wang, Jinniu; Wu, Ning; Wu, Yan; Shi, Fusun

2018-01-01

Soil microbial activity varies seasonally in frozen alpine soils during cold seasons and plays a crucial role in available N pool accumulation in soil. The intra- and interannual patterns of microbial and nutrient dynamics reflect the influences of changing weather factors, and thus provide important insights into the biogeochemical cycles and ecological functions of ecosystems. We documented the seasonal and interannual dynamics of soil microbial and available N in an alpine meadow in the eastern part of Qinghai-Tibet Plateau, China, between April 2011 and October 2013. Soil was collected in the middle of each month and analyzed for water content, microbial biomass C (MBC) and N (MBN), dissolved organic C and N, and inorganic N. Soil microbial community composition was measured by the dilution-plate method. Fungi and actinomycetes dominated the microbial community during the nongrowing seasons, and the proportion of bacteria increased considerably during the early growing seasons. Trends of consistently increasing MBC and available N pools were observed during the nongrowing seasons. MBC sharply declined during soil thaw and was accompanied by a peak in available N pool. Induced by changes in soil temperatures, significant shifts in the structures and functions of microbial communities were observed during the winter-spring transition and largely contributed to microbial reduction. The divergent seasonal dynamics of different N forms showed a complementary nutrient supply pattern during the growing season. Similarities between the interannual dynamics of microbial biomass and available N pools were observed, and soil temperature and water conditions were the primary environmental factors driving interannual fluctuations. Owing to the changes in climate, seasonal soil microbial activities and nutrient supply patterns are expected to change further, and these changes may have crucial implications for the productivity and biodiversity of alpine ecosystems.

Microbial Community Response to Warming and Correlations to Organic Carbon Degradation in an Arctic Tundra Soil

NASA Astrophysics Data System (ADS)

Yang, Z.; Yang, S.; Zhou, J.; Wullschleger, S. D.; Graham, D. E.; Yang, Y.; Gu, B.

2016-12-01

Climate warming increases microbial activity and thus decomposition of soil organic carbon (SOC) stored in Arctic tundra, but changes in microbial community and its correlations to SOC decomposition are poorly understood. Using a microbial functional gene array (GeoChip 5.0), we examined the microbial functional community structure changes with temperature (-2 and +8 °C) in an anoxic incubation experiment with a high-centered polygon trough soil from Barrow, Alaska. Through a 122-day incubation, we show that functional community structure was significantly altered (P < 0.05) by 8 °C warming, with functional diversity decreasing in response to warming and rapid degradation of the labile soil organic substrates. In contrast, microbial community structure was largely unchanged by -2 °C incubation. In the organic layer soil, gene abundances associated with fermentation, methanogenesis, and iron reduction all decreased significantly (P < 0.05) following the incubation at 8 °C. These observations corroborate strongly with decreased methane and reducing sugar production rates and iron reduction during the incubation. These results demonstrate a rapid and sensitive microbial response to increasing soil temperature, and suggest important roles of microbial communities in moderating SOC degradation and iron cycling in warming Arctic tundra.

Changes in organic - C, N, P and K and enzyme activities in vermicompost of biodegradable organic wastes under liming and microbial inoculants.

PubMed

Pramanik, P; Ghosh, G K; Ghosal, P K; Banik, P

2007-09-01

The aim of this work was to study the effect of different organic wastes, viz. cow dung, grass, aquatic weeds and municipal solid waste with lime and microbial inoculants on chemical and biochemical properties of vermicompost. Cow dung was the best substrate for vermicomposting. Application of lime (5 g/kg) and inoculation of microorganisms increased the nutrient content in vermicompost and also phosphatases and urease activities. Bacillus polymyxa, the free-living N-fixer, increased N-content of vermicompost significantly (p < or = 0.01) as compared to other inoculants.

Application of Nanoparticle Technologies in the Combat against Anti-Microbial Resistance.

PubMed

Kumar, Mayur; Curtis, Anthony; Hoskins, Clare

2018-01-14

Anti-microbial resistance is a growing problem that has impacted the world and brought about the beginning of the end for the old generation of antibiotics. Increasingly, more antibiotics are being prescribed unnecessarily and this reckless practice has resulted in increased resistance towards these drugs, rendering them useless against infection. Nanotechnology presents a potential answer to anti-microbial resistance, which could stimulate innovation and create a new generation of antibiotic treatments for future medicines. Preserving existing antibiotic activity through novel formulation into or onto nanotechnologies can increase clinical longevity of action against infection. Additionally, the unique physiochemical properties of nanoparticles can provide new anti-bacterial modes of action which can also be explored. Simply concentrating on antibiotic prescribing habits will not resolve the issue but rather mitigate it. Thus, new scientific approaches through the development of novel antibiotics and formulations is required in order to employ a new generation of therapies to combat anti-microbial resistance.

Ongoing modification of Mediterranean Pleistocene sapropels mediated by prokaryotes.

PubMed

Coolen, Marco J L; Cypionka, Heribert; Sass, Andrea M; Sass, Henrik; Overmann, Jörg

2002-06-28

Late Pleistocene organic-rich sediments (sapropels) from the eastern Mediterranean Sea harbor unknown, metabolically active chemoorganotrophic prokaryotes. As compared to the carbon-lean intermediate layers, sapropels exhibit elevated cell numbers, increased activities of hydrolytic exoenzymes, and increased anaerobic glucose degradation rates, suggesting that microbial carbon substrates originate from sapropel layers up to 217,000 years old. 16S ribosomal RNA gene analyses revealed that as-yet-uncultured green nonsulfur bacteria constitute up to 70% of the total microbial biomass. Crenarchaeota constitute a smaller fraction (on average, 16%). A slow but significant turnover of glucose could be detected. Apparently, sapropels are still altered by the metabolic activity of green nonsulfur bacteria and crenarchaeota.

Soil microbial properties after 5 years of consecutive amendment with composted tannery sludge.

PubMed

Araujo, Ademir Sérgio Ferreira; Miranda, Ana Roberta Lima; Oliveira, Mara Lucia Jacinto; Santos, Vilma Maria; Nunes, Luís Alfredo Pinheiro Leal; Melo, Wanderley José

2015-01-01

Composting has been recognised an alternative method to tannery sludge recycling and afterwards to be used in agriculture. As the tannery sludge contains salts and chromium, the application of composted tannery sludge (CTS) should be performed carefully to minimise negative effects on soil microbial properties. Therefore, this study evaluated the effects of 5-year repeated CTS amendment on soil microbial biomass (SMB) and enzyme activities in a tropical soil. CTS was applied during 5 years at 0, 2.5, 5, 10 and 20 Mg ha(-1), and at the fifth year, the microbial biomass C (MBC) and N (MBN), basal and substrate-induced respiration (SIR), metabolic quotient (qCO₂) and dehydrogenase (DHA) and fluorescein diacetate (FDA) hydrolysis were determined in the soil samples. Soil MBC and MBN showed the highest values with the amendment of 5 Mg ha(-1) CTS. Soil respiration increased with the increase in CTS rates, while SIR showed the highest values with the amendment of 0, 2.5 and 5 Mg ha(-1) CTS. DHA activity showed the highest values with the amendment up to 2.5 Mg ha(-1), while FDA hydrolysis increased up to the rate of 5 Mg ha(-1) CTS. The results show that after 5 years of permanent amendment of CTS, soils amended with 2.5 Mg ha(-1) have SMB and enzymatic activities similar to those in unamended soil.

Short-term effect of aniline on soil microbial activity: a combined study by isothermal microcalorimetry, glucose analysis, and enzyme assay techniques.

PubMed

Chen, Huilun; Zhuang, Rensheng; Yao, Jun; Wang, Fei; Qian, Yiguang; Masakorala, Kanaji; Cai, Minmin; Liu, Haijun

2014-01-01

The accidents of aniline spill and explosion happened almost every year in China, whereas the toxic effect of aniline on soil microbial activity remained largely unexplored. In this study, isothermal microcalorimetric technique, glucose analysis, and soil enzyme assay techniques were employed to investigate the toxic effect of aniline on microbial activity in Chinese soil for the first time. Soil samples were treated with aniline from 0 to 2.5 mg/g soil to tie in with the fact of aniline spill. Results from microcalorimetric analysis showed that the introduction of aniline had a significant adverse effect on soil microbial activity at the exposure concentrations ≥0.4 mg/g soil (p < 0.05) and ≥0.8 mg/g soil (p < 0.01), and the activity was totally inhibited when the concentration increased to 2.5 mg/g soil. The glucose analysis indicated that aniline significantly decreased the soil microbial respiratory activity at the concentrations ≥0.8 mg/g soil (p < 0.05) and ≥1.5 mg/g soil (p < 0.01). Soil enzyme activities for β-glucosidase, urease, acid-phosphatase, and dehydrogenase revealed that aniline had a significant effect (p < 0.05) on the nutrient cycling of C, N, and P as well as the oxidative capacity of soil microorganisms, respectively. All of these results showed an intensively toxic effect of aniline on soil microbial activity. The proposed methods can provide toxicological information of aniline to soil microbes from the metabolic and biochemical point of views which are consistent with and correlated to each other.

Finding the best windows: An apparent environmental threshold determines which diffuse flows are dominated by subsurface microbes

NASA Astrophysics Data System (ADS)

Olins, H. C.; Rogers, D.; Scholin, C. A.; Preston, C. J.; Vidoudez, C.; Ussler, W.; Pargett, D.; Jensen, S.; Roman, B.; Birch, J. M.; Girguis, P. R.

2014-12-01

Hydrothermal vents are hotspots of microbial primary productivity often described as "windows into the subsurface biosphere." High temperature vents have received the majority of research attention, but cooler diffuse flows are as, if not more, important a source of heat and chemicals to the overlying ocean. We studied patterns of in situ gene expression and co-registered geochemistry in order to 1) describe the diversity and physiological poise of active microbial communities that span thermal and geochemical gradients from active diffuse flow to background vent field seawater, and 2) determine to what extent seawater or subsurface microbes were active throughout this environment. Analyses of multiple metatranscriptomes from 5 geochemically distinct sites (some from samples preserved in situ) show that proximate diffuse flows showed strikingly different transcription profiles. Specifically, caldera background and some diffuse flows were similar, both dominated by seawater-derived Gammaproteobacteria despite having distinct geochemistries. Intra-field community shows evidence of increased primary productivity throughout the entire vent field and not just at individual diffuse flows. In contrast, a more spatially limited, Epsilonproteobacteria-dominated transcription profile from the most hydrothermally-influenced diffuse flow appeared to be driven by the activity of vent-endemic microbes, likely reflecting subsurface microbial activity. We suggest that the microbial activity within many diffuse flow vents is primarily attributable to seawater derived Gammaproteobacterial sulfur oxidizers, while in certain other flows vent-endemic Epsilonproteobactiera are most active. These data reveal a diversity in microbial activity at diffuse flows that has not previously been recognized, and reshapes our thinking about the relative influence that different microbial communities may have on local processes (such as primary production) and potentially global biogeochemical cycles.

Effects of nutrient load on microbial activities within a seagrass-dominated ecosystem: Implications of changes in seagrass blue carbon.

PubMed

Liu, Songlin; Jiang, Zhijian; Wu, Yunchao; Zhang, Jingping; Arbi, Iman; Ye, Feng; Huang, Xiaoping; Macreadie, Peter Ian

2017-04-15

Nutrient loading is a leading cause of global seagrass decline, triggering shifts from seagrass- to macroalgal-dominance. Within seagrass meadows of Xincun Bay (South China Sea), we found that nutrient loading (due to fish farming) increased sediment microbial biomass and extracellular enzyme activity associated with carbon cycling (polyphenol oxidase, invertase and cellulase), with a corresponding decrease in percent sediment organic carbon (SOC), suggesting that nutrients primed microorganism and stimulated SOC remineralization. Surpisingly, however, the relative contribution of seagrass-derived carbon to bacteria (δ 13 C bacteria ) increased with nutrient loading, despite popular theory being that microbes switch to consuming macroalgae which are assumed to provide a more labile carbon source. Organic carbon sources of fungi were unaffected by nutrient loading. Overall, this study suggests that nutrient loading changes the relative contribution of seagrass and algal sources to SOC pools, boosting sediment microbial biomass and extracellular enzyme activity, thereby possibly changing seagrass blue carbon. Copyright © 2017 Elsevier Ltd. All rights reserved.

Effects of nutrient enrichment on the decomposition of wood and associated microbial activity in streams

USGS Publications Warehouse

Gulis, V.; Rosemond, A.D.; Suberkropp, K.; Weyers, H.S.; Benstead, J.P.

2004-01-01

1. We determined the effects of nutrient enrichment on wood decomposition rates and microbial activity during a 3-year study in two headwater streams at Coweeta Hydrologic Laboratory, NC, U.S.A. After a 1-year pretreatment period, one of the streams was continuously enriched with inorganic nutrients (nitrogen and phosphorus) for 2 years while the other stream served as a reference. We determined the effects of enrichment on both wood veneers and sticks, which have similar carbon quality but differ in physical characteristics (e.g. surface area to volume ratios, presence of bark) that potentially affect microbial colonisation and activity. 2. Oak wood veneers (0.5 mm thick) were placed in streams monthly and allowed to decompose for approximately 90 days. Nutrient addition stimulated ash-free dry mass loss and increased mean nitrogen content, fungal biomass and microbial respiration on veneers in the treatment stream compared with the reference. The magnitude of the response to enrichment was great, with mass loss 6.1 times, and per cent N, fungal biomass and microbial respiration approximately four times greater in the treatment versus reference stream. 3. Decomposition rate and nitrogen content of maple sticks (ca. 1-2 cm diameter) also increased; however, the effect was less pronounced than for veneers. Wood response overall was greater than that determined for leaves in a comparable study, supporting the hypothesis that response to enrichment may be greater for lower quality organic matter (high C:N) than for higher quality (low C:N) substrates. 4. Our results show that moderate nutrient enrichment can profoundly affect decomposition rate and microbial activity on wood in streams. Thus, the timing and availability of wood that provides retention, structure, attachment sites and food in stream ecosystems may be affected by nutrient concentrations raised by human activities.

Plant-mediated effects on extracellular enzyme activities in distinct soil aggregate size classes in field

NASA Astrophysics Data System (ADS)

Kumar, Amit; Dorodnikov, Maxim; Splettstößer, Thomas; Kuzyakov, Yakov; Pausch, Johanna

2017-04-01

Soil aggregation and microbial activities within the aggregates are important factors regulating soil carbon (C) turnover. A reliable and sensitive proxy for microbial activity is activity of extracellular enzymes (EEA). In the present study, effects of soil aggregates on EEA were investigated under three maize plant densities (Low, Normal, and High). Bulk soil was fractionated into three aggregate size classes (>2000 µm large macroaggregates; 2000-250 µm small macroaggregates; <250 µm microaggregates) by optimal-moisture sieving. Microbial biomass and EEA (β-1,4-glucosidase (BG), β-1,4-N-acetylglucosaminidase (NAG), L-leucine aminopeptidase (LAP) and acid phosphatase (acP)) catalyzing soil organic matter (SOM) decomposition were measured in rooted soil of maize and soil from bare fallow. Microbial biomass C (Cmic) decreased with decreasing aggregate size classes. Potential and specific EEA (per unit of Cmic) increased from macro- to microaggregates. In comparison with bare fallow soil, specific EEA of microaggregates in rooted soil was higher by up to 73%, 31%, 26%, and 92% for BG, NAG, acP and LAP, respectively. Moreover, high plant density decreased macroaggregates by 9% compared to bare fallow. Enhanced EEA in three aggregate size classes demonstrated activation of microorganisms by roots. Strong EEA in microaggregates can be explained by microaggregates' localization within the soil. Originally adhering to surfaces of macroaggregates, microaggregates were preferentially exposed to C substrates and nutrients, thereby promoting microbial activity.

Influence of Calcium on Microbial Reduction of Solid Phase Uranium (VI)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Chongxuan; Jeon, Byong-Hun; Zachara, John M.

2007-06-27

The effect of calcium on microbial reduction of a solid phase U(VI), sodium boltwoodite (NaUO2SiO3OH ∙1.5H2O), was evaluated in a culture of a dissimilatory metal-reducing bacterium (DMRB), Shewanella oneidensis strain MR-1. Batch experiments were performed in a non-growth bicarbonate medium with lactate as electron donor at pH 7 buffered with PIPES. Calcium increased both the rate and extent of Na-boltwoodite dissolution by increasing its solubility through the formation of a ternary aqueous calcium-uranyl-carbonate species. The ternary species, however, decreased the rates of microbial reduction of aqueous U(VI). Laser-induced fluorescence spectroscopy (LIFS) and transmission electron microscopy (TEM) revealed that microbial reductionmore » of solid phase U(VI) is a sequentially coupled process of Na-boltwoodite dissolution, U(VI) aqueous speciation, and microbial reduction of dissolved U(VI) to U(IV) that accumulated on bacterial surfaces/periplasm. The overall rates of microbial reduction of solid phase U(VI) can be described by the coupled rates of dissolution and microbial reduction that were both influenced by calcium. The results demonstrated that dissolved U(VI) concentration during microbial reduction was a complex function of solid phase U(VI) dissolution kinetics, aqueous U(VI) speciation, and microbial activity.« less

Effect of rice straw application on microbial community and activity in paddy soil under different water status.

PubMed

Pan, Fuxia; Li, Yaying; Chapman, Stephen James; Yao, Huaiying

2016-03-01

Rice straw application and flooding are common practices in rice production, both of which can induce changes in the microbial community. This study used soil microcosms to investigate the impact of water status (saturated and nonsaturated) and straw application (10 g kg(-1) soil) on soil microbial composition (phospholipid fatty acid analysis) and activity (MicroResp(™) method). Straw application significantly increased total PLFA amount and individual PLFA components independent of soil moisture level. The amount of soil fungal PLFA was less than Gram-negative, Gram-positive, and actinomycete PLFA, except the drained treatment with rice straw application, which had higher fungal PLFA than actinomycete PLFA at the initial incubation stage. Straw amendment and waterlogging had different effects on microbial community structure and substrate-induced pattern. PLFA profiles were primarily influenced by straw application, whereas soil water status had the greater influence on microbial respiration. Of the variation in PLFA and respiration data, straw accounted for 30.1 and 16.7 %, while soil water status explained 7.5 and 29.1 %, respectively. Our results suggest that (1) the size of microbial communities in paddy soil is more limited by carbon substrate availability rather than by the anaerobic conditions due to waterlogging and (2) that soil water status is more important as a control of fungal growth and microbial community activity.

Dynamics of microorganism populations in recirculating nutrient solutions

NASA Technical Reports Server (NTRS)

Strayer, R. F.

1994-01-01

This overview covers the basic microbial ecology of recirculating hydroponic solutions. Examples from NASA and Soviet CELSS tests and the commercial hydroponic industry will be used. The sources of microorganisms in nutrient solutions include air, water, seeds, plant containers and plumbing, biological vectors, and personnel. Microbial fates include growth, death, and emigration. Important microbial habitats within nutrient delivery systems are root surfaces, hardware surfaces (biofilms), and solution suspension. Numbers of bacteria on root surfaces usually exceed those from the other habitats by several orders of magnitude. Gram negative bacteria dominate the microflora with fungal counts usually much lower. Trends typically show a decrease in counts with increasing time unless stressed plants increase root exudates. Important microbial activities include carbon mineralization and nitrogen transformations. Important detrimental interactions include competition with plants, and human and plant pathogenesis.

Soil microbial community structure and function responses to successive planting of Eucalyptus.

PubMed

Chen, Falin; Zheng, Hua; Zhang, Kai; Ouyang, Zhiyun; Li, Huailin; Wu, Bing; Shi, Qian

2013-10-01

Many studies have shown soil degradation after the conversion of native forests to exotic Eucalyptus plantations. However, few studies have investigated the long-term impacts of short-rotation forestry practices on soil microorganisms. The impacts of Eucalyptus successive rotations on soil microbial communities were evaluated by comparing phospholipid fatty acid (PLFA) abundances, compositions, and enzyme activities of native Pinus massoniana plantations and adjacent 1st, 2nd, 3rd, 4th generation Eucalyptus plantations. The conversion from P. massoniana to Eucalyptus plantations significantly decreased soil microbial community size and enzyme activities, and increased microbial physiological stress. However, the PLFA abundances formed "u" shaped quadratic functions with Eucalyptus plantation age. Alternatively, physiological stress biomarkers, the ratios of monounsaturated to saturated fatty acid and Gram+ to Gram- bacteria, formed "n"' shaped quadratic functions, and the ratio of cy17:0 to 16:1omega7c decreased with plantation age. The activities of phenol oxidase, peroxidase, and acid phosphatase increased with Eucalyptus plantation age, while the cellobiohydrolase activity formed "u" shaped quadratic functions. Soil N:P, alkaline hydrolytic nitrogen, soil organic carbon, and understory cover largely explained the variation in PLFA profiles while soil N:P, alkaline hydrolytic nitrogen, and understory cover explained most of the variability in enzyme activity. In conclusion, soil microbial structure and function under Eucalyptus plantations were strongly impacted by plantation age. Most of the changes could be explained by altered soil resource availability and understory cover associated with successive planting of Eucalyptus. Our results highlight the importance of plantation age for assessing the impacts of plantation conversion as well as the importance of reducing disturbance for plantation management.

Long-term exposure to benzalkonium chloride disinfectants results in change of microbial community structure and increased antimicrobial resistance.

PubMed

Tandukar, Madan; Oh, Seungdae; Tezel, Ulas; Konstantinidis, Konstantinos T; Pavlostathis, Spyros G

2013-09-03

The effect of benzalkonium chlorides (BACs), a widely used class of quaternary ammonium disinfectants, on microbial community structure and antimicrobial resistance was investigated using three aerobic microbial communities: BACs-unexposed (DP, fed a mixture of dextrin/peptone), BACs-exposed (DPB, fed a mixture of dextrin/peptone and BACs), and BACs-enriched (B, fed only BACs). Long-term exposure to BACs reduced community diversity and resulted in the enrichment of BAC-resistant species, predominantly Pseudomonas species. Exposure of the two microbial communities to BACs significantly decreased their susceptibility to BACs as well as three clinically relevant antibiotics (penicillin G, tetracycline, ciprofloxacin). Increased resistance to BACs and penicillin G of the two BACs-exposed communities is predominantly attributed to degradation or transformation of these compounds, whereas resistance to tetracycline and ciprofloxacin is largely due to the activity of efflux pumps. Quantification of several key multidrug resistance genes showed a much higher number of copies of these genes in the DPB and B microbial communities compared to the DP community. Collectively, our findings indicate that exposure of a microbial community to BACs results in increased antibiotic resistance, which has important implications for both human and environmental health.

Modeling the Response of Soil Organic Matter Decomposition to Warming: Effects of Dynamical Enzyme Productivity and Nuanced Representation of Respiration.

NASA Astrophysics Data System (ADS)

Sihi, D.; Gerber, S.; Inglett, K. S.; Inglett, P.

2014-12-01

Recent development in modeling soil organic carbon (SOC) decomposition includes the explicit incorporation of enzyme and microbial dynamics. A characteristic of these models is a feedback between substrate and consumers which is absent in traditional first order decay models. Second, microbial decomposition models incorporate carbon use efficiency (CUE) as a function of temperature which proved to be critical to prediction of SOC with warming. Our main goal is to explore microbial decomposition models with respect to responses of microbes to enzyme activity, costs to enzyme production, and to incorporation of growth vs. maintenance respiration. In order to simplify the modeling setup we assumed quick adjustment of enzyme activity and depolymerized carbon to microbial and SOC pools. Enzyme activity plays an important role to decomposition if its production is scaled to microbial biomass. In fact if microbes are allowed to optimize enzyme productivity the microbial enzyme model becomes unstable. Thus if the assumption of enzyme productivity is relaxed, other limiting factors must come into play. To stabilize the model, we account for two feedbacks that include cost of enzyme production and diminishing return of depolymerization with increasing enzyme concentration and activity. These feedback mechanisms caused the model to behave in a similar way to traditional, first order decay models. Most importantly, we found, that under warming, the changes in SOC carbon were more severe in enzyme synthesis is costly. In turn, carbon use efficiency (CUE) and its dynamical response to temperature is mainly determined by 1) the rate of turnover of microbes 2) the partitioning of dead microbial matter into different quality pools, and 3) and whether growth, maintenance respiration and microbial death rate have distinct responses to changes in temperature. Abbreviations: p: decay of enzyme, g: coefficient for growth respiration, : fraction of material from microbial turnover that enters the DOC pool, loss of C scaled to microbial mass, half saturation constant.

Regulation of Hydrolytic Enzyme Activity in Aquatic Microbial Communities Hosted by Carnivorous Pitcher Plants.

PubMed

Young, Erica B; Sielicki, Jessica; Grothjan, Jacob J

2018-04-20

Carnivorous pitcher plants Sarracenia purpurea host diverse eukaryotic and bacterial communities which aid in insect prey digestion, but little is known about the functional processes mediated by the microbial communities. This study aimed to connect pitcher community diversity with functional nutrient transformation processes, identifying bacterial taxa, and measuring regulation of hydrolytic enzyme activity in response to prey and alternative nutrient sources. Genetic analysis identified diverse bacterial taxa known to produce hydrolytic enzyme activities. Chitinase, protease, and phosphatase activities were measured using fluorometric assays. Enzyme activity in field pitchers was positively correlated with bacterial abundance, and activity was suppressed by antibiotics suggesting predominantly bacterial sources of chitinase and protease activity. Fungi, algae, and rotifers observed could also contribute enzyme activity, but fresh insect prey released minimal chitinase activity. Activity of chitinase and proteases was upregulated in response to insect additions, and phosphatase activity was suppressed by phosphate additions. Particulate organic P in prey was broken down, appearing as increasing dissolved organic and inorganic P pools within 14 days. Chitinase and protease were not significantly suppressed by availability of dissolved organic substrates, though organic C and N stimulated bacterial growth, resulting in elevated enzyme activity. This comprehensive field and experimental study show that pitcher plant microbial communities dynamically regulate hydrolytic enzyme activity, to digest prey nutrients to simpler forms, mediating biogeochemical nutrient transformations and release of nutrients for microbial and host plant uptake.

Suitability of the microbial community composition and function in a semiarid mine soil for assessing phytomanagement practices based on mycorrhizal inoculation and amendment addition.

PubMed

Kohler, J; Caravaca, F; Azcón, R; Díaz, G; Roldán, A

2016-03-15

The recovery of species composition and functions of soil microbial community of degraded lands is crucial in order to guarantee the long-term self-sustainability of the ecosystems. A field experiment was carried out to test the influence of combining fermented sugar beet residue (SBR) addition and inoculation with the arbuscular mycorrhizal (AM) fungus Funneliformis mosseae on the plant growth parameters and microbial community composition and function in the rhizosphere of two autochthonous plant species (Dorycnium pentaphyllum L. and Asteriscus maritimus L.) growing in a semiarid soil contaminated by heavy metals. We analysed the phospholipid fatty acids (PLFAs), neutral lipids fatty acids (NLFAs) and enzyme activities to study the soil microbial community composition and function, respectively. The combined treatment was not effective for increasing plant growth. The SBR promoted the growth of both plant species, whilst the AM fungus was effective only for D. pentaphyllum. The effect of the treatments on plant growth was linked to shifts in the rhizosphere microbial community composition and function. The highest increase in dehydrogenase and β-glucosidase activities was recorded in SBR-amended soil. The SBR increased the abundance of marker PLFAs for saprophytic fungi, Gram+ and Gram- bacteria and actinobacteria, whereas the AM fungus enhanced the abundance of AM fungi-related NLFA and marker PLFAs for Gram- bacteria. Measurement of the soil microbial community composition and function was useful to assess the success of phytomanagement technologies in a semiarid, contaminated soil. Copyright © 2016 Elsevier Ltd. All rights reserved.

Metabolically active microbial communities in marine sediment under high-CO2 and low-pH extremes

PubMed Central

Yanagawa, Katsunori; Morono, Yuki; de Beer, Dirk; Haeckel, Matthias; Sunamura, Michinari; Futagami, Taiki; Hoshino, Tatsuhiko; Terada, Takeshi; Nakamura, Ko-ichi; Urabe, Tetsuro; Rehder, Gregor; Boetius, Antje; Inagaki, Fumio

2013-01-01

Sediment-hosting hydrothermal systems in the Okinawa Trough maintain a large amount of liquid, supercritical and hydrate phases of CO2 in the seabed. The emission of CO2 may critically impact the geochemical, geophysical and ecological characteristics of the deep-sea sedimentary environment. So far it remains unclear whether microbial communities that have been detected in such high-CO2 and low-pH habitats are metabolically active, and if so, what the biogeochemical and ecological consequences for the environment are. In this study, RNA-based molecular approaches and radioactive tracer-based respiration rate assays were combined to study the density, diversity and metabolic activity of microbial communities in CO2-seep sediment at the Yonaguni Knoll IV hydrothermal field of the southern Okinawa Trough. In general, the number of microbes decreased sharply with increasing sediment depth and CO2 concentration. Phylogenetic analyses of community structure using reverse-transcribed 16S ribosomal RNA showed that the active microbial community became less diverse with increasing sediment depth and CO2 concentration, indicating that microbial activity and community structure are sensitive to CO2 venting. Analyses of RNA-based pyrosequences and catalyzed reporter deposition-fluorescence in situ hybridization data revealed that members of the SEEP-SRB2 group within the Deltaproteobacteria and anaerobic methanotrophic archaea (ANME-2a and -2c) were confined to the top seafloor, and active archaea were not detected in deeper sediments (13–30 cm in depth) characterized by high CO2. Measurement of the potential sulfate reduction rate at pH conditions of 3–9 with and without methane in the headspace indicated that acidophilic sulfate reduction possibly occurs in the presence of methane, even at very low pH of 3. These results suggest that some members of the anaerobic methanotrophs and sulfate reducers can adapt to the CO2-seep sedimentary environment; however, CO2 and pH in the deep-sea sediment were found to severely impact the activity and structure of the microbial community. PMID:23096400

Microbial diversity in restored wetlands of San Francisco Bay

DOE Office of Scientific and Technical Information (OSTI.GOV)

Theroux, Susanna; Hartman, Wyatt; He, Shaomei

Wetland ecosystems may serve as either a source or a sink for atmospheric carbon and greenhouse gases. This delicate carbon balance is influenced by the activity of belowground microbial communities that return carbon dioxide and methane to the atmosphere. Wetland restoration efforts in the San Francisco Bay-Delta region may help to reverse land subsidence and possibly increase carbon storage in soils. However, the effects of wetland restoration on microbial communities, which mediate soil metabolic activity and carbon cycling, are poorly studied. In an effort to better understand the underlying factors which shape the balance of carbon flux in wetland soils,more » we targeted the microbial communities in a suite of restored and historic wetlands in the San Francisco Bay-Delta region. Using DNA and RNA sequencing, coupled with greenhouse gas monitoring, we profiled the diversity and metabolic potential of the wetland soil microbial communities along biogeochemical and wetland age gradients. Our results show relationships among geochemical gradients, availability of electron acceptors, and microbial community composition. Our study provides the first genomic glimpse into microbial populations in natural and restored wetlands of the San Francisco Bay-Delta region and provides a valuable benchmark for future studies.« less

[Effects of different fertilization patterns on soil enzyme activities in greenhouse vegetable field.

PubMed

Wang, Wen Feng; Li, Chun Hua; Huang, Shao Wen; Gao, Wei; Tang, Ji Wei

2016-03-01

A fixed-site greenhouse vegetable fertilization experiment was carried out to study effects of 6 fertilization patterns on soil enzyme activities in Tianjin City, Northern China. The results showed that during the growing stages of tomato, activities of soil α-glucosidase, β-xylosidase, β-glucosidase, β-cellobiosidase, chitinase and phosphatase in different treatments all increased first and then decreased, while soil urease activities increased first and then became flat. Compared with the chemical nitrogen fertilizer treatment, soil enzyme activities were much higher in treatments of combined application of organic materials with chemical fertilizers, and rose with the increasing input of pig manure and especially the application of straw. A significant positive correlation was found between soil enzyme activities, microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), and dissolved organic carbon (DOC) and dissolved organic nitrogen (DON) contents at different growing stages of tomato. Under the condition of same nutrient input, the combined application of inorganic fertilizers with organic materials, especially a certain amount of corn straw, was capable of increasing soil enzyme activities and keeping soil fertility and sustainability in greenhouse vegetable production.

Is DOM driver of the microbial carrying capacity in pristine porous groundwater ecosystems? - lab-scale experiments in 2D sediment flow-through microcosms

NASA Astrophysics Data System (ADS)

Hofmann, Roland; Griebler, Christian

2017-04-01

Groundwater ecosystems are an essential resource for drinking water and at the same time constitute fascinating habitats subject to increasing (anthropogenic) disturbances. In our research, we look for ways to qualitatively and quantitatively access, and predict the resistance and resilience (potential) of groundwater ecosystems in consequence of selected disturbances. As a central goal we hope to identify and quantify the underlying biological and ecological key drivers of the microbial Carrying Capacity (mCC) - an ecological concept established in macro-ecology - we assume directly connected to the ecosystem's productivity and the resistance and resilience of aquifers. We further hypothesize, that the ecosystems' mCC is a result of available energy and constitutes a promising proxy for the potential of groundwater ecosystems to withstand impacts and recover from it. In a first approach we studied the dynamics of the microbial standing stock (biomass) and growth (productivity) productivity of a natural groundwater microbial community in parallel 2-D sediment flow-through systems. Selected zones of the model aquifers were disturbed by elevated DOM concentrations. Both the 'mobile' (free floating) and 'sessile' (sediment attached) microbial components were followed over time in terms of biomass, growth, and specific activities (ATP, carbon use efficiency) and taxonomic composition. Sediment regions supplied with elevated concentrations of natural DOM showed increased biomass, activities and taxonomic richness with the sediment community, while differences in the mobile microbial were marginal. Specifically, the carbon use efficiency was significantly increased in the DOM amended sediment zones. In contrast, the microbial community that received the mainly refractory natural background DOM was able to metabolize polymers more efficiently in substrate use tests (ECOLOG), seen as an adaptation to the energy-poor subsurface. Quasi-stationary conditions were reached in the model aquifers only after several weeks. The quantitative link between microbial productivity and mCC is currently evaluated.

Plant–microbial competition for nitrogen increases microbial activities and carbon loss in invaded soils

Treesearch

Matthew E. Craig; Jennifer M. Fraterrigo

2017-01-01

Many invasive plant species show high rates of nutrient acquisition relative to their competitors. Yet the mechanisms underlying this phenomenon, and its implications for ecosystem functioning, are poorly understood, particularly in nutrient-limited systems. Here, we test the hypothesis that an invasive plant species (Microstegium vimineum...

Impact of protists on a hydrocarbon-degrading bacterial community from deep-sea Gulf of Mexico sediments: A microcosm study

NASA Astrophysics Data System (ADS)

Beaudoin, David J.; Carmichael, Catherine A.; Nelson, Robert K.; Reddy, Christopher M.; Teske, Andreas P.; Edgcomb, Virginia P.

2016-07-01

In spite of significant advancements towards understanding the dynamics of petroleum hydrocarbon degrading microbial consortia, the impacts (direct or indirect via grazing activities) of bacterivorous protists remain largely unknown. Microcosm experiments were used to examine whether protistan grazing affects the petroleum hydrocarbon degradation capacity of a deep-sea sediment microbial community from an active Gulf of Mexico cold seep. Differences in n-alkane content between native sediment microcosms and those treated with inhibitors of eukaryotes were assessed by comprehensive two-dimensional gas chromatography following 30-90 day incubations and analysis of shifts in microbial community composition using small subunit ribosomal RNA gene clone libraries. More biodegradation was observed in microcosms supplemented with eukaryotic inhibitors. SSU rRNA gene clone libraries from oil-amended treatments revealed an increase in the number of proteobacterial clones (particularly γ-proteobacteria) after spiking sediments with diesel oil. Bacterial community composition shifted, and degradation rates increased, in treatments where protists were inhibited, suggesting protists affect the hydrocarbon degrading capacity of microbial communities in sediments collected at this Gulf of Mexico site.

Effects of gamma irradiation on physicochemical properties, antioxidant and microbial activities of sour cherry juice

NASA Astrophysics Data System (ADS)

Arjeh, Edris; Barzegar, Mohsen; Ali Sahari, Mohammad

2015-09-01

Recently, due to the beneficial effects of bioactive compounds, demand for minimally processed fruits and fruit juices has increased rapidly in the world. In this study, sour cherry juice (SCJ) was exposed to gamma irradiation at 0.0, 0.5, 1.5, 3.0, 4.5, and 6.0 kGy and then stored at 4 °C for 60 days. Total soluble solids (TSS), total acidity (TA), color, total phenolic content (TPC), total monomeric anthocyanin content (TMC), antioxidant activity, organic acid profile, and microbial analysis were evaluated at regular intervals during the storage. Results indicated that irradiation did not have any significant effect on TSS, while level of TA increased significantly at the dose of 6 kGy (p<0.05). Furthermore, irradiation treatment and storage time led to a significant increase in L* and b* values and a decrease in a* values. Total monomeric anthocyanin content of the irradiated SCJ was lower than that of the non-irradiated one (24% at 3.0 kGy) and also changed toward a more negative direction during the storage (63% at 3.0 kGy for 60 days). There was a significant decrease in the antioxidant activity (DPPH radical scavenging and FRAP assay) in both irradiated and stored SCJs. After irradiation (0-6 kGy), the results showed that the concentration of malic and oxalic acid significantly increased; but, the concentration of ascorbic, citric, fumaric, and succinic acids significantly decreased. Gamma irradiation with doses of ≥3 kGy resulted in overall reduction in microbial loads. Based on the results obtained from the changes of physicochemical properties, antioxidant activity, and microbial analysis, irradiation of SCJ at doses of higher than 3.0 kGy is not recommended.

Limitations of microbial hydrocarbon degradation at the Amon Mud Volcano (Nile Deep Sea Fan)

NASA Astrophysics Data System (ADS)

Felden, J.; Lichtschlag, A.; Wenzhöfer, F.; de Beer, D.; Feseker, T.; Pop Ristova, P.; de Lange, G.; Boetius, A.

2013-01-01

The Amon mud volcano (MV), located at 1250 m water depth on the Nile Deep Sea Fan, is known for its active emission of methane and non-methane hydrocarbons into the hydrosphere. Previous investigations showed a low efficiency of hydrocarbon-degrading anaerobic microbial communities inhabiting the Amon MV center in the presence of sulphate and hydrocarbons in the seeping subsurface fluids. By comparing spatial and temporal patterns of in situ biogeochemical fluxes, temperature gradients, pore water composition and microbial activities over three years, we investigated why the activity of anaerobic hydrocarbon degraders can be low despite high energy supplies. We found that the central dome of the Amon MV, as well as a lateral mud flow at its base, showed signs of recent exposure of hot subsurface muds lacking active hydrocarbon degrading communities. In these highly disturbed areas, anaerobic degradation of methane was less than 2% of the methane flux. Rather high oxygen consumption rates compared to low sulphide production suggest a faster development of more rapidly growing aerobic hydrocarbon degraders in highly disturbed areas. In contrast, the more stabilized muds surrounding the central gas and fluid conduits hosted active anaerobic hydrocarbon-degrading microbial communities. Furthermore, within three years, cell numbers and hydrocarbon degrading activity increased at the gas-seeping sites. The low microbial activity in the hydrocarbon-vented areas of Amon mud volcano is thus a consequence of kinetic limitations by heat and mud expulsion, whereas most of the outer mud volcano area is limited by hydrocarbon transport.

Microbial Species Richness and Metabolic Activities in Hypersaline Microbial Mats: Insight into Biosignature Formation Through Lithification

NASA Astrophysics Data System (ADS)

Baumgartner, Laura K.; Dupraz, Christophe; Buckley, Daniel H.; Spear, John R.; Pace, Norman R.; Visscher, Pieter T.

2009-11-01

Microbial mats in the hypersaline lake of Salt Pan, Eleuthera, Bahamas, display a gradient of lithification along a transect from the center to the shore of the lake. These mats exist under similar geochemical conditions, with light quantity and quality as the sole major environmental difference. Therefore, we hypothesized that the microbial community may be driving the differences in lithification and, by extension, mineral biosignature formation. The lithifying and non-lithifying mat communities were compared (via 16S rRNA gene sequencing, 485 and 464 sequences, respectively) over both temporal and spatial scales. Seven bacterial groups dominated in all the microbial mat libraries: bacteriodetes, alphaproteobacteria, deltaproetobacteria, chloroflexi, spirochaetes, cyanobacteria, and planctomycetes. The mat communities were all significantly different over space, time, and lithification state. Species richness is significantly higher in the non-lithifying mats, potentially due to differences in mat structure and activity. This increased richness may impact lithification and, hence, biosignature production.

Activated carbon derived from chitosan as air cathode catalyst for high performance in microbial fuel cells

NASA Astrophysics Data System (ADS)

Liu, Yi; Zhao, Yong; Li, Kexun; Wang, Zhong; Tian, Pei; Liu, Di; Yang, Tingting; Wang, Junjie

2018-02-01

Chitosan with rich of nitrogen is used as carbon precursor to synthesis activated carbon through directly heating method in this study. The obtained carbon is activated by different amount of KOH at different temperatures, and then prepared as air cathodes for microbial fuel cells. Carbon sample treated with double amount of KOH at 850 °C exhibits maximum power density (1435 ± 46 mW m-2), 1.01 times improved, which ascribes to the highest total surface area, moderate micropore and mesoporous structure and the introduction of nitrogen. The electrochemical impedance spectroscopy and powder resistivity state that carbon treated with double amount of KOH at 850 °C possesses lower resistance. The other electrochemical measurements demonstrate that the best kinetic activity make the above treated sample to show the best oxygen reduction reaction activity. Besides, the degree of graphitization of samples increases with the activated temperature increasing, which is tested by Raman. According to elemental analysis and X-ray photoelectron spectroscopy, all chitosan samples are nitrogen-doped carbon, and high content nitrogen (pyridinic-N) improves the electrochemical activity of carbon treated with KOH at 850 °C. Thus, carbon materials derived from chitosan would be an optimized catalyst for oxygen reduction reaction in microbial fuel cell.

[Microbial air monitoring in operating theatre: active and passive samplings].

PubMed

Pasquarella, C; Masia, M D; Nnanga, Nga; Sansebastiano, G E; Savino, A; Signorelli, C; Veronesi, L

2004-01-01

Microbial air contamination was evaluated in 11 operating theatres using active and passive samplings. SAS (Surface Air System) air sampling was used to evaluate cfu/m3 and settle plates were used to measure the index of microbial air contamination (IMA). Samplings were performed at the same time on three different days, at three different times (before, during and after the surgical activity). Two points were monitored (patient area and perimeter of the operating theatre). Moreover, the cfu/m3 were evaluated at the air inlet of the conditioner system. 74.7% of samplings performed at the air inlet and 66.7% of the samplings performed at the patient area before the beginning of the surgical activity (at rest) exceeded the 35 cfu/m3 used as threshold value. 100% of IMA values exceeded the threshold value of 5. Using both active and passive sampling, the microbial contamination was shown to increase significantly during activity. The cfu values were higher at the patient area than at the perimeter of the operating theatre. Mean values of the cfu/m3 during activity at the patient area ranged from a minimum of 61+/-41 cfu/m3 to a maximum of 242+/-136 cfu/m3; IMA values ranged from a minimum of 19+/-10 to a maximum of 129+/-60. 15.2% of samplings performed at the patient area using SAS and 75.8% of samplings performed using settle plates exceeded the threshold values of 180 cfu/m3 and 25 respectively, with a significant difference of the percentages. The highest values were found in the operating theatre with inadequate structural and managerial conditions. These findings confirm that the microbiological quality of air may be considered a mirror of the hygienic conditions of the operating theatre. Settle plates proved to be more sensitive in detecting the increase of microbial air contamination related to conditions that could compromise the quality of the air in operating theatres.

Microbial Community Dynamics from Permafrost Across the Pleistocene-Holocene Boundary and Response to Abrupt Climate Change

NASA Astrophysics Data System (ADS)

Hammad, A.; Mahony, M.; Froese, D. G.; Lanoil, B. D.

2014-12-01

Earth is currently undergoing rapid warming similar to that observed about 10,000 years ago at the end of the Pleistocene. We know a considerable amount about the adaptations and extinctions of mammals and plants at the Pleistocene/Holocene (P/H) boundary, but relatively little about changes at the microbial level. Due to permafrost soils' freezing anoxic conditions, they act as microbial diversity archives allowing us to determine how microbial communities adapted to the abrupt warming at the end of P. Since microbial community composition only helps differentiate viable and extant microorganisms in frozen permafrost, microbial activity in thawing permafrost must be investigated to provide a clear understanding of microbial response to climate change. Current increased temperatures will result in warming and potential thaw of permafrost and release of stored organic carbon, freeing it for microbial utilization; turning permafrost into a carbon source. Studying permafrost viable microbial communities' diversity and activity will provide a better understanding of how these microorganisms respond to soil edaphic variability due to climate change across the P/H boundary, providing insight into the changes that the soil community is currently undergoing in this modern era of rapid climate change. Modern soil, H and P permafrost cores were collected from Lucky Lady II site outside Dawson City, Yukon. 16S rRNA high throughput sequencing of permafrost DNA showed the same trends for total and viable community richness and diversity with both decreasing with permafrost depth and only the richness increasing in mid and early P. The modern, H and P soils had 50.9, 33.9, and 27.3% unique viable species and only 14% of the total number of viable species were shared by all soils. Gas flux measurements of thawed permafrost showed metabolic activity in modern and permafrost soils, aerobic CH­­4 consumption in modern, some H and P soils, and anaerobic CH­­4 production in one H sample. Soil chemistry analysis showed that older permafrost, P, had higher pH, lower total nitrogen, ammonium, and organic carbon than younger permafrost, H.

A Survey of Environmental Microbial Flora During Closed Chamber Studies

NASA Technical Reports Server (NTRS)

Ott, C. Mark; Groves, Theron O.; Bell-Robinson, Denetia; Pierson, Duane L.; Paloski, W. H. (Technical Monitor)

1999-01-01

Services, Inc. and NASA Johnson Space Center, Houston, TX As NASA prepares for long-term missions aboard the International Space Station and the eventual exploration of Mars, closed-environment chambers on Earth have become important test beds for systems evaluations. During 2 separate studies of a selfcontained ecosystem containing 4 crewmembers, microbial surveys of samples from 13 surface and 3 air sites were performed. Microbial concentration of samples from surface sites with frequent water contact (e.g., urinal, sink) did not indicate significantly higher levels of contamination than drier areas, though surface cleaning by the crew may have influenced this conclusion. Changes in bacterial diversity on surface sites implied that the number of transient species was high, suggesting movement by crew activities, aerosols, or both. A non-linear relationship between bacterial diversity and enumeration from surface samples indicated that a rapid increase occurred in the number of species as cell concentration increased to 5 CFU/sq cm. Above this concentration, the number of different bacterial species varied between 11 and 16. Airborne bacteria and fungi averaged only 160 and 1 CFU/m3, respectively. Microbial contamination of the potable water system primarily consisted of 3 species of Gram negative bacteria; however, after 60 days during one study, several species of Bacillus became the dominant flora. This study suggests that under these conditions, microbial contamination in the air and water was suppressed by the life-support systems, though contamination was possible. Conversely, the crew and their activities controlled microbial levels on surfaces. Understanding the factors that affect microbial control will improve the design of microbial testing both during space flight and in analogous Earth-based environments.

Segregation of the Anodic Microbial Communities in a Microbial Fuel Cell Cascade

PubMed Central

Hodgson, Douglas M.; Smith, Ann; Dahale, Sonal; Stratford, James P.; Li, Jia V.; Grüning, André; Bushell, Michael E.; Marchesi, Julian R.; Avignone Rossa, C.

2016-01-01

Metabolic interactions within microbial communities are essential for the efficient degradation of complex organic compounds, and underpin natural phenomena driven by microorganisms, such as the recycling of carbon-, nitrogen-, and sulfur-containing molecules. These metabolic interactions ultimately determine the function, activity and stability of the community, and therefore their understanding would be essential to steer processes where microbial communities are involved. This is exploited in the design of microbial fuel cells (MFCs), bioelectrochemical devices that convert the chemical energy present in substrates into electrical energy through the metabolic activity of microorganisms, either single species or communities. In this work, we analyzed the evolution of the microbial community structure in a cascade of MFCs inoculated with an anaerobic microbial community and continuously fed with a complex medium. The analysis of the composition of the anodic communities revealed the establishment of different communities in the anodes of the hydraulically connected MFCs, with a decrease in the abundance of fermentative taxa and a concurrent increase in respiratory taxa along the cascade. The analysis of the metabolites in the anodic suspension showed a metabolic shift between the first and last MFC, confirming the segregation of the anodic communities. Those results suggest a metabolic interaction mechanism between the predominant fermentative bacteria at the first stages of the cascade and the anaerobic respiratory electrogenic population in the latter stages, which is reflected in the observed increase in power output. We show that our experimental system represents an ideal platform for optimization of processes where the degradation of complex substrates is involved, as well as a potential tool for the study of metabolic interactions in complex microbial communities. PMID:27242723

Fate and Effects of Crude Oil Spilled on Subarctic Permafrost Terrain in Interior Alaska: Fifteen Years Later

DTIC Science & Technology

1993-08-01

tundra ecosystems of Alas- (75 m2) having surface oil visible. In contrast, most ka and northern Canada (Deneke et al. 1974, Atlas of the crude oil...Overall soil microbial activity was growing black spruce (Picea mariana) forest with an increased, with some components of the microbial understory of...terrestrial environments, in the heavily affected portions of the site; they 3. Determine the effect of crude oil spills on soil found that microbial

Pesticide dissipation and microbial community changes in a biopurification system: influence of the rhizosphere.

PubMed

Diez, M C; Elgueta, S; Rubilar, O; Tortella, G R; Schalchli, H; Bornhardt, C; Gallardo, F

2017-12-01

The dissipation of atrazine, chlorpyrifos and iprodione in a biopurification system and changes in the microbial and some biological parameters influenced by the rhizosphere of Lolium perenne were studied in a column system packed with an organic biomixture. Three column depths were analyzed for residual pesticides, peroxidase, fluorescein diacetate activity and microbial communities. Fungal colonization was analyzed by confocal laser scanning microscopy to assess the extent of its proliferation in wheat straw. The L. perenne rhizosphere enhanced pesticide dissipation and negligible pesticide residues were detected at 20-30 cm column depth. Atrazine, chlorpyrifos and iprodione removal was 82, 89 and 74% respectively in the first 10 cm depth for columns with vegetal cover. The presence of L. perenne in contaminated columns stimulated peroxidase activity in all three column depth sections. Fluorescein diacetate activity decreased over time in all column sections with the highest values in biomixtures with vegetal cover. Microbial communities, analyzed by PCR-DGGE, were not affected by the pesticide mixture application, presenting high values of similarity (>65%) with and without vegetal cover. Microbial abundance of Actinobacteria varied according to treatment and no clear link was observed. However, bacterial abundance increased over time and was similar with and without vegetal cover. On the other hand, fungal abundance decreased in all sections of columns after 40 days, but an increase was observed in response to pesticide application. Fungal colonization and straw degradation during pesticide dissipation were verified by monitoring the lignin autofluorescence loss.

Soil microbial properties after long-term swine slurry application to conventional and no-tillage systems in Brazil.

PubMed

Balota, Elcio L; Machineski, Oswaldo; Hamid, Karima I A; Yada, Ines F U; Barbosa, Graziela M C; Nakatani, Andre S; Coyne, Mark S

2014-08-15

Swine waste can be used as an agricultural fertilizer, but large amounts may accumulate excess nutrients in soil or contaminate the surrounding environment. This study evaluated long-term soil amendment (15 years) with different levels of swine slurry to conventional (plow) tillage (CT) and no tillage (NT) soils. Long-term swine slurry application did not affect soil organic carbon. Some chemical properties, such as calcium, base saturation, and aluminum saturation were significantly different within and between tillages for various application rates. Available P and microbial parameters were significantly affected by slurry addition. Depending on tillage, soil microbial biomass and enzyme activity increased up to 120 m(3) ha(-1) year(-1) in all application rates. The NT system had higher microbial biomass and activity than CT at all application levels. There was an inverse relationship between the metabolic quotient (qCO2) and MBC, and the qCO2 was 53% lower in NT than CT. Swine slurry increased overall acid phosphatase activity, but the phosphatase produced per unit of microbial biomass decreased. A comparison of data obtained in the 3rd and 15th years of swine slurry application indicated that despite slurry application the CT system degraded with time while the NT system had improved values of soil quality indicators. For these Brazilian oxisols, swine slurry amendment was insufficient to maintain soil quality parameters in annual crop production without additional changes in tillage management. Copyright © 2014 Elsevier B.V. All rights reserved.

Effects of poultry manure on soil biochemical properties in phthalic acid esters contaminated soil.

PubMed

Gao, Jun; Qin, Xiaojian; Ren, Xuqin; Zhou, Haifeng

2015-12-01

This study aimed to evaluate the effects of poultry manure (PM) on soil biological properties in DBP- and DEHP-contaminated soils. An indoor incubation experiment was conducted. Soil microbial biomass C (Cmic), soil enzymatic activities, and microbial phospholipid fatty acid (PLFA) concentrations were measured during incubation period. The results indicated that except alkaline phosphatase activity, DBP and DEHP had negative effects on Cmic, dehydrogenase, urease, protease activities, and contents of total PLFA. However, 5 % PM treatment alleviated the negative effects of PAEs on the above biochemical parameters. In DBP-contaminated soil, 5 % PM amendment even resulted in dehydroenase activity and Cmic content increasing by 17.8 and 11.8 % on the day 15 of incubation, respectively. During the incubation periods, the total PLFA contents decreased maximumly by 17.2 and 11.6 % in DBP- and DEHP-contaminated soils without PM amendments, respectively. Compared with those in uncontaminated soil, the total PLFA contents increased slightly and the value of bacPLFA/fugalPLFA increased significantly in PAE-contaminated soils with 5 % PM amendment. Nevertheless, in both contaminated soils, the effects of 5 % PM amendment on the biochemical parameters were not observed with 10 % PM amendment. In 10 % PM-amended soils, DBP and DEHP had little effect on Cmic, soil enzymatic activities, and microbial community composition. At the end of incubation, the effects of PAEs on these parameters disappeared, irrespective of PM amendment. The application of PM ameliorated the negative effect of PAEs on soil biological environment. However, further work is needed to study the effect of PM on soil microbial gene expression in order to explain the change mechanisms of soil biological properties.

Small-scale spatial heterogeneity of ecosystem properties, microbial community composition and microbial activities in a temperate mountain forest soil.

PubMed

Štursová, Martina; Bárta, Jiří; Šantrůčková, Hana; Baldrian, Petr

2016-12-01

Forests are recognised as spatially heterogeneous ecosystems. However, knowledge of the small-scale spatial variation in microbial abundance, community composition and activity is limited. Here, we aimed to describe the heterogeneity of environmental properties, namely vegetation, soil chemical composition, fungal and bacterial abundance and community composition, and enzymatic activity, in the topsoil in a small area (36 m 2 ) of a highly heterogeneous regenerating temperate natural forest, and to explore the relationships among these variables. The results demonstrated a high level of spatial heterogeneity in all properties and revealed differences between litter and soil. Fungal communities had substantially higher beta-diversity than bacterial communities, which were more uniform and less spatially autocorrelated. In litter, fungal communities were affected by vegetation and appeared to be more involved in decomposition. In the soil, chemical composition affected both microbial abundance and the rates of decomposition, whereas the effect of vegetation was small. Importantly, decomposition appeared to be concentrated in hotspots with increased activity of multiple enzymes. Overall, forest topsoil should be considered a spatially heterogeneous environment in which the mean estimates of ecosystem-level processes and microbial community composition may confound the existence of highly specific microenvironments. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Nitrogen Stimulates the Growth of Subsurface Basalt-associated Microorganisms at the Western Flank of the Mid-Atlantic Ridge

PubMed Central

Zhang, Xinxu; Fang, Jing; Bach, Wolfgang; Edwards, Katrina J.; Orcutt, Beth N.; Wang, Fengping

2016-01-01

Oceanic crust constitutes the largest aquifer system on Earth, and microbial activity in this environment has been inferred from various geochemical analyses. However, empirical documentation of microbial activity from subsurface basalts is still lacking, particularly in the cool (<25°C) regions of the crust, where are assumed to harbor active iron-oxidizing microbial communities. To test this hypothesis, we report the enrichment and isolation of crust-associated microorganisms from North Pond, a site of relatively young and cold basaltic basement on the western flank of the Mid-Atlantic Ridge that was sampled during Expedition 336 of the Integrated Ocean Drilling Program. Enrichment experiments with different carbon (bicarbonate, acetate, methane) and nitrogen (nitrate and ammonium) sources revealed significant cell growth (one magnitude higher cell abundance), higher intracellular DNA content, and increased Fe3+/ΣFe ratios only when nitrogen substrates were added. Furthermore, a Marinobacter strain with neutrophilic iron-oxidizing capabilities was isolated from the basalt. This work reveals that basalt-associated microorganisms at North Pond had the potential for activity and that microbial growth could be stimulated by in vitro nitrogen addition. Furthermore, iron oxidation is supported as an important process for microbial communities in subsurface basalts from young and cool ridge flank basement. PMID:27199959

Effect of exogenous carbon addition and the freeze-thaw cycle on soil microbes and mineral nitrogen pools1

NASA Astrophysics Data System (ADS)

Hu, Xia; Yin, Peng; Nong, Xiang; Liao, Jinhua

2018-01-01

To elucidate the alpine soil process in winter, the response mechanism of soil mineral nitrogen and soil microbes to exogenous carbon (0 mg C, 1 mg C, 2 mg C, 4 mg C and 8 mg C·g-1 dry soil) and the freeze-thaw cycle (-2 °C, -2 ∼ 2 °C, -20 ∼2°C) were studied by laboratory simulation. The freeze-thaw treatment had no significant effect on microbial biomass nitrogen and the number of bacteria. The soil mineral N pool, the number of fungi, and enzyme activities were obviously affected by the freeze-thaw cycle. A mild freeze-thaw cycle (-2∼2°C) significantly increased the number of fungi and catalase activity, while severe freeze-thaw cycle (-20∼2°C) obviously decreased invertase activity. The results suggested that both the freeze-thaw rate and freeze-thaw temperature amplitudes have a strong effect on soil microbial dynamics in the alpine zone in winter. The results showed that exogenous carbon addition significantly decreased soil NO3-N and NH4 +-N contents, increased soil microbial biomass, the number of microbes, and soil enzyme activities. The results showed that microbial growth in the eastern Tibetan Plateau was somewhat limited by available C. It may represent a larger potential pulse of soil nutrient for alpine plants in the next spring, and may be instrumental for plant community shifts under future climate change predictions due to the possible increased litter addition.

Monitoring microbial growth and activity using spectral induced polarization and low-field nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Zhang, Chi; Keating, Kristina; Revil, Andre

2015-04-01

Microbes and microbial activities in the Earth's subsurface play a significant role in shaping subsurface environments and are involved in environmental applications such as remediation of contaminants in groundwater and oil fields biodegradation. Stimulated microbial growth in such applications could cause wide variety of changes of physical/chemical properties in the subsurface. It is critical to monitor and determine the fate and transportation of microorganisms in the subsurface during such applications. Recent geophysical studies demonstrate the potential of two innovative techniques, spectral induced polarization (SIP) and low-field nuclear magnetic resonance (NMR), for monitoring microbial growth and activities in porous media. The SIP measures complex dielectric properties of porous media at low frequencies of exciting electric field, and NMR studies the porous structure of geologic media and characterizes fluids subsurface. In this laboratory study, we examined both SIP and NMR responses from bacterial growth suspension as well as suspension mixed with silica sands. We focus on the direct contribution of microbes to the SIP and NMR signals in the absence of biofilm formation or biomineralization. We used Zymomonas mobilis and Shewanella oneidensis (MR-1) for SIP and NMR measurements, respectively. The SIP measurements were collected over the frequency range of 0.1 - 1 kHz on Z. mobilis growth suspension and suspension saturated sands at different cell densities. SIP data show two distinct peaks in imaginary conductivity spectra, and both imaginary and real conductivities increased as microbial density increased. NMR data were collected using both CPMG pulse sequence and D-T2 mapping to determine the T2-distribution and diffusion properties on S. oneidensis suspension, pellets (live and dead), and suspension mixed with silica sands. NMR data show a decrease in the T2-distribution in S. oneidensis suspension saturated sands as microbial density increase. A clear distinction in the T2-distribution and D-T2 plots between live and dead cell pellets was also observed. These results will provide a basis for understanding the effect of microbes within geologic media on SIP and low-field NMR measurements. This research suggests that both SIP and NMR have the potential to monitor microbial growth and activities in the subsurface and could provide spatiotemporal variations in bacterial abundance in porous media.

Effect of light wavelength on hot spring microbial mat biodiversity

PubMed Central

Nishida, Akifumi; Thiel, Vera; Nakagawa, Mayuko; Ayukawa, Shotaro

2018-01-01

Hot spring associated phototrophic microbial mats are purely microbial communities, in which phototrophic bacteria function as primary producers and thus shape the community. The microbial mats at Nakabusa hot springs in Japan harbor diverse photosynthetic bacteria, mainly Thermosynechococcus, Chloroflexus, and Roseiflexus, which use light of different wavelength for energy conversion. The aim of this study was to investigate the effect of the phototrophs on biodiversity and community composition in hot spring microbial mats. For this, we specifically activated the different phototrophs by irradiating the mats with different wavelengths in situ. We used 625, 730, and 890 nm wavelength LEDs alone or in combination and confirmed the hypothesized increase in relative abundance of different phototrophs by 16S rRNA gene sequencing. In addition to the increase of the targeted phototrophs, we studied the effect of the different treatments on chemotrophic members. The specific activation of Thermosynechococcus led to increased abundance of several other bacteria, whereas wavelengths specific to Chloroflexus and Roseiflexus induced a decrease in >50% of the community members as compared to the dark conditions. This suggests that the growth of Thermosynechococcus at the surface layer benefits many community members, whereas less benefit is obtained from an increase in filamentous anoxygenic phototrophs Chloroflexus and Roseiflexus. The increases in relative abundance of chemotrophs under different light conditions suggest a relationship between the two groups. Aerobic chemoheterotrophs such as Thermus sp. and Meiothermus sp. are thought to benefit from aerobic conditions and organic carbon in the form of photosynthates by Thermosynechococcus, while the oxidation of sulfide and production of elemental sulfur by filamentous anoxygenic phototrophs benefit the sulfur-disproportionating Caldimicrobium thiodismutans. In this study, we used an experimental approach under controlled environmental conditions for the analysis of natural microbial communities, which proved to be a powerful tool to study interspecies relationships in the microbiome. PMID:29381713

Effect of light wavelength on hot spring microbial mat biodiversity.

PubMed

Nishida, Akifumi; Thiel, Vera; Nakagawa, Mayuko; Ayukawa, Shotaro; Yamamura, Masayuki

2018-01-01

Hot spring associated phototrophic microbial mats are purely microbial communities, in which phototrophic bacteria function as primary producers and thus shape the community. The microbial mats at Nakabusa hot springs in Japan harbor diverse photosynthetic bacteria, mainly Thermosynechococcus, Chloroflexus, and Roseiflexus, which use light of different wavelength for energy conversion. The aim of this study was to investigate the effect of the phototrophs on biodiversity and community composition in hot spring microbial mats. For this, we specifically activated the different phototrophs by irradiating the mats with different wavelengths in situ. We used 625, 730, and 890 nm wavelength LEDs alone or in combination and confirmed the hypothesized increase in relative abundance of different phototrophs by 16S rRNA gene sequencing. In addition to the increase of the targeted phototrophs, we studied the effect of the different treatments on chemotrophic members. The specific activation of Thermosynechococcus led to increased abundance of several other bacteria, whereas wavelengths specific to Chloroflexus and Roseiflexus induced a decrease in >50% of the community members as compared to the dark conditions. This suggests that the growth of Thermosynechococcus at the surface layer benefits many community members, whereas less benefit is obtained from an increase in filamentous anoxygenic phototrophs Chloroflexus and Roseiflexus. The increases in relative abundance of chemotrophs under different light conditions suggest a relationship between the two groups. Aerobic chemoheterotrophs such as Thermus sp. and Meiothermus sp. are thought to benefit from aerobic conditions and organic carbon in the form of photosynthates by Thermosynechococcus, while the oxidation of sulfide and production of elemental sulfur by filamentous anoxygenic phototrophs benefit the sulfur-disproportionating Caldimicrobium thiodismutans. In this study, we used an experimental approach under controlled environmental conditions for the analysis of natural microbial communities, which proved to be a powerful tool to study interspecies relationships in the microbiome.

Effects of Non-Indigenous Oysters on Microbial Diversity and Ecosystem Functioning

PubMed Central

Green, Dannielle S.; Boots, Bas; Crowe, Tasman P.

2012-01-01

Invasive ecosystem engineers can physically and chemically alter the receiving environment, thereby affecting biodiversity and ecosystem functioning. The Pacific oyster, Crassostrea gigas, invasive throughout much of the world, can establish dense populations monopolising shorelines and possibly altering ecosystem processes including decomposition and nutrient cycling. The effects of increasing cover of invasive C. gigas on ecosystem processes and associated microbial assemblages in mud-flats were tested experimentally in the field. Pore-water nutrients (NH4 + and total oxidised nitrogen), sediment chlorophyll content, microbial activity, total carbon and nitrogen, and community respiration (CO2 and CH4) were measured to assess changes in ecosystem functioning. Assemblages of bacteria and functionally important microbes, including methanogens, methylotrophs and ammonia-oxidisers were assessed in the oxic and anoxic layers of sediment using terminal restriction length polymorphism of the bacterial 16S rRNA, mxaF, amoA and archaeal mcrA genes respectively. At higher covers (40 and 80%) of oysters there was significantly greater microbial activity, increased chlorophyll content, CO2 (13 fold greater) and CH4 (6 fold greater) emission from the sediment compared to mud-flats without C. gigas. At 10% cover, C. gigas increased the concentration of total oxidised nitrogen and altered the assemblage structure of ammonia-oxidisers and methanogens. Concentrations of pore-water NH4 + were increased by C. gigas regardless of cover. Invasive species can alter ecosystem functioning not only directly, but also indirectly, by affecting microbial communities vital for the maintenance of ecosystem processes, but the nature and magnitude of these effects can be non-linear, depending on invader abundance. PMID:23144762

Soil organic carbon (SOC) accumulation in rice paddies under long-term agro-ecosystem experiments in southern China - VI. Changes in microbial community structure and respiratory activity

NASA Astrophysics Data System (ADS)

Liu, D.; Liu, X.; Liu, Y.; Li, L.; Pan, G.; Crowley, D.; Tippkötter, R.

2011-02-01

Biological stabilization within accumulated soil organic carbon (SOC) has not been well understood, while its role in physical and chemical protection as well as of chemical recalcitrance had been addressed in Chinese rice paddies. In this study, topsoil samples were collected and respiratory activity measured in situ following rice harvest under different fertilization treatments of three long-term experimental sites across southern China in 2009. The SOC contents, microbial biomass carbon (SMBC) and nitrogen (SMBN) were analysed using chemical digestion and microbial community structure assessment via clony dilute plate counting methods. While SOC contents were consistently higher under compound chemical fertilization (Comp-Fert) or combined organic and inorganic fertilization (Comb-Fert) compared to N fertilization only (N-Fert), there was significantly higher fungal-bacterial ratio under Comb-Fert than under N-Fert and Comp-Fert. When subtracting the background effect under no fertilization treatment (Non-Fert), the increase both in SMBC and SMBN under fertilization treatment was found very significantly correlated to the increase in SOC over controls across the sites. Also, the ratio of culturable fungal to bacterial population numbers (F/B ratio) was well correlated with soil organic carbon contents in all samples across the sites studied. SOC accumulation favoured a build-up the microbial community with increasing fungal dominance in the rice paddies under fertilization treatments. While soil respiration rates were high under Comb-Fert as a result of enhanced microbial community build-up, the specific soil respiratory activity based on microbial biomass carbon was found in a significantly negatively correlation with the SOC contents for overall samples. Thus, a fungal-dominated microbial community seemed to slow SOC turnover, thereby favouring SOC accumulation under Comp-Fert or under Comb-Fert in the rice paddies. Therefore, the biological stabilization process is of importance in SOC sequestration in the rice paddies, operating with physical and chemical protection and chemical recalcitrance. However, sufficient understanding and prediction of SOM dynamics needs further quantitative characterization of the simultaneous operation of several mechanisms.

Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning.

PubMed

He, Zhili; Zhang, Ping; Wu, Linwei; Rocha, Andrea M; Tu, Qichao; Shi, Zhou; Wu, Bo; Qin, Yujia; Wang, Jianjun; Yan, Qingyun; Curtis, Daniel; Ning, Daliang; Van Nostrand, Joy D; Wu, Liyou; Yang, Yunfeng; Elias, Dwayne A; Watson, David B; Adams, Michael W W; Fields, Matthew W; Alm, Eric J; Hazen, Terry C; Adams, Paul D; Arkin, Adam P; Zhou, Jizhong

2018-02-20

Contamination from anthropogenic activities has significantly impacted Earth's biosphere. However, knowledge about how environmental contamination affects the biodiversity of groundwater microbiomes and ecosystem functioning remains very limited. Here, we used a comprehensive functional gene array to analyze groundwater microbiomes from 69 wells at the Oak Ridge Field Research Center (Oak Ridge, TN), representing a wide pH range and uranium, nitrate, and other contaminants. We hypothesized that the functional diversity of groundwater microbiomes would decrease as environmental contamination (e.g., uranium or nitrate) increased or at low or high pH, while some specific populations capable of utilizing or resistant to those contaminants would increase, and thus, such key microbial functional genes and/or populations could be used to predict groundwater contamination and ecosystem functioning. Our results indicated that functional richness/diversity decreased as uranium (but not nitrate) increased in groundwater. In addition, about 5.9% of specific key functional populations targeted by a comprehensive functional gene array (GeoChip 5) increased significantly ( P < 0.05) as uranium or nitrate increased, and their changes could be used to successfully predict uranium and nitrate contamination and ecosystem functioning. This study indicates great potential for using microbial functional genes to predict environmental contamination and ecosystem functioning. IMPORTANCE Disentangling the relationships between biodiversity and ecosystem functioning is an important but poorly understood topic in ecology. Predicting ecosystem functioning on the basis of biodiversity is even more difficult, particularly with microbial biomarkers. As an exploratory effort, this study used key microbial functional genes as biomarkers to provide predictive understanding of environmental contamination and ecosystem functioning. The results indicated that the overall functional gene richness/diversity decreased as uranium increased in groundwater, while specific key microbial guilds increased significantly as uranium or nitrate increased. These key microbial functional genes could be used to successfully predict environmental contamination and ecosystem functioning. This study represents a significant advance in using functional gene markers to predict the spatial distribution of environmental contaminants and ecosystem functioning toward predictive microbial ecology, which is an ultimate goal of microbial ecology. Copyright © 2018 He et al.

Salinity stress accelerates the effect of cadmium toxicity on soil N dynamics and cycling: Does joint effect of these stresses matter?

PubMed

Raiesi, Fayez; Razmkhah, Mahshid; Kiani, Shahram

2018-05-30

The objective of this study was to determine responses of soil nitrogen (N) transformation, microbial biomass N, and urease activity to the combined effect of cadmium (Cd) toxicity (0 and 30 mg kg -1 ) and NaCl stress (0, 7.5 and 15 dS m -1 ) in a clay loam soil unamended (0%) or amended with alfalfa residues (1%, w/w). Cd, NaCl, and alfalfa residues were added to the soil, and the mixtures were incubated for 90 days under standard laboratory conditions (25 ± 1 °C and 70% of water holding capacity [WHC]). The results showed that salinity increased soil Cd availability and toxicity and subsequently decreased soil microbial N transformations (i.e., potential ammonification and nitrification as well as net N mineralization), arginine ammonification and nitrification rates, microbial biomass N, and urease activity. The adverse effects of salinity on soil microbial properties were greater in Cd-polluted than unpolluted soils, at high than low salinity levels, but were lower in residue-amended than unamended soils. These effects were mainly attributed to the increased Cd availability under saline conditions or the decreased Cd availability with residue addition. All the measured soil microbial attributes showed a negative correlation with the available Cd content in the soil. The interaction or combined effects of Cd and NaCl on soil microbial attributes were mostly synergistic in residue-unamended soils but antagonistic in residue-amended soils. The addition of organic residues to Cd-polluted soils may moderate salinity effect, and thus could stimulate the activity of ammonifiers and nitrifiers, as well as urease. Copyright © 2018 Elsevier Inc. All rights reserved.

Effects of elevated sulfate concentration on the mobility of arsenic in the sediment-water interface.

PubMed

Li, Shiyu; Yang, Changliang; Peng, Changhui; Li, Haixia; Liu, Bin; Chen, Chuan; Chen, Bingyu; Bai, Jinyue; Lin, Chen

2018-06-15

The adsorption/desorption of arsenic (As) at the sediment-water interface in lakes is the key to understanding whether As can enter the ecosystem and participate in material circulation. In this study, the concentrations of As(III), total arsenic [As(T)], sulfide, iron (Fe), and dissolved organic carbon (DOC) in overlying water were observed after the initial sulfate (SO 4 2- ) concentrations were increased by four gradients in the presence and absence of microbial systems. The results indicate that increased SO 4 2- concentrations in overlying water triggered As desorption from sediments. Approximately 10% of the desorbed As was desorbed directly as arsenite or arsenate by competitive adsorption sites on the iron salt surface; 21% was due to the reduction of iron (hydr)oxides; and 69% was due to microbial activity, as compared with a system with no microbial activity. The intensity of microbial activity was controlled by the SO 4 2- and DOC concentrations in the overlying water. In anaerobic systems, which had SO 4 2- and DOC concentrations higher than 47 and 7 mg/L, respectively, microbial activity was promoted by SO 4 2- and DOC; As(III) was desorbed under these indoor simulation conditions. When either the SO 4 2- or DOC concentration was lower than its respective threshold of 47 or 7 mg/L, or when either of these indices was below its concentration limit, it was difficult for microorganisms to use SO 4 2- and DOC to enhance their own activities. Therefore, conditions were insufficient for As desorption. The migration of As in lake sediments was dominated by microbial activity, which was co-limited by SO 4 2- and DOC. The concentrations of SO 4 2- and DOC in the overlying water are thus important for the prevention and control of As pollution in lakes. We recommend controlling SO 4 2- and DOC concentrations as a method for controlling As inner-source pollution in lake water. Copyright © 2018 Elsevier Inc. All rights reserved.

Long-term carbon exclusion alters soil microbial function but not community structure across forests of contrasting productivity

NASA Astrophysics Data System (ADS)

Hart, S. C.; Dove, N. C.; Stark, J.

2017-12-01

While it is well-documented that distinct heterotrophic microbial communities emerge under different conditions of carbon (C) availability, the response of soil microbial communities and their function to long-term conditions of C exclusion in situ has yet to be investigated. We evaluated the role of C in controlling soil microbial communities and function by experimentally excluding plant C inputs for nine years at four forest sites along a productivity gradient in Oregon, USA. Carbon exclusion treatments were implemented by root trenching to a depth of 30 cm using 25-cm diameter steel pipe, and minimizing aboveground inputs as plant litter by covering the pipe with a 1-mm mesh screen. After nine years, we measured rates of gross and net nitrogen (N) transformations and microbial respiration in situ in the upper 15-cm of mineral soil in both C excluded plots and undisturbed control soils. We measured the soil total C and N concentration and potential extracellular enzyme activities. We used phospholipid fatty acid (PLFA) analysis to determine potential changes in the microbial community structure. Nine years of C exclusion reduced soil total C by about 20%, except at the highest productivity site where no statistically significant change was observed. Although PLFA community structure and microbial C were unchanged, microbial respiration was reduced by 15-45% at all sites. Similarly, specific extracellular enzyme activities for all enzymes increased at these sites with C exclusion, suggesting that the microbial communities were substrate-limited. Although gross N mineralization decreased under C exclusion, decreases in gross N immobilization were greater, resulting in increased net N mineralization rates in all but the lowest productivity site. Furthermore, C exclusion only increased net nitrification in the highest productivity site. Although these field-based results are largely consistent with previous laboratory studies indicating a strong coupling between C and N biogeochemical cycles, they build upon this earlier research by suggesting that the "C connection" to the N cycle depends on the rate of C cycling within the ecosystem.

Milankovitch-scale correlations between deeply buried microbial populations and biogenic ooze lithology

USGS Publications Warehouse

Aiello, I.W.; Bekins, B.A.

2010-01-01

The recent discoveries of large, active populations of microbes in the subseafloor of the world's oceans supports the impact of the deep biosphere biota on global biogeochemical cycles and raises important questions concerning the functioning of these extreme environments for life. These investigations demonstrated that subseafloor microbes are unevenly distributed and that cell abundances and metabolic activities are often independent from sediment depths, with increased prokaryotic activity at geochemical and/or sedimentary interfaces. In this study we demonstrate that microbial populations vary at the scale of individual beds in the biogenic oozes of a drill site in the eastern equatorial Pacific (Ocean Drilling Program Leg 201, Site 1226). We relate bedding-scale changes in biogenic ooze sediment composition to organic carbon (OC) and microbial cell concentrations using high-resolution color reflectance data as proxy for lithology. Our analyses demonstrate that microbial concentrations are an order of magnitude higher in the more organic-rich diatom oozes than in the nannofossil oozes. The variations mimic small-scale variations in diatom abundance and OC, indicating that the modern distribution of microbial biomass is ultimately controlled by Milankovitch-frequency variations in past oceanographic conditions. ?? 2010 Geological Society of America.

Discovery of New Compounds Active against Plasmodium falciparum by High Throughput Screening of Microbial Natural Products.

PubMed

Pérez-Moreno, Guiomar; Cantizani, Juan; Sánchez-Carrasco, Paula; Ruiz-Pérez, Luis Miguel; Martín, Jesús; El Aouad, Noureddine; Pérez-Victoria, Ignacio; Tormo, José Rubén; González-Menendez, Víctor; González, Ignacio; de Pedro, Nuria; Reyes, Fernando; Genilloud, Olga; Vicente, Francisca; González-Pacanowska, Dolores

2016-01-01

Due to the low structural diversity within the set of antimalarial drugs currently available in the clinic and the increasing number of cases of resistance, there is an urgent need to find new compounds with novel modes of action to treat the disease. Microbial natural products are characterized by their large diversity provided in terms of the chemical complexity of the compounds and the novelty of structures. Microbial natural products extracts have been underexplored in the search for new antiparasitic drugs and even more so in the discovery of new antimalarials. Our objective was to find new druggable natural products with antimalarial properties from the MEDINA natural products collection, one of the largest natural product libraries harboring more than 130,000 microbial extracts. In this work, we describe the optimization process and the results of a phenotypic high throughput screen (HTS) based on measurements of Plasmodium lactate dehydrogenase. A subset of more than 20,000 extracts from the MEDINA microbial products collection has been explored, leading to the discovery of 3 new compounds with antimalarial activity. In addition, we report on the novel antiplasmodial activity of 4 previously described natural products.

The nanostructure of microbially-reduced graphene oxide fosters thick and highly-performing electrochemically-active biofilms

NASA Astrophysics Data System (ADS)

Virdis, Bernardino; Dennis, Paul G.

2017-07-01

Biofilms of electrochemically-active organisms are used in microbial electrochemical technologies (METs) to catalyze bioreactions otherwise not possible at bare electrodes. At present, however, achievable current outputs are still below levels considered sufficient for economic viability of large-scale METs implementations. Here, we report three-dimensional, self-aggregating biofilm composites comprising of microbial cells embedded with microbially-reduced graphene oxide (rGO) nanoparticles to form a thick macro-porous network with superior electrochemical properties. In the presence of metabolic substrate, these hybrid biofilms are capable of producing up to five times more catalytic current than the control biofilms. Cyclic voltammetry, linear sweep voltammetry, and electrochemical impedance spectroscopy, show that in spite of the increased thickness, the biofilms amended with GO display lower polarization/charge transfer resistance compared to the controls, which we ascribe to the incorporation of rGO into the biofilms, which (1) promotes fast electron transfer, yet conserving a macroporous structure that allows free diffusion of reactants and products, and (2) enhances the interfacial dynamics by allowing a higher load of microbial cells per electrode surface area. These results suggest an easy-to-apply and cost-effective method to produce high-performing electrochemically-active biofilms in situ.

Effects of nitrogen deposition and cattle grazing on productivity, invasion impact, and soil microbial processes in a serpentine grassland

NASA Astrophysics Data System (ADS)

Pasari, J.; Hernandez, D.; Selmants, P. C.; Keck, D.

2010-12-01

In recent decades, human activities have vastly increased the amount of biologically available nitrogen (N) in the biosphere. The resulting increase in N availability has broadly affected ecosystems through increased productivity, changes in species composition, altered nutrient cycles, and increases in invasion by exotic plant species, especially in systems that were historically low in N. California serpentine grasslands are N-limited ecosystems historically dominated by native species including several threatened and endangered plants and animals. Cattle grazing has emerged as the primary tool for controlling the impact of nitrophilic exotic grasses whose increased abundance has paralleled the regional traffic-derived increase in atmospheric N deposition. We examined the interactive effects of cattle grazing and N deposition on plant community composition, productivity, invasion resistance, and microbial processes in the Bay Area's largest serpentine grassland to determine the efficacy of current management strategies as well as the biogeochemical consequences of exotic species invasion. In the first two years of the study, aboveground net primary productivity decreased in response to grazing and increased in response to nitrogen addition. However, contrary to our hypotheses the change in productivity was not due to an increase in exotic species cover as there was little overall effect of grazing or N addition on species composition. Microbial activity was more responsive to grazing and N. Potential net N mineralization rates increased with N addition, but were not affected by grazing. In contrast, soil respiration rates were inhibited by grazing, but were not affected by N addition; suggesting strong carbon-limitation of soil microbial activity, particularly under grazing. Site differences in soil depth and grazing intensity were often more important than treatment effects. We suspect that the unusually dry conditions in the first two growing seasons inhibited the growth of exotic species and minimized the effects of cattle exclusion and N addition on species composition.

Dynamics of microorganism populations in recirculating nutrient solutions

NASA Technical Reports Server (NTRS)

Strayer, R. F.

1994-01-01

This overview covers the basic microbial ecology of recirculating hydroponic solutions. Examples from NASA and Soviet Controlled Ecological Life Support Systems (CELSS) tests and the commercial hydroponic industry will be used. The sources of microorganisms in nutrient solutions include air, water, seeds, plant containers and plumbing, biological vectors, and personnel. Microbial fates include growth, death, and emigration. Important microbial habitats within nutrient delivery systems are root surfaces, hardware surfaces (biofilms), and solution suspension. Numbers of bacteria on root surfaces usually exceed those from the other habitats by several orders of magnitude. Gram negative bacteria dominate the microflora with fungal counts usually much lower. Trends typically show a decrease in counts with increasing time unless stressed plants increase root exudates. Important microbial activities include carbon mineralization and nitrogen transformations. Important detrimental interactions include competition with plants, and human and plant pathogenesis.

The complicated substrates enhance the microbial diversity and zinc leaching efficiency in sphalerite bioleaching system.

PubMed

Xiao, Yunhua; Xu, YongDong; Dong, Weiling; Liang, Yili; Fan, Fenliang; Zhang, Xiaoxia; Zhang, Xian; Niu, Jiaojiao; Ma, Liyuan; She, Siyuan; He, Zhili; Liu, Xueduan; Yin, Huaqun

2015-12-01

This study used an artificial enrichment microbial consortium to examine the effects of different substrate conditions on microbial diversity, composition, and function (e.g., zinc leaching efficiency) through adding pyrite (SP group), chalcopyrite (SC group), or both (SPC group) in sphalerite bioleaching systems. 16S rRNA gene sequencing analysis showed that microbial community structures and compositions dramatically changed with additions of pyrite or chalcopyrite during the sphalerite bioleaching process. Shannon diversity index showed a significantly increase in the SP (1.460), SC (1.476), and SPC (1.341) groups compared with control (sphalerite group, 0.624) on day 30, meanwhile, zinc leaching efficiencies were enhanced by about 13.4, 2.9, and 13.2%, respectively. Also, additions of pyrite or chalcopyrite could increase electric potential (ORP) and the concentrations of Fe3+ and H+, which were the main factors shaping microbial community structures by Mantel test analysis. Linear regression analysis showed that ORP, Fe3+ concentration, and pH were significantly correlated to zinc leaching efficiency and microbial diversity. In addition, we found that leaching efficiency showed a positive and significant relationship with microbial diversity. In conclusion, our results showed that the complicated substrates could significantly enhance microbial diversity and activity of function.

Hydrolytic microbial communities in terrestrial ecosystems

NASA Astrophysics Data System (ADS)

Manucharova, Natalia; Chernov, Timofey; Kolcova, Ekaterina; Zelezova, Alena; Lukacheva, Euhenia; Zenova, Galina

2014-05-01

Hydrolytic microbial communities in terrestrial ecosystems Manucharova N.A., Chernov T.I., Kolcova E.M., Zelezova A.D., Lukacheva E.G. Lomonosov Moscow State University, Russia Vertical differentiation of terrestrial biogeocenoses is conditioned by the formation of vertical tiers that differ considerably in the composition and structure of microbial communities. All the three tiers, phylloplane, litter and soil, are united by a single flow of organic matter, and are spatially separated successional stages of decomposition of organic substances. Decomposition of organic matter is mainly due to the activity of microorganisms producing enzymes - hydrolase and lyase - which destroy complex organic compounds. Application of molecular biological techniques (FISH) in environmental studies provides a more complete information concerning the taxonomic diversity and potential hydrolytic activity of microbial complexes of terrestrial ecosystems that exist in a wide range of environmental factors (moisture, temperature, redox potential, organic matter). The combination of two molecular biological techniques (FISH and DGGE-analysis of fragments of gene 16S rRNA total amplificate) enables an informative assessment of the differences in the structure of dominant and minor components of hydrolytic complexes formed in different tiers of terrestrial ecosystems. The functional activity of hydrolytic microbial complexes of terrestrial ecosystems is determined by the activity of dominant and minor components, which also have a high gross enzymatic activity. Degradation of biopolymers in the phylloplane is mainly due to the representatives of the Proteobacteria phylogenetic group (classes alpha and beta). In mineral soil horizons, the role of hydrolytic representatives of Firmicutes and Actinobacteria increases. Among the key environmental parameters that determine the functional activity of the hydrolytic (chitinolytic) complex of soil layer (moisture, nutrient supply, successional time), the most significant one is moisture. Moisture levels providing maximum activity of a hydrolytic microbial complex depend on the soil type. Development of a hydrolytic microbial complex occurs in a very wide moisture range - from values close to field capacity to those close to the wilting moisture point. The functional role of mycelial actinobacteria in the metabolism of chitin consists, on the one hand, in active decomposition of this biopolymer, and on the other hand, in the regulation of microbial hydrolytic complex activity through the production of biologically active regulatory metabolites, which occurs in a wide range of environmental parameters (moisture, temperature, organic matter, successional time). Experimental design is applicable to identify in situ optimal values of environmental factors that considerably affect the functional parameters of hydrolytic microbial complexes.

Co-composting of biowaste and wood ash, influence on a microbially driven-process.

PubMed

Fernández-Delgado Juárez, Marina; Prähauser, Barbara; Walter, Andreas; Insam, Heribert; Franke-Whittle, Ingrid H

2015-12-01

A trial at semi-industrial scale was conducted to evaluate the effect of wood ash amendment on communal biowaste in a composting process and on the final composts produced. For this purpose, three treatments including an unamended control (C0) and composts with additions of 6% (C6), and 12% (C12) of wood ash (w/w) were studied, and physico-chemical parameters as well as microbial activity and community composition were investigated. At the end of the process, composts were tested for toxicity and quality, and microbial physiological activity. The influence of ash addition on compost temperature, pH, microbial activity and composition was stronger during the early composting stages and diminished with time, whereby composts became more similar. Using the COMPOCHIP microarray, a reduction in the pathogenic genera Listeria and Clostridium was observed, which together with the temperature increases of the composting process helped in the hygienisation of composts. Lactobacillus species were also affected, such that reduced hybridisation signals were observed with increased ash addition, due to the increased pH values in amended composts. Organic matter mineralisation was also increased through ash addition, and no negative effects on the composting process were observed. The nutrient content of the final products was increased through the addition of ash, and no toxic effects were observed. Nonetheless, greater concentrations of heavy metals were found in composts amended with more ash, which resulted in a downgrading of the compost quality according to the Austrian Compost Ordinance. Thus, regulation of both input materials and end-product quality is essential in optimising composting processes. Copyright © 2015 Elsevier Ltd. All rights reserved.

[Effects of different crop rotations on growth of continuous cropping sorghum and its rhizosphere soil micro-environment.

PubMed

Wang, Jin Song; Fan, Fang Fang; Guo, Jun; Wu, Ai Lian; Dong, Er Wei; Bai, Wen Bin; Jiao, Xiao Yan

2016-07-01

The effects of crop rotation on sorghum [Sorghum biocolor (L) Moench] growth, rhizosphere microbial community and the activity of soil enzymes for successive crops of sorghum were evaluated. Five years of continuous monoculture sorghum as the control (CK) was compared to alfalfa and scallion planted in the fourth year. The results showed that incorporation of alfalfa and scallion into the rotation significantly improved sorghum shoot growth. Specifically, sorghum grain yield increased by 16.5% in the alfalfa rotation plots compared to the CK. The rotations also increased sorghum root system growth, with alfalfa or scallion rotation increasing sorghum total root length by 0.3 and 0.4 times, total root surface area by 0.6 and 0.5 times, root volume by 1.2 and 0.6 times, and root biomass by 1.0 and 0.3 times, respectively. Alfalfa rotation also expanded sorghum root distribution below the 10 cm soil depth. A Biolog analysis on biome functions in the sorghum flowering period indicated significantly higher microbial activity in the rotation plots. The alfalfa and scallion rotation increased the Shannon index by 0.2 and 0.1 times compared to the CK, and improved the sucrose activity in the rhizosphere soil. It was concluded that including alfalfa in rotation with sorghum improved sorghum rhizosphere soil environment, enhanced soil microbial enzyme activity, alleviated the obstacle of continuous cropping and thus increased the sorghum yield.

Assessing impacts of unconventional natural gas extraction on microbial communities in headwater stream ecosystems in Northwestern Pennsylvania

PubMed Central

Trexler, Ryan; Solomon, Caroline; Brislawn, Colin J.; Wright, Justin R.; Rosenberger, Abigail; McClure, Erin E.; Grube, Alyssa M.; Peterson, Mark P.; Keddache, Mehdi; Mason, Olivia U.; Hazen, Terry C.; Grant, Christopher J.; Lamendella, Regina

2014-01-01

Hydraulic fracturing and horizontal drilling have increased dramatically in Pennsylvania Marcellus shale formations, however the potential for major environmental impacts are still incompletely understood. High-throughput sequencing of the 16S rRNA gene was performed to characterize the microbial community structure of water, sediment, bryophyte, and biofilm samples from 26 headwater stream sites in northwestern Pennsylvania with different histories of fracking activity within Marcellus shale formations. Further, we describe the relationship between microbial community structure and environmental parameters measured. Approximately 3.2 million 16S rRNA gene sequences were retrieved from a total of 58 samples. Microbial community analyses showed significant reductions in species richness as well as evenness in sites with Marcellus shale activity. Beta diversity analyses revealed distinct microbial community structure between sites with and without Marcellus shale activity. For example, operational taxonomic units (OTUs) within the Acetobacteracea, Methylocystaceae, Acidobacteriaceae, and Phenylobacterium were greater than three log-fold more abundant in MSA+ sites as compared to MSA− sites. Further, several of these OTUs were strongly negatively correlated with pH and positively correlated with the number of wellpads in a watershed. It should be noted that many of the OTUs enriched in MSA+ sites are putative acidophilic and/or methanotrophic populations. This study revealed apparent shifts in the autochthonous microbial communities and highlighted potential members that could be responding to changing stream conditions as a result of nascent industrial activity in these aquatic ecosystems. PMID:25408683

Interactive effects of wildfire and permafrost on microbial communities and soil processes in an Alaskan black spruce forest.

Treesearch

Mark P. Waldrop; Jennifer W. Harden

2008-01-01

Boreal forests contain significant quantities of soil carbon that may be oxidized to CO2 given future increases in climate warming and wildfire behavior. At the ecosystem scale, decomposition and heterotrophic respiration are strongly controlled by temperature and moisture, but we questioned whether changes in microbial biomass, activity, or...

Bioremediation of hydrocarbon degradation in a petroleum-contaminated soil and microbial population and activity determination.

PubMed

Wu, Manli; Li, Wei; Dick, Warren A; Ye, Xiqiong; Chen, Kaili; Kost, David; Chen, Liming

2017-02-01

Bioremediation of hydrocarbon degradation in petroleum-polluted soil is carried out by various microorganisms. However, little information is available for the relationships between hydrocarbon degradation rates in petroleum-contaminated soil and microbial population and activity in laboratory assay. In a microcosm study, degradation rate and efficiency of total petroleum hydrocarbons (TPH), alkanes, and polycyclic aromatic hydrocarbons (PAH) in a petroleum-contaminated soil were determined using an infrared photometer oil content analyzer and a gas chromatography mass spectrometry (GC-MS). Also, the populations of TPH, alkane, and PAH degraders were enumerated by a modified most probable number (MPN) procedure, and the hydrocarbon degrading activities of these degraders were determined by the Biolog (MT2) MicroPlates assay. Results showed linear correlations between the TPH and alkane degradation rates and the population and activity increases of TPH and alkane degraders, but no correlation was observed between the PAH degradation rates and the PAH population and activity increases. Petroleum hydrocarbon degrading microbial population measured by MPN was significantly correlated with metabolic activity in the Biolog assay. The results suggest that the MPN procedure and the Biolog assay are efficient methods for assessing the rates of TPH and alkane, but not PAH, bioremediation in oil-contaminated soil in laboratory. Copyright © 2016 Elsevier Ltd. All rights reserved.

Microbial environmental contamination in Italian dental clinics: A multicenter study yielding recommendations for standardized sampling methods and threshold values.

PubMed

Pasquarella, Cesira; Veronesi, Licia; Napoli, Christian; Castiglia, Paolo; Liguori, Giorgio; Rizzetto, Rolando; Torre, Ida; Righi, Elena; Farruggia, Patrizia; Tesauro, Marina; Torregrossa, Maria V; Montagna, Maria T; Colucci, Maria E; Gallè, Francesca; Masia, Maria D; Strohmenger, Laura; Bergomi, Margherita; Tinteri, Carola; Panico, Manuela; Pennino, Francesca; Cannova, Lucia; Tanzi, Marialuisa

2012-03-15

A microbiological environmental investigation was carried out in ten dental clinics in Italy. Microbial contamination of water, air and surfaces was assessed in each clinic during the five working days, for one week per month, for a three-month period. Water and surfaces were sampled before and after clinical activity; air was sampled before, after, and during clinical activity. A wide variation was found in microbial environmental contamination, both within the participating clinics and for the different sampling times. Before clinical activity, microbial water contamination in tap water reached 51,200cfu/mL (colony forming units per milliliter), and that in Dental Unit Water Systems (DUWSs) reached 872,000cfu/mL. After clinical activity, there was a significant decrease in the Total Viable Count (TVC) in tap water and in DUWSs. Pseudomonas aeruginosa was found in 2.38% (7/294) of tap water samples and in 20.06% (59/294) of DUWS samples; Legionella spp. was found in 29.96% (89/297) of tap water samples and 15.82% (47/297) of DUWS samples, with no significant difference between pre- and post-clinical activity. Microbial air contamination was highest during dental treatments, and decreased significantly at the end of the working activity (p<0.05). The microbial buildup on surfaces increased significantly during the working hours. This study provides data for the establishment of standardized sampling methods, and threshold values for contamination monitoring in dentistry. Some very critical situations have been observed which require urgent intervention. Furthermore, the study emphasizes the need for research aimed at defining effective managing strategies for dental clinics. Copyright © 2012 Elsevier B.V. All rights reserved.

Microbial communities change in an anaerobic digestion after application of microbial electrolysis cells.

PubMed

Lee, Beom; Park, Jun-Gyu; Shin, Won-Beom; Tian, Dong-Jie; Jun, Hang-Bae

2017-06-01

Microbial electrolysis cells (MECs) are being studied to improve the efficiency of anaerobic digesters and biogas production. In the present study, we investigated the effects of electrochemical reactions in AD-MEC (anaerobic digester combined with MECs) on changes in the microbial communities of bulk sludge through 454-pyrosequencing analysis, as well as the effect of these changes on anaerobic digestion. Methanobacterium beijingense and Methanobacterium petrolearium were the dominant archaeal species in AD, while Methanosarcina thermophila and Methanobacterium formicicum were dominant in AD-MEC at steady-state. There were no substantial differences in dominant bacterial species. Clostridia class was more abundant than Bacteroidia class in both reactors. Compared to AD, AD-MEC showed a 40% increase in overall bacterial population, increasing the removal of organic matters and the conversion of volatile fatty acids (VFAs). Thus, the MEC reaction more effectively converts organic matters to VFAs and activates microbial communities favorable for methane production. Copyright © 2017 Elsevier Ltd. All rights reserved.

Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Filippis, Francesca; Genovese, Alessandro; Ferranti, Pasquale

Traditional cheeses harbour complex microbial consortia that play an important role in shaping typical sensorial properties. However, the microbial metabolism is considered difficult to control. Microbial community succession and the related gene expression were analysed during ripening of a traditional Italian cheese, identifying parameters that could be modified to accelerate ripening. Afterwards, we modulated ripening conditions and observed consistent changes in microbial community structure and function. We provide concrete evidence of the essential contribution of non-starter lactic acid bacteria in ripening-related activities. An increase in the ripening temperature promoted the expression of genes related to proteolysis, lipolysis and amino acid/lipidmore » catabolism and significantly increases the cheese maturation rate. Moreover, temperature-promoted microbial metabolisms were consistent with the metabolomic profiles of proteins and volatile organic compounds in the cheese. Finally, the results clearly indicate how processing-driven microbiome responses can be modulated in order to optimize production efficiency and product quality.« less

Enhanced microbial reduction of vanadium (V) in groundwater with bioelectricity from microbial fuel cells

NASA Astrophysics Data System (ADS)

Hao, Liting; Zhang, Baogang; Tian, Caixing; Liu, Ye; Shi, Chunhong; Cheng, Ming; Feng, Chuanping

2015-08-01

Bioelectricity generated from the microbial fuel cell (MFC) is applied to the bioelectrical reactor (BER) directly to enhance microbial reduction of vanadium (V) (V(V)) in groundwater. With the maximum power density of 543.4 mW m-2 from the MFC, V(V) removal is accelerated with efficiency of 93.6% during 12 h operation. Higher applied voltage can facilitate this process. V(V) removals decrease with the increase of initial V(V) concentration, while extra addition of chemical oxygen demand (COD) has little effect on performance improvement. Microbial V(V) reduction is enhanced and then suppressed with the increase of conductivity. High-throughput 16S rRNA gene pyrosequencing analysis implies the accumulated Enterobacter and Lactococcus reduce V(V) with products from fermentative microorganisms such as Macellibacteroides. The presentation of electrochemically active bacteria as Enterobacter promotes electron transfers. This study indicates that application of bioelectricity from MFCs is a promising strategy to improve the efficiency of in-situ bioremediation of V(V) polluted groundwater.

Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate

DOE PAGES

De Filippis, Francesca; Genovese, Alessandro; Ferranti, Pasquale; ...

2016-02-25

Traditional cheeses harbour complex microbial consortia that play an important role in shaping typical sensorial properties. However, the microbial metabolism is considered difficult to control. Microbial community succession and the related gene expression were analysed during ripening of a traditional Italian cheese, identifying parameters that could be modified to accelerate ripening. Afterwards, we modulated ripening conditions and observed consistent changes in microbial community structure and function. We provide concrete evidence of the essential contribution of non-starter lactic acid bacteria in ripening-related activities. An increase in the ripening temperature promoted the expression of genes related to proteolysis, lipolysis and amino acid/lipidmore » catabolism and significantly increases the cheese maturation rate. Moreover, temperature-promoted microbial metabolisms were consistent with the metabolomic profiles of proteins and volatile organic compounds in the cheese. Finally, the results clearly indicate how processing-driven microbiome responses can be modulated in order to optimize production efficiency and product quality.« less

Leaf Treatments with a Protein-Based Resistance Inducer Partially Modify Phyllosphere Microbial Communities of Grapevine

PubMed Central

Cappelletti, Martina; Perazzolli, Michele; Antonielli, Livio; Nesler, Andrea; Torboli, Esmeralda; Bianchedi, Pier L.; Pindo, Massimo; Puopolo, Gerardo; Pertot, Ilaria

2016-01-01

Protein derivatives and carbohydrates can stimulate plant growth, increase stress tolerance, and activate plant defense mechanisms. However, these molecules can also act as a nutritional substrate for microbial communities living on the plant phyllosphere and possibly affect their biocontrol activity against pathogens. We investigated the mechanisms of action of a protein derivative (nutrient broth, NB) against grapevine downy mildew, specifically focusing on the effects of foliar treatments on plant defense stimulation and on the composition and biocontrol features of the phyllosphere microbial populations. NB reduced downy mildew symptoms and induced the expression of defense-related genes in greenhouse- and in vitro-grown plants, indicating the activation of grapevine resistance mechanisms. Furthermore, NB increased the number of culturable phyllosphere bacteria and altered the composition of bacterial and fungal populations on leaves of greenhouse-grown plants. Although, NB-induced changes on microbial populations were affected by the structure of indigenous communities originally residing on grapevine leaves, degrees of disease reduction and defense gene modulation were consistent among the experiments. Thus, modifications in the structure of phyllosphere populations caused by NB application could partially contribute to downy mildew control by competition for space or other biocontrol strategies. Particularly, changes in the abundance of phyllosphere microorganisms may provide a contribution to resistance induction, partially affecting the hormone-mediated signaling pathways involved. Modifying phyllosphere populations by increasing natural biocontrol agents with the application of selected nutritional factors can open new opportunities in terms of sustainable plant protection strategies. PMID:27486468

Heterotrophic Soil Respiration in Warming Experiments: Using Microbial Indicators to Partition Contributions from Labile and Recalcitrant Soil Organic Carbon. Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bradford, M A; Melillo, J M; Reynolds, J F

2010-06-10

The central objective of the proposed work was to develop a genomic approach (nucleic acid-based) that elucidates the mechanistic basis for the observed impacts of experimental soil warming on forest soil respiration. The need to understand the mechanistic basis arises from the importance of such information for developing effective adaptation strategies for dealing with projected climate change. Specifically, robust predictions of future climate will permit the tailoring of the most effective adaptation efforts. And one of the greatest uncertainties in current global climate models is whether there will be a net loss of carbon from soils to the atmosphere asmore » climate warms. Given that soils contain approximately 2.5 times as much carbon as the atmosphere, a net loss could lead to runaway climate warming. Indeed, most ecosystem models predict that climate warming will stimulate microbial decomposition of soil carbon, producing such a positive feedback to rising global temperatures. Yet the IPCC highlights the uncertainty regarding this projected feedback. The uncertainty arises because although warming-experiments document an initial increase in the loss of carbon from soils, the increase in respiration is short-lived, declining to control levels in a few years. This attenuation could result from changes in microbial physiology with temperature. We explored possible microbial responses to warming using experiments and modeling. Our work advances our understanding of how soil microbial communities and their activities are structured, generating insight into how soil carbon might respond to warming. We show the importance of resource partitioning in structuring microbial communities. Specifically, we quantified the relative abundance of fungal taxa that proliferated following the addition of organic substrates to soil. We added glycine, sucrose, cellulose, lignin, or tannin-protein to soils in conjunction with 3-bromo-deoxyuridine (BrdU), a nucleotide analog. Active microbes absorb BrdU from the soil solution; if they multiply in response to substrate additions, they incorporate the BrdU into their DNA. After allowing soils to incubate, we extracted BrdU-labeled DNA and sequenced the ITS regions of fungal rDNA. Fungal taxa that proliferated following substrate addition were likely using the substrate as a resource for growth. We found that the structure of active fungal communities varied significantly among substrates. The active fungal community under glycine was significantly different from those under other conditions, while the active communities under sucrose and cellulose were marginally different from each other and the control. These results indicate that the overall community structure of active fungi was altered by the addition of glycine, sucrose, and cellulose and implies that some fungal taxa respond to changes in resource availability. The community composition of active fungi is also altered by experimental warming. We found that glycine-users tended to increase under warming, while lignin-, tannin/protein-, and sucrose-users declined. The latter group of substrates requires extracellular enzymes for use, but glycine does not. It is possible that warming selects for fungal species that target, in particular, labile substrates. Linking these changes in microbial communities and resource partitioning to soil carbon dynamics, we find that substrate mineralization rates are, in general, significantly lower in soils exposed to long-term warming. This suggests that microbial use of organic substrates is impaired by warming. Yet effects are dependent on substrate identity. There are fundamental differences in the metabolic capabilities of the communities in the control and warmed soils. These differences might relate to the changes in microbial community composition, which appeared to be associated with groups specialized on different resources. We also find that functional responses indicate temperature acclimation of the microbial community. There are distinct seasonal patterns and to long-term soil warming, with higher-temperature optima for soils exposed to warmer temperatures. To relate these changes within the microbial community to potential positive feedbacks between climate warming and soil respiration, we develop a microbial-enzyme model to simulate the responses of soil carbon to warming. We find that declines in microbial biomass and degradative enzymes can explain the observed attenuation of soil-carbon emissions in response to warming. Specifically, reduced carbon-use efficiency limits the biomass of microbial decomposers and mitigates loss of soil carbon. However, microbial adaptation or a change in microbial communities could lead to an upward adjustment of the efficiency of carbon use, counteracting the decline in microbial biomass and accelerating soil-carbon loss. We conclude that the soil-carbon response to climate warming depends on the efficiency of soil microbes in using carbon.« less

Effect of residual H2O2 from advanced oxidation processes on subsequent biological water treatment: A laboratory batch study.

PubMed

Wang, Feifei; van Halem, Doris; Liu, Gang; Lekkerkerker-Teunissen, Karin; van der Hoek, Jan Peter

2017-10-01

H 2 O 2 residuals from advanced oxidation processes (AOPs) may have critical impacts on the microbial ecology and performance of subsequent biological treatment processes, but little is known. The objective of this study was to evaluate how H 2 O 2 residuals influence sand systems with an emphasis on dissolved organic carbon (DOC) removal, microbial activity change and bacterial community evolution. The results from laboratory batch studies showed that 0.25 mg/L H 2 O 2 lowered DOC removal by 10% while higher H 2 O 2 concentrations at 3 and 5 mg/L promoted DOC removal by 8% and 28%. A H 2 O 2 dosage of 0.25 mg/L did not impact microbial activity (as measured by ATP) while high H 2 O 2 dosages, 1, 3 and 5 mg/L, resulted in reduced microbial activity of 23%, 37% and 37% respectively. Therefore, DOC removal was promoted by the increase of H 2 O 2 dosage while microbial activity was reduced. The pyrosequencing results illustrated that bacterial communities were dominated by Proteobacteria. The presence of H 2 O 2 showed clear influence on the diversity and composition of bacterial communities, which became more diverse under 0.25 mg/L H 2 O 2 but conversely less diverse when the dosage increased to 5 mg/L H 2 O 2 . Anaerobic bacteria were found to be most sensitive to H 2 O 2 as their growth in batch reactors was limited by both 0.25 and 5 mg/L H 2 O 2 (17-88% reduction). In conclusion, special attention should be given to effects of AOPs residuals on microbial ecology before introducing AOPs as a pre-treatment to biological (sand) processes. Additionally, the guideline on the maximum allowable H 2 O 2 concentration should be properly evaluated. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Soil water availability and microsite mediate fungal and bacterial phospholipid fatty acid biomarker abundances in Mojave Desert soils exposed to elevated atmospheric CO2

NASA Astrophysics Data System (ADS)

Jin, V. L.; Schaeffer, S. M.; Ziegler, S. E.; Evans, R. D.

2011-06-01

Changes in the rates of nitrogen (N) cycling, microbial carbon (C) substrate use, and extracellular enzyme activities in a Mojave Desert ecosystem exposed to elevated atmospheric CO2 suggest shifts in the size and/or functional characteristics of microbial assemblages in two dominant soil microsites: plant interspaces and under the dominant shrub Larrea tridentata. We used ester-linked phospholipid fatty acid (PLFA) biomarkers as a proxy for microbial biomass to quantify spatial and temporal differences in soil microbial communities from February 2003 to May 2005. Further, we used the 13C signature of the fossil CO2 source for elevated CO2 plots to trace recent plant C inputs into soil organic matter (SOM) and broad microbial groups using δ13C (‰). Differences between individual δ13CPLFA and δ13CSOM for fungal biomarkers indicated active metabolism of newer C in elevated CO2 soils. Total PLFA-C was greater in shrub microsites compared to plant interspaces, and CO2 treatment differences within microsites increased under higher soil water availability. Total, fungal, and bacterial PLFA-C increased with decreasing soil volumetric water content (VWC) in both microsites, suggesting general adaptations to xeric desert conditions. Increases in fungal-to-bacterial PLFA-C ratio with decreasing VWC reflected functional group-specific responses to changing soil water availability. While temporal and spatial extremes in resource availability in desert ecosystems contribute to the difficulty in identifying common trends or mechanisms driving microbial responses in less extreme environments, we found that soil water availability and soil microsite interacted with elevated CO2 to shift fungal and bacterial biomarker abundances in Mojave Desert soils.

Effects of sulphamethazine and zinc on the functional diversity of microbial communities during composting.

PubMed

Duan, Manli; Yang, Jiu; Gu, Jie; Qian, Xun; Sun, Wei; Gao, Hua; Wang, Xiaojuan

2016-01-01

The changes in the functional diversity of the microbial community in a compost matrix with a single or compound addition of zinc (Zn; 0, 600, and 1800 mg/kg) and sulphamethazine (SM2; 0, 1, and 25 mg/kg) were studied with the Biolog method during composting. The microbial community was extracted from the compost matrix comprising swine manure and wheat straw at day 6 (themophilic period) and day 25 (mature period) of composting. Results proved that the Shannon index, average well-colour development, and substrate utilization significantly decreased as the concentrations of SM2 and Zn increased on day 6. The negative effect of the combined addition of SM2 and Zn was lower than that of the individual addition of SM2 and Zn. On day 25, the inhibition effect disappeared, and microbial metabolic activities were higher than those on day 6. The effects of SM2 and Zn could be further differentiated via the principal component analysis (PCA) and cluster analysis. On day 6, the treatments were divided into three groups by PC1 and PC2. The separation of the different treatments in the PCA plots became increasingly apparent on day 25. In conclusion, the effects of SM2 and Zn on the microbial community during composting became evident in the themophilic period and that the microbial activity recovered in the mature period. The combination of SM2 and Zn decreased the inhibition with the addition of individual additive.

A Prospective Metagenomic and Metabolomic Analysis of the Impact of Exercise and/or Whey Protein Supplementation on the Gut Microbiome of Sedentary Adults.

PubMed

Cronin, Owen; Barton, Wiley; Skuse, Peter; Penney, Nicholas C; Garcia-Perez, Isabel; Murphy, Eileen F; Woods, Trevor; Nugent, Helena; Fanning, Aine; Melgar, Silvia; Falvey, Eanna C; Holmes, Elaine; Cotter, Paul D; O'Sullivan, Orla; Molloy, Michael G; Shanahan, Fergus

2018-01-01

Many components of modern living exert influence on the resident intestinal microbiota of humans with resultant impact on host health. For example, exercise-associated changes in the diversity, composition, and functional profiles of microbial populations in the gut have been described in cross-sectional studies of habitual athletes. However, this relationship is also affected by changes in diet, such as changes in dietary and supplementary protein consumption, that coincide with exercise. To determine whether increasing physical activity and/or increased protein intake modulates gut microbial composition and function, we prospectively challenged healthy but sedentary adults with a short-term exercise regime, with and without concurrent daily whey protein consumption. Metagenomics- and metabolomics-based assessments demonstrated modest changes in gut microbial composition and function following increases in physical activity. Significant changes in the diversity of the gut virome were evident in participants receiving daily whey protein supplementation. Results indicate that improved body composition with exercise is not dependent on major changes in the diversity of microbial populations in the gut. The diverse microbial characteristics previously observed in long-term habitual athletes may be a later response to exercise and fitness improvement. IMPORTANCE The gut microbiota of humans is a critical component of functional development and subsequent health. It is important to understand the lifestyle and dietary factors that affect the gut microbiome and what impact these factors may have. Animal studies suggest that exercise can directly affect the gut microbiota, and elite athletes demonstrate unique beneficial and diverse gut microbiome characteristics. These characteristics are associated with levels of protein consumption and levels of physical activity. The results of this study show that increasing the fitness levels of physically inactive humans leads to modest but detectable changes in gut microbiota characteristics. For the first time, we show that regular whey protein intake leads to significant alterations to the composition of the gut virome.

Relationships between waste physicochemical properties, microbial activity and vegetation at coal ash and sludge disposal sites.

PubMed

Woch, Marcin W; Radwańska, Magdalena; Stanek, Małgorzata; Łopata, Barbara; Stefanowicz, Anna M

2018-06-11

The aim of the study was to assess the relationships between vegetation, physicochemical and microbial properties of substrate at coal ash and sludge disposal sites. The study was performed on 32 plots classified into 7 categories: dried ash sedimentation ponds, dominated by a grass Calamagrostis epigejos (AH-Ce), with the admixture of Pinus sylvestris (AH-CePs) or Robinia pseudoacacia (AH-CeRp), dry ash landfill dominated by Betula pendula and Pinus sylvestris (AD-BpPs) or Salix viminalis (AD-Sv) and coal sludge pond with drier parts dominated by Tussilago farfara (CS-Tf) and the wetter ones by Cyperus flavescens (CS-Cf). Ash sites were covered with soil layer imported as a part of technical reclamation. Ash had relatively high concentrations of some alkali and alkaline earth metals, Mn and pH, while coal sludge had high water and C, S, P and K contents. Concentrations of heavy metals were lower than allowable limits in all substrate types. Microbial biomass and, particularly, enzymatic activity in ash and sludge were generally low. The only exception were CS-Tf plots characterized by the highest microbial biomass, presumably due to large deposits of organic matter that became available for aerobic microbial biomass when water level fell. The properties of ash and sludge adversely affected microbial biomass and enzymatic activity as indicated by significant negative correlations between the content of alkali/alkaline earth metals, heavy metals, and macronutrients with enzymatic activity and/or microbial biomass, as well as positive correlations of these parameters with metabolic quotient (qCO 2 ). Plant species richness and cover were relatively high, which may be partly associated with alleviating influence of soil covering the ash. The effect of the admixture of R. pseudoacacia or P. sylvestris to stands dominated by C. epigejos was smaller than expected. The former species increased NNH 4 , NNO 3 and arylsulfatase activity, while the latter reduced activity of the enzyme. Copyright © 2018 Elsevier B.V. All rights reserved.

Mechanisms of microbial destabilization of soil C shifts over decades of warming

NASA Astrophysics Data System (ADS)

DeAngelis, K.; Pold, G.; Chowdhury, P. R.; Schnabel, J.; Grandy, S.; Melillo, J. M.

2017-12-01

Microbes are major actors in regulating the earth's biogeochemical cycles, with temperature-sensitive microbial tradeoffs improving ecosystem biogeochemical models. Meanwhile, the Earth's climate is changing, with decades of warming undercutting the ability of soil to store carbon. Our work explores trends of 26 years of experimental warming in temperate deciduous forest soils, which is associated with cycles of soil carbon degradation punctuated by periods of changes in soil microbial dynamics. Using a combination of biogeochemistry and molecular analytical methods, we explore the hypotheses that substrate availability, community structure, altered temperature sensitivity of microbial turnover-growth efficiency tradeoff, and microbial evolution are responsible for observations of accelerated degradation of soil carbon over time. Amplicon sequencing of microbial communities suggests a small role of changing microbial community composition over decades of warming, but a sustained suppression of fungal biomass is accompanied by increased biomass of Actinobacteria, Actinobacteria, Alphaproteobacteria, Verrucomicrobia and Planctomycetes. Substrate availability plays an important role in microbial dynamics, with depleted labile carbon in the first decade and depleted lignin in the second decade. Increased lignin-degrading enzyme activity supports the suggestion that lignin-like organic matter is an important substrate in chronically warmed soils. Metatranscriptomics data support the suggestion that increased turnover is associated with long-term warming, with metagenomic signals of increased carbohydrate-degrading enzymes in the organic horizon but decreased in the mineral soils. Finally, traits analysis of over 200 cultivated isolates of bacterial species from heated and control soils suggests an expanded ability for degradation of cellulose and hemicellulose but not chitin, supporting the hypothesis that long-term warming is exerting evolutionary pressure on microbial species. Together, these data suggest that after decades of warming both direct kinetic effects and indirect effects of altered substrate availability are affecting microbial ecology and evolution in ways that conspire to destabilize soil organic matter.

Changes in Labile Organic Carbon Fractions and Soil Enzyme Activities after Marshland Reclamation and Restoration in the Sanjiang Plain in Northeast China

NASA Astrophysics Data System (ADS)

Song, Yanyu; Song, Changchun; Yang, Guisheng; Miao, Yuqing; Wang, Jiaoyue; Guo, Yuedong

2012-09-01

The extensive reclamation of marshland into cropland has tremendously impacted the ecological environment of the Sanjiang Plain in northeast China. To understand the impacts of marshland reclamation and restoration on soil properties, we investigated the labile organic carbon fractions and the soil enzyme activities in an undisturbed marshland, a cultivated marshland and three marshlands that had been restored for 3, 6 and 12 years. Soil samples collected from the different management systems at a depth of 0-20 cm in July 2009 were analyzed for soil organic carbon (SOC), dissolved organic carbon (DOC), microbial biomass carbon (MBC) and easily degradable organic carbon. In addition, the activities of the invertase, β-glucosidase, urease and acid phosphatase were determined. These enzymes are involved in C, N and P cycling, respectively. Long-term cultivation resulted in decreased SOC, DOC, MBC, microbial quotient and C (invertase, β-glucosidase) and N-transforming (urease) enzyme activities compared with undisturbed marshland. After marshland restoration, the MBC and DOC concentrations and the soil invertase, β-glucosidase and urease activities increased. Soil DOC and MBC concentrations are probably the main factors responsible for the different invertase, β-glucosidase and urease activities. In addition, marshland restoration caused a significant increase in the microbial quotient, which reflects enhanced efficiency of organic substrate use by microbial biomass. Our observations demonstrated that soil quality recovered following marshland restoration. DOC, MBC and invertase, β-glucosidase and urease activities were sensitive for discriminating soil ecosystems under the different types of land use. Thus, these parameters should be considered to be indicators for detecting changes in soil quality and environmental impacts in marshlands.

Application of Nanoparticle Technologies in the Combat against Anti-Microbial Resistance

PubMed Central

Kumar, Mayur; Curtis, Anthony

2018-01-01

Anti-microbial resistance is a growing problem that has impacted the world and brought about the beginning of the end for the old generation of antibiotics. Increasingly, more antibiotics are being prescribed unnecessarily and this reckless practice has resulted in increased resistance towards these drugs, rendering them useless against infection. Nanotechnology presents a potential answer to anti-microbial resistance, which could stimulate innovation and create a new generation of antibiotic treatments for future medicines. Preserving existing antibiotic activity through novel formulation into or onto nanotechnologies can increase clinical longevity of action against infection. Additionally, the unique physiochemical properties of nanoparticles can provide new anti-bacterial modes of action which can also be explored. Simply concentrating on antibiotic prescribing habits will not resolve the issue but rather mitigate it. Thus, new scientific approaches through the development of novel antibiotics and formulations is required in order to employ a new generation of therapies to combat anti-microbial resistance. PMID:29342903

Soil mineral assemblage influences on microbial communities and carbon cycling under fresh organic matter input

NASA Astrophysics Data System (ADS)

Finley, B. K.; Schwartz, E.; Koch, B.; Dijkstra, P.; Hungate, B. A.

2017-12-01

The interactions between soil mineral assemblages and microbial communities are important drivers of soil organic carbon (SOC) cycling and storage, although the mechanisms driving these interactions remain unclear. There is increasing evidence supporting the importance of associations with poorly crystalline, short-range order (SRO) minerals in protection of SOC from microbial utilization. However, how the microbial processing of SRO-associated SOC may be influenced by fresh organic matter inputs (priming) remains poorly understood. The influence on SRO minerals on soil microbial community dynamics is uncertain as well. Therefore, we conducted a priming incubation by adding either a simulated root exudate mixture or conifer needle litter to three soils from a mixed-conifer ecosystem. The parent material of the soils were andesite, basalt, and granite and decreased in SRO mineral content, respectively. We also conducted a parallel quantitative stable isotope probing incubation by adding 18O-labelled water to the soils to isotopically label microbial DNA in situ. This allowed us to characterize and identify the active bacterial and archaeal community and taxon-specific growth under fresh organic matter input. While the granite soil (lowest SRO content), had the largest total mineralization, the least priming occurred. The andesite and basalt soils (greater SRO content) had lower total respiration, but greater priming. Across all treatments, the granite soil, while having the lowest species richness of the entire community (249 taxa, both active and inactive), had a larger active community (90%) in response to new SOC input. The andesite and basalt soils, while having greater total species richness of the entire community at 333 and 325 taxa, respectively, had fewer active taxa in response to new C compared to the granite soil (30% and 49% taxa, respectively). These findings suggest that the soil mineral assemblage is an important driver on SOC cycling under fresh organic matter inputs, as well as on the activity and diversity of the microbial community. Often, microbial diversity is associated with function. Our results suggest that the soil environment, in this case SRO mineral content, may be more important on SOC cycling and storage than microbial diversity alone.

Ecological effects of soil properties and metal concentrations on the composition and diversity of microbial communities associated with land use patterns in an electronic waste recycling region.

PubMed

Wu, Wencheng; Dong, Changxun; Wu, Jiahui; Liu, Xiaowen; Wu, Yingxin; Chen, Xianbin; Yu, Shixiao

2017-12-01

Soil microbes play vital roles in ecosystem functions, and soil microbial communities may be strongly structured by land use patterns associated with electronic waste (e-waste) recycling activities, which can increase the heavy metal concentration in soils. In this study, a suite of soils from five land use types (paddy field, vegetable field, dry field, forest field, and e-waste recycling site) were collected in Longtang Town, Guangdong Province, South China. Soil physicochemical properties and heavy metal concentrations were measured, and the indigenous microbial assemblages were profiled using 16S rRNA high-throughput sequencing and clone library analyses. The results showed that mercury concentration was positively correlated with both Faith's PD and Chao1 estimates, suggesting that the soil microbial alpha diversity was predominantly regulated by mercury. In addition, redundancy analysis indicated that available phosphorus, soil moisture, and mercury were the three major drivers affecting the microbial assemblages. Overall, the microbial composition was determined primarily by land use patterns, and this study provides a novel insight on the composition and diversity of microbial communities in soils associated with e-waste recycling activities. Copyright © 2017 Elsevier B.V. All rights reserved.

Shifts of methanogenic communities in response to permafrost thaw results in rising methane emissions and soil property changes.

PubMed

Wei, Shiping; Cui, Hongpeng; Zhu, Youhai; Lu, Zhenquan; Pang, Shouji; Zhang, Shuai; Dong, Hailiang; Su, Xin

2018-05-01

Permafrost thaw can bring negative consequences in terms of ecosystems, resulting in permafrost collapse, waterlogging, thermokarst lake development, and species composition changes. Little is known about how permafrost thaw influences microbial community shifts and their activities. Here, we show that the dominant archaeal community shifts from Methanomicrobiales to Methanosarcinales in response to the permafrost thaw, and the increase in methane emission is found to be associated with the methanogenic archaea, which rapidly bloom with nearly tenfold increase in total number. The mcrA gene clone libraries analyses indicate that Methanocellales/Rice Cluster I was predominant both in the original permafrost and in the thawed permafrost. However, only species belonging to Methanosarcinales showed higher transcriptional activities in the thawed permafrost, indicating a shift of methanogens from hydrogenotrophic to partly acetoclastic methane-generating metabolic processes. In addition, data also show the soil texture and features change as a result of microbial reproduction and activity induced by this permafrost thaw. Those data indicate that microbial ecology under warming permafrost has potential impacts on ecosystem and methane emissions.

[Effects of bio-organic fertilizer on soil enzyme activities and microbial community in kiwifruit orchard.

PubMed

Sun, Jia Un; Fu, Qing Xia; Gu, Jie; Wang, Xiao Juan; Gao, Hua

2016-03-01

A field experiment was conducted to compare the effects of three fertilizer managements (bio-organic fertilizer, traditional organic fertilizer and chemical fertilizer) and a no-fertilizer control on soil enzyme activities and microbial community functional diversity in a kiwifruit orchard. The results showed that the soil invertase and FDA hydrolase activities in the bio-organic fertilizer treatment were 12.2%-129.4% and 18.8%-87.4% higher than those in the no-fertilizer control during kiwifruit growth period, respectively. The application of bio-organic fertilizer also increased soil urease and acid phosphatase activities at the expanding stage and maturity stage. The Biolog results suggested that bio-organic fertilizer treatment improved the average well color development (AWCD) and increased the species diversity, richness and evenness. The relative ratios of six groups of carbon sources by microbes were changed to some extent after the application of bio-organic fertilizer. Compared with the no-fertilizer control, bio-organic fertilizer application decreased the capacity of microbes in using amino acids, but enhanced the utilization of polyphenols and polyamines. The principal components analysis demonstrated that the differentiation of microbial community was mainly in utilization of carbohydrates, amino acids and carboxylic acids.

Impacts of Projected Climate Warming and Wetting on Soil Microbial Communities in Alpine Grassland Ecosystems of the Tibetan Plateau.

PubMed

Zeng, Jun; Shen, Ju-Pei; Wang, Jun-Tao; Hu, Hang-Wei; Zhang, Cui-Jing; Bai, Ren; Zhang, Li-Mei; He, Ji-Zheng

2018-05-01

Climate change is projected to have impacts on precipitation and temperature regimes in drylands of high elevation regions, with especially large effects in the Qinghai-Tibetan Plateau. However, there was limited information about how the projected climate change will impact on the soil microbial community and their activity in the region. Here, we present results from a study conducted across 72 soil samples from 24 different sites along a temperature and precipitation gradient (substituted by aridity index ranging from 0.079 to 0.89) of the Plateau, to assess how changes in aridity affect the abundance, community composition, and diversity of bacteria, ammonia-oxidizers, and denitrifers (nirK/S and nosZ genes-containing communities) as well as nitrogen (N) turnover enzyme activities. We found V-shaped or inverted V-shaped relationships between the aridity index (AI) and soil microbial parameters (gene abundance, community structures, microbial diversity, and N turnover enzyme activities) with a threshold at AI = 0.27. The increasing or decreasing rates of the microbial parameters were higher in areas with AI < 0.27 (alpine steppes) than in mesic areas with 0.27 < AI < 0.89 (alpine meadow and swamp meadow). The results indicated that the projected warming and wetting have a strong impact on soil microbial communities in the alpine steppes.

Microbial communities of the deep unfrozen: Do microbes in taliks increase permafrost carbon vulnerability? (Invited)

NASA Astrophysics Data System (ADS)

Waldrop, M. P.; Blazewicz, S.; Jones, M.; Mcfarland, J. W.; Harden, J. W.; Euskirchen, E. S.; Turetsky, M.; Hultman, J.; Jansson, J.

2013-12-01

The vast frozen terrain of northern latitude ecosystems is typically thought of as being nearly biologically inert for the winter period. Yet deep within the frozen ground of northern latitude soils reside microbial communities that can remain active during the winter months. As we have shown previously, microbial communities may remain active in permafrost soils just below the freezing point of water. Though perhaps more importantly, microbial communities persist in unfrozen areas of water, soil, and sediment beneath water bodies the entire year. Microbial activity in taliks may have significant impacts on biogeochemical cycling in northern latitude ecosystems because their activity is not limited by the winter months. Here we present compositional and functional data, including long term incubation data, for microbial communities within permafrost landscapes, in permafrost and taliks, and the implications of these activities on permafrost carbon decomposition and the flux of CO2 and CH4. Our experiment was conducted at the Alaska Peatland Experiment (APEX) within the Bonanza Creek LTER in interior Alaska. Our site consists of a black spruce forest on permafrost that has degraded into thermokarst bogs at various times over the last five hundred years. We assume the parent substrate of the deep (1-1.5m) thermokarst peat was similar to the nearby forest soil and permafrost C before thaw. At this site, flux tower and autochamber data show that the thermokarst bog is a sink of CO2 , but a significant source of CH4. Yet this does not tell the whole story as these data do not fully capture microbial activity within the deep unfrozen talik layer. There is published evidence that within thermokarst bogs, relatively rapid decomposition of old forest floor material may be occurring. There are several possible mechanisms for this pattern; one possible mechanism for accelerated decomposition is the overwintering activities of microbial communities in taliks of thermokarst soils. To test this idea, we conducted anaerobic incubations of deep (1m) bog soils at two different temperatures to determine microbial temperature response functions. We also measured soil profile CO2 and CH4 concentrations and functional gene assays of the deep bog microbial community. Incubation data in combination with overwinter temperature profiles show that the talik has high potential rates of CO2 and CH4 production compared to the mass of C from forest floor and permafrost C to 1m depth. Results highlight the potential importance of taliks affecting the vulnerability of permafrost carbon to decomposition and reduction to methane.

Corn residue removal and CO2 emissions

USDA-ARS?s Scientific Manuscript database

Carbon dioxide (CO2), nitrous oxide (N2O), and methane (CH4) are the primary greenhouse gases (GHG) emitted from the soil due to agricultural activities. In the short-term, increases in CO2 emissions indicate increased soil microbial activity. Soil micro-organisms decompose crop residues and release...

Effects of Cd and Pb on soil microbial community structure and activities.

PubMed

Khan, Sardar; Hesham, Abd El-Latif; Qiao, Min; Rehman, Shafiqur; He, Ji-Zheng

2010-02-01

Soil contamination with heavy metals occurs as a result of both anthropogenic and natural activities. Heavy metals could have long-term hazardous impacts on the health of soil ecosystems and adverse influences on soil biological processes. Soil enzymatic activities are recognized as sensors towards any natural and anthropogenic disturbance occurring in the soil ecosystem. Similarly, microbial biomass carbon (MBC) is also considered as one of the important soil biological activities frequently influenced by heavy metal contamination. The polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) has recently been used to investigate changes in soil microbial community composition in response to environmental stresses. Soil microbial community structure and activities are difficult to elucidate using single monitoring approach; therefore, for a better insight and complete depiction of the soil microbial situation, different approaches need to be used. This study was conducted in a greenhouse for a period of 12 weeks to evaluate the changes in indigenous microbial community structure and activities in the soil amended with different application rates of Cd, Pb, and Cd/Pb mix. In a field environment, soil is contaminated with single or mixed heavy metals; so that, in this research, we used the selected metals in both single and mixed forms at different application rates and investigated their toxic effects on microbial community structure and activities, using soil enzyme assays, plate counting, and advanced molecular DGGE technique. Soil microbial activities, including acid phosphatase (ACP), urease (URE), and MBC, and microbial community structure were studied. A soil sample (0-20 cm) with an unknown history of heavy metal contamination was collected and amended with Cd, Pb, and Cd/Pb mix using the CdSO(4) and Pb(NO(3))(2) solutions at different application rates. The amended soils were incubated in the greenhouse at 25 +/- 4 degrees C and 60% water-holding capacity for 12 weeks. During the incubation period, samples were collected from each pot at 0, 2, 9, and 12 weeks for enzyme assays, MBC, numeration of microbes, and DNA extraction. Fumigation-extraction method was used to measure the MBC, while plate counting techniques were used to numerate viable heterotrophic bacteria, fungi, and actinomycetes. Soil DNAs were extracted from the samples and used for DGGE analysis. ACP, URE, and MBC activities of microbial community were significantly lower (p < 0.05) in the metal-amended samples than those in the control. The enzyme inhibition extent was obvious between different incubation periods and varied as the incubation proceeded, and the highest rate was detected in the samples after 2 weeks. However, the lowest values of ACP and URE activities (35.6% and 36.6% of the control, respectively) were found in the Cd(3)/Pb(3)-treated sample after 2 weeks. Similarly, MBC was strongly decreased in both Cd/Pb-amended samples and highest reduction (52.4%) was detected for Cd(3)/Pb(3) treatment. The number of bacteria and actinomycetes were significantly decreased in the heavy metal-amended samples compared to the control, while fungal cells were not significantly different (from 2.3% to 23.87%). In this study, the DGGE profile indicated that the high dose of metal amendment caused a greater change in the number of bands. DGGE banding patterns confirmed that the addition of metals had a significant impact on microbial community structure. In soil ecosystem, heavy metals exhibit toxicological effects on soil microbes which may lead to the decrease of their numbers and activities. This study demonstrated that toxicological effects of heavy metals on soil microbial community structure and activities depend largely on the type and concentration of metal and incubation time. The inhibition extent varied widely among different incubation periods for these enzymes. Furthermore, the rapid inhibition in microbial activities such as ACP, URE, and MBC were observed in the 2 weeks, which should be related to the fact that the microbes were suddenly exposed to heavy metals. The increased inhibition of soil microbial activities is likely to be related to tolerance and adaptation of the microbial community, concentration of pollutants, and mechanisms of heavy metals. The DGGE profile has shown that the structure of the bacterial community changed in amended heavy metal samples. In this research, the microbial community structure was highly affected, consistent with the lower microbial activities in different levels of heavy metals. Furthermore, a great community change in this study, particularly at a high level of contamination, was probably a result of metal toxicity and also unavailability of nutrients because no nutrients were supplied during the whole incubation period. The added concentrations of heavy metals have changed the soil microbial community structure and activities. The highest inhibitory effects on soil microbial activities were observed at 2 weeks of incubation. The bacteria were more sensitive than actinomycetes and fungi. The DGGE profile indicated that bacterial community structure was changed in the Cd/Pb-amended samples, particularly at high concentrations. The investigation of soil microbial community structure and activities together could give more reliable and accurate information about the toxic effects of heavy metals on soil health.

Gaseous oxygen uptake in porous media at different moisture contents and airflow velocities.

PubMed

Sharma, Prabhakar; Poulsen, Tjalfe G; Kalluri, Prasad N V

2009-06-01

The presence and distribution of water in the pore space is a critical factor for flow and transport of gases through unsaturated porous media. The water content also affects the biological activity necessary for treatment of polluted gas streams in biofilters. In this research, microbial activity and quantity of inactive volume in a porous medium as a function of moisture content and gas flow rate were investigated. Yard waste compost was used as a test medium, and oxygen uptake rate measurements were used to quantify microbial activity and effective active compost volume using batch and column flow-through systems. Compost water contents were varied from air-dry to field capacity and gas flows ranged from 0.2 to 2 L x min(-1). The results showed that overall microbial activity and the relative fraction of active compost medium volume increased with airflow velocity for all levels of water content up to a certain flow rate above which the oxygen uptake rate assumed a constant value independent of gas flow. The actual value of the maximum oxygen uptake rate was controlled by the water content. The oxygen uptake rate also increased with increasing water content and reached a maximum between 42 and 48% volumetric water content, above which it decreased, again likely because of formation of inactive zones in the compost medium. Overall, maximum possible oxygen uptake rate as a function of gas flow rate across all water contents and gas flows could be approximated by a linear expression. The relative fraction of active volume also increased with gas flow rate and reached approximately 80% for the highest gas flows used.

Increased gut microbiota diversity and abundance of Faecalibacterium prausnitzii and Akkermansia after fasting: a pilot study.

PubMed

Remely, Marlene; Hippe, Berit; Geretschlaeger, Isabella; Stegmayer, Sonja; Hoefinger, Ingrid; Haslberger, Alexander

2015-05-01

An impaired gut microbiota has been reported as an important factor in the pathogenesis of obesity. Weight reduction has already been mentioned to improve gut microbial subpopulations involved in inflammatory processes, though other subpopulations still need further investigation. Thus, weight reduction in the context of a fasting program together with a probiotic intervention may improve the abundance and diversity of gut microbiota. In this pilot study, overweight people underwent a fasting program with laxative treatment for 1 week followed by a 6 week intervention with a probiotic formula. Gut microbiota were analyzed on the basis of 16s rDNA with a quantitative real time polymerase chain reaction. Additionally, a food frequency questionnaire with questions about nutritional behavior, lifestyle, and physical activity was administered before and after the intervention. We observed an increase in microbial diversity over the study period. No significant changes in abundance of total bacteria, or of Bacteroidetes, Prevotella, Clostridium cluster XIVa, or Clostridium cluster IV were found, although Faecalibacterium prausnitzii showed an increase over the study period. In addition, Akkermanisa and Bifidobacteria increased in abundance due to intervention. The inflammation-associated gut microbes Enterobacteria and Lactobacilli increased during the first week and then declined by the end of the intervention. Two-thirds of the study participants harbored Archaea. No significant improvements of eating habits were reported, although physical activity improved due to the intervention. Our results show that caloric restriction affects gut microbiota by proliferating mucin-degrading microbial subpopulations. An additional intervention with a probiotic formula increased probiotic-administered gut microbial populations.

[Effects of tree species fine root decomposition on soil active organic carbon].

PubMed

Liu, Yan; Wang, Si-Long; Wang, Xiao-Wei; Yu, Xiao-Jun; Yang, Yue-Jun

2007-03-01

With incubation test, this paper studied the effects of fine root decomposition of Alnus cremastogyne, Cunninghamia lanceolata and Michelia macclurei on the content of soil active organic carbon at 9 degrees C , 14 degrees C , 24 degrees C and 28 degrees C. The results showed that the decomposition rate of fine root differed significantly with test tree species, which was decreased in the order of M. macclurei > A. cremastogyne > C. lanceolata. The decomposition rate was increased with increasing temperature, but declined with prolonged incubation time. Fine root source, incubation temperature, and incubation time all affected the contents of soil microbial biomass carbon and water-soluble organic carbon. The decomposition of fine root increased soil microbial biomass carbon and water-soluble organic carbon significantly, and the effect decreased in the order of M. macclurei > A. cremastogyne > C. lanceolata. Higher contents of soil microbial biomass carbon and water-soluble organic carbon were observed at medium temperature and middle incubation stage. Fine root decomposition had less effect on the content of soil readily oxidized organic carbon.

The impact on the soil microbial community and enzyme activity of two earthworm species during the bioremediation of pentachlorophenol-contaminated soils.

PubMed

Lin, Zhong; Zhen, Zhen; Wu, Zhihao; Yang, Jiewen; Zhong, Laiyuan; Hu, Hanqiao; Luo, Chunling; Bai, Jing; Li, Yongtao; Zhang, Dayi

2016-01-15

The ecological effect of earthworms on the fate of soil pentachlorophenol (PCP) differs with species. This study addressed the roles and mechanisms by which two earthworm species (epigeic Eisenia fetida and endogeic Amynthas robustus E. Perrier) affect the soil microbial community and enzyme activity during the bioremediation of PCP-contaminated soils. A. robustus removed more soil PCP than did E. foetida. A. robustus improved nitrogen utilisation efficiency and soil oxidation more than did E. foetida, whereas the latter promoted the organic matter cycle in the soil. Both earthworm species significantly increased the amount of cultivable bacteria and actinomyces in soils, enhancing the utilisation rate of the carbon source (i.e. carbohydrates, carboxyl acids, and amino acids) and improving the richness and evenness of the soil microbial community. Additionally, earthworm treatment optimized the soil microbial community and increased the amount of the PCP-4-monooxygenase gene. Phylogenic classification revealed stimulation of indigenous PCP bacterial degraders, as assigned to the families Flavobacteriaceae, Pseudomonadaceae and Sphingobacteriacea, by both earthworms. A. robustus and E. foetida specifically promoted Comamonadaceae and Moraxellaceae PCP degraders, respectively. Copyright © 2015 Elsevier B.V. All rights reserved.

Preparation and Application of LDPE/ZnO Nanocomposites for Extending Shelf Life of Fresh Strawberries

PubMed Central

Mohammadizadeh, Mehri

2015-01-01

Summary Strawberries have a very short post-harvest life mostly due to their relatively high water content, intense metabolic activity and susceptibility to microbial rot. Antimicrobial low-density polyethylene nanocomposite films containing ZnO nanoparticles at different mass fractions were prepared by melt mixing and followed by compression moulding using a hot press machine. Fresh strawberries were packed in nanocomposite films and stored at 4 °C. Their microbial stability, ascorbic acid content and titratable acidity were evaluated after 0, 4, 8, 12 and 16 days of storage. Microbial growth rate was significantly reduced up to 16 days as a result of the use of nanocomposite packaging material containing ZnO nanoparticles. By increasing the ZnO nanoparticle mass fraction to 5%, the antimicrobial activity of the film increased. All packages containing the ZnO nanoparticles kept the microbial load of fresh strawberries below the level that affects shelf life (5 log CFU/g) up to 16 days. The lowest degradation of ascorbic acid content (6.55 mg per 100 g), and loss of acidity (0.68%) were observed in packages containing 3% of ZnO nanoparticles with 10% polyethylene-grafted maleic anhydride. PMID:27904384

Preparation and Application of LDPE/ZnO Nanocomposites for Extending Shelf Life of Fresh Strawberries.

PubMed

Emamifar, Aryou; Mohammadizadeh, Mehri

2015-12-01

Strawberries have a very short post-harvest life mostly due to their relatively high water content, intense metabolic activity and susceptibility to microbial rot. Antimicrobial low-density polyethylene nanocomposite films containing ZnO nanoparticles at different mass fractions were prepared by melt mixing and followed by compression moulding using a hot press machine. Fresh strawberries were packed in nanocomposite films and stored at 4 °C. Their microbial stability, ascorbic acid content and titratable acidity were evaluated after 0, 4, 8, 12 and 16 days of storage. Microbial growth rate was significantly reduced up to 16 days as a result of the use of nanocomposite packaging material containing ZnO nanoparticles. By increasing the ZnO nanoparticle mass fraction to 5%, the antimicrobial activity of the film increased. All packages containing the ZnO nanoparticles kept the microbial load of fresh strawberries below the level that affects shelf life (5 log CFU/g) up to 16 days. The lowest degradation of ascorbic acid content (6.55 mg per 100 g), and loss of acidity (0.68%) were observed in packages containing 3% of ZnO nanoparticles with 10% polyethylene-grafted maleic anhydride.

[Effects of biochar and sheep manure on rhizospheric soil microbial community in continuous ratooning tea orchards].

PubMed

Li, Yan Chun; Li, Zhao Wei; Lin, Wei Wei; Jiang, Yu Hang; Weng, Bo Qi; Lin, Wen Xiong

2018-04-01

Long-term continuous ratooning of tea could lead to serious soil acidification, nutritional imbalance, and the deterioration of the rhizosphere micro-ecological environment. Understanding the effects of biochar and sheep manure on the growth of tea plants and the rhizosphere microbial community structure and function would provide theoretical basis to improve the soil micro-ecological environment of continuous ratooning tea orchards. Biolog technology combined with phospholipid fatty acid (PLFA) approaches were employed to quantify the effects of biochar (40 t·hm -2 ) and sheep manure on the growth of 20 years continuous ratooning tea plants, soil chemical properties, and the soil microbial community structure and function. The results showed that after one year treatment, biochar and sheep manure both improved soil pH and nutrition, and significantly enhanced tea production. Compared with the routine fertilizer application (CK), the biochar and sheep manure treatments significantly increased the carbon metabolic activity (AWCD) and microorganism diversity in the rhizosphere soils, and increased the relative utilization of the carbon sources such as amines, carbohydrates, and polymers. The total PLFA concentrations in the biochar and sheep manure treatments were significantly increased by 20.9% and 47.5% than that in the routine fertilizers application. In addition, sheep manure treatment significantly decreased the saturated/monosaturated fatty acids In conclusion, biochar and sheep manure could alleviate soil acidification, enhance soil nutrition and the growth of tea plants. Both management strategies could increase the soil microbial activity and biomass, enhance the diversity, and improve the microbial community structure, which could be taken as effective measures to regulate the rhizosphere micro-environment of tea plants.

Rhizobial Inoculation Increases Soil Microbial Functioning and Gum Arabic Production of 13-Year-Old Senegalia senegal (L.) Britton, Trees in the North Part of Senegal.

PubMed

Fall, Dioumacor; Bakhoum, Niokhor; Nourou Sall, Saïdou; Zoubeirou, Alzouma Mayaki; Sylla, Samba N; Diouf, Diegane

2016-01-01

Rhizobial inoculation has been widely used in controlled conditions as a substitute for chemical fertilizers to increase plants growth and productivity. However, very little is known about such effects on mature trees in natural habitats. In this study, we investigated the effect of rhizobial inoculation on soil total microbial biomass, mineral nitrogen content, potential CO2 respiration, fluorescein diacetate (FDA), acid phosphatase activities, and gum arabic production by 13-year-old Senegalia senegal (synonym: Acacia senegal) under natural conditions in the north part of Senegal during two consecutive years. Rhizobial inoculation was performed at the beginning of the rainy season (July) for both years with a cocktail of four strains (CIRADF 300, CIRADF 301, CIRADF 302, and CIRADF 303). Rhizospheric soils were collected in both dry and rainy seasons to a depth of 0-25 cm under uninoculated and inoculated trees. Trees were tapped in November (beginning of dry season) using traditional tools. Gum arabic was harvested every 15 days from December to March. The results obtained from both years demonstrated that rhizobial inoculation increased significantly the percentage of trees producing gum arabic, gum arabic production per tree, soil microbial biomass, FDA, and acid phosphatase activities. However, there was no significant effect on C mineralization and mineral nitrogen (N) content. Gum arabic production was positively correlated to rainfall, soil microbial biomass, and mineral nitrogen content. Our results showed a positive effect of rhizobial inoculation on soil microbial functioning and gum arabic production by mature S. senegal trees. These important findings deserve to be conducted in several contrasting sites in order to improve gum arabic production and contribute to increase rural population incomes.

Rhizobial Inoculation Increases Soil Microbial Functioning and Gum Arabic Production of 13-Year-Old Senegalia senegal (L.) Britton, Trees in the North Part of Senegal

PubMed Central

Fall, Dioumacor; Bakhoum, Niokhor; Nourou Sall, Saïdou; Zoubeirou, Alzouma Mayaki; Sylla, Samba N.; Diouf, Diegane

2016-01-01

Rhizobial inoculation has been widely used in controlled conditions as a substitute for chemical fertilizers to increase plants growth and productivity. However, very little is known about such effects on mature trees in natural habitats. In this study, we investigated the effect of rhizobial inoculation on soil total microbial biomass, mineral nitrogen content, potential CO2 respiration, fluorescein diacetate (FDA), acid phosphatase activities, and gum arabic production by 13-year-old Senegalia senegal (synonym: Acacia senegal) under natural conditions in the north part of Senegal during two consecutive years. Rhizobial inoculation was performed at the beginning of the rainy season (July) for both years with a cocktail of four strains (CIRADF 300, CIRADF 301, CIRADF 302, and CIRADF 303). Rhizospheric soils were collected in both dry and rainy seasons to a depth of 0–25 cm under uninoculated and inoculated trees. Trees were tapped in November (beginning of dry season) using traditional tools. Gum arabic was harvested every 15 days from December to March. The results obtained from both years demonstrated that rhizobial inoculation increased significantly the percentage of trees producing gum arabic, gum arabic production per tree, soil microbial biomass, FDA, and acid phosphatase activities. However, there was no significant effect on C mineralization and mineral nitrogen (N) content. Gum arabic production was positively correlated to rainfall, soil microbial biomass, and mineral nitrogen content. Our results showed a positive effect of rhizobial inoculation on soil microbial functioning and gum arabic production by mature S. senegal trees. These important findings deserve to be conducted in several contrasting sites in order to improve gum arabic production and contribute to increase rural population incomes. PMID:27656192

Effects of lead contamination on soil enzymatic activities, microbial biomass, and rice physiological indices in soil-lead-rice (Oryza sativa L.) system.

PubMed

Zeng, Lu S; Liao, Min; Chen, Cheng L; Huang, Chang Y

2007-05-01

The effect of lead (Pb) treatment on the soil enzymatic activities, soil microbial biomass, rice physiological indices and rice biomass were studied in a greenhouse pot experiment. Six levels of Pb viz. 0(CK), 100, 300, 500, 700, 900 mg/kg soil were applied in two types of paddy soils. The results showed that Pb treatment had a stimulating effect on soil enzymatic activities and microbial biomass carbon (Cmic) at low concentration and an inhibitory influence at higher concentration. The degree of influence on enzymatic activities and Cmic by Pb was related to the clay and organic matter contents of the soils. When the Pb treatment was raised to the level of 500 mg/kg, ecological risk appeared both to soil microorganisms and plants. The results also revealed a consistent trend of increased chlorophyll contents and rice biomass initially, maximum at a certain Pb treatment, and then decreased gradually with the increase in Pb concentration. Pb was effective in inducing proline accumulation and its toxicity causes oxidative stress in rice plants. Therefore, it was concluded that soil enzymatic activities, Cmic and rice physiological indices, could be sensitive indicators to reflect environmental stress in soil-lead-rice system.

Effects of Different Organic Manures on the Biochemical and Microbial Characteristics of Albic Paddy Soil in a Short-Term Experiment

PubMed Central

Zhang, Qian; Zhou, Wei; Liang, Guoqing; Wang, Xiubin; Sun, Jingwen; He, Ping; Li, Lujiu

2015-01-01

This study aimed to evaluate the effects of chemical fertilizer (NPK), NPK with livestock manure (NPK+M), NPK with straw (NPK+S), and NPK with green manure (NPK+G) on soil enzyme activities and microbial characteristics of albic paddy soil, which is a typical soil with low productivity in China. The responses of extracellular enzyme activities and the microbial community diversity (determined by phospholipid fatty acid analysis [PLFA] and denaturing gradient gel electrophoresis [DGGE]) were measured. The results showed that NPK+M and NPK+S significantly increased rice yield, with NPK+M being approximately 24% greater than NPK. The NPK+M significantly increased soil organic carbon (SOC) and available phosphate (P) and enhanced phosphatase, β-cellobiosidase, L-leucine aminopeptidase and urease activities. The NPK+S significantly increased SOC and available potassium (K) and significantly enhanced N-acetyl-glucosamidase, β-xylosidase, urease, and phenol oxidase activities. The NPK+G significantly improved total nitrogen (N), ammonium N, available P, and N-acetyl-glucosamidase activity. The PLFA biomass was highest under NPK+S, followed by NPK+M and NPK+G treatments. Principal component analysis (PCA) of the PLFA indicated that soils with NPK+M and NPK+S contained higher proportions of unsaturated and cyclopropane fatty acids (biomarkers of fungi and gram-negative bacteria) and soil under NPK+G contained more straight chain saturated fatty acids (representing gram-positive bacteria). PCA of the DGGE patterns showed that organic amendments had a greater influence on fungal community. Cluster analysis of fungal DGGE patterns revealed that NPK+G was clearly separated. Meanwhile, the bacterial community of NPK+M treatment was the most distinct. RDA analysis revealed changes of microbial community composition mostly depended on β-xylosidase, β-cellobiosidase activities, total N and available K contents. The abundances of gram-negative bacterial and fungal PLFAs probably effective in improving fertility of low-yield albic paddy soil because of their significant influence on DGGE profile. PMID:25879759

Effects of different organic manures on the biochemical and microbial characteristics of albic paddy soil in a short-term experiment.

PubMed

Zhang, Qian; Zhou, Wei; Liang, Guoqing; Wang, Xiubin; Sun, Jingwen; He, Ping; Li, Lujiu

2015-01-01

This study aimed to evaluate the effects of chemical fertilizer (NPK), NPK with livestock manure (NPK+M), NPK with straw (NPK+S), and NPK with green manure (NPK+G) on soil enzyme activities and microbial characteristics of albic paddy soil, which is a typical soil with low productivity in China. The responses of extracellular enzyme activities and the microbial community diversity (determined by phospholipid fatty acid analysis [PLFA] and denaturing gradient gel electrophoresis [DGGE]) were measured. The results showed that NPK+M and NPK+S significantly increased rice yield, with NPK+M being approximately 24% greater than NPK. The NPK+M significantly increased soil organic carbon (SOC) and available phosphate (P) and enhanced phosphatase, β-cellobiosidase, L-leucine aminopeptidase and urease activities. The NPK+S significantly increased SOC and available potassium (K) and significantly enhanced N-acetyl-glucosamidase, β-xylosidase, urease, and phenol oxidase activities. The NPK+G significantly improved total nitrogen (N), ammonium N, available P, and N-acetyl-glucosamidase activity. The PLFA biomass was highest under NPK+S, followed by NPK+M and NPK+G treatments. Principal component analysis (PCA) of the PLFA indicated that soils with NPK+M and NPK+S contained higher proportions of unsaturated and cyclopropane fatty acids (biomarkers of fungi and gram-negative bacteria) and soil under NPK+G contained more straight chain saturated fatty acids (representing gram-positive bacteria). PCA of the DGGE patterns showed that organic amendments had a greater influence on fungal community. Cluster analysis of fungal DGGE patterns revealed that NPK+G was clearly separated. Meanwhile, the bacterial community of NPK+M treatment was the most distinct. RDA analysis revealed changes of microbial community composition mostly depended on β-xylosidase, β-cellobiosidase activities, total N and available K contents. The abundances of gram-negative bacterial and fungal PLFAs probably effective in improving fertility of low-yield albic paddy soil because of their significant influence on DGGE profile.

Application of manures to mitigate the harmful effects of electrokinetic remediation of heavy metals on soil microbial properties in polluted soils.

PubMed

Tahmasbian, Iman; Safari Sinegani, Ali Akbar; Nguyen, Thi Thu Nhan; Che, Rongxiao; Phan, Thuc D; Hosseini Bai, Shahla

2017-12-01

Ethylenediaminetetraacetic acid (EDTA) used with electrokinetic (EK) to remediate heavy metal-polluted soils is a toxic chelate for soil microorganisms. Therefore, this study aimed to evaluate the effects of alternative organic chelates to EDTA on improving the microbial properties of a heavy metal-polluted soil subjected to EK. Cow manure extract (CME), poultry manure extract (PME) and EDTA were applied to a lead (Pb) and zinc (Zn)-polluted calcareous soil which were subjected to two electric intensities (1.1 and 3.3 v/cm). Soil carbon pools, microbial activity, microbial abundance (e.g., fungal, actinomycetes and bacterial abundances) and diethylenetriaminepentaacetic acid (DTPA)-extractable Pb and Zn (available forms) were assessed in both cathodic and anodic soils. Applying the EK to soil decreased all the microbial variables in the cathodic and anodic soils in the absence or presence of chelates. Both CME and PME applied with two electric intensities decreased the negative effect of EK on soil microbial variables. The lowest values of soil microbial variables were observed when EK was combined with EDTA. The following order was observed in values of soil microbial variables after treating with EK and chelates: EK + CME or EK + PME > EK > EK + EDTA. The CME and PME could increase the concentrations of available Pb and Zn, although the increase was less than that of EDTA. Overall, despite increasing soil available Pb and Zn, the combination of EK with manures (CME or PME) mitigated the negative effects of using EK on soil microbial properties. This study suggested that the synthetic chelates such as EDTA could be replaced with manures to alleviate the environmental risks of EK application.

Changes in soil microbial community structure influenced by agricultural management practices in a mediterranean agro-ecosystem.

PubMed

García-Orenes, Fuensanta; Morugán-Coronado, Alicia; Zornoza, Raul; Cerdà, Artemi; Scow, Kate

2013-01-01

Agricultural practices have proven to be unsuitable in many cases, causing considerable reductions in soil quality. Land management practices can provide solutions to this problem and contribute to get a sustainable agriculture model. The main objective of this work was to assess the effect of different agricultural management practices on soil microbial community structure (evaluated as abundance of phospholipid fatty acids, PLFA). Five different treatments were selected, based on the most common practices used by farmers in the study area (eastern Spain): residual herbicides, tillage, tillage with oats and oats straw mulching; these agricultural practices were evaluated against an abandoned land after farming and an adjacent long term wild forest coverage. The results showed a substantial level of differentiation in the microbial community structure, in terms of management practices, which was highly associated with soil organic matter content. Addition of oats straw led to a microbial community structure closer to wild forest coverage soil, associated with increases in organic carbon, microbial biomass and fungal abundances. The microbial community composition of the abandoned agricultural soil was characterised by increases in both fungal abundances and the metabolic quotient (soil respiration per unit of microbial biomass), suggesting an increase in the stability of organic carbon. The ratio of bacteria:fungi was higher in wild forest coverage and land abandoned systems, as well as in the soil treated with oat straw. The most intensively managed soils showed higher abundances of bacteria and actinobacteria. Thus, the application of organic matter, such as oats straw, appears to be a sustainable management practice that enhances organic carbon, microbial biomass and activity and fungal abundances, thereby changing the microbial community structure to one more similar to those observed in soils under wild forest coverage.

Urbanization Effects on the Vertical Distribution of Soil Microbial Communities and Soil C Storage across Edge-to-Interior Urban Forest Gradients

NASA Astrophysics Data System (ADS)

Rosier, C. L.; Van Stan, J. T., II; Trammell, T. L.

2017-12-01

Urbanization alters environmental conditions such as temperature, moisture, carbon (C) and nitrogen (N) deposition affecting critical soil processes (e.g., C storage). Urban soils experience elevated N deposition (e.g., transportation, industry) and decreased soil moisture via urban heat island that can subsequently alter soil microbial community structure and activity. However, there is a critical gap in understanding how increased temperatures and pollutant deposition influences soil microbial community structure and soil C/N cycling in urban forests. Furthermore, canopy structural differences between individual tree species is a potentially important mechanism facilitating the deposition of pollutants to the soil. The overarching goal of this study is to investigate the influence of urbanization and tree species structural differences on the bacterial and fungal community and C and N content of soils experiencing a gradient of urbanization pressures (i.e., forest edge to interior; 150-m). Soil cores (1-m depth) were collected near the stem (< 0.5 meter) of two tree species with contrasting canopy and bark structure (Fagus grandifolia, vs. Liriodendron tulipifera), and evaluated for soil microbial structure via metagenomic analysis and soil C/N content. We hypothesize that soil moisture constraints coupled with increases in recalcitrant C will decrease gram negative bacteria (i.e., dependent on labile C) while increasing saprophytic fungal community abundance (i.e., specialist consuming recalcitrant C) within both surface and subsurface soils experiencing the greatest urban pressure (i.e., forest edge). We further expect trees located on the edge of forest fragments will maintain greater surface soil (< 20 cm) C concentrations due to decreased soil moisture constraining microbial activity (e.g., slower decay), and increased capture of recalcitrant C stocks from industrial/vehicle emission sources (e.g., black C). Our initial results support our hypotheses that urbanization alters soil microbial community composition via reduced soil moisture and carbon storage potential via deposition gradients. Further analyses will answer important questions regarding how individual tree species alters urban soil C storage, N retention, and microbial dynamics.

Enhanced microbial adaptation to p-nitrophenol using activated sludge retained in porous carrier particles and simultaneous removal of nitrite released from degradation of p-nitrophenol.

PubMed

Xing, X H; Inoue, T; Tanji, Y; Unno, H

1999-01-01

In order to examine the microbial degradation of p-nitrophenol (PNP) by a mixed culture system and simultaneous removal of nitrite released via the degradation, an activated sludge retained in porous carrier particles and a suspension culture as a control were acclimated to artificial sewage containing PNP as the sole carbon source. The adaptation of microbes retained in porous carrier particles to PNP was faster than that of suspended microbes by more than 20 d. After microbial adaptation to PNP, it was degraded completely without significant accumulation of intermediate metabolites. The PNP degradation activity of the retained microbes was more than 2 times higher than that of the suspended microbes. By increasing the retained microbial concentration, nitrite released from the degraded PNP was removed by denitrification. This research demonstrates that using microbes retained in porous carrier particles is not only effective for reduction of acclimation time but also enables simultaneous removal of the nitrogen compounds resulting from the degradation of nitroaromatics.

The mechanisms of granulation of activated sludge in wastewater treatment, its optimization, and impact on effluent quality.

PubMed

Wilén, Britt-Marie; Liébana, Raquel; Persson, Frank; Modin, Oskar; Hermansson, Malte

2018-06-01

Granular activated sludge has gained increasing interest due to its potential in treating wastewater in a compact and efficient way. It is well-established that activated sludge can form granules under certain environmental conditions such as batch-wise operation with feast-famine feeding, high hydrodynamic shear forces, and short settling time which select for dense microbial aggregates. Aerobic granules with stable structure and functionality have been obtained with a range of different wastewaters seeded with different sources of sludge at different operational conditions, but the microbial communities developed differed substantially. In spite of this, granule instability occurs. In this review, the available literature on the mechanisms involved in granulation and how it affects the effluent quality is assessed with special attention given to the microbial interactions involved. To be able to optimize the process further, more knowledge is needed regarding the influence of microbial communities and their metabolism on granule stability and functionality. Studies performed at conditions similar to full-scale such as fluctuation in organic loading rate, hydrodynamic conditions, temperature, incoming particles, and feed water microorganisms need further investigations.

Effect of zinc oxide nanoparticles on nitrogen removal, microbial activity and microbial community of CANON process in a membrane bioreactor.

PubMed

Zhang, Xiaojing; Zhang, Nan; Fu, Haoqiang; Chen, Tao; Liu, Sa; Zheng, Shuhua; Zhang, Jie

2017-11-01

In this study, a membrane bioreactor (MBR) was adopted for completely autotrophic nitrogen removal over nitrite (CANON) process. Zinc oxide nanoparticles (ZnO NPs) was step-wise increased to analyze the influence on nitrogen removal, microbial activity and microbial communities. Finally ZnO NPs was removed to study its recovery capability. The bioactivities of ammonia-oxidizing bacteria (AOB), anaerobic ammonia-oxidizing bacteria (AAOB) and nitrite-oxidizing bacteria (NOB) were detected by batch experiments. Results showed that the ZnO NPs with low concentration (≤5mgL -1 ) was profitable for nitrogen removal while the high concentration performed inhibition, and it lowered the abundance of both AOB and NOB while enhanced that of AAOB. ZnO NPs with high concentration (≥10mgL -1 ) suppressed both AOB and AAOB, and long-term exposure within ZnO NPs led to microbial diversity decrease. The inhibition threshold of ZnO NPs on CANON process was 10mgL -1 , and the profitable concentration was 1mgL -1 . Copyright © 2017 Elsevier Ltd. All rights reserved.

No tillage combined with crop rotation improves soil microbial community composition and metabolic activity.

PubMed

Sun, Bingjie; Jia, Shuxia; Zhang, Shixiu; McLaughlin, Neil B; Liang, Aizhen; Chen, Xuewen; Liu, Siyi; Zhang, Xiaoping

2016-04-01

Soil microbial community can vary with different agricultural managements, which in turn can affect soil quality. The objective of this work was to evaluate the effects of long-term tillage practice (no tillage (NT) and conventional tillage (CT)) and crop rotation (maize-soybean (MS) rotation and monoculture maize (MM)) on soil microbial community composition and metabolic capacity in different soil layers. Long-term NT increased the soil organic carbon (SOC) and total nitrogen (TN) mainly at the 0-5 cm depth which was accompanied with a greater microbial abundance. The greater fungi-to-bacteria (F/B) ratio was found in NTMS at the 0-5 cm depth. Both tillage and crop rotation had a significant effect on the metabolic activity, with the greatest average well color development (AWCD) value in NTMS soil at all three soil depths. Redundancy analysis (RDA) showed that the shift in microbial community composition was accompanied with the changes in capacity of utilizing different carbon substrates. Therefore, no tillage combined with crop rotation could improve soil biological quality and make agricultural systems more sustainable.

Microbial Diversity in Sediment Ecosystems (Evaporites Domes, Microbial Mats, and Crusts) of Hypersaline Laguna Tebenquiche, Salar de Atacama, Chile.

PubMed

Fernandez, Ana B; Rasuk, Maria C; Visscher, Pieter T; Contreras, Manuel; Novoa, Fernando; Poire, Daniel G; Patterson, Molly M; Ventosa, Antonio; Farias, Maria E

2016-01-01

We combined nucleic acid-based molecular methods, biogeochemical measurements, and physicochemical characteristics to investigate microbial sedimentary ecosystems of Laguna Tebenquiche, Atacama Desert, Chile. Molecular diversity, and biogeochemistry of hypersaline microbial mats, rhizome-associated concretions, and an endoevaporite were compared with: The V4 hypervariable region of the 16S rRNA gene was amplified by pyrosequencing to analyze the total microbial diversity (i.e., bacteria and archaea) in bulk samples, and in addition, in detail on a millimeter scale in one microbial mat and in one evaporite. Archaea were more abundant than bacteria. Euryarchaeota was one of the most abundant phyla in all samples, and particularly dominant (97% of total diversity) in the most lithified ecosystem, the evaporite. Most of the euryarchaeal OTUs could be assigned to the class Halobacteria or anaerobic and methanogenic archaea. Planctomycetes potentially also play a key role in mats and rhizome-associated concretions, notably the aerobic organoheterotroph members of the class Phycisphaerae. In addition to cyanobacteria, members of Chromatiales and possibly the candidate family Chlorotrichaceae contributed to photosynthetic carbon fixation. Other abundant uncultured taxa such as the candidate division MSBL1, the uncultured MBGB, and the phylum Acetothermia potentially play an important metabolic role in these ecosystems. Lithifying microbial mats contained calcium carbonate precipitates, whereas endoevoporites consisted of gypsum, and halite. Biogeochemical measurements revealed that based on depth profiles of O2 and sulfide, metabolic activities were much higher in the non-lithifying mat (peaking in the least lithified systems) than in lithifying mats with the lowest activity in endoevaporites. This trend in decreasing microbial activity reflects the increase in salinity, which may play an important role in the biodiversity.

Microbial Diversity in Sediment Ecosystems (Evaporites Domes, Microbial Mats, and Crusts) of Hypersaline Laguna Tebenquiche, Salar de Atacama, Chile

PubMed Central

Fernandez, Ana B.; Rasuk, Maria C.; Visscher, Pieter T.; Contreras, Manuel; Novoa, Fernando; Poire, Daniel G.; Patterson, Molly M.; Ventosa, Antonio; Farias, Maria E.

2016-01-01

We combined nucleic acid-based molecular methods, biogeochemical measurements, and physicochemical characteristics to investigate microbial sedimentary ecosystems of Laguna Tebenquiche, Atacama Desert, Chile. Molecular diversity, and biogeochemistry of hypersaline microbial mats, rhizome-associated concretions, and an endoevaporite were compared with: The V4 hypervariable region of the 16S rRNA gene was amplified by pyrosequencing to analyze the total microbial diversity (i.e., bacteria and archaea) in bulk samples, and in addition, in detail on a millimeter scale in one microbial mat and in one evaporite. Archaea were more abundant than bacteria. Euryarchaeota was one of the most abundant phyla in all samples, and particularly dominant (97% of total diversity) in the most lithified ecosystem, the evaporite. Most of the euryarchaeal OTUs could be assigned to the class Halobacteria or anaerobic and methanogenic archaea. Planctomycetes potentially also play a key role in mats and rhizome-associated concretions, notably the aerobic organoheterotroph members of the class Phycisphaerae. In addition to cyanobacteria, members of Chromatiales and possibly the candidate family Chlorotrichaceae contributed to photosynthetic carbon fixation. Other abundant uncultured taxa such as the candidate division MSBL1, the uncultured MBGB, and the phylum Acetothermia potentially play an important metabolic role in these ecosystems. Lithifying microbial mats contained calcium carbonate precipitates, whereas endoevoporites consisted of gypsum, and halite. Biogeochemical measurements revealed that based on depth profiles of O2 and sulfide, metabolic activities were much higher in the non-lithifying mat (peaking in the least lithified systems) than in lithifying mats with the lowest activity in endoevaporites. This trend in decreasing microbial activity reflects the increase in salinity, which may play an important role in the biodiversity. PMID:27597845

Effects of inorganic and organic amendment on soil chemical properties, enzyme activities, microbial community and soil quality in yellow clayey soil.

PubMed

Liu, Zhanjun; Rong, Qinlei; Zhou, Wei; Liang, Guoqing

2017-01-01

Understanding the effects of external organic and inorganic components on soil fertility and quality is essential for improving low-yielding soils. We conducted a field study over two consecutive rice growing seasons to investigate the effect of applying chemical fertilizer (NPK), NPK plus green manure (NPKG), NPK plus pig manure (NPKM), and NPK plus straw (NPKS) on the soil nutrient status, enzyme activities involved in C, N, P, and S cycling, microbial community and rice yields of yellow clayey soil. Results showed that the fertilized treatments significantly improved rice yields over the first three experimental seasons. Compared with the NPK treatment, organic amendments produced more favorable effects on soil productivity. Notably, the NPKM treatment exhibited the highest levels of nutrient availability, microbial biomass carbon (MBC), activities of most enzymes and the microbial community. This resulted in the highest soil quality index (SQI) and rice yield, indicating better soil fertility and quality. Significant differences in enzyme activities and the microbial community were observed among the treatments, and redundancy analysis showed that MBC and available N were the key determinants affecting the soil enzyme activities and microbial community. The SQI score of the non-fertilized control (0.72) was comparable to that of the NPK (0.77), NPKG (0.81) and NPKS (0.79) treatments but significantly lower compared with NPKM (0.85). The significant correlation between rice yield and SQI suggests that SQI can be a useful to quantify soil quality changes caused by different agricultural management practices. The results indicate that application of NPK plus pig manure is the preferred option to enhance SOC accumulation, improve soil fertility and quality, and increase rice yield in yellow clayey soil.

Effect of dietary fiber on microbial activity and microbial gas production in various regions of the gastrointestinal tract of pigs.

PubMed Central

Jensen, B B; Jørgensen, H

1994-01-01

The microbial activity, composition of the gas phase, and gas production rates in the gastrointestinal tract of pigs fed either a low- or a high-fiber diet were investigated. Dense populations of culturable anaerobic bacteria, high ATP concentrations, and high adenylate energy charges were found for the last third of the small intestine, indicating that substantial microbial activity takes place in that portion of the gut. The highest microbial activity (highest bacterium counts, highest ATP concentration, high adenylate energy charge, and low pH) was found in the cecum and proximal colon. Greater microbial activity was found in the stomach and all segments of the hindgut in the pigs fed the high-fiber diet than in the pigs fed the low-fiber diet. Considerable amounts of O2 were found in the stomach (around 5%), while the content of O2 in gas samples taken from all other parts of the gastrointestinal tract was < 1%. The highest concentrations and highest production rates for H2 were found in the last third of the small intestine. No methane could be detected in the stomach or the small intestine. The rate of production and concentration of methane in the cecum and the proximal colon were low, followed by a steady increase in the successive segments of the hindgut. A very good correlation between in vivo and in vitro measurements of methane production was found. The amount of CH4 produced by pigs fed the low-fiber diet was 1.4 liters/day per animal. Substantially larger amounts of CH4 were produced by pigs fed the high-fiber diet (12.5 liters/day)(ABSTRACT TRUNCATED AT 250 WORDS) PMID:8031085

Effects of inorganic and organic amendment on soil chemical properties, enzyme activities, microbial community and soil quality in yellow clayey soil

PubMed Central

Liu, Zhanjun; Rong, Qinlei; Zhou, Wei; Liang, Guoqing

2017-01-01

Understanding the effects of external organic and inorganic components on soil fertility and quality is essential for improving low-yielding soils. We conducted a field study over two consecutive rice growing seasons to investigate the effect of applying chemical fertilizer (NPK), NPK plus green manure (NPKG), NPK plus pig manure (NPKM), and NPK plus straw (NPKS) on the soil nutrient status, enzyme activities involved in C, N, P, and S cycling, microbial community and rice yields of yellow clayey soil. Results showed that the fertilized treatments significantly improved rice yields over the first three experimental seasons. Compared with the NPK treatment, organic amendments produced more favorable effects on soil productivity. Notably, the NPKM treatment exhibited the highest levels of nutrient availability, microbial biomass carbon (MBC), activities of most enzymes and the microbial community. This resulted in the highest soil quality index (SQI) and rice yield, indicating better soil fertility and quality. Significant differences in enzyme activities and the microbial community were observed among the treatments, and redundancy analysis showed that MBC and available N were the key determinants affecting the soil enzyme activities and microbial community. The SQI score of the non-fertilized control (0.72) was comparable to that of the NPK (0.77), NPKG (0.81) and NPKS (0.79) treatments but significantly lower compared with NPKM (0.85). The significant correlation between rice yield and SQI suggests that SQI can be a useful to quantify soil quality changes caused by different agricultural management practices. The results indicate that application of NPK plus pig manure is the preferred option to enhance SOC accumulation, improve soil fertility and quality, and increase rice yield in yellow clayey soil. PMID:28263999

The responses of microbial temperature relationships to seasonal change and winter warming in a temperate grassland.

PubMed

Birgander, Johanna; Olsson, Pål Axel; Rousk, Johannes

2018-01-18

Microorganisms dominate the decomposition of organic matter and their activities are strongly influenced by temperature. As the carbon (C) flux from soil to the atmosphere due to microbial activity is substantial, understanding temperature relationships of microbial processes is critical. It has been shown that microbial temperature relationships in soil correlate with the climate, and microorganisms in field experiments become more warm-tolerant in response to chronic warming. It is also known that microbial temperature relationships reflect the seasons in aquatic ecosystems, but to date this has not been investigated in soil. Although climate change predictions suggest that temperatures will be mostly affected during winter in temperate ecosystems, no assessments exist of the responses of microbial temperature relationships to winter warming. We investigated the responses of the temperature relationships of bacterial growth, fungal growth, and respiration in a temperate grassland to seasonal change, and to 2 years' winter warming. The warming treatments increased winter soil temperatures by 5-6°C, corresponding to 3°C warming of the mean annual temperature. Microbial temperature relationships and temperature sensitivities (Q 10 ) could be accurately established, but did not respond to winter warming or to seasonal temperature change, despite significant shifts in the microbial community structure. The lack of response to winter warming that we demonstrate, and the strong response to chronic warming treatments previously shown, together suggest that it is the peak annual soil temperature that influences the microbial temperature relationships, and that temperatures during colder seasons will have little impact. Thus, mean annual temperatures are poor predictors for microbial temperature relationships. Instead, the intensity of summer heat-spells in temperate systems is likely to shape the microbial temperature relationships that govern the soil-atmosphere C exchange. © 2018 John Wiley & Sons Ltd.

[Soil microbial functional diversity of different altitude Pinus koraiensis forests].

PubMed

Han, Dong-xue; Wang, Ning; Wang, Nan-nan; Sun, Xue; Feng, Fu-juan

2015-12-01

In order to comprehensively understand the soil microbial carbon utilization characteristics of Pinus koraiensis forests, we took the topsoil (0-5 cm and 5-10 cm) along the 700-1100 m altitude in Changbai Mountains and analyzed the vertical distributed characteristics and variation of microbial functional diversity along the elevation gradient by Biolog microplate method. The results showed that there were significant differences in functional diversity of microbial communities at different elevations. AWCD increased with the extension of incubation time and AWCD at the same soil depth gradually decreased along with increasing altitude; Shannon, Simpson and McIntosh diversity index also showed the same trend with AWCD and three different diversity indices were significantly different along the elevation gradient; Species diversity and functional diversity showed the same variation. The utilization intensities of six categories carbon sources had differences while amino acids were constantly the most dominant carbon source. Principal component analysis (PCA) identified that soil microbial carbon utilization at different altitudes had obvious spatial differentiation, as reflected in the use of carbohydrates, amino acids and carboxylic acids. In addition, the cluster of the microbial diversity indexes and AWCD values of different altitudes showed that the composition of vegetation had a significant impact on soil microbial composition and functional activity.

[Characteristics of microbial community and operation efficiency in biofilter process for drinking water purification].

PubMed

Xiang, Hong; Lü, Xi-Wu; Yang, Fei; Yin, Li-Hong; Zhu, Guang-Can

2011-04-01

In order to explore characteristics of microbial community and operation efficiency in biofilter (biologically-enhanced active filter and biological activated carbon filter) process for drinking water purification, Biolog and polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) techniques were applied to analyze the metabolic function and structure of microbial community developing in biofilters. Water quality parameters, such as NH; -N, NO; -N, permanganate index, UV254 and BDOC etc, were determined in inflow and outflow of biofilters for investigation of operation efficiency of the biofilters. The results show that metabolic capacity of microbial community of the raw water is reduced after the biofilters, which reflect that metabolically active microbial communities in the raw water can be intercepted by biofilters. After 6 months operation of biofilters, the metabolic profiles of microbial communities are similar between two kinds of biologically-enhanced active filters, and utilization of carbon sources of microbial communities in the two filters are 73.4% and 75.5%, respectively. The metabolic profiles of microbial communities in two biological activated carbon filters showed significant difference. The carbon source utilization rate of microbial community in granule-activated carbon filter is 79.6%, which is obviously higher than 53.8% of the rate in the columnar activated carbon filter (p < 0.01). The analysis results of PCR-SSCP indicate that microbial communities in each biofilter are variety, but the structure of dominant microorganisms is similar among different biofilters. The results also show that the packing materials had little effect on the structure and metabolic function of microbial community in biologically-enhanced active filters, and the difference between two biofilters for the water purification efficiency was not significant (p > 0.05). However, in biological activated carbon filters, granule-activated carbon is conducive to microbial growth and reproduction, and the microbial communities in the biofilter present high metabolic activities, and the removal efficiency for NH4(+)-N, permanganate index and BDOC is better than the columnar activated carbon filter(p < 0.05). The results also suggest that operation efficiency of biofilter is related to the metabolic capacity of microbial community in biofilter.

Microbial expression profiles in the rhizosphere of willows depend on soil contamination

PubMed Central

Yergeau, Etienne; Sanschagrin, Sylvie; Maynard, Christine; St-Arnaud, Marc; Greer, Charles W

2014-01-01

The goal of phytoremediation is to use plants to immobilize, extract or degrade organic and inorganic pollutants. In the case of organic contaminants, plants essentially act indirectly through the stimulation of rhizosphere microorganisms. A detailed understanding of the effect plants have on the activities of rhizosphere microorganisms could help optimize phytoremediation systems and enhance their use. In this study, willows were planted in contaminated and non-contaminated soils in a greenhouse, and the active microbial communities and the expression of functional genes in the rhizosphere and bulk soil were compared. Ion Torrent sequencing of 16S rRNA and Illumina sequencing of mRNA were performed. Genes related to carbon and amino-acid uptake and utilization were upregulated in the willow rhizosphere, providing indirect evidence of the compositional content of the root exudates. Related to this increased nutrient input, several microbial taxa showed a significant increase in activity in the rhizosphere. The extent of the rhizosphere stimulation varied markedly with soil contamination levels. The combined selective pressure of contaminants and rhizosphere resulted in higher expression of genes related to competition (antibiotic resistance and biofilm formation) in the contaminated rhizosphere. Genes related to hydrocarbon degradation were generally more expressed in contaminated soils, but the exact complement of genes induced was different for bulk and rhizosphere soils. Together, these results provide an unprecedented view of microbial gene expression in the plant rhizosphere during phytoremediation. PMID:24067257

Experimental evidence that microbial activity lowers the albedo of glacier surfaces: the cryoconite casserole experiment.

NASA Astrophysics Data System (ADS)

Musilova, M.; Tranter, M.; Takeuchi, N.; Anesio, A. M.

2014-12-01

Darkened glacier and ice sheet surfaces have lower albedos, absorb more solar radiation and consequently melt more rapidly. The increase in glacier surface darkening is an important positive feedback to warming global temperatures, leading to ever growing world-wide ice mass loss. Most studies focus primarily on glacial albedo darkening caused by the physical properties of snow and ice surfaces, and the deposition of dark impurities on glaciers. To date, however, the important effects of biological activity have not been included in most albedo reduction models. This study provides the first experimental evidence that microbial activity can significantly decrease the albedo of glacier surfaces. An original laboratory experiment, the cryoconite casserole, was designed to test the microbial darkening of glacier surface debris (cryoconite) under simulated Greenlandic summer conditions. It was found that minor fertilisation of the cryoconite (at nutrient concentrations typical of glacial ice melt) stimulated extensive microbial activity. Microbes intensified their organic carbon fixation and even mined phosphorous out of the glacier surface sediment. Furthermore, the microbial organic carbon production, accumulation and transformation caused the glacial debris to darken further by 17.3% reflectivity (albedo analogue). These experiments are consistent with the hypothesis that enhanced fertilisation by anthropogenic inputs results in substantial amounts of organic carbon fixation, debris darkening and ultimately to a considerable decrease in the ice albedo of glacier surfaces on global scales. The sizeable amounts of microbially produced glacier surface organic matter and nutrients can thus be a vital source of bioavailable nutrients for subglacial and downstream environments.

Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance

PubMed Central

Bokulich, Nicholas A; Bergsveinson, Jordyn; Ziola, Barry; Mills, David A

2015-01-01

Distinct microbial ecosystems have evolved to meet the challenges of indoor environments, shaping the microbial communities that interact most with modern human activities. Microbial transmission in food-processing facilities has an enormous impact on the qualities and healthfulness of foods, beneficially or detrimentally interacting with food products. To explore modes of microbial transmission and spoilage-gene frequency in a commercial food-production scenario, we profiled hop-resistance gene frequencies and bacterial and fungal communities in a brewery. We employed a Bayesian approach for predicting routes of contamination, revealing critical control points for microbial management. Physically mapping microbial populations over time illustrates patterns of dispersal and identifies potential contaminant reservoirs within this environment. Habitual exposure to beer is associated with increased abundance of spoilage genes, predicting greater contamination risk. Elucidating the genetic landscapes of indoor environments poses important practical implications for food-production systems and these concepts are translatable to other built environments. DOI: http://dx.doi.org/10.7554/eLife.04634.001 PMID:25756611

Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology.

PubMed

Binga, Erik K; Lasken, Roger S; Neufeld, Josh D

2008-03-01

Microbial ecology is a field that applies molecular techniques to analyze genes and communities associated with a plethora of unique environments on this planet. In the past, low biomass and the predominance of a few abundant community members have impeded the application of techniques such as PCR, microarray analysis and metagenomics to complex microbial populations. In the absence of suitable cultivation methods, it was not possible to obtain DNA samples from individual microorganisms. Recently, a method called multiple displacement amplification (MDA) has been used to circumvent these limitations by amplifying DNA from microbial communities in low-biomass environments, individual cells from uncultivated microbial species and active organisms obtained through stable isotope probing incubations. This review describes the development and applications of MDA, discusses its strengths and limitations and highlights the impact of MDA on the field of microbial ecology. Whole genome amplification via MDA has increased access to the genomic DNA of uncultivated microorganisms and low-biomass environments and represents a 'power tool' in the molecular toolbox of microbial ecologists.

Profiling of Indigenous Microbial Community Dynamics and Metabolic Activity During Enrichment in Molasses-Supplemented Crude Oil-Brine Mixtures for Improved Understanding of Microbial Enhanced Oil Recovery.

PubMed

Halim, Amalia Yunita; Pedersen, Dorthe Skou; Nielsen, Sidsel Marie; Lantz, Anna Eliasson

2015-06-01

Anaerobic incubations using crude oil and brine from a North Sea reservoir were conducted to gain increased understanding of indigenous microbial community development, metabolite production, and the effects on the oil-brine system after addition of a complex carbon source, molasses, with or without nitrate to boost microbial growth. Growth of the indigenous microbes was stimulated by addition of molasses. Pyrosequencing showed that specifically Anaerobaculum, Petrotoga, and Methanothermococcus were enriched. Addition of nitrate favored the growth of Petrotoga over Anaerobaculum. The microbial growth caused changes in the crude oil-brine system: formation of oil emulsions, and reduction of interfacial tension (IFT). Reduction in IFT was associated with microbes being present at the oil-brine interphase. These findings suggest that stimulation of indigenous microbial growth by addition of molasses has potential as microbial enhanced oil recovery (MEOR) strategy in North Sea oil reservoirs.

Effect of immobilized rhizobacteria and organic amendment in bulk and rhizospheric soil of Cistus albidus L.

NASA Astrophysics Data System (ADS)

Mengual, Carmen Maria; del Mar Alguacil, Maria; Roldan, Antonio; Schoebitz, Mauricio

2013-04-01

A field experiment was carried out to assess the effectiveness of the immobilized microbial inoculant and the addition of organic olive residue. The microbial inoculant contained two rhizobacterial species identified as Azospirillum brasilense and Pantoea dispersa immobilized in a natural inert support. Bacterial population densities were 3.5×109 and 4.1×109 CFU g-1 of A. brasilense M3 and P. dispersa C3, respectively. The amendment used was the organic fraction extracted with KOH from composted "alperujo". The raw material was collected from an olive-mill and mixed with fresh cow bedding as bulking agent for composting. The inoculation of rhizobacteria and the addition of organic residue were employed for plant growth promotion of Cistus albidus L. and enhancement of soil physicochemical, biochemical and biological properties in a degraded semiarid Mediterranean area. One year after planting, the available phosphorus and potassium content in the amended soils was about 100 and 70% respectively higher than in the non-amended soil. Microbial inoculant and their interaction with organic residue increased the aggregate stability of the rhizosphere soil of C. albidus (by 12% with respect to control soil) while the organic residue alone not increased the aggregate stability of the rhizosphere of C. albidus. Microbial biomass C content and enzyme activities (dehydrogenase, urease, protease-BAA and alkaline phosphatase) of the rhizosphere of C. albidus were increased by microbial inoculant and organic residue interaction but not by microbial inoculation alone. The microbial inoculant and organic residue interaction were the most effective treatment for stimulating the roots dry weight of C. albidus (by 133% with respect to control plants) and microbial inoculant was the most effective treatment for increase the shoot dry weigh of plants (by 106% with respect to control plants). The combined treatment, involving microbial inoculant and addition of the organic residue directly into the soil, had additive effect on the root growth of C. albidus and chemical and biological quality of soil.

Concentrations of viable oil-degrading microorganisms are increased in feces from Calanus finmarchicus feeding in petroleum oil dispersions.

PubMed

Størdal, Ingvild Fladvad; Olsen, Anders Johny; Jenssen, Bjørn Munro; Netzer, Roman; Hansen, Bjørn Henrik; Altin, Dag; Brakstad, Odd Gunnar

2015-09-15

Zooplankton are suggested to be biotic contributors to the transport and weathering of oil in marine environments due to their ingestion of oil. In the present experiment, feeding activity and microbial communities in feces from Calanus finmarchicus feeding in oil dispersions were characterized. Feeding activity was significantly reduced in oil dispersions. The microbial communities in clean and oil-containing copepod feces were dominated by Rhodobacteraceae family bacteria (Lesingera, Phaeobacter, Rugeria, and Sulfitobacter), which were suggested to be indigenous to copepod feces. The results also indicated that these bacteria were metabolizing oil compounds, as a significant increase in the concentrations of viable oil degrading microorganisms was observed in oil-containing feces. This study shows that bacteria in feces from copepods feeding in dilute oil dispersions have capacity for degradation of oil. Zooplankton may therefore contribute to weathering of oil by excreting feces with microbial communities already adapted to degradation of oil. Copyright © 2015 Elsevier Ltd. All rights reserved.

Microbial response to triepthylphosphate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hazen, T.C.; Santo Domingo, J.W.; Berry, C.J.

1997-05-01

The effect of triethylphosphate (TEP) on the activity of a landfill aquifer microbial community was evaluated using standard techniques and in situ hybridizations with phylogenetic probes. Benzene was used as an external carbon source to monitor degradation of an aromatic compound in TEP amended microcosms. Microscopical and viable counts were higher in TEP containing microcosms when compared to unamended controls. A significant increase in metabolic activity was also observed for TEP amended samples as determined by the number of cells hybridizing to an eubacterial probe. In addition, the number of beta and gamma Proteobacteria increased from undetectable levels prior tomore » the study to 15-29% of the total bacteria in microcosms containing TEP and benzene. In these microcosms, nearly 40% of the benzene was degraded during the incubation period compared to less than 5% in unamended microcosms. While TEP has previously been used as an alternate phosphate source in the bioremediation of chlorinated aliphatics, this study shows that it can also stimulate the microbial degradation of aromatics in phosphate limited aquifers.« less

Microbial Community Structure of an Alluvial Aquifer Treated to Encourage Microbial Induced Calcite Precipitation

NASA Astrophysics Data System (ADS)

Ohan, J.; Saneiyan, S.; Lee, J.; Ntarlagiannis, D.; Burns, S.; Colwell, F. S.

2017-12-01

An oligotrophic aquifer in the Colorado River floodplain (Rifle, CO) was treated with molasses and urea to encourage microbial induced calcite precipitation (MICP). This would stabilize the soil mass by reducing porosity and strengthening the mineral fabric. Over the course of a 15-day treatment period, microbial biomass was collected from monitoring well groundwater for DNA extraction and sequencing. Bromide, a conservative tracer, was co-injected and subsequently detected in downgradient wells, confirming effective nutrient delivery. Conductivity increased during the injection regime and an overall decrease in pH was observed. Groundwater chemistry showed a marked increase in ammonia, suggesting urea hydrolysis - a process catalyzed by the enzyme urease - the primary enzyme implicated in MICP. Additionally, soluble iron was detected, suggesting a general increase in microbial activity; possibly as iron-reducing bacteria changed insoluble ferric oxide to soluble ferrous hydroxide in the anoxic aquifer. DNA sequencing of the 16S rRNA gene confirmed the presence of iron reducing bacteria, including Shewanella and Desulfuromonadales. Generally, a decrease in microbial community diversity was observed when pre-injection community taxa were compared with post-injection community taxa. Phyla indicative of anoxic aquifers were represented in accordance with previous literature at the Rifle site. Linear discriminant analysis showed significant differences in representative phyla over the course of the injection series. Geophysical monitoring of the site further suggested changes that could be due to MICP. Induced polarization increased the phase shift in the primary treated area, in agreement with laboratory experiments. Cross-hole seismic testing confirmed that the shear wave velocities increased in the treated soil mass, implying the soil matrix became more stable. Future investigations will help elucidate the viability and efficacy of MICP treatment in changing microbial community structure, and the functional attributes associated with community change, so that physical strengthening of soils by microbial action can be accomplished.

Volatile fatty acids productions by mesophilic and thermophilic sludge fermentation: Biological responses to fermentation temperature.

PubMed

Hao, Jiuxiao; Wang, Hui

2015-01-01

The volatile fatty acids (VFAs) productions, as well as hydrolases activities, microbial communities, and homoacetogens, of mesophilic and thermophilic sludge anaerobic fermentation were investigated to reveal the microbial responses to different fermentation temperatures. Thermophilic fermentation led to 10-fold more accumulation of VFAs compared to mesophilic fermentation. α-glucosidase and protease had much higher activities in thermophilic reactor, especially protease. Illumina sequencing manifested that raising fermentation temperature increased the abundances of Clostridiaceae, Microthrixaceae and Thermotogaceae, which could facilitate either hydrolysis or acidification. Real-time PCR analysis demonstrated that under thermophilic condition the relative abundance of homoacetogens increased in batch tests and reached higher level at stable fermentation, whereas under mesophilic condition it only increased slightly in batch tests. Therefore, higher fermentation temperature increased the activities of key hydrolases, raised the proportions of bacteria involved in hydrolysis and acidification, and promoted the relative abundance of homoacetogens, which all resulted in higher VFAs production. Copyright © 2014 Elsevier Ltd. All rights reserved.

Transformation of ecofunctional parameters of soil microbial cenoses in clearings for power transmission lines in Central Siberia

NASA Astrophysics Data System (ADS)

Bogorodskaya, A. V.; Ponomareva, T. V.; Efimov, D. Yu.; Shishikin, A. S.

2017-06-01

Changes in soil microbial processes and phytocenotic parameters were studied in clearings made for power transmission lines in the subtaiga and southern taiga of Central Siberia. In these clearings, secondary meadow communities play the main environmental role. The substitution of meadow vegetation for forest vegetation, the increase in the phytomass by 40-120%, and the transformation of the hydrothermic regime in the clearings led to the intensification of the humus-accumulative process, growth of the humus content, reduction in acidity and oligotrophy of the upper horizons in the gray soils of the meadow communities, and more active microbial mineralization of organic matter. In the humus horizon of the soils under meadows, the microbial biomass (Cmicr) increased by 20-90%, and the intensity of basal respiration became higher by 60-90%. The values of the microbial metabolic quotient were also higher in these soils than in the soils under the native forests. In the 0- to 50-cm layer of the gray soils under the meadows, the total Cmicr reserves were 35-45% greater and amounted to 230-320 g/m3; the total microbial production of CO2 was 1.5-2 times higher than that in the soil of the adjacent forest and reached 770-840 mg CO2-C/m3 h. The predominance of mineralization processes in the soils under meadows in the clearings reflected changes in edaphic and trophic conditions of the soils and testified to an active inclusion of the herb falloff into the biological cycle.

Integrated ‘omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boaro, Amy A.; Kim, Young-Mo; Konopka, Allan

2014-12-01

Integrated ‘omics have been used on pure cultures and co-cultures, yet they have not been applied to complex microbial communities to examine questions of perturbation response. In this study, we used integrated ‘omics to measure the perturbation response of a cellulose-degrading bioreactor community fed with microcrystalline cellulose (Avicel). We predicted that a pH decrease by addition of a pulse of acid would reduce microbial community diversity and temporarily reduce reactor function such as cellulose degradation. However, 16S rDNA pyrosequencing results revealed increased alpha diversity in the microbial community after the perturbation, and a persistence of the dominant community members overmore » the duration of the experiment. Proteomics results showed a decrease in activity of proteins associated with Fibrobacter succinogenes two days after the perturbation followed by increased protein abundances six days after the perturbation. The decrease in cellulolytic activity suggested by the proteomics was confirmed by the accumulation of Avicel in the reactor. Metabolomics showed a pattern similar to that of the proteome, with amino acid production decreasing two days after the perturbation and increasing after six days. This study demonstrated that community ‘omics data provides valuable information about the interactions and function of anaerobic cellulolytic community members after a perturbation.« less

Dynamics of organic matter and microbial populations in amended soil: a multidisciplinary approach

NASA Astrophysics Data System (ADS)

Gigliotti, Giovanni; Pezzolla, Daniela; Zadra, Claudia; Albertini, Emidio; Marconi, Gianpiero; Turchetti, Benedetta; Buzzini, Pietro

2013-04-01

The application of organic amendments to soils, such as pig slurry, sewage sludge and compost is considered a tool for improving soil fertility and enhancing C stock. The addition of these different organic materials allows a good supply of nutrients for plants but also contributes to C sequestration, affects the microbial activity and the transformation of soil organic matter (SOM). Moreover, the addition of organic amendment has gained importance as a source of greenhouse gas (GHG) emissions and then as a cause of the "Global Warming". Therefore, it is important to investigate the factors controlling the SOM mineralization in order to improve soil C sequestration and decreasing at the same time the GHG emissions. The quality of organic matter added to the soil will play an important role in these dynamics, affecting the microbial activity and the changes in microbial community structure. A laboratory, multidisciplinary experiment was carried out to test the effect of the amendment by anaerobic digested livestock-derived organic materials on labile organic matter evolution and on dynamics of microbial population, this latter both in terms of consistence of microbial biomass, as well as in terms of microbial biodiversity. Different approaches were used to study the microbial community structure: chemical (CO2 fluxes, WEOC, C-biomass, PLFA), microbiological (microbial enumeration) and molecular (DNA extraction and Roche 454, Next Generation Sequencing, NGS). The application of fresh digestate, derived from the anaerobic treatment of animal wastes, affected the short-term dynamics of microbial community, as reflected by the increase of CO2 emissions immediately after the amendment compared to the control soil. This is probably due to the addition of easily available C added with the digestate, demonstrating that this organic material was only partially stabilized by the anaerobic process. In fact, the digestate contained a high amounts of available C, which led to increase WEOC concentration in digestate treated soil compared to the control soil. The depletion of C, likely due to the microbial activity, was confirmed by the gradual decrease of WEOC concentration in soils amended with digestate. The SUVA254 measurement showed an influence of digestate on the quality of soil WEOM, with higher values in the control rather than in the digestate amended soil, indicating a great amount of aromatic compounds in native SOM. The results of the PLFAs showed that the addition of digestate did not lead overall changes in the microbial community structure compared to the control, except for a shallow decrease of fungi. This probably suggests that the slow rate of mineralization of the organic matter added with digestate does not induce to a rapid shift of microbial community structure. The NGS showed the most important bacterial phyla and fungi species that were involved in the SOM turnover. Furthermore, this approach might be useful to trace the residence time of microbial pathogens supplied with digestates.

Contribution of above- and below-ground plant traits to the structure and function of grassland soil microbial communities

PubMed Central

Legay, N.; Baxendale, C.; Grigulis, K.; Krainer, U.; Kastl, E.; Schloter, M.; Bardgett, R. D.; Arnoldi, C.; Bahn, M.; Dumont, M.; Poly, F.; Pommier, T.; Clément, J. C.; Lavorel, S.

2014-01-01

Background and Aims Abiotic properties of soil are known to be major drivers of the microbial community within it. Our understanding of how soil microbial properties are related to the functional structure and diversity of plant communities, however, is limited and largely restricted to above-ground plant traits, with the role of below-ground traits being poorly understood. This study investigated the relative contributions of soil abiotic properties and plant traits, both above-ground and below-ground, to variations in microbial processes involved in grassland nitrogen turnover. Methods In mountain grasslands distributed across three European sites, a correlative approach was used to examine the role of a large range of plant functional traits and soil abiotic factors on microbial variables, including gene abundance of nitrifiers and denitrifiers and their potential activities. Key Results Direct effects of soil abiotic parameters were found to have the most significant influence on the microbial groups investigated. Indirect pathways via plant functional traits contributed substantially to explaining the relative abundance of fungi and bacteria and gene abundances of the investigated microbial communities, while they explained little of the variance in microbial activities. Gene abundances of nitrifiers and denitrifiers were most strongly related to below-ground plant traits, suggesting that they were the most relevant traits for explaining variation in community structure and abundances of soil microbes involved in nitrification and denitrification. Conclusions The results suggest that consideration of plant traits, and especially below-ground traits, increases our ability to describe variation in the abundances and the functional characteristics of microbial communities in grassland soils. PMID:25122656

Quantification of microbial activity in subsurface environments using a hydrogenase enzyme assay

NASA Astrophysics Data System (ADS)

Adhikari, R. R.; Nickel, J.; Kallmeyer, J.

2012-04-01

The subsurface biosphere is the largest microbial ecosystem on Earth. Despite its large size and extensive industrial exploitation, very little is known about the role of microbial activity in the subsurface. Subsurface microbial activity plays a fundamental role in geochemical cycles of carbon and other biologically important elements. How the indigenous microbial communities are supplied with energy is one of the most fundamental questions in subsurface research. It is still an enigma how these communities can survive with such recalcitrant carbon over geological time scales. Despite its usually very low concentration, hydrogen is an important element in subsurface environments. Heterotrophic and chemoautotrophic microorganisms use hydrogen in their metabolic pathways; they either obtain protons from the radiolysis of water and/or cleavage of hydrogen generated by the alteration of basaltic crust, or they dispose of protons by formation of water. Hydrogenase (H2ase) is a ubiquitous intracellular enzyme that catalyzes the interconversion of molecular hydrogen and/or water into protons and electrons. The protons are used for the synthesis of ATP, thereby coupling energy-generating metabolic processes to electron acceptors such as carbon dioxide or sulfate. H2ase activity can therefore be used as a measure for total microbial activity as it targets a key metabolic compound rather than a specific turnover process. Using a highly sensitive tritium assay we measured H2ase enzyme activity in the organic-rich sediments of Lake Van, a saline, alkaline lake in eastern Turkey and in marine subsurface sediments of the Barents Sea. Additionally, sulfate reduction rates (SRRs) were measured to compare the results of the H2ase enzyme assay with the quantitatively most important electron acceptor process. H2ase activity was found at all sites, measured values and distribution of activity varied widely with depth and between sites. At the Lake Van sites H2ase activity ranged from ca. 20 mmol H2 cm-3 d-1 close to the sediment-water interface to 0.5 mmol H2 cm-3 d-1 at a depth of 0.8 m. In samples from the Barents Sea H2ase activity ranged between 0.1 to 2.5 mmol H2 cm-3 d-1 down to a depth of 1.60 m. At all sites the SRR profile followed the H2ase activity profile until SRR declined to values close to the minimum detection limit (~10 pmol cm-3 d-1). H2ase activity increased again after SRR declined, indicating that other microbial processes are becoming quantitatively more important. The H2ase and SRR data show that our assay has a potential to become a valuable tool to measure total subsurface microbial activity.

Above- and belowground linkages in Sphagnum peatland: climate warming affects plant-microbial interactions.

PubMed

Jassey, Vincent E J; Chiapusio, Geneviève; Binet, Philippe; Buttler, Alexandre; Laggoun-Défarge, Fatima; Delarue, Frédéric; Bernard, Nadine; Mitchell, Edward A D; Toussaint, Marie-Laure; Francez, André-Jean; Gilbert, Daniel

2013-03-01

Peatlands contain approximately one third of all soil organic carbon (SOC). Warming can alter above- and belowground linkages that regulate soil organic carbon dynamics and C-balance in peatlands. Here we examine the multiyear impact of in situ experimental warming on the microbial food web, vegetation, and their feedbacks with soil chemistry. We provide evidence of both positive and negative impacts of warming on specific microbial functional groups, leading to destabilization of the microbial food web. We observed a strong reduction (70%) in the biomass of top-predators (testate amoebae) in warmed plots. Such a loss caused a shortening of microbial food chains, which in turn stimulated microbial activity, leading to slight increases in levels of nutrients and labile C in water. We further show that warming altered the regulatory role of Sphagnum-polyphenols on microbial community structure with a potential inhibition of top predators. In addition, warming caused a decrease in Sphagnum cover and an increase in vascular plant cover. Using structural equation modelling, we show that changes in the microbial food web affected the relationships between plants, soil water chemistry, and microbial communities. These results suggest that warming will destabilize C and nutrient recycling of peatlands via changes in above- and belowground linkages, and therefore, the microbial food web associated with mosses will feedback positively to global warming by destabilizing the carbon cycle. This study confirms that microbial food webs thus constitute a key element in the functioning of peatland ecosystems. Their study can help understand how mosses, as ecosystem engineers, tightly regulate biogeochemical cycling and climate feedback in peatlands. © 2012 Blackwell Publishing Ltd.

Polyhydroxyalkanoate (PHA) accumulation potential and PHA-accumulating microbial communities in various activated sludge processes of municipal wastewater treatment plants.

PubMed

Sakai, K; Miyake, S; Iwama, K; Inoue, D; Soda, S; Ike, M

2015-01-01

To clarify the polyhydroxyalkanoate (PHA) accumulation potential and the PHA-accumulating microbial community structure in activated sludge in municipal wastewater treatment plants (WWTPs) and to identify their influential factors. Nine activated sludge samples were collected from municipal WWTPs employing various biological treatment processes. In acetate-fed 24-h batch experiments under aerobic and nitrogen- and phosphorus-limited conditions, polyhydroxybutyrate (PHB) content of activated sludge increased from 0-1·3 wt% to 7·9-24 wt%, with PHB yields of 0·22-0·50 C-mol 3-hydroxybutyrate (C-mol acetate)(-1). Microbial community analyses found that activated sludge samples that accumulated >20 wt% of PHB after 24-h PHA accumulation experiments had >5·0 × 10(8) copies g(-1)-mixed liquor-suspended solid of phaC genes. Results indicated that (i) activated sludge in municipal WWTPs can accumulate up to approx. 20 wt% of PHA without enrichment processes, (ii) PHA accumulation potential of activated sludge varied depending on the operational conditions (treatment processes) of WWTPs, and (iii) phaC gene number can provide a simple indication of PHA accumulation potential. This is the first study to compare the PHA accumulation potential and PHA-accumulating microbial communities in activated sludge of various treatment processes. Our findings may be useful for enhancing the resource recovery potential of wastewater treatment systems. © 2014 The Society for Applied Microbiology.

Microbial diversity and impact on carbonate geochemistry across a changing geochemical gradient in a karst aquifer

PubMed Central

Gray, Cassie J; Engel, Annette S

2013-01-01

Although microbes are known to influence karst (carbonate) aquifer ecosystem-level processes, comparatively little information is available regarding the diversity of microbial activities that could influence water quality and geological modification. To assess microbial diversity in the context of aquifer geochemistry, we coupled 16S rRNA Sanger sequencing and 454 tag pyrosequencing to in situ microcosm experiments from wells that cross the transition from fresh to saline and sulfidic water in the Edwards Aquifer of central Texas, one of the largest karst aquifers in the United States. The distribution of microbial groups across the transition zone correlated with dissolved oxygen and sulfide concentration, and significant variations in community composition were explained by local carbonate geochemistry, specifically calcium concentration and alkalinity. The waters were supersaturated with respect to prevalent aquifer minerals, calcite and dolomite, but in situ microcosm experiments containing these minerals revealed significant mass loss from dissolution when colonized by microbes. Despite differences in cell density on the experimental surfaces, carbonate loss was greater from freshwater wells than saline, sulfidic wells. However, as cell density increased, which was correlated to and controlled by local geochemistry, dissolution rates decreased. Surface colonization by metabolically active cells promotes dissolution by creating local disequilibria between bulk aquifer fluids and mineral surfaces, but this also controls rates of karst aquifer modification. These results expand our understanding of microbial diversity in karst aquifers and emphasize the importance of evaluating active microbial processes that could affect carbonate weathering in the subsurface. PMID:23151637

Microbial diversity and impact on carbonate geochemistry across a changing geochemical gradient in a karst aquifer.

PubMed

Gray, Cassie J; Engel, Annette S

2013-02-01

Although microbes are known to influence karst (carbonate) aquifer ecosystem-level processes, comparatively little information is available regarding the diversity of microbial activities that could influence water quality and geological modification. To assess microbial diversity in the context of aquifer geochemistry, we coupled 16S rRNA Sanger sequencing and 454 tag pyrosequencing to in situ microcosm experiments from wells that cross the transition from fresh to saline and sulfidic water in the Edwards Aquifer of central Texas, one of the largest karst aquifers in the United States. The distribution of microbial groups across the transition zone correlated with dissolved oxygen and sulfide concentration, and significant variations in community composition were explained by local carbonate geochemistry, specifically calcium concentration and alkalinity. The waters were supersaturated with respect to prevalent aquifer minerals, calcite and dolomite, but in situ microcosm experiments containing these minerals revealed significant mass loss from dissolution when colonized by microbes. Despite differences in cell density on the experimental surfaces, carbonate loss was greater from freshwater wells than saline, sulfidic wells. However, as cell density increased, which was correlated to and controlled by local geochemistry, dissolution rates decreased. Surface colonization by metabolically active cells promotes dissolution by creating local disequilibria between bulk aquifer fluids and mineral surfaces, but this also controls rates of karst aquifer modification. These results expand our understanding of microbial diversity in karst aquifers and emphasize the importance of evaluating active microbial processes that could affect carbonate weathering in the subsurface.

[Characterization and microbial community shifts of rice strawdegrading microbial consortia].

PubMed

Wang, Chunfang; Ma, Shichun; Huang, Yan; Liu, Laiyan; Fan, Hui; Deng, Yu

2016-12-04

To study the relationship between microbial community and degradation rate of rice straw, we compared and analyzed cellulose-decomposing ability, microbial community structures and shifts of microbial consortia F1 and F2. We determined exoglucanase activity by 3, 5-dinitrosalicylic acid colorimetry. We determined content of cellulose, hemicellulose and lignin in rice straw by Van Soest method, and calculated degradation rates of rice straw by the weight changes before and after a 10-day incubation. We analyzed and compared the microbial communities and functional microbiology shifts by clone libraries, Miseq analysis and real time-PCR based on the 16S rRNA gene and cel48 genes. Total degradation rate, cellulose, and hemicellulose degradation rate of microbial consortia F1 were significantly higher than that of F2. The variation trend of exoglucanase activity in both microbial consortia F1 and F2 was consistent with that of cel48 gene copies. Microbial diversity of F1 was complex with aerobic bacteria as dominant species, whereas that of F2 was simple with a high proportion of anaerobic cellulose decomposing bacteria in the later stage of incubation. In the first 4 days, unclassified Bacillales and Bacillus were dominant in both F1 and F2. The dominant species and abundance became different after 4-day incubation, Bacteroidetes and Firmicutes were dominant phyla of F1 and F2, respectively. Although Petrimonas and Pusillimonas were common dominant species in F1 and F2, abundance of Petrimonas in F2 (38.30%) was significantly higher than that in F1 (9.47%), and the abundance of Clostridiales OPB54 in F2 increased to 14.85% after 8-day incubation. The abundance of cel48 gene related with cellulose degradation rate and exoglucanase activity, and cel48 gene has the potential as a molecular marker to monitor the process of cellulose degradation. Microbial community structure has a remarkable impact on the degradation efficiency of straw cellulose, and Petrimonas, Paenibacillus, Bacillales, Clostridiales were vital species for microbial consortia F1 and F2 decomposing rice straw.

The Impact of Climate Change on Microbial Communities and Carbon Cycling in High Arctic Permafrost Soil from Spitsbergen, Northern Norway

NASA Astrophysics Data System (ADS)

de Leon, K. C.; Schwery, D.; Yoshikawa, K.; Christiansen, H. H.; Pearce, D.

2014-12-01

Permafrost-affected soils are among the most fragile ecosystems in which current microbial controls on organic matter decomposition are changing as a result of climate change. Warmer conditions in the high Arctic will lead to a deepening of the seasonal active layer of permafrost, provoking changes in microbial processes and possibly resulting in exacerbated carbon degradation under increasing anoxic conditions. The viable and non-viable fractions of the microbial community in a permafrost soil from Adventdalen, Spitsbergen, Norway were subjected to a comprehensive investigation using culture-dependent and culture-independent methods. Molecular analyses using FISH (with CTC-DAPI) and amplified rDNA restriction analysis (ARDRA) on a 257cm deep core, revealed the presence of all major microbial soil groups, with the active layer having more viable cells, and a higher microbial community diversity. Carbon dioxide (CO2) and methane (CH4) flux measurements were performed to show the amount of C stored in the sample. We demonstrated that the microbial community composition from the soil in the center of the core was most likely influenced by small scale variations in environmental conditions. Community structure showed distinct shift of presence of bacterial groups along the vertical temperature gradient profile and microbial counts and diversity was found to be highest in the surface layers, decreasing with depth. It was observed that soil properties driving microbial diversity and functional potential varied across the permafrost table. Data on the variability of CO2 and CH4 distribution described in peat structure heterogeneity are important for modeling emissions on a larger scale. Furthermore, linking microbial biomass to gas distribution may elucidate the cause of peak CO2 and CH4 and their changes in relation to environmental change and peat composition.

Linking N2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community

PubMed Central

Harter, Johannes; Krause, Hans-Martin; Schuettler, Stefanie; Ruser, Reiner; Fromme, Markus; Scholten, Thomas; Kappler, Andreas; Behrens, Sebastian

2014-01-01

Nitrous oxide (N2O) contributes 8% to global greenhouse gas emissions. Agricultural sources represent about 60% of anthropogenic N2O emissions. Most agricultural N2O emissions are due to increased fertilizer application. A considerable fraction of nitrogen fertilizers are converted to N2O by microbiological processes (that is, nitrification and denitrification). Soil amended with biochar (charcoal created by pyrolysis of biomass) has been demonstrated to increase crop yield, improve soil quality and affect greenhouse gas emissions, for example, reduce N2O emissions. Despite several studies on variations in the general microbial community structure due to soil biochar amendment, hitherto the specific role of the nitrogen cycling microbial community in mitigating soil N2O emissions has not been subject of systematic investigation. We performed a microcosm study with a water-saturated soil amended with different amounts (0%, 2% and 10% (w/w)) of high-temperature biochar. By quantifying the abundance and activity of functional marker genes of microbial nitrogen fixation (nifH), nitrification (amoA) and denitrification (nirK, nirS and nosZ) using quantitative PCR we found that biochar addition enhanced microbial nitrous oxide reduction and increased the abundance of microorganisms capable of N2-fixation. Soil biochar amendment increased the relative gene and transcript copy numbers of the nosZ-encoded bacterial N2O reductase, suggesting a mechanistic link to the observed reduction in N2O emissions. Our findings contribute to a better understanding of the impact of biochar on the nitrogen cycling microbial community and the consequences of soil biochar amendment for microbial nitrogen transformation processes and N2O emissions from soil. PMID:24067258

Quorum sensing molecules in activated sludge could trigger microalgae lipid synthesis.

PubMed

Zhang, Chaofan; Li, Qingcheng; Fu, Liang; Zhou, Dandan; Crittenden, John C

2018-05-18

Cultivating microalgae using wastewater is an economical strategy to produce biofuel; however, microbial contamination has to be controlled strictly. Microalgae lipid accumulation can be triggered by environmental pressures, and here, we studied whether microbial contamination is the pressure for microalgae. We hypothesized this pressure was forced via cell-to-cell communication with quorum sensing molecules (QSMs). In this work, we verified the impacts of QSMs produced by activated sludge (wastewater-born microbial consortiums) on both lipid content and biomass production of the microalgae Chlorophyta sp., since in combination, they determined lipid productivity. With QSMs stress, the lipid content of Chlorophyta sp. increased by ∼84%, while biomass production decreased only slightly. Consistently, enzymes on the fatty acid synthesis pathways were generally up-regulated, while they were slightly down-regulated for DNA replication. In summary, the total lipid production improved by 86%. These results revealed the positive effects of microbial contamination on microalgae biofuel production. Copyright © 2018 Elsevier Ltd. All rights reserved.

The impact of long-term hydrocarbon exposure on the structure, activity, and biogeochemical functioning of microbial mats.

PubMed

Aubé, Johanne; Senin, Pavel; Pringault, Olivier; Bonin, Patricia; Deflandre, Bruno; Bouchez, Olivier; Bru, Noëlle; Biritxinaga-Etchart, Edurne; Klopp, Christophe; Guyoneaud, Rémy; Goñi-Urriza, Marisol

2016-10-15

Photosynthetic microbial mats are metabolically structured systems driven by solar light. They are ubiquitous and can grow in hydrocarbon-polluted sites. Our aim is to determine the impact of chronic hydrocarbon contamination on the structure, activity, and functioning of a microbial mat. We compared it to an uncontaminated mat harboring similar geochemical characteristics. The mats were sampled in spring and fall for 2years. Seasonal variations were observed for the reference mat: sulfur cycle-related bacteria dominated spring samples, while Cyanobacteria dominated in autumn. The contaminated mat showed minor seasonal variation; a progressive increase of Cyanobacteria was noticed, indicating a perturbation of the classical seasonal behavior. Hydrocarbon content was the main factor explaining the differences in the microbial community structure; however, hydrocarbonoclastic bacteria were among rare or transient Operational Taxonomic Units (OTUs) in the contaminated mat. We suggest that in long-term contaminated systems, hydrocarbonoclastic bacteria cannot be considered a sentinel of contamination. Copyright © 2016 Elsevier Ltd. All rights reserved.

Enhanced biomethane production rate and yield from lignocellulosic ensiled forage ley by in situ anaerobic digestion treatment with endogenous cellulolytic enzymes.

PubMed

Speda, Jutta; Johansson, Mikaela A; Odnell, Anna; Karlsson, Martin

2017-01-01

Enzymatic treatment of lignocellulosic material for increased biogas production has so far focused on pretreatment methods. However, often combinations of enzymes and different physicochemical treatments are necessary to achieve a desired effect. This need for additional energy and chemicals compromises the rationale of using enzymes for low energy treatment to promote biogas production. Therefore, simpler and less energy intensive in situ anaerobic digester treatment with enzymes is desirable. However, investigations in which exogenous enzymes are added to treat the material in situ have shown mixed success, possibly because the enzymes used originated from organisms not evolutionarily adapted to the environment of anaerobic digesters. In this study, to examine the effect of enzymes endogenous to methanogenic microbial communities, cellulolytic enzymes were instead overproduced and collected from a dedicated methanogenic microbial community. By this approach, a solution with very high endogenous microbial cellulolytic activity was produced and tested for the effect on biogas production from lignocellulose by in situ anaerobic digester treatment. Addition of enzymes, endogenous to the environment of a mixed methanogenic microbial community, to the anaerobic digestion of ensiled forage ley resulted in significantly increased rate and yield of biomethane production. The enzyme solution had an instant effect on more readily available cellulosic material. More importantly, the induced enzyme solution also affected the biogas production rate from less accessible cellulosic material in a second slower phase of lignocellulose digestion. Notably, this effect was maintained throughout the experiment to completely digested lignocellulosic substrate. The induced enzyme solution collected from a microbial methanogenic community contained enzymes that were apparently active and stable in the environment of anaerobic digestion. The enzymatic activity had a profound effect on the biogas production rate and yield, comparable with the results of many pretreatment methods. Thus, application of such enzymes could enable efficient low energy in situ anaerobic digester treatment for increased biomethane production from lignocellulosic material.

Bioreactor Scalability: Laboratory-Scale Bioreactor Design Influences Performance, Ecology, and Community Physiology in Expanded Granular Sludge Bed Bioreactors

PubMed Central

Connelly, Stephanie; Shin, Seung G.; Dillon, Robert J.; Ijaz, Umer Z.; Quince, Christopher; Sloan, William T.; Collins, Gavin

2017-01-01

Studies investigating the feasibility of new, or improved, biotechnologies, such as wastewater treatment digesters, inevitably start with laboratory-scale trials. However, it is rarely determined whether laboratory-scale results reflect full-scale performance or microbial ecology. The Expanded Granular Sludge Bed (EGSB) bioreactor, which is a high-rate anaerobic digester configuration, was used as a model to address that knowledge gap in this study. Two laboratory-scale idealizations of the EGSB—a one-dimensional and a three- dimensional scale-down of a full-scale design—were built and operated in triplicate under near-identical conditions to a full-scale EGSB. The laboratory-scale bioreactors were seeded using biomass obtained from the full-scale bioreactor, and, spent water from the distillation of whisky from maize was applied as substrate at both scales. Over 70 days, bioreactor performance, microbial ecology, and microbial community physiology were monitored at various depths in the sludge-beds using 16S rRNA gene sequencing (V4 region), specific methanogenic activity (SMA) assays, and a range of physical and chemical monitoring methods. SMA assays indicated dominance of the hydrogenotrophic pathway at full-scale whilst a more balanced activity profile developed during the laboratory-scale trials. At each scale, Methanobacterium was the dominant methanogenic genus present. Bioreactor performance overall was better at laboratory-scale than full-scale. We observed that bioreactor design at laboratory-scale significantly influenced spatial distribution of microbial community physiology and taxonomy in the bioreactor sludge-bed, with 1-D bioreactor types promoting stratification of each. In the 1-D laboratory bioreactors, increased abundance of Firmicutes was associated with both granule position in the sludge bed and increased activity against acetate and ethanol as substrates. We further observed that stratification in the sludge-bed in 1-D laboratory-scale bioreactors was associated with increased richness in the underlying microbial community at species (OTU) level and improved overall performance. PMID:28507535

The Resilience of Microbial Community under Drying and Rewetting Cycles of Three Forest Soils.

PubMed

Zhou, Xue; Fornara, Dario; Ikenaga, Makoto; Akagi, Isao; Zhang, Ruifu; Jia, Zhongjun

2016-01-01

Forest soil ecosystems are associated with large pools and fluxes of carbon (C) and nitrogen (N), which could be strongly affected by variation in rainfall events under current climate change. Understanding how dry and wet cycle events might influence the metabolic state of indigenous soil microbes is crucial for predicting forest soil responses to environmental change. We used 454 pyrosequencing and quantitative PCR to address how present (DNA-based) and potentially active (RNA-based) soil bacterial communities might response to the changes in water availability across three different forest types located in two continents (Africa and Asia) under controlled drying and rewetting cycles. Sequencing of rRNA gene and transcript indicated that Proteobacteria, Actinobacteria, and Acidobacteria were the most responsive phyla to changes in water availability. We defined the ratio of rRNA transcript to rRNA gene abundance as a key indicator of potential microbial activity and we found that this ratio was increased following soil dry-down process whereas it decreased after soil rewetting. Following rewetting Crenarchaeota-like 16S rRNA gene transcript increased in some forest soils and this was linked to increases in soil nitrate levels suggesting greater nitrification rates under higher soil water availability. Changes in the relative abundance of (1) different microbial phyla and classes, and (2) 16S and amoA genes were found to be site- and taxa-specific and might have been driven by different life-strategies. Overall, we found that, after rewetting, the structure of the present and potentially active bacterial community structure as well as the abundance of bacterial (16S), archaeal (16S) and ammonia oxidizers (amoA), all returned to pre-dry-down levels. This suggests that microbial taxa have the ability to recover from desiccation, a critical response, which will contribute to maintaining microbial biodiversity in harsh ecosystems under environmental perturbations, such as significant changes in water availability.

The Resilience of Microbial Community under Drying and Rewetting Cycles of Three Forest Soils

PubMed Central

Zhou, Xue; Fornara, Dario; Ikenaga, Makoto; Akagi, Isao; Zhang, Ruifu; Jia, Zhongjun

2016-01-01

Forest soil ecosystems are associated with large pools and fluxes of carbon (C) and nitrogen (N), which could be strongly affected by variation in rainfall events under current climate change. Understanding how dry and wet cycle events might influence the metabolic state of indigenous soil microbes is crucial for predicting forest soil responses to environmental change. We used 454 pyrosequencing and quantitative PCR to address how present (DNA-based) and potentially active (RNA-based) soil bacterial communities might response to the changes in water availability across three different forest types located in two continents (Africa and Asia) under controlled drying and rewetting cycles. Sequencing of rRNA gene and transcript indicated that Proteobacteria, Actinobacteria, and Acidobacteria were the most responsive phyla to changes in water availability. We defined the ratio of rRNA transcript to rRNA gene abundance as a key indicator of potential microbial activity and we found that this ratio was increased following soil dry-down process whereas it decreased after soil rewetting. Following rewetting Crenarchaeota-like 16S rRNA gene transcript increased in some forest soils and this was linked to increases in soil nitrate levels suggesting greater nitrification rates under higher soil water availability. Changes in the relative abundance of (1) different microbial phyla and classes, and (2) 16S and amoA genes were found to be site- and taxa-specific and might have been driven by different life-strategies. Overall, we found that, after rewetting, the structure of the present and potentially active bacterial community structure as well as the abundance of bacterial (16S), archaeal (16S) and ammonia oxidizers (amoA), all returned to pre-dry-down levels. This suggests that microbial taxa have the ability to recover from desiccation, a critical response, which will contribute to maintaining microbial biodiversity in harsh ecosystems under environmental perturbations, such as significant changes in water availability. PMID:27486444

Soil Microbial Responses to Elevated CO2 and O3 in a Nitrogen-Aggrading Agroecosystem

PubMed Central

Cheng, Lei; Booker, Fitzgerald L.; Burkey, Kent O.; Tu, Cong; Shew, H. David; Rufty, Thomas W.; Fiscus, Edwin L.; Deforest, Jared L.; Hu, Shuijin

2011-01-01

Climate change factors such as elevated atmospheric carbon dioxide (CO2) and ozone (O3) can exert significant impacts on soil microbes and the ecosystem level processes they mediate. However, the underlying mechanisms by which soil microbes respond to these environmental changes remain poorly understood. The prevailing hypothesis, which states that CO2- or O3-induced changes in carbon (C) availability dominate microbial responses, is primarily based on results from nitrogen (N)-limiting forests and grasslands. It remains largely unexplored how soil microbes respond to elevated CO2 and O3 in N-rich or N-aggrading systems, which severely hinders our ability to predict the long-term soil C dynamics in agroecosystems. Using a long-term field study conducted in a no-till wheat-soybean rotation system with open-top chambers, we showed that elevated CO2 but not O3 had a potent influence on soil microbes. Elevated CO2 (1.5×ambient) significantly increased, while O3 (1.4×ambient) reduced, aboveground (and presumably belowground) plant residue C and N inputs to soil. However, only elevated CO2 significantly affected soil microbial biomass, activities (namely heterotrophic respiration) and community composition. The enhancement of microbial biomass and activities by elevated CO2 largely occurred in the third and fourth years of the experiment and coincided with increased soil N availability, likely due to CO2-stimulation of symbiotic N2 fixation in soybean. Fungal biomass and the fungi∶bacteria ratio decreased under both ambient and elevated CO2 by the third year and also coincided with increased soil N availability; but they were significantly higher under elevated than ambient CO2. These results suggest that more attention should be directed towards assessing the impact of N availability on microbial activities and decomposition in projections of soil organic C balance in N-rich systems under future CO2 scenarios. PMID:21731722

Bacillus licheniformis affects the microbial community and metabolic profile in the spontaneous fermentation of Daqu starter for Chinese liquor making.

PubMed

Wang, Peng; Wu, Qun; Jiang, Xuejian; Wang, Zhiqiang; Tang, Jingli; Xu, Yan

2017-06-05

Chinese liquor is produced from spontaneous fermentation starter (Daqu) that provides the microbes, enzymes and flavors for liquor fermentation. To improve the flavor character of Daqu, we inoculated Bacillus licheniformis and studied the effect of this strain on the community structure and metabolic profile in Daqu fermentation. The microbial relative abundance changed after the inoculation, including the increase in Bacillus, Clavispora and Aspergillus, and the decrease in Pichia, Saccharomycopsis and some other genera. This variation was also confirmed by pure culture and coculture experiments. Seventy-three metabolites were identified during Daqu fermentation process. After inoculation, the average content of aromatic compounds were significantly enriched from 0.37mg/kg to 0.90mg/kg, and the average content of pyrazines significantly increased from 0.35mg/kg to 5.71mg/kg. The increase in pyrazines was positively associated with the metabolism of the inoculated Bacillus and the native genus Clavispora, because they produced much more pyrazines in their cocultures. Whereas the increase in aromatic compounds might be related to the change of in situ metabolic activity of several native genera, in particular, Aspergillus produced more aromatic compounds in cocultures with B. licheniformis. It indicated that the inoculation of B. licheniformis altered the flavor character of Daqu by both its own metabolic activity and the variation of in situ metabolic activity. Moreover, B. licheniformis inoculation influenced the enzyme activity of Daqu, including the significant increase in amylase activity (from 1.3gstarch/g/h to 1.7gstarch/g/h), and the significant decrease in glucoamylase activity (from 627.6mgglucose/g/h to 445.6mgglucose/g/h) and esterase activity (from 28.1mgethylcaproate/g/100h to 17.2mgethylcaproate/g/100h). These effects of inoculation were important factors for regulating the metabolism of microbial communities, hence for improving the flavor profile Daqu. Copyright © 2017 Elsevier B.V. All rights reserved.

Effect of florfenicol on performance and microbial community of a sequencing batch biofilm reactor treating mariculture wastewater.

PubMed

Gao, Feng; Li, Zhiwei; Chang, Qingbo; Gao, Mengchun; She, Zonglian; Wu, Juan; Jin, Chunji; Zheng, Dong; Guo, Liang; Zhao, Yangguo; Wang, Sen

2018-02-01

The effects of florfenicol (FF) on the performance, microbial activity and microbial community of a sequencing batch biofilm reactor (SBBR) were evaluated in treating mariculture wastewater. The chemical oxygen demand (COD) and nitrogen removal were inhibited at high FF concentrations. The specific oxygen utilization rate (SOUR), specific ammonium oxidation rate (SAOR), specific nitrite oxidation rate (SNOR) and specific nitrate reduction rate (SNRR) were decreased with an increase in the FF concentration from 0 to 35 mg/L. The chemical compositions of loosely bound extracellular polymeric substances (LB-EPS) and tightly bound EPS (TB-EPS) could be affected with an increase in the FF concentration. The high-throughput sequencing indicated some obvious variations in the microbial community at different FF concentrations. The relative abundance of Nitrosomonas and Nitrospira showed a decreasing tendency with an increase in the FF concentration, suggesting that FF could affect the nitrification process of SBBR. Some genera capable of reducing nitrate to nitrogen gas could be inhibited by the addition of FF in the influent, such as Azospirillum and Hyphomicrobium.

Nitrogen Deposition Enhances Carbon Sequestration by Plantations in Northern China

PubMed Central

Du, Zhihong; Wang, Wei; Zeng, Wenjing; Zeng, Hui

2014-01-01

Nitrogen (N) deposition and its ecological effects on forest ecosystems have received global attention. Plantations play an important role in mitigating climate change through assimilating atmospheric CO2. However, the mechanisms by which increasing N additions affect net ecosystem production (NEP) of plantations remain poorly understood. A field experiment was initialized in May 2009, which incorporated additions of four rates of N (control (no N addition), low-N (5 g N m−2 yr−1), medium-N (10 g N m−2 yr−1), and high-N (15 g N m−2 yr−1)) at the Saihanba Forestry Center, Hebei Province, northern China, a locality that contains the largest area of plantations in China. Net primary production (NPP), soil respiration, and its autotrophic and heterotrophic components were measured. Plant tissue carbon (C) and N concentrations (including foliage, litter, and fine roots), microbial biomass, microbial community composition, extracellular enzyme activities, and soil pH were also measured. N addition significantly increased NPP, which was associated with increased litter N concentrations. Autotrophic respiration (AR) increased but heterotrophic respiration (HR) decreased in the high N compared with the medium N plots, although the HR in high and medium N plots did not significantly differ from that in the control. The increased AR may derive from mycorrhizal respiration and rhizospheric microbial respiration, not live root respiration, because fine root biomass and N concentrations showed no significant differences. Although the HR was significantly suppressed in the high-N plots, soil microbial biomass, composition, or activity of extracellular enzymes were not significantly changed. Reduced pH with fertilization also could not explain the pattern of HR. The reduction of HR may be related to altered microbial C use efficiency. NEP was significantly enhanced by N addition, from 149 to 426.6 g C m−2 yr−1. Short-term N addition may significantly enhance the role of plantations as an important C sink. PMID:24498416

Microbial Community Activity is Insensitive to Passive Warming in a Semiarid Ecosystem

NASA Astrophysics Data System (ADS)

Espinosa, N. J.; Gallery, R. E.; Fehmi, J. S.

2016-12-01

Soil microorganisms drive ecosystem nutrient cycling through the production of extracellular enzymes, which facilitate organic matter decomposition, and the flux of large amounts of carbon dioxide to the atmosphere. Although aird and semiarid ecosystems occupy over 40% of land cover and are projected to expand due to climate change, much of our current understanding of these processes comes from mesic temperate ecosystems. Semiarid ecosystems have added complexity due to the widespread biological adaptations to infrequent and discreet precipitation pulses, which enable biological activity to persist throughout dry periods and thrive following seasonal precipitation events. Additionally, the intricacies of plant-microbe interactions and the response of these interactions to a warmer climate and increased precipitation variability in semiarid ecosystems present a continued challenge for climate change research. In this study, we used a passive warming experiment with added plant debris as either woodchip or biochar, to simulate different long-term carbon additions to two common semiarid soils. The response of soil respiration, plant biomass, and microbial activity was monitored bi-annually. We hypothesized that microbial activity would increase with temperature manipulations when soil moisture limitation was alleviated by summer precipitation. The passive warming treatment was most pronounced during periods of daily and seasonal temperature maxima. For all seven hydrolytic enzymes examined, there was no significant response to experimental warming, regardless of seasonal climatic and soil moisture variation. Surprisingly, soil respiration responded positively to warming for certain carbon additions and seasons, which did not correspond with a similar response in plant biomass. The enzyme results observed here are consistent with the few other experimental results for warming in semiarid ecosystems and indicate that the soil microbial community activity of semiarid ecosystems is potentially resilient to a warmer environment.

Decline in Topsoil Microbial Quotient, Fungal Abundance and C Utilization Efficiency of Rice Paddies under Heavy Metal Pollution across South China

PubMed Central

Liu, Yongzhuo; Zhou, Tong; Crowley, David; Li, Lianqing; Liu, Dawen; Zheng, Jinwei; Yu, Xinyan; Pan, Genxing; Hussain, Qaiser; Zhang, Xuhui; Zheng, Jufeng

2012-01-01

Agricultural soils have been increasingly subject to heavy metal pollution worldwide. However, the impacts on soil microbial community structure and activity of field soils have been not yet well characterized. Topsoil samples were collected from heavy metal polluted (PS) and their background (BGS) fields of rice paddies in four sites across South China in 2009. Changes with metal pollution relative to the BGS in the size and community structure of soil microorganisms were examined with multiple microbiological assays of biomass carbon (MBC) and nitrogen (MBN) measurement, plate counting of culturable colonies and phospholipids fatty acids (PLFAs) analysis along with denaturing gradient gel electrophoresis (DGGE) profile of 16S rRNA and 18S rRNA gene and real-time PCR assay. In addition, a 7-day lab incubation under constantly 25°C was conducted to further track the changes in metabolic activity. While the decrease under metal pollution in MBC and MBN, as well as in culturable population size, total PLFA contents and DGGE band numbers of bacteria were not significantly and consistently seen, a significant reduction was indeed observed under metal pollution in microbial quotient, in culturable fungal population size and in ratio of fungal to bacterial PLFAs consistently across the sites by an extent ranging from 6% to 74%. Moreover, a consistently significant increase in metabolic quotient was observed by up to 68% under pollution across the sites. These observations supported a shift of microbial community with decline in its abundance, decrease in fungal proportion and thus in C utilization efficiency under pollution in the soils. In addition, ratios of microbial quotient, of fungal to bacterial and qCO2 are proved better indicative of heavy metal impacts on microbial community structure and activity. The potential effects of these changes on C cycling and CO2 production in the polluted rice paddies deserve further field studies. PMID:22701725

Distance-dependent varieties of microbial community structure and metabolic functions in the rhizosphere of Sedum alfredii Hance during phytoextraction of a cadmium-contaminated soil.

PubMed

Yang, Wenhao; Zhang, Taoxiang; Lin, Sen; Ni, Wuzhong

2017-06-01

The recovery of microbial community and activities is crucial to the remediation of contaminated soils. Distance-dependent variations of microbial community composition and metabolic characteristics in the rhizospheric soil of hyperaccumulator during phytoextraction are poorly understood. A 12-month phytoextraction experiment with Sedum alfredii in a Cd-contaminated soil was conducted. A pre-stratified rhizobox was used for separating sub-layer rhizospheric (0-2, 2-4, 4-6, 6-8, 8-10 mm from the root mat)/bulk soils. Soil microbial structure and function were analyzed by phospholipid fatty acid (PLFA) and MicroResp™ methods. The concentrations of total and specified PLFA biomarkers and the utilization rates for the 14 substrates (organic carbon) in the 0-2-mm sub-layer rhizospheric soil were significantly increased, as well as decreased with the increase in the distance from the root mat. Microbial structure measured by the ratios of different groups of PLFAs such as fungal/bacterial, monounsaturated/saturated, ratios of Gram-positive to Gram-negative (GP/GN) bacterial, and cyclopropyl/monoenoic precursors and 19:0 cyclo/18:1ω7c were significantly changed in the 0-2-mm soil. The PLFA contents and substrate utilization rates were negatively correlated with pH and total, acid-soluble, and reducible fractions of Cd, while positively correlated with labile carbon. The dynamics of microbial community were likely due to root exudates and Cd uptake by S. alfredii. This study revealed the stimulations and gradient changes of rhizosphere microbial community through phytoextraction, as reduced Cd concentration, pH, and increased labile carbons are due to the microbial community responses.

Response of soil microbial activity and biodiversity in soils polluted with different concentrations of cypermethrin insecticide.

PubMed

Tejada, Manuel; García, Carlos; Hernández, Teresa; Gómez, Isidoro

2015-07-01

We performed a laboratory study into the effect of cypermethrin insecticide applied to different concentrations on biological properties in two soils [Typic Xerofluvent (soil A) and Xerollic Calciorthid (soil B)]. Two kg of each soil were polluted with cypermethrin at a rate of 60, 300, 600, and 1,200 g ha(-1) (C1, C2, C3, and C4 treatments). A nonpolluted soil was used as a control (C0 treatment). For all treatments and each experimental soil, soil dehydrogenase, urease, β-glucosidase, phosphatase, and arylsulphatase activities and soil microbial community were analysed by phospholipid fatty acids, which were measured at six incubation times (3, 7, 15, 30, 60, and 90 days). The behavior of the enzymatic activities and microbial population were dependent on the dose of insecticide applied to the soil. Compared with the C0 treatment, in soil A, the maximum inhibition of the enzymatic activities was at 15, 30, 45, and 90 days for the C1, C2, C3, and C4 treatments, respectively. However, in soil B, the maximum inhibition occurred at 7, 15, 30, and 45 days for the C1, C2, C3, and C4 treatments, respectively. These results suggest that the cypermethrin insecticide caused a negative effect on soil enzymatic activities and microbial diversity. This negative impact was greater when a greater dose of insecticide was used; this impact was also greater in soil with lower organic matter content. For both soils, and from these respective days onward, the enzymatic activities and microbial populations progressively increased by the end of the experimental period. This is possibly due to the fact that the insecticide or its breakdown products and killed microbial cells, subsequently killed by the insecticide, are being used as a source of energy or as a carbon source for the surviving microorganisms for cell proliferation.

Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds.

PubMed

Wurzbacher, Christian; Nilsson, R Henrik; Rautio, Milla; Peura, Sari

2017-08-01

In the transition zone of the shifting permafrost border, thaw ponds emerge as hotspots of microbial activity, processing the ancient carbon freed from the permafrost. We analyzed the microbial succession across a gradient of recently emerged to older ponds using three molecular markers: one universal, one bacterial and one fungal. Age was a major modulator of the microbial community of the thaw ponds. Surprisingly, typical freshwater taxa comprised only a small fraction of the community. Instead, thaw ponds of all age classes were dominated by enigmatic bacterial and fungal phyla. Our results on permafrost thaw ponds lead to a revised perception of the thaw pond ecosystem and their microbes, with potential implications for carbon and nutrient cycling in this increasingly important class of freshwaters.

Bi-layered nanocomposite bandages for controlling microbial infections and overproduction of matrix metalloproteinase activity.

PubMed

Anjana, J; Mohandas, Annapoorna; Seethalakshmy, S; Suresh, Maneesha K; Menon, Riju; Biswas, Raja; Jayakumar, R

2018-04-15

Chronic diabetic wounds is characterised by increased microbial contamination and overproduction of matrix metalloproteases that would degrade the extracellular matrix. A bi-layer bandage was developed, that promotes the inhibition of microbial infections and matrix metalloprotease (MMPs) activity. Bi-layer bandage containing benzalkonium chloride loaded gelatin nanoparticles (BZK GNPs) in chitosan-Hyaluronic acid (HA) as a bottom layer and sodium alendronate containing chitosan as top layer was developed. We hypothesized that the chitosan-gelatin top layer with sodium alendronate could inhibit the MMPs activity, whereas the chitosan-HA bottom layer with BZK GNPs (240±66nm) would enable the elimination of microbes. The porosity, swelling and degradation nature of the prepared Bi-layered bandage was studied. The bottom layer could degrade within 4days whereas the top layer remained upto 7days. The antimicrobial activity of the BZK NPs loaded bandage was determined using normal and clinical strains. Gelatin zymography shows that the proteolytic activity of MMP was inhibited by the bandage. Copyright © 2017 Elsevier B.V. All rights reserved.

Diet rapidly and reproducibly alters the human gut microbiome

PubMed Central

David, Lawrence A.; Maurice, Corinne F.; Carmody, Rachel N.; Gootenberg, David B.; Button, Julie E.; Wolfe, Benjamin E.; Ling, Alisha V.; Devlin, A. Sloan; Varma, Yug; Fischbach, Michael A.; Biddinger, Sudha B.; Dutton, Rachel J.; Turnbaugh, Peter J.

2013-01-01

Long-term diet influences the structure and activity of the trillions of microorganisms residing in the human gut1–5, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here, we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila, and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale, and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals2, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi, and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids, and the outgrowth of microorganisms capable of triggering inflammatory bowel disease6. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles. PMID:24336217

Microbial transformation of ginsenoside Rb1, Re and Rg1 and its contribution to the improved anti-inflammatory activity of ginseng.

PubMed

Yu, Shanshan; Zhou, Xiaoli; Li, Fan; Xu, Chunchun; Zheng, Fei; Li, Jing; Zhao, Huanxi; Dai, Yulin; Liu, Shuying; Feng, Yan

2017-03-10

Microbial transformation of ginsenosides to increase its pharmaceutical effect is gaining increasing attention in recent years. In this study, Cellulosimicrobium sp. TH-20, which was isolated from soil samples on which ginseng grown, exhibited effective ginsenoside-transforming activity. After protopanaxadiol (PPD)-type ginsenoside (Rb1) and protopanaxatriol (PPT)-type ginsenosides (Re and Rg1) were fed to C. sp. TH20, a total of 12 metabolites, including 6 new intermediate metabolites, were identified. Stepwise deglycosylation and dehydrogenation on the feeding precursors have been observed. The final products were confirmed to be rare ginsenosides Rd, GypXVII, Rg2 and PPT after 96 h transformation with 38-96% yields. The four products showed improved anti-inflammatory activities by using lipopolysaccharide (LPS)-induced murine RAW 264.7 macrophages and the xylene-induced acute inflammatory model of mouse ear edema. The results indicated that they could dramatically attenuate the production of TNF-α more effectively than the precursors. Our study would provide an example of a unique and powerful microbial cell factory for efficiently converting both PPD-type and PPT-type ginsenosides to rare natural products, which extends the drug candidates as novel anti-inflammatory remedies.

Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation.

PubMed

Kantor, Rose S; Huddy, Robert J; Iyer, Ramsunder; Thomas, Brian C; Brown, Christopher T; Anantharaman, Karthik; Tringe, Susannah; Hettich, Robert L; Harrison, Susan T L; Banfield, Jillian F

2017-03-07

Remediation of industrial wastewater is important for preventing environmental contamination and enabling water reuse. Biological treatment for one industrial contaminant, thiocyanate (SCN - ), relies upon microbial hydrolysis, but this process is sensitive to high loadings. To examine the activity and stability of a microbial community over increasing SCN - loadings, we established and operated a continuous-flow bioreactor fed increasing loadings of SCN - . A second reactor was fed ammonium sulfate to mimic breakdown products of SCN - . Biomass was sampled from both reactors for metagenomics and metaproteomics, yielding a set of genomes for 144 bacteria and one rotifer that constituted the abundant community in both reactors. We analyzed the metabolic potential and temporal dynamics of these organisms across the increasing loadings. In the SCN - reactor, Thiobacillus strains capable of SCN - degradation were highly abundant, whereas the ammonium sulfate reactor contained nitrifiers and heterotrophs capable of nitrate reduction. Key organisms in the SCN - reactor expressed proteins involved in SCN - degradation, sulfur oxidation, carbon fixation, and nitrogen removal. Lower performance at higher loadings was linked to changes in microbial community composition. This work provides an example of how meta-omics can increase our understanding of industrial wastewater treatment and inform iterative process design and development.

[Microbial and physiological mechanisms for alleviating fusarium wilt of faba bean in intercropping system.

PubMed

Dong, Yan; Dong, Kun; Yang, Zhi Xian; Zheng, Yi; Tang, Li

2016-06-01

A field trial was conducted to investigate effects of wheat and faba bean intercropping on incidence and index of fusarium wilt, amount of Fusarium oxysporum of faba bean, oxidase activity and membrane peroxidation of faba bean roots. Functional diversity of microbial community in rhizosphere soil of faba bean was analyzed by using Biolog microbial analysis system, contents of pheno-lic acids in faba bean rhizosphere soil were determined with high performance liquid chromatography (HPLC). Results showed that in comparison with that of monocropped faba bean, wheat and faba bean intercropping tended to reduce the incidence and disease index of faba bean. The fusarium wilt was significantly decreased by 15.8% and 22.8% during the peak infection and late infection stages, and the average well color development (AWCD value) was promoted obviously. The Shannon diversity (H) and richness (S) increased by 4.4% and 19.4% during the peak infection stage and 5.3% and 37.1% during the late infection stage, respectively. Principal component analysis demonstrated that intercropping significantly changed the rhizospheric microbial community composition. The amount of F. oxysporum in rhizosphere soil of intercropped faba bean was significantly decreased by 53.8% and 33.1%, respectively, during the peak infection and late infection stages, and contents of 4-hydroxy benzoic acid, vanillic acid, syringic acid, ferulic acid, benzoic acid and cinnamic acid also significantly decreased, peroxidase (POD), catalases (CAT) activities in roots of intercropped faba bean increased significantly by 20.0% and 31.3%, respectively during the peak infection stage and 38.5% and 66.7% respectively during the late infection stage, and the malondialdehyd (MDA) content decreased significantly by 36.3% and 46.3%, respectively during peak infection stage and late infection stage. It was concluded that wheat with faba bean intercropping could significantly promote the soil microbial activity and diversity, reduce the accumulation of phenolic allelochemicals and the amount of F. oxysporum in rhizosphere soil, increase the activities of CAT and POD, reduce MDA content in roots, and thus promote the resistance of faba bean to F. oxysporum infection.

Over 150 years of long-term fertilization alters spatial scaling of microbial biodiversity

DOE PAGES

Liang, Yuting; Wu, Liyou; Clark, Ian M.; ...

2015-04-07

Spatial scaling is a critical issue in ecology, but how anthropogenic activities like fertilization affect spatial scaling is poorly understood, especially for microbial communities. Here, we determined the effects of long-term fertilization on the spatial scaling of microbial functional diversity and its relationships to plant diversity in the 150-year-old Park Grass Experiment, the oldest continuous grassland experiment in the world. Nested samples were taken from plots with contrasting inorganic fertilization regimes, and community DNAs were analyzed using the GeoChip-based functional gene array. The slopes of microbial gene-area relationships (GARs) and plant species-area relationships (SARs) were estimated in a plot receivingmore » nitrogen (N), phosphorus (P), and potassium (K) and a control plot without fertilization. Our results indicated that long-term inorganic fertilization significantly increased both microbial GARs and plant SARs. Microbial spatial turnover rates (i.e., z values) were less than 0.1 and were significantly higher in the fertilized plot (0.0583) than in the control plot (0.0449) (P < 0.0001). The z values also varied significantly with different functional genes involved in carbon (C), N, P, and sulfur (S) cycling and with various phylogenetic groups (archaea, bacteria, and fungi). Similarly, the plant SARs increased significantly (P < 0.0001), from 0.225 in the control plot to 0.419 in the fertilized plot. Soil fertilization, plant diversity, and spatial distance had roughly equal contributions in shaping the microbial functional community structure, while soil geochemical variables contributed less. These results indicated that long-term agricultural practice could alter the spatial scaling of microbial biodiversity. Determining the spatial scaling of microbial biodiversity and its response to human activities is important but challenging in microbial ecology. Most studies to date are based on different sites that may not be truly comparable or on short-term perturbations, and hence, the results observed could represent transient responses. This study examined the spatial patterns of microbial communities in response to different fertilization regimes at the Rothamsted Research Experimental Station, which has become an invaluable resource for ecologists, environmentalists, and soil scientists. The current study is the first showing that long-term fertilization has dramatic impacts on the spatial scaling of microbial communities. By identifying the spatial patterns in response to long-term fertilization and their underlying mechanisms, this study makes fundamental contributions to predictive understanding of microbial biogeography.« less

Over 150 years of long-term fertilization alters spatial scaling of microbial biodiversity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liang, Yuting; Wu, Liyou; Clark, Ian M.

Spatial scaling is a critical issue in ecology, but how anthropogenic activities like fertilization affect spatial scaling is poorly understood, especially for microbial communities. Here, we determined the effects of long-term fertilization on the spatial scaling of microbial functional diversity and its relationships to plant diversity in the 150-year-old Park Grass Experiment, the oldest continuous grassland experiment in the world. Nested samples were taken from plots with contrasting inorganic fertilization regimes, and community DNAs were analyzed using the GeoChip-based functional gene array. The slopes of microbial gene-area relationships (GARs) and plant species-area relationships (SARs) were estimated in a plot receivingmore » nitrogen (N), phosphorus (P), and potassium (K) and a control plot without fertilization. Our results indicated that long-term inorganic fertilization significantly increased both microbial GARs and plant SARs. Microbial spatial turnover rates (i.e., z values) were less than 0.1 and were significantly higher in the fertilized plot (0.0583) than in the control plot (0.0449) (P < 0.0001). The z values also varied significantly with different functional genes involved in carbon (C), N, P, and sulfur (S) cycling and with various phylogenetic groups (archaea, bacteria, and fungi). Similarly, the plant SARs increased significantly (P < 0.0001), from 0.225 in the control plot to 0.419 in the fertilized plot. Soil fertilization, plant diversity, and spatial distance had roughly equal contributions in shaping the microbial functional community structure, while soil geochemical variables contributed less. These results indicated that long-term agricultural practice could alter the spatial scaling of microbial biodiversity. Determining the spatial scaling of microbial biodiversity and its response to human activities is important but challenging in microbial ecology. Most studies to date are based on different sites that may not be truly comparable or on short-term perturbations, and hence, the results observed could represent transient responses. This study examined the spatial patterns of microbial communities in response to different fertilization regimes at the Rothamsted Research Experimental Station, which has become an invaluable resource for ecologists, environmentalists, and soil scientists. The current study is the first showing that long-term fertilization has dramatic impacts on the spatial scaling of microbial communities. By identifying the spatial patterns in response to long-term fertilization and their underlying mechanisms, this study makes fundamental contributions to predictive understanding of microbial biogeography.« less

[Change in soil enzymes activities after adding biochar or straw by fluorescent microplate method].

PubMed

Zhang, Yu-Lan; Chen, Li-Jun; Duan, Zheng-Hu; Wu, Zhi-Jie; Sun, Cai-Xia; Wang, Jun-Yu

2014-02-01

The present work was aimed to study soil a-glucosidase and beta-glucosidase activities of and red soils based on fluorescence detection method combined with 96 microplates with TECAN Infinite 200 Multi-Mode Microplate Reader. We added biochar or straw (2.5 g air dry sample/50g air dry soil sample) into and red soils and the test was carried under fixed temperature and humidity condition (25 degrees C, 20% soil moisture content). The results showed that straw addition enhances soil alpha-glucosidase and beta-glucosidase activities, beta-glucosidase activity stimulated by rice straw treatment was higher than that of corn straw treatment, and activity still maintains strong after 40 days, accounting for increasing soil carbon transformation with straw inputting. Straw inputting increased soil nutrients contents and may promote microbial activity, which also lead to the increase oin enzyme Straw inputting increased soil nutrients contents and may promote microbial activity, which also lead to the increase oin enzyme activities. Different effects of straw kinds may be related to material source that needs further research. However, biochar inputting has little effect on soil alpha-glucosidase and beta-glucosidase activity. Biochar contains less available nutrients than straw and have degradation-resistant characteristics. Compared with the conventional spectrophotometric method, fluorescence microplate method is more sensitive to soil enzyme activities in suspension liquid, which can be used in a large number of samples. In brief, fluorescence microplate method is fast, accurate, and simple to determine soil enzymes activities.

Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil.

PubMed

Su, Jian-Qiang; Ding, Long-Jun; Xue, Kai; Yao, Huai-Ying; Quensen, John; Bai, Shi-Jie; Wei, Wen-Xue; Wu, Jin-Shui; Zhou, Jizhong; Tiedje, James M; Zhu, Yong-Guan

2015-01-01

The influence of long-term chemical fertilization on soil microbial communities has been one of the frontier topics of agricultural and environmental sciences and is critical for linking soil microbial flora with soil functions. In this study, 16S rRNA gene pyrosequencing and a functional gene array, geochip 4.0, were used to investigate the shifts in microbial composition and functional gene structure in paddy soils with different fertilization treatments over a 22-year period. These included a control without fertilizers; chemical nitrogen fertilizer (N); N and phosphate (NP); N and potassium (NK); and N, P and K (NPK). Based on 16S rRNA gene data, both species evenness and key genera were affected by P fertilization. Functional gene array-based analysis revealed that long-term fertilization significantly changed the overall microbial functional structures. Chemical fertilization significantly increased the diversity and abundance of most genes involved in C, N, P and S cycling, especially for the treatments NK and NPK. Significant correlations were found among functional gene structure and abundance, related soil enzymatic activities and rice yield, suggesting that a fertilizer-induced shift in the microbial community may accelerate the nutrient turnover in soil, which in turn influenced rice growth. The effect of N fertilization on soil microbial functional genes was mitigated by the addition of P fertilizer in this P-limited paddy soil, suggesting that balanced chemical fertilization is beneficial to the soil microbial community and its functions. © 2014 John Wiley & Sons Ltd.

Effects of different soil management practices on soil properties and microbial diversity

NASA Astrophysics Data System (ADS)

Gajda, Anna M.; Czyż, Ewa A.; Dexter, Anthony R.; Furtak, Karolina M.; Grządziel, Jarosław; Stanek-Tarkowska, Jadwiga

2018-01-01

The effects of different tillage systems on the properties and microbial diversity of an agricultural soil was investigated. In doing so, soil physical, chemical and biological properties were analysed in 2013-2015, on a long-term field experiment on a loamy sand at the IUNG-PIB Experimental Station in Grabów, Poland. Winter wheat was grown under two tillage treatments: conventional tillage using a mouldboard plough and traditional soil tillage equipment, and reduced tillage based on soil crushing-loosening equipment and a rigid-tine cultivator. Chopped wheat straw was used as a mulch on both treatments. Reduced tillage resulted in increased water content throughout the whole soil profile, in comparison with conventional tillage. Under reduced tillage, the content of readily dispersible clay was also reduced, and, therefore, soil stability was increased in the toplayers, compared with conventional tillage. In addition, the beneficial effects of reduced tillage were reflected in higher soil microbial activity as measured with dehydrogenases and hydrolysis of fluorescein diacetate, compared with conventional tillage. Moreover, the polimerase chain reaction - denaturing gradient gel electrophoresis analysis showed that soil under reduced till-age had greater diversity of microbial communities, compared with conventionally-tilled soil. Finally, reduced tillage increased organic matter content, stability in water and microbial diversity in the top layer of the soil.

Spreading topsoil encourages ecological restoration on embankments: soil fertility, microbial activity and vegetation cover.

PubMed

Rivera, Desirée; Mejías, Violeta; Jáuregui, Berta M; Costa-Tenorio, Marga; López-Archilla, Ana Isabel; Peco, Begoña

2014-01-01

The construction of linear transport infrastructure has severe effects on ecosystem functions and properties, and the restoration of the associated roadslopes contributes to reduce its impact. This restoration is usually approached from the perspective of plant cover regeneration, ignoring plant-soil interactions and the consequences for plant growth. The addition of a 30 cm layer of topsoil is a common practice in roadslope restoration projects to increase vegetation recovery. However topsoil is a scarce resource. This study assesses the effects of topsoil spreading and its depth (10 to 30 cm) on two surrogates of microbial activity (β-glucosidase and phosphatase enzymes activity and soil respiration), and on plant cover, plant species richness and floristic composition of embankment vegetation. The study also evaluates the differences in selected physic-chemical properties related to soil fertility between topsoil and the original embankment substrate. Topsoil was found to have higher values of organic matter (11%), nitrogen (44%), assimilable phosphorous (50%) and silt content (54%) than the original embankment substrate. The topsoil spreading treatment increased microbial activity, and its application increased β-glucosidase activity (45%), phosphatase activity (57%) and soil respiration (60%). Depth seemed to affect soil respiration, β-glucosidase and phosphatase activity. Topsoil application also enhanced the species richness of restored embankments in relation to controls. Nevertheless, the depth of the spread topsoil did not significantly affect the resulting plant cover, species richness or floristic composition, suggesting that both depths could have similar effects on short-term recovery of the vegetation cover. A significant implication of these results is that it permits the application of thinner topsoil layers, with major savings in this scarce resource during the subsequent slope restoration work, but the quality of topsoil relative to the original substrate should be previously assessed on a site by site basis.

Long-term reactive nitrogen loading alters soil carbon and microbial community properties in a subalpine forest ecosystem

USGS Publications Warehouse

Boot, Claudia M.; Hall, Ed K.; Denef, Karolien; Baron, Jill S.

2016-01-01

Elevated nitrogen (N) deposition due to increased fossil fuel combustion and agricultural practices has altered global carbon (C) cycling. Additions of reactive N to N-limited environments are typically accompanied by increases in plant biomass. Soil C dynamics, however, have shown a range of different responses to the addition of reactive N that seem to be ecosystem dependent. We evaluated the effect of N amendments on biogeochemical characteristics and microbial responses of subalpine forest organic soils in order to develop a mechanistic understanding of how soils are affected by N amendments in subalpine ecosystems. We measured a suite of responses across three years (2011–2013) during two seasons (spring and fall). Following 17 years of N amendments, fertilized soils were more acidic (control mean 5.09, fertilized mean 4.68), and had lower %C (control mean 33.7% C, fertilized mean 29.8% C) and microbial biomass C by 22% relative to control plots. Shifts in biogeochemical properties in fertilized plots were associated with an altered microbial community driven by reduced arbuscular mycorrhizal (control mean 3.2 mol%, fertilized mean 2.5 mol%) and saprotrophic fungal groups (control mean 17.0 mol%, fertilized mean 15.2 mol%), as well as a decrease in N degrading microbial enzyme activity. Our results suggest that decreases in soil C in subalpine forests were in part driven by increased microbial degradation of soil organic matter and reduced inputs to soil organic matter in the form of microbial biomass.

The Role of Microbial Community Composition in Controlling Soil Respiration Responses to Temperature

PubMed Central

Khachane, Amit; Dungait, Jennifer A. J.; Fraser, Fiona; Hopkins, David W.; Wookey, Philip A.; Singh, Brajesh K.; Freitag, Thomas E.; Hartley, Iain P.; Prosser, James I.

2016-01-01

Rising global temperatures may increase the rates of soil organic matter decomposition by heterotrophic microorganisms, potentially accelerating climate change further by releasing additional carbon dioxide (CO2) to the atmosphere. However, the possibility that microbial community responses to prolonged warming may modify the temperature sensitivity of soil respiration creates large uncertainty in the strength of this positive feedback. Both compensatory responses (decreasing temperature sensitivity of soil respiration in the long-term) and enhancing responses (increasing temperature sensitivity) have been reported, but the mechanisms underlying these responses are poorly understood. In this study, microbial biomass, community structure and the activities of dehydrogenase and β-glucosidase enzymes were determined for 18 soils that had previously demonstrated either no response or varying magnitude of enhancing or compensatory responses of temperature sensitivity of heterotrophic microbial respiration to prolonged cooling. The soil cooling approach, in contrast to warming experiments, discriminates between microbial community responses and the consequences of substrate depletion, by minimising changes in substrate availability. The initial microbial community composition, determined by molecular analysis of soils showing contrasting respiration responses to cooling, provided evidence that the magnitude of enhancing responses was partly related to microbial community composition. There was also evidence that higher relative abundance of saprophytic Basidiomycota may explain the compensatory response observed in one soil, but neither microbial biomass nor enzymatic capacity were significantly affected by cooling. Our findings emphasise the key importance of soil microbial community responses for feedbacks to global change, but also highlight important areas where our understanding remains limited. PMID:27798702

Microbial Communities as Environmental Indicators of Ecological Disturbance in Restored Carbonate Fen-Results of 10 Years of Studies.

PubMed

Mieczan, Tomasz; Tarkowska-Kukuryk, Monika

2017-08-01

Interactions between bacteria and protists are essential to the ecosystem ecology of fens. Until now, however, there has been almost no information on how restoration procedures in carbonate fens affect the functioning of microbial food webs. Changes in vegetation patterns resulting from restoration may take years to be observed, whereas microbial processes display effects even after short-term exposure to changes in environmental conditions caused by restoration. Therefore, microbial processes and patterns can be used as sensitive indicators of changes in environmental conditions. The present study attempts to verify the hypothesis that the species richness and abundance of microbial loop components would differ substantially before and after restoration. The effect of restoration processes on the functioning of the food web was investigated for a 10 years in a carbonate-rich fen, before and after restoration. The restoration procedure (particularly the improvement in hydrological conditions) distinctly modified the taxonomic composition and functioning of microbial food webs. This is reflected in the increased abundance and diversity of testate amoeba, i.e. top predators, within the microbial food web and in the pronounced increase in the abundance of bacteria. This study suggests potential use of microbial loop components as bio-indicators and bio-monitoring tools for hydrological status of fens and concentrations of nutrients. Better understanding of what regulates microbial populations and activity in fens and unravelling of these fundamental mechanisms are particularly critical in order to more accurately predict how fens will respond to global change or anthropogenic disturbances.

The Role of Microbial Community Composition in Controlling Soil Respiration Responses to Temperature.

PubMed

Auffret, Marc D; Karhu, Kristiina; Khachane, Amit; Dungait, Jennifer A J; Fraser, Fiona; Hopkins, David W; Wookey, Philip A; Singh, Brajesh K; Freitag, Thomas E; Hartley, Iain P; Prosser, James I

2016-01-01

Rising global temperatures may increase the rates of soil organic matter decomposition by heterotrophic microorganisms, potentially accelerating climate change further by releasing additional carbon dioxide (CO2) to the atmosphere. However, the possibility that microbial community responses to prolonged warming may modify the temperature sensitivity of soil respiration creates large uncertainty in the strength of this positive feedback. Both compensatory responses (decreasing temperature sensitivity of soil respiration in the long-term) and enhancing responses (increasing temperature sensitivity) have been reported, but the mechanisms underlying these responses are poorly understood. In this study, microbial biomass, community structure and the activities of dehydrogenase and β-glucosidase enzymes were determined for 18 soils that had previously demonstrated either no response or varying magnitude of enhancing or compensatory responses of temperature sensitivity of heterotrophic microbial respiration to prolonged cooling. The soil cooling approach, in contrast to warming experiments, discriminates between microbial community responses and the consequences of substrate depletion, by minimising changes in substrate availability. The initial microbial community composition, determined by molecular analysis of soils showing contrasting respiration responses to cooling, provided evidence that the magnitude of enhancing responses was partly related to microbial community composition. There was also evidence that higher relative abundance of saprophytic Basidiomycota may explain the compensatory response observed in one soil, but neither microbial biomass nor enzymatic capacity were significantly affected by cooling. Our findings emphasise the key importance of soil microbial community responses for feedbacks to global change, but also highlight important areas where our understanding remains limited.

Production-related petroleum microbiology: progress and prospects.

PubMed

Voordouw, Gerrit

2011-06-01

Microbial activity in oil reservoirs is common. Methanogenic consortia hydrolyze low molecular weight components to methane and CO2, transforming light oil to heavy oil to bitumen. The presence of sulfate in injection water causes sulfate-reducing bacteria to produce sulfide. This souring can be reversed by nitrate, stimulating nitrate-reducing bacteria. Removing biogenic sulfide is important, because it contributes to pitting corrosion and resulting pipeline failures. Increased water production eventually makes oil production uneconomic. Microbial fermentation products can lower oil viscosity or interfacial tension and produced biomass can block undesired flow paths to produce more oil. These biotechnologies benefit from increased understanding of reservoir microbial ecology through new sequence technologies and help to decrease the environmental impact of oil production. Copyright © 2010 Elsevier Ltd. All rights reserved.

Simulated nitrogen deposition causes a decline of intra- and extraradical abundance of arbuscular mycorrhizal fungi and changes in microbial community structure in northern hardwood forests

Treesearch

Linda T.A. van Diepen; Erik A. Lilleskov; Kurt S. Pregitzer; R. Michael Miller

2010-01-01

Increased nitrogen (N) deposition caused by human activities has altered ecosystem functioning and biodiversity. To understand the effects of altered N availability, we measured the abundance of arbuscular mycorrhizal fungi (AMF) and the microbial community in northern hardwood forests exposed to long-term (12 years) simulated N deposition (30 kg N ha-1...

Using fluorescence spectroscopy coupled with chemometric analysis to investigate the origin, composition, and dynamics of dissolved organic matter in leachate-polluted groundwater.

PubMed

He, Xiao-Song; Xi, Bei-Dou; Gao, Ru-Tai; Wang, Lei; Ma, Yan; Cui, Dong-Yu; Tan, Wen-Bing

2015-06-01

Groundwater was collected in 2011 and 2012, and fluorescence spectroscopy coupled with chemometric analysis was employed to investigate the composition, origin, and dynamics of dissolved organic matter (DOM) in the groundwater. The results showed that the groundwater DOM comprised protein-, fulvic-, and humic-like substances, and the protein-like component originated predominantly from microbial production. The groundwater pollution by landfill leachate enhanced microbial activity and thereby increased microbial by-product-like material such as protein-like component in the groundwater. Excitation-emission matrix fluorescence spectra combined with parallel factor analysis showed that the protein-like matter content increased from 2011 to 2012 in the groundwater, whereas the fulvic- and humic-like matter concentration exhibited no significant changes. In addition, synchronous-scan fluorescence spectra coupled with two-dimensional correlation analysis showed that the change of the fulvic- and humic-like matter was faster than that of the protein-like substances, as the groundwater flowed from upstream to downstream in 2011, but slower than that of the protein-like substance in 2012 due to the enhancement of microbial activity. Fluorescence spectroscopy combined with chemometric analysis can investigate groundwater pollution characteristics and monitor DOM dynamics in groundwater.

Product quality and microbial dynamics during vermicomposting and maturation of compost from pig manure.

PubMed

Villar, Iria; Alves, David; Mato, Salustiano

2017-11-01

This research evaluates, through microbial dynamics, the use of earthworms Eisenia andrei for maturation of pre-composted pig manure in comparison with maturation under static conditions and with vermicomposting of fresh pig manure. Therefore, two substrates were used (fresh and pre-composted pig manure) and four treatments were developed: fresh manure vermicomposting, control of fresh manure without earthworms, pre-composting followed by vermicomposting and static maturation of pre-composted manure. In order to determine the microbial dynamics, the enzymatic activities and profiles of phospholipid fatty acids (PLFAs) were evaluated over a 112-days period. Physicochemical and biological parameters of the obtained products were also analyzed. The presence of earthworms significantly reduced (p<0.05) microbial biomass and all the microbial groups (Gram+bacteria, Gram-bacteria, and fungi) in both substrates. The enzymatic activities (cellulase, β-glucosidase and acid phosphatase) behaved in a significantly distinctive manner (p<0.05) depending on the treatment. Microbial communities had significant correlations (p<0.05) with hydrolytic activities during static maturation of pre-composted manure. This indicates a direct effect of microbiota evolution on the degradative processes; however, complex earthworm-microbiota interactions were established in the presence of E. andrei. After earthworms' removal from vermicompost of fresh substrate at 70day, an increase in Gram + (4.4 times), Gram - (3.8 times) and fungi (2.8 times) were observed and, although the vermicompost achieved quality values, it is necessary to optimize the vermicompost aging phase period to improve the stability. Static maturation presented stability on microbial dynamics that indicated a slow degradation of organic compounds so that, maturation of pre-composted manure through vermicomposting is better option. Copyright © 2017 Elsevier Ltd. All rights reserved.

Italian multicentre study on microbial environmental contamination in dental clinics: a pilot study.

PubMed

Pasquarella, Cesira; Veronesi, Licia; Castiglia, Paolo; Liguori, Giorgio; Montagna, Maria Teresa; Napoli, Christian; Rizzetto, Rolando; Torre, Ida; Masia, Maria Dolores; Di Onofrio, Valeria; Colucci, Maria Eugenia; Tinteri, Carola; Tanzi, Marialuisa

2010-09-01

The dental practice is associated with a high risk of infections, both for patients and healthcare operators, and the environment may play an important role in the transmission of infectious diseases. A microbiological environmental investigation was carried out in six dental clinics as a pilot study for a larger multicentre study that will be performed by the Italian SItI (Society of Hygiene, Preventive Medicine and Public Health) working group "Hygiene in Dentistry". Microbial contamination of water, air and surfaces was assessed in each clinic during the five working days of the week, before and during treatments. Air and surfaces were also examined at the end of the daily activity. A wide variation was found in microbial environmental contamination, both within the participating clinics and relative to the different sampling times. Microbial water contamination in Dental Unit Water Systems (DUWS) reached values of up to 26x10(4)cfu/mL (colony forming units per millilitre). P. aeruginosa was found in 33% of the sampled DUWS and Legionella spp. in 50%. A significant decrease in the Total Viable Count (TVC) was recorded during the activity. Microbial air contamination showed the highest levels during dental treatments and tended to decrease at the end of the working activity (p<0.05). Microbial buildup on surfaces increased significantly during the working hours. As these findings point out, research on microbial environmental contamination and the related risk factors in dental clinics should be expanded and should also be based on larger collections of data, in order to provide the essential knowledge aimed at targeted preventive interventions. Copyright 2010 Elsevier B.V. All rights reserved.

An Evaluation of Subsurface Microbial Activity Conditional to Subsurface Temperature, Porosity, and Permeability at North American Carbon Sequestration Sites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilson, B.; Mordensky, S.; Verba, Circe

Several nations, including the United States, recognize global climate change as a force transforming the global ecosphere. Carbon dioxide (CO 2) is a greenhouse gas that contributes to the evolving climate. Reduction of atmospheric CO 2 levels is a goal for many nations and carbon sequestration which traps CO 2 in the Earth’s subsurface is one method to reduce atmospheric CO 2 levels. Among the variables that must be considered in developing this technology to a national scale is microbial activity. Microbial activity or biomass can change rock permeability, alter artificial seals around boreholes, and play a key role inmore » biogeochemistry and accordingly may determine how CO 2 is sequestered underground. Certain physical parameters of a reservoir found in literature (e.g., temperature, porosity, and permeability) may indicate whether a reservoir can host microbial communities. In order to estimate which subsurface formations may host microbes, this report examines the subsurface temperature, porosity, and permeability of underground rock formations that have high potential to be targeted for CO 2 sequestration. Of the 268 North American wellbore locations from the National Carbon Sequestration Database (NATCARB; National Energy and Technology Laboratory, 2015) and 35 sites from Nelson and Kibler (2003), 96 sequestration sites contain temperature data. Of these 96 sites, 36 sites have temperatures that would be favorable for microbial survival, 48 sites have mixed conditions for supporting microbial populations, and 11 sites would appear to be unfavorable to support microbial populations. Future studies of microbe viability would benefit from a larger database with more formation parameters (e.g. mineralogy, structure, and groundwater chemistry), which would help to increase understanding of where CO 2 sequestration could be most efficiently implemented.« less

Changes in Soil Organic Matter Abundance, Molecular Composition, and Diversity in an Arid Ecosystem in Response to Long-term Elevated CO2 Manipulation.

NASA Astrophysics Data System (ADS)

Hess, N. J.; Tfaily, M.; Evans, R. D.; Koyama, A.

2017-12-01

Little is known about how soils in arid ecosystems will respond to rising atmospheric CO2 concentration yet arid and semi-arid ecosystems cover more than 40% of Earth's land surface. Previous work in the Mojave Desert (Evans et al., 2014 Nature Climate Change) reported higher soil organic carbon (SOC) and total nitrogen (N) concentrations following 10 years exposure to elevated atmospheric CO2 at the Nevada Desert Free-Air-Carbon dioxide-Enrichment (FACE) Facility (NDFF). In this study, we investigated potential mechanisms that resulted in increased SOC and total N accumulation and stabilization using high resolution mass spectrometry at the NDFF site. Samples were collected from soil profiles to 1 m in depth with a 0.2 m a increment under the dominant evergreen shrub Larrea tridentata. The differences in the molecular composition and diversity of soil organic matter (SOM) were more evident in surface soils and declined with depth, and were consistent with higher SOC and total N concentrations under elevated than ambient CO2. Our molecular analysis also suggested increased root exudation and/or microbial necromass from stabilization of labile C and N contributed to SOM and N stocks. Increased microbial activity and metabolism under elevated CO2 compared to ambient plots suggested that elevated CO2 altered microbial carbon (C) use patterns, reflecting changes in the quality and quantity of SOC inputs. We found that plant-derived compounds were primary substrates for microbial activity under elevated CO2 and microbial products were the main constituents of stabilized SOM. Our results suggest that arid ecosystems are a potential large C sink under elevated CO2, give the extensive coverage of the land surface, and that labile compounds are transformed to stable SOM via microbial processes. Arid systems are limited by water, and thus may have a different C storage potential under changing climates than other ecosystems that are limited by nitrogen or phosphorus.

Different effects of plant-derived dissolved organic matter (DOM) and urea on the priming of soil organic carbon.

PubMed

Qiu, Qingyan; Wu, Lanfang; Ouyang, Zhu; Li, Binbin; Xu, Yanyan

2016-03-01

Soil organic carbon (SOC) mineralization is important for the regulation of the global climate and soil fertility. Decomposition of SOC may be significantly affected by the supply of plant-derived labile carbon (C). To investigate the impact of plant-derived dissolved organic matter (DOM) and urea (N) additions on the decomposition of native SOC as well as to elucidate the underlying mechanisms of priming effects (PEs), a batch of incubation experiments was conducted for 250 days by application of (13)C-labeled plant-derived DOM and urea to soils. The direction of PE induced by the addition of DOM was different from the addition of N, i.e. it switched from negative to positive in DOM-amended soils, whereas in the N-treated soil it switched from positive to negative. Adding DOM alone was favorable for soil C sequestration (59 ± 5 mg C per kg soil), whereas adding N alone or together with DOM accelerated the decomposition of native SOC, causing net C losses (-62 ± 4 and -34 ± 31 mg C per kg soil, respectively). These findings indicate that N addition and its interaction with DOM are not favorable for soil C sequestration. Adding DOM alone increased the level of dissolved organic carbon (DOC), but it did not increase the level of soil mineral N. Changes in the ratio of microbial biomass carbon (MBC) to microbial biomass nitrogen (MBN) and microbial metabolic quotient (qCO2) after the addition of DOM and N suggest that a possible shift in the microbial community composition may occur in the present study. Adding DOM with or without N increased the activities of β-glucosidase and urease. Changes in the direction and magnitude of PE were closely related to changes in soil C and N availability. Soil C and N availability might influence the PE through affecting the microbial biomass and extracellular enzyme activity as well as causing a possible shift in the microbial community composition.

Strong linkage between active microbial communities and microbial carbon usage in a deglaciated terrain of the High Arctic

NASA Astrophysics Data System (ADS)

Kim, M.; Gyeong, H. R.; Lee, Y. K.

2017-12-01

Soil microorganisms play pivotal roles in ecosystem development and carbon cycling in newly exposed glacier forelands. However, little is known about carbon utilization pattern by metabolically active microbes over the course of ecosystem succession in these nutrient-poor environments. We investigated RNA-based microbial community dynamics and its relation to microbial carbon usage along the chronosequence of a High Arctic glacier foreland. Among microbial taxa surveyed (bacteria, archaea and fungi), bacteria are among the most metabolically active taxa with a dominance of Cyanobacteria and Actinobacteria. There was a strong association between microbial carbon usage and active Actinobacterial communities, suggesting that member of Actinobacteria are actively involved in organic carbon degradation in glacier forelands. Both bacterial community and microbial carbon usage are converged towards later stage of succession, indicating that the composition of soil organic carbon plays important roles in structuring bacterial decomposer communities during ecosystem development.

Exercise Is More Effective at Altering Gut Microbial Composition and Producing Stable Changes in Lean Mass in Juvenile versus Adult Male F344 Rats

PubMed Central

Mika, Agnieszka; Van Treuren, Will; González, Antonio; Herrera, Jonathan J.; Knight, Rob; Fleshner, Monika

2015-01-01

The mammalian intestine harbors a complex microbial ecosystem that influences many aspects of host physiology. Exposure to specific microbes early in development affects host metabolism, immune function, and behavior across the lifespan. Just as the physiology of the developing organism undergoes a period of plasticity, the developing microbial ecosystem is characterized by instability and may also be more sensitive to change. Early life thus presents a window of opportunity for manipulations that produce adaptive changes in microbial composition. Recent insights have revealed that increasing physical activity can increase the abundance of beneficial microbial species. We therefore investigated whether six weeks of wheel running initiated in the juvenile period (postnatal day 24) would produce more robust and stable changes in microbial communities versus exercise initiated in adulthood (postnatal day 70) in male F344 rats. 16S rRNA gene sequencing was used to characterize the microbial composition of juvenile versus adult runners and their sedentary counterparts across multiple time points during exercise and following exercise cessation. Alpha diversity measures revealed that the microbial communities of young runners were less even and diverse, a community structure that reflects volatility and malleability. Juvenile onset exercise altered several phyla and, notably, increased Bacteroidetes and decreased Firmicutes, a configuration associated with leanness. At the genus level of taxonomy, exercise altered more genera in juveniles than in the adults and produced patterns associated with adaptive metabolic consequences. Given the potential of these changes to contribute to a lean phenotype, we examined body composition in juvenile versus adult runners. Interestingly, exercise produced persistent increases in lean body mass in juvenile but not adult runners. Taken together, these results indicate that the impact of exercise on gut microbiota composition as well as body composition may depend on the developmental stage during which exercise is initiated. PMID:26016739

Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients.

PubMed

Fierer, Noah; Lauber, Christian L; Ramirez, Kelly S; Zaneveld, Jesse; Bradford, Mark A; Knight, Rob

2012-05-01

Terrestrial ecosystems are receiving elevated inputs of nitrogen (N) from anthropogenic sources and understanding how these increases in N availability affect soil microbial communities is critical for predicting the associated effects on belowground ecosystems. We used a suite of approaches to analyze the structure and functional characteristics of soil microbial communities from replicated plots in two long-term N fertilization experiments located in contrasting systems. Pyrosequencing-based analyses of 16S rRNA genes revealed no significant effects of N fertilization on bacterial diversity, but significant effects on community composition at both sites; copiotrophic taxa (including members of the Proteobacteria and Bacteroidetes phyla) typically increased in relative abundance in the high N plots, with oligotrophic taxa (mainly Acidobacteria) exhibiting the opposite pattern. Consistent with the phylogenetic shifts under N fertilization, shotgun metagenomic sequencing revealed increases in the relative abundances of genes associated with DNA/RNA replication, electron transport and protein metabolism, increases that could be resolved even with the shallow shotgun metagenomic sequencing conducted here (average of 75 000 reads per sample). We also observed shifts in the catabolic capabilities of the communities across the N gradients that were significantly correlated with the phylogenetic and metagenomic responses, indicating possible linkages between the structure and functioning of soil microbial communities. Overall, our results suggest that N fertilization may, directly or indirectly, induce a shift in the predominant microbial life-history strategies, favoring a more active, copiotrophic microbial community, a pattern that parallels the often observed replacement of K-selected with r-selected plant species with elevated N.

Colonization-Induced Host-Gut Microbial Metabolic Interaction

PubMed Central

Claus, Sandrine P.; Ellero, Sandrine L.; Berger, Bernard; Krause, Lutz; Bruttin, Anne; Molina, Jérôme; Paris, Alain; Want, Elizabeth J.; de Waziers, Isabelle; Cloarec, Olivier; Richards, Selena E.; Wang, Yulan; Dumas, Marc-Emmanuel; Ross, Alastair; Rezzi, Serge; Kochhar, Sunil; Van Bladeren, Peter; Lindon, John C.; Holmes, Elaine; Nicholson, Jeremy K.

2011-01-01

The gut microbiota enhances the host’s metabolic capacity for processing nutrients and drugs and modulate the activities of multiple pathways in a variety of organ systems. We have probed the systemic metabolic adaptation to gut colonization for 20 days following exposure of axenic mice (n = 35) to a typical environmental microbial background using high-resolution 1H nuclear magnetic resonance (NMR) spectroscopy to analyze urine, plasma, liver, kidney, and colon (5 time points) metabolic profiles. Acquisition of the gut microbiota was associated with rapid increase in body weight (4%) over the first 5 days of colonization with parallel changes in multiple pathways in all compartments analyzed. The colonization process stimulated glycogenesis in the liver prior to triggering increases in hepatic triglyceride synthesis. These changes were associated with modifications of hepatic Cyp8b1 expression and the subsequent alteration of bile acid metabolites, including taurocholate and tauromuricholate, which are essential regulators of lipid absorption. Expression and activity of major drug-metabolizing enzymes (Cyp3a11 and Cyp2c29) were also significantly stimulated. Remarkably, statistical modeling of the interactions between hepatic metabolic profiles and microbial composition analyzed by 16S rRNA gene pyrosequencing revealed strong associations of the Coriobacteriaceae family with both the hepatic triglyceride, glucose, and glycogen levels and the metabolism of xenobiotics. These data demonstrate the importance of microbial activity in metabolic phenotype development, indicating that microbiota manipulation is a useful tool for beneficially modulating xenobiotic metabolism and pharmacokinetics in personalized health care. PMID:21363910

Enhancing antioxidant activity, microbial and sensory quality of mango (Mangifera indica L.) juice by γ-irradiation and its in vitro radioprotective potential.

PubMed

Naresh, Kondapalli; Varakumar, Sadineni; Variyar, Prasad Shekhar; Sharma, Arun; Reddy, Obulam Vijaya Sarathi

2015-07-01

Gamma irradiation is an effective method currently being used for microbial decontamination and insect disinfestations of foods. In the present study, mango (Mangifera indica L.) juice was irradiated at doses of 0, 1.0, 3.0 and 5.0 kGy and microbial load, total polyphenols, flavonoids, ascorbic acid content, antioxidant activities, colour and sensory properties were evaluated immediately after irradiation and also during storage. Microbiological assay of the fresh and stored mango juice showed better quality after γ-irradiation. The total polyphenols and flavonoids were significantly (p < 0.05) increased while the ascorbic acid content decreased with the irradiation doses applied. As a result of γ-irradiation, a significant increment in gallic, syringic and chlorogenic acids and a significant reduction in ferulic and synapic acids were noted when analyzed by HPLC. In vitro antioxidant potentials were measured using DPPH, FRAP and NO scavenging assays; the results showed significant enhancement in the activities after irradiation, that correlated well with the increase in phenolic and flavonoid content. γ-irradiation improved the colour of mango juice without any adverse changes in the sensory qualities. Significant in vitro plasmid DNA protection was observed in the presence of mango juice against radiation induced damage, even at the dose of 5 kGy. This study confirmed the potential of γ-irradiation as a method for microbial decontamination and improving the quality of the mango juice without compromising on the sensory attributes.

Impact of Microbial Growth on Subsurface Perfluoroalkyl Acid Transport

NASA Astrophysics Data System (ADS)

Weathers, T. S.; Higgins, C. P.; Sharp, J.

2014-12-01

The fate and transport of poly and perfluoroalkyl substances (PFASs) in the presence of active microbial communities has not been widely investigated. These emerging contaminants are commonly utilized in aqueous film-forming foams (AFFF) and have often been detected in groundwater. This study explores the transport of a suite of perfluorocarboxylic acids and perfluoroalkylsulfonates, including perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS), in microbially active settings. Single point organic carbon normalized sorption coefficients derived by exposing inactive cellular material to PFASs result in more than an order of magnitude increase in sorption compared to soil organic carbon sorption coefficients found in literature. For example, the sorption coefficients for PFOS are 4.05±0.07 L/kg and 2.80±0.08 L/kg for cellular organic carbon and soil organic carbon respectively. This increase in sorption, coupled with enhanced extracellular polymeric substance production observed during growth of a common hydrocarbon degrading soil microbe exposed to source-level concentrations of PFASs (10 mg/L of 11 analytes, 110 mg/L total) may result in PFAS retardation in situ. To address the upscaling of this phenomenon, flow-through columns packed with low-organic carbon sediment and biostimulated with 10 mg/L glucose were exposed to PFAS concentrations from 15 μg/L to 10 mg/L of each 11 analytes. Breakthrough and tailing of each analyte was measured and modeled with Hydrus-1D to explore sorption coefficients over time for microbially active columns.

Deciphering biodegradable chelant-enhanced phytoremediation through microbes and nitrogen transformation in contaminated soils.

PubMed

Fang, Linchuan; Wang, Mengke; Cai, Lin; Cang, Long

2017-06-01

Biodegradable chelant-enhanced phytoremediation offers an alternative treatment technique for metal contaminated soils, but most studies to date have addressed on phytoextraction efficiency rather than comprehensive understanding of the interactions among plant, soil microbes, and biodegradable chelants. In the present study, we investigated the impacts of biodegradable chelants, including nitrilotriacetate, S,S-ethylenediaminedisuccinic acid (EDDS), and citric acid on soil microbes, nitrogen transformation, and metal removal from contaminated soils. The EDDS addition to soil showed the strongest ability to promote the nitrogen cycling in soil, ryegrass tissue, and microbial metabolism in comparison with other chelants. Both bacterial community-level physiological profiles and soil mass specific heat rates demonstrated that soil microbial activity was inhibited after the EDDS application (between day 2 and 10), but this effect completely vanished on day 30, indicating the revitalization of microbial activity and community structure in the soil system. The results of quantitative real-time PCR revealed that the EDDS application stimulated denitrification in soil by increasing nitrite reductase genes, especially nirS. These new findings demonstrated that the nitrogen release capacity of biodegradable chelants plays an important role in accelerating nitrogen transformation, enhancing soil microbial structure and activity, and improving phytoextraction efficiency in contaminated soil.

Response of rhizosphere microbial community structure and diversity to heavy metal co-pollution in arable soil.

PubMed

Deng, Linjing; Zeng, Guangming; Fan, Changzheng; Lu, Lunhui; Chen, Xunfeng; Chen, Ming; Wu, Haipeng; He, Xiaoxiao; He, Yan

2015-10-01

Due to the emerging environmental issues related to heavy metals, concern about the soil quality of farming lands near manufacturing district is increasing. Investigating the function of soil microorganisms exposed to long-term heavy metal contamination is meaningful and important for agricultural soil utilization. This article studied the potential influence of several heavy metals on microbial biomass, activity, abundance, and community composition in arable soil near industrial estate in Zhuzhou, Hunan province, China. The results showed that soil organic contents (SOC) were significantly positive correlated with heavy metals, whereas dehydrogenase activity (DHA) was greatly depressed by the heavy metal stress. Negative correlation was found between heavy metals and basal soil respiration (BSR), and no correlation was found between heavy metals and microbial biomass content (MBC). The quantitative PCR (QPCR) and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis could suggest that heavy metal pollution has significantly decreased abundance of bacteria and fungi and also changed their community structure. The results could contribute to evaluate heavy metal pollution level in soil. By combining different environmental parameters, it would promote the better understanding of heavy metal effect on the size, structure, and activity of microbial community in arable soil.

Carbon input increases microbial nitrogen demand, but not microbial nitrogen mining in boreal forest soils

NASA Astrophysics Data System (ADS)

Wild, Birgit; Alaei, Saeed; Bengtson, Per; Bodé, Samuel; Boeckx, Pascal; Schnecker, Jörg; Mayerhofer, Werner; Rütting, Tobias

2016-04-01

Plant primary production at mid and high latitudes is often limited by low soil N availability. It has been hypothesized that plants can indirectly increase soil N availability via root exudation, i.e., via the release of easily degradable organic compounds such as sugars into the soil. These compounds can stimulate microbial activity and extracellular enzyme synthesis, and thus promote soil organic matter (SOM) decomposition ("priming effect"). Even more, increased C availability in the rhizosphere might specifically stimulate the synthesis of enzymes targeting N-rich polymers such as proteins that store most of the soil N, but are too large for immediate uptake ("N mining"). This effect might be particularly important in boreal forests, where plants often maintain high primary production in spite of low soil N availability. We here tested the hypothesis that increased C availability promotes protein depolymerization, and thus soil N availability. In a laboratory incubation experiment, we added 13C-labeled glucose to a range of soil samples derived from boreal forests across Sweden, and monitored the release of CO2 by C mineralization, distinguishing between CO2 from the added glucose and from the native, unlabeled soil organic C (SOC). Using a set of 15N pool dilution assays, we further measured gross rates of protein depolymerization (the breakdown of proteins into amino acids) and N mineralization (the microbial release of excess N as ammonium). Comparing unamended control samples, we found a high variability in C and N mineralization rates, even when normalized by SOC content. Both C and N mineralization were significantly correlated to SOM C/N ratios, with high C mineralization at high C/N and high N mineralization at low C/N, suggesting that microorganisms adjusted C and N mineralization rates to the C/N ratio of their substrate and released C or N that was in excess. The addition of glucose significantly stimulated the mineralization of native SOC in soils where C availability was initially low, but this priming effect was not linked to increased gross protein depolymerization rates. Similarly, we found no connection to increased activities of enzymes targeting N-containing polymers such as proteins or chitin. Instead, glucose addition increased the microbial efficiency to use the N already available, as indicated by lower gross N mineralization rates and lower concentrations of inorganic N in the soil. We emphasize that these findings do not generally preclude that higher C availability can induce microbial N mining and thus enhance soil N availability in some soils, but that such an effect cannot be universally assumed. In contrast, the changes in microbial N dynamics observed across our range of boreal forest soils suggest that higher C availability can at least in some soils increase N storage within microbial bio- and necromass, thus reducing N availability for plants, but also constraining soil N losses, e.g., by nitrate leaching and denitrification.

High concentrations of single-walled carbon nanotubes lower soil enzyme activity and microbial biomass.

PubMed

Jin, Lixia; Son, Yowhan; Yoon, Tae Kyung; Kang, Yu Jin; Kim, Woong; Chung, Haegeun

2013-02-01

Nanomaterials such as single-walled carbon nanotubes (SWCNTs) may enter the soil environment with unknown consequences resulting from the development of nanotechnology for a variety of applications. We determined the effects of SWCNTs on soil enzyme activity and microbial biomass through a 3-week incubation of urban soils treated with different concentrations of SWCNTs ranging from 0 to 1000 μg g(-1) soil. The activities of cellobiohydrolase, β-1,4-glucosidase, β-1,4-xylosidase, β-1,4-N-acetylglucosaminidase, L-leucine aminopeptidase, and acid phosphatase and microbial biomass were measured in soils treated with powder and suspended forms of SWCNTs. SWCNTs of concentrations at 300-1000 μg g(-1) soil significantly lowered activities of most enzymes and microbial biomass. It is noteworthy that the SWCNTs showed similar effects to that of multi-walled carbon nanotubes (MWCNTs), but at a concentration approximately 5 times lower; we suggest that this is mainly due to the higher surface area of SWCNTs than that of MWCNTs. Indeed, our results show that surface area of CNTs has significant negative relationship with relative enzyme activity and biomass, which suggests that greater microorganism-CNT interactions could increase the negative effect of CNTs on microorganisms. Current work may contribute to the preparation of a regulatory guideline for the release of CNTs to the soil environment. Copyright © 2012 Elsevier Inc. All rights reserved.

Effect of three typical sulfide mineral flotation collectors on soil microbial activity.

PubMed

Guo, Zunwei; Yao, Jun; Wang, Fei; Yuan, Zhimin; Bararunyeretse, P; Zhao, Yue

2016-04-01

The sulfide mineral flotation collectors are wildly used in China, whereas their toxic effect on soil microbial activity remains largely unexplored. In this study, isothermal microcalorimetric technique and soil enzyme assay techniques were employed to investigate the toxic effect of typical sulfide mineral flotation collectors on soil microbial activity. Soil samples were treated with different concentrations (0-100 μg•g - 1 soil) of butyl xanthate, butyl dithiophosphate, and sodium diethyldithiocarbamate. Results showed a significant adverse effect of butyl xanthate (p < 0.05), butyl dithiophosphate, and sodium diethyldithiocarbamate (p < 0.01) on soil microbial activity. The growth rate constants k decreased along with the increase of flotation collectors concentration from 20.0 to 100.0 μg•g(-1). However, the adverse effects of these three floatation collectors showed significant difference. The IC 20 of the investigated flotation reagents followed such an order: IC 20 (butyl xanthate) > IC 20 (sodium diethyldithiocarbamate) > IC 20 (butyl dithiophosphate) with their respective inhibitory concentration as 47.03, 38.36, and 33.34 μg•g(-1). Besides, soil enzyme activities revealed that these three flotation collectors had an obvious effect on fluorescein diacetate hydrolysis (FDA) enzyme and catalase (CAT) enzyme. The proposed methods can provide meaningful toxicological information of flotation reagents to soil microbes in the view of metabolism and biochemistry, which are consistent and correlated to each other.

[Effects of re-vegetation on soil microbial functional diversity in purple soils at different re-vegetation stages on sloping-land in Hengyang, Hunan Province, China.

PubMed

Wen, Dong Xin; Yang, Ning; Yang, Man Yuan

2016-08-01

The aim of the study was to explore the effects of re-vegetation on soil microbial functio-nal diversity in purple soils at different re-vegetation stages on sloping-land in Hengyang, Hunan Province, China. By using the spatial series to replace time series, four typical sampling plots, grass (Setaria viridi, GS), frutex and grass (Lagerstroemia indica-Setaria viridi, FG), frutex (Vitex negundo var. cannabifolia+Robinia pseudoacacia, FX), as well as arbor and frutex (Liquidamdar formosana+Melia azedarach-Vitex negundo var. cannabifolia, AF) community were selected to study the soil microbial functional diversity by using the Biolog-ECO micro-plate technique. The four communities in purple soils on sloping-land were similar and denoted four different re-vegetation stages. The results showed that the soil microbial metabolic activity increased after re-vegetation significantly, and the average well color development (AWCD) which represented soil microbial activity and functional diversity followed the order of AF community＞FX community＞FG community＞GS community at different re-vegetation stages, and followed the order of 0-10 cm ＞10-20 cm in different soil layers. Principal component analysis (PCA) identified that FG and FX community had similar C sources utilization mode and metabolic function, and GS and AF community were diffe-rent. The carbohydrates, amino acids, intermediate metabolites, and secondary metabolites were the main carbon sources separating the two principal component factors. The Shannon species richness index (H), Shannon evenness index (E), Simpson dominance index (D), McIntosh index (U) at four re-vegetation stages were the highest in AF community, the second in FG and FX community, and the lowest in GS community. The results of correlation analysis indicated that the content of soil water content (SWC), soil total organic carbon (STOC), total nitrogen (TN), total phospho-rus (TP) and available phosphorus (AP) had important influence on the soil microbial metabolic function and functional diversity indices. There existed significant correlation between the activities of urease (URE), alk-phosphatase (APE), invertase (INV), catalase (CAT) and the soil microbial metabolic function and functional diversity indices. All the results indicated that re-vegetation could enhance the soil microbial metabolic function, which was beneficial to the reproduction of soil micro-organisms, thereby promoting an increase of soil carbon source utilization intensity.

Enhanced sulfide removal and bioelectricity generation in microbial fuel cells with anodes modified by vertically oriented nanosheets.

PubMed

Yang, Meng; Zhong, Yuezhi; Zhang, Baogang; Shi, Jiaxin; Huang, Xueyang; Xing, Yi; Su, Lin; Liu, Huipeng; Borthwick, Alistair G L

2018-01-31

Anode materials and structures are of critical importance for microbial fuel cells (MFCs) recovering energy from toxic substrates. Carbon-fiber-felt anodes modified by layers of vertically oriented TiO 2 and Fe 2 O 3 nanosheets were applied in the present study. Enhanced sulfide removal efficiencies (both over 90%) were obtained after a 48-h operation, with maximum power densities improved by 1.53 and 1.36 folds compared with MFCs with raw carbon-fiber-felt anode. The modified anodes provided more active sites for microbial adhesion with increasing biomass densities. High-throughput 16S rRNA gene sequencing analysis also indicated the increase in microbial diversities. Bacteroidetes responsible for bioelectricity generation with Thiobacillus and Spirochaeta dominating sulfide removal were found in the MFCs with the modified anodes, with less anaerobic fermentative bacteria as Firmicutes appeared. This indicates that the proposed materials are competitive for applications of MFCs generating bioelectricity from toxic sulfide.

Social dynamics within decomposer communities lead to nitrogen retention and organic matter build-up in soils

PubMed Central

Kaiser, Christina; Franklin, Oskar; Richter, Andreas; Dieckmann, Ulf

2015-01-01

The chemical structure of organic matter has been shown to be only marginally important for its decomposability by microorganisms. The question of why organic matter does accumulate in the face of powerful microbial degraders is thus key for understanding terrestrial carbon and nitrogen cycling. Here we demonstrate, based on an individual-based microbial community model, that social dynamics among microbes producing extracellular enzymes (‘decomposers') and microbes exploiting the catalytic activities of others (‘cheaters') regulate organic matter turnover. We show that the presence of cheaters increases nitrogen retention and organic matter build-up by downregulating the ratio of extracellular enzymes to total microbial biomass, allowing nitrogen-rich microbial necromass to accumulate. Moreover, increasing catalytic efficiencies of enzymes are outbalanced by a strong negative feedback on enzyme producers, leading to less enzymes being produced at the community level. Our results thus reveal a possible control mechanism that may buffer soil CO2 emissions in a future climate. PMID:26621582

Microbial Adhesion and Biofilm Formation on Microfiltration Membranes: A Detailed Characterization Using Model Organisms with Increasing Complexity

PubMed Central

Vanysacker, L.; Denis, C.; Declerck, P.; Piasecka, A.; Vankelecom, I. F. J.

2013-01-01

Since many years, membrane biofouling has been described as the Achilles heel of membrane fouling. In the present study, an ecological assay was performed using model systems with increasing complexity: a monospecies assay using Pseudomonas aeruginosa or Escherichia coli separately, a duospecies assay using both microorganisms, and a multispecies assay using activated sludge with or without spiked P. aeruginosa. The microbial adhesion and biofilm formation were evaluated in terms of bacterial cell densities, species richness, and bacterial community composition on polyvinyldifluoride, polyethylene, and polysulfone membranes. The data show that biofouling formation was strongly influenced by the kind of microorganism, the interactions between the organisms, and the changes in environmental conditions whereas the membrane effect was less important. The findings obtained in this study suggest that more knowledge in species composition and microbial interactions is needed in order to understand the complex biofouling process. This is the first report describing the microbial interactions with a membrane during the biofouling development. PMID:23986906

Effects of water stress, organic amendment and mycorrhizal inoculation on soil microbial community structure and activity during the establishment of two heavy metal-tolerant native plant species.

PubMed

Fernández, D A; Roldán, A; Azcón, R; Caravaca, F; Bååth, E

2012-05-01

Our aim was to examine the effect of water stress on plant growth and development of two native plant species (Tetraclinis articulata and Crithmum maritimum) and on microbial community composition and activity in the rhizosphere soil, following the addition of an organic amendment, namely sugar beet residue (SBR), and/or the inoculation with an arbuscular mycorrhizal (AM) fungus, namely Glomus mosseae, in a non-sterile heavy metal-polluted soil. The AM inoculation did not have any significant effect on plant growth of both species. In T. articulata, SBR increased shoot growth, foliar P, total phospholipid fatty acids (PLFA), fungi-related PLFA, AM fungi-related neutral lipid fatty acid, bacterial gram-positive/gram-negative PLFA ratio and the β-glucosidase and dehydrogenase activities. SBR and AM inoculation increased phosphatase activity in T. articulata plants grown under drought conditions. In both plants, there was a synergistic effect between AM inoculation and SBR on mycorrhizal colonisation under drought conditions. In C. maritimum, the increase produced by the SBR on total amounts of PLFA, bacterial gram-positive-related PLFA and bacterial gram-negative-related PLFA was considerably higher under drought conditions. Our results suggest that the effectiveness of the amendment with regard to stimulating microbial communities and plant growth was largely limited by drought, particularly for plant species with a low degree of mycorrhizal colonisation.

Biochar in co-contaminated soil manipulates arsenic solubility and microbiological community structure, and promotes organochlorine degradation.

PubMed

Gregory, Samuel J; Anderson, Christopher W N; Camps-Arbestain, Marta; Biggs, Patrick J; Ganley, Austen R D; O'Sullivan, Justin M; McManus, Michael T

2015-01-01

We examined the effect of biochar on the water-soluble arsenic (As) concentration and the extent of organochlorine degradation in a co-contaminated historic sheep-dip soil during a 180-d glasshouse incubation experiment. Soil microbial activity, bacterial community and structure diversity were also investigated. Biochar made from willow feedstock (Salix sp) was pyrolysed at 350 or 550°C and added to soil at rates of 10 g kg-1 and 20 g kg-1 (representing 30 t ha-1 and 60 t ha-1). The isomers of hexachlorocyclohexane (HCH) alpha-HCH and gamma-HCH (lindane), underwent 10-fold and 4-fold reductions in concentration as a function of biochar treatment. Biochar also resulted in a significant reduction in soil DDT levels (P < 0.01), and increased the DDE:DDT ratio. Soil microbial activity was significantly increased (P < 0.01) under all biochar treatments after 60 days of treatment compared to the control. 16S amplicon sequencing revealed that biochar-amended soil contained more members of the Chryseobacterium, Flavobacterium, Dyadobacter and Pseudomonadaceae which are known bioremediators of hydrocarbons. We hypothesise that a recorded short-term reduction in the soluble As concentration due to biochar amendment allowed native soil microbial communities to overcome As-related stress. We propose that increased microbiological activity (dehydrogenase activity) due to biochar amendment was responsible for enhanced degradation of organochlorines in the soil. Biochar therefore partially overcame the co-contaminant effect of As, allowing for enhanced natural attenuation of organochlorines in soil.

Microbial factories for recombinant pharmaceuticals

PubMed Central

Ferrer-Miralles, Neus; Domingo-Espín, Joan; Corchero, José Luis; Vázquez, Esther; Villaverde, Antonio

2009-01-01

Most of the hosts used to produce the 151 recombinant pharmaceuticals so far approved for human use by the Food and Drug Administration (FDA) and/or by the European Medicines Agency (EMEA) are microbial cells, either bacteria or yeast. This fact indicates that despite the diverse bottlenecks and obstacles that microbial systems pose to the efficient production of functional mammalian proteins, namely lack or unconventional post-translational modifications, proteolytic instability, poor solubility and activation of cell stress responses, among others, they represent convenient and powerful tools for recombinant protein production. The entering into the market of a progressively increasing number of protein drugs produced in non-microbial systems has not impaired the development of products obtained in microbial cells, proving the robustness of the microbial set of cellular systems (so far Escherichia coli and Saccharomyces cerevisae) developed for protein drug production. We summarize here the nature, properties and applications of all those pharmaceuticals and the relevant features of the current and potential producing hosts, in a comparative way. PMID:19317892

Effect of probiotics (Saccharomyces boulardii) on microbial translocation and inflammation in HIV-treated patients: a double-blind, randomized, placebo-controlled trial.

PubMed

Villar-García, Judit; Hernández, Juan J; Güerri-Fernández, Robert; González, Alicia; Lerma, Elisabet; Guelar, Ana; Saenz, David; Sorlí, Lluisa; Montero, Milagro; Horcajada, Juan P; Knobel Freud, Hernando

2015-03-01

Microbial translocation has been associated with an increase in immune activation and inflammation in HIV infection despite effective highly active antiretroviral therapy. It has been shown that some probiotics have a beneficial effect by reducing intestinal permeability and, consequently, microbial translocation. To assess changes in microbial translocation and inflammation after treatment with probiotics (Saccharomyces boulardii) in HIV-1-infected patients with virologic suppression. A double-blind, randomized, placebo-controlled trial was conducted in 44 nonconsecutive HIV-1-infected patients with viral load of <20 copies per milliliter for at least 2 years. Patients were randomized to oral supplementation with probiotics or placebo during 12 weeks. Markers of microbial translocation (lipopolysaccharide-binding protein [LBP] and soluble CD14), inflammation (interleukin 6 [IL-6], tumor necrosis factor alpha, interferon gamma, high-sensitivity C-reactive protein), and immunological and clinical data were determined before and after the intervention and 3 months after treatment discontinuation. Quantitative variables were compared using the Mann-Whitney U test, and categorical variables were compared using the Fisher exact test. After 12 weeks of treatment, differences between the probiotic arm and the placebo arm were observed in LBP values (-0.30 vs +0.70 pg/mL) and IL-6 (-0.60 vs +0.78 pg/mL). These differences were also noted at 3 months after treatment withdrawal. Qualitative analysis was performed, defining a variable as "decreased" or "increased" from baseline LBP. A significant decrease of LBP at 12 weeks of treatment was observed (57.9% patients in the probiotic group vs 6.2% in the placebo group, P = 0.002). Treatment with S. boulardii decreases microbial translocation (LBP) and inflammation parameters (IL-6) in HIV-1-infected patients with long-term virologic suppression.

Influence of triethyl phosphate on phosphatase activity in shooting range soil: Isolation of a zinc-resistant bacterium with an acid phosphatase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Story, Sandra; Brigmon, Robin L.

Phosphatase-mediated hydrolysis of organic phosphate may be a viable means of stabilizing heavy metals via precipitation as a metal phosphate in bioremediation applications. We investigated the effect of triethyl phosphate (TEP) on soil microbial-phosphatase activity in a heavy-metal contaminated soil. Gaseous TEP has been used at subsurface sites for bioremediation of organic contaminants but not applied in heavy-metal contaminated areas. Little is known about how TEP affects microbial activity in soils and it is postulated that TEP can serve as a phosphate source in nutrient-poor groundwater and soil/sediments. Over a 3-week period, TEP amendment to microcosms containing heavy-metal contaminated soilmore » resulted in increased activity of soil acid-phosphatase and repression of alkaline phosphatase, indicating a stimulatory effect on the microbial population. A soil-free enrichment of microorganisms adapted to heavy-metal and acidic conditions was derived from the TEP-amended soil microcosms using TEP as the sole phosphate source and the selected microbial consortium maintained a high acid-phosphatase activity with repression of alkaline phosphatase. Addition of 5 mM zinc to soil-free microcosms had little effect on acid phosphatase but inhibited alkaline phosphatase. One bacterial member from the consortium, identified as Burkholderia cepacia sp., expressed an acid-phosphatase activity uninhibited by high concentrations of zinc and produced a soluble, indigo pigment under phosphate limitation. The pigment was produced in a phosphate-free medium and was not produced in the presence of TEP or phosphate ion, indicative of purple acid-phosphatase types that are pressed by bioavailable phosphate. Finally, these results demonstrate that TEP amendment was bioavailable and increased overall phosphatase activity in both soil and soil-free microcosms supporting the possibility of positive outcomes in bioremediation applications.« less

Influence of triethyl phosphate on phosphatase activity in shooting range soil: Isolation of a zinc-resistant bacterium with an acid phosphatase

DOE PAGES

Story, Sandra; Brigmon, Robin L.

2016-12-19

Phosphatase-mediated hydrolysis of organic phosphate may be a viable means of stabilizing heavy metals via precipitation as a metal phosphate in bioremediation applications. We investigated the effect of triethyl phosphate (TEP) on soil microbial-phosphatase activity in a heavy-metal contaminated soil. Gaseous TEP has been used at subsurface sites for bioremediation of organic contaminants but not applied in heavy-metal contaminated areas. Little is known about how TEP affects microbial activity in soils and it is postulated that TEP can serve as a phosphate source in nutrient-poor groundwater and soil/sediments. Over a 3-week period, TEP amendment to microcosms containing heavy-metal contaminated soilmore » resulted in increased activity of soil acid-phosphatase and repression of alkaline phosphatase, indicating a stimulatory effect on the microbial population. A soil-free enrichment of microorganisms adapted to heavy-metal and acidic conditions was derived from the TEP-amended soil microcosms using TEP as the sole phosphate source and the selected microbial consortium maintained a high acid-phosphatase activity with repression of alkaline phosphatase. Addition of 5 mM zinc to soil-free microcosms had little effect on acid phosphatase but inhibited alkaline phosphatase. One bacterial member from the consortium, identified as Burkholderia cepacia sp., expressed an acid-phosphatase activity uninhibited by high concentrations of zinc and produced a soluble, indigo pigment under phosphate limitation. The pigment was produced in a phosphate-free medium and was not produced in the presence of TEP or phosphate ion, indicative of purple acid-phosphatase types that are pressed by bioavailable phosphate. Finally, these results demonstrate that TEP amendment was bioavailable and increased overall phosphatase activity in both soil and soil-free microcosms supporting the possibility of positive outcomes in bioremediation applications.« less

Influence of triethyl phosphate on phosphatase activity in shooting range soil: Isolation of a zinc-resistant bacterium with an acid phosphatase.

PubMed

Story, Sandra; Brigmon, Robin L

2017-03-01

Phosphatase-mediated hydrolysis of organic phosphate may be a viable means of stabilizing heavy metals via precipitation as a metal phosphate in bioremediation applications. We investigated the effect of triethyl phosphate (TEP) on soil microbial-phosphatase activity in a heavy-metal contaminated soil. Gaseous TEP has been used at subsurface sites for bioremediation of organic contaminants but not applied in heavy-metal contaminated areas. Little is known about how TEP affects microbial activity in soils and it is postulated that TEP can serve as a phosphate source in nutrient-poor groundwater and soil/sediments. Over a 3-week period, TEP amendment to microcosms containing heavy-metal contaminated soil resulted in increased activity of soil acid-phosphatase and repression of alkaline phosphatase, indicating a stimulatory effect on the microbial population. A soil-free enrichment of microorganisms adapted to heavy-metal and acidic conditions was derived from the TEP-amended soil microcosms using TEP as the sole phosphate source and the selected microbial consortium maintained a high acid-phosphatase activity with repression of alkaline phosphatase. Addition of 5mM zinc to soil-free microcosms had little effect on acid phosphatase but inhibited alkaline phosphatase. One bacterial member from the consortium, identified as Burkholderia cepacia sp., expressed an acid-phosphatase activity uninhibited by high concentrations of zinc and produced a soluble, indigo pigment under phosphate limitation. The pigment was produced in a phosphate-free medium and was not produced in the presence of TEP or phosphate ion, indicative of purple acid-phosphatase types that are pressed by bioavailable phosphate. These results demonstrate that TEP amendment was bioavailable and increased overall phosphatase activity in both soil and soil-free microcosms supporting the possibility of positive outcomes in bioremediation applications. Copyright © 2016. Published by Elsevier Inc.

Potential microbial contamination during sampling of permafrost soil assessed by tracers

NASA Astrophysics Data System (ADS)

Bang-Andreasen, Toke; Schostag, Morten; Priemé, Anders; Elberling, Bo; Jacobsen, Carsten S.

2017-02-01

Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores.

Potential microbial contamination during sampling of permafrost soil assessed by tracers.

PubMed

Bang-Andreasen, Toke; Schostag, Morten; Priemé, Anders; Elberling, Bo; Jacobsen, Carsten S

2017-02-23

Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores.

Potential microbial contamination during sampling of permafrost soil assessed by tracers

PubMed Central

Bang-Andreasen, Toke; Schostag, Morten; Priemé, Anders; Elberling, Bo; Jacobsen, Carsten S.

2017-01-01

Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores. PMID:28230151

Study on distribution of reservoir endogenous microbe and oil displacement mechanism.

PubMed

Yue, Ming; Zhu, Weiyao; Song, Zhiyong; Long, Yunqian; Song, Hongqing

2017-02-01

In order to research oil displacement mechanism by indigenous microbial communities under reservoir conditions, indigenous microbial flooding experiments using the endogenous mixed bacterium from Shengli Oilfield were carried out. Through microscopic simulation visual model, observation and analysis of distribution and flow of the remaining oil in the process of water flooding and microbial oil displacement were conducted under high temperature and high pressure conditions. Research has shown that compared with atmospheric conditions, the growth of the microorganism metabolism and attenuation is slowly under high pressure conditions, and the existence of the porous medium for microbial provides good adhesion, also makes its growth cycle extension. The microbial activities can effectively launch all kinds of residual oil, and can together with metabolites, enter the blind holes off which water flooding, polymer flooding and gas flooding can't sweep, then swap out remaining oil, increase liquidity of the crude oil and remarkably improve oil displacement effect.

Priming effects and enzymatic activity in Israeli soils under treated wastewater and freshwater irrigation

NASA Astrophysics Data System (ADS)

Anissimova, Marina; Heinze, Stefanie; Chen, Yona; Tarchitzky, Jorge; Marschner, Bernd

2014-05-01

Irrigation of soils with treated wastewater (TWW) directly influences microbial processes of soil. TWW contains easily decomposable organic material, which can stimulate the activity of soil microorganisms and, as a result, lead to the excessive consumption of soil organic carbon pool. We investigated the effects of irrigation with TWW relative to those of irrigation with freshwater (FW) on the microbial parameters in soils with low (7%) and medium (13%) clay content in a lysimeter experiment. The objectives of our study were to (i) determine the impact of water quality on soil respiration and enzymatic activity influenced by clay content and depth, and (ii) work out the changes in the turnover of soil organic matter (PE, priming effects). Samples were taken from three soil depths (0-10, 10-20, and 40-60 cm). Soil respiration and PE were determined in a 21-days incubation experiment after addition of uniformly 14C-labeled fructose. Activity of 10 extracellular enzymes (EEA, from C-, N-, P-, and S-cycle), phenol oxidase and peroxidase activity (PO+PE), and dehydrogenase activity (DHA) were assayed. Microbial Community-Level Physiological Profiles (CLPP) using four substrates, and microbial biomass were determined. The results showed that the clay content acted as the main determinative factor. In the soil with low clay content the water quality had a greater impact: the highest PE (56%) was observed in the upper layer (0-10cm) under FW irrigation; EEA of C-, P-, and S-cycles was significantly higher in the upper soil layer under TWW irrigation. Microbial biomass was higher in the soil under TWW irrigation and decreased with increasing of depth (50 μg/g soil in the upper layer, 15 μg/g soil in the lowest layer). This tendency was also observed for DHA. Contrary to the low clay content, in the soil with medium clay content both irrigation types caused the highest PE in the lowest layer (65% under FW irrigation, 48% under TWW irrigation); the higher substrate mineralization (10%) and the highest phosphatase activity (in the case of FW irrigation) was observed. The PO+PE activity was two to three times higher than in the soil with low clay content and increased clearly with increasing of soil depth. The last tendency was also valid generally for the enzymes of C-, N-, and P-cycles under both types of irrigation. The upper layer in the soil under TWW irrigation was characterized by the highest microbial biomass value (74 μg/g soil). DHA in all soil depths under both types of irrigation was significantly higher than in the corresponding depths of soil with low clay content. CLPP data showed the highest consumption of ascorbic acid and D-glucosamine hydrochloride in comparison to consumption of D-glucose and L-glutamine in both irrigation types.

Evaluation of anti-microbial activities of ZnO, citric acid and a mixture of both against Propionibacterium acnes.

PubMed

Bae, J Y; Park, S N

2016-12-01

In this study, anti-microbial activities of ZnO of three different particle sizes of citric acid (CA) and of mixtures of ZnO and CA were confirmed against Propionibacterium acnes. ZnO with the smallest particle size showed relatively high anti-microbial activity by disc diffusion assay and broth macrodilution assay. The mixtures of ZnO and CA also showed relatively high anti-microbial activity when the particle size of ZnO was the smallest. Furthermore, anti-microbial activities of ZnO, CA and the mixtures of ZnO and CA were compared through the checkerboard assay. The results indicated that a 1 : 1 ratio of ZnO and CA resulted in the highest anti-microbial activity. The substances were confirmed to have synergic anti-microbial effects. With the time-kill curve assay, the mixture of ZnO-containing CA reduced the surviving microbial content the most after 24 h. The results of our study suggest that ZnO may not only be an anti-microbial ingredient for the prevention of and treatment of acne. The results of our study suggest that ZnO may be an anti-microbial ingredient for the prevention of and treatment of acne when mixed with CA. © 2016 Society of Cosmetic Scientists and the Société Française de Cosmétologie.

Methanogenic and Sulfate-Reducing Activities in a Hypersaline Microbial Mat and Associated Microbial Diversity.

PubMed

Cadena, Santiago; García-Maldonado, José Q; López-Lozano, Nguyen E; Cervantes, Francisco J

2018-05-01

Methanogenesis and sulfate reduction are important microbial processes in hypersaline environments. However, key aspects determining substrate competition between these microbial processes have not been well documented. We evaluated competitive and non-competitive substrates for stimulation of both processes through microcosm experiments of hypersaline microbial mat samples from Guerrero Negro, Baja California Sur, Mexico, and we assessed the effect of these substrates on the microbial community composition. Methylotrophic methanogenesis evidenced by sequences belonging to methanogens of the family Methanosarcinaceae was found as the dominant methanogenic pathway in the studied hypersaline microbial mat. Nevertheless, our results showed that incubations supplemented with acetate and lactate, performed in absence of sulfate, also produced methane after 40 days of incubation, apparently driven by hydrogenotrophic methanogens affiliated to the family Methanomicrobiaceae. Sulfate reduction was mainly stimulated by addition of acetate and lactate; however, after 40 days of incubation, an increase of the H 2 S concentrations in microcosms amended with trimethylamine and methanol was also observed, suggesting that these substrates are putatively used for sulfate reduction. Moreover, 16S rRNA gene sequencing analysis showed remarkable differences in the microbial community composition among experimental treatments. In the analyzed sample amended with acetate, sulfate-reducing bacteria (SRB) belonging to the family Desulfobacteraceae were dominant, while members of Desulfohalobiaceae, Desulfomicrobiaceae, and Desulfovibrionaceae were found in the incubation with lactate. Additionally, we detected an unexpected high abundance of unclassified Hydrogenedentes (near 25%) in almost all the experimental treatments. This study contributes to better understand methanogenic and sulfate-reducing activities, which play an important role in the functioning of hypersaline environments.

Response of the microbial community structure of biofilms to ferric iron in microbial fuel cells.

PubMed

Liu, Qian; Yang, Yang; Mei, Xiaoxue; Liu, Bingfeng; Chen, Chuan; Xing, Defeng

2018-08-01

Ferric iron can affect the current generation of microbial electrochemical system (MES); however, how it influences microbial biofilm formation and metabolic activity has not been reported. Here, we describe the response of microbial electrode biofilm communities to insoluble ferric iron (Fe 3+ ) at different concentrations in microbial fuel cells (MFCs). Insoluble ferric iron (200μM) improved electrochemical activity of the MFCs microbial biofilms during start-up and resulted in a higher maximum power density of 0.95W/m 2 , compared with the control (0.76W/m 2 ), 500μM Fe 3+ (0.83W/m 2 ), 1000μM Fe 3+ (0.73W/m 2 ), and 2000μM Fe 3+ (0.59W/m 2 ) treatments. Illumina Hiseq sequencing of 16S rRNA gene amplicons indicated that the predominant populations in the anode biofilms of the MFCs belonged to Geobacter, with relative abundance of 66-75%. Microbial cathode biofilm communities were more susceptible to Fe 3+ , as an obvious shift in the cathode biofilm community structures occurred as Fe 3+ concentration was increased. The most predominant populations in the MFC cathode biofilms without Fe 3+ and with 200μM Fe 3+ were affiliated with Thauera (46% and 35%), whereas no absolutely predominant populations were present in the MFC cathode biofilm with 1000μM Fe 3+ . The results demonstrate that a low concentration of Fe 3+ facilitated the power output of MFCs and shaped community structures of the electrode biofilm. Copyright © 2018 Elsevier B.V. All rights reserved.

Invited review: Essential oils as modifiers of rumen microbial fermentation.

PubMed

Calsamiglia, S; Busquet, M; Cardozo, P W; Castillejos, L; Ferret, A

2007-06-01

Microorganisms in the rumen degrade nutrients to produce volatile fatty acids and synthesize microbial protein as an energy and protein supply for the ruminant, respectively. However, this fermentation process has energy (losses of methane) and protein (losses of ammonia N) inefficiencies that may limit production performance and contribute to the release of pollutants to the environment. Antibiotic ionophores have been very successful in reducing these energy and protein losses in the rumen, but the use of antibiotics in animal feeds is facing reduced social acceptance, and their use has been banned in the European Union since January 2006. For this reason, scientists have become interested in evaluating other alternatives to control specific microbial populations to modulate rumen fermentation. Essential oils can interact with microbial cell membranes and inhibit the growth of some gram-positive and gram-negative bacteria. As a result of such inhibition, the addition of some plant extracts to the rumen results in an inhibition of deamination and methanogenesis, resulting in lower ammonia N, methane, and acetate, and in higher propionate and butyrate concentrations. Results have indicated that garlic oil, cinnamaldehyde (the main active component of cinnamon oil), eugenol (the main active component of the clove bud), capsaicin (the active component of hot peppers), and anise oil, among others, may increase propionate production, reduce acetate or methane production, and modify proteolysis, peptidolysis, or deamination in the rumen. However, the effects of some of these essential oils are pH and diet dependent, and their use may be beneficial only under specific conditions and production systems. For example, capsaicin appears to have small effects in high-forage diets, whereas the changes observed in high-concentrate diets (increases in dry matter intake and total VFA, and reduction in the acetateto-propionate ratio and ammonia N concentration) may be beneficial. Because plant extracts may act at different levels in the carbohydrate and protein degradation pathways, their careful selection and combination may provide a useful tool to manipulate rumen microbial fermentation effectively. However, additional research is required to establish the optimal dose in vivo in units of the active component, to consider the potential adaptation of microbial populations to their activities, to examine the presence of residues in the products (milk or meat), and to demonstrate improvements in animal performance.

How do microlocal environmental variations affect microbial activities of a Pinus halepensis litter in a Mediterranean coastal area?

PubMed

Qasemian, Leila; Guiral, Daniel; Farnet, Anne-Marie

2014-10-15

Mediterranean coastal ecosystems suffer many different types of natural and anthropogenic environmental pressure. Microbial communities, major conductors of organic matter decomposition are also subject to these environmental constraints. In this study, our aim was to understand how microbial activities vary at a small spatio-temporal scale in a Mediterranean coastal environment. Microbial activities were monitored in a Pinus halepensis litter collected from two areas, one close to (10 m) and one far from (300 m) the French Mediterranean coast. Litters were transferred from one area to the other using litterbags and studied via different microbial indicators after 2, 5 and 13 months. Microbial Basal Respiration, qCO₂, certain enzyme activities (laccase, cellulase, β-glucosidase and acid phosphatase) and functional diversity via Biolog microplates were assayed in litterbags left in the area of origin as well as in litterbags transferred from one area to the other. Results highlight that microbial activities differ significantly in this short spatial scale over time. The influence of microlocal conditions more intensified for litters situated close to the sea, especially during summer seems to have a stressful effect on microbial communities, leading to less efficient functional activities. However, microbial activities were more strongly influenced by temporal variations linked to seasonality than by location. Copyright © 2014 Elsevier B.V. All rights reserved.

Impacts of shallow geothermal energy production on redox processes and microbial communities.

PubMed

Bonte, Matthijs; Röling, Wilfred F M; Zaura, Egija; van der Wielen, Paul W J J; Stuyfzand, Pieter J; van Breukelen, Boris M

2013-12-17

Shallow geothermal systems are increasingly being used to store or harvest thermal energy for heating or cooling purposes. This technology causes temperature perturbations exceeding the natural variations in aquifers, which may impact groundwater quality. Here, we report the results of laboratory experiments on the effect of temperature variations (5-80 °C) on redox processes and associated microbial communities in anoxic unconsolidated subsurface sediments. Both hydrochemical and microbiological data showed that a temperature increase from 11 °C (in situ) to 25 °C caused a shift from iron-reducing to sulfate-reducing and methanogenic conditions. Bioenergetic calculations could explain this shift. A further temperature increase (>45 °C) resulted in the emergence of a thermophilic microbial community specialized in fermentation and sulfate reduction. Two distinct maxima in sulfate reduction rates, of similar orders of magnitude (5 × 10(-10) M s(-1)), were observed at 40 and 70 °C. Thermophilic sulfate reduction, however, had a higher activation energy (100-160 kJ mol(-1)) than mesophilic sulfate reduction (30-60 kJ mol(-1)), which might be due to a trade-off between enzyme stability and activity with thermostable enzymes being less efficient catalysts that require higher activation energies. These results reveal that while sulfate-reducing functionality can withstand a substantial temperature rise, other key biochemical processes appear more temperature sensitive.

Dissolved organic carbon leaching from plastics stimulates microbial activity in the ocean.

PubMed

Romera-Castillo, Cristina; Pinto, Maria; Langer, Teresa M; Álvarez-Salgado, Xosé Antón; Herndl, Gerhard J

2018-04-12

Approximately 5.25 trillion plastic pieces are floating at the sea surface. The impact of plastic pollution on the lowest trophic levels of the food web, however, remains unknown. Here we show that plastics release dissolved organic carbon (DOC) into the ambient seawater stimulating the activity of heterotrophic microbes. Our estimates indicate that globally up to 23,600 metric tons of DOC are leaching from marine plastics annually. About 60% of it is available to microbial utilization in less than 5 days. If exposed to solar radiation, however, this DOC becomes less labile. Thus, plastic pollution of marine surface waters likely alters the composition and activity of the base of the marine food webs. It is predicted that plastic waste entering the ocean will increase by a factor of ten within the next decade, resulting in an increase in plastic-derived DOC that might have unaccounted consequences for marine microbes and for the ocean system.

Microbial communities and soil fertility in flood irrigated orchards under different management systems in eastern spain

NASA Astrophysics Data System (ADS)

Morugán-Coronado, Alicia; García-Orenes, Fuensanta; Caravaca, Fuensanta; Roldán, Antonio

2016-04-01

Unsuitable land management such as the excessive use of herbicides can lead to a loss of soil fertility and a drastic reduction in the abundance of microbial populations and their functions related to nutrient cycling. Microbial communities are the most sensitive and rapid indicators of perturbations in agroecosystems. A field experiment was performed in an orange-trees orchard (Citrus sinensis) to assess the long-term effect of three different management systems on the soil microbial community biomass, structure and composition (phospholipid fatty acids (PLFAs) total, pattern, and abundance). The three agricultural systems assayed were established 30 years ago: herbicides (Glyphosate (N-(phosphonomethyl)glycine) with inorganic fertilizers (H), intensive ploughing and inorganic fertilizers (NPK 15%) (P) and organic farming (chipped pruned branches and weeds, manure from sheep and goats) (O). Nine soil samples were taken from each system. The results showed that the management practices including herbicides and intensive ploughing had similar results on soil microbial properties, while organic fertilization significantly increased microbial biomass, shifted the structure and composition of the soil microbial community, and stimulated microbial activity, when compared to inorganic fertilization systems; thus, enhancing the sustainability of this agroecosystem under semiarid conditions.

Growth rates of rhizosphere microorganisms depend on competitive abilities of plants for nitrogen

NASA Astrophysics Data System (ADS)

Blagodatskaya, Evgenia; Littschwager, Johanna; Lauerer, Marianna; Kuzyakov, Yakov

2010-05-01

Rhizosphere - one of the most important ‘hot spots' in soil - is characterized not only by accelerated turnover of microbial biomass and nutrients but also by strong intra- and inter-specific competition. Intra-specific competition occurs between individual plants of the same species, while inter-specific competition can occur both at population level (plant species-specific, microbial species-specific interactions) and at community level (plant - microbial interactions). Such plant - microbial interactions are mainly governed by competition for available N sources, since N is one of the main growth limiting nutrients in natural ecosystems. Functional structure and activity of microbial community in rhizosphere is not uniform and is dependent on quantity and quality of root exudates which are plant specific. It is still unclear how microbial growth and turnover in the rhizosphere are dependent on the features and competitive abilities of plants for N. Depending on C and N availability, acceleration and even retardation of microbial activity and carbon mineralization can be expected in the rhizosphere of plants with high competitive abilities for N. We hypothesized slower microbial growth rates in the rhizosphere of plants with smaller roots, as they usually produce less exudates compared to plants with small shoot-to-root ratio. As the first hypothesis is based solely on C availability, we also expected the greater effect of N availability on microbial growth in rhizosphere of plants with smaller root mass. These hypothesis were tested for two plant species of strawberry: Fragaria vesca L. (native species), and Duchesnea indica (Andrews) Focke (an invasive plant in central Europe) growing in intraspecific and interspecific competition. Microbial biomass and the kinetic parameters of microbial growth in the rhizosphere were estimated by dynamics of CO2 emission from the soil amended with glucose and nutrients. Specific growth rate (µ) of soil microorganisms was estimated by fitting the parameters of the equation: CO2(t) = A + B × exp(µ×t), to the measured CO2 production rate (CO2(t)) after glucose addition, where A is the initial respiration rate uncoupled from ATP production, B the initial rate of the growing fraction of total respiration coupled with ATP generation and cell growth, and t time. Our study revealed the linkage between growth strategies of rhizosphere microorganisms and different adaptation strategies of F. vesca and D. indica to N limitation. Plant - strong competitor for N (D. indica) did not change root mass under N limitation causing the deficit of N in the rhizosphere and altering the structure of rhizosphere microbial community. Benefiting of slow growing microorganisms with K-strategy under N limiting conditions was indicated by strong decrease in specific microbial growth rates in the rhizosphere of D. indica. Root mass of the plant with weak competitive abilities for N (F. vesca) increased under lack of N to compensate the lack of nutrients. The increase in root mass and possible increase in amount of root exudates coincided with no structural changes in microbial community in rhizosphere of F. vesca. By intraspecific competition at low N level a 2.4-fold slower microbial specific growth rates were observed under D. indica (0.09 h-1) characterized by smaller root biomass and lower N content in roots compared with F. vesca. The generation time of actively growing microbial biomass was for the 6 hours longer in rhizosphere of D. indica than under F. vesca (10.7 to 4.6 h, respectively). Thus, under N limitation the strong competition for N between plant and microorganisms decreased microbial growth rates and carbon turnover in rhizosphere. By interspecific competition of both plants at low N level, microbial growth rates were similar to those for D. indica indicating that plant with stronger competitive abilities for N controls microbial community in the rhizosphere. At high N availability the root biomass did not differ significantly between both plants. This resulted in similar microbial growth rates for intra- and interspecific plant competition. Since high N level smoothed the differences between plant species in root and microbial biomass as well as in microbial growth rates, we conclude that competitive abilities of plant species were responsible for microbial growth in rhizosphere only under N imitation. As it is common that fine root proliferation and root exudation decrease at high N level, N addition smoothed the differences in microbial growth independently on plant competitive abilities.

Microbial Community Structure and Enzyme Activities in Semiarid Agricultural Soils

NASA Astrophysics Data System (ADS)

Acosta-Martinez, V. A.; Zobeck, T. M.; Gill, T. E.; Kennedy, A. C.

2002-12-01

The effect of agricultural management practices on the microbial community structure and enzyme activities of semiarid soils of different textures in the Southern High Plains of Texas were investigated. The soils (sandy clay loam, fine sandy loam and loam) were under continuous cotton (Gossypium hirsutum L.) or in rotations with peanut (Arachis hypogaea L.), sorghum (Sorghum bicolor L.) or wheat (Triticum aestivum L.), and had different water management (irrigated or dryland) and tillage (conservation or conventional). Microbial community structure was investigated using fatty acid methyl ester (FAME) analysis by gas chromatography and enzyme activities, involved in C, N, P and S cycling of soils, were measured (mg product released per kg soil per h). The activities of b-glucosidase, b-glucosaminidase, alkaline phosphatase, and arylsulfatase were significantly (P<0.05) increased in soils under cotton rotated with sorghum or wheat, and due to conservation tillage in comparison to continuous cotton under conventional tillage. Principal component analysis showed FAME profiles of these soils separated distinctly along PC1 (20 %) and PC2 (13 %) due to their differences in soil texture and management. No significant differences were detected in FAME profiles due to management practices for the same soils in this sampling period. Enzyme activities provide early indications of the benefits in microbial populations and activities and soil organic matter under crop rotations and conservation tillage in comparison to the typical practices in semiarid regions of continuous cotton and conventional tillage.

Profiling microbial lignocellulose degradation and utilization by emergent omics technologies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rosnow, Joshua J.; Anderson, Lindsey N.; Nair, Reji N.

2016-07-20

The use of plant materials to generate renewable biofuels and other high-value chemicals is the sustainable and preferable option, but will require considerable improvements to increase the rate and efficiency of lignocellulose depolymerization. This review highlights novel and emergent technologies that are being developed and deployed to characterize the process of lignocellulose degradation. The review will also illustrate how microbial communities deconstruct and metabolize lignocellulose by identifying the necessary genes and enzyme activities along with the reaction products. These technologies include multi-omic measurements, cell sorting and isolation, nuclear magnetic resonance spectroscopy (NMR), activity-based protein profiling, and direct measurement of enzymemore » activity. The recalcitrant nature of lignocellulose necessitates the need to characterize the methods microbes employ to deconstruct lignocellulose to inform new strategies on how to greatly improve biofuel conversion processes. New technologies are yielding important insights into microbial functions and strategies employed to degrade lignocellulose, providing a mechanistic blueprint to advance biofuel production.« less

Profiling microbial lignocellulose degradation and utilization by emergent omics technologies.

PubMed

Rosnow, Joshua J; Anderson, Lindsey N; Nair, Reji N; Baker, Erin S; Wright, Aaron T

2017-08-01

The use of plant materials to generate renewable biofuels and other high-value chemicals is the sustainable and preferable option, but will require considerable improvements to increase the rate and efficiency of lignocellulose depolymerization. This review highlights novel and emerging technologies that are being developed and deployed to characterize the process of lignocellulose degradation. The review will also illustrate how microbial communities deconstruct and metabolize lignocellulose by identifying the necessary genes and enzyme activities along with the reaction products. These technologies include multi-omic measurements, cell sorting and isolation, nuclear magnetic resonance spectroscopy (NMR), activity-based protein profiling, and direct measurement of enzyme activity. The recalcitrant nature of lignocellulose necessitates the need to characterize the methods microbes employ to deconstruct lignocellulose to inform new strategies on how to greatly improve biofuel conversion processes. New technologies are yielding important insights into microbial functions and strategies employed to degrade lignocellulose, providing a mechanistic blueprint in order to advance biofuel production.

Effects of Manure Compost Application on Soil Microbial Community Diversity and Soil Microenvironments in a Temperate Cropland in China

PubMed Central

Zhen, Zhen; Liu, Haitao; Wang, Na; Guo, Liyue; Meng, Jie; Ding, Na; Wu, Guanglei; Jiang, Gaoming

2014-01-01

The long-term application of excessive chemical fertilizers has resulted in the degeneration of soil quality parameters such as soil microbial biomass, communities, and nutrient content, which in turn affects crop health, productivity, and soil sustainable productivity. The objective of this study was to develop a rapid and efficient solution for rehabilitating degraded cropland soils by precisely quantifying soil quality parameters through the application of manure compost and bacteria fertilizers or its combination during maize growth. We investigated dynamic impacts on soil microbial count, biomass, basal respiration, community structure diversity, and enzyme activity using six different treatments [no fertilizer (CK), N fertilizer (N), N fertilizer + bacterial fertilizer (NB), manure compost (M), manure compost + bacterial fertilizer (MB), and bacterial fertilizer (B)] in the plowed layer (0–20 cm) of potted soil during various maize growth stages in a temperate cropland of eastern China. Denaturing gradient electrophoresis (DGGE) fingerprinting analysis showed that the structure and composition of bacterial and fungi communities in the six fertilizer treatments varied at different levels. The Shannon index of bacterial and fungi communities displayed the highest value in the MB treatments and the lowest in the N treatment at the maize mature stage. Changes in soil microorganism community structure and diversity after different fertilizer treatments resulted in different microbial properties. Adding manure compost significantly increased the amount of cultivable microorganisms and microbial biomass, thus enhancing soil respiration and enzyme activities (p<0.01), whereas N treatment showed the opposite results (p<0.01). However, B and NB treatments minimally increased the amount of cultivable microorganisms and microbial biomass, with no obvious influence on community structure and soil enzymes. Our findings indicate that the application of manure compost plus bacterial fertilizers can immediately improve the microbial community structure and diversity of degraded cropland soils. PMID:25302996

Photochemical and microbial alterations of DOM spectroscopic properties in the estuarine system Ria de Aveiro.

PubMed

Santos, L; Santos, E B H; Dias, J M; Cunha, A; Almeida, A

2014-08-01

The influence of photochemical transformations of chromophoric dissolved organic matter (CDOM) on microbial communities was evaluated in the estuarine system Ria de Aveiro. Two sites, representative of the marine and brackish water zones of the estuary, were surveyed regularly in order to determine seasonal and vertical profiles of variation of CDOM properties. Optical parameters of CDOM indicative of aromaticity and molecular weight were used to establish CDOM sources, and microbial abundance and activity was characterized. Additionally, microcosm experiments were performed in order to simulate photochemical reactions of CDOM and to evaluate microbial responses to light-induced changes in CDOM composition. The CDOM of the two estuarine zones showed different spectral characteristics, with significantly higher values of the specific ultra-violet absorbance at 254 nm (SUVA254) (5.5 times) and of the absorption coefficient at 350 nm (a350) (12 times) and lower SR (S275-295/S350-400) ratio at brackish water compared with the marine zone, reflecting the different amounts and prevailing sources of organic matter, as well as distinct riverine and oceanic influences. At the marine zone, the abundance of bacteria and the activity of Leu-AMPase correlated with a350 and a254, suggesting a microbial contribution to the HMW CDOM pool. The irradiation of DOM resulted in a decrease of the values of a254 and a350 and an increase of the slope S275-295 and of the ratios E2 : E3 (a250/a365) and SR, which in turn increase its bioavailability. However, the extent of photoinduced transformations and microbial responses was dependent on the initial optical characteristics of CDOM. In Ria de Aveiro both photochemical and microbial processes yielded optical changes in CDOM and the overall results of these combined processes determine the fate of CDOM in the estuarine system and have an influence on local productivity and in adjacent coastal areas.

Comparative effects of sulfuric and nitric acid rain on litter decomposition and soil microbial community in subtropical plantation of Yangtze River Delta region.

PubMed

Liu, Xin; Zhang, Bo; Zhao, Wenrui; Wang, Ling; Xie, Dejin; Huo, Wentong; Wu, Yanwen; Zhang, Jinchi

2017-12-01

Acid rain is mainly caused by dissolution of sulfur dioxide and nitrogen oxides in the atmosphere, and has a significant negative effect on ecosystems. The relative composition of acid rain is changing gradually from sulfuric acid rain (SAR) to nitric acid rain (NAR) with the rapidly growing amount of nitrogen deposition. In this study, we investigated the impact of simulated SAR and NAR on litter decomposition and the soil microbial community over four seasons since March 2015. Results first showed that the effects of acid rain on litter decomposition and soil microbial were positive in the early period of the experiment, except for SAR on soil microbes. Second, soil pH with NAR decreased more rapidly with the amount of acid rain increased in summer than with SAR treatments. Only strongly acid rain (both SAR and NAR) was capable of depressing litter decomposition and its inhibitory effect was stronger on leaf than on fine root litter. Meanwhile, NAR had a higher inhibitory effect on litter decomposition than SAR. Third, in summer, autumn and winter, PLFAs were negatively impacted by the increased acidity level resulting from both SAR and NAR. However, higher acidity level of NAR (pH=2.5) had the strongest inhibitory impact on soil microbial activity, especially in summer. In addition, Gram-negative bacteria (cy19:0) and fungi (18:1ω9) were more sensitive to both SAR and NAR, and actinomycetes was more sensitive to SAR intensity. Finally, soil total carbon, total nitrogen and pH were the most important soil property factors affecting soil microbial activity, and high microbial indices (fungi/bacteria) with high soil pH. Our results suggest that the ratio of SO 4 2- to NO 3 - in acid rain is an important factor which could affect litter decomposition and soil microbial in subtropical forest of China. Copyright © 2017. Published by Elsevier B.V.

Effect of redox conditions on MTBE biodegradation in surface water Sediments

USGS Publications Warehouse

Bradley, P.M.; Chapelle, F.H.; Landmeyer, J.E.

2001-01-01

Microbial degradation of methyl tert-butyl ether (MTBE) was observed in surface water-sediment microcosms under anaerobic conditions. The efficiency and products of anaerobic MTBE biodegradation were dependent on the predominant terminal electron-accepting conditions. In the presence of substantial methanogenic activity, MTBE biodegradation was nominal and involved reduction of MTBE to the toxic product, tert-butyl alcohol (TBA). In the absence of significant methanogenic activity, accumulation of [14C]TBA generally decreased, and mineralization of [U-14C]MTBE to 14CO2 generally increased as the oxidative potential of the predominant terminal electron acceptor increased in the order of SO4, Fe(III), Mn(IV) < NO3 < O2. Microbial mineralization of MTBE to CO2 under Mn(IV)or SO4-reducing conditions has not been reported previously. The results of this study indicate that microorganisms inhabiting the sediments of streams and lakes can degrade MTBE effectively under a range of anaerobic terminal electron-accepting conditions. Thus, anaerobic bed sediment microbial processes may provide a significant environmental sink for MTBE in surface water systems throughout the United States.

Influences of iron and calcium carbonate on wastewater treatment performances of algae based reactors.

PubMed

Zhao, Zhimiao; Song, Xinshan; Wang, Wei; Xiao, Yanping; Gong, Zhijie; Wang, Yuhui; Zhao, Yufeng; Chen, Yu; Mei, Mengyuan

2016-09-01

The influences of iron and calcium carbonate (CaCO3) addition in wastewater treatments reactors performance were investigated. Adding different concentrations of Fe(3+) (5, 10, 30 and 50mmol/m(3)), iron and CaCO3 powder led to changes in algal characteristics and physico-chemical and microbiological properties. According to the investigation results, nutrient removal efficiency in algae based reactors was obviously increased by the addition of 10mmol/m(3) Fe(3+), iron (5mmol/m(3)) and CaCO3 powder (0.2gm(-3)) and the removal efficiencies of BOD5, TN, and TP in Stage 2 were respectively increased by 28%, 8.9%, and 22%. The improvements in physico-chemical performances were verified by microbial community tests (bacteria quantity, activity and community measured in most probable number, extracellular enzymes activity, and Biolog Eco Plates). Microbial variations indicated the coexistence of Fe ions and carbonate-bicarbonate, which triggered the synergistic effect of physico-chemical action and microbial factors in algae based reactors. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effects of Soil Organic Matter Properties and Microbial Community Composition on Enzyme Activities in Cryoturbated Arctic Soils

PubMed Central

Schnecker, Jörg; Wild, Birgit; Hofhansl, Florian; Eloy Alves, Ricardo J.; Bárta, Jiří; Čapek, Petr; Fuchslueger, Lucia; Gentsch, Norman; Gittel, Antje; Guggenberger, Georg; Hofer, Angelika; Kienzl, Sandra; Knoltsch, Anna; Lashchinskiy, Nikolay; Mikutta, Robert; Šantrůčková, Hana; Shibistova, Olga; Takriti, Mounir; Urich, Tim; Weltin, Georg; Richter, Andreas

2014-01-01

Enzyme-mediated decomposition of soil organic matter (SOM) is controlled, amongst other factors, by organic matter properties and by the microbial decomposer community present. Since microbial community composition and SOM properties are often interrelated and both change with soil depth, the drivers of enzymatic decomposition are hard to dissect. We investigated soils from three regions in the Siberian Arctic, where carbon rich topsoil material has been incorporated into the subsoil (cryoturbation). We took advantage of this subduction to test if SOM properties shape microbial community composition, and to identify controls of both on enzyme activities. We found that microbial community composition (estimated by phospholipid fatty acid analysis), was similar in cryoturbated material and in surrounding subsoil, although carbon and nitrogen contents were similar in cryoturbated material and topsoils. This suggests that the microbial community in cryoturbated material was not well adapted to SOM properties. We also measured three potential enzyme activities (cellobiohydrolase, leucine-amino-peptidase and phenoloxidase) and used structural equation models (SEMs) to identify direct and indirect drivers of the three enzyme activities. The models included microbial community composition, carbon and nitrogen contents, clay content, water content, and pH. Models for regular horizons, excluding cryoturbated material, showed that all enzyme activities were mainly controlled by carbon or nitrogen. Microbial community composition had no effect. In contrast, models for cryoturbated material showed that enzyme activities were also related to microbial community composition. The additional control of microbial community composition could have restrained enzyme activities and furthermore decomposition in general. The functional decoupling of SOM properties and microbial community composition might thus be one of the reasons for low decomposition rates and the persistence of 400 Gt carbon stored in cryoturbated material. PMID:24705618

Seasonal Variation in Soil Microbial Biomass, Bacterial Community Composition and Extracellular Enzyme Activity in Relation to Soil Respiration in a Northern Great Plains Grassland

NASA Astrophysics Data System (ADS)

Wilton, E.; Flanagan, L. B.

2014-12-01

Soil respiration rate is affected by seasonal changes in temperature and moisture, but is this a direct effect on soil metabolism or an indirect effect caused by changes in microbial biomass, bacterial community composition and substrate availability? In order to address this question, we compared continuous measurements of soil and plant CO2 exchange made with an automatic chamber system to analyses conducted on replicate soil samples collected on four dates during June-August. Microbial biomass was estimated from substrate-induced respiration rate, bacterial community composition was determined by 16S rRNA amplicon pyrosequencing, and β-1,4-N-acetylglucosaminidase (NAGase) and phenol oxidase enzyme activities were assayed fluorometrically or by absorbance measurements, respectively. Soil microbial biomass declined from June to August in strong correlation with a progressive decline in soil moisture during this time period. Soil bacterial species richness and alpha diversity showed no significant seasonal change. However, bacterial community composition showed a progressive shift over time as measured by Bray-Curtis dissimilarity. In particular, the change in community composition was associated with increasing relative abundance in the alpha and delta classes, and declining abundance of the beta and gamma classes of the Proteobacteria phylum during June-August. NAGase showed a progressive seasonal decline in potential activity that was correlated with microbial biomass and seasonal changes in soil moisture. In contrast, phenol oxidase showed highest potential activity in mid-July near the time of peak soil respiration and ecosystem photosynthesis, which may represent a time of high input of carbon exudates into the soil from plant roots. This input of exudates may stimulate the activity of phenol oxidase, a lignolytic enzyme involved in the breakdown of soil organic matter. These analyses indicated that seasonal change in soil respiration is a complex interaction between temporal changes in soil environmental factors and biological changes in the plant and microbial community that affect soil respiratory metabolism.

The effect of coal bed dewatering and partial oxidation on biogenic methane potential

USGS Publications Warehouse

Jones, Elizabeth J.P.; Harris, Steve H.; Barnhart, Elliott P.; Orem, William H.; Clark, Arthur C.; Corum, Margo D.; Kirshtein, Julie D.; Varonka, Matthew S.; Voytek, Mary A.

2013-01-01

Coal formation dewatering at a site in the Powder River Basin was associated with enhanced potential for secondary biogenic methane determined by using a bioassay. We hypothesized that dewatering can stimulate microbial activity and increase the bioavailability of coal. We analyzed one dewatered and two water-saturated coals to examine possible ways in which dewatering influences coal bed natural gas biogenesis by looking at differences with respect to the native coal microbial community, coal-methane organic intermediates, and residual coal oxidation potential. Microbial biomass did not increase in response to dewatering. Small Subunit rRNA sequences retrieved from all coals sampled represented members from genera known to be aerobic, anaerobic and facultatively anaerobic. A Bray Curtis similarity analysis indicated that the microbial communities in water-saturated coals were more similar to each other than to the dewatered coal, suggesting an effect of dewatering. There was a higher incidence of long chain and volatile fatty acid intermediates in incubations of the dewatered coal compared to the water-saturated coals, and this could either be due to differences in microbial enzymatic activities or to chemical oxidation of the coal associated with O2 exposure. Dilute H2O2 treatment of two fractions of structural coal (kerogen and bitumen + kerogen) was used as a proxy for chemical oxidation by O2. The dewatered coal had a low residual oxidation potential compared to the water-saturated coals. Oxidation with 5% H2O2 did increase the bioavailability of structural coal, and the increase in residual oxidation potential in the water saturated coals was approximately equivalent to the higher methanogenic potential measured in the dewatered coal. Evidence from this study supports the idea that coal bed dewatering could stimulate biogenic methanogenesis through partial oxidation of the structural organics in coal once anaerobic conditions are restored.

Effects of redox fluctuations on microbial community ecology post-wildfire in a high elevation mixed-conifer catchment in northern New Mexico.

NASA Astrophysics Data System (ADS)

Fairbanks, D.; Green, K.; Murphy, M. A.; Shepard, C.; Chorover, J.; Rich, V. I.; Gallery, R. E.

2015-12-01

Wildfires are increasing in size and severity across the western United States with impacts on regional biogeochemical cycling. The resiliency of resident soil microbial communities determines rates of nutrient transformations as well as forest structure and recovery. Redox conditions in soil determine metabolic activities of microorganisms, which first consume oxygen and a succession of alternative terminal electron acceptors to support growth and metabolism using a variety of carbon sources. Controls on redox zonation are largely unknown in dominantly oxic soils, and microbial community adaptation and response to fluctuations in redox potential in a sub-alpine forested post-disturbance catchment has not been studied. Previous work has shown that fluctuating or rising water tables result in redox-dynamic sites, which can be 'hot spots' of biogeochemical activity depending on landscape position. Fire-induced tree mortality results in altered hydrologic flow paths and decreased evapotranspiration, leading to potential for intensified hot spot activity. We are testing such coupling of microbial activity with fluctuations in redox status using field measurements and laboratory incubation experiments. The 2013 Thompson Ridge Fire in the Jemez River Basin (NM) Critical Zone Observatory provides a highly-contextualized opportunity to examine how disturbance regime affects changes in soil microbial community dynamics and fluctuations in reduction-oxidation potential (as quantified by continuous CZO measurements of O2, CO2 and Eh as a function of soil depth and landscape location). We hypothesize that areas of depositional convergence in the catchment, which have been shown to exhibit more reducing conditions, will host microbial communities that are better adapted to fluctuating redox conditions and exhibit a greater diversity in functional capabilities. In these mixed conifer forests we find shifts in redox potential status in relation to depth and topography where more reducing conditions typically occur in convergent zones and at depth. These results highlight the significance of fluctuating oxygen-depleted zones in aerobic soils on microbial community activity and structure, linking community response to larger scale ecosystem processes.

Microbial Priming and Protected Carbon Responses to Elevated CO2 at Local to Global Scales: a New Modeling Approach

NASA Astrophysics Data System (ADS)

Sulman, B. N.; Oishi, C.; Shevliakova, E.; Pacala, S. W.

2013-12-01

The soil carbon formulations commonly used in global carbon cycle models and Earth System models (ESMs) are based on first-order decomposition equations, where turnover of carbon is determined only by the size of the carbon pool and empirical functions of responses to temperature and moisture. These models do not include microbial dynamics or protection of carbon in microaggregates and mineral complexes, making them incapable of simulating important soil processes like priming and the influence of soil physical structure on carbon turnover. We present a new soil carbon dynamics model - Carbon, Organisms, Respiration, and Protection in the Soil Environment (CORPSE) - that explicitly represents microbial biomass and protected carbon pools. The model includes multiple types of carbon with different chemically determined turnover rates that interact with a single dynamic microbial biomass pool, allowing the model to simulate priming effects. The model also includes the formation and turnover of protected carbon that is inaccessible to microbial decomposers. The rate of protected carbon formation increases with microbial biomass. CORPSE has been implemented both as a stand-alone model and as a component of the NOAA Geophysical Fluid Dynamics Laboratory (GFDL) ESM. We calibrated the model against measured soil carbon stocks from the Duke FACE experiment. The model successfully simulated the seasonal pattern of heterotrophic CO2 production. We investigated the roles of priming and protection in soil carbon accumulation by running the model using measured inputs of leaf litter, fine roots, and root exudates from the ambient and elevated CO2 plots at the Duke FACE experiment. Measurements from the experiment showed that elevated CO2 caused enhanced root exudation, increasing soil carbon turnover in the rhizosphere due to priming effects. We tested the impact of increased root exudation on soil carbon accumulation by comparing model simulations of carbon accumulation under elevated CO2 with and without increased root exudation. Increased root exudation stimulated microbial activity in the model, resulting in reduced accumulation of chemically recalcitrant carbon, but increasing the formation of protected carbon. This indicates that elevated CO2 could cause decreases in soil carbon storage despite increases in productivity in ecosystems where protection of soil carbon is limited. These effects have important implications for simulations of soil carbon response to elevated CO2 in current terrestrial carbon cycle models. The CORPSE model has been implemented in LM3, the terrestrial component of the GFDL ESM. In addition to the functionality described above, this model adds vertically resolved carbon pools and vertical transfers of carbon, leading to a decrease in carbon turnover rates with depth due to leaching of priming agents from the surface. We present preliminary global simulations using this model, including the variation of microbial activity and protected carbon with latitude and the resulting impacts on the sensitivity of soil carbon to climatic warming.

Long-Term Field Study of Microbial Community and Dechlorinating Activity Following Carboxymethyl Cellulose-Stabilized Nanoscale Zero-Valent Iron Injection.

PubMed

Kocur, Chris M D; Lomheim, Line; Molenda, Olivia; Weber, Kela P; Austrins, Leanne M; Sleep, Brent E; Boparai, Hardiljeet K; Edwards, Elizabeth A; O'Carroll, Denis M

2016-07-19

Nanoscale zerovalent iron (nZVI) is an emerging technology for the remediation of contaminated sites. However, there are concerns related to the impact of nZVI on in situ microbial communities. In this study, the microbial community composition at a contaminated site was monitored over two years following the injection of nZVI stabilized with carboxymethyl cellulose (nZVI-CMC). Enhanced dechlorination of chlorinated ethenes to nontoxic ethene was observed long after the expected nZVI oxidation. The abundance of Dehalococcoides (Dhc) and vinyl chloride reductase (vcrA) genes, monitored using qPCR, increased by over an order of magnitude in nZVI-CMC-impacted wells. The entire microbial community was tracked using 16S rRNA gene amplicon pyrosequencing. Following nZVI-CMC injection, a clear shift in microbial community was observed, with most notable increases in the dechlorinating genera Dehalococcoides and Dehalogenimonas. This study suggests that coupled abiotic degradation (i.e., from reaction with nZVI) and biotic degradation fueled by CMC led to the long-term degradation of chlorinated ethenes at this field site. Furthermore, nZVI-CMC addition stimulated dehalogenator growth (e.g., Dehalococcoides) and biotic degradation of chlorinated ethenes.

Soil warming alters microbial substrate use in alpine soils.

PubMed

Streit, Kathrin; Hagedorn, Frank; Hiltbrunner, David; Portmann, Magdalena; Saurer, Matthias; Buchmann, Nina; Wild, Birgit; Richter, Andreas; Wipf, Sonja; Siegwolf, Rolf T W

2014-04-01

Will warming lead to an increased use of older soil organic carbon (SOC) by microbial communities, thereby inducing C losses from C-rich alpine soils? We studied soil microbial community composition, activity, and substrate use after 3 and 4 years of soil warming (+4 °C, 2007-2010) at the alpine treeline in Switzerland. The warming experiment was nested in a free air CO2 enrichment experiment using depleted (13)CO2 (δ(13)C = -30‰, 2001-2009). We traced this depleted (13)C label in phospholipid fatty acids (PLFA) of the organic layer (0-5 cm soil depth) and in C mineralized from root-free soils to distinguish substrate ages used by soil microorganisms: fixed before 2001 ('old'), from 2001 to 2009 ('new') or in 2010 ('recent'). Warming induced a sustained stimulation of soil respiration (+38%) without decline in mineralizable SOC. PLFA concentrations did not reveal changes in microbial community composition due to soil warming, but soil microbial metabolic activity was stimulated (+66%). Warming decreased the amount of new and recent C in the fungal biomarker 18:2ω6,9 and the amount of new C mineralized from root-free soils, implying a shift in microbial substrate use toward a greater use of old SOC. This shift in substrate use could indicate an imbalance between C inputs and outputs, which could eventually decrease SOC storage in this alpine ecosystem. © 2013 John Wiley & Sons Ltd.

Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology.

PubMed

von Bergen, Martin; Jehmlich, Nico; Taubert, Martin; Vogt, Carsten; Bastida, Felipe; Herbst, Florian-Alexander; Schmidt, Frank; Richnow, Hans-Hermann; Seifert, Jana

2013-10-01

The recent development of metaproteomics has enabled the direct identification and quantification of expressed proteins from microbial communities in situ, without the need for microbial enrichment. This became possible by (1) significant increases in quality and quantity of metagenome data and by improvements of (2) accuracy and (3) sensitivity of modern mass spectrometers (MS). The identification of physiologically relevant enzymes can help to understand the role of specific species within a community or an ecological niche. Beside identification, relative and absolute quantitation is also crucial. We will review label-free and label-based methods of quantitation in MS-based proteome analysis and the contribution of quantitative proteome data to microbial ecology. Additionally, approaches of protein-based stable isotope probing (protein-SIP) for deciphering community structures are reviewed. Information on the species-specific metabolic activity can be obtained when substrates or nutrients are labeled with stable isotopes in a protein-SIP approach. The stable isotopes ((13)C, (15)N, (36)S) are incorporated into proteins and the rate of incorporation can be used for assessing the metabolic activity of the corresponding species. We will focus on the relevance of the metabolic and phylogenetic information retrieved with protein-SIP studies and for detecting and quantifying the carbon flux within microbial consortia. Furthermore, the combination of protein-SIP with established tools in microbial ecology such as other stable isotope probing techniques are discussed.

Earthworm Effects without Earthworms: Inoculation of Raw Organic Matter with Worm-Worked Substrates Alters Microbial Community Functioning

PubMed Central

Aira, Manuel; Domínguez, Jorge

2011-01-01

Background Earthworms are key organisms in organic matter decomposition because of the interactions they establish with soil microorganisms. They enhance decomposition rates through the joint action of direct effects (i.e. effects due to direct earthworm activity such as digestion, burrowing, etc) and indirect effects (i.e. effects derived from earthworm activities such as cast ageing). Here we test whether indirect earthworm effects affect microbial community functioning in the substrate, as when earthworms are present (i. e., direct effects). Methodology/Principal Findings To address these questions we inoculated fresh organic matter (pig manure) with worm-worked substrates (vermicompost) produced by three different earthworm species. Two doses of each vermicompost were used (2.5 and 10%). We hypothesized that the presence of worm-worked material in the fresh organic matter will result in an inoculum of different microorganisms and nutrients. This inoculum should interact with microbial communities in fresh organic matter, thus promoting modifications similar to those found when earthworms are present. Inoculation of worm-worked substrates provoked significant increases in microbial biomass and enzyme activities (β-glucosidase, cellulase, phosphatase and protease). These indirect effects were similar to, although lower than, those obtained in pig manure with earthworms (direct and indirect earthworm effects). In general, the effects were not dose-dependent, suggesting the existence of a threshold at which they were triggered. Conclusion/Significance Our data reveal that the relationships between earthworms and microorganisms are far from being understood, and suggest the existence of several positive feedbacks during earthworm activity as a result of the interactions between direct and indirect effects, since their combination produces stronger modifications to microbial biomass and enzyme activity. PMID:21298016

Characterization of Microbial Community Structure in Gulf of Mexico Gas Hydrates: Comparative Analysis of DNA- and RNA-Derived Clone Libraries

PubMed Central

Mills, Heath J.; Martinez, Robert J.; Story, Sandra; Sobecky, Patricia A.

2005-01-01

The characterization of microbial assemblages within solid gas hydrate, especially those that may be physiologically active under in situ hydrate conditions, is essential to gain a better understanding of the effects and contributions of microbial activities in Gulf of Mexico (GoM) hydrate ecosystems. In this study, the composition of the Bacteria and Archaea communities was determined by 16S rRNA phylogenetic analyses of clone libraries derived from RNA and DNA extracted from sediment-entrained hydrate (SEH) and interior hydrate (IH). The hydrate was recovered from an exposed mound located in the northern GoM continental slope with a hydrate chipper designed for use on the manned-submersible Johnson Sea Link (water depth, 550 m). Previous geochemical analyses indicated that there was increased metabolic activity in the SEH compared to the IH layer (B. N. Orcutt, A. Boetius, S. K. Lugo, I. R. Macdonald, V. A. Samarkin, and S. Joye, Chem. Geol. 205:239-251). Phylogenetic analysis of RNA- and DNA-derived clones indicated that there was greater diversity in the SEH libraries than in the IH libraries. A majority of the clones obtained from the metabolically active fraction of the microbial community were most closely related to putative sulfate-reducing bacteria and anaerobic methane-oxidizing archaea. Several novel bacterial and archaeal phylotypes for which there were no previously identified closely related cultured isolates were detected in the RNA- and DNA-derived clone libraries. This study was the first phylogenetic analysis of the metabolically active fraction of the microbial community extant in the distinct SEH and IH layers of GoM gas hydrate. PMID:15933026

Effect of Elevated Salt Concentrations on the Aerobic Granular Sludge Process: Linking Microbial Activity with Microbial Community Structure▿

PubMed Central

Bassin, J. P.; Pronk, M.; Muyzer, G.; Kleerebezem, R.; Dezotti, M.; van Loosdrecht, M. C. M.

2011-01-01

The long- and short-term effects of salt on biological nitrogen and phosphorus removal processes were studied in an aerobic granular sludge reactor. The microbial community structure was investigated by PCR-denaturing gradient gel electrophoresis (DGGE) on 16S rRNA and amoA genes. PCR products obtained from genomic DNA and from rRNA after reverse transcription were compared to determine the presence of bacteria as well as the metabolically active fraction of bacteria. Fluorescence in situ hybridization (FISH) was used to validate the PCR-based results and to quantify the dominant bacterial populations. The results demonstrated that ammonium removal efficiency was not affected by salt concentrations up to 33 g/liter NaCl. Conversely, a high accumulation of nitrite was observed above 22 g/liter NaCl, which coincided with the disappearance of Nitrospira sp. Phosphorus removal was severely affected by gradual salt increase. No P release or uptake was observed at steady-state operation at 33 g/liter NaCl, exactly when the polyphosphate-accumulating organisms (PAOs), “Candidatus Accumulibacter phosphatis” bacteria, were no longer detected by PCR-DGGE or FISH. Batch experiments confirmed that P removal still could occur at 30 g/liter NaCl, but the long exposure of the biomass to this salinity level was detrimental for PAOs, which were outcompeted by glycogen-accumulating organisms (GAOs) in the bioreactor. GAOs became the dominant microorganisms at increasing salt concentrations, especially at 33 g/liter NaCl. In the comparative analysis of the diversity (DNA-derived pattern) and the activity (cDNA-derived pattern) of the microbial population, the highly metabolically active microorganisms were observed to be those related to ammonia (Nitrosomonas sp.) and phosphate removal (“Candidatus Accumulibacter”). PMID:21926194

Capturing the genetic makeup of the active microbiome in situ.

PubMed

Singer, Esther; Wagner, Michael; Woyke, Tanja

2017-09-01

More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and that have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions.

Capturing the genetic makeup of the active microbiome in situ

PubMed Central

Singer, Esther; Wagner, Michael; Woyke, Tanja

2017-01-01

More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and that have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions. PMID:28574490

[Effects of bio-crust on soil microbial biomass and enzyme activities in copper mine tailings].

PubMed

Chen, Zheng; Yang, Gui-de; Sun, Qing-ye

2009-09-01

Bio-crust is the initial stage of natural primary succession in copper mine tailings. With the Yangshanchong and Tongguanshan copper mine tailings in Tongling City of Anhui Province as test objects, this paper studied the soil microbial biomass C and N and the activities of dehydrogenase, catalase, alkaline phosphatase, and urease under different types of bio-crust. The bio-crusts improved the soil microbial biomass and enzyme activities in the upper layer of the tailings markedly. Algal crust had the best effect in improving soil microbial biomass C and N, followed by moss-algal crust, and moss crust. Soil microflora also varied with the type of bio-crust. No'significant difference was observed in the soil enzyme activities under the three types of bio-crust. Soil alkaline phosphatase activity was significantly positively correlated with soil microbial biomass and dehydrogenase and urease activities, but negatively correlated with soil pH. In addition, moss rhizoid could markedly enhance the soil microbial biomass and enzyme activities in moss crust rhizoid.

N2O and N2 emissions from contrasting soil environments - interactive effects of soil nitrogen, hydrology and microbial communities

NASA Astrophysics Data System (ADS)

Christiansen, Jesper; Elberling, Bo; Ribbons, Relena; Hedo, Javier; José Fernández Alonso, Maria; Krych, Lukasz; Sandris Nielsen, Dennis; Kitzler, Barbara

2016-04-01

Reactive nitrogen (N) in the environment has doubled relative to the natural global N cycle with consequences for biogeochemical cycling of soil N. Also, climate change is expected to alter precipitation patterns and increase soil temperatures which in Arctic environments may accelerate permafrost thawing. The combination of changes in the soil N cycle and hydrological regimes may alter microbial transformations of soil N with unknown impacts on N2O and N2 emissions from temperate and Arctic soils. We present the first results of soil N2O and N2 emissions, chemistry and microbial communities over soil hydrological gradients (upslope, intermediate and wet) across a global N deposition gradient. The global gradient covered an N-limited high Arctic tundra (Zackenberg-ZA), a pacific temperate rain forest (Vancouver Island-VI) and an N saturated forest in Austria (Klausenleopoldsdorf-KL). The N2O and N2 emissions were measured from intact cores at field moisture in a He-atmosphere system. Extractable NH4+ and NO3-, organic and microbial C and N and potential enzyme-activities were determined on soil samples. Soil genomic DNA was subjected to MiSeq-based tag-encoded 16S rRNA and ITS gene amplicon sequencing for the bacterial and fungal community structure. Similar soil moisture levels were observed for the upslope, intermediate and wet locations at ZA, VI and KL, respectively. Extractable NO3- was highest at the N rich KL and lowest at ZA and showed no trend with soil moisture similar to NH4+. At ZA and VI soil NH4+ was higher than NO3- indicating a tighter N cycling. N2O emissions increased with soil moisture at all sites. The N2O emissions for the wet locations ranked similarly to NO3- with the largest response to soil moisture at KL. N2 emissions were remarkably similar across the sites and increased with soil wetness. Microbial C and N also increased with soil moisture and were overall lowest at the N rich KL site. The potential activity of protease enzyme was site dependent indicating different capacities for N turnover of the microbial community. These findings indicate a positive feedback between increased soil N and wetter soils that promotes N2O relative to N2. These interactions may be site specific due to differential functional diversity of the soil microbial community. Future characterization of the community structure will shed light on the link between the role of microbial groups related to soil N cycling pathways and the resultant partitioning of N2O and N2 emissions in these contrasting environments.

Soil microbes shift C-degrading activity along an ambient and experimental nitrogen gradient

NASA Astrophysics Data System (ADS)

Moore, J.; Frey, S. D.

2017-12-01

The balance between soil carbon (C) accumulation and decomposition is determined in large part by the activity and biomass of soil microbes, and yet their sensitivity to global changes remains unresolved. Atmospheric nitrogen (N) deposition has increased 22% (for NH4+) in the last two decades despite initiation of the Clean Air Act. Nitrogen deposition alters ecosystem processes by changing nutrient availability and soil pH, creating physiologically stressful environments that select for stress tolerant microbes. The functional fungal community may switch from domination by species with traits associated with decomposition via oxidative enzymes to traits associated with stress tolerance if global changes push fungal physiological limits. We examined changes in soil microbial activity across seven sites representing a gradient of ambient atmospheric N deposition, and five of these sites also had long-term N addition experiments. We measured changes in abundance of decomposition genes and C mineralization rates as indicators of microbial activity. We expected microbes to be less active with high N deposition, thus decreasing C mineralization rates. We found that C mineralization rates declined with total N deposition (ambient plus experimental additions), and this decline was more sensitive to N deposition where it occurred naturally compared to experimental treatments. Carbon mineralization declined by 3% in experimentally fertilized soils compared to 10% in control soils for every 1 kg/ha/y increase in ambient N deposition. Thus, microbes exposed to ambient levels of N deposition (2 - 12 kg/ha/y) had a stronger response than those exposed to fertilized soils (20 - 50 kg/ha/y). Long-term experimental N-addition seems to have selected for a microbial community that is tolerant of high N deposition. In sum, we provide evidence that soil microbial activity responded to N deposition, and may shift over time to a community capable of tolerating environmental change.

Responses of the functional structure of soil microbial community to livestock grazing in the Tibetan alpine grassland.

PubMed

Yang, Yunfeng; Wu, Linwei; Lin, Qiaoyan; Yuan, Mengting; Xu, Depeng; Yu, Hao; Hu, Yigang; Duan, Jichuang; Li, Xiangzhen; He, Zhili; Xue, Kai; van Nostrand, Joy; Wang, Shiping; Zhou, Jizhong

2013-02-01

Microbes play key roles in various biogeochemical processes, including carbon (C) and nitrogen (N) cycling. However, changes of microbial community at the functional gene level by livestock grazing, which is a global land-use activity, remain unclear. Here we use a functional gene array, GeoChip 4.0, to examine the effects of free livestock grazing on the microbial community at an experimental site of Tibet, a region known to be very sensitive to anthropogenic perturbation and global warming. Our results showed that grazing changed microbial community functional structure, in addition to aboveground vegetation and soil geochemical properties. Further statistical tests showed that microbial community functional structures were closely correlated with environmental variables, and variations in microbial community functional structures were mainly controlled by aboveground vegetation, soil C/N ratio, and NH4 (+) -N. In-depth examination of N cycling genes showed that abundances of N mineralization and nitrification genes were increased at grazed sites, but denitrification and N-reduction genes were decreased, suggesting that functional potentials of relevant bioprocesses were changed. Meanwhile, abundances of genes involved in methane cycling, C fixation, and degradation were decreased, which might be caused by vegetation removal and hence decrease in litter accumulation at grazed sites. In contrast, abundances of virulence, stress, and antibiotics resistance genes were increased because of the presence of livestock. In conclusion, these results indicated that soil microbial community functional structure was very sensitive to the impact of livestock grazing and revealed microbial functional potentials in regulating soil N and C cycling, supporting the necessity to include microbial components in evaluating the consequence of land-use and/or climate changes. © 2012 Blackwell Publishing Ltd.

Effects of phosphorus and nitrogen additions on tropical soil microbial activity in the context of experimental warming

NASA Astrophysics Data System (ADS)

Foley, M.; Nottingham, A.; Turner, B. L.

2017-12-01

Soil warming is generally predicted to increase microbial mineralization rates and accelerate soil C losses which could establish a positive feedback to climatic warming. Tropical rain forests account for a third of global soil C, yet the responseto of tropical soil C a warming climate remains poorly understood. Despite predictions of soil C losses, decomposition of soil organic matter (SOM) in tropical soils may be constrained by several factors including microbial nutrient deficiencies. We performed an incubation experiment in conjunction with an in-situ soil warming experiment in a lowland tropical forest on Barro Colorado Island, Panama, to measure microbial response to two key nutrient additions in shallow (0-10cm) and deep (50-100 cm) soils. We compared the response of lowland tropical soils to montane tropical soils, predicting that lowland soils would display the strongest response to phosphorus additions. Soils were treated with either carbon alone (C), nitrogen (CN), phosphorus (CP) or nitrogen and phosphorus combined (CNP). Carbon dioxide (CO2) production was measured by NaOH capture and titrimetric analysis for 10 days. Cumulative CO2 production in montane soils increased significantly with all additions, suggesting these soils are characterized by a general microbial nutrient deficiency. The cumulative amount of C respired in deep soils from the lowland site increased significantly with CP and CNP additions, suggesting that microbial processes in deep lowland tropical soils are phosphorus-limited. These results support the current understanding that lowland tropical forests are growing on highly weathered, phosphorus-deplete soils, and provide novel insight that deep tropical SOM may be stabilized by a lack of biologically-available phosphorus. Further, this data suggests tropical soil C losses under elevated temperature may be limited by a strong microbial phosphorus deficiency.

Changes in the Structure and Function of Microbial Communities in Drinking Water Treatment Bioreactors upon Addition of Phosphorus▿ †

PubMed Central

Li, Xu; Upadhyaya, Giridhar; Yuen, Wangki; Brown, Jess; Morgenroth, Eberhard; Raskin, Lutgarde

2010-01-01

Phosphorus was added as a nutrient to bench-scale and pilot-scale biologically active carbon (BAC) reactors operated for perchlorate and nitrate removal from contaminated groundwater. The two bioreactors responded similarly to phosphorus addition in terms of microbial community function (i.e., reactor performance), while drastically different responses in microbial community structure were detected. Improvement in reactor performance with respect to perchlorate and nitrate removal started within a few days after phosphorus addition for both reactors. Microbial community structures were evaluated using molecular techniques targeting 16S rRNA genes. Clone library results showed that the relative abundance of perchlorate-reducing bacteria (PRB) Dechloromonas and Azospira in the bench-scale reactor increased from 15.2% and 0.6% to 54.2% and 11.7% after phosphorus addition, respectively. Real-time quantitative PCR (qPCR) experiments revealed that these increases started within a few days after phosphorus addition. In contrast, after phosphorus addition, the relative abundance of Dechloromonas in the pilot-scale reactor decreased from 7.1 to 0.6%, while Zoogloea increased from 17.9 to 52.0%. The results of this study demonstrated that similar operating conditions for bench-scale and pilot-scale reactors resulted in similar contaminant removal performances, despite dramatically different responses from microbial communities. These findings suggest that it is important to evaluate the microbial community compositions inside bioreactors used for drinking water treatment, as they determine the microbial composition in the effluent and impact downstream treatment requirements for drinking water production. This information could be particularly relevant to drinking water safety, if pathogens or disinfectant-resistant bacteria are detected in the bioreactors. PMID:20889793

The effects of ionic liquid 1-ethyl-3-methylimidazolium trifluoromethanesulfonate on the production of 1,3-propanediol from crude glycerol by microbial consortium.

PubMed

Jiang, Lili; Dai, Jianying; Sun, Yaqin; Xiu, Zhilong

2018-04-12

Ionic liquids (ILs) as "green" solvents have been widely used owing to their excellent properties, e.g., for biodiesel production. Crude glycerol as a by-product in biodiesel production is an ideal feedstock for the microbial production of 1,3-propanediol (PDO), which is a versatile bulk chemical. PDO can be produced by microbial consortium with the advantages of high substrate tolerance and narrow by-product profile. In the present study, the effect of IL 1-ethyl-3-methylimidazolium trifluoromethanesulfonate ([Emim][TfO]) was evaluated on the capacity of PDO production from crude glycerol by microbial consortium DL38-BH. In the batch fermentation at 60 g/L crude glycerol and 10 g/L [Emim][TfO], the concentration and yield of PDO from glycerol increased from 23.14 g/L and 0.45 mol/mol to 31.17 g/L and 0.60 mol/mol, respectively. Our results showed that [Emim][TfO] decreased the ratio of intracellular NADH to NAD + and increased the concentration of 3-HPA during batch fermentation. The activities of three key enzymes in glycerol metabolism were stimulated by [Emim][TfO] during the batch fermentation by microbial consortium DL38-BH. Compared to the control, the proportion of Klebsiella genus which could convert glycerol to PDO increased significantly from 79.19% to 89.49% and the other genera that did not produce PDO were dramatically decreased (P < 0.05) at the end of batch fermentation. This work demonstrated that [Emim][TfO] significantly improved the concentration and yield of PDO from crude glycerol by adjusting microbial community during batch fermentation by microbial consortium.

Plant community influence on soil microbial response after a wildfire in Sierra Nevada National Park (Spain).

PubMed

Bárcenas-Moreno, Gema; García-Orenes, Fuensanta; Mataix-Solera, Jorge; Mataix-Beneyto, Jorge

2016-12-15

Plant community influence on microbial response after fire has been studied in a Sierra Nevada National Park area affected by a wildfire in 2005. Two different plant communities adapted to different altitudes were selected to analyse possible differences on soil microbial recolonisation process after fire, in oak forest and high mountain shrub communities. Microbial abundance, activity and community composition were monitored to evaluate medium-term changes. Microbial abundance was studied by mean of microbial biomass carbon and plate count methods; microbial activity was analysed by microbial respiration and bacterial growth while microbial community composition was determined by analysing phospholipid fatty acid pattern. Under unburnt conditions oak forest showed higher nutrient content, pH and microbial abundance and activity values than the high mountain shrubs community. Different parameters studied showed different trends with time, highlighting important changes in microbial community composition in high mountain shrubs from first sampling to the second one. Post-fire recolonisation process was different depending on plant community studied. Highlighting fungal response and microbial activity were stimulated in burnt high mountain shrubs community whilst it was negatively affected in oak forest. Fire induced changes in oak forest were almost neutralized 20months after the fire, while high mountain shrubs community still showed fire-induced changes at the end of the study. Copyright © 2016 Elsevier B.V. All rights reserved.

Genetic Linkage of Soil Carbon Pools and Microbial Functions in Subtropical Freshwater Wetlands in Response to Experimental Warming

PubMed Central

Wang, Hang; He, Zhili; Lu, Zhenmei; Zhou, Jizhong; Van Nostrand, Joy D.; Xu, Xinhua

2012-01-01

Rising climate temperatures in the future are predicted to accelerate the microbial decomposition of soil organic matter. A field microcosm experiment was carried out to examine the impact of soil warming in freshwater wetlands on different organic carbon (C) pools and associated microbial functional responses. GeoChip 4.0, a functional gene microarray, was used to determine microbial gene diversity and functional potential for C degradation. Experimental warming significantly increased soil pore water dissolved organic C and phosphorus (P) concentrations, leading to a higher potential for C emission and P export. Such losses of total organic C stored in soil could be traced back to the decomposition of recalcitrant organic C. Warming preferentially stimulated genes for degrading recalcitrant C over labile C. This was especially true for genes encoding cellobiase and mnp for cellulose and lignin degradation, respectively. We confirmed this with warming-enhanced polyphenol oxidase and peroxidase activities for recalcitrant C acquisition and greater increases in recalcitrant C use efficiency than in labile C use efficiency (average percentage increases of 48% versus 28%, respectively). The relative abundance of lignin-degrading genes increased by 15% under warming; meanwhile, soil fungi, as the primary decomposers of lignin, were greater in abundance by 27%. This work suggests that future warming may enhance the potential for accelerated fungal decomposition of lignin-like compounds, leading to greater microbially mediated C losses than previously estimated in freshwater wetlands. PMID:22923398

The engineered biofiltration system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pisotti, D.A.

1997-12-31

For years, biofiltration has meant compost, peat, bark, leave mulch, or any combination of these as the substrate to house microorganisms. This has lead to a number of operational and maintenance problems, including: compaction, channeling, anaerobic zones, dry spots, pressure drop, and media degradation. All of these cause reduced efficiency and increased maintenance and increased operational costs. For these reasons inert media, including plastic beads and low grade carbons have been added to the media for buffering capacity, resists compaction, channeling and to increase efficiency. This has led to search for a more reliable and sturdy media. The media themore » authors chose was activated carbon. Pelletized activated carbon was the ideal candidate due to its uniform size and shape, its inherent hardness, adsorptive capacity, and its ability to withstand microbial degradation. The pressure drop of the system will remain constant after microbial growth occurs, due to the ability to wash the media bed. Carbon allows for the removal of excess biomass which can not be performed on organic media, this is one of the problems leading to media degradation, too many microbes and not enough food (i.e. VOCs). Carbon also allows for spike or increased loads to be treated without performance suffering. Carbon also has tremendous surface area, which allows more microorganisms to be present in a smaller volume, therefore reducing the overall size of the biofilter vessel. This paper will discuss further the findings of a pilot test that was performed using activated carbon as the media for microbial growth. This paper will show the performance of the carbon based biofilter system with respect to pressure drop, residence time, removal efficiency, microbial populations, temperature, moisture, and water requirements. The pilot unit is 350 acfm and operated for 4 months on an air stream in which the contaminant concentrations varied greatly every few minutes.« less

[Development of Sediment Micro-Interface Under Physical and Chironomus plumosus Combination Disturbance].

PubMed

Wang, Ren; Li, Da-peng; Huang, Yong; Liu, Yan-jian; Chen, Jun

2015-11-01

Synergistic effect of physical and Chironomus plumosus combination disturbance on the characteristics of the micro-environment and micro-interface was investigated by the Rhizon samplers and Unisense micro sensor system. The results showed that the oxygen penetration depth (OPD), total oxygen exchange (TOE), water content and total microbial activity increased under the combination disturbance and bioturbation and were kept at the higher level, compared with the control. These parameters increased with the physical intensity under combination disturbance. However, the content of Fe2+ decreased under the combination disturbance and bioturbation and the decrease was more obvious than that in the control. The changes of the Fe2+, the water content and the total microbial activity were large at 0-4 cm depth in the sediments. Therefore, the area might be the active area for the transformation of internal sedimentary phosphorus forms. The curve fitting was used for the OPD, TOE, the content of Fe2+, the water content and the total microbial activity with the physical intensity under combination disturbance. It was observed that the second-order polynomial equation was suitable for the curve fitting. In addition, jump type synergistic effect was presented in the above mentioned parameters under combination disturbance when the physical intensity was higher than 34 r x min(-1). The remodeling on the sediment micro-interface and micro-environment might be the main inducing mechanism for the transformation of internal phosphorus.

Impact of antiretroviral drugs on the microbiome: unknown answers to important questions

PubMed Central

Pinto-Cardoso, Sandra; Klatt, Nichole R.; Reyes-Terán, Gustavo

2018-01-01

Purpose of review Little is known on how different antiretroviral (ARV) drugs affect the gut microbiome in HIV infection; and conflicting data exists on the effect of ARV drugs on residual inflammation/immune activation and microbial translocation. Recent findings Gut microbiome involvement in the transmission and pathogenesis of HIV infection is increasingly being recognized. Various studies have shown that antiretroviral therapy (ART) is unable to restore gut health despite effective suppression of plasma HIV viremia. Indeed, the resolution of residual inflammation and gut microbial translocation is partial under ART. Very recent studies have provided new evidence that ARV combinations can differentially affect the gut microbiome, immune activation and microbial translocation. Furthermore, a recent article uncovered a link between drug metabolism and specific microbial species indicating that microbes can directly metabolically degrade ARV drugs when administered topically. Summary There are still many unanswered questions regarding ARVs and the gut microbiome. It is, therefore, critical for researchers to address the effect of distinct ARV drugs on the microbiome and vice versa: the effects of the microbiome on ARV drug metabolism, and speculate about possible therapeutic avenues. PMID:29028667

Microbial production of metabolites and associated enzymatic reactions under high pressure.

PubMed

Dong, Yongsheng; Jiang, Hua

2016-11-01

High environmental pressure exerts an external stress on the survival of microorganisms that are commonly found under normal pressure. In response, many growth traits alter, including cell morphology and physiology, cellular structure, metabolism, physical and chemical properties, the reproductive process, and defense mechanisms. The high-pressure technology (HP) has been industrially utilized in pressurized sterilization, synthesis of stress-induced products, and microbial/enzymatic transformation of chemicals. This article reviews current research on pressure-induced production of metabolites in normal-pressure microbes and their enzymatic reactions. Factors that affect the production of such metabolites are summarized, as well as the effect of pressure on the performance of microbial fermentation and the yield of flavoring compounds, different categories of induced enzymatic reactions and their characteristics in the supercritical carbon dioxide fluid, effects on enzyme activity, and the selection of desirable bacterial strains. Technological challenges are discussed, and future research directions are proposed. Information presented here will benefit the research, development, and application of the HP technology to improve microbial fermentation and enzymatic production of biologically active substances, thereby help to meet their increasing demand from the ever-expanding market.

Interaction effects and mechanism of Pb pollution and soil microorganism in the presence of earthworm.

PubMed

Liu, Gao; Ling, Siyuan; Zhan, Xiuping; Lin, Zhifen; Zhang, Wei; Lin, Kuangfei

2017-04-01

Heavy metals usually cause great damage to soil ecosystem. Lead (Pb) was chosen as a research object in the present study. Here repeated exposure of Pb was designed for the soil artificially contaminated. A laboratory study was conducted to determine the changes in the Pb availability and biological activity in the presence of earthworm, and the risk assessment code (RAC) was applied to evaluate the remediated soil. Results demonstrated that Pb gradually transformed to more stable fractions (OMB- and FeMnOX-Pb) under microbial action, indicating the risk level of Pb was declined. On the other hand, Pb also caused the inhibition of soil respiration and microbial biomass, and the higher the concentration of Pb, the stronger the inhibition; While in the presence of earthworm, it could absorb Pb and facilitate microbial activity, reflected the decrease of Pb content and the increase of respiration intensity in soil, as well as microbial biomass. Additionally, a good dose-response relationship between EXCH-Pb content and respiration intensity might provide a basis for ecological risk assessment. Copyright © 2017 Elsevier Ltd. All rights reserved.

Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kantor, Rose S.; Huddy, Robert J.; Iyer, Ramsunder

Remediation of industrial wastewater is important for preventing environmental contamination and allowing water reuse. Biological treatment for one industrial contaminant, thiocyanate (SCN - ), relies upon microbial hydrolysis, but this process is sensitive to high loadings. To examine the activity and stability of a microbial community over increasing SCN - loadings, we established and operated a continuous-flow bioreactor fed increasing loadings of SCN - . A second reactor was fed ammonium sulfate to mimic breakdown products of SCN - . Biomass was sampled from both reactors for metagenomics and metaproteomics, yielding a set of genomes for 144 bacteria and onemore » rotifer that constituted the abundant community in both reactors. We analyzed the metabolic potential and temporal dynamics of these organisms across the increasing loadings. In the SCN - reactor, Thiobacillus strains capable of SCN - degradation were highly abundant, whereas the ammonium sulfate reactor contained nitrifiers and heterotrophs capable of nitrate reduction. Key organisms in the SCN - reactor expressed proteins involved in SCN - degradation, sulfur oxidation, carbon fixation, and nitrogen removal. Lower performance at higher loadings was linked to changes in microbial community composition. This work provides an example of how meta-omics can increase our understanding of industrial wastewater treatment and inform iterative process design and development.« less

Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation

DOE PAGES

Kantor, Rose S.; Huddy, Robert J.; Iyer, Ramsunder; ...

2017-01-31

Remediation of industrial wastewater is important for preventing environmental contamination and allowing water reuse. Biological treatment for one industrial contaminant, thiocyanate (SCN - ), relies upon microbial hydrolysis, but this process is sensitive to high loadings. To examine the activity and stability of a microbial community over increasing SCN - loadings, we established and operated a continuous-flow bioreactor fed increasing loadings of SCN - . A second reactor was fed ammonium sulfate to mimic breakdown products of SCN - . Biomass was sampled from both reactors for metagenomics and metaproteomics, yielding a set of genomes for 144 bacteria and onemore » rotifer that constituted the abundant community in both reactors. We analyzed the metabolic potential and temporal dynamics of these organisms across the increasing loadings. In the SCN - reactor, Thiobacillus strains capable of SCN - degradation were highly abundant, whereas the ammonium sulfate reactor contained nitrifiers and heterotrophs capable of nitrate reduction. Key organisms in the SCN - reactor expressed proteins involved in SCN - degradation, sulfur oxidation, carbon fixation, and nitrogen removal. Lower performance at higher loadings was linked to changes in microbial community composition. This work provides an example of how meta-omics can increase our understanding of industrial wastewater treatment and inform iterative process design and development.« less

Investigating the Differences in the Total and Active Microbial Community of Mid-Atlantic Ridge Sediments

NASA Astrophysics Data System (ADS)

Sobol, M. S.; Zinke, L. A.; Orcutt, B.; Mills, H. J.; Edwards, K. J.; Girguis, P. R.; Reese, B. K.

2016-02-01

Microbes in the marine deep subsurface are key mediators of many geochemical cycles. It is important to understand how microbial communities and the diversity of those communities impacts geochemical cycling. Sediment cores were collected from IODP (Integrated Ocean Drilling Program) Expedition 336 to the western flank of the mid-Atlantic ridge also referred to as North Pond. The dissolved oxygen concentration decreased with depth for 60-70 mbsf, followed by a sharp increase in oxygen until it terminated at the basement. The 16S rRNA genes (DNA) and transcripts (RNA) were extracted simultaneously using a method designed by Reese et al. (2013) to differentiate between the total and active microbial community structures, respectively, as well as correlate the putative metabolism with the geochemistry. We observed many differences between the active and total communities. Sequences most closely related to Cyanobacteria were found to dominate the total community at both sites, but were found in small numbers in the active community. The most abundant phyla in the active community were Alphaproteobacteria, which suggests that they may have high activity even though the abundance was not as great in the total community. This suggests that, even in small numbers, bacteria are capable of contributing greatly to their environment. Principal Component Analysis (PCA) and Singular Value Decomposition (SVD) showed that iron-reducing bacteria in the active (RNA) community correlated strongly with solid phase iron oxides. SVD also showed that the putative nitrate reducers in the active community were found in greater abundance where porewater NO3- and NO2- total concentrations were elevated. Overall, the active (RNA) community correlated significantly with the geochemistry whereas the total (DNA) community did not. Therefore, RNA analysis yields a more accurate representation of how microbial communities impact geochemical cycling.

Organic matter dynamics in Technosols created with metalliferous mine residues, biochar and marble waste

NASA Astrophysics Data System (ADS)

Moreno-Barriga, Fabián; Acosta, José A.; Ángeles Muñoz, M.; Faz, Ángel; Zornoza, Raúl

2017-04-01

Creation of Technosols by use of different materials can be a sustainable strategy to reclaim mine tailings spread on the environment. A proper selection of materials is critical to efficiently contribute to soil creation, with development of soil structure, organic matter stabilization and stimulation of microbial growth. For this purpose, a short-term incubation experiment was designed with biochars derived from different feedstocks, added to tailings alone or in combination with marble waste (MaW). We aimed to assess the effects of the different materials on the evolution of C and N contents and pools, greenhouse gas (GHG) emissions, aggregate stability, and microbial biomass and activity. Results showed that carbonates provided by MaW increased pH around the target value of 8, with significant decrease in salinity by precipitation of soluble salts. Organic C and total N remained stable during the incubation, with high recalcitrant indices. Labile and soluble C and N pools were low in Technosols, with no differences with unamended tailings at the end of incubation. All biochars increased aggregate stability with regard to control by 40%, with no effect of addition of MaW. Biochars significantly increased microbial biomass C during the first 7 days of incubation; however, from this date, there were no significant differences with unamended tailings. The β-glucosidase activity was below detection limit in all samples, while arylesterase activity increased in biochar-amended samples favored by increases in pH. CO2 emissions were not significantly affected by any amendment, while N2O emissions increased with the addition of biochars with lower recalcitrance. CH4 emissions decreased in all Technosols receiving biochar. Thus, the combined use of biochar and MaW contributed to soil C sequestration and improved soil structure. However, labile sources of organic compounds would be needed to stimulate microbial populations in the Technosols. Acknowledgements This work was supported by Fundación Séneca (Agency of Science and Technology of the Region of Murcia, Spain) [grant number 18920/JLI/13].

Changes in deep-sea carbonate-hosted microbial communities associated with high and low methane flux

NASA Astrophysics Data System (ADS)

Case, D. H.; Steele, J. A.; Chadwick, G.; Mendoza, G. F.; Levin, L. A.; Orphan, V. J.

2012-12-01

Methane seeps on continental shelves are rich in authigenic carbonates built of methane-derived carbon. These authigenic carbonates are home to micro- and macroscopic communities whose compositions are thus far poorly constrained but are known to broadly depend on local methane flux. The formation of authigenic carbonates is itself a result of microbial metabolic activity, as associations of anaerobic methane oxidizing archaea (ANME) and sulfate reducing bacteria (SRB) in the sediment subsurface increase both dissolved inorganic carbon (DIC) and alkalinity in pore waters. This 1:1 increase in DIC and alkalinity promotes the precipitation of authigenic carbonates. In this study, we performed in situ manipulations to test the response of micro- and macrofaunal communities to a change in methane flux. Methane-derived authigenic carbonates from two locations at Hydrate Ridge, OR, USA (depth range 595-604 mbsl), were transplanted from "active" cold seep sites (high methane flux) to "inactive" background sites (low methane flux), and vise versa, for one year. Community diversity surveys using T-RFLP and 16S rRNA clone libraries revealed how both bacterial and archaeal assemblages respond to this change in local environment, specifically demonstrating reproducible shifts in different ANME groups (ANME-1 vs. ANME-2). Animal assemblage composition also shifted during transplantation; gastropod representation increased (relative to control rocks) when substrates were moved from inactive to active sites and polychaete, crustacean and echinoderm representation increased when substrates were moved from active to inactive sites. Combined with organic and inorganic carbon δ13C measurements and mineralogy, this unique in situ experiment demonstrates that authigenic carbonates are viable habitats, hosting microbial and macrofaunal communities capable of responding to changes in external environment over relatively short time periods.

Effect of Malathion on the Microbial Ecology of Activated Sludge

DTIC Science & Technology

2015-03-26

EFFECT OF MALATHION ON THE MICROBIAL ECOLOGY OF ACTIVATED SLUDGE THESIS Seth K. Martin, Senior Master Sergeant, USAF AFIT-ENV-MS-15-M-095 DEPARTMENT...Government and is not subject to copyright protection in the United States. AFIT-ENV-MS-15-M-095 EFFECT OF MALATHION ON THE MICROBIAL ECOLOGY OF ACTIVATED...UNLIMITED. AFIT-ENV-MS-15-M-095 EFFECT OF MALATHION ON THE MICROBIAL ECOLOGY OF ACTIVATED SLUDGE THESIS Seth K. Martin, B.S. Senior Master Sergeant

Policing the intestinal epithelial barrier: Innate immune functions of intraepithelial lymphocytes.

PubMed

Hu, Madeleine D; Jia, Luo; Edelblum, Karen L

2018-03-01

This review will explore the contribution of IELs to mucosal innate immunity and highlight the similarities in IEL functional responses to bacteria, viruses and protozoan parasite invasion. IELs rapidly respond to microbial invasion by activating host defense responses, including the production of mucus and antimicrobial peptides to prevent microbes from reaching the epithelial surface. During active infection, IELs promote epithelial cytolysis, cytokine and chemokine production to limit pathogen invasion, replication and dissemination. Commensal-induced priming of IEL effector function or continuous surveillance of the epithelium may be important contributing factors to the rapidity of response. Impaired microbial recognition, dysregulated innate immune signaling or microbial dysbiosis may limit the protective function of IELs and increase susceptibility to disease. Further understanding of the mechanisms regulating IEL surveillance and sentinel function may provide insight into the development of more effective targeted therapies designed to reinforce the mucosal barrier.

Metaproteomics reveals major microbial players and their biodegradation functions in a large-scale aerobic composting plant

PubMed Central

Liu, Dongming; Li, Mingxiao; Xi, Beidou; Zhao, Yue; Wei, Zimin; Song, Caihong; Zhu, Chaowei

2015-01-01

Composting is an appropriate management alternative for municipal solid waste; however, our knowledge about the microbial regulation of this process is still scare. We employed metaproteomics to elucidate the main biodegradation pathways in municipal solid waste composting system across the main phases in a large-scale composting plant. The investigation of microbial succession revealed that Bacillales, Actinobacteria and Saccharomyces increased significantly with respect to abundance in composting process. The key microbiologic population for cellulose degradation in different composting stages was different. Fungi were found to be the main producers of cellulase in earlier phase. However, the cellulolytic fungal communities were gradually replaced by a purely bacterial one in active phase, which did not support the concept that the thermophilic fungi are active through the thermophilic phase. The effective decomposition of cellulose required the synergy between bacteria and fungi in the curing phase. PMID:25989417

An improved biofilter to control the dissolved organic nitrogen concentration during drinking water treatment.

PubMed

Zhang, Huining; Gu, Li; Liu, Bing; Gan, Huihui; Zhang, Kefeng; Jin, Huixia; Yu, Xin

2016-09-01

Dissolved organic nitrogen (DON) is a key precursor of numerous disinfection by-products (DBPs), especially nitrogenous DBPs (N-DBPs) formed during disinfection in drinking water treatment. To effectively control DBPs, reduction of the DON concentration before the disinfection process is critical. Traditional biofilters can increase the DON concentration in the effluent, so an improved biofilter is needed. In this study, an improved biofilter was set up with two-layer columns using activated carbon and quartz sand under different influent patterns. Compared with the single-layer filter, the two-layer biofilter controlled the DON concentration more efficiently. The two-point influent biofilter controlled the DON concentration more effectively than the single-point influent biofilter. The improved biofilter resulted in an environment (including matrix, DO, and pH) suitable for microbial growth. Along the depth of the biofilter column, the environment affected the microbial biomass and microbial activity and thus affected the DON concentration.

Sequential biodegradation of TNT, RDX and HMX in a mixture.

PubMed

Sagi-Ben Moshe, S; Ronen, Z; Dahan, O; Weisbrod, N; Groisman, L; Adar, E; Nativ, R

2009-01-01

We describe TNT's inhibition of RDX and HMX anaerobic degradation in contaminated soil containing indigenous microbial populations. Biodegradation of RDX or HMX alone was markedly faster than their degradation in a mixture with TNT, implying biodegradation inhibition by the latter. The delay caused by the presence of TNT continued even after its disappearance and was linked to the presence of its intermediate, tetranitroazoxytoluene. PCR-DGGE analysis of cultures derived from the soil indicated a clear reduction in microbial biomass and diversity with increasing TNT concentration. At high-TNT concentrations (30 and 90 mg/L), only a single band, related to Clostridium nitrophenolicum, was observed after 3 days of incubation. We propose that the mechanism of TNT inhibition involves a cytotoxic effect on the RDX- and HMX-degrading microbial population. TNT inhibition in the top active soil can therefore initiate rapid transport of RDX and HMX to the less active subsurface and groundwater.

Microbial activity in Alaskan taiga soils contaminated by crude oil in 1976

DOE Office of Scientific and Technical Information (OSTI.GOV)

Monroe, E.M.; Lindstrom, J.E.; Brown, E.J.

1995-12-31

Biodegradation, often measured via microbial activity, includes destruction of environmental pollutants by living microorganisms and is dependent upon many physical and chemical factors. Effects of mineral nutrients and organic matter on biodegradation of Prudhoe Bay crude oil were investigated at a nineteen-year-old oil spill site in Alaskan taiga. Microcosms of two different soil types from the spill site; one undeveloped soil with forest litter and detritus (O horizon) and one more developed with lower organic content (A horizon), were treated with various nitrogen and phosphorus amendments, and incubated for up to six weeks. Each microcosm was sampled periodically and assayedmore » for hydrocarbon mineralization potential using radiorespirometry, for total carbon dioxide respired using gas chromatography, and for numbers of hydrocarbon-degrading bacteria and heterotrophic bacteria using most probable number counting techniques. Organic matter in the O horizon soil along with combinations of mineral nutrients were found to stimulate microbial activity. No combination of mineral nutrient additions to the A horizon soil stimulated any of the parameters above those measured in control microcosms. The results of this study indicate that adding mineral nutrients and tilling the O horizon into the A horizon of subarctic soils contaminated with crude oil, would stimulate microbial activity, and therefore the biodegradation potential, ultimately increasing the rate of destruction of crude oil in these soils.« less

A Relationship Between Microbial Activity in Soils and Phosphate Levels in Tributaries to Lake Champlain

NASA Astrophysics Data System (ADS)

Larose, R.; Lee, S.; Lane, T.

2015-12-01

Lake Champlain is a large natural freshwater lake. It forms the western boundary of Vermont and drains over half of the state. It is bordered by the state of New York on its western side and drains to the north into Quebec, Canada. Lake Champlain is the source of fresh drinking water for over quarter of a million people and provides for the livelihoods and recreational opportunities of many well beyond its borders. The health of this lake is important. During the summer month's algae blooms plague the lake. These unsightly growths, which affect other aquatic organisms, are the result of excess phosphate flowing into the lake from many sources. Examining whether there is a relationship between microbial activity in the soils bordering tributaries to Lake Champlain and phosphate levels in those tributaries sheds insight into the origins and paths by which phosphate moves into Lake Champlain. Understanding the how phosphate moves into the water system may assist in mitigation efforts.Total Phosphate levels and Total Suspended Solids were measured in second and third order streams in the Lake Champlain Basin over a three-year period. In addition microbial activity was measured within the toe, bank and upland riparian zone areas of these streams during the summer months. In general in areas showing greater microbial activity in the soil(s) there were increased levels of phosphate in the streams.

Air-cathode microbial fuel cell array: a device for identifying and characterizing electrochemically active microbes.

PubMed

Hou, Huijie; Li, Lei; de Figueiredo, Paul; Han, Arum

2011-01-15

Microbial fuel cells (MFCs) have generated excitement in environmental and bioenergy communities due to their potential for coupling wastewater treatment with energy generation and powering diverse devices. The pursuit of strategies such as improving microbial cultivation practices and optimizing MFC devices has increased power generating capacities of MFCs. However, surprisingly few microbial species with electrochemical activity in MFCs have been identified because current devices do not support parallel analyses or high throughput screening. We have recently demonstrated the feasibility of using advanced microfabrication methods to fabricate an MFC microarray. Here, we extend these studies by demonstrating a microfabricated air-cathode MFC array system. The system contains 24 individual air-cathode MFCs integrated onto a single chip. The device enables the direct and parallel comparison of different microbes loaded onto the array. Environmental samples were used to validate the utility of the air-cathode MFC array system and two previously identified isolates, 7Ca (Shewanella sp.) and 3C (Arthrobacter sp.), were shown to display enhanced electrochemical activities of 2.69 mW/m(2) and 1.86 mW/m(2), respectively. Experiments using a large scale conventional air-cathode MFC validated these findings. The parallel air-cathode MFC array system demonstrated here is expected to promote and accelerate the discovery and characterization of electrochemically active microbes. Copyright © 2010 Elsevier B.V. All rights reserved.

[Characteristics of soil microbes and enzyme activities in different degraded alpine meadows].

PubMed

Yin, Ya Li; Wang, Yu Qin; Bao, Gen Sheng; Wang, Hong Sheng; Li, Shi Xiong; Song, Mei Ling; Shao, Bao Lian; Wen, Yu Cun

2017-12-01

Soil microbial biomass C and N, microbial diversities and enzyme activity in 0-10 cm and 10-20 cm soil layers of different degraded grasslands (non-degradation, ND; light degradation, LD; moderate degradation, MD; sever degradation, SD; and black soil beach, ED) were measured by Biolog and other methods. The results showed that: 1) There were significant diffe-rences between 0-10 cm and 10-20 cm soil layers in soil microbial biomass, diversities and inver-tase activities in all grasslands. 2) The ratio of soil microbial biomass C to N decreased significantly with the grassland degradation. In the 0-10 cm soil layer, microbial biomass C and N in ND and LD were significantly higher than that in MD, SD and ED. Among the latter three kinds of grasslands, there was no difference for microbial biomass C, but microbial biomass N was lower in MD than in the other grasslands. The average color change rate (AWCD) and McIntosh Index (U) also decreased with grassland degradation, but only the reduction from ND to MD was significant. There were no differences among all grasslands for Shannon index (H) and Simpson Index (D). The urease activity was highest in MD and SD, and the activity of phosphatase and invertase was lowest in ED. In the 10-20 cm soil layer, microbial biomass C in ND and LD were significantly higher than that in the other grasslands. Microbial biomass N in LD and ED were significantly higher than that in the other grasslands. Carbon metabolism index in MD was significantly lower than that in LD and SD. AWCD and U index in ND and LD were significantly higher than that in ED. H index and D index showed no difference among different grasslands. The urease activity in ND and MD was significantly higher than that in the other grasslands. The phosphatase activity was highest in MD, and the invertase activity was lowest in MD. 3) The belowground biomass was significantly positively correlated with microbial biomass, carbon metabolic index and phosphatase activity, and the urease activity was negatively correlated with microbial biomass N, H index and D index.