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.

Microbial community dynamics in soil aggregates shape biogeochemical gas fluxes from soil profiles - upscaling an aggregate biophysical model.

PubMed

Ebrahimi, Ali; Or, Dani

2016-09-01

Microbial communities inhabiting soil aggregates dynamically adjust their activity and composition in response to variations in hydration and other external conditions. These rapid dynamics shape signatures of biogeochemical activity and gas fluxes emitted from soil profiles. Recent mechanistic models of microbial processes in unsaturated aggregate-like pore networks revealed a highly dynamic interplay between oxic and anoxic microsites jointly shaped by hydration conditions and by aerobic and anaerobic microbial community abundance and self-organization. The spatial extent of anoxic niches (hotspots) flicker in time (hot moments) and support substantial anaerobic microbial activity even in aerated soil profiles. We employed an individual-based model for microbial community life in soil aggregate assemblies represented by 3D angular pore networks. Model aggregates of different sizes were subjected to variable water, carbon and oxygen contents that varied with soil depth as boundary conditions. The study integrates microbial activity within aggregates of different sizes and soil depth to obtain estimates of biogeochemical fluxes from the soil profile. The results quantify impacts of dynamic shifts in microbial community composition on CO2 and N2 O production rates in soil profiles in good agreement with experimental data. Aggregate size distribution and the shape of resource profiles in a soil determine how hydration dynamics shape denitrification and carbon utilization rates. Results from the mechanistic model for microbial activity in aggregates of different sizes were used to derive parameters for analytical representation of soil biogeochemical processes across large scales of practical interest for hydrological and climate models. © 2016 John Wiley & Sons Ltd.

Microbial survey of a full-scale, biologically active filter for treatment of drinking water.

PubMed

White, Colin P; Debry, Ronald W; Lytle, Darren A

2012-09-01

The microbial community of a full-scale, biologically active drinking water filter was surveyed using molecular techniques. Nitrosomonas, Nitrospira, Sphingomonadales, and Rhizobiales dominated the clone libraries. The results elucidate the microbial ecology of biological filters and demonstrate that biological treatment of drinking water should be considered a viable alternative to physicochemical methods.

Increased resiliency and activity of microbial mediated carbon cycling enzymes in diversified bioenergy cropping systems

NASA Astrophysics Data System (ADS)

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

2017-12-01

Microbes are mediators of soil carbon (C) and are influenced in membership and activity by nitrogen (N) fertilization and inter-annual abiotic factors. Microbial communities and their extracellular enzyme activities (EEA) are important parameters that influence ecosystem C cycling properties and are often included in microbial explicit C cycling models. In an effort to generate model relevant, empirical findings, we investigated how both microbial community structure and C degrading enzyme activity are influenced by inter-annual variability and N inputs in bioenergy crops. Our study was performed at the Comparison of Biofuel Systems field-site from 2011 to 2014, in three bioenergy cropping systems, continuous corn (CC) and two restored prairies, both fertilized (FP) and unfertilized (P). We hypothesized microbial community structure would diverge during the prairie restoration, leading to changes in C cycling enzymes over time. Using a sequencing approach (16S and ITS) we determined the bacterial and fungal community structure response to the cropping system, fertilization, and inter-annual variability. Additionally, we used EEA of β-glucosidase, cellobiohydrolase, and β-xylosidase to determine inter-annual and ecosystem impacts on microbial activity. Our results show cropping system was a main effect for microbial community structure, with corn diverging from both prairies to be less diverse. Inter-annual changes showed that a drought occurring in 2012 significantly impacted microbial community structure in both the P and CC, decreasing microbial richness. However, FP increased in microbial richness, suggesting the application of N increased resiliency to drought. Similarly, the only year in which C cycling enzymes were impacted by ecosystem was 2012, with FP supporting higher potential enzymatic activity then CC and P. The highest EEA across all ecosystems occurred in 2014, suggesting the continued root biomass and litter build-up in this no till system provides increased C cycling activity. Our results showed that diverse cropping systems still benefit from N fertilization to confer resiliency to abiotic stress factors. Long-term studies for microbial mediation of soil C are necessary for modeling the impacts of restoration on SOC to assure inclusion of sustainability and resiliency.

Abundance and activity of soil microorganisms in Cedrus atlantica forests are more related to land use than to altitude or latitude

NASA Astrophysics Data System (ADS)

Ramírez Rojas, Irene; Perez Fernandez, María; Moreno Gallardo, Laura; Lechuga Ordoñez, Victor; Linares, Juan Carlos

2016-04-01

Several environmental traits might change the abundance and the function of soil microorganisms in forest soils by plant-mediated reactions. Few studies have related the landscape-scale forest structural diversity with the micro-scale distribution of microorganism and their activities. High mountain environments harbor ecosystems that are very sensitive to global change and hence highly vulnerable, as those of Atlantic cedar. Altitudinal gradients in mountains are orrelated with changes in vegetation. We propose that altitudinal gradients drive shifts in microbial communities and are correlated with land uses. Thus, the latitudinal and longitudinal pattern of abundance and activity of soil micro-organisms was studied in an intercontinental comparison. We investigate soil extractable organic carbon (EOC) and nitrogen and carbon, microbial biomass and microbial metabolic activities at eight different sites along the latitudinal range of Cedrus atlantica, covering different altitudes and soils characteristics both in Southern Spain and Northern Morocco. Analyses of the abundances of total bacteria, (16S rRNA gene), was conducted using the Ilumina metagenomics technique. Results show that the stands at the highest altitudes had distinct microbial and biochemical characteristics compared with other areas. Overall, microbial activity, as measured by soil respiration, is higher in forests subjected to lower human pressure than in stands highly degraded, probably reflecting the quality of litter input that results of the influence of local assemblage of different tree, shrub and annual species, though changes in the soil N and C contents. Indeed, total soil C and N contents explained the microbial properties at every scale. Our results suggest that in contrast to the observed pronounced altitudinal changes, the kind of human-mediate land management has a stronger role in defining changes in microbial composition and activities in the investigated forest systems.

Addition of Rubber to soil damages the functional diversity of soil.

PubMed

Goswami, Madhurankhi; Bhattacharyya, Purnita; Tribedi, Prosun

2017-07-01

Rubber is a polymer of isoprene, consisting mainly of cis-1,4-polyisoprene units. The unmanageable production and its irresponsible disposal pose severe threats to environmental ecology. Therefore, the current study focuses extensively on the ill-effects of Rubber disposal on soil microbial functional diversity as it reflects the health of ecosystem by acting as a key component in ecosystem productivity. To investigate the effect of Rubber on soil microbial functional diversity, soil samples were collected from landfill sites and three different soil microcosms (Rubber treated, untreated, and sterile soil) were prepared. The soil enzymatic activity was determined by fluorescein diacetate hydrolysis followed by the determination of the microbial metabolic potential and functional diversity by average well color development and Shannon-Weaver index (H), respectively. BiOLOG ECO plates were used for determining the microbial functional diversity of the soil microcosms. Higher heterotrophic microbial count as well as higher soil microbial activity was observed in Rubber untreated soil than Rubber treated soil microcosm. The result indicated that the addition of Rubber to soil reduced soil heterotrophic microbial count and soil microbial activity considerably. Similarly, soil microbial metabolic potential as well as microbial functional diversity of soil had been decreased by the addition of Rubber gloves in it. Variation in soil microbial metabolic spectrum between Rubber treated and untreated microcosm was confirmed by multivariate analysis. Collectively, all the results demonstrated that the addition of Rubber to soil reduced the soil microbial functional diversity considerably. Therefore, it is necessary for the commission of serious steps regarding Rubber disposal and protection of the environment from serious environmental issues.

Microbial Survey of a Full-Scale, Biologically Active Filter for Treatment of Drinking Water

PubMed Central

DeBry, Ronald W.; Lytle, Darren A.

2012-01-01

The microbial community of a full-scale, biologically active drinking water filter was surveyed using molecular techniques. Nitrosomonas, Nitrospira, Sphingomonadales, and Rhizobiales dominated the clone libraries. The results elucidate the microbial ecology of biological filters and demonstrate that biological treatment of drinking water should be considered a viable alternative to physicochemical methods. PMID:22752177

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

Root and Rhizosphere Bacterial Phosphatase Activity Varies with Tree Species and Soil Phosphorus Availability in Puerto Rico Tropical Forest

DOE PAGES

Cabugao, Kristine Grace M.; Timm, Collin M.; Carrell, Alyssa A.; ...

2017-10-30

Climatic conditions in tropical forests combined with the immobility of phosphorus due to sorption on mineral surfaces or result in soils typically lacking in the form of phosphorus (orthophosphate) most easily metabolized by plants and microbes. In these soils, mineralization of organic phosphorus can be the major source for labile inorganic P available for uptake. Both plants and microbes encode for phosphatase enzymes capable of mineralizing a range of organic phosphorus compounds. However, the activity of these enzymes depends on several edaphic factors including P availability and tree or microbial species. Thus, phosphatase activity in both roots and the rootmore » microbial community constitute an important role in P mineralization and P nutrient dynamics that are not well studied in tropical forests. We measured phosphatase activity in roots and bacterial isolates from the microbial community of six tree species from three forest sites differing in phosphorus availability in the Luquillo Mountains of Puerto Rico. Root and microbial phosphatase activity were both influenced by tree identity and soil phosphorus availability. However, tree identity had a larger effect on phosphatase activity (effect size = 0.12) than soil phosphorus availability (effect size = 0.07). In addition, lower amounts of P availability corresponded with higher levels of enzyme activity. In contrast, ANOSIM analysis of the weighted UniFrac distance matrix indicates that microbial community composition was more strongly controlled by soil P availability (P value < 0.05). These results indicate that root and rhizosphere microbial phosphatase activity are similarly expressed despite the slightly stronger influence of tree identity on root function and the stronger influence of P availability on microbial community composition. The low levels of orthophosphate in tropical forests, rather than prohibiting growth, have encouraged a variety of functions to adapt to minimal levels of an essential nutrient. Phosphatase activity is one such mechanism that varies in both roots and microbial community members. A thorough understanding of phosphatase activity provides insight into P mineralization in tropical forests, providing not only perspective on ecosystem function of tropical trees and microbial communities, but also in advancing efforts to improve representations of tropical forests in future climates.« less

Root and Rhizosphere Bacterial Phosphatase Activity Varies with Tree Species and Soil Phosphorus Availability in Puerto Rico Tropical Forest

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

Cabugao, Kristine Grace M.; Timm, Collin M.; Carrell, Alyssa A.

Climatic conditions in tropical forests combined with the immobility of phosphorus due to sorption on mineral surfaces or result in soils typically lacking in the form of phosphorus (orthophosphate) most easily metabolized by plants and microbes. In these soils, mineralization of organic phosphorus can be the major source for labile inorganic P available for uptake. Both plants and microbes encode for phosphatase enzymes capable of mineralizing a range of organic phosphorus compounds. However, the activity of these enzymes depends on several edaphic factors including P availability and tree or microbial species. Thus, phosphatase activity in both roots and the rootmore » microbial community constitute an important role in P mineralization and P nutrient dynamics that are not well studied in tropical forests. We measured phosphatase activity in roots and bacterial isolates from the microbial community of six tree species from three forest sites differing in phosphorus availability in the Luquillo Mountains of Puerto Rico. Root and microbial phosphatase activity were both influenced by tree identity and soil phosphorus availability. However, tree identity had a larger effect on phosphatase activity (effect size = 0.12) than soil phosphorus availability (effect size = 0.07). In addition, lower amounts of P availability corresponded with higher levels of enzyme activity. In contrast, ANOSIM analysis of the weighted UniFrac distance matrix indicates that microbial community composition was more strongly controlled by soil P availability (P value < 0.05). These results indicate that root and rhizosphere microbial phosphatase activity are similarly expressed despite the slightly stronger influence of tree identity on root function and the stronger influence of P availability on microbial community composition. The low levels of orthophosphate in tropical forests, rather than prohibiting growth, have encouraged a variety of functions to adapt to minimal levels of an essential nutrient. Phosphatase activity is one such mechanism that varies in both roots and microbial community members. A thorough understanding of phosphatase activity provides insight into P mineralization in tropical forests, providing not only perspective on ecosystem function of tropical trees and microbial communities, but also in advancing efforts to improve representations of tropical forests in future climates.« less

Soil microbial biomass, activity and community composition along altitudinal gradients in the High Arctic (Billefjorden, Svalbard)

NASA Astrophysics Data System (ADS)

Kotas, Petr; Šantrůčková, Hana; Elster, Josef; Kaštovská, Eva

2018-03-01

The unique and fragile High Arctic ecosystems are vulnerable to global climate warming. The elucidation of factors driving microbial distribution and activity in arctic soils is essential for a comprehensive understanding of ecosystem functioning and its response to environmental change. The goals of this study were to investigate microbial biomass and activity, microbial community structure (MCS), and their environmental controls in soils along three elevational transects in the coastal mountains of Billefjorden, central Svalbard. Soils from four different altitudes (25, 275, 525 and 765 m above sea level) were analyzed for a suite of characteristics including temperature regimes, organic matter content, base cation availability, moisture, pH, potential respiration, and microbial biomass and community structure using phospholipid fatty acids (PLFAs). We observed significant spatial heterogeneity of edaphic properties among transects, resulting in transect-specific effects of altitude on most soil parameters. We did not observe any clear elevation pattern in microbial biomass, and microbial activity revealed contrasting elevational patterns between transects. We found relatively large horizontal variability in MCS (i.e., between sites of corresponding elevation in different transects), mainly due to differences in the composition of bacterial PLFAs, but also a systematic altitudinal shift in MCS related to different habitat preferences of fungi and bacteria, which resulted in high fungi-to-bacteria ratios at the most elevated sites. The biological soil crusts on these most elevated, unvegetated sites can host microbial assemblages of a size and activity comparable to those of the arctic tundra ecosystem. The key environmental factors determining horizontal and vertical changes in soil microbial properties were soil pH, organic carbon content, soil moisture and Mg2+ availability.

Stoichiometry constrains microbial response to root exudation - insights from a model and a field experiment in a temperate forest

NASA Astrophysics Data System (ADS)

Drake, J. E.; Darby, B. A.; Giasson, M.-A.; Kramer, M. A.; Phillips, R. P.; Finzi, A. C.

2012-06-01

Healthy plant roots release a wide range of chemicals into soils. This process, termed root exudation, is thought to increase the activity of microbes and the exo-enzymes they synthesize, leading to accelerated rates of carbon (C) mineralization and nutrient cycling in rhizosphere soils relative to bulk soils. The causal role of exudation, however, is difficult to isolate with in-situ observations, given the complex nature of the rhizosphere environment. We investigated the potential effects of root exudation on microbial and exo-enzyme activity using a theoretical model of decomposition and a field experiment, with a specific focus on the stoichiometric constraint of nitrogen (N) availability. The field experiment isolated the effect of exudation by pumping solutions of exudate mimics through microlysimeter "root simulators" into intact forest soils over two 50-day periods. Using a combined model-experiment approach, we tested two hypotheses: (1) exudation alone is sufficient to stimulate microbial and exo-enzyme activity in rhizosphere soils, and (2) microbial response to C-exudates (carbohydrates and organic acids) is constrained by N-limitation. Experimental delivery of exudate mimics containing C and N significantly increased microbial respiration, microbial biomass, and the activity of exo-enzymes that decompose labile components of soil organic matter (SOM, e.g., cellulose, amino sugars), while decreasing the activity of exo-enzymes that degrade recalcitrant SOM (e.g., polyphenols, lignin). However, delivery of C-only exudates had no effect on microbial biomass or overall exo-enzyme activity, and only increased microbial respiration. The theoretical decomposition model produced complementary results; the modeled microbial response to C-only exudates was constrained by limited N supply to support the synthesis of N-rich microbial biomass and exo-enzymes, while exuding C and N together elicited an increase in modeled microbial biomass, exo-enzyme activity, and decomposition. Thus, hypothesis (2) was supported, while hypothesis (1) was only supported when C and N compounds were exuded together. This study supports a cause-and-effect relationship between root exudation and enhanced microbial activity, and suggests that exudate stoichiometry is an important and underappreciated driver of microbial activity in rhizosphere soils.

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.

Methane Seep Carbonates Host Distinct, Diverse, and Dynamic Microbial Assemblages

PubMed Central

Pasulka, Alexis L.; Marlow, Jeffrey J.; Grupe, Benjamin M.; Levin, Lisa A.

2015-01-01

ABSTRACT Marine methane seeps are globally distributed geologic features in which reduced fluids, including methane, are advected upward from the subsurface. As a result of alkalinity generation during sulfate-coupled methane oxidation, authigenic carbonates form slabs, nodules, and extensive pavements. These carbonates shape the landscape within methane seeps, persist long after methane flux is diminished, and in some cases are incorporated into the geologic record. In this study, microbial assemblages from 134 native and experimental samples across 5,500 km, representing a range of habitat substrates (carbonate nodules and slabs, sediment, bottom water, and wood) and seepage conditions (active and low activity), were analyzed to address two fundamental questions of seep microbial ecology: (i) whether carbonates host distinct microbial assemblages and (ii) how sensitive microbial assemblages are to habitat substrate type and temporal shifts in methane seepage flux. Through massively parallel 16S rRNA gene sequencing and statistical analysis, native carbonates are shown to be reservoirs of distinct and highly diverse seep microbial assemblages. Unique coupled transplantation and colonization experiments on the seafloor demonstrated that carbonate-associated microbial assemblages are resilient to seep quiescence and reactive to seep activation over 13 months. Various rates of response to simulated seep quiescence and activation are observed among similar phylogenies (e.g., Chloroflexi operational taxonomic units) and similar metabolisms (e.g., putative S oxidizers), demonstrating the wide range of microbial sensitivity to changes in seepage flux. These results imply that carbonates do not passively record a time-integrated history of seep microorganisms but rather host distinct, diverse, and dynamic microbial assemblages. PMID:26695630

The effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon.

PubMed

Xu, Weihui; Wang, Zhigang; Wu, Fengzhi

2015-01-01

The growth of watermelon is often threatened by Fusarium oxysporum f. sp. niveum (Fon) in successively monocultured soil, which results in economic loss. The objective of this study was to investigate the effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon and to explore the relationship between the effect and the incidence of wilt caused by Fon. The results showed that the activities of soil polyphenol oxidase, urease and invertase were increased, the microbial biomass nitrogen (MBN) and microbial biomass phosphorus (MBP) were significantly increased, and the ratio of MBC/MBN was decreased (P < 0.05). Real-time PCR analysis showed that the Fon population declined significantly in the watermelon/wheat companion system compared with the monoculture system (P < 0.05). The analysis of microbial communities showed that the relative abundance of microbial communities was changed in the rhizosphere of watermelon. Compared with the monoculture system, the relative abundances of Alphaproteobacteria, Actinobacteria, Gemmatimonadetes and Sordariomycetes were increased, and the relative abundances of Gammaproteobacteria, Sphingobacteria, Cytophagia, Pezizomycetes, and Eurotiomycetes were decreased in the rhizosphere of watermelon in the watermelon/wheat companion system; importantly, the incidence of Fusarium wilt was also decreased in the watermelon/wheat companion system. In conclusion, this study indicated that D123 wheat as a companion crop increased soil enzyme activities and microbial biomass, decreased the Fon population, and changed the relative abundance of microbial communities in the rhizosphere of watermelon, which may be related to the reduction of Fusarium wilt in the watermelon/wheat companion system.

Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments.

PubMed

Thureborn, Petter; Franzetti, Andrea; Lundin, Daniel; Sjöling, Sara

2016-01-01

Baltic Sea deep water and sediments hold one of the largest anthropogenically induced hypoxic areas in the world. High nutrient input and low water exchange result in eutrophication and oxygen depletion below the halocline. As a consequence at Landsort Deep, the deepest point of the Baltic Sea, anoxia in the sediments has been a persistent condition over the past decades. Given that microbial communities are drivers of essential ecosystem functions we investigated the microbial community metabolisms and functions of oxygen depleted Landsort Deep sediments by metatranscriptomics. Results show substantial expression of genes involved in protein metabolism demonstrating that the Landsort Deep sediment microbial community is active. Identified expressed gene suites of metabolic pathways with importance for carbon transformation including fermentation, dissimilatory sulphate reduction and methanogenesis were identified. The presence of transcripts for these metabolic processes suggests a potential for heterotrophic-autotrophic community synergism and indicates active mineralisation of the organic matter deposited at the sediment as a consequence of the eutrophication process. Furthermore, cyanobacteria, probably deposited from the water column, are transcriptionally active in the anoxic sediment at this depth. Results also reveal high abundance of transcripts encoding integron integrases. These results provide insight into the activity of the microbial community of the anoxic sediment at the deepest point of the Baltic Sea and its possible role in ecosystem functioning.

Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments

PubMed Central

Franzetti, Andrea; Lundin, Daniel; Sjöling, Sara

2016-01-01

Baltic Sea deep water and sediments hold one of the largest anthropogenically induced hypoxic areas in the world. High nutrient input and low water exchange result in eutrophication and oxygen depletion below the halocline. As a consequence at Landsort Deep, the deepest point of the Baltic Sea, anoxia in the sediments has been a persistent condition over the past decades. Given that microbial communities are drivers of essential ecosystem functions we investigated the microbial community metabolisms and functions of oxygen depleted Landsort Deep sediments by metatranscriptomics. Results show substantial expression of genes involved in protein metabolism demonstrating that the Landsort Deep sediment microbial community is active. Identified expressed gene suites of metabolic pathways with importance for carbon transformation including fermentation, dissimilatory sulphate reduction and methanogenesis were identified. The presence of transcripts for these metabolic processes suggests a potential for heterotrophic-autotrophic community synergism and indicates active mineralisation of the organic matter deposited at the sediment as a consequence of the eutrophication process. Furthermore, cyanobacteria, probably deposited from the water column, are transcriptionally active in the anoxic sediment at this depth. Results also reveal high abundance of transcripts encoding integron integrases. These results provide insight into the activity of the microbial community of the anoxic sediment at the deepest point of the Baltic Sea and its possible role in ecosystem functioning. PMID:26823996

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.

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.

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.

mRNA-Based Parallel Detection of Active Methanotroph Populations by Use of a Diagnostic Microarray

PubMed Central

Bodrossy, Levente; Stralis-Pavese, Nancy; Konrad-Köszler, Marianne; Weilharter, Alexandra; Reichenauer, Thomas G.; Schöfer, David; Sessitsch, Angela

2006-01-01

A method was developed for the mRNA-based application of microbial diagnostic microarrays to detect active microbial populations. DNA- and mRNA-based analyses of environmental samples were compared and confirmed via quantitative PCR. Results indicated that mRNA-based microarray analyses may provide additional information on the composition and functioning of microbial communities. PMID:16461725

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

USGS Publications Warehouse

Waldrop, M.P.; Harden, J.W.

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 community structure induced by fire might also affect these processes. We particularly wanted to understand whether postfire reductions in microbial biomass could affect rates of decomposition. Additionally, we compared the short-term effects of wildfire to the long-term effects of climate warming and permafrost decline. We compared soil microbial communities between control and recently burned soils that were located in areas with and without permafrost near Delta Junction, AK. In addition to soil physical variables, we quantified changes in microbial biomass, fungal biomass, fungal community composition, and C cycling processes (phenol oxidase enzyme activity, lignin decomposition, and microbial respiration). Five years following fire, organic surface horizons had lower microbial biomass, fungal biomass, and dissolved organic carbon (DOC) concentrations compared with control soils. Reductions in soil fungi were associated with reductions in phenol oxidase activity and lignin decomposition. Effects of wildfire on microbial biomass and activity in the mineral soil were minor. Microbial community composition was affected by wildfire, but the effect was greater in nonpermafrost soils. Although the presence of permafrost increased soil moisture contents, effects on microbial biomass and activity were limited to mineral soils that showed lower fungal biomass but higher activity compared with soils without permafrost. Fungal abundance and moisture were strong predictors of phenol oxidase enzyme activity in soil. Phenol oxidase enzyme activity, in turn, was linearly related to both 13C lignin decomposition and microbial respiration in incubation studies. Taken together, these results indicate that reductions in fungal biomass in postfire soils and lower soil moisture in nonpermafrost soils reduced the potential of soil heterotrophs to decompose soil carbon. Although in the field increased rates of microbial respiration can be observed in postfire soils due to warmer soil conditions, reductions in fungal biomass and activity may limit rates of decomposition. ?? 2008 The Authors Journal compilation ?? 2008 Blackwell Publishing.

The relation between growth of four microbes on six different plasterboards and biological activity of spores.

PubMed

Murtoniemi, T; Hirvonen, M-R; Nevalainen, A; Suutari, M

2003-03-01

Microbial growth on water-damaged building materials is commonly associated with adverse health effects in the occupants. We examined the growth of Stachybotrys chartarum, Aspergillus versicolor, Penicillium spinulosum, and Streptomyces californicus, isolated from water-damaged buildings, on six different brands of plasterboards. The microbial growth was compared with the biological activity of the spores, that is the potential to induce cytotoxicity and proinflammatory mediators in RAW264.7 macrophages. These results showed that the microbial growth on plasterboard depended on both the microbial strain and the brand of plasterboard used. The biological activity of spores appeared to be regulated by different growth conditions on plasterboards so that good microbial growth was associated with a low bioactivity of the spores, whereas the spores collected from plasterboard supporting only weak growth usually were biologically active. Cytotoxicity of either S. chartarum or A. versicolor did not correlate with any particular growth conditions or induced inflammatory responses. Instead, there were positive correlations between cytotoxicity and levels of induced proinflammatory cytokines for P. spinulosum and S. californicus. These data suggest that both the microbial growth on plasterboard and the resulting bioactivity of spores vary and might be affected by changing the growth conditions provided by the plasterboards.

[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.

Microbial Biomass and Activity in Geomorphic Features in Forested and Urban Restored and Degraded Streams

EPA Science Inventory

Geomorphic spatial heterogeneity affects sediment denitrification, an anaerobic microbial process that results in the loss of nitrogen (N), and other anaerobic microbial processes such as methanogenesis in urban streams. We measured sediment denitrification potential (DEA), metha...

MICROBIAL ENZYME ACTIVITY FOR CHARACTERIZING NUTRIENT LOADING TO GREAT LAKES COASTAL WETLANDS

EPA Science Inventory

Energy and material flows in aquatic ecosystems are mediated by microbial carbon and nutrient cycling. Extracellular enzymes produced by the microbial community aid in the degradation of organic matter and the resultant acquisition of limiting nutrients. Organic carbon sequestrat...

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

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.

Are Microbial Nanowires Responsible for Geoelectrical Changes at Hydrocarbon Contaminated Sites?

NASA Astrophysics Data System (ADS)

Hager, C.; Atekwana, E. A.; Gorby, Y. A.; Duris, J. W.; Allen, J. P.; Atekwana, E. A.; Ownby, C.; Rossbach, S.

2007-05-01

Significant advances in near-surface geophysics and biogeophysics in particular, have clearly established a link between geoelectrical response and the growth and enzymatic activities of microbes in geologic media. Recent studies from hydrocarbon contaminated sites suggest that the activities of distinct microbial populations, specifically syntrophic, sulfate reducing, and dissimilatory iron reducing microbial populations are a contributing factor to elevated sediment conductivity. However, a fundamental mechanistic understanding of the processes and sources resulting in the measured electrical response remains uncertain. The recent discovery of bacterial nanowires and their electron transport capabilities suggest that if bacterial nanowires permeate the subsurface, they may in part be responsible for the anomalous conductivity response. In this study we investigated the microbial population structure, the presence of nanowires, and microbial-induced alterations of a hydrocarbon contaminated environment and relate them to the sediments' geoelectrical response. Our results show that microbial communities varied substantially along the vertical gradient and at depths where hydrocarbons saturated the sediments, ribosomal intergenic spacer analysis (RISA) revealed signatures of microbial communities adapted to hydrocarbon impact. In contrast, RISA profiles from a background location showed little community variations with depth. While all sites showed evidence of microbial activity, a scanning electron microscope (SEM) study of sediment from the contaminated location showed pervasive development of "nanowire-like structures" with morphologies consistent with nanowires from laboratory experiments. SEM analysis suggests extensive alteration of the sediments by microbial Activity. We conclude that, excess organic carbon (electron donor) but limited electron acceptors in these environments cause microorganisms to produce nanowires to shuttle the electrons as they seek for distant electron acceptors. Hence, electron flow via bacterial nanowires may contribute to the geoelectrical response.

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.

Temporal dynamics of the compositions and activities of soil microbial communities post-application of the insecticide chlorantraniliprole in paddy soils.

PubMed

Wu, Meng; Liu, Jia; Li, Weitao; Liu, Ming; Jiang, Chunyu; Li, Zhongpei

2017-10-01

Chlorantraniliprole (CAP) is a newly developed insecticide widely used in rice fields in China. There has been few studies evaluating the toxicological effects of CAP on soil-associated microbes. An 85-day microcosm experiment was performed to reveal the dissipation dynamics of CAP in three types of paddy soils in subtropical China. The effects of CAP on microbial activities (microbial biomass carbon-MBC, basal soil respiration-BSR, microbial metabolic quotient-qCO 2 , acid phosphatase and sucrose invertase activities) in the soils were periodically evaluated. Microbial phospholipid fatty acid (PLFA) analysis was used to evaluate the change of soil microbial community composition on day 14 and 50 of the experiment. CAP residues were extracted using the quick, easy, cheap, effective, rugged, and safe (QuChERS) method and quantification was measured by high performance liquid chromatography (HPLC). The half-lives (DT 50 ) of CAP were in the range of 41.0-53.0 days in the three soils. The results showed that CAP did not impart negative effects on MBC during the incubation. CAP inhibited BSR, qCO 2 , acid phosphatase and sucrose invertase activities in the first 14 days of incubation in all the soils. After day 14, the soil microbial parameters of CAP-treated soils became statistically at par with their controls. Principal component analysis (PCA) determining abundance of biomarker PLFAs indicated that the application of CAP significantly changed the compositions of microbial communities in all three paddy soils on day 14 but the compositions of soil microbial communities recovered by day 50. This study indicates that CAP does not ultimately impair microbial activities and microbial compositions of these three paddy soil types. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

[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.

Biogeography and Biodiversity in Sulfide Structures of Active and Inactive Vents at Deep-Sea Hydrothermal Fields of the Southern Mariana Trough▿ †

PubMed Central

Kato, Shingo; Takano, Yoshinori; Kakegawa, Takeshi; Oba, Hironori; Inoue, Kazuhiko; Kobayashi, Chiyori; Utsumi, Motoo; Marumo, Katsumi; Kobayashi, Kensei; Ito, Yuki; Ishibashi, Jun-ichiro; Yamagishi, Akihiko

2010-01-01

The abundance, diversity, activity, and composition of microbial communities in sulfide structures both of active and inactive vents were investigated by culture-independent methods. These sulfide structures were collected at four hydrothermal fields, both on- and off-axis of the back-arc spreading center of the Southern Mariana Trough. The microbial abundance and activity in the samples were determined by analyzing total organic content, enzymatic activity, and copy number of the 16S rRNA gene. To assess the diversity and composition of the microbial communities, 16S rRNA gene clone libraries including bacterial and archaeal phylotypes were constructed from the sulfide structures. Despite the differences in the geological settings among the sampling points, phylotypes related to the Epsilonproteobacteria and cultured hyperthermophilic archaea were abundant in the libraries from the samples of active vents. In contrast, the relative abundance of these phylotypes was extremely low in the libraries from the samples of inactive vents. These results suggest that the composition of microbial communities within sulfide structures dramatically changes depending on the degree of hydrothermal activity, which was supported by statistical analyses. Comparative analyses suggest that the abundance, activity and diversity of microbial communities within sulfide structures of inactive vents are likely to be comparable to or higher than those in active vent structures, even though the microbial community composition is different between these two types of vents. The microbial community compositions in the sulfide structures of inactive vents were similar to those in seafloor basaltic rocks rather than those in marine sediments or the sulfide structures of active vents, suggesting that the microbial community compositions on the seafloor may be constrained by the available energy sources. Our findings provide helpful information for understanding the biogeography, biodiversity and microbial ecosystems in marine environments. PMID:20228114

[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.

Effect of gamma irradiation on the microbial load, nutrient composition and free radical scavenging activity of Nelumbo nucifera rhizome

NASA Astrophysics Data System (ADS)

Khattak, Khanzadi Fatima; Simpson, Thomas James; Ihasnullah

2009-03-01

The assurance of microbial quality is necessary to make plant materials suitable for human consumption and commercialization. The aim of the present study was to evaluate the possibility to apply the gamma radiation treatment on the rhizome samples of Nelumbo nucifera for microbial decontamination. The radiation processing was carried out at dose levels of 1, 2, 4 and 6 kGy. The irradiated and control samples were analyzed for microbial load, organoleptic acceptance, extraction yield, proximate composition, phenolic contents and DPPH scavenging activity. The results indicated that gamma radiation treatment significantly reduced microbial load and increased the storability of the irradiated samples. The treated samples were also acceptable sensorically. The extraction yield and phenolic contents increased with the increase of radiation dose. Gamma radiation also enhanced the DPPH scavenging activity.

Microbial and diagenetic steps leading to the mineralisation of Great Salt Lake microbialites

NASA Astrophysics Data System (ADS)

Pace, Aurélie; Bourillot, Raphaël; Bouton, Anthony; Vennin, Emmanuelle; Galaup, Serge; Bundeleva, Irina; Patrier, Patricia; Dupraz, Christophe; Thomazo, Christophe; Sansjofre, Pierre; Yokoyama, Yusuke; Franceschi, Michel; Anguy, Yannick; Pigot, Léa; Virgone, Aurélien; Visscher, Pieter T.

2016-08-01

Microbialites are widespread in modern and fossil hypersaline environments, where they provide a unique sedimentary archive. Authigenic mineral precipitation in modern microbialites results from a complex interplay between microbial metabolisms, organic matrices and environmental parameters. Here, we combined mineralogical and microscopic analyses with measurements of metabolic activity in order to characterise the mineralisation of microbial mats forming microbialites in the Great Salt Lake (Utah, USA). Our results show that the mineralisation process takes place in three steps progressing along geochemical gradients produced through microbial activity. First, a poorly crystallized Mg-Si phase precipitates on alveolar extracellular organic matrix due to a rise of the pH in the zone of active oxygenic photosynthesis. Second, aragonite patches nucleate in close proximity to sulfate reduction hotspots, as a result of the degradation of cyanobacteria and extracellular organic matrix mediated by, among others, sulfate reducing bacteria. A final step consists of partial replacement of aragonite by dolomite, possibly in neutral to slightly acidic porewater. This might occur due to dissolution-precipitation reactions when the most recalcitrant part of the organic matrix is degraded. The mineralisation pathways proposed here provide pivotal insight for the interpretation of microbial processes in past hypersaline environments.

Microbial activity in the marine deep biosphere: progress and prospects.

PubMed

Orcutt, Beth N; Larowe, Douglas E; Biddle, Jennifer F; Colwell, Frederick S; Glazer, Brian T; Reese, Brandi Kiel; Kirkpatrick, John B; Lapham, Laura L; Mills, Heath J; Sylvan, Jason B; Wankel, Scott D; Wheat, C Geoff

2013-01-01

The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists-all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these "extreme" environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) "theme team" on microbial activity (www.darkenergybiosphere.org).

Microbial activity in the marine deep biosphere: progress and prospects

PubMed Central

Orcutt, Beth N.; LaRowe, Douglas E.; Biddle, Jennifer F.; Colwell, Frederick S.; Glazer, Brian T.; Reese, Brandi Kiel; Kirkpatrick, John B.; Lapham, Laura L.; Mills, Heath J.; Sylvan, Jason B.; Wankel, Scott D.; Wheat, C. Geoff

2013-01-01

The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists—all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these “extreme” environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) “theme team” on microbial activity (www.darkenergybiosphere.org). PMID:23874326

Anion effects on anti-microbial activity of poly[1-vinyl-3-(2-sulfoethyl imidazolium betaine)].

PubMed

Garg, Godawari; Chauhan, Ghanshyam S; Gupta, Reena; Ahn, J-H

2010-04-01

Recent investigations in the anti-microbial properties of the functional polymers are predominantly focused on the structure of the cationic moieties. In the present study, we investigated that the nature of the anion present in polysulfobetaines affects activity against certain microorganisms and their anti-microbial properties have been rationalized in terms of the structure-activity relationship. Vinyl imidazolium-based polysulfobetaines were prepared by the quaternization of poly(N-vinyl imidazole) with sodium salt of 2-bromo ethanesulfonic acid. The bromide counter anion of the resulting polymer was exchanged with different anions to generate a series of polymers. These were characterized by FTIR, DSC, XRD, SEM, elemental analysis (C, H, N and S) and viscosity measurements. The anti-microbial activity studies were carried against three fungi (Aspergillus niger, Byssochlamys fulva and Mucor circenelliods) and two bacteria (Bacillus coagulans BTS-3 and Pseudomonas aeruginosa BTS-2). The nature of the anion affects the structure of polysulfobetaine by realignment of polymer chains. The anion-dependent anti-microbial properties of polysulfobetaines result from the interaction of the microbes at the polymer interface. Copyright 2009 Elsevier Inc. All rights reserved.

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...

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.

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

Nearing the cold-arid limits of microbial life in permafrost of an upper dry valley, Antarctica.

PubMed

Goordial, Jacqueline; Davila, Alfonso; Lacelle, Denis; Pollard, Wayne; Marinova, Margarita M; Greer, Charles W; DiRuggiero, Jocelyn; McKay, Christopher P; Whyte, Lyle G

2016-07-01

Some of the coldest and driest permafrost soils on Earth are located in the high-elevation McMurdo Dry Valleys (MDVs) of Antarctica, but little is known about the permafrost microbial communities other than that microorganisms are present in these valleys. Here, we describe the microbiology and habitable conditions of highly unique dry and ice-cemented permafrost in University Valley, one of the coldest and driest regions in the MDVs (1700 m above sea level; mean temperature -23 °C; no degree days above freezing), where the ice in permafrost originates from vapour deposition rather than liquid water. We found that culturable and total microbial biomass in University Valley was extremely low, and microbial activity under ambient conditions was undetectable. Our results contrast with reports from the lower-elevation Dry Valleys and Arctic permafrost soils where active microbial populations are found, suggesting that the combination of severe cold, aridity, oligotrophy of University Valley permafrost soils severely limit microbial activity and survival.

Nearing the cold-arid limits of microbial life in permafrost of an upper dry valley, Antarctica

PubMed Central

Goordial, Jacqueline; Davila, Alfonso; Lacelle, Denis; Pollard, Wayne; Marinova, Margarita M; Greer, Charles W; DiRuggiero, Jocelyn; McKay, Christopher P; Whyte, Lyle G

2016-01-01

Some of the coldest and driest permafrost soils on Earth are located in the high-elevation McMurdo Dry Valleys (MDVs) of Antarctica, but little is known about the permafrost microbial communities other than that microorganisms are present in these valleys. Here, we describe the microbiology and habitable conditions of highly unique dry and ice-cemented permafrost in University Valley, one of the coldest and driest regions in the MDVs (1700 m above sea level; mean temperature −23 °C; no degree days above freezing), where the ice in permafrost originates from vapour deposition rather than liquid water. We found that culturable and total microbial biomass in University Valley was extremely low, and microbial activity under ambient conditions was undetectable. Our results contrast with reports from the lower-elevation Dry Valleys and Arctic permafrost soils where active microbial populations are found, suggesting that the combination of severe cold, aridity, oligotrophy of University Valley permafrost soils severely limit microbial activity and survival. PMID:27323892

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

Soil Microbial Properties and Plant Growth Responses to Carbon and Water Addition in a Temperate Steppe: The Importance of Nutrient Availability

PubMed Central

Guo, Chengyuan; Wang, Renzhong; Xiao, Chunwang

2012-01-01

Background Global climatic change is generally expected to stimulate net primary production, and consequently increase soil carbon (C) input. The enhanced C input together with potentially increased precipitation may affect soil microbial processes and plant growth. Methodology/Principal Findings To examine the effects of C and water additions on soil microbial properties and plant growth, we conducted an experiment lasting two years in a temperate steppe of northeastern China. We found that soil C and water additions significantly affected microbial properties and stimulated plant growth. Carbon addition significantly increased soil microbial biomass and activity but had a limited effect on microbial community structure. Water addition significantly increased soil microbial activity in the first year but the response to water decreased in the second year. The water-induced changes of microbial activity could be ascribed to decreased soil nitrogen (N) availability and to the shift in soil microbial community structure. However, no water effect on soil microbial activity was visible under C addition during the two years, likely because C addition alleviated nutrient limitation of soil microbes. In addition, C and water additions interacted to affect plant functional group composition. Water addition significantly increased the ratio of grass to forb biomass in C addition plots but showed only minor effects under ambient C levels. Our results suggest that soil microbial activity and plant growth are limited by nutrient (C and N) and water availability, and highlight the importance of nutrient availability in modulating the responses of soil microbes and plants to potentially increased precipitation in the temperate steppe. Conclusions/Significance Increased soil C input and precipitation would show significant effects on soil microbial properties and plant growth in the temperate steppe. These findings will improve our understanding of the responses of soil microbes and plants to the indirect and direct climate change effects. PMID:22496905

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.

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

RHIZOSPHERE MICROBIOLOGY OF CHLORINATED ETHENE CONTAMINATED SOILS: EFFECTS ON PHOSPHOLIPID FATTY ACID CONTENT

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

Brigmon, R. L.; Stanhopc, A.; Franck, M. M.

2005-05-26

Microbial degradation of chlorinated ethenes (CE) in rhizosphere soils was investigated at seepline areas impacted by CE plumes. Successful bioremediation of CE in rhizosphere soils is dependent on microbial activity, soil types, plant species, and groundwater CE concentrations. Seepline soils were exposed to trichloroethylene (TCE) and perchloroethylene (PCE) in the 10-50 ppb range. Greenhouse soils were exposed to 2-10 ppm TCE. Plants at the seepline were poplar and pine while the greenhouse contained sweet gum, willow, pine, and poplar. Phospholipid fatty acid (PLFA) analyses were performed to assess the microbial activity in rhizosphere soils. Biomass content was lowest in themore » nonvegetated control soil and highest in the Sweet Gum soil. Bacterial rhizhosphere densities, as measured by PLFA, were similar in different vegetated soils while fungi biomass was highly variable. The PLFA soil profiles showed diverse microbial communities primarily composed of Gram-negative bacteria. Adaptation of the microbial community to CE was determined by the ratio of {omega}7t/{omega}7c fatty acids. Ratios (16:1{omega}7v16:1{omega}7c and 18:l{omega}7t/18:1{omega}7c) greater than 0.1 were demonstrated in soils exposed to higher CE concentrations (10-50 ppm), indicating an adaptation to CE resulting in decreased membrane permeability. Ratios of cyclopropyl fatty acids showed that the vegetated control soil sample contained the fastest microbial turnover rate and least amount of environmental stress. PLFA results provide evidence that sulfate reducing bacteria (SRB) are active in these soils. Microcosm studies with these soils showed CE dechlorinating activity was occurring. This study demonstrates microbial adaptation to environmental contamination and supports the application of natural soil rhizosphere activity as a remedial strategy.« less

Microbial translocation and microbiome dsybiosis in HIV-associated immune activation

PubMed Central

Zevin, Alexander S.; McKinnon, Lyle; Burgener, Adam; Klatt, Nichole R.

2016-01-01

Purpose of Review To describe the mechanisms and consequences of both microbial translocation and microbial dysbiosis in HIV infection. Recent Findings Microbes in HIV are likely playing a large role in contributing to HIV pathogenesis, morbidities and mortality. Two major disruptions to microbial systems in HIV infection include microbial translocation and microbiome dysbiosis. Microbial translocation occurs when the bacteria (or bacterial products) that should be in the lumen of the intestine translocate across the tight epithelial barrier into systemic circulation, where they contribute to inflammation and pathogenesis. This is associated with poorer health outcomes in HIV infected individuals. In addition, microbial populations in the GI tract are also altered after HIV infection, resulting in microbiome dysbiosis, which further exacerbates microbial translocation, epithelial barrier disruption, inflammation, and mucosal immune functioning. Summary Altered microbial regulation in HIV infection can lead to poor health outcomes, and understanding the mechanisms underlying microbial dysbiosis and translocation may result in novel pathways for therapeutic interventions. PMID:26679414

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

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

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

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.

Microbial stress-response physiology and its implications for ecosystem function.

PubMed

Schimel, Joshua; Balser, Teri C; Wallenstein, Matthew

2007-06-01

Microorganisms have a variety of evolutionary adaptations and physiological acclimation mechanisms that allow them to survive and remain active in the face of environmental stress. Physiological responses to stress have costs at the organismal level that can result in altered ecosystem-level C, energy, and nutrient flows. These large-scale impacts result from direct effects on active microbes' physiology and by controlling the composition of the active microbial community. We first consider some general aspects of how microbes experience environmental stresses and how they respond to them. We then discuss the impacts of two important ecosystem-level stressors, drought and freezing, on microbial physiology and community composition. Even when microbial community response to stress is limited, the physiological costs imposed on soil microbes are large enough that they may cause large shifts in the allocation and fate of C and N. For example, for microbes to synthesize the osmolytes they need to survive a single drought episode they may consume up to 5% of total annual net primary production in grassland ecosystems, while acclimating to freezing conditions switches Arctic tundra soils from immobilizing N during the growing season to mineralizing it during the winter. We suggest that more effectively integrating microbial ecology into ecosystem ecology will require a more complete integration of microbial physiological ecology, population biology, and process ecology.

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.

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.

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.

[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.

Effect of plant harvesting on the performance of constructed wetlands during winter: radial oxygen loss and microbial characteristics.

PubMed

Wang, Qian; Xie, Huijun; Zhang, Jian; Liang, Shuang; Ngo, Huu Hao; Guo, Wenshan; Liu, Chen; Zhao, Congcong; Li, Hao

2015-05-01

The aboveground tissue of plants is important for providing roots with constant photosynthetic resources. However, the aboveground biomass is usually harvested before winter to maintain the permanent removal of nutrients. In this work, the effects of harvest on plants' involvement in oxygen input as well as in microbial abundance and activity were investigated in detail. Three series of constructed wetlands with integrated plants ("unharvested"), harvested plants ("harvested"), and fully cleared plants ("cleared") were set up. Better performance was found in the unharvested units, with the radial oxygen loss (ROL) rates ranging from 0.05 to 0.59 μmol O₂/h/plant, followed by the harvested units that had relatively lower ROL rates (0.01 to 0.52 μmol O₂/h/plant). The cleared units had the lowest removal efficiency, which had no rhizome resources from the plants. The microbial population and activity were highest in the unharvested units, followed by the harvested and cleared units. Results showed that bacterial abundances and enhanced microbial activity were ten times higher on root surfaces compared with sands. These results indicate that late autumn harvesting of the aboveground biomass exhibited negative effects on plant ROL as well as on the microbial population and activity during the following winter.

Do Aloe vera and Ageratum conyzoides enhance the anti-microbial activity of traditional medicinal soft soaps (Osedudu)?

PubMed

Moody, J O; Adebiyi, O A; Adeniyi, B A

2004-05-01

The Nigerian traditional soft soaps prepared using varied locally sourced raw materials such as cocoa pod ash (Theobroma cacao) palm kernel shaft ash (Elaies guineensis) have been evaluated for their physico-chemical properties and anti-microbial activities using standard pharmacopoeia protocols and an in-vitro agar diffusion bioassay method. The anti-microbial evaluation was done with and without incorporation of Aloe vera and Ageratum conyzoides extractives into the soap samples. Results showed that the physico-chemical properties of the soaps are dependent on the raw materials utilised. The incorporated medicinal plants used in this study, however, did not show any significant effect on the anti-microbial activities exhibited by the various soaps against the bacterial and fungal test organisms. Copyright 2004 Elsevier Ireland Ltd.

Microbial catabolic activities are naturally selected by metabolic energy harvest rate.

PubMed

González-Cabaleiro, Rebeca; Ofiţeru, Irina D; Lema, Juan M; Rodríguez, Jorge

2015-12-01

The fundamental trade-off between yield and rate of energy harvest per unit of substrate has been largely discussed as a main characteristic for microbial established cooperation or competition. In this study, this point is addressed by developing a generalized model that simulates competition between existing and not experimentally reported microbial catabolic activities defined only based on well-known biochemical pathways. No specific microbial physiological adaptations are considered, growth yield is calculated coupled to catabolism energetics and a common maximum biomass-specific catabolism rate (expressed as electron transfer rate) is assumed for all microbial groups. Under this approach, successful microbial metabolisms are predicted in line with experimental observations under the hypothesis of maximum energy harvest rate. Two microbial ecosystems, typically found in wastewater treatment plants, are simulated, namely: (i) the anaerobic fermentation of glucose and (ii) the oxidation and reduction of nitrogen under aerobic autotrophic (nitrification) and anoxic heterotrophic and autotrophic (denitrification) conditions. The experimentally observed cross feeding in glucose fermentation, through multiple intermediate fermentation pathways, towards ultimately methane and carbon dioxide is predicted. Analogously, two-stage nitrification (by ammonium and nitrite oxidizers) is predicted as prevailing over nitrification in one stage. Conversely, denitrification is predicted in one stage (by denitrifiers) as well as anammox (anaerobic ammonium oxidation). The model results suggest that these observations are a direct consequence of the different energy yields per electron transferred at the different steps of the pathways. Overall, our results theoretically support the hypothesis that successful microbial catabolic activities are selected by an overall maximum energy harvest rate.

Respiration and enzymatic activities as indicators of stabilization of sewage sludge composting.

PubMed

Nikaeen, Mahnaz; Nafez, Amir Hossein; Bina, Bijan; Nabavi, BiBi Fatemeh; Hassanzadeh, Akbar

2015-05-01

The objective of this work was to study the evolution of physico-chemical and microbial parameters in the composting process of sewage sludge (SS) with pruning wastes (PW) in order to compare these parameters with respect to their applicability in the evaluation of organic matter (OM) stabilization. To evaluate the composting process and organic matter stability, different microbial activities were compared during composting of anaerobically digested SS with two volumetric ratios, 1:1 and 3:1 of PW:SS and two aeration techniques including aerated static piles (ASP) and turned windrows (TW). Dehydrogenase activity, fluorescein diacetate hydrolysis, and specific oxygen uptake rate (SOUR) were used as microbial activity indices. These indices were compared with traditional parameters, including temperature, pH, moisture content, organic matter, and C/N ratio. The results showed that the TW method and 3:1 (PW:SS) proportion was superior to the ASP method and 1:1 proportion, since the former accelerate the composting process by catalyzing the OM stabilization. Enzymatic activities and SOUR, which reflect microbial activity, correlated well with temperature fluctuations. Based on these results it appears that SOUR and the enzymatic activities are useful parameters to monitor the stabilization of SS compost. Copyright © 2015 Elsevier Ltd. All rights reserved.

Soil Microbial Biomass, Basal Respiration and Enzyme Activity of Main Forest Types in the Qinling Mountains

PubMed Central

Cheng, Fei; Peng, Xiaobang; Zhao, Peng; Yuan, Jie; Zhong, Chonggao; Cheng, Yalong; Cui, Cui; Zhang, Shuoxin

2013-01-01

Different forest types exert essential impacts on soil physical-chemical characteristics by dominant tree species producing diverse litters and root exudates, thereby further regulating size and activity of soil microbial communities. However, the study accuracy is usually restricted by differences in climate, soil type and forest age. Our objective is to precisely quantify soil microbial biomass, basal respiration and enzyme activity of five natural secondary forest (NSF) types with the same stand age and soil type in a small climate region and to evaluate relationship between soil microbial and physical-chemical characters. We determined soil physical-chemical indices and used the chloroform fumigation-extraction method, alkali absorption method and titration or colorimetry to obtain the microbial data. Our results showed that soil physical-chemical characters remarkably differed among the NSFs. Microbial biomass carbon (Cmic) was the highest in wilson spruce soils, while microbial biomass nitrogen (Nmic) was the highest in sharptooth oak soils. Moreover, the highest basal respiration was found in the spruce soils, but mixed, Chinese pine and spruce stands exhibited a higher soil qCO2. The spruce soils had the highest Cmic/Nmic ratio, the greatest Nmic/TN and Cmic/Corg ratios were found in the oak soils. Additionally, the spruce soils had the maximum invertase activity and the minimum urease and catalase activities, but the maximum urease and catalase activities were found in the mixed stand. The Pearson correlation and principle component analyses revealed that the soils of spruce and oak stands obviously discriminated from other NSFs, whereas the others were similar. This suggested that the forest types affected soil microbial properties significantly due to differences in soil physical-chemical features. PMID:23840671

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.

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

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.

Effect of monospecific and mixed sea-buckthorn (Hippophae rhamnoides) plantations on the structure and activity of soil microbial communities.

PubMed

Yu, Xuan; Liu, Xu; Zhao, Zhong; Liu, Jinliang; Zhang, Shunxiang

2015-01-01

This study aims to evaluate the effect of different afforestation models on soil microbial composition in the Loess Plateau in China. In particular, we determined soil physicochemical properties, enzyme activities, and microbial community structures in the top 0 cm to 10 cm soil underneath a pure Hippophae rhamnoides (SS) stand and three mixed stands, namely, H. rhamnoides and Robinia pseucdoacacia (SC), H. rhamnoides and Pinus tabulaeformis (SY), and H. rhamnoides and Platycladus orientalis (SB). Results showed that total organic carbon (TOC), total nitrogen, and ammonium (NH4(+)) contents were higher in SY and SB than in SS. The total microbial biomass, bacterial biomass, and Gram+ biomass of the three mixed stands were significantly higher than those of the pure stand. However, no significant difference was found in fungal biomass. Correlation analysis suggested that soil microbial communities are significantly and positively correlated with some chemical parameters of soil, such as TOC, total phosphorus, total potassium, available phosphorus, NH4(+) content, nitrate content (NH3(-)), and the enzyme activities of urease, peroxidase, and phosphatase. Principal component analysis showed that the microbial community structures of SB and SS could clearly be discriminated from each other and from the others, whereas SY and SC were similar. In conclusion, tree species indirectly but significantly affect soil microbial communities and enzyme activities through soil physicochemical properties. In addition, mixing P. tabulaeformis or P. orientalis in H. rhamnoides plantations is a suitable afforestation model in the Loess Plateau, because of significant positive effects on soil nutrient conditions, microbial community, and enzyme activities over pure plantations.

Soil microbial activities in a constructed soil reed-bed under cheese-dairy farm effluents.

PubMed

Farnet, A M; Prudent, P; Cigna, M; Gros, R

2008-09-01

Soil microbial activities in a reed-bed used for effluent purification of a small cheese-dairy farm under a Mediterranean climate were described and studied. This work aims to demonstrate (i) whether certain enzyme activities used as bioindicators of dairy waste degradation (beta-galactosidase and protease) vary over time, which might influence organic matter degradation and (ii) whether specific microbial communities are selected through contact with the discarded effluent using community level catabolic profiles (CLCPs). beta-galactosidase and protease activities were followed in a 14-month monitoring experiment. These enzyme activities were strongly expressed during the whey-discarding period from February to May. CLCPs using Biolog Ecoplate showed great microbial diversity, as described by Shannon-Weaver index, and no difference was observed in microbial diversity between areas at the receiving end of the reed-bed (where effluent was discarded) and those at the opposite end. This may be explained by successive environmental factors which made enzyme activities vary: whey discarded from February to May and Mediterranean climate conditions (drying-rewetting effects on summer). Microbial enumeration using epifluorescence microscopy also showed a pattern linked to Mediterranean conditions with a drastic decrease in biomass during summer drought. These results on functional biodiversity were correlated with high purification yields: the minimum decrease in Biological Demand in Oxygen was 84% and that in suspended solids was 75%.

Assessment of Anaerobic Metabolic Activity and Microbial Diversity in a Petroleum-Contaminated Aquifer Using Push-Pull Tests in Combination With Molecular Tools and Stable Isotopes

NASA Astrophysics Data System (ADS)

Schroth, M. H.; Kleikemper, J.; Pombo, S. A.; Zeyer, J.

2002-12-01

In the past, studies on microbial communities in natural environments have typically focused on either their structure or on their metabolic function. However, linking structure and function is important for understanding microbial community dynamics, in particular in contaminated environments. We will present results of a novel combination of a hydrogeological field method (push-pull tests) with molecular tools and stable isotope analysis, which was employed to quantify anaerobic activities and associated microbial diversity in a petroleum-contaminated aquifer in Studen, Switzerland. Push-pull tests consisted of the injection of test solution containing a conservative tracer and reactants (electron acceptors, 13C-labeled carbon sources) into the aquifer anoxic zone. Following an incubation period, the test solution/groundwater mixture was extracted from the same location. Metabolic activities were computed from solute concentrations measured during extraction. Simultaneously, microbial diversity in sediment and groundwater was characterized by using fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE), as well as phospholipids fatty acid (PLFA) analysis in combination with 13C isotopic measurements. Results from DGGE analyses provided information on the general community structure before, during and after the tests, while FISH yielded information on active populations. Moreover, using 13C-labeling of microbial PLFA we were able to directly link carbon source assimilation in an aquifer to indigenous microorganisms while providing quantitative information on respective carbon source consumption.

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.

Two-dimensional distribution of microbial activity and flow patterns within naturally fractured chalk.

PubMed

Arnon, Shai; Ronen, Zeev; Adar, Eilon; Yakirevich, Alexander; Nativ, Ronit

2005-10-01

The two-dimensional distribution of flow patterns and their dynamic change due to microbial activity were investigated in naturally fractured chalk cores. Long-term biodegradation experiments were conducted in two cores ( approximately 20 cm diameter, 31 and 44 cm long), intersected by a natural fracture. 2,4,6-tribromophenol (TBP) was used as a model contaminant and as the sole carbon source for aerobic microbial activity. The transmissivity of the fractures was continuously reduced due to biomass accumulation in the fracture concurrent with TBP biodegradation. From multi-tracer experiments conducted prior to and following the microbial activity, it was found that biomass accumulation causes redistribution of the preferential flow channels. Zones of slow flow near the fracture inlet were clogged, thus further diverting the flow through zones of fast flow, which were also partially clogged. Quantitative evaluation of biodegradation and bacterial counts supported the results of the multi-tracer tests, indicating that most of the bacterial activity occurs close to the inlet. The changing flow patterns, which control the nutrient supply, resulted in variations in the concentrations of the chemical constituents (TBP, bromide and oxygen), used as indicators of biodegradation.

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.

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

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.

Sediment microbial activity and its relation to environmental variables along the eastern Gulf of Finland coastline

NASA Astrophysics Data System (ADS)

Polyak, Yulia; Shigaeva, Tatyana; Gubelit, Yulia; Bakina, Ludmila; Kudryavtseva, Valentina; Polyak, Mark

2017-07-01

Sediment microbial activity and its relationship with the main environmental factors and pollutants were examined in the coastal area of the eastern Gulf of Finland, Baltic Sea. The activity of two common oxidoreductase enzymes: dehydrogenase (DA) and catalase (CA) varied significantly between 13 study sites. In the Neva Bay the highest microbial activities (DA: 2.64 mg TFF (10 g- 1) day- 1, CA: 6.29 mg H2O2 g- 1) were recorded, while in the outer estuary the minimum values of dehydrogenase and catalase were measured. DA, CA, and abundances of culturable heterotrophic bacteria (CHB) were positively correlated with each other, while biomass of green opportunistic algae was independent of both microbial activities and CHB. Enzymatic activity was found to be strongly positively correlated with sediment particle size and organic matter content, but unrelated to the other studied environmental parameters (temperature, pH, and salinity). Principal components analysis (PCA), controlling for environmental variables, supported direct effects of metal and oil contamination on sediment microbial activity. Also it had shown the similar patterns for algal biomass and metals. Our results suggest that copper and hydrocarbons are the main anthropogenic variables influencing enzyme distribution along the eastern Gulf of Finland coastline.

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.

Microbial enzymatic activity and secondary production in sediments affected by the sedimentation pulse following the Deepwater Horizon oil spill

NASA Astrophysics Data System (ADS)

Ziervogel, Kai; Joye, Samantha B.; Arnosti, Carol

2016-07-01

A large fraction of the spilled oil from the Deepwater Horizon (DwH) blowout in April 2010 reached the seafloor via sinking oil aggregates (oil snow) in a massive sedimentation that continued until late summer 2010 (;Dirty blizzard;). We measured heterotrophic microbial metabolic rates as well as porewater and sedimentary geochemical parameters at sites proximate to and distant from the wellhead to investigate microbial responses to the "Dirty Blizzard". Lipase activity and rates of bacterial protein production were highest and leucine-aminopeptidase activity was lowest in 0-2 cm sediment layers at the sites proximate to the wellhead. These results suggest that the presence of the oil snow stimulated benthic microbial enzymatic hydrolysis of oil-derived organic matter that was depleted in peptide substrates at the time of our sampling. The strong gradients in porewater DOC, NH4+, and HPO43- concentrations in the upper 6 cm of the sediments near the wellhead likewise indicate elevated heterotrophic responses to recently-sedimented organic matter. In addition to enhanced microbial activities in the 0-2 cm sediment layers, we found peaks of total organic carbon and elevated microbial metabolic rates down to 10 cm at the sites closest to the wellhead. Our results indicate distinct benthic metabolic responses of heterotrophic microbial communities, even three months after the ending of the "Dirty Blizzard". Compared to other deep-sea environments, however, metabolic rates associated with the recently deposited particulate matter around the wellhead were only moderately enhanced. Oil contaminants at the seafloor may therefore have prolonged residence times, enhancing the potential for longer-term ecological consequences in deep-sea environments.

[Spatiotemporal evolvement of soil microbiological characteristics in upland fields with different utilization duration in Cixi, Zhejiang Province].

PubMed

Hu, Jun-Li; Lin, Xian-Gui; Yin, Rui; Chu, Hai-Yan; Zhang, Hua-Yong; Wang, Jun-Hua; Cao, Zhi-Hong

2008-09-01

The microbial number, microbial biomass, and enzymatic activities in five upland soils under agricultural utilization for 50-700 years were determined, with the correlations between soil microbiological characteristics and agricultural utilization duration analyzed. In the meantime, the functional diversity of microbes in soils having been utilized for 50, 100, and 700 years were investigated. The results showed that at the early stage (< 100 years) of agricultural utilization, the number of soil fungi (F) had a slight increase, while the bacterial number (B), B/F ratio, microbial biomass C (C(mic)), microbial biomass N (N(mic)), and the activities of catalase, invertase and urease all decreased markedly. After utilized for more than 100 years, the F decreased significantly, while the B, B/F ratio, C(mic), N(mic), and the activities of test enzymes all tended to increase. During the whole utilization period from 50 to 700 years, the C(mic)/N(mic) ratio had a significant increase with year. The Shannon, Simpson, and McIntosh indices of soil microbial community had the same responses to the agricultural utilization duration as the bacterial number, microbial biomass, and enzymatic activities. All of these indicated that in the upland fields in Cixi of Zhejiang Province, shifts of soil microbial community occurred with increasing agricultural utilization duration, and soil microbiological quality had an overall increase after 100 years agricultural utilization.

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.

Microbially mediated alteration of crystalline basalts as identified from analogical reactive percolation experiments

NASA Astrophysics Data System (ADS)

Moore, Rachael; Ménez, Bénédicte; Stéphant, Sylvian; Dupraz, Sébastien; Ranchou-Peyruse, Magali; Ranchou-Peyruse, Anthony; Gérard, Emmanuelle

2017-04-01

Alteration in the ocean crust through fluid circulation is an ongoing process affecting the first kilometers and at low temperatures some alteration may be microbially mediated. Hydrothermal activity through the hard rock basement supports diverse microbial communities within the rock by providing nutrient and energy sources. Currently, the impact of basement hosted microbial communities on alteration is poorly understood. In order to identify and quantify the nature of microbially mediated alteration two reactive percolation experiments mimicking circulation of CO2 enriched ground water were performed at 35 °C and 30 bar for 21 days each. The experiments were performed using a crystalline basalt substrate from an earlier drilled deep Icelandic aquifer. One experiment was conducted on sterile rock while the other was conducted with the addition of a microbial inoculate derived from groundwater enrichment cultures obtained from the same aquifer. µCT on the experimental basaltic substrate before and after the reactive percolation experiment along with synchrotron radiation x-ray tomographic microscopy and the mineralogical characterization of resulting material allows for the comparative volumetric quantification of dissolution and precipitation. The unique design of this experiment allows for the identification of alteration which occurs solely abiotically and of microbially mediated alteration. Experimental results are compared to natural basaltic cores from Iceland retrieved following a large field CO2 injection experiment that stimulated microbial activity at depth.

[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.

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.

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.

[Effect of tillage system on soil animal, microorganism and enzyme activity in paddy field].

PubMed

Gao, Ming; Zhou, Baotong; Wei, Chaofu; Xie, Deti; Zhang, Lei

2004-07-01

A long-term experiment showed that under ridge-no-tillage, the amount of soil animal in 0 - 20 cm layer was 14700 ind. x m(-2), while under no-tillage and fallow in winter, paddy-upland rotation, and conventional tillage, it was 10450, 7950 and 6275 ind. x m(-2), respectively. Soil microbial biomass and microbial biomass N were more in spring and autumn, and less in summer. Soil enzyme activity was higher in surface soil layer and lower in bottom soil layer. The amount of soil animal, microbial biomass and microbial biomass N and soil enzyme activity was in order of ridge-no-tillage > paddy-upland rotation > no-tillage and fallow in winter > conventional tillage. The results also indicated that ridge-no-tillage was advantageous to improve soil ecological environment and soil fertility in paddy field.

Molecular phylogenetic and chemical analyses of the microbial mats in deep-sea cold seep sediments at the northeastern Japan Sea.

PubMed

Arakawa, Shizuka; Sato, Takako; Sato, Rumi; Zhang, Jing; Gamo, Toshitaka; Tsunogai, Urumu; Hirota, Akinari; Yoshida, Yasuhiko; Usami, Ron; Inagaki, Fumio; Kato, Chiaki

2006-08-01

Microbial communities inhabiting deep-sea cold seep sediments at the northeastern Japan Sea were characterized by molecular phylogenetic and chemical analyses. White patchy microbial mats were observed along the fault offshore the Hokkaido Island and sediment samples were collected from two stations at the southern foot of the Shiribeshi seamount (M1 site at a depth of 2,961 m on the active fault) and off the Motta Cape site (M2 site at a depth of 3,064 m off the active fault). The phylogenetic and terminal-restriction fragment polymorphism analyses of PCR-amplified 16S rRNA genes revealed that microbial community structures were different between two sampling stations. The members of ANME-2 archaea and diverse bacterial components including sulfate reducers within Deltaproteobacteria were detected from M1 site, indicating the occurrence of biologically mediated anaerobic oxidation of methane, while microbial community at M2 site was predominantly composed of members of Marine Crenarchaeota group I, sulfate reducers of Deltaproteobacteria, and sulfur oxidizers of Epsilonproteobacteria. Chemical analyses of seawater above microbial mats suggested that concentrations of sulfate and methane at M1 site were largely decreased relative to those at M2 site and carbon isotopic composition of methane at M1 site shifted heavier ((13)C-enriched), the results of which are consistent with molecular analyses. These results suggest that the mat microbial communities in deep-sea cold seep sediments at the northeastern Japan Sea are significantly responsible for sulfur and carbon circulations and the geological activity associated with plate movements serves unique microbial habitats in deep-sea environments.

Antibiotic activity and microbial community of the temperate sponge, Haliclona sp.

PubMed

Hoppers, A; Stoudenmire, J; Wu, S; Lopanik, N B

2015-02-01

Sessile marine invertebrates engage in a diverse array of beneficial interactions with bacterial symbionts. One feature of some of these relationships is the presence of bioactive natural products that can defend the holobiont from predation, competition or disease. In this study, we investigated the antimicrobial activity and microbial community of a common temperate sponge from coastal North Carolina. The sponge was identified as a member of the genus Haliclona, a prolific source of bioactive natural products, based on its 18S rRNA gene sequence. The crude chemical extract and methanol partition had broad activity against the assayed Gram-negative and Gram-positive pathogenic bacteria. Further fractionation resulted in two groups of compounds with differing antimicrobial activity, primarily against Gram-positive test organisms. There was, however, notable activity against the Gram-negative marine pathogen, Vibrio parahaemolyticus. Microbial community analysis of the sponge and surrounding sea water via denaturing gradient gel electrophoresis (DGGE) indicates that it harbours a distinct group of bacterial associates. The common temperate sponge, Haliclona sp., is a source of multiple antimicrobial compounds and has some consistent microbial community members that may play a role in secondary metabolite production. These data suggest that common temperate sponges can be a source of bioactive chemical and microbial diversity. Further studies may reveal the importance of the microbial associates to the sponge and natural product biosynthesis. © 2014 The Society for Applied Microbiology.

Nutrient Limitation of Microbial Mediated Decomposition and Arctic Soil Chronology

NASA Astrophysics Data System (ADS)

Melle, C. J.; Darrouzet-Nardi, A.; Wallenstein, M. D.

2012-12-01

Soils of northern permafrost regions currently contain twice as much carbon as the entire Earth's atmosphere. Traditionally, environmental constraints have limited microbial activity resulting in restricted decomposition of soil organic matter in these systems and accumulation of massive amounts of soil organic carbon (SOC), however climate change is reducing the constraints of decomposition in arctic permafrost regions. Carbon cycling in nutrient poor, arctic ecosystems is tightly coupled to other biogeochemical cycles. Several studies have suggested strong nitrogen limitations of primary productivity and potentially warm-season microbial activity in these nutrient deficient soils. Nitrogen is required for microbial extracellular enzyme production which drives the decomposition of soil organic matter (SOM). Nitrogen limited arctic soils may also experience limitation via labile carbon availability despite the SOM rich environment due to low extracellular enzyme production. Few studies have directly addressed nutrient induced microbial limitation in SOC rich arctic tundra soils, and even less is known about the potential for nutrient co-limitation. Additionally, through the process of becoming deglaciated, sites within close proximity to one another may have experienced drastic differences in their effective soil ages due to the varied length of their active histories. Many soil properties and nutrient deficiencies are directly related to soil age, however this chronology has not previously been a focus of research on nutrient limitation of arctic soil microbial activity. Understanding of nutrient limitations, as well as potential co-limitation, on arctic soil microbial activity has important implications for carbon cycling and the ultimate fate of the current arctic SOC reservoir. Analyses of nutrient limitation on soils of a single site are not adequate for fully understanding the controls on soil microbial activity across a vast land mass with large variation in effective soil age. My research is focused on addressing the questions of the extent of microbial N limitation in arctic tundra soils, the potential for co-limitation of labile C despite a high SOC environment, and the dependence, if any, nutrient limitation may have on the effective age of the soil. I have addressed these questions by conducting a laboratory soil incubation of factorial design with treatments of amended glucose, amended ammonium nitrate, and a control consisting of an addition of an equivalent volume of deionized water. Moist acid tundra soils possessing similar soil properties from two arctic sites of close proximity yet with varying deglaciation chronologies were utilized in my study. Soil properties of C-mineralization via respiration, microbial biomass, and nitrogen content in the forms of ammonium, nitrate, and total free amino acids and microbial extra-cellular enzyme production were assayed to determine the microbial response to the experimental treatments. Through the results of this work, I hope to better our understanding of biogeochemical cycling within arctic tundra ecosystems and the response to climate change by contributing to existing knowledge of nutrient limitation on microbial mediated decomposition of SOC in the arctic and how this may differ in soils of varying effective age.

Effect of Monospecific and Mixed Sea-Buckthorn (Hippophae rhamnoides) Plantations on the Structure and Activity of Soil Microbial Communities

PubMed Central

Yu, Xuan; Liu, Xu; Zhao, Zhong; Liu, Jinliang; Zhang, Shunxiang

2015-01-01

This study aims to evaluate the effect of different afforestation models on soil microbial composition in the Loess Plateau in China. In particular, we determined soil physicochemical properties, enzyme activities, and microbial community structures in the top 0 cm to 10 cm soil underneath a pure Hippophae rhamnoides (SS) stand and three mixed stands, namely, H. rhamnoides and Robinia pseucdoacacia (SC), H. rhamnoides and Pinus tabulaeformis (SY), and H. rhamnoides and Platycladus orientalis (SB). Results showed that total organic carbon (TOC), total nitrogen, and ammonium (NH4 +) contents were higher in SY and SB than in SS. The total microbial biomass, bacterial biomass, and Gram+ biomass of the three mixed stands were significantly higher than those of the pure stand. However, no significant difference was found in fungal biomass. Correlation analysis suggested that soil microbial communities are significantly and positively correlated with some chemical parameters of soil, such as TOC, total phosphorus, total potassium, available phosphorus, NH4 + content, nitrate content (NH3 −), and the enzyme activities of urease, peroxidase, and phosphatase. Principal component analysis showed that the microbial community structures of SB and SS could clearly be discriminated from each other and from the others, whereas SY and SC were similar. In conclusion, tree species indirectly but significantly affect soil microbial communities and enzyme activities through soil physicochemical properties. In addition, mixing P. tabulaeformis or P. orientalis in H. rhamnoides plantations is a suitable afforestation model in the Loess Plateau, because of significant positive effects on soil nutrient conditions, microbial community, and enzyme activities over pure plantations. PMID:25658843

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.

Evaluating digestion efficiency in full-scale anaerobic digesters by identifying active microbial populations through the lens of microbial activity

NASA Astrophysics Data System (ADS)

Mei, Ran; Narihiro, Takashi; Nobu, Masaru K.; Kuroda, Kyohei; Liu, Wen-Tso

2016-09-01

Anaerobic digestion is a common technology to biologically stabilize wasted solids produced in municipal wastewater treatment. Its efficiency is usually evaluated by calculating the reduction in volatile solids, which assumes no biomass growth associated with digestion. To determine whether this assumption is valid and further evaluate digestion efficiency, this study sampled 35 digester sludge from different reactors at multiple time points together with the feed biomass in a full-scale water reclamation plant at Chicago, Illinois. The microbial communities were characterized using Illumina sequencing technology based on 16S rRNA and 16S rRNA gene (rDNA). 74 core microbial populations were identified and represented 58.7% of the entire digester community. Among them, active populations were first identified using the ratio of 16S rRNA and 16S rDNA (rRNA/rDNA) for individual populations, but this approach failed to generate consistent results. Subsequently, a recently proposed mass balance model was applied to calculate the specific growth rate (μ), and this approach successfully identified active microbial populations in digester (positive μ) that could play important roles than those with negative μ. It was further estimated that 82% of microbial populations in the feed sludge were digested in comparison with less than 50% calculated using current equations.

Potential Research and Development Synergies between Life support and Planetary protection

NASA Astrophysics Data System (ADS)

Lasseur, Ch.; Kminek, G.; Mergeay, M.

Long term manned missions of our Russian colleagues have demonstrated the risks associated with microbial contamination These risks concern both crew health via the metabolic consumables contamination water air but and also the hardware degradation Over the last six years ESA and IBMP have developed a collaboration to elaborate and document these microbial contamination issues The collaboration involved the mutual exchanges of knowledge as well as microbial samples and leads up to the microbial survey of the Russian module of the ISS Based on these results and in addition to an external expert report commissioned by ESA the agency initiated the development of a rapid and automated microbial detection and identification tool for use in future space missions In parallel to these developments and via several international meetings planetary protection experts have agreed to place clear specification of the microbial quality of future hardware landing on virgin planets as well as elaborate the preliminary requirements of contamination for manned missions on surface For these activities its is necessary to have a better understanding of microbial activity to create culture collection and to develop on-line detection tools Within this paper we present more deeply the life support activities related to microbial issues we identify some potential synergies with Planetary protection developments and we propose some pathway for collaboration between these two communities

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.

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.

Review of Concrete Biodeterioration in Relation to Buried Nuclear Waste

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

Turick, C; Berry, C.

Long-term storage of low level radioactive material in below ground concrete disposal units (DUs) (Saltstone Disposal Facility) is a means of depositing wastes generated from nuclear operations of the U.S. Department of Energy. Based on the currently modeled degradation mechanisms, possible microbial induced effects on the structural integrity of buried low level wastes must be addressed. Previous international efforts related to microbial impacts on concrete structures that house low level radioactive waste showed that microbial activity can play a significant role in the process of concrete degradation and ultimately structural deterioration. This literature review examines the recent research in thismore » field and is focused on specific parameters that are applicable to modeling and prediction of the fate of concrete vaults housing stored wastes and the wastes themselves. Rates of concrete biodegradation vary with the environmental conditions, illustrating a need to understand the bioavailability of key compounds involved in microbial activity. Specific parameters require pH and osmotic pressure to be within a certain range to allow for microbial growth as well as the availability and abundance of energy sources like components involved in sulfur, iron and nitrogen oxidation. Carbon flow and availability are also factors to consider in predicting concrete biodegradation. The results of this review suggest that microbial activity in Saltstone, (grouted low level radioactive waste) is unlikely due to very high pH and osmotic pressure. Biodegradation of the concrete vaults housing the radioactive waste however, is a possibility. The rate and degree of concrete biodegradation is dependent on numerous physical, chemical and biological parameters. Results from this review point to parameters to focus on for modeling activities and also, possible options for mitigation that would minimize concrete biodegradation. In addition, key chemical components that drive microbial activity on concrete surfaces are discussed.« less

[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.

Uncoupling of microbial community structure and function in decomposing litter across beech forest ecosystems in Central Europe.

PubMed

Purahong, Witoon; Schloter, Michael; Pecyna, Marek J; Kapturska, Danuta; Däumlich, Veronika; Mital, Sanchit; Buscot, François; Hofrichter, Martin; Gutknecht, Jessica L M; Krüger, Dirk

2014-11-12

The widespread paradigm in ecology that community structure determines function has recently been challenged by the high complexity of microbial communities. Here, we investigate the patterns of and connections between microbial community structure and microbially-mediated ecological function across different forest management practices and temporal changes in leaf litter across beech forest ecosystems in Central Europe. Our results clearly indicate distinct pattern of microbial community structure in response to forest management and time. However, those patterns were not reflected when potential enzymatic activities of microbes were measured. We postulate that in our forest ecosystems, a disconnect between microbial community structure and function may be present due to differences between the drivers of microbial growth and those of microbial function.

Microbial Indicators of Soil Quality under Different Land Use Systems in Subtropical Soils

NASA Astrophysics Data System (ADS)

Maharjan, M.

2016-12-01

Land-use change from native forest to intensive agricultural systems can negatively impact numerous soil parameters. Understanding the effects of forest ecosystem transformations on markers of long-term soil health is particularly important in rapidly developing regions such as Nepal, where unprecedented levels of agriculturally-driven deforestation have occurred in recent decades. However, the effects of widespread land use changes on soil quality in this region have yet to be properly characterized. Microbial indicators (soil microbial biomass, metabolic quotient and enzymes activities) are particularly suited to assessing the consequences of such ecosystem disturbances, as microbial communities are especially sensitive to environmental change. Thus, the aim of this study was to assess the effect of land use system; i.e. forest, organic and conventional farming, on soil quality in Chitwan, Nepal using markers of microbial community size and activity. Total organic C and N contents were higher in organic farming compared with conventional farming and forest, suggesting higher nutrient retention and soil preservation with organic farming practices compared to conventional. These differences in soil composition were reflected in the health of the soil microbial communities: Organic farm soil exhibited higher microbial biomass C, elevated β-glucosidase and chitinase activities, and a lower metabolic quotient relative to other soils, indicating a larger, more active, and less stressed microbial community, respectively. These results collectively demonstrate that application of organic fertilizers and organic residues positively influence nutrient availability, with subsequent improvements in soil quality and productivity. Furthermore, the sensitivity of microbial indicators to different management practices demonstrated in this study supports their use as effective markers of ecosystem disturbance in subtropical soils.

Responses of microbial respiration in grazed and ungrazed grasslands to glucose addition

NASA Astrophysics Data System (ADS)

Xu, Xingliang; Liu, Qianyuan; Pang, Rui

2017-04-01

Grazing can change species composition, alter soil properties, and thus modify microbial activities, affecting biogeochemical processes in grasslands. However, it remains unclear how microbial respiration in grazed and ungrazed grasslands responds to glucose addition. Here we hypothesize that microbial respiration in grazed grasslands will respond more strongly to glucose addition than in ungrazed grasslands because moderate grazing can enhance microbial activity. To examine the hypothesis above, we collected the upper 10 cm soil from grazed and ungrazed grasslands at five sites of China. Three sites (Hulunbuir 1, Hulunbuir 2 and Xielingele) were located in Inner Mongolia and two in the Tibet Plateau) Soils were incubated with low glucose input (50% MBC), high glucose input (150% MBC), and water for 60 days in 21oC. CO2 released from soil was trapped with 1 M NaOH. The results showed that the effect of grazing on microbial respiration has two distinct patterns, depending on soil types and addition amount. After glucose addition, cumulative CO2 efflux from grazed soils was significantly higher than from ungrazed soils in two temperate grasslands (Hulunbuir 1 and Xielingele). This may be ascribed to that moderate grazing promoted microbial activity. On the contrary, microbial respirations from grazed soils were lower than ungrazed soils in two alpine meadows of Haibei and Dangxiong and in Hulunbuir 2. This effect of grazing was not obvious in Hulunbeier 2 soils at low carbon addition level. Grazing may decrease soil organic carbon, nitrogen availability and thus microbial activity in alpine grasslands. These findings indicate that soil microorganisms could have different adaptation mechanisms to grazing in temperate and alpine grasslands.

Microbial mats as a biological treatment approach for saline wastewaters: the case of produced water from hydraulic fracturing.

PubMed

Akyon, Benay; Stachler, Elyse; Wei, Na; Bibby, Kyle

2015-05-19

Treatment of produced water, i.e. wastewater from hydraulic fracturing, for reuse or final disposal is challenged by both high salinity and the presence of organic compounds. Organic compounds in produced water may foul physical-chemical treatment processes or support microbial corrosion, fouling, and sulfide release. Biological approaches have potential applications in produced water treatment, including reducing fouling of physical-chemical treatment processes and decreasing biological activity during produced water holding; however, conventional activated sludge treatments are intolerant of high salinity. In this study, a biofilm treatment approach using constructed microbial mats was evaluated for biodegradation performance, microbial community structure, and metabolic potential in both simulated and real produced water. Results demonstrated that engineered microbial mats are active at total dissolved solids (TDS) concentrations up to at least 100,000 mg/L, and experiments in real produced water showed a biodegradation capacity of 1.45 mg COD/gramwet-day at a TDS concentration of 91,351 mg/L. Additionally, microbial community and metagenomic analyses revealed an adaptive microbial community that shifted based upon the sample being treated and has the metabolic potential to degrade a wide array of contaminants, suggesting the potential of this approach to treat produced waters with varying composition.

Divergence of dominant factors in soil microbial communities and functions in forest ecosystems along a climatic gradient

NASA Astrophysics Data System (ADS)

Xu, Zhiwei; Yu, Guirui; Zhang, Xinyu; He, Nianpeng; Wang, Qiufeng; Wang, Shengzhong; Xu, Xiaofeng; Wang, Ruili; Zhao, Ning

2018-03-01

Soil microorganisms play an important role in regulating nutrient cycling in terrestrial ecosystems. Most of the studies conducted thus far have been confined to a single forest biome or have focused on one or two controlling factors, and few have dealt with the integrated effects of climate, vegetation, and soil substrate availability on soil microbial communities and functions among different forests. In this study, we used phospholipid-derived fatty acid (PLFA) analysis to investigate soil microbial community structure and extracellular enzymatic activities to evaluate the functional potential of soil microbes of different types of forests in three different climatic zones along the north-south transect in eastern China (NSTEC). Both climate and forest type had significant effects on soil enzyme activities and microbial communities with considerable interactive effects. Except for soil acid phosphatase (AP), the other three enzyme activities were much higher in the warm temperate zone than in the temperate and the subtropical climate zones. The soil total PLFAs and bacteria were much higher in the temperate zone than in the warm temperate and the subtropical zones. The soil β-glucosidase (BG) and N-acetylglucosaminidase (NAG) activities were highest in the coniferous forest. Except for the soil fungi and fungi-bacteria (F/B), the different groups of microbial PLFAs were much higher in the conifer broad-leaved mixed forests than in the coniferous forests and the broad-leaved forests. In general, soil enzyme activities and microbial PLFAs were higher in primary forests than in secondary forests in temperate and warm temperate regions. In the subtropical region, soil enzyme activities were lower in the primary forests than in the secondary forests and microbial PLFAs did not differ significantly between primary and secondary forests. Different compositions of the tree species may cause variations in soil microbial communities and enzyme activities. Our results showed that the main controls on soil microbes and functions vary in different climatic zones and that the effects of soil moisture content, soil temperature, clay content, and the soil N / P ratio were considerable. This information will add value to the modeling of microbial processes and will contribute to carbon cycling in large-scale carbon models.

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.

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.

Co-composting of organic fraction of municipal solid waste mixed with different bulking waste: characterization of physicochemical parameters and microbial enzymatic dynamic.

PubMed

Awasthi, Mukesh Kumar; Pandey, Akhilesh Kumar; Bundela, Pushpendra Singh; Khan, Jamaluddin

2015-04-01

The effect of various bulking waste such as wood shaving, agricultural and yard trimming waste combined with organic fraction of municipal solid waste (OFMSW) composting was investigated through assessing their influence on microbial enzymatic activities and quality of finished compost. All three piles of OFMSW with different bulking waste were inoculated with microbial consortium. The results revealed that OFMSW combined with wood shaving and microbial consortium (Phanerochaete chrysosporium, Trichoderma viride and Pseudomonas aeruginosa) were helpful tool to facilitate the enzymatic activity and shortened composting period within 4 weeks. Maximum enzymatic activity were observed in pile 1 and 3 during the first 3 weeks, while in pile 2 relatively very low. But phosphatase activity was relatively higher in all piles until the end of the process. Maturity parameters of compost quality also favored the pile 1 as the best formulation for OFMSW composting. Copyright © 2015 Elsevier Ltd. All rights reserved.

Lactose digestion by yogurt beta-galactosidase: influence of pH and microbial cell integrity.

PubMed

Martini, M C; Bollweg, G L; Levitt, M D; Savaiano, D A

1987-02-01

Lactase-deficient subjects more effectively digest lactose in yogurt than lactose in other dairy products, apparently due to yogurt microbial beta-galactosidase (beta-gal) which is active in the GI tract. We evaluated the effects of buffering capacity of yogurt, gastric pH, and microbial cell disruption on beta-gal activity and lactose digestion. Three times more acid was required to acidify yogurt than to acidify milk. Yogurt beta-gal was stable at pH 4.0 but inactivated at lower pH. When yogurt was sonicated to disrupt microbial cell structure, only 20% activity remained after incubation at pH 4.0 for 60 min. In vivo gastric pH remained greater than 2.7 for 3 h after ingestion of yogurt. Acidified milk alone or with disrupted yogurt microorganisms caused twice as much lactose malabsorption as did acidified milk containing intact yogurt microorganisms. The results provide a possible explanation for the survival of beta-gal activity from yogurt in the GI tract.

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.

Microbial Response to Experimentally Controlled Redox Transitions at the Sediment Water Interface.

PubMed

Frindte, Katharina; Allgaier, Martin; Grossart, Hans-Peter; Eckert, Werner

2015-01-01

The sediment-water interface of freshwater lakes is characterized by sharp chemical gradients, shaped by the interplay between physical, chemical and microbial processes. As dissolved oxygen is depleted in the uppermost sediment, the availability of alternative electron acceptors, e.g. nitrate and sulfate, becomes the limiting factor. We performed a time series experiment in a mesocosm to simulate the transition from aerobic to anaerobic conditions at the sediment-water interface. Our goal was to identify changes in the microbial activity due to redox transitions induced by successive depletion of available electron acceptors. Monitoring critical hydrochemical parameters in the overlying water in conjunction with a new sampling strategy for sediment bacteria enabled us to correlate redox changes in the water to shifts in the active microbial community and the expression of functional genes representing specific redox-dependent microbial processes. Our results show that during several transitions from oxic-heterotrophic condition to sulfate-reducing condition, nitrate-availability and the on-set of sulfate reduction strongly affected the corresponding functional gene expression. There was evidence of anaerobic methane oxidation with NOx. DGGE analysis revealed redox-related changes in microbial activity and expression of functional genes involved in sulfate and nitrite reduction, whereas methanogenesis and methanotrophy showed only minor changes during redox transitions. The combination of high-frequency chemical measurements and molecular methods provide new insights into the temporal dynamics of the interplay between microbial activity and specific redox transitions at the sediment-water interface.

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.

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

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.

Microorganism-regulated mechanisms of temperature effects on the performance of anaerobic digestion.

PubMed

Lin, Qiang; He, Guihua; Rui, Junpeng; Fang, Xiaoyu; Tao, Yong; Li, Jiabao; Li, Xiangzhen

2016-06-03

Temperature is an important factor determining the performance and stability of the anaerobic digestion process. However, the microorganism-regulated mechanisms of temperature effects on the performance of anaerobic digestion systems remain further elusive. To address this issue, we investigated the changes in composition, diversity and activities of microbial communities under temperature gradient from 25 to 55 °C using 16S rRNA gene amplicon sequencing approach based on genomic DNA (refer to as "16S rDNA") and total RNA (refer to as "16S rRNA"). Microbial community structure and activities changed dramatically along the temperature gradient, which corresponded to the variations in digestion performance (e.g., daily CH4 production, total biogas production and volatile fatty acids concentration). The ratios of 16S rRNA to 16S rDNA of microbial taxa, as an indicator of the potentially relative activities in situ, and whole activities of microbial community assessed by the similarity between microbial community based on 16S rDNA and rRNA, varied strongly along the temperature gradient, reflecting different metabolic activities. The daily CH4 production increased with temperature from 25 to 50 °C and declined at 55 °C. Among all the examined microbial properties, the whole activities of microbial community and alpha-diversity indices of both microbial communities and potentially relative activities showed highest correlations to the performance. The whole activities of microbial community and alpha-diversity indices of both microbial communities and potentially relative activities were sensitive indicators for the performance of anaerobic digestion systems under temperature gradient, while beta-diversity could predict functional differences. Microorganism-regulated mechanisms of temperature effects on anaerobic digestion performance were likely realized through increasing alpha-diversity of both microbial communities and potentially relative activities to supply more functional pathways and activities for metabolic network, and increasing the whole activities of microbial community, especially methanogenesis, to improve the strength and efficiency in anaerobic digestion process.

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 in Aquatic Environments Measured by Dimethyl Sulfoxide Reduction and Intercomparison with Commonly Used Methods

PubMed Central

Griebler, Christian; Slezak, Doris

2001-01-01

A new method to determine microbial (bacterial and fungal) activity in various freshwater habitats is described. Based on microbial reduction of dimethyl sulfoxide (DMSO) to dimethyl sulfide (DMS), our DMSO reduction method allows measurement of the respiratory activity in interstitial water, as well as in the water column. DMSO is added to water samples at a concentration (0.75% [vol/vol] or 106 mM) high enough to compete with other naturally occurring electron acceptors, as determined with oxygen and nitrate, without stimulating or inhibiting microbial activity. Addition of NaN3, KCN, and formaldehyde, as well as autoclaving, inhibited the production of DMS, which proves that the reduction of DMSO is a biotic process. DMSO reduction is readily detectable via the formation of DMS even at low microbial activities. All water samples showed significant DMSO reduction over several hours. Microbially reduced DMSO is recovered in the form of DMS from water samples by a purge and trap system and is quantified by gas chromatography and detection with a flame photometric detector. The DMSO reduction method was compared with other methods commonly used for assessment of microbial activity. DMSO reduction activity correlated well with bacterial production in predator-free batch cultures. Cell-production-specific DMSO reduction rates did not differ significantly in batch cultures with different nutrient regimes but were different in different growth phases. Overall, a cell-production-specific DMSO reduction rate of 1.26 × 10−17 ± 0.12 × 10−17 mol of DMS per produced cell (mean ± standard error; R2 = 0.78) was calculated. We suggest that the relationship of DMSO reduction rates to thymidine and leucine incorporation is linear (the R2 values ranged from 0.783 to 0.944), whereas there is an exponential relationship between DMSO reduction rates and glucose uptake, as well as incorporation (the R2 values ranged from 0.821 to 0.931). Based on our results, we conclude that the DMSO reduction method is a nonradioactive alternative to other methods commonly used to assess microbial activity. PMID:11133433

Microbial activity in aquatic environments measured by dimethyl sulfoxide reduction and intercomparison with commonly used methods.

PubMed

Griebler, C; Slezak, D

2001-01-01

A new method to determine microbial (bacterial and fungal) activity in various freshwater habitats is described. Based on microbial reduction of dimethyl sulfoxide (DMSO) to dimethyl sulfide (DMS), our DMSO reduction method allows measurement of the respiratory activity in interstitial water, as well as in the water column. DMSO is added to water samples at a concentration (0.75% [vol/vol] or 106 mM) high enough to compete with other naturally occurring electron acceptors, as determined with oxygen and nitrate, without stimulating or inhibiting microbial activity. Addition of NaN(3), KCN, and formaldehyde, as well as autoclaving, inhibited the production of DMS, which proves that the reduction of DMSO is a biotic process. DMSO reduction is readily detectable via the formation of DMS even at low microbial activities. All water samples showed significant DMSO reduction over several hours. Microbially reduced DMSO is recovered in the form of DMS from water samples by a purge and trap system and is quantified by gas chromatography and detection with a flame photometric detector. The DMSO reduction method was compared with other methods commonly used for assessment of microbial activity. DMSO reduction activity correlated well with bacterial production in predator-free batch cultures. Cell-production-specific DMSO reduction rates did not differ significantly in batch cultures with different nutrient regimes but were different in different growth phases. Overall, a cell-production-specific DMSO reduction rate of 1.26 x 10(-17) +/- 0. 12 x 10(-17) mol of DMS per produced cell (mean +/- standard error; R(2) = 0.78) was calculated. We suggest that the relationship of DMSO reduction rates to thymidine and leucine incorporation is linear (the R(2) values ranged from 0.783 to 0.944), whereas there is an exponential relationship between DMSO reduction rates and glucose uptake, as well as incorporation (the R(2) values ranged from 0.821 to 0.931). Based on our results, we conclude that the DMSO reduction method is a nonradioactive alternative to other methods commonly used to assess microbial activity.

High shear enrichment improves the performance of the anodophilic microbial consortium in a microbial fuel cell

PubMed Central

Pham, Hai The; Boon, Nico; Aelterman, Peter; Clauwaert, Peter; De Schamphelaire, Liesje; Van Oostveldt, Patrick; Verbeken, Kim; Rabaey, Korneel; Verstraete, Willy

2008-01-01

Summary In many microbial bioreactors, high shear rates result in strong attachment of microbes and dense biofilms. In this study, high shear rates were applied to enrich an anodophilic microbial consortium in a microbial fuel cell (MFC). Enrichment at a shear rate of about 120 s−1 resulted in the production of a current and power output two to three times higher than those in the case of low shear rates (around 0.3 s−1). Biomass and biofilm analyses showed that the anodic biofilm from the MFC enriched under high shear rate conditions, in comparison with that under low shear rate conditions, had a doubled average thickness and the biomass density increased with a factor 5. The microbial community of the former, as analysed by DGGE, was significantly different from that of the latter. The results showed that enrichment by applying high shear rates in an MFC can result in a specific electrochemically active biofilm that is thicker and denser and attaches better, and hence has a better performance. PMID:21261869

Formation of recent Pb-Ag-Au mineralization by potential sub-surface microbial activity

NASA Astrophysics Data System (ADS)

Tornos, Fernando; Velasco, Francisco; Menor-Salván, César; Delgado, Antonio; Slack, John F.; Escobar, Juan Manuel

2014-08-01

Las Cruces is a base-metal deposit in the Iberian Pyrite Belt, one of the world’s best-known ore provinces. Here we report the occurrence of major Pb-Ag-Au mineralization resulting from recent sub-surface replacement of supergene oxyhydroxides by carbonate and sulphide minerals. This is probably the largest documented occurrence of recent microbial activity producing an ore assemblage previously unknown in supergene mineralizing environments. The presence of microbial features in the sulphides suggests that these may be the first-described natural bacteriomorphs of galena. The low δ13C values of the carbonate minerals indicate formation by deep anaerobic microbial processes. Sulphur isotope values of sulphides are interpreted here as reflecting microbial reduction in a system impoverished in sulphate. We suggest that biogenic activity has produced around 3.1 × 109 moles of reduced sulphur and 1010 moles of CO2, promoting the formation of ca. 1.19 Mt of carbonates, 114,000 t of galena, 638 t of silver sulphides and 6.5 t of gold.

Microbial Functioning and Community Structure Variability in the Mesopelagic and Epipelagic Waters of the Subtropical Northeast Atlantic Ocean

PubMed Central

Arístegui, Javier; Gasol, Josep M.; Herndl, Gerhard J.

2012-01-01

We analyzed the regional distribution of bulk heterotrophic prokaryotic activity (leucine incorporation) and selected single-cell parameters (cell viability and nucleic acid content) as parameters for microbial functioning, as well as bacterial and archaeal community structure in the epipelagic (0 to 200 m) and mesopelagic (200 to 1,000 m) subtropical Northeast Atlantic Ocean. We selectively sampled three contrasting regions covering a wide range of surface productivity and oceanographic properties within the same basin: (i) the eddy field south of the Canary Islands, (ii) the open-ocean NE Atlantic Subtropical Gyre, and (iii) the upwelling filament off Cape Blanc. In the epipelagic waters, a high regional variation in hydrographic parameters and bacterial community structure was detected, accompanied, however, by a low variability in microbial functioning. In contrast, mesopelagic microbial functioning was highly variable between the studied regions despite the homogeneous abiotic conditions found therein. More microbial functioning parameters indicated differences among the three regions within the mesopelagic (i.e., viability of cells, nucleic acid content, cell-specific heterotrophic activity, nanoflagellate abundance, prokaryote-to-nanoflagellate abundance ratio) than within the epipelagic (i.e., bulk activity, nucleic acid content, and nanoflagellate abundance) waters. Our results show that the mesopelagic realm in the Northeast Atlantic is, in terms of microbial activity, more heterogeneous than its epipelagic counterpart, probably linked to mesoscale hydrographical variations. PMID:22344670

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.

Ecohydrological Impacts of Groundwater Drawdown : Effects on Microbial Activity in the Hyporheic Zone

NASA Astrophysics Data System (ADS)

Auhl, A.; Rutlidge, H.; Andersen, M. S.; Eberhard, S. M.; Baker, A.; Holley, C.

2016-12-01

Our current understanding of ecohydrological processes in the ecotone between surface water and groundwater - the hyporheic zone - is limited. Groundwater drawdown is a key stressor for many groundwater dependent ecosystems, as groundwater levels are declining globally. It is caused by different perturbations, including agriculture, mine dewatering and climate change. Therefore, there is a pressing need to examine how different ecohydrological systems work under different types of stress. This research aims to investigate the impacts of groundwater drawdown on hyporheic zone microbial activity. For two six week sampling campaigns (winter and summer) at Maules Creek, Namoi, New South Wales, Australia, microbial activity was measured using the cotton strip degradation method. Unprimed cotton canvas was affixed to rulers which were then placed for six weeks in different habitats (dry bar, hyporheic zone and surface waters) at three different water regimes found at different sections of the creek (perennial, ephemeral, and losing). The microbial activity was related to the loss of cotton strip tensile strength. The water regimes were used as proxies for different stages of groundwater drawdown. Key physico-chemical variables were also measured. The preliminary results show that there is a positive correlation between moisture status (i.e. the degree of habitat saturation over six weeks) and microbial activity.This suggests that groundwater drawdown and desaturation of streambed sediments may lead to a decrease in microbial activity and therefore, the recycling of organic carbon and nutrients. This research has local implications for environmental impact assessments and global implications for the assessment and management of ecological impacts of declining shallow groundwater levels.

Physical Factors Correlate to Microbial Community Structure and Nitrogen Cycling Gene Abundance in a Nitrate Fed Eutrophic Lagoon.

PubMed

Highton, Matthew P; Roosa, Stéphanie; Crawshaw, Josie; Schallenberg, Marc; Morales, Sergio E

2016-01-01

Nitrogenous run-off from farmed pastures contributes to the eutrophication of Lake Ellesmere, a large shallow lagoon/lake on the east coast of New Zealand. Tributaries periodically deliver high loads of nitrate to the lake which likely affect microbial communities therein. We hypothesized that a nutrient gradient would form from the potential sources (tributaries) creating a disturbance resulting in changes in microbial community structure. To test this we first determined the existence of such a gradient but found only a weak nitrogen (TN) and phosphorous gradient (DRP). Changes in microbial communities were determined by measuring functional potential (quantification of nitrogen cycling genes via nifH , nirS , nosZI , and nosZII using qPCR), potential activity (via denitrification enzyme activity), as well as using changes in total community (via 16S rRNA gene amplicon sequencing). Our results demonstrated that changes in microbial communities at a phylogenetic (relative abundance) and functional level (proportion of the microbial community carrying nifH and nosZI genes) were most strongly associated with physical gradients (e.g., lake depth, sediment grain size, sediment porosity) and not nutrient concentrations. Low nitrate influx at the time of sampling is proposed as a factor contributing to the observed patterns.

Methanogenesis at low temperatures by microflora of tundra wetland soil.

PubMed

Kotsyurbenko, O R; Nozhevnikova, A N; Soloviova, T I; Zavarzin, G A

1996-01-01

Active methanogenesis from organic matter contained in soil samples from tundra wetland occurred even at 6 degrees C. Methane was the only end product in balanced microbial community with H2/CO2 as a substrate, besides acetate was produced as an intermediate at temperatures below 10 degrees C. The activity of different microbial groups of methanogenic community in the temperature range of 6-28 degrees C was investigated using 5% of tundra soil as inoculum. Anaerobic microflora of tundra wetland fermented different organic compounds with formation of hydrogen, volatile fatty acids (VFA) and alcohols. Methane was produced at the second step. Homoacetogenic and methanogenic bacteria competed for such substrates as hydrogen, formate, carbon monoxide and methanol. Acetogens out competed methanogens in an excess of substrate and low density of microbial population. Kinetic analysis of the results confirmed the prevalence of hydrogen acetogenesis on methanogenesis. Pure culture of acetogenic bacteria was isolated at 6 degrees C. Dilution of tundra soil and supply with the excess of substrate disbalanced the methanoigenic microbial community. It resulted in accumulation of acetate and other VFA. In balanced microbial community obviously autotrophic methanogens keep hydrogen concentration below a threshold for syntrophic degradation of VFA. Accumulation of acetate- and H2/CO2-utilising methanogens should be very important in methanogenic microbial community operating at low temperatures.

Diet simplification selects for high gut microbial diversity and strong fermenting ability in high-altitude pikas.

PubMed

Li, Huan; Qu, Jiapeng; Li, Tongtong; Wirth, Stephan; Zhang, Yanming; Zhao, Xinquan; Li, Xiangzhen

2018-06-03

The gut microbiota in mammals plays a key role in host metabolism and adaptation. However, relatively little is known regarding to how the animals adapts to extreme environments through regulating gut microbial diversity and function. Here, we investigated the diet, gut microbiota, short-chain fatty acid (SCFA) profiles, and cellulolytic activity from two common pika (Ochotona spp.) species in China, including Plateau pika (Ochotona curzoniae) from the Qinghai-Tibet Plateau and Daurian pika (Ochotona daurica) from the Inner Mongolia Grassland. Despite a partial diet overlap, Plateau pikas harbored lower diet diversity than Daurian pikas. Some bacteria (e.g., Prevotella and Ruminococcus) associated with fiber degradation were enriched in Plateau pikas. They harbored higher gut microbial diversity, total SCFA concentration, and cellulolytic activity than Daurian pikas. Interestingly, cellulolytic activity was positively correlated with the gut microbial diversity and SCFAs. Gut microbial communities and SCFA profiles were segregated structurally between host species. PICRUSt metagenome predictions demonstrated that microbial genes involved in carbohydrate metabolism and energy metabolism were overrepresented in the gut microbiota of Plateau pikas. Our results demonstrate that Plateau pikas harbor a stronger fermenting ability for the plant-based diet than Daurian pikas via gut microbial fermentation. The enhanced ability for utilization of plant-based diets in Plateau pikas may be partly a kind of microbiota adaptation for more energy requirements in cold and hypoxic high-altitude environments.

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.

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.

Are biological effects of desert shrubs more important than physical effects on soil microorganisms?

PubMed

Berg, Naama; Steinberger, Yosef

2010-01-01

Vegetation cover plays a major role in providing organic matter and in acting as a physical barrier, with both together contributing to the formation of "fertile islands," which play an active role in prolonging biological activity in desert ecosystems. By undertaking this study, a longterm research, we designed an experiment to separate the two components-the physical and biotic parts of the perennial plants-and to identify the factor that contributes the most to the ecosystem. The study site was located in the northern Negev Desert, Israel, where 50 Hammada scoparia shrubs and 50 artificial plants were randomly marked. Soil samples were collected monthly over 3 years of research at three locations: under the canopy of H. scoparia shrubs, in the vicinity of the artificial plants, and between the shrubs (control). The contribution to microbial activity was measured by evaluation of the microbial community functions in soil. The functional aspects of the microbial community that were measured were CO2 evolution, microbial biomass, microbial functional diversity, and the physiological profile of the community. The results of this study are presented in two ways: (1) according to the three locations/treatments; and (2) according to the phenological situation of the vegetation (annual and perennial plants) in the research field: the growing phase, the drying process, and the absence of annual plants. The only parameters that were found to affect microbial activity were the contribution of the organic matter of perennial shrubs and the growth of vegetation (annual and perennial) during the growing seasons. The physical component was found to have no effect on soil microbial functional diversity, which elucidates the important contribution of the desert shrub in enhancing biological multiplicity and activity.

Experimental removal of wetland emergent vegetation leads to decreased methylmercury production in surface sediment

USGS Publications Warehouse

Windham-Myers, L.; Marvin-DiPasquale, M.; Krabbenhoft, D.P.; Agee, J.L.; Cox, M.H.; Heredia-Middleton, P.; Coates, C.; Kakouros, E.

2009-01-01

We performed plant removal (devegetation) experiments across a suite of ecologically diverse wetland settings (tidal salt marshes, river floodplain, rotational rice fields, and freshwater wetlands with permanent or seasonal flooding) to determine the extent to which the presence (or absence) of actively growing plants influences the activity of the Hg(II)-methylating microbial community and the availability of Hg(II) to those microbes. Vegetated control plots were paired with neighboring devegetated plots in which photosynthetic input was terminated 4-8 months prior to measurements, through clipping aboveground biomass, severing belowground connections, and shading the sediment surface to prevent regrowth. Across all wetlands, devegetation decreased the activity of the Hg(II)-methylating microbial community (kmeth) by 38%, calculated MeHg production potential (MP) rates by 36%, and pore water acetate concentration by 78%. Decreases in MP were associated with decreases in microbial sulfate reduction in salt marsh settings. In freshwater agricultural wetlands, decreases in MP were related to indices of microbial iron reduction. Sediment MeHg concentrations were also significantly lower in devegetated than in vegetated plots in most wetland settings studied. Devegetation effects were correlated with live root density (percent volume) and were most profound in vegetated sites with higher initial pore water acetate concentrations. Densely rooted wetlands had the highest rates of microbial Hg(II)-methylation activity but often the lowest concentrations of bioavailable reactive Hg(II). We conclude that the exudation of labile organic carbon (e.g., acetate) by plants leads to enhanced microbial sulfate and iron reduction activity in the rhizosphere, which results in high rates of microbial Hg(II)-methyation and high MeHg concentrations in wetland sediment.

Experimental removal of wetland emergent vegetation leads to decreased methylmercury production in surface sediment

USGS Publications Warehouse

Windham-Myers, Lisamarie; Marvin-DiPasquale, Mark; Krabbenhoft, David P.; Agee, Jennifer L.; Cox, Marisa H.; Heredia-Middleton, Pilar; Coates, Carolyn; Kakouros, Evangelos

2009-01-01

We performed plant removal (devegetation) experiments across a suite of ecologically diverse wetland settings (tidal salt marshes, river floodplain, rotational rice fields, and freshwater wetlands with permanent or seasonal flooding) to determine the extent to which the presence (or absence) of actively growing plants influences the activity of the Hg(II)-methylating microbial community and the availability of Hg(II) to those microbes. Vegetated control plots were paired with neighboring devegetated plots in which photosynthetic input was terminated 4–8 months prior to measurements, through clipping aboveground biomass, severing belowground connections, and shading the sediment surface to prevent regrowth. Across all wetlands, devegetation decreased the activity of the Hg(II)-methylating microbial community (kmeth) by 38%, calculated MeHg production potential (MP) rates by 36%, and pore water acetate concentration by 78%. Decreases in MP were associated with decreases in microbial sulfate reduction in salt marsh settings. In freshwater agricultural wetlands, decreases in MP were related to indices of microbial iron reduction. Sediment MeHg concentrations were also significantly lower in devegetated than in vegetated plots in most wetland settings studied. Devegetation effects were correlated with live root density (percent volume) and were most profound in vegetated sites with higher initial pore water acetate concentrations. Densely rooted wetlands had the highest rates of microbial Hg(II)-methylation activity but often the lowest concentrations of bioavailable reactive Hg(II). We conclude that the exudation of labile organic carbon (e.g., acetate) by plants leads to enhanced microbial sulfate and iron reduction activity in the rhizosphere, which results in high rates of microbial Hg(II)-methyation and high MeHg concentrations in wetland sediment.

[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.

Deposition and postdeposition mechanisms as possible drivers of microbial population variability in glacier ice.

PubMed

Xiang, Shu-Rong; Shang, Tian-Cui; Chen, Yong; Yao, Tan-Dong

2009-11-01

Glaciers accumulate airborne microorganisms year by year and thus are good archives of microbial communities and their relationship to climatic and environmental changes. Hypotheses have focused on two possible drivers of microbial community composition in glacier systems. One is aeolian deposition, in which the microbial load by aerosol, dust, and precipitation events directly determines the amount and composition of microbial species in glacier ice. The other is postdepositional selection, in which the metabolic activity in surface snow causes microbial community shifts in glacier ice. An additional possibility is that both processes occur simultaneously. Aeolian deposition initially establishes a microbial community in the ice, whereas postdeposition selection strengthens the deposition patterns of microorganisms with the development of tolerant species in surface snow, resulting in varying structures of microbial communities with depth. In this minireview, we examine these postulations through an analysis of physical-chemical and biological parameters from the Malan and Vostok ice cores, and the Kuytun 51 Glacial surface and deep snow. We discuss these and other recent results in the context of the hypothesized mechanisms driving microbial community succession in glaciers. We explore our current gaps in knowledge and point out future directions for research on microorganisms in glacial ecosystems.

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.

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.

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.

The microbiology of malting and brewing.

PubMed

Bokulich, Nicholas A; Bamforth, Charles W

2013-06-01

Brewing beer involves microbial activity at every stage, from raw material production and malting to stability in the package. Most of these activities are desirable, as beer is the result of a traditional food fermentation, but others represent threats to the quality of the final product and must be controlled actively through careful management, the daily task of maltsters and brewers globally. This review collates current knowledge relevant to the biology of brewing yeast, fermentation management, and the microbial ecology of beer and brewing.

The Microbiology of Malting and Brewing

PubMed Central

Bokulich, Nicholas A.

2013-01-01

SUMMARY Brewing beer involves microbial activity at every stage, from raw material production and malting to stability in the package. Most of these activities are desirable, as beer is the result of a traditional food fermentation, but others represent threats to the quality of the final product and must be controlled actively through careful management, the daily task of maltsters and brewers globally. This review collates current knowledge relevant to the biology of brewing yeast, fermentation management, and the microbial ecology of beer and brewing. PMID:23699253

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.

Comparative Activity and Functional Ecology of Permafrost Soils and Lithic Niches in a Hyper-Arid Polar Desert

NASA Technical Reports Server (NTRS)

Goordial, J.; Davila, A.; Greer, C. W.; Cannam, R.; DiRuggiero, J.; McKay, C. P.; Whyte, L. G.

2016-01-01

This study represents the first metagenomic interrogation of Antarctic permafrost and polar cryptoendolithic microbial communities. The results underlie two different habitability conditions in the same location under extreme cold and dryness: the permafrost habitat where viable microbial life and activity is questionable, and the cryptoendolithic habitat which contains organisms capable of growth under the extreme conditions of the Antarctic Dry Valleys.

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

Effect of dry mycelium of Penicillium chrysogenum fertilizer on soil microbial community composition, enzyme activities and snap bean growth.

PubMed

Wang, Bing; Liu, Huiling; Cai, Chen; Thabit, Mohamed; Wang, Pu; Li, Guomin; Duan, Ziheng

2016-10-01

The dry mycelium fertilizer (DMF) was produced from penicillin fermentation fungi mycelium (PFFM) following an acid-heating pretreatment to degrade the residual penicillin. In this study, it was applied into soil as fertilizer to investigate its effects on soil properties, phytotoxicity, microbial community composition, enzyme activities, and growth of snap bean in greenhouse. As the results show, pH, total nitrogen, total phosphorus, total potassium, and organic matter of soil with DMF treatments were generally higher than CON treatment. In addition, the applied DMF did not cause heavy metal and residual drug pollution of the modified soil. The lowest GI values (<0.3) were recorded at DMF8 (36 kg DMF/plat) on the first days after applying the fertilizer, indicating that severe phytotoxicity appeared in the DMF8-modified soil. Results of microbial population and enzyme activities illustrated that DMF was rapidly decomposed and the decomposition process significantly affected microbial growth and enzyme activities. The DMF-modified soil phytotoxicity decreased at the late fertilization time. DMF1 was considered as the optimum amount of DMF dose based on principal component analysis scores. Plant height and plant yield of snap bean were remarkably enhanced with the optimum DMF dose.

Trophic structure and microbial activity in a spawning area of Engraulis encrasicolus

NASA Astrophysics Data System (ADS)

Zaccone, R.; Azzaro, M.; Azzaro, F.; Caruso, G.; Caroppo, C.; Decembrini, F.; Diociaiuti, T.; Fonda Umani, S.; Leonardi, M.; Maimone, G.; Monticelli, L. S.; Paranhos, R.; Placenti, F.; Cuttitta, A.; Patti, B.; La Ferla, R.

2018-07-01

The abundance, biomass and size-structure of planktonic populations, and the microbial metabolic processes were studied in the Sicily Channel, one of the most important spawning areas in the Mediterranean for anchovy (Engraulis encrasicolus), a pelagic species of commercial interest. Results showed that prokaryotes contribute for the 83% of total carbon biomass. Microphytoplankton abundances and biomasses were dominated by autotrophic nanoflagellates and dinoflagellates (36 identified species) and contribute 11% of total biomass. The microzooplanktonic biomass showed its maximum at the surface or subsurface and its contribution was low (4%). In agreement with the general oligotrophy of the investigated area, the study highlights the prevalence of pico-sized fractions within the whole phytoplankton biomass expressed as chlorophyll content, suggesting the importance of picophytoplankton in sustaining the microbial food web. At the same time, the levels of microbial hydrolytic activities are related to productive processes recycling the organic matter and releasing nutrients (P and N), indicating also an active functioning of ecosystem at low trophic levels. Autotrophic production exceeded oxidation by respiration; at the same time, the co-variation of prokaryotic activities and eggs distribution with temperature in summer was observed. The results obtained confirmed that the area acted as a nursery for small fish and both autotrophic and heterotrophic processes supported by microorganisms were in synergy.

Deep-Subterranean Microbial Habitats in the Hishikari Epithermal Gold Mine: Active Thermophilic Microbial Communities and Endolithic Ancient Microbial Relicts.

NASA Astrophysics Data System (ADS)

Hirayama, H.; Takai, K.; Inagaki, F.; Horikoshi, K.

2001-12-01

Deep subterranean microbial community structures in an epithermal gold-silver deposit, Hishikari gold mine, southern part of Kyusyu Japan, were evaluated through the combined use of enrichment culture methods and culture-independent molecular surveys. The geologic setting of the Hishikari deposit is composed of three lithologies; basement oceanic sediments of the Cretaceous Shimanto Supergroup, Quaternary andesites, and auriferous quartz vein. We studied the drilled core rock of these, and the geothermal hot waters from the basement aquifers collected by means of the dewatering system located at the deepest level in the mining sites. Culture-independent molecular phylogenetic analyses of PCR-amplified ribosomal DNA (rDNA) recovered from drilled cores suggested that the deep-sea oceanic microbial communities were present as ancient indigenous relicts confined in the Shimanto basement. On the other hand, genetic signals of active thermophilic microbial communities, mainly consisting of thermophilic hydrogen-oxidizer within Aquificales, thermophilic methanotroph within g-Proteobacteria and yet-uncultivated bacterium OPB37 within b-Proteobacteria, were detected with these of oceanic relicts from the subterranean geothermal hot aquifers (temp. 70-100ºC). Successful cultivation and FISH analyses strongly supported that these thermophilic lithotrophic microorganisms could be exactly active and they grew using geochemically produced hydrogen and methane gasses as nutrients. Based on these results, the deep-subsurface biosphere occurring in the Hishikari epithermal gold mine was delineated as endolithic ancient microbial relicts and modern habitats raising active lithotrophic thermophiles associated with the geological and geochemical features of the epithermal gold deposit.

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.

Biochar, activated carbon, and carbon nanotubes have different effects on fate of (14)C-catechol and microbial community in soil.

PubMed

Shan, Jun; Ji, Rong; Yu, Yongjie; Xie, Zubin; Yan, Xiaoyuan

2015-10-30

This study investigated the effects of biochar, activated carbon (AC)-, and single-walled and multi-walled carbon nanotubes (SWCNTs and MWCNTs) in various concentrations (0, 0.2, 20, and 2,000 mg/kg dry soil) on the fate of (14)C-catechol and microbial community in soil. The results showed that biochar had no effect on the mineralization of (14)C-catechol, whereas AC at all amendment rates and SWCNTs at 2,000 mg/kg significantly reduced mineralization. Particularly, MWCNTs at 0.2 mg/kg significantly stimulated mineralization compared with the control soil. The inhibitory effects of AC and SWCNTs on the mineralization were attributed to the inhibited soil microbial activities and the shifts in microbial communities, as suggested by the reduced microbial biomass C and the separated phylogenetic distance. In contrast, the stimulatory effects of MWCNTs on the mineralization were attributed to the selective stimulation of specific catechol-degraders by MWCNTs at 0.2 mg/kg. Only MWCNTs amendments and AC at 2,000 mg/kg significantly changed the distribution of (14)C residues within the fractions of humic substances. Our findings suggest biochar, AC, SWCNTs and MWCNTs have different effects on the fate of (14)C-catechol and microbial community in soil.

Biochar, activated carbon, and carbon nanotubes have different effects on fate of 14C-catechol and microbial community in soil

PubMed Central

Shan, Jun; Ji, Rong; Yu, Yongjie; Xie, Zubin; Yan, Xiaoyuan

2015-01-01

This study investigated the effects of biochar, activated carbon (AC)-, and single-walled and multi-walled carbon nanotubes (SWCNTs and MWCNTs) in various concentrations (0, 0.2, 20, and 2,000 mg/kg dry soil) on the fate of 14C-catechol and microbial community in soil. The results showed that biochar had no effect on the mineralization of 14C-catechol, whereas AC at all amendment rates and SWCNTs at 2,000 mg/kg significantly reduced mineralization. Particularly, MWCNTs at 0.2 mg/kg significantly stimulated mineralization compared with the control soil. The inhibitory effects of AC and SWCNTs on the mineralization were attributed to the inhibited soil microbial activities and the shifts in microbial communities, as suggested by the reduced microbial biomass C and the separated phylogenetic distance. In contrast, the stimulatory effects of MWCNTs on the mineralization were attributed to the selective stimulation of specific catechol-degraders by MWCNTs at 0.2 mg/kg. Only MWCNTs amendments and AC at 2,000 mg/kg significantly changed the distribution of 14C residues within the fractions of humic substances. Our findings suggest biochar, AC, SWCNTs and MWCNTs have different effects on the fate of 14C-catechol and microbial community in soil. PMID:26515132

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.

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.

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.

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.

Synthesis of coumarin-theophylline hybrids as a new class of anti-tubercular and anti-microbial agents.

PubMed

Mangasuli, Sumitra N; Hosamani, Kallappa M; Devarajegowda, Hirihalli C; Kurjogi, Mahantesh M; Joshi, Shrinivas D

2018-02-25

A series of novel coumarin-theophylline hybrids were synthesized and examined for their anti-tubercular activity in vitro against Mycobacterium tuberculosis H 37 Rv, anti-microbial activity in vitro against gram-positive bacteria (Staphylococcus aureus) and gram-negative bacterias (Escherichia coli, Salmonella typhi) as well as fungi (Candida albicans). The compound (3a) has shown excellent anti-tubercular activity with MIC of 0.12 μg/mL. Electron donating compounds (3a, 3f) have displayed significant anti-microbial activity. The compounds have also been precisely elucidated using single crystal X-ray diffraction techniques. Molecular docking study has been performed against 4DQU enzyme of Mycobacterium tuberculosis showed good binding interactions and is in agreement with the in vitro results. Copyright © 2018. Published by Elsevier Masson SAS.

Tracking dynamics of plant biomass composting by changes in substrate structure, microbial community, and enzyme activity

PubMed Central

2012-01-01

Background Understanding the dynamics of the microbial communities that, along with their secreted enzymes, are involved in the natural process of biomass composting may hold the key to breaking the major bottleneck in biomass-to-biofuels conversion technology, which is the still-costly deconstruction of polymeric biomass carbohydrates to fermentable sugars. However, the complexity of both the structure of plant biomass and its counterpart microbial degradation communities makes it difficult to investigate the composting process. Results In this study, a composter was set up with a mix of yellow poplar (Liriodendron tulipifera) wood-chips and mown lawn grass clippings (85:15 in dry-weight) and used as a model system. The microbial rDNA abundance data obtained from analyzing weekly-withdrawn composted samples suggested population-shifts from bacteria-dominated to fungus-dominated communities. Further analyses by an array of optical microscopic, transcriptional and enzyme-activity techniques yielded correlated results, suggesting that such population shifts occurred along with early removal of hemicellulose followed by attack on the consequently uncovered cellulose as the composting progressed. Conclusion The observed shifts in dominance by representative microbial groups, along with the observed different patterns in the gene expression and enzymatic activities between cellulases, hemicellulases, and ligninases during the composting process, provide new perspectives for biomass-derived biotechnology such as consolidated bioprocessing (CBP) and solid-state fermentation for the production of cellulolytic enzymes and biofuels. PMID:22490508

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.

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.

Active subsurface cellular function in the Baltic Sea Basin, IODP Exp 347

NASA Astrophysics Data System (ADS)

Reese, B. K.; Zinke, L. A.; Bird, J. T.; Lloyd, K. G.; Marshall, I.; Amend, J.; Jørgensen, B. B.

2016-12-01

The Baltic Sea Basin is a unique depositional setting that has experienced periods of glaciation and deglaciation as a result of global temperature fluctuations over the course of several hundred thousand years. This has resulted in laminated sediments formed during periods with strong permanent salinity stratification. The high sedimentation rates (100-500 cm/1000 y) make this an ideal setting to understand the microbial structure of a deep biosphere community in a high-organic matter environment. The responses of deep sediment microbial communities to variations in conditions during and after deposition are poorly understood. Samples were collected through scientific drilling during the International Ocean Discovery Program (IODP) Expedition 347 on board the Greatship Manisha, September-November 2013. We examined the active microbial community structure using the 16S rRNA gene transcript and active functional genes through metatranscriptome sequencing. Major biogeochemical shifts have been observed in response to the depositional history between the limnic, brackish, and marine phases. The microbial community structure in the BSB is diverse and reflective of the unique changes in the geochemical profile. These data further define the existence life in the deep subsurface and the survival mechanisms required for this extreme environment.

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.

Antimicrobial activity of organometallic isonicotinyl and pyrazinyl ferrocenyl-derived complexes

USDA-ARS?s Scientific Manuscript database

The discovery of new drugs against microbial diseases is imperative to human and animal health. In this study, we synthesized a novel set of iron-based compounds and tested them against three widespread microbial diseases –tuberculosis, malaria, and trichomoniasis. Our results identified several lea...

Climate change and human activities altered the diversity and composition of soil microbial community in alpine grasslands of the Qinghai-Tibetan Plateau.

PubMed

Zhang, Yong; Dong, Shikui; Gao, Qingzhu; Liu, Shiliang; Zhou, Huakun; Ganjurjav, Hasbagan; Wang, Xuexia

2016-08-15

Alpine ecosystems are known to be sensitive to climate change and human disturbances. However, the knowledge about the changes of their underground microbial communities is inadequate. We explored the diversity and structure of soil bacterial and fungal communities using Ilumina MiSeq sequencing in native alpine grasslands (i.e. the alpine meadow, alpine steppe) and cultivated grassland of the Qinghai-Tibetan Plateau (QTP) under three-year treatments of overgrazing, warming and enhanced rainfall. Enhanced rainfall rather than warming significantly reduced soil microbial diversity in native alpine grasslands. Variable warming significantly reduced it in the cultivated grassland. Over 20% and 40% variations of microbial diversity could be explained by soil nutrients and moisture in the alpine meadow and cultivated grassland, separately. Soil microbial communities could be clustered into different groups according to different treatments in the alpine meadow and cultivated grassland. For the alpine steppe, with the lowest soil nutrients and moistures, <10% variations of microbial diversity was explained by soil properties; and the soil microbial communities among different treatments were similar. The soil microbial community in the cultivated grassland was varied from it in native grasslands. Over 50% variations of soil microbial communities among different treatments were explained by soil nutrients and moisture in each grassland type. Our results suggest that climate change and human activities strongly affected soil microbial communities by changing soil nutrients and moistures in alpine grassland ecosystems. Copyright © 2016 Elsevier B.V. All rights reserved.

Reactivation of Deep Subsurface Microbial Community in Response to Methane or Methanol Amendment

PubMed Central

Rajala, Pauliina; Bomberg, Malin

2017-01-01

Microbial communities in deep subsurface environments comprise a large portion of Earth’s biomass, but the microbial activity in these habitats is largely unknown. Here, we studied how microorganisms from two isolated groundwater fractures at 180 and 500 m depths of the Outokumpu Deep Drillhole (Finland) responded to methane or methanol amendment, in the presence or absence of sulfate as an additional electron acceptor. Methane is a plausible intermediate in the deep subsurface carbon cycle, and electron acceptors such as sulfate are critical components for oxidation processes. In fact, the majority of the available carbon in the Outokumpu deep biosphere is present as methane. Methanol is an intermediate of methane oxidation, but may also be produced through degradation of organic matter. The fracture fluid samples were incubated in vitro with methane or methanol in the presence or absence of sulfate as electron acceptor. The metabolic response of microbial communities was measured by staining the microbial cells with fluorescent redox sensitive dye combined with flow cytometry, and DNA or cDNA-derived amplicon sequencing. The microbial community of the fracture zone at the 180 m depth was originally considerably more respiratory active and 10-fold more numerous (105 cells ml-1 at 180 m depth and 104 cells ml-1 at 500 m depth) than the community of the fracture zone at the 500 m. However, the dormant microbial community at the 500 m depth rapidly reactivated their transcription and respiration systems in the presence of methane or methanol, whereas in the shallower fracture zone only a small sub-population was able to utilize the newly available carbon source. In addition, the composition of substrate activated microbial communities differed at both depths from original microbial communities. The results demonstrate that OTUs representing minor groups of the total microbial communities play an important role when microbial communities face changes in environmental conditions. PMID:28367144

3-(1,3,4-Thiadiazole-2-yl)quinoline derivatives: synthesis, characterization and anti-microbial activity.

PubMed

Bhat, Abdul R; Tazeem; Azam, Amir; Choi, Inho; Athar, Fareeda

2011-07-01

A new series of thiadiazoles and intermediate thiosemicarbazones were synthesized from the chloroquinone molecule, with an aim to explore their effect on in vitro growth of microorganisms causing microbial infection. The chemical structures of the compound were elucidated by elemental analysis, FTIR, 1H and 13C NMR and ESI-MS spectral data. In vitro anti-microbial activity was performed against Staphylococcusaureus, Streptococcuspyogenes, Salmonellatyphimurium, and Escherichiacoli. The MIC was detected using the double dilution method. The results were compared by calculating percent inhibit area/μg of the compounds and the standard "amoxicillin". The selected compounds were tested for cytotoxic results using MTT assay H9c2 cardiac myoblasts cell line and the results showed that all the compounds offered remarkable >80% viability to a concentration of 200 μg/mL. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

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.

Synthetic microbial ecology and the dynamic interplay between microbial genotypes.

PubMed

Dolinšek, Jan; Goldschmidt, Felix; Johnson, David R

2016-11-01

Assemblages of microbial genotypes growing together can display surprisingly complex and unexpected dynamics and result in community-level functions and behaviors that are not readily expected from analyzing each genotype in isolation. This complexity has, at least in part, inspired a discipline of synthetic microbial ecology. Synthetic microbial ecology focuses on designing, building and analyzing the dynamic behavior of ‘ecological circuits’ (i.e. a set of interacting microbial genotypes) and understanding how community-level properties emerge as a consequence of those interactions. In this review, we discuss typical objectives of synthetic microbial ecology and the main advantages and rationales of using synthetic microbial assemblages. We then summarize recent findings of current synthetic microbial ecology investigations. In particular, we focus on the causes and consequences of the interplay between different microbial genotypes and illustrate how simple interactions can create complex dynamics and promote unexpected community-level properties. We finally propose that distinguishing between active and passive interactions and accounting for the pervasiveness of competition can improve existing frameworks for designing and predicting the dynamics of microbial assemblages.

Effects and bioavailability of 2,4,6-trinitrotoluene in spiked and field-contaminated soils to indigenous microorganisms

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

Gong, P.; Siciliano, S.D.; Greer, C.W.

1999-12-01

The response of potential nitrification activity (PNA), nitrogen-fixation activity (NFA), and dehydrogenase activity (DHA) in soil to 2,4,6-trinitrotoluene (TNT) was assessed. Two garden soils of contrasting texture were spiked with TNT. Soil microbial activities and TNT residues were analyzed 1 week later. The estimated IC50 ranged from 39 to 533 mg/kg of the acetonitrile-extractable (AE) TNT, depending on indicators and soils. The lowest LOEC (lowest-observed-effect concentration) was 1 mg AE TNT/kg. Field soil was collected from three known contaminated sites in an abandoned TNT manufacturing facility. Microbial toxicity significantly correlated to TNT levels in these soils. The LOEC and NOECmore » (no-observed-effect concentration) values were site and indicator specific, with the lowest LOEC being 1 mg AE TNT/kg and the lowest NOEC being 0.4 mg AE TNT/kg. The IC50 of the pooled field samples was 51 mg AE TNT/kg for PNA or 157 mg AE TNT/kg for DHA. These results indicate that microbial responses were consistent and comparable between the laboratory and the field and that TNT could significantly inhibit soil microbial activities at very low levels. Both AE TNT and deionized water-extractable (DW) TNT concentrations correlated well with microbial toxicity, but AE TNT provided a better evaluation of TNT bioavailability than did DW TNT.« less

Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances.

PubMed

Xu, Jianping

2006-06-01

Microbial ecology examines the diversity and activity of micro-organisms in Earth's biosphere. In the last 20 years, the application of genomics tools have revolutionized microbial ecological studies and drastically expanded our view on the previously underappreciated microbial world. This review first introduces the basic concepts in microbial ecology and the main genomics methods that have been used to examine natural microbial populations and communities. In the ensuing three specific sections, the applications of the genomics in microbial ecological research are highlighted. The first describes the widespread application of multilocus sequence typing and representational difference analysis in studying genetic variation within microbial species. Such investigations have identified that migration, horizontal gene transfer and recombination are common in natural microbial populations and that microbial strains can be highly variable in genome size and gene content. The second section highlights and summarizes the use of four specific genomics methods (phylogenetic analysis of ribosomal RNA, DNA-DNA re-association kinetics, metagenomics, and micro-arrays) in analysing the diversity and potential activity of microbial populations and communities from a variety of terrestrial and aquatic environments. Such analyses have identified many unexpected phylogenetic lineages in viruses, bacteria, archaea, and microbial eukaryotes. Functional analyses of environmental DNA also revealed highly prevalent, but previously unknown, metabolic processes in natural microbial communities. In the third section, the ecological implications of sequenced microbial genomes are briefly discussed. Comparative analyses of prokaryotic genomic sequences suggest the importance of ecology in determining microbial genome size and gene content. The significant variability in genome size and gene content among strains and species of prokaryotes indicate the highly fluid nature of prokaryotic genomes, a result consistent with those from multilocus sequence typing and representational difference analyses. The integration of various levels of ecological analyses coupled to the application and further development of high throughput technologies are accelerating the pace of discovery in microbial ecology.

Exploitation of starch industry liquid by-product to produce bioactive peptides from rice hydrolyzed proteins.

PubMed

Dei Piu', Lucilla; Tassoni, Annalisa; Serrazanetti, Diana Isabella; Ferri, Maura; Babini, Elena; Tagliazucchi, Davide; Gianotti, Andrea

2014-07-15

Small peptides show higher antioxidant capacity than native proteins and may be absorbed in the intestine without further digestion. In our study, a protein by-product from rice starch industry was hydrolyzed with commercial proteolytic enzymes (Alcalase, Neutrase, Flavourzyme) and microbial whole cells of Bacillus spp. and the released peptides were tested for antioxidant activity. Among enzymes, Alcalase was the most performing, while microbial proteolytic activity was less efficient. Conversely, the antioxidant activity was higher in the samples obtained by microbial hydrolysis and particularly with Bacillus pumilus AG1. The sequences of low molecular weight antioxidant peptides were determined and analyzed for aminoacidic composition. The results obtained so far suggest that the hydrolytic treatment of this industrial by-product, with selected enzymes and microbial systems, can allow its exploitation for the production of functional additives and supplements rich in antioxidant peptides, to be used in new food formulas for human consumption. Copyright © 2014 Elsevier Ltd. All rights reserved.

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.

Microbial Assimilation of Atmospheric CO2 to Synthesize Organic Matter in Soils

NASA Astrophysics Data System (ADS)

Ge, Tida

2014-05-01

Like higher plants, microbial autotrophs possess photosynthetic systems that enable them to fix CO2. Whilst present in large numbers in soils, the capacity for soil microorganisms to fix CO2 and their importance in terrestrial C cycling has not been quantified. To measure the activities of microbial autotrophs in assimilating atmospheric CO2, seven different soils were incubated with 14C labelled CO2 for 80 d, and the 14C-labelled organic C synthesized was determined. The results indicate that the synthesis rates of 14C-lablled organic C ranged from 0.0134 to 0.103 g C m-2 d-1, and were closely related to RubisCO activities and the abundance of cbbL-genes in the soils, indicating that the synthesis could be attributed to soil microbial autotrophs. This finding suggests that microbial assimilation of atmospheric CO2 is an important process in the sequestration and cycling of terrestrial C that, until now, has been largely ignored.

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.

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.

Substrate and environmental controls on microbial assimilation of soil organic carbon: a framework for Earth System Models

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

Xu, Xiaofeng; Schimel, Joshua; Thornton, Peter E

2014-01-01

Microbial assimilation of soil organic carbon is one of the fundamental processes of global carbon cycling and it determines the magnitude of microbial biomass in soils. Mechanistic understanding of microbial assimilation of soil organic carbon and its controls is important for to improve Earth system models ability to simulate carbon-climate feedbacks. Although microbial assimilation of soil organic carbon is broadly considered to be an important parameter, it really comprises two separate physiological processes: one-time assimilation efficiency and time-dependent microbial maintenance energy. Representing of these two mechanisms is crucial to more accurately simulate carbon cycling in soils. In this study, amore » simple modeling framework was developed to evaluate the substrate and environmental controls on microbial assimilation of soil organic carbon using a new term: microbial annual active period (the length of microbes remaining active in one year). Substrate quality has a positive effect on microbial assimilation of soil organic carbon: higher substrate quality (lower C:N ratio) leads to higher ratio of microbial carbon to soil organic carbon and vice versa. Increases in microbial annual active period from zero stimulate microbial assimilation of soil organic carbon; however, when microbial annual active period is longer than an optimal threshold, increasing this period decreases microbial biomass. The simulated ratios of soil microbial biomass to soil organic carbon are reasonably consistent with a recently compiled global dataset at the biome-level. The modeling framework of microbial assimilation of soil organic carbon and its controls developed in this study offers an applicable ways to incorporate microbial contributions to the carbon cycling into Earth system models for simulating carbon-climate feedbacks and to explain global patterns of microbial biomass.« less

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

Defining boundaries for the distribution of microbial communities beneath the sediment-buried, hydrothermally active seafloor

PubMed Central

Yanagawa, Katsunori; Ijiri, Akira; Breuker, Anja; Sakai, Sanae; Miyoshi, Youko; Kawagucci, Shinsuke; Noguchi, Takuroh; Hirai, Miho; Schippers, Axel; Ishibashi, Jun-ichiro; Takaki, Yoshihiro; Sunamura, Michinari; Urabe, Tetsuro; Nunoura, Takuro; Takai, Ken

2017-01-01

Subseafloor microbes beneath active hydrothermal vents are thought to live near the upper temperature limit for life on Earth. We drilled and cored the Iheya North hydrothermal field in the Mid-Okinawa Trough, and examined the phylogenetic compositions and the products of metabolic functions of sub-vent microbial communities. We detected microbial cells, metabolic activities and molecular signatures only in the shallow sediments down to 15.8 m below the seafloor at a moderately distant drilling site from the active hydrothermal vents (450 m). At the drilling site, the profiles of methane and sulfate concentrations and the δ13C and δD isotopic compositions of methane suggested the laterally flowing hydrothermal fluids and the in situ microbial anaerobic methane oxidation. In situ measurements during the drilling constrain the current bottom temperature of the microbially habitable zone to ~45 °C. However, in the past, higher temperatures of 106–198 °C were possible at the depth, as estimated from geochemical thermometry on hydrothermally altered clay minerals. The 16S rRNA gene phylotypes found in the deepest habitable zone are related to those of thermophiles, although sequences typical of known hyperthermophilic microbes were absent from the entire core. Overall our results shed new light on the distribution and composition of the boundary microbial community close to the high-temperature limit for habitability in the subseafloor environment of a hydrothermal field. PMID:27754478

Defining boundaries for the distribution of microbial communities beneath the sediment-buried, hydrothermally active seafloor.

PubMed

Yanagawa, Katsunori; Ijiri, Akira; Breuker, Anja; Sakai, Sanae; Miyoshi, Youko; Kawagucci, Shinsuke; Noguchi, Takuroh; Hirai, Miho; Schippers, Axel; Ishibashi, Jun-Ichiro; Takaki, Yoshihiro; Sunamura, Michinari; Urabe, Tetsuro; Nunoura, Takuro; Takai, Ken

2017-02-01

Subseafloor microbes beneath active hydrothermal vents are thought to live near the upper temperature limit for life on Earth. We drilled and cored the Iheya North hydrothermal field in the Mid-Okinawa Trough, and examined the phylogenetic compositions and the products of metabolic functions of sub-vent microbial communities. We detected microbial cells, metabolic activities and molecular signatures only in the shallow sediments down to 15.8 m below the seafloor at a moderately distant drilling site from the active hydrothermal vents (450 m). At the drilling site, the profiles of methane and sulfate concentrations and the δ 13 C and δD isotopic compositions of methane suggested the laterally flowing hydrothermal fluids and the in situ microbial anaerobic methane oxidation. In situ measurements during the drilling constrain the current bottom temperature of the microbially habitable zone to ~45 °C. However, in the past, higher temperatures of 106-198 °C were possible at the depth, as estimated from geochemical thermometry on hydrothermally altered clay minerals. The 16S rRNA gene phylotypes found in the deepest habitable zone are related to those of thermophiles, although sequences typical of known hyperthermophilic microbes were absent from the entire core. Overall our results shed new light on the distribution and composition of the boundary microbial community close to the high-temperature limit for habitability in the subseafloor environment of a hydrothermal field.

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

Contrasting digestive strategies in four New Zealand herbivorous fishes as reflected by carbohydrase activity profiles.

PubMed

Skea, G L; Mountfort, D O; Clements, K D

2007-01-01

Enzymatic degradation of algal carbohydrates was examined in the New Zealand herbivorous fishes Parma alboscapularis (Pomacentridae), Aplodactylus etheridgii (Aplodactylidae), Girella tricuspidata and G. cyanea (Girellidae). Enzyme extract taken from the anterior gut wall, gut fluid and microbial pellet from sections sampled along the gut were tested for activity against starch, carrageenan, agarose and carboxymethylcellulose. Hydrolysis of starch was greater than for all other substrates tested. Endogenous (host-produced) activity in the anterior gut fluid varied between species in the order G. tricuspidata (7700 units mL(-1))>G. cyanea (2300 units mL(-1))>P. alboscapularis (2000)>A. etheridgii (1400 units mL(-1)) where one unit is equivalent to 1 mug of reducing sugar released per minute. Activity decreased markedly along the gut in all cases, so that at the posterior end of the gut only 0.3-8% of the anterior activity remained in the gut fluid. Enzyme activity against structural carbohydrates was lower than that against starch, and was of exogenous (produced by resident microbiota) origin in all species although the location of activity along the gut differed. The microbial extract of A. etheridgii displayed the highest activity against carrageenan and agarose in all gut sections, reaching maxima of 47 units mL(-1) against carrageenan and 35 units mL(-1) against agarose in the mid-gut microbial extract. Carrageenase and agarase activity in the other three species was <10 units mL(-1) for all gut sections. Results suggest that carrageenan and agarose are potentially important substrates for microbial fermentation, particularly in A. etheridgii, and that there is microbial activity in the mid-gut of this species, rather than primarily in the hind-gut as in other herbivorous species.

Modeling of Sustainable Base Production by Microbial Electrolysis Cell.

PubMed

Blatter, Maxime; Sugnaux, Marc; Comninellis, Christos; Nealson, Kenneth; Fischer, Fabian

2016-07-07

A predictive model for the microbial/electrochemical base formation from wastewater was established and compared to experimental conditions within a microbial electrolysis cell. A Na2 SO4 /K2 SO4 anolyte showed that model prediction matched experimental results. Using Shewanella oneidensis MR-1, a strong base (pH≈13) was generated using applied voltages between 0.3 and 1.1 V. Due to the use of bicarbonate, the pH value in the anolyte remained unchanged, which is required to maintain microbial activity. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ionic Strength Is a Barrier to the Habitability of Mars.

PubMed

Fox-Powell, Mark G; Hallsworth, John E; Cousins, Claire R; Cockell, Charles S

2016-06-01

The thermodynamic availability of water (water activity) strictly limits microbial propagation on Earth, particularly in hypersaline environments. A considerable body of evidence indicates the existence of hypersaline surface waters throughout the history of Mars; therefore it is assumed that, as on Earth, water activity is a major limiting factor for martian habitability. However, the differing geological histories of Earth and Mars have driven variations in their respective aqueous geochemistry, with as-yet-unknown implications for habitability. Using a microbial community enrichment approach, we investigated microbial habitability for a suite of simulated martian brines. While the habitability of some martian brines was consistent with predictions made from water activity, others were uninhabitable even when the water activity was biologically permissive. We demonstrate experimentally that high ionic strength, driven to extremes on Mars by the ubiquitous occurrence of multivalent ions, renders these environments uninhabitable despite the presence of biologically available water. These findings show how the respective geological histories of Earth and Mars, which have produced differences in the planets' dominant water chemistries, have resulted in different physicochemical extremes which define the boundary space for microbial habitability. Habitability-Mars-Salts-Water activity-Life in extreme environments. Astrobiology 16, 427-442.

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.

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

Pilot-scale vadose zone microbial biobarriers removed nitrate leaching from a cattle corral

USDA-ARS?s Scientific Manuscript database

activities that involve animal wastes can result in the contamination of subsurface soils by nitrates. In saturated or nearly saturated soils microbial biobarriers are a common method used to remove contaminants from water. This field study was conducted beneath a cattle pen in northeast Colorado a...

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.

Long-term effects of nickel oxide nanoparticles on performance, microbial enzymatic activity, and microbial community of a sequencing batch reactor.

PubMed

Wang, Sen; Li, Zhiwei; Gao, Mengchun; She, Zonglian; Guo, Liang; Zheng, Dong; Zhao, Yangguo; Ma, Bingrui; Gao, Feng; Wang, Xuejiao

2017-02-01

The nitrogen and phosphorus removal, microbial enzymatic activity, and microbial community of a sequencing batch reactor (SBR) were evaluated under long-term exposure to nickel oxide nanoparticles (NiO NPs). High NiO NP concentration (over 5 mg L -1 ) affected the removal of chemical oxygen demand, nitrogen, and phosphorus. The presence of NiO NP inhibited the microbial enzymatic activities and reduced the nitrogen and phosphorus removal rates of activated sludge. The microbial enzymatic activities of the activated sludge showed a similar variation trend to the nitrogen and phosphorus removal rates with the increase in NiO NP concentration from 0 to 60 mg L -1 . The Ni content in the effluent and activated sludge showed an increasing trend with the increase in NiO NP concentration. Some NiO NPs were absorbed on the sludge surface or penetrate the cell membrane into the interior of microbial cells in the activated sludge. NiO NP facilitated the increase in reactive oxygen species by disturbing the balance between the oxidation and anti-oxidation processes, and the variation in lactate dehydrogenase demonstrated that NiO NP could destroy the cytomembrane and cause variations in the microbial morphology and physiological function. High-throughput sequencing demonstrated that the microbial community of SBR had some obvious changes at 0-60 mg L -1 NiO NPs at the phyla, class and genus levels. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

Representing Microbial Dormancy in Soil Decomposition Models Improves Model Performance and Reveals Key Ecosystem Controls on Microbial Activity

NASA Astrophysics Data System (ADS)

He, Y.; Yang, J.; Zhuang, Q.; Wang, G.; Liu, Y.

2014-12-01

Climate feedbacks from soils can result from environmental change and subsequent responses of plant and microbial communities and nutrient cycling. Explicit consideration of microbial life history traits and strategy may be necessary to predict climate feedbacks due to microbial physiology and community changes and their associated effect on carbon cycling. In this study, we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of dormancy at six temperate forest sites with observed soil efflux ranged from 4 to 10 years across different forest types. We then extrapolated the model to all temperate forests in the Northern Hemisphere (25-50°N) to investigate spatial controls on microbial and soil C dynamics. Both models captured the observed soil heterotrophic respiration (RH), yet no-dormancy model consistently exhibited large seasonal amplitude and overestimation in microbial biomass. Spatially, the total RH from temperate forests based on dormancy model amounts to 6.88PgC/yr, and 7.99PgC/yr based on no-dormancy model. However, no-dormancy model notably overestimated the ratio of microbial biomass to SOC. Spatial correlation analysis revealed key controls of soil C:N ratio on the active proportion of microbial biomass, whereas local dormancy is primarily controlled by soil moisture and temperature, indicating scale-dependent environmental and biotic controls on microbial and SOC dynamics. These developments should provide essential support to modeling future soil carbon dynamics and enhance the avenue for collaboration between empirical soil experiment and modeling in the sense that more microbial physiological measurements are needed to better constrain and evaluate the models.

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

Microbial functional diversity plays an important role in the degradation of polyhydroxybutyrate (PHB) in soil.

PubMed

Dey, Samrat; Tribedi, Prosun

2018-03-01

Towards bioremediation of recalcitrant materials like synthetic polymer, soil has been recognized as a traditional site for disposal and subsequent degradation as some microorganisms in soil can degrade the polymer in a non-toxic, cost-effective, and environment friendly way. Microbial functional diversity is a constituent of biodiversity that includes wide range of metabolic activities that can influence numerous aspects of ecosystem functioning like ecosystem stability, nutrient availability, ecosystem dynamics, etc. Thus, in the current study, we assumed that microbial functional diversity could play an important role in polymer degradation in soil. To verify this hypothesis, we isolated soil from five different sites of landfill and examined several microbiological parameters wherein we observed a significant variation in heterotrophic microbial count as well as microbial activities among the soil microcosms tested. Multivariate analysis (principle component analysis) based on the carbon sources utilization pattern revealed that soil microcosms showed different metabolic patterns suggesting the variable distribution of microorganisms among the soil microcosms tested. Since microbial functional diversity depends on both microbial richness and evenness, Shannon diversity index was determined to measure microbial richness and Gini coefficient was determined to measure microbial evenness. The tested soil microcosms exhibited variation in both microbial richness and evenness suggesting the considerable difference in microbial functional diversity among the tested microcosms. We then measured polyhydroxybutyrate (PHB) degradation in soil microcosms after desired period of incubation of PHB in soil wherein we found that soil microcosms having higher functional diversity showed enhanced PHB degradation and soil microcosms having lower functional diversity showed reduced PHB degradation. We also noticed that all the tested soil microcosms showed similar pattern in both microbial functional diversity and PHB degradation suggesting a strong positive correlation ( r  = 0.95) between microbial functional diversity and PHB degradation. Thus, the results demonstrate that microbial functional diversity plays an important role in PHB degradation in soil by exhibiting versatile microbial metabolic potentials that lead to the enhanced degradation of PHB.

Carbon availability structures microbial community composition and function in soil aggregate fractions

NASA Astrophysics Data System (ADS)

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

2014-12-01

Identifying the microbial metabolic pathways that most strongly influence ecosystem carbon (C) cycling requires a deeper understanding of the availability and accessibility of microbial substrates. A first step towards this goal is characterizing the relationships between microbial community function and soil C chemistry in a field context. For this perspective, soil aggregate fractions can be used as model systems that scale between microbe-substrate interactions and ecosystem C cycling and storage. The present study addresses how physicochemical variation among soil aggregate fractions influences the composition and functional potential of C cycling microbial communities. We report variation across soil aggregates using plot scale biological replicates from biofuel agroecosystems (fertilized, reconstructed, tallgrass prairie). Our results suggest that C and nitrogen (N) chemistry significantly differ among aggregate fractions. This leads to variation in microbial community composition, which was better characterized among aggregates than by using the whole soil. In fact by considering soil aggregation, we were able to characterize almost 2000 more taxa than whole soil alone, resulting in 65% greater community richness. Availability of C and N strongly influenced the composition of microbial communities among soil aggregate fractions. The normalized abundance of microbial functional guilds among aggregate fractions correlated with C and N chemistry, as did functional potential, measured by extracellular enzyme activity. Metagenomic results suggest that soil aggregate fractions select for functionally distinct microbial communities, which may significantly influence decomposition and soil C storage. Our study provides support for the premise that integration of soil aggregate chemistry, especially microaggregates that have greater microbial richness and occur at spatial scales relevant to microbial community functioning, may be necessary to understand the role of microbial communities on terrestrial C and N cycling.

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.

Changes of soil organic matter and microbial activity in irrigated and non irrigated olive groves

NASA Astrophysics Data System (ADS)

Kavvadias, Victor; Papadopoulou, Maria; Theocharopoulos, Sideris; Vavoulidou, Evagelia; Doula, Maria; Reppas, Spiros

2014-05-01

The implementation of olive cultivation techniques in Greece has not been systematically tested under the prevailing Mediterranean conditions. A LIFE+ project was initiated (oLIVE-CLIMA; LIFE 11/ENV/000942) aiming to introduce new management practices in olive tree crops that lead to increased carbon dioxide uptake by plants as well as carbon sequestration from the atmosphere and reverse the trend of soil organic matter decline, erosion and desertification. This paper presents data on soil organic matter and microbial activity from a soil campaign in a pilot region in Greece, and particularly in the area of Chora, prefecture of Messinia, South west Peloponnese. The soil campaign took place during the period December 2012-February 2013. Twelve soil parcels of olive groves were selected (6 irrigated and 6 rainfed) and in each soil parcel six composite soil samples were taken from 0-10 cm depth at equal intervals along a straight line of the trunk of the tree to the middle of the distance from the nearest tree of the next tree series. The first three samples were under olive tree canopy. An additional composite sample was taken at depth of 10-40 cm. Soil samples were analyzed for soil physicochemical and biological properties. In this study results for total organic carbon (TOC), soil basal microbial respiration (BR), microbial biomass C (MB-C) from the region of Messinia, are presented. Organic matter was determined by dichromate oxidation. The microbial activity was measured by the amount of CO2 evolution, while microbial biomass C was determined by substrate-induced respiration, after the addition of glucose. The results showed considerable differences in TOC, BR and MB-C associated with the sampling position and soil depth. The higher TOC, BR and MB-C values, in most cases, were determined in samples taken from points under the canopy, but not close to the tree trunk compared to the sampling points outside the canopy. This indicates the positive effect of rhizosphere and the favorable soil moisture conditions under tree canopy on soil microbial activities. TOC, BR and MB-C values were considerably lower in soil depth of 10-40cm compared with 0-10 cm in both irrigated and rainfed soil parcels. Moreover BR and MB-C was higher in irrigated soil parcels compared with rainfed ones suggesting that the periodic irrigation significantly enhances the soil microbial activity. There were no considerable differences in TOC. For this the TOC and potential activity of microbial community can contribute in the soil nutrient and irrigation management guidelines in order to exploit the utilization of productive soils in the region under studied.

Microbial community diversity associated with moonmilk deposits in a karstic cave system in Ireland

NASA Astrophysics Data System (ADS)

Rooney, D.; Hutchens, E.; Clipson, Nick; McDermott, Frank

2009-04-01

Microbial ecology in subterranean systems has yet to be fully studied. Cave systems present highly unusual and extreme habitats, where microbial activity can potentially play a major role in nutrient cycling and possibly contribute to the formation of characteristic subaerial structures. How microorganisms actually function in cave systems, and what ecological roles they may perform, has yet to be widely addressed, although recent studies using molecular techniques combined with analytical geochemistry have begun to answer some questions surrounding subterranean microbial ecology (Northup et al., 2003). Moonmilk has a ‘cottage-cheese' like consistency, comprised of fine crystal aggregates of carbonate minerals, commonly calcite, hydromagnesite and gypsum, and is believed to be at least partially precipitated by microbial activity (Baskar et al., 2006). Microbial metabolic processes have been implicated in the formation of moonmilk, probably a result of biochemical corrosion of bedrock under high moisture conditions. Mineral weathering via bacterial activity has become accepted as a major influence on subsurface geochemistry and formation of belowground structures (Summers-Engel et al., 2004). While many studies focus on bacterial communities in subterranean systems, fungal community structure is also likely to be important in cave systems, given the important role fungi play in the transformations of organic and inorganic substrates (Gadd, 2004) and the significant role of fungi in mineral dissolution and secondary mineral formation (Burford et al., 2003). In general, it is agreed that both biotic and abiotic processes influence moonmilk formation, yet the diversity of the microbial community associated with moonmilk formations has not been characterised to date. Ballinamintra Cave (Waterford County, Ireland) is largely protected from human influence due to accessibility difficulties and thereby offers an opportunity to study microbial community structure that has been unaltered by human disturbance or practices. The aim of this study was to examine microbial community diversity associated with moonmilk deposits at Ballynamintra Cave, Ireland using automated ribosomal intergenic spacer analysis (ARISA). The results revealed considerable bacterial and fungal diversity associated with moonmilk in a karstic cave system, suggesting that the microbial community implicated in moonmilk formation may be more diverse than previously thought. These results suggest that microbes may have important functional roles in subterranean environments. Although the moonmilk in this study was largely comprised of calcite, microbial involvement in calcite precipitation could result in the bioavailability of a range of organic compounds for subsequent microbial metabolism. References: Baskar, S., Baskar, R., Mauclaire, L., and McKenzie, J.A. 2006. Microbially induced calcite precipitation in culture experiments: Possible origin for stalactites in Sahastradhara caves, Dehradun, India. Current Science 90: 58-64. Burford, E.P., Fomina, M., Gadd, G. 2003. Fungal involvement in bioweathering and biotrasformations of rocks and minerals. Min Mag 67(6):1172-1155. Engel, A.S., Stern, L.A., Bennett, P.C. 2004. Microbial contributions to cave formation: new insights into sulfuric acid speleogenesis. Geology 32(5): 369-372. Gadd, G.M. (2004). Mycotransformation of organic and inorganic substrates. Mycologist 18: 60-70. Northup, D., Barns, S.M., Yu, Laura, E., Spilde, M.N., Schelble, R.T., Dano, K.E., Crossey, L.J., Connolly, C.A., Boston, P.J., and Dahm, C.N. 2003. Diverse microbial communities inhabiting ferromanganese deposits in Lechuguilla and Spider Caves. Environmental Microbiology 5(11): 1071-1086.

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.

Toxic effects of ionic liquid 1-octyl-3-methylimidazolium tetrafluoroborate on soil enzyme activity and soil microbial community diversity.

PubMed

Sun, Xi; Zhu, Lusheng; Wang, Jinhua; Wang, Jun; Su, Benying; Liu, Tong; Zhang, Cheng; Gao, Chong; Shao, Yuting

2017-01-01

Ionic liquids (ILs) were considered as "green" solvents and have been used widely because of their excellent properties. But ILs are not as "green" as has been suggested, and the toxic effects of ILs on organisms have been shown in recent years. In the present study, the toxic effects of the IL 1-octyl-3-methylimidazolium tetrafluoroborate ([Omim]BF 4 ) on soil enzyme activity and soil microbial communities at three different concentrations (1.0, 5.0 and 10.0mg/kg) and a control treatment over 40 days of incubation time (sampled on days 10, 20, 30 and 40) were examined under laboratory conditions. The concentrations of [Omim]BF 4 in soils were detected by high performance liquid chromatography (HPLC) and the results indicated that [Omim]BF 4 were maintained stable in the soil during the exposure period. However, the enzyme activity results showed that urease activity was stimulated on day 20 and then decreased after 30 days of incubation. The activity of β-glucosidase was stimulated after 20 days of incubation in both treatment groups. Moreover, both dehydrogenase and acid phosphatase were inhibited at a high level (10.0mg/kg) only on day 20. The analysis of terminal restriction fragment length polymorphism (T-RFLP) revealed that the soil microbial community structures were altered by [Omim]BF 4 and that the soil microbial diversity and evenness of high levels (5.0mg/kg and 10.0mg/kg) treatments were decreased. Moreover, the dominant structure of the microbial communities was not changed by [Omim]BF 4 . Furthermore, the abundance of the ammonia monooxygenase (amoA) genes of both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) was examined using real time polymerase chain reaction (RT-PCR). The results revealed that the copy numbers of the amoA-gene were decreased by [Omim]BF 4 with the 5.0 and 10.0mg/kg treatments. Based on the experiment, we concluded that high levels (5.0 and 10.0mg/kg) of [Omim]BF 4 could have significantly toxic effects on soil enzyme activities and the diversity of the microbial communities. Copyright © 2016 Elsevier Inc. All rights reserved.

Analysis of the coral associated bacterial community structures in healthy and diseased corals from off-shore of southern Taiwan.

PubMed

Chiou, Shu-Fen; Kuo, Jimmy; Wong, Tit-Yee; Fan, Tung-Yung; Tew, Kwee Siong; Liu, Jong-Kang

2010-07-01

The methods of denaturing gradient gel electrophoresis (DGGE) and DNA sequencing were used to analyze the ribotypes of microbial communities associated with corals. Both healthy and diseased coral of different species were collected at three locations off the southern coast of Taiwan. Ribotyping results suggested that the microbial communities were diverse. The microbial community profiles, even among the same species of corals from different geographical locations, differ significantly. The coral-associated bacterial communities contain many bacteria common to the habitants of various invertebrates. However, some bacteria were unexpected. The presence of some unusual species, such as Staphylococcus, Clostridium and Legionella, associated with corals that were likely the results of human activities. Human activities, such as thermal pollution from the nearby nuclear plant, active fishing and tourism industries in the region might have all contributed to the change in bacterial communities and the death of coral colonies around the region.

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.

Effects of plastic film residues on occurrence of phthalates and microbial activity in soils.

PubMed

Wang, Jun; Lv, Shenghong; Zhang, Manyun; Chen, Gangcai; Zhu, Tongbin; Zhang, Shen; Teng, Ying; Christie, Peter; Luo, Yongming

2016-05-01

Plastic film mulching has played an important role in Chinese agriculture, especially in vegetable production, but large amounts of film residues can accumulate in the soil. The present study investigated the effects of plastic film residues on the occurrence of soil PAEs and microbial activities using a batch pot experiment. PAE concentrations increased with increasing plastic film residues but the soil microbial carbon and nitrogen, enzyme activities and microbial diversity decreased significantly. At the end of the experiment the PAE concentrations were 0-2.02 mg kg(-1) in the different treatments. Soil microbial C and N, enzyme activities, AWCD value, and Shannon-Weaver and Simpson indices declined by about 28.9-76.2%, 14.9-59.0%, 4.9-22.7%, 23.0-42.0% and 1.8-18.7%, respectively. Soil microbial activity was positively correlated with soil PAE concentration, and soil PAE concentrations were impacted by plastic color and residue volume. Correlations among, and molecular mechanisms of, plastic film residues, PAE occurrence and microbial activity require further study. Copyright © 2016 Elsevier Ltd. All rights reserved.

Leaf and root C-to-N ratios are poor predictors of soil microbial biomass C and respiration across 32 tree species.

PubMed

Ferlian, Olga; Wirth, Christian; Eisenhauer, Nico

2017-11-01

Soil microorganisms are the main primary decomposers of plant material and drive biogeochemical processes like carbon and nitrogen cycles. Hence, knowledge of their nutritional demands and limitations for activity and growth is of particular importance. However, potential effects of the stoichiometry of soil and plant species on soil microbial activity and carbon use efficiency are poorly understood. Soil properties and plant traits are assumed to drive microbial carbon and community structure. We investigated the associations between C and N concentrations of leaf, root, and soil as well as their ratios and soil microbial biomass C and activity (microbial basal respiration and specific respiratory quotient) across 32 young native angiosperm tree species at two locations in Central Germany. Correlations between C:N ratios of leaves, roots, and soil were positive but overall weak. Only regressions between root and leaf C:N ratios as well as between root and soil C:N ratios were significant at one site. Soil microbial properties differed significantly between the two sites and were significantly correlated with soil C:N ratio across sites. Soil C concentrations rather than N concentrations drove significant effects of soil C:N ratio on soil microbial properties. No significant correlations between soil microbial properties and leaf as well as root C:N ratios were found. We found weak correlations of C:N ratios between plant aboveground and belowground tissues. Furthermore, microorganisms were not affected by the stoichiometry of plant tissues in the investigated young trees. The results suggest that soil stoichiometry represents a consistent determinant of soil microbial biomass and respiration. Our study indicates that stoichiometric relationships among tree organs can be weak and poor predictors of soil microbial properties in young tree stands. Further research in controlled experimental settings with a wide range of tree species is needed to study the role of plant chemical traits like the composition and stoichiometry of root exudates in determining interactions between above- and belowground compartments.

Plant rhizosphere species-specific stoichiometry and regulation of extracellular enzyme and microbial community structure

NASA Astrophysics Data System (ADS)

Bell, C. W.; Calderon, F.; Pendall, E.; Wallenstein, M. D.

2012-12-01

Plant communities affect the activity and composition of soil microbial communities through alteration of the soil environment during root growth; substrate availability through root exudation; nutrient availability through plant uptake; and moisture regimes through transpiration. As a result, positive feedbacks in soil properties can result from alterations in microbial community composition and function in the rhizosphere zone. At the ecosystem-scale, many properties of soil microbial communities can vary between forest stands dominated by different species, including community composition and stoichiometry. However, the influence of smaller individual plants on grassland soils and microbial communities is less well documented. There is evidence to suggest that some plants can modify their soil environment in a manner that favors their persistence. For example, when Bromus tectorum plants invade, soil microbial communities tend to have higher N mineralization rates (in the rhizosphere zone) relative to native plants. If tight linkages between individual plant species and microbial communities inhabiting the rhizosphere exist, we hypothesized that any differences among plant species specific rhizosphere zones could be observed by shifts in: 1) soil -rhizosphere microbial community structure, 2) enzymatic C:N:P acquisition activities, 3) alterations in the soil C chemistry composition in the rhizosphere, and 4) plant - soil - microbial C:N:P elemental stoichiometry. We selected and grew 4 different C3 grasses species including three species native to the Shortgrass Steppe region (Pascopyrum smithii, Koeleria macrantha, and Vulpia octoflora) and one exotic invasive plant species (B. tectorum) in root-boxes that are designed to allow for easy access to the rhizosphere. The field soil was homogenized using a 4mm sieve and mixed 1:1 with sterile sand and seeded as monocultures (24 replicate root - boxes for each species). Plant and soil samples (along with no - plant control soil samples) were collected on day 28, 78, and 148 (N = 4 /sample period/species). Microbial community structure was quantified using the barcoded pyrosequencing protocols. We measured the potential activity of seven hydrolytic soil enzymes to represent the degradation of C, N, and P-rich substrates. Soil microbial C:N biomass responses to specific plant rhizospheres (MBC and MBN) were measured using the chloroform fumigation extraction method followed by DOC & N analysis. Fourier Transform Infrared Spectroscopy was used to assess differences in plant and soil C chemistry. We found that species specific rhizospheres are characteristic of very different soil chemical, edaphic, and microbial properties. These plant species act as gateways that introduce variability into soil C, N, and P ecosystem functional dynamics directly facilitated by rhizosphere - microbe associations. Our results suggest that nutrient stoichiometry within plant species' rhizospheres is a useful tool for identifying intra-ecosystem functional patterns. By identifying what and how specific species rhizospheres differ among the overall plant community, we can better predict how below-ground microbial community function and subsequent ecosystem processes can be influenced by alterations in plant community shifts based on the rhizosphere effects.

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.

Quantitative analysis of microbial biomass yield in aerobic bioreactor.

PubMed

Watanabe, Osamu; Isoda, Satoru

2013-12-01

We have studied the integrated model of reaction rate equations with thermal energy balance in aerobic bioreactor for food waste decomposition and showed that the integrated model has the capability both of monitoring microbial activity in real time and of analyzing biodegradation kinetics and thermal-hydrodynamic properties. On the other hand, concerning microbial metabolism, it was known that balancing catabolic reactions with anabolic reactions in terms of energy and electron flow provides stoichiometric metabolic reactions and enables the estimation of microbial biomass yield (stoichiometric reaction model). We have studied a method for estimating real-time microbial biomass yield in the bioreactor during food waste decomposition by combining the integrated model with the stoichiometric reaction model. As a result, it was found that the time course of microbial biomass yield in the bioreactor during decomposition can be evaluated using the operational data of the bioreactor (weight of input food waste and bed temperature) by the combined model. The combined model can be applied to manage a food waste decomposition not only for controlling system operation to keep microbial activity stable, but also for producing value-added products such as compost on optimum condition. Copyright © 2013 The Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.

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.

The role of microbial low-molecular-weight autoregulatory factors (alkylhydroxybenzenes) in resistance of microorganisms to radiation and heat shock

NASA Astrophysics Data System (ADS)

El-Registan, Galina I.; Mulyukin, Andrey L.; Nikolaev, Yuri A.; Stepanenko, Irina Yu.; Kozlova, Alla N.; Martirosova, Elena I.; Shanenko, Elena F.; Strakhovskaya, Marina G.; Revina, Aleksandra A.

Low-molecular-weight cell-to-cell communication factors are produced by various pro- and eukaryotes and involved in autoregulation of the growth and development of microbial cultures. As for some bacterial and yeast species, these factors were identified as isomers and homologues of alkylhydroxybenzenes (AHB). Depending on the concentration, they participate in controlling the transition to stationary phase, entering the resting state, and stress resistance of vegetative cells to gamma-irradiation, photooxidation (singlet oxygen), and heat shock. Chemical analogues of microbial AHB protected microbial cultures from stressful situations and exerted (1) the stabilizing activity toward macromolecules and (2) the ability to scavenge active oxygen species. The stabilizing effect of AHBs resulted from their complex formation with protected macromolecules due to intermolecular hydrogen bonds, hydrophobic and electrostatic interactions and was demonstrated on models of individual enzymes (trypsin). Particularly, AHBs protected the yeast from the action of (a) active oxygen species formed during gamma-irradiation (500 Gy, 1.96 Gy/s) or (b) singlet oxygen generated in cells photosensitized by chlorin e 6 (10 μg/L). It is important that microbial AHBs were not species-specific and defended cultured microbial and animal cells from the action of organic toxicants. The use of AHBs as protectants and adaptogens is discussed as well as perspectives of further investigations.

Are antimicrobial defences in bird eggs related to climatic conditions associated with risk of trans-shell microbial infection?

PubMed Central

2014-01-01

Introduction All bird eggs are exposed to microbes in the environment, which if transmitted to the developing embryo, could cause hatching failure. However, the risk of trans-shell infection varies with environmental conditions and is higher for eggs laid in wetter environments. This might relate to generally higher microbial abundances and diversity in more humid environments, including on the surface of eggshells, as well as the need for moisture to facilitate microbial penetration of the eggshell. To protect against microbial infection, the albumen of avian eggs contains antimicrobial proteins, including lysozyme and ovotransferrin. We tested whether lysozyme and ovotransferrin activities varied in eggs of larks (Alaudidae) living along an arid-mesic gradient of environmental aridity, which we used as a proxy for risk of trans-shell infection. Results Contrary to expectations, lysozyme activity was highest in eggs from hotter, more arid locations, where we predicted the risk of trans-shell infection would be lower. Ovotransferrin concentrations did not vary with climatic factors. Temperature was a much better predictor of antimicrobial protein activity than precipitation, a result inconsistent with studies stressing the importance of moisture for trans-shell infection. Conclusions Our study raises interesting questions about the links between temperature and lysozyme activity in eggs, but we find no support for the hypothesis that antimicrobial protein deposition is higher in eggs laid in wetter environments. PMID:25057281

Ecological guild and enzyme activities of rhizosphere soil microbial communities associated with Bt-maize cultivation under field conditions in North West Province of South Africa.

PubMed

van Wyk, Deidré A B; Adeleke, Rasheed; Rhode, Owen H J; Bezuidenhout, Carlos C; Mienie, Charlotte

2017-09-01

Insecticidal proteins expressed by genetically modified Bt maize may alter the enzymatic and microbial communities associated with rhizosphere soil. This study investigated the structure and enzymatic activity of rhizosphere soil microbial communities associated with field grown Bt and non-Bt maize. Rhizosphere soil samples were collected from Bt and non-Bt fields under dryland and irrigated conditions. Samples were subjected to chemical tests, enzyme analyses, and next generation sequencing. Results showed that nitrate and phosphorus concentrations were significantly higher in non-Bt maize dryland soils, while organic carbon was significantly higher in non-Bt maize irrigated field soil. Acid phosphatase and β-glucosidase activities were significantly reduced in soils under Bt maize cultivation. The species diversity differed between fields and Bt and non-Bt maize soils. Results revealed that Actinobacteria, Proteobacteria, and Acidobacteria were the dominant phyla present in these soils. Redundancy analyses indicated that some chemical properties and enzyme activities could explain differences in bacterial community structures. Variances existed in microbial community structures between Bt and non-Bt maize fields. There were also differences between the chemical and biochemical properties of rhizosphere soils under Bt and non-Bt maize cultivation. These differences could be related to agricultural practices and cultivar type. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Microbial population and functional dynamics associated with surface potential and carbon metabolism

PubMed Central

Ishii, Shun'ichi; Suzuki, Shino; Norden-Krichmar, Trina M; Phan, Tony; Wanger, Greg; Nealson, Kenneth H; Sekiguchi, Yuji; Gorby, Yuri A; Bretschger, Orianna

2014-01-01

Microbial extracellular electron transfer (EET) to solid surfaces is an important reaction for metal reduction occurring in various anoxic environments. However, it is challenging to accurately characterize EET-active microbial communities and each member's contribution to EET reactions because of changes in composition and concentrations of electron donors and solid-phase acceptors. Here, we used bioelectrochemical systems to systematically evaluate the synergistic effects of carbon source and surface redox potential on EET-active microbial community development, metabolic networks and overall electron transfer rates. The results indicate that faster biocatalytic rates were observed under electropositive electrode surface potential conditions, and under fatty acid-fed conditions. Temporal 16S rRNA-based microbial community analyses showed that Geobacter phylotypes were highly diverse and apparently dependent on surface potentials. The well-known electrogenic microbes affiliated with the Geobacter metallireducens clade were associated with lower surface potentials and less current generation, whereas Geobacter subsurface clades 1 and 2 were associated with higher surface potentials and greater current generation. An association was also observed between specific fermentative phylotypes and Geobacter phylotypes at specific surface potentials. When sugars were present, Tolumonas and Aeromonas phylotypes were preferentially associated with lower surface potentials, whereas Lactococcus phylotypes were found to be closely associated with Geobacter subsurface clades 1 and 2 phylotypes under higher surface potential conditions. Collectively, these results suggest that surface potentials provide a strong selective pressure, at the species and strain level, for both solid surface respirators and fermentative microbes throughout the EET-active community development. PMID:24351938

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.

Marine metagenomics: strategies for the discovery of novel enzymes with biotechnological applications from marine environments

PubMed Central

Kennedy, Jonathan; Marchesi, Julian R; Dobson, Alan DW

2008-01-01

Metagenomic based strategies have previously been successfully employed as powerful tools to isolate and identify enzymes with novel biocatalytic activities from the unculturable component of microbial communities from various terrestrial environmental niches. Both sequence based and function based screening approaches have been employed to identify genes encoding novel biocatalytic activities and metabolic pathways from metagenomic libraries. While much of the focus to date has centred on terrestrial based microbial ecosystems, it is clear that the marine environment has enormous microbial biodiversity that remains largely unstudied. Marine microbes are both extremely abundant and diverse; the environments they occupy likewise consist of very diverse niches. As culture-dependent methods have thus far resulted in the isolation of only a tiny percentage of the marine microbiota the application of metagenomic strategies holds great potential to study and exploit the enormous microbial biodiversity which is present within these marine environments. PMID:18717988

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.

HSQC-TOCSY Fingerprinting for Prioritization of Polyketide- and Peptide-Producing Microbial Isolates.

PubMed

Buedenbender, Larissa; Habener, Leesa J; Grkovic, Tanja; Kurtböke, D İpek; Duffy, Sandra; Avery, Vicky M; Carroll, Anthony R

2018-04-27

Microbial products are a promising source for drug leads as a result of their unique structural diversity. However, reisolation of already known natural products significantly hampers the discovery process, and it is therefore important to incorporate effective microbial isolate selection and dereplication protocols early in microbial natural product studies. We have developed a systematic approach for prioritization of microbial isolates for natural product discovery based on heteronuclear single-quantum correlation-total correlation spectroscopy (HSQC-TOCSY) nuclear magnetic resonance profiles in combination with antiplasmodial activity of extracts. The HSQC-TOCSY experiments allowed for unfractionated microbial extracts containing polyketide and peptidic natural products to be rapidly identified. Here, we highlight how this approach was used to prioritize extracts derived from a library of 119 ascidian-associated actinomycetes that possess a higher potential to produce bioactive polyketides and peptides.

Patterns of extracellular enzyme activities and microbial metabolism in an Arctic fjord of Svalbard and in the northern Gulf of Mexico: contrasts in carbon processing by pelagic microbial communities

PubMed Central

Arnosti, Carol; Steen, Andrew D.

2013-01-01

The microbial community composition of polar and temperate ocean waters differs substantially, but the potential functional consequences of these differences are largely unexplored. We measured bacterial production, glucose metabolism, and the abilities of microbial communities to hydrolyze a range of polysaccharides in an Arctic fjord of Svalbard (Smeerenburg Fjord), and thus to initiate remineralization of high-molecular weight organic matter. We compared these data with similar measurements previously carried out in the northern Gulf of Mexico in order to investigate whether differences in the spectrum of enzyme activities measurable in Arctic and temperate environments are reflected in “downstream” aspects of microbial metabolism (metabolism of monomers and biomass production). Only four of six polysaccharide substrates were hydrolyzed in Smeerenburg Fjord; all were hydrolyzed in the upper water column of the Gulf. These patterns are consistent on an interannual basis. Bacterial protein production was comparable at both locations, but the pathways of glucose utilization differed. Glucose incorporation rate constants were comparatively higher in Svalbard, but glucose respiration rate constants were higher in surface waters of the Gulf. As a result, at the time of sampling ca. 75% of the glucose was incorporated into biomass in Svalbard, but in the northern Gulf of Mexico most of the glucose was respired to CO2. A limited range of enzyme activities is therefore not a sign of a dormant community or one unable to further process substrates resulting from extracellular enzymatic hydrolysis. The ultimate fate of carbohydrates in marine waters, however, is strongly dependent upon the specific capabilities of heterotrophic microbial communities in these disparate environments. PMID:24198812

Developing and using artificial soils to analyze soil microbial processes

NASA Astrophysics Data System (ADS)

Gao, X.; Cheng, H. Y.; Boynton, L.; Masiello, C. A.; Silberg, J. J.

2017-12-01

Microbial diversity and function in soils are governed by soil characteristics such as mineral composition, particles size and aggregations, soil organic matter (SOM), and availability of nutrients and H2O. The spatial and temporal heterogeneity of soils creates a range of niches (hotspots) differing in the availability of O2, H2O, and nutrients, which shapes microbial activities at scales ranging from nanometer to landscape. Synthetic biologists often examine microbial response trigged by their environment conditions in nutrient-rich aqueous media using single strain microbes. While these studies provided useful insight in the role of soil microbes in important soil biogeochemical processes (e.g., C cycling, N cycling, etc.), the results obtained from the over-simplified model systems are often not applicable natural soil systems. On the contrary, soil microbiologists examine microbial processes in natural soils using longer incubation time. However, due to its physical, chemical and biological complexity of natural soils, it is often difficult to examine soil characteristics independently and understand how each characteristic influences soil microbial activities and their corresponding soil functioning. Therefore, it is necessary to bridge the gap and develop a model matrix to exclude unpredictable influences from the environment while still reliably mimicking real environmental conditions. The objective of this study is to design a range of ecologically-relevant artificial soils with varying texture (particle size distribution), structure, mineralogy, SOM content, and nutrient heterogeneity. We thoroughly characterize the artificial soils for pH, active surface area and surface morphology, cation exchange capacity (CEC), and water retention curve. We demonstrate the effectiveness of the artificial soils as useful matrix for microbial processes, such as microbial growth and horizontal gene transfer (HGT), using the gas-reporting biosensors recently developed in our lab.

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.

Microbial Extracellular Enzyme Activity and Community Assembly Processes Post Fire Disturbance Amanda Labrado, University of Texas at El Paso; Emily B. Graham, University of Colorado Boulder; Joseph E. Knelman, University of Colorado Boulder; Scott Ferrenberg, University of Colorado Boulder; Diana R. Nemergut, University of Colorado Boulder

NASA Astrophysics Data System (ADS)

Labrdo, A.; Knelman, J. E.; Graham, E. B.; Ferrenberg, S.; Nemergut, D. R.

2013-12-01

Microbes control major biogeochemical cycles and can directly impact the carbon, nitrogen, and phosphorus pools and fluxes of soils. However, many questions remain regarding when and where data on microbial community structure are necessary to accurately predict biogeochemical processes. In particular, it is unknown how shifts in microbial assembly processes may relate to changes in the relationship between community structure and ecosystem function. Here, we examine soil microbial community assembly processes and extracellular enzyme activity (EEA) at 4-weeks and 16-weeks after the Fourmile Canyon Fire in Boulder, CO in order to determine the effects of disturbance on community assembly and EEA. Microbial community structure was determined from 16S rRNA gene pyrosequencing, edaphic properties were determined using standard biogeochemical assays, and extracellular enzyme activity for β-1, 4-glucosidase (BG) and β-1, 4-N-acetylglucosaminidase (NAG) enzymes were determined using fluorimetric assays. Stepwise linear regressions were used to determine the effects of microbial community structure and edaphic factors on EEA. We determined that in 4-week post fire samples EEA was only correlated with microbial predictors. However, we observed a shift with 16-week samples in which EEA was significantly related to edaphic predictors. Null derivation analysis of community assembly revealed that communities in the 4-week samples were more neutrally assembled than communities in the 16-week samples. Together, these results support a conceptual model in which the relationship between edaphic factors and ecosystem processes is somewhat decoupled in more neutrally assembled communities, and data on microbial community structure is important to most accurately predict function.

Real-time monitoring of subsurface microbial metabolism with graphite electrodes

DOE PAGES

Wardman, Colin; Nevin, Kelly P.; Lovley, Derek R.

2014-11-21

Monitoring in situ microbial activity in anoxic submerged soils and aquatic sediments can be labor intensive and technically difficult, especially in dynamic environments in which a record of changes in microbial activity over time is desired. Microbial fuel cell concepts have previously been adapted to detect changes in the availability of relatively high concentrations of organic compounds in waste water but, in most soils and sediments, rates of microbial activity are not linked to the concentrations of labile substrates, but rather to the turnover rates of the substrate pools with steady state concentrations in the nM-μ M range. In ordermore » to determine whether levels of current produced at a graphite anode would correspond to the rates of microbial metabolism in anoxic sediments, small graphite anodes were inserted in sediment cores and connected to graphite brush cathodes in the overlying water. Currents produced were compared with the rates of [2- 14C]-acetate metabolism. There was a direct correlation between current production and the rate that [2- 14C]-acetate was metabolized to 14CO 2 and 14CH 4 in sediments in which Fe(III) reduction, sulfate reduction, or methane production was the predominant terminal electron-accepting process. At comparable acetate turnover rates, currents were higher in the sediments in which sulfate-reduction or Fe(III) reduction predominated than in methanogenic sediments. This was attributed to reduced products (Fe(II), sulfide) produced at distance from the anode contributing to current production in addition to the current that was produced from microbial oxidation of organic substrates with electron transfer to the anode surface in all three sediment types. In conclusion, the results demonstrate that inexpensive graphite electrodes may provide a simple strategy for real-time monitoring of microbial activity in a diversity of anoxic soils and sediments.« less

Field and lab conditions alter microbial enzyme and biomass dynamics driving decomposition of the same leaf litter

PubMed Central

Rinkes, Zachary L.; Sinsabaugh, Robert L.; Moorhead, Daryl L.; Grandy, A. Stuart; Weintraub, Michael N.

2013-01-01

Fluctuations in climate and edaphic factors influence field decomposition rates and preclude a complete understanding of how microbial communities respond to plant litter quality. In contrast, laboratory microcosms isolate the intrinsic effects of litter chemistry and microbial community from extrinsic effects of environmental variation. Used together, these paired approaches provide mechanistic insights to decomposition processes. In order to elucidate the microbial mechanisms underlying how environmental conditions alter the trajectory of decay, we characterized microbial biomass, respiration, enzyme activities, and nutrient dynamics during early (<10% mass loss), mid- (10–40% mass loss), and late (>40% mass loss) decay in parallel field and laboratory litter bag incubations for deciduous tree litters with varying recalcitrance (dogwood < maple < maple-oak mixture < oak). In the field, mass loss was minimal (<10%) over the first 50 days (January–February), even for labile litter types, despite above-freezing soil temperatures and adequate moisture during these winter months. In contrast, microcosms displayed high C mineralization rates in the first week. During mid-decay, the labile dogwood and maple litters in the field had higher mass loss per unit enzyme activity than the lab, possibly due to leaching of soluble compounds. Microbial biomass to litter mass (B:C) ratios peaked in the field during late decay, but B:C ratios declined between mid- and late decay in the lab. Thus, microbial biomass did not have a consistent relationship with litter quality between studies. Higher oxidative enzyme activities in oak litters in the field, and higher nitrogen (N) accumulation in the lab microcosms occurred in late decay. We speculate that elevated N suppressed fungal activity and/or biomass in microcosms. Our results suggest that differences in microbial biomass and enzyme dynamics alter the decay trajectory of the same leaf litter under field and lab conditions. PMID:24027563

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

A Comparison of Response Surface Methodology and a One-Factor-At-A-Time Approach as Calibration Techniques for the Bioplume-II Simulation Model of Contaminant Biodegradation

DTIC Science & Technology

1995-12-01

Technology, 26:1404-1410 (July 1992). 4. Atlas , Ronald M. and Richard Bartha . Microbial Ecology , Fundamentals and Applica- tions (3rd Edition). Redwood... microbial metabolic activity. Leahy and Colwell (35:307) note the impact of physical factors on microbial activity. They cite research by Atlas and... Bartha observing that low temperatures inhibit microbial activity and research by Bossert and Bartha observing that higher temperatures increase activity

Microbial Community Structure and Activity Linked to Contrasting Biogeochemical Gradients in Bog and Fen Environments of the Glacial Lake Agassiz Peatland

PubMed Central

Lin, X.; Green, S.; Tfaily, M. M.; Prakash, O.; Konstantinidis, K. T.; Corbett, J. E.; Chanton, J. P.; Cooper, W. T.

2012-01-01

The abundances, compositions, and activities of microbial communities were investigated at bog and fen sites in the Glacial Lake Agassiz Peatland of northwestern Minnesota. These sites contrast in the reactivity of dissolved organic matter (DOM) and the presence or absence of groundwater inputs. Microbial community composition was characterized using pyrosequencing and clone library construction of phylogenetic marker genes. Microbial distribution patterns were linked to pH, concentrations of dissolved organic carbon and nitrogen, C/N ratios, optical properties of DOM, and activities of laccase and peroxidase enzymes. Both bacterial and archaeal richness and rRNA gene abundance were >2 times higher on average in the fen than in the bog, in agreement with a higher pH, labile DOM content, and enhanced enzyme activities in the fen. Fungi were equivalent to an average of 1.4% of total prokaryotes in gene abundance assayed by quantitative PCR. Results revealed statistically distinct spatial patterns between bacterial and fungal communities. Fungal distribution did not covary with pH and DOM optical properties and was vertically stratified, with a prevalence of Ascomycota and Basidiomycota near the surface and much higher representation of Zygomycota in the subsurface. In contrast, bacterial community composition largely varied between environments, with the bog dominated by Acidobacteria (61% of total sequences), while the Firmicutes (52%) dominated in the fen. Acetoclastic Methanosarcinales showed a much higher relative abundance in the bog, in contrast to the dominance of diverse hydrogenotrophic methanogens in the fen. This is the first quantitative and compositional analysis of three microbial domains in peatlands and demonstrates that the microbial abundance, diversity, and activity parallel with the pronounced differences in environmental variables between bog and fen sites. PMID:22843538

'FloraArray' for screening of specific DNA probes representing the characteristics of a certain microbial community.

PubMed

Yokoi, Takahide; Kaku, Yoshiko; Suzuki, Hiroyuki; Ohta, Masayuki; Ikuta, Hajime; Isaka, Kazuichi; Sumino, Tatsuo; Wagatsuma, Masako

2007-08-01

To investigate uncharacterized microbial communities, a custom DNA microarray named 'FloraArray' was developed for screening specific probes that would represent the characteristics of a microbial community. The array was prepared by spotting 2000 plasmid DNAs from a genomic shotgun library of a sludge sample on a DNA microarray. By comparative hybridization of the array with two different samples of genomic DNA, one from the activated sludge and the other from a nonactivated sludge sample of an anaerobic ammonium oxidation (anammox) bacterial community, specific spots were visualized as a definite fluctuating profile in an MA (differential intensity ratio vs. spot intensity) plot. About 300 spots of the array accounted for the candidate probes to represent anammox reaction of the activated sludge. After sequence analysis of the probes and examination of the results of blastn searches against the reported anammox reference sequence, complete matches were found for 161 probes (58.3%) and >90% matches were found for 242 probes (87.1%). These results demonstrate that 'FloraArray' could be a useful tool for screening specific DNA molecules of unknown microbial communities.

Snow surface microbiome on the High Antarctic Plateau (DOME C).

PubMed

Michaud, Luigi; Lo Giudice, Angelina; Mysara, Mohamed; Monsieurs, Pieter; Raffa, Carmela; Leys, Natalie; Amalfitano, Stefano; Van Houdt, Rob

2014-01-01

The cryosphere is an integral part of the global climate system and one of the major habitable ecosystems of Earth's biosphere. These permanently frozen environments harbor diverse, viable and metabolically active microbial populations that represent almost all the major phylogenetic groups. In this study, we investigated the microbial diversity in the surface snow surrounding the Concordia Research Station on the High Antarctic Plateau through a polyphasic approach, including direct prokaryotic quantification by flow cytometry and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH), and phylogenetic identification by 16S RNA gene clone library sequencing and 454 16S amplicon pyrosequencing. Although the microbial abundance was low (<10(3) cells/ml of snowmelt), concordant results were obtained with the different techniques. The microbial community was mainly composed of members of the Alpha-proteobacteria class (e.g. Kiloniellaceae and Rhodobacteraceae), which is one of the most well-represented bacterial groups in marine habitats, Bacteroidetes (e.g. Cryomorphaceae and Flavobacteriaceae) and Cyanobacteria. Based on our results, polar microorganisms could not only be considered as deposited airborne particles, but as an active component of the snowpack ecology of the High Antarctic Plateau.

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.

Anti-microbial screening and cytotoxic activity of aerial part of Thymelaea hirsuta L. essential oil growing in south-west Tunisia.

PubMed

Felhi, Samir; Chaaibia, Mouna; Bakari, Sana; Mansour, Riadh Ben; Békir, Ahmed; Gharsallah, Néji; Kadri, Adel

2017-01-01

This study aimed to investigate the antimicrobial and cytotoxic activities of essential oil isolated by the hydro-distillation of aerial parts of Thymelaea hirsuta. The antimicrobial activity of the oil was evaluated against eight bacterial and three fungal pathogenic strains. The results revealed that the essential oil exhibited a moderate-to-potent anti-microbial activity against all the microorganisms tested. Gram-positive bacteria were noted to be more sensitive to the oil than gram-negative bacteria and yeasts. In vitro cytotoxicity evaluation against HeLa cell lines showed that the essential oil exhibited moderate cytotoxicity on human tumor cells, with a high IC 50 value of 175μg/mL. To the author's knowledge, this is the first study reporting on the antimicrobial and cytotoxic activities of Thymelaea hirsuta essential oil. Overall, the results indicate that the T. hirsuta essential oil has a number of attractive properties that might open new promising opportunities for the control or prevention of a wide range of microbial infections and cancers and can facilitate the use of essential oils as natural preservatives against spoilage microorganisms in food systems.

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

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.

Linking leach chemistry and microbiology of low-grade copper ore bioleaching at different temperatures

NASA Astrophysics Data System (ADS)

Jia, Yan; Sun, He-yun; Tan, Qiao-yi; Gao, Hong-shan; Feng, Xing-liang; Ruan, Ren-man

2018-03-01

The effects of temperature on chalcocite/pyrite oxidation and the microbial population in the bioleaching columns of a low-grade chalcocite ore were investigated in this study. Raffinate from the industrial bioleaching heap was used as an irrigation solution for columns operated at 20, 30, 45, and 60°C. The dissolution of copper and iron were investigated during the bioleaching processes, and the microbial community was revealed by using a high-throughput sequencing method. The genera of Ferroplasma, Acidithiobacillus, Leptospirillum, Acidiplasma, and Sulfobacillus dominated the microbial community, and the column at a higher temperature favored the growth of moderate thermophiles. Even though microbial abundance and activity were highest at 30°C, the column at a higher temperature achieved a much higher Cu leaching efficiency and recovery, which suggested that the promotion of chemical oxidation by elevated temperature dominated the dissolution of Cu. The highest pyrite oxidation percentage was detected at 45°C. Higher temperature resulted in precipitation of jarosite in columns, especially at 60°C. The results gave implications to the optimization of heap bioleaching of secondary copper sulfide in both enhanced chalcocite leaching and acid/iron balance, from the perspective of leaching temperature and affected microbial community and activity.

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

Microbial diversity and activity of an aged soil contaminated by polycyclic aromatic hydrocarbons.

PubMed

Zhao, Xiaohui; Fan, Fuqiang; Zhou, Huaidong; Zhang, Panwei; Zhao, Gaofeng

2018-06-01

In-depth understanding of indigenous microbial assemblages resulted from aged contamination by polycyclic aromatic hydrocarbons (PAHs) is of vital importance in successful in situ bioremediation treatments. Soil samples of three boreholes were collected at 12 different vertical depths. Overall, the dominating three-ring PAHs (76.2%) were closely related to distribution patterns of soil dehydrogenase activity, microbial cell numbers, and Shannon biodiversity index (H') of indigenous microorganisms. High-molecular-weight PAHs tend to yield more diverse communities. Results from 16S rRNA analysis indicated that possible functional groups of PAH degradation include three species in Bacillus cereus group, Bacillus sp. SA Ant14, Nocardioides sp., and Ralstonia pickettii. Principal component analysis indicates significant positive correlations between the content of high-molecular-weight PAHs and the distribution of Bacillus weihenstephanensis KBAB4 and Nocardioides sp. The species B. cereus 03BB102, Bacillus thuringiensis, B. weihenstephanensis KBAB4, and Nocardioides sp. were recognized as main PAH degraders and thus recommended to be utilized in further bioremediation applications. The vertical distribution characteristics of PAHs in soil profiles (1-12 m) and the internal relationship between the transport mechanisms of PAHs and the response of soil biological properties help further understand the microbial diversity and activity in an aged site.

Consumption of freons CFC-11 and CFC-12 by anaerobic sediments and soils

USGS Publications Warehouse

Lovley, D.R.; Woodward, J.C.

1992-01-01

A variety of anaerobic sediments and soils consumed CFC-11 (CFCl3) and CFC-12 (CF2Cl2). An aerobic soil did not. Active microbial metabolism was required for CFC-12 uptake in all of the sediments examined. CFC-11 uptake was faster in the presence of microbial activity, but reduced components in the sediments also resulted in nonenzymatic CFC-11 consumption in most instances. CFC-12 uptake in a culture of Clostridium pasteurianum provided a model for the sediment uptake of CFC-11 and CFC-12 that required active microbial metabolism. Consumption of CFC-11 in the presence of reduced hematin demonstrated a potential mechanism for nonenzymatic CFC-11 consumption. These findings demonstrate that CFC-11 and CFC-12 are not biochemically inert under anaerobic conditions. This suggests that anaerobic degradation of CFC-11 and CFC-12 in anaerobic landfills might prevent some disposed CFC-11 and CFC-12 from entering the atmosphere. The results also suggest that CFC-11 and CFC-12 cannot be used as stable tracers in anaerobic environments. Furthermore, although the microbial sink for atmospheric CFC-11 and CFC-12 is much less than current anthropogenic release, this sink could have a significant long-term effect on the amount of CFC-11 and CFC-12 reaching the stratosphere.

HIV enteropathy and aging: gastrointestinal immunity, mucosal epithelial barrier, and microbial translocation.

PubMed

Wang, Hongyin; Kotler, Donald P

2014-07-01

Despite decreases in morbidity and mortality as a result of antiretroviral therapy, gastrointestinal dysfunction remains common in HIV infection. Treated patients are at risk for complications of 'premature' aging, such as cardiovascular disease, osteopenia, neurocognitive decline, malignancies, and frailty. This review summarizes recent observations in this field. Mucosal CD4 lymphocytes, especially Th17 cells, are depleted in acute HIV and simian immune deficiency virus (SIV) infections, although other cell types also are affected. Reconstitution during therapy often is incomplete, especially in mucosa. Mucosal barrier function is affected by both HIV infection and aging and includes paracellular transport via tight junctions and uptake through areas of apoptosis; other factors may affect systemic antigen exposure. The resultant microbial translocation is associated with systemic immune activation in HIV and SIV infections. There is evidence of immune activation and microbial translocation in the elderly. The immune phenotypes of immunosenescence in HIV infection and aging appear similar. There are several targets for intervention; blockage of residual mucosal virus replication, preventing antigen uptake, modulating the microbiome, improving T cell recovery, combining therapies aimed at mucosal integrity, augmenting mucosal immunity, and managing traditional risk factors for premature aging in the general population. Aging may interact with HIV enteropathy to enhance microbial translocation and immune activation.

Soil microbial carbon utilization, enzyme activities and nutrient availability responses to Bidens pilosa and a non-invasive congener under different irradiances.

PubMed

Wei, Hui; Yan, Wenbin; Quan, Guoming; Zhang, Jiaen; Liang, Kaiming

2017-09-12

Two Bidens species (Bidens pilosa and B. bipinnata) that originate from America have been introduced widely in pan-tropics, with the former regarded as a noxious invasive weed whereas the latter naturalized as a plant resource. Whether the two species exhibit different effects on the belowground system remains rarely studied. This study was conducted to investigate soil microbial carbon (C) utilization, enzyme activities and available nitrogen, phosphorus and potassium contents under the two species in a subtropical garden soil of southern China under different levels of light intensity. Results showed that the microbial C utilization and enzyme activities were not significantly different under the two species, implying that the strong invasiveness of B. pilosa could not be due to the plant-soil microbe interactions, at least plant-induced alterations of microbial community function to utilize C substrates. Alternatively, available soil nitrogen and potassium contents were significantly higher under B. pilosa than under B. bipinnata in full sun, indicating that the strong invasiveness of B. pilosa could result from rapid nutrient mobilizations by B. pilosa. However, the differences turned non-significant as light intensity decreased, suggesting that light availability could substantially alter the plant effects on soil nutrient mobilizations.

Microbial processes and factors controlling their activities in alkaline lakes of the Mongolian plateau

NASA Astrophysics Data System (ADS)

Namsaraev, Zorigto B.; Zaitseva, Svetlana V.; Gorlenko, Vladimir M.; Kozyreva, Ludmila P.; Namsaraev, Bair B.

2015-11-01

A striking feature of the Mongolian plateau is the wide range of air temperatures during a year, -30 to 30°C. High summer temperatures, atmospheric weathering and the arid climate lead to formation of numerous alkaline soda lakes that are covered by ice during 6-7 months per year. During the study period, the lakes had pH values between 8.1 to 10.4 and salinity between 1.8 and 360 g/L. According to chemical composition, the lakes belong to sodium carbonate, sodium chloride-carbonate and sodium sulfate-carbonate types. This paper presents the data on the water chemical composition, results of the determination of the rates of microbial processes in microbial mats and sediments in the lakes studied, and the results of a Principal Component Analysis of environmental variables and microbial activity data. Temperature was the most important factor that influenced both chemical composition and microbial activity. pH and salinity are also important factors for the microbial processes. Dark CO2 fixation is impacted mostly by salinity and the chemical composition of the lake water. Total photosynthesis and sulfate-reduction are impacted mostly by pH. Photosynthesis is the dominant process of primary production, but the highest rate (386 mg C/(L•d)) determined in the lakes studied were 2-3 times lower than in microbial mats of lakes located in tropical zones. This can be explained by the relatively short warm period that lasts only 3-4 months per year. The highest measured rate of dark CO2 assimilation (59.8 mg C/(L•d)) was much lower than photosynthesis. The highest rate of sulfate reduction was 60 mg S/(L•d), while that of methanogenesis was 75.6 μL CN4/(L•d) in the alkaline lakes of Mongolian plateau. The rate of organic matter consumption during sulfate reduction was 3-4 orders of magnitude higher than that associated with methanogenesis.

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.

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.

Optimization of biomass composition explains microbial growth-stoichiometry relationships

USGS Publications Warehouse

Franklin, O.; Hall, E.K.; Kaiser, C.; Battin, T.J.; Richter, A.

2011-01-01

Integrating microbial physiology and biomass stoichiometry opens far-reaching possibilities for linking microbial dynamics to ecosystem processes. For example, the growth-rate hypothesis (GRH) predicts positive correlations among growth rate, RNA content, and biomass phosphorus (P) content. Such relationships have been used to infer patterns of microbial activity, resource availability, and nutrient recycling in ecosystems. However, for microorganisms it is unclear under which resource conditions the GRH applies. We developed a model to test whether the response of microbial biomass stoichiometry to variable resource stoichiometry can be explained by a trade-off among cellular components that maximizes growth. The results show mechanistically why the GRH is valid under P limitation but not under N limitation. We also show why variability of growth rate-biomass stoichiometry relationships is lower under P limitation than under N or C limitation. These theoretical results are supported by experimental data on macromolecular composition (RNA, DNA, and protein) and biomass stoichiometry from two different bacteria. In addition, compared to a model with strictly homeostatic biomass, the optimization mechanism we suggest results in increased microbial N and P mineralization during organic-matter decomposition. Therefore, this mechanism may also have important implications for our understanding of nutrient cycling in ecosystems.

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.

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

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.

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.

Easily degradable carbon - an indicator of microbial hotspots and soil degradation

NASA Astrophysics Data System (ADS)

Wolińska, Agnieszka; Banach, Artur; Szafranek-Nakonieczna, Anna; Stępniewska, Zofia; Błaszczyk, Mieczysław

2018-01-01

The effect of arable soil was quantified against non-cultivated soil on easily degradable carbon and other selected microbiological factors, i.e. soil microbial biomass, respiration activity, and dehydrogenase activity. The intent was to ascertain whether easily degradable carbo can be useful as a sensitive indicator of both soil biological degradation and microbial hot-spots indication. As a result, it was found that soil respiration activity was significantly higher (p <0.0001) in all controls, ranging between 30-60 vs. 11.5-23.7 μmol CO2 kg d.m.-1 h-1 for the arable soils. Dehydrogenase activity was significantly lower in the arable soil (down to 35-40% of the control values, p <0.001) varying depending on the soil type. The microbial biomass was also significantly higher at the non-cultivated soil (512-2807 vs. 416-1429 µg g-1 d.m., p <0.001), while easily degradable carbon ranged between 620-1209 mg kg-1 non-cultivated soil and 497-877 mg kg-1 arable soil (p <0.0001). It was demonstrated that agricultural practices affected soil properties by significantly reducing the levels of the studied parameters in relation to the control soils. The significant correlations of easily degradable carbon-respiration activity (ρ = 0.77*), easily degradable carbon-dehydrogenase activity (ρ = 0.42*), and easily degradable carbon-microbial biomass (ρ = 0.53*) reveal that easily degradable carbon is a novel, suitable factor indicative of soil biological degradation. It, therefore, could be used for evaluating the degree of soil degradation and for choosing a proper management procedure.

Microbial biomass carbon and enzyme activities of urban soils in Beijing.

PubMed

Wang, Meie; Markert, Bernd; Shen, Wenming; Chen, Weiping; Peng, Chi; Ouyang, Zhiyun

2011-07-01

To promote rational and sustainable use of soil resources and to maintain the urban soil quality, it is essential to assess urban ecosystem health. In this study, the microbiological properties of urban soils in Beijing and their spatial distribution patterns across the city were evaluated based on measurements of microbial biomass carbon and urease and invertase activities of the soils for the purpose of assessing the urban ecosystem health of Beijing. Grid sampling design, normal Kriging technique, and the multiple comparisons among different land use types were used in soil sampling and data treatment. The inherent chemical characteristics of urban soils in Beijing, e.g., soil pH, electronic conductivity, heavy metal contents, total N, P and K contents, and soil organic matter contents were detected. The size and diversity of microbial community and the extent of microbial activity in Beijing urban soils were measured as the microbial biomass carbon content and the ratio of microbial biomass carbon content to total soil organic carbon. The microbial community health measured in terms of microbial biomass carbon, urease, and invertase activities varied with the organic substrate and nutrient contents of the soils and were not adversely affected by the presence of heavy metals at p < 0.01. It was shown that the older and the biologically more stable part of city exhibited higher microbial activity levels than the more recently developed part of the city and the road areas of heavy traffic. It was concluded that the land use patterns in Beijing urban soils influenced the nature and activities of the microbial communities.

Influence of different forms of acidities on soil microbiological properties and enzyme activities at an acid mine drainage contaminated site.

PubMed

Sahoo, Prafulla Kumar; Bhattacharyya, Pradip; Tripathy, Subhasish; Equeenuddin, Sk Md; Panigrahi, M K

2010-07-15

Assessment of microbial parameters, viz. microbial biomass, fluorescence diacetate, microbial respiration, acid phosphatase, beta-glucosidase and urease with respect to acidity helps in evaluating the quality of soils. This study was conducted to investigate the effects of different forms of acidities on soil microbial parameters in an acid mine drainage contaminated site around coal deposits in Jainta Hills of India. Total potential and exchangeable acidity, extractable and exchangeable aluminium were significantly higher in contaminated soil compared to the baseline (p<0.01). Different forms of acidity were significantly and positively correlated with each other (p<0.05). Further, all microbial properties were positively and significantly correlated with organic carbon and clay (p<0.05). The ratios of microbial parameters with organic carbon were negatively correlated with different forms of acidity. Principal component analysis and cluster analyses showed that the microbial activities are not directly influenced by the total potential acidity and extractable aluminium. Though acid mine drainage affected soils had higher microbial biomass and activities due to higher organic matter content than those of the baseline soils, the ratios of microbial parameters/organic carbon indicated suppression of microbial growth and activities due to acidity stress. 2010 Elsevier B.V. All rights reserved.

Forest understory plant and soil microbial response to an experimentally induced drought and heat-pulse event: the importance of maintaining the continuum.

PubMed

von Rein, Isabell; Gessler, Arthur; Premke, Katrin; Keitel, Claudia; Ulrich, Andreas; Kayler, Zachary E

2016-08-01

Drought duration and intensity are expected to increase with global climate change. How changes in water availability and temperature affect the combined plant-soil-microorganism response remains uncertain. We excavated soil monoliths from a beech (Fagus sylvatica L.) forest, thus keeping the understory plant-microbe communities intact, imposed an extreme climate event, consisting of drought and/or a single heat-pulse event, and followed microbial community dynamics over a time period of 28 days. During the treatment, we labeled the canopy with (13) CO2 with the goal of (i) determining the strength of plant-microbe carbon linkages under control, drought, heat and heat-drought treatments and (ii) characterizing microbial groups that are tightly linked to the plant-soil carbon continuum based on (13) C-labeled PLFAs. Additionally, we used 16S rRNA sequencing of bacteria from the Ah horizon to determine the short-term changes in the active microbial community. The treatments did not sever within-plant transport over the experiment, and carbon sinks belowground were still active. Based on the relative distribution of labeled carbon to roots and microbial PLFAs, we determined that soil microbes appear to have a stronger carbon sink strength during environmental stress. High-throughput sequencing of the 16S rRNA revealed multiple trajectories in microbial community shifts within the different treatments. Heat in combination with drought had a clear negative effect on microbial diversity and resulted in a distinct shift in the microbial community structure that also corresponded to the lowest level of label found in the PLFAs. Hence, the strongest changes in microbial abundances occurred in the heat-drought treatment where plants were most severely affected. Our study suggests that many of the shifts in the microbial communities that we might expect from extreme environmental stress will result from the plant-soil-microbial dynamics rather than from direct effects of drought and heat on soil microbes alone. © 2016 John Wiley & Sons Ltd.

Nitrogen Fixation in Thermophilic Chemosynthetic Microbial Communities Depending on Hydrogen, Sulfate, and Carbon Dioxide

PubMed Central

Nishihara, Arisa; Haruta, Shin; McGlynn, Shawn E.; Thiel, Vera; Matsuura, Katsumi

2018-01-01

The activity of nitrogen fixation measured by acetylene reduction was examined in chemosynthetic microbial mats at 72–75°C in slightly-alkaline sulfidic hot springs in Nakabusa, Japan. Nitrogenase activity markedly varied from sampling to sampling. Nitrogenase activity did not correlate with methane production, but was detected in samples showing methane production levels less than the maximum amount, indicating a possible redox dependency of nitrogenase activity. Nitrogenase activity was not affected by 2-bromo-ethane sulfonate, an inhibitor of methanogenesis. However, it was inhibited by the addition of molybdate, an inhibitor of sulfate reduction and sulfur disproportionation, suggesting the involvement of sulfate-reducing or sulfur-disproportionating organisms. Nitrogenase activity was affected by different O2 concentrations in the gas phase, again supporting the hypothesis of a redox potential dependency, and was decreased by the dispersion of mats with a homogenizer. The loss of activity that occurred from dispersion was partially recovered by the addition of H2, sulfate, and carbon dioxide. These results suggested that the observed activity of nitrogen fixation was related to chemoautotrophic sulfate reducers, and fixation may be active in a limited range of ambient redox potential. Since thermophilic chemosynthetic communities may resemble ancient microbial communities before the appearance of photosynthesis, the present results may be useful when considering the ancient nitrogen cycle on earth. PMID:29367473

Habitat management affects soil chemistry and allochthonous organic inputs mediating microbial structure and exo-enzyme activity in Wadden Sea salt-marsh soils

NASA Astrophysics Data System (ADS)

Mueller, Peter; Granse, Dirk; Thi Do, Hai; Weingartner, Magdalena; Nolte, Stefanie; Hoth, Stefan; Jensen, Kai

2016-04-01

The Wadden Sea (WS) region is Europe's largest wetland and home to approximately 20% of its salt marsh area. Mainland salt marshes of the WS are anthropogenically influenced systems and have traditionally been used for livestock grazing in wide parts. After foundation of WS National Parks in the late 1980s and early 1990s, artificial drainage has been abandoned; however, livestock grazing is still common in many areas of the National Parks and is under ongoing discussion as a habitat-management practice. While studies so far focused on effects of livestock grazing on biodiversity, little is known about how biogeochemical processes, element cycling, and particularly carbon sequestration are affected. Here, we present data from a recent field study focusing on grazing effects on soil properties, microbial exo-enzyme activity, microbial abundance and structure. Exo-enzyme activity was studied conducting digestive enzyme assays for various enzymes involved in C- and N cycling. Microbial abundance and structure was assessed measuring specific gene abundance of fungi and bacteria using quantitative PCR. Soil compaction induced by grazing led to higher bulk density and decreases in soil redox (Δ >100 mV). Soil pH was significantly lower in grazed parts. Further, the proportion of allochthonous organic matter (marine input) was significantly smaller in grazed vs. ungrazed sites, likely caused by a higher sediment trapping capacity of the taller vegetation in the ungrazed sites. Grazing induced changes in bulk density, pH and redox resulted in reduced activity of enzymes involved in microbial C acquisition; however, there was no grazing effect on enzymes involved in N acquisition. While changes in pH, bulk density or redox did not affect microbial abundance and structure, the relative amount of marine organic matter significantly reduced the relative abundance of fungi (F:B ratio). We conclude that livestock grazing directly affects microbial exo-enzyme activity, thus slowing down C turnover, and indirectly changes microbial structure, namely relative fungal abundance, by reducing high-quality marine organic matter inputs.

Adaptation of microbial community of the anode biofilm in microbial fuel cells to temperature.

PubMed

Mei, Xiaoxue; Xing, Defeng; Yang, Yang; Liu, Qian; Zhou, Huihui; Guo, Changhong; Ren, Nanqi

2017-10-01

Temperature as an important ecological factor affects biofilm development and microbial metabolic activity. Here, the performances and microbial communities of microbial fuel cells (MFCs) at different temperature were analyzed. As the temperature decreased, the power output of MFCs declined. A maximum power density of 894.3±48.6mW/m 2 was obtained in MFCs operating at 30°C, which was 18.5% and 64.5% higher than that in MFCs at 20°C and 10°C, respectively. Illumina sequencing of 16S rRNA gene amplicons showed that a distinct difference in microbial community structure of the anode biofilms occurred. This resulted in different power outputs of MFCs. Species diversity analyses indicated that species evenness of the anode biofilms shifted beyond species richness at different temperatures. The predominant populations of the anode biofilm shifted from Geobacter and Azonexus (30°C) to Pelobacter (20°C) or Acidovorax, Zoogloea and Simplicispira, (10°C). These results indicate that temperature plays an important role in shaping microbial communities of the anode biofilms in MFCs through changes in species evenness. Copyright © 2017 Elsevier B.V. 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.

Influence of petroleum hydrocarbon contamination on microalgae and microbial activities in a long-term contaminated soil.

PubMed

Megharaj, M; Singleton, I; McClure, N C; Naidu, R

2000-05-01

Petroleum hydrocarbons are widespread environmental pollutants. Although biodegradation of petroleum hydrocarbons has been the subject of numerous investigations, information on their toxicity to microorganisms in soil is limited, with virtually no work conducted on soil algae. We carried out a screening experiment for total petroleum hydrocarbons (TPH) and their toxicity to soil algal populations, microbial biomass, and soil enzymes (dehydrogenase and urease) in a long-term TPH-polluted site with reference to an adjacent unpolluted site. Microbial biomass, soil enzyme activity, and microalgae declined in medium to high-level (5,200-21,430 mg kg(-1) soil) TPH-polluted soils, whereas low-level (<2,120 mg kg(-1) soil) pollution stimulated the algal populations and showed no effect on microbial biomass and enzymes. However, inhibition of all the tested parameters was more severe in soil considered to have medium-level pollution than in soils that were highly polluted. This result could not be explained by chemical analysis alone. Of particular interest was an observed shift in the species composition of algae in polluted soils with elimination of sensitive species in the medium to high polluted soils. Also, an algal growth inhibition test carried out using aqueous eluates prepared from polluted soils supported these results. Given the sensitivity of algae to synthetic pollutants, alteration in the algal species composition can serve as a useful bioindicator of pollution. The results of this experiment suggest that chemical analysis alone is not adequate for toxicological estimations and should be used in conjunction with bioassays. Furthermore, changes in species composition of algae proved to be more sensitive than microbial biomass and soil enzyme activity measurements.

Probing Metabolic Activity of Deep Subseafloor Life with NanoSIMS

NASA Astrophysics Data System (ADS)

Morono, Y.; Terada, T.; Itoh, M.; Inagaki, F.

2014-12-01

There are very few natural environments where life is absent in the Earth's surface biosphere. However, uninhabitable region is expected to be exist in the deep subsurface biosphere, of which extent and constraining factor(s) have still remained largly unknown. Scientific ocean drilling have revealed that microbial communities in sediments are generally phylogenetically distinct from known spieces isolated from the Earth's surface biosphere, and hence metabolic functions of the deep subseafloor life remain unknown. In addition, activity of subseafloor microbial cells are thought to be extraordinally slow, as indicated by limited supply of neutrient and energy substrates. To understand the limits of the Earth's subseafloor biosphere and metabolic functions of microbial populations, detection and quantification of the deeply buried microbial cells in geological habitats are fundamentary important. Using newly developed cell separation techniques as well as an discriminative cell detection system, the current quantification limit of sedimentary microbial cells approaches to 102 cells/cm3. These techniques allow not only to assess very small microbial population close to the subsurface biotic fringe, but also to separate and sort the target cells using flow cytometric cell sorter. Once the deep subseafloor microbial cells are detached from mineral grains and sorted, it opens new windows to subsequent molecular ecological and element/isotopic analyses. With a combined use of nano-scale secondary ion masspectrometry (NanoSIMS) and stable isotope-probing techniques, it is possible to detect and measure activity of substrate incorporation into biomass, even for extremely slow metabolic processes such as uncharacteriszed deep subseafloor life. For example, it was evidenced by NanoSIMS that at least over 80% of microbial cells at ~200 meters-deep, 460,000-year-old sedimentary habitat are indeed live, which substrate incooporation was found to be low (10-15 gC/cell/day) even under the lab incubation condition. Also microbial activity in ultraoligotrophic biosphere samples such as the South Pacific Gyre (i.e., IODP Expeditions 329) will be shown. Our results demonstrates metabolic potential of microbes that have been survived for geological timescale in extremely starved condition.

[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.

Capturing the genetic makeup of the active microbiome in situ

DOE PAGES

Singer, Esther; Wagner, Michael; Woyke, Tanja

2017-06-02

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 thatmore » 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.« less

Capturing the genetic makeup of the active microbiome in situ

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

Singer, Esther; Wagner, Michael; Woyke, Tanja

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 thatmore » 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.« less

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.

Life in Ice: Microbial Growth Dynamics and Greenhouse Gas Production During Winter in a Thermokarst Bog Revealed by Stable Isotope Probing Targeted Metagenomics

NASA Astrophysics Data System (ADS)

Blazewicz, S.; White, R. A., III; Tas, N.; Euskirchen, E. S.; Mcfarland, J. W.; Jansson, J.; Waldrop, M. P.

2016-12-01

Permafrost contains a reservoir of frozen C estimated to be twice the size of the current atmospheric C pool. In response to changing climate, permafrost is rapidly warming which could result in widespread seasonal thawing. When permafrost thaws, soils that are rich in ice and C often transform into thermokarst wetlands with anaerobic conditions and significant production of atmospheric CH4. While most C flux research in recently thawed permafrost concentrates on the few summer months when seasonal thaw has occurred, there is mounting evidence that sizeable portions of annual CO2 and CH4 efflux occurs over winter or during a rapid burst of emissions associated with seasonal thaw. A potential mechanism for such efflux patterns is microbial activity in frozen soils over winter where gasses produced are partially trapped within ice until spring thaw. In order to better understand microbial transformation of soil C to greenhouse gas over winter, we applied stable isotope probing (SIP) targeted metagenomics combined with process measurements and field flux data to reveal activities of microbial communities in `frozen' soil from an Alaskan thermokarst bog. Field studies revealed build-up of CO2 and CH4 in frozen soils suggesting that microbial activity persisted throughout the winter in soils poised just below the freezing point. Laboratory incubations designed to simulate in-situ winter conditions (-1.5 °C and anaerobic) revealed continuous CH4 and CO2 production. Strikingly, the quantity of CH4 produced in 6 months in frozen soil was equivalent to approximately 80% of CH4 emitted during the 3 month summer `active' season. Heavy water SIP targeted iTag sequencing revealed growing bacteria and archaea in the frozen anaerobic soil. Growth was primarily observed in two bacterial phyla, Firmicutes and Bacteroidetes, suggesting that fermentation was likely the major C mineralization pathway. SIP targeted metagenomics facilitated characterization of the primary metabolic pathways in growing organisms that likely drove C mineralization. Results indicate that winter microbial activities can play an important role in controlling seasonal C flux in recent thawed permafrost and characterization of growing organisms leads to stronger mechanistic linkages between the soil microbial community and ecosystem processes.

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.

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.

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.

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.

Aerobic Microbial Respiration in Oceanic Oxygen Minimum Zones

NASA Astrophysics Data System (ADS)

Kalvelage, Tim; Lavik, Gaute; Jensen, Marlene M.; Revsbech, Niels Peter; Schunck, Harald; Loescher, Carolin; Desai, Dhwani K.; LaRoche, Julie; Schmitz-Streit, Ruth; Kuypers, Marcel M. M.

2014-05-01

In the oxygen minimum zones (OMZs) of the tropical oceans, sluggish ventilation combined with strong microbial respiration of sinking organic matter results in the depletion of oxygen (O2). When O2 concentrations drop below ~5 µmol/L, organic matter is generally assumed to be respired with nitrate, ultimately leading to the loss of fixed inorganic nitrogen via anammox and denitrification. However, direct measurements of microbial O2 consumption at low O2 levels are - apart from a single experiment conducted in the OMZ off Peru - so far lacking. At the same time, consistently observed active aerobic ammonium and nitrite oxidation at non-detectable O2 concentrations (<1 µmol/L) in all major OMZs, suggests aerobic microorganisms, likely including heterotrophs, to be well adapted to near-anoxic conditions. Consequently, microaerobic (≤5 µmol/L) remineralization of organic matter, and thus release of ammonium, in low- O2 environments might be significantly underestimated at present. Here we present extensive measurements of microbial O2 consumption in OMZ waters, combined with highly sensitive O2 (STOX) measurements and meta-omic functional gene analyses. Short-term incubation experiments with labelled O2 (18-18O2) carried out in the Namibian and Peruvian OMZ, revealed persistent aerobic microbial activity at depths with non-detectable concentrations of O2 (≤50 nmol/L). In accordance, examination of metagenomes and metatranscriptomes from Chilean and Peruvian OMZ waters identified genes encoding for terminal respiratory oxidases with high O2 affinities as well as their expression by diverse microbial communities. Oxygen consumption was particularly enhanced near the upper OMZ boundaries and could mostly (~80%) be assigned to heterotrophic microbial activity. Compared to previously identified anaerobic microbial processes, microaerobic organic matter respiration was the dominant remineralization pathway and source of ammonium (~90%) in the upper Namibian and Peruvian OMZ. Our results reconcile so-far existing mismatches between ammonium sources and sinks in OMZs, and may help to improve biogeochemical modelling of the effects of future ocean de-oxygenation on aerobic and anaerobic organic matter remineralization in these zones.

Phylogenetically conserved resource partitioning in the coastal microbial loop

DOE PAGES

Bryson, Samuel; Li, Zhou; Chavez, Francisco; ...

2017-08-11

Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six 13C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA. Both sequencing approaches indicated distinct substrate-specific community shifts. However, observed changes in relative abundance for individual populationsmore » did not correlate well with directly measured substrate assimilation. The complementary SIP techniques identified assimilation of all six substrates by diverse taxa, but also revealed differential assimilation of substrates into protein and ribonucleotide biomass between taxa. Substrate assimilation trends indicated significantly conserved resource partitioning among populations within the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria classes, suggesting that functional guilds within marine microbial communities are phylogenetically cohesive. However, populations within these classes exhibited heterogeneity in biosynthetic activity, which distinguished high-activity copiotrophs from low-activity oligotrophs. These results indicate distinct growth responses between populations that is not apparent by genome sequencing alone.« less

Phylogenetically conserved resource partitioning in the coastal microbial loop

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

Bryson, Samuel; Li, Zhou; Chavez, Francisco

Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six 13C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA. Both sequencing approaches indicated distinct substrate-specific community shifts. However, observed changes in relative abundance for individual populationsmore » did not correlate well with directly measured substrate assimilation. The complementary SIP techniques identified assimilation of all six substrates by diverse taxa, but also revealed differential assimilation of substrates into protein and ribonucleotide biomass between taxa. Substrate assimilation trends indicated significantly conserved resource partitioning among populations within the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria classes, suggesting that functional guilds within marine microbial communities are phylogenetically cohesive. However, populations within these classes exhibited heterogeneity in biosynthetic activity, which distinguished high-activity copiotrophs from low-activity oligotrophs. These results indicate distinct growth responses between populations that is not apparent by genome sequencing alone.« less

Phylogenetically conserved resource partitioning in the coastal microbial loop

PubMed Central

Bryson, Samuel; Li, Zhou; Chavez, Francisco; Weber, Peter K; Pett-Ridge, Jennifer; Hettich, Robert L; Pan, Chongle; Mayali, Xavier; Mueller, Ryan S

2017-01-01

Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six 13C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA. Both sequencing approaches indicated distinct substrate-specific community shifts. However, observed changes in relative abundance for individual populations did not correlate well with directly measured substrate assimilation. The complementary SIP techniques identified assimilation of all six substrates by diverse taxa, but also revealed differential assimilation of substrates into protein and ribonucleotide biomass between taxa. Substrate assimilation trends indicated significantly conserved resource partitioning among populations within the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria classes, suggesting that functional guilds within marine microbial communities are phylogenetically cohesive. However, populations within these classes exhibited heterogeneity in biosynthetic activity, which distinguished high-activity copiotrophs from low-activity oligotrophs. These results indicate distinct growth responses between populations that is not apparent by genome sequencing alone. PMID:28800138

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.

Effects of the novel pyrimidynyloxybenzoic herbicide ZJ0273 on enzyme activities, microorganisms and its degradation in Chinese soils.

PubMed

Cai, Zhiqiang; Li, Shanshan; Zhang, Wenjie; Ma, Jiangtao; Wang, Jing; Cai, Jinyan; Yang, Guanghua

2015-03-01

Enzyme activity and microbial population in soils have important roles in keeping soil fertility. ZJ0273 is a novel pyrimidynyloxybenzoic-based herbicide, which was recently developed in China. The effect of ZJ0273 on soil enzyme activity and microbial population in two different soils was investigated in this study for the first time. The protease activity was significantly inhibited by ZJ0273 and this inhibiting effect gradually weakened after 60-day incubation. The results also showed that ZJ0273 had different stimulating effects on the activities of dehydrogenase, urease, and catalase. Dehydrogenase was consistently stimulated by all the applied concentrations of ZJ0273. The stimulating effect on urease weakened after 60-day incubation. Catalase activity was subject to variations during the period of the experiments. The results of microbial population showed that the number of bacteria and actinomycetes increased in ZJ0273-treated soil compared with the control after 20 days of incubation, while fungal number decreased after only 10 days of incubation in soils. DT50 (half-life value) and k (degradation rate constant) of ZJ0273 in S1 (marine-fluvigenic yellow loamy soil) and S2 (Huangshi soil) were found 69.31 and 49.50 days and 0.010 and 0.014 day(-1), respectively.

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.

Influence of diesel contamination on the benthic microbial/meiofaunal food web of a Louisiana salt marsh

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

Carman, K.R.; Fleeger, J.W.; Pomarico, S.

The authors studied the influence of diesel-contaminated sediments on the benthic microbial/meiofaunal food web from a Louisiana salt marsh. Diesel-contaminated sediment was added to microcosms (intact cores of marsh mud) in a range of doses, and a suite of microbial and meiofaunal responses were measured over a 28-day period. The authors measured bacterial and microalgal (Chl a) abundance, bacterial and microalgal activity using radiotracers ({sup 14}C-acetate and {sup 14}CO{sub 2}, respectively), meiofaunal grazing on microalgae, meiofaunal community structure, and meiofaunal physiological condition. Preliminary results indicate that diesel-contaminated sediments influence microalgal biomass and activity, as well as the life histories ofmore » benthic copepod species.« less

Seasonal dynamics of microbial community composition and function in oak canopy and open grassland soils

USGS Publications Warehouse

Waldrop, M.P.; Firestone, M.K.

2006-01-01

Soil microbial communities are closely associated with aboveground plant communities, with multiple potential drivers of this relationship. Plants can affect available soil carbon, temperature, and water content, which each have the potential to affect microbial community composition and function. These same variables change seasonally, and thus plant control on microbial community composition may be modulated or overshadowed by annual climatic patterns. We examined microbial community composition, C cycling processes, and environmental data in California annual grassland soils from beneath oak canopies and in open grassland areas to distinguish factors controlling microbial community composition and function seasonally and in association with the two plant overstory communities. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid (PLFA) analysis, microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups using isotope labeling of PLFA biomarkers (13C-PLFA) . Distinct microbial communities were associated with oak canopy soils and open grassland soils and microbial communities displayed seasonal patterns from year to year. The effects of plant species and seasonal climate on microbial community composition were similar in magnitude. In this Mediterranean ecosystem, plant control of microbial community composition was primarily due to effects on soil water content, whereas the changes in microbial community composition seasonally appeared to be due, in large part, to soil temperature. Available soil carbon was not a significant control on microbial community composition. Microbial community composition (PLFA) and 13C-PLFA ordination values were strongly related to intra-annual variability in soil enzyme activities and soil respiration, but microbial biomass was not. In this Mediterranean climate, soil microclimate appeared to be the master variable controlling microbial community composition and function. ?? 2006 Springer Science+Business Media, Inc.

Anti-Bacterial and Anti-Fungal Activity of Xanthones Obtained via Semi-Synthetic Modification of α-Mangostin from Garcinia mangostana.

PubMed

Narasimhan, Srinivasan; Maheshwaran, Shanmugam; Abu-Yousef, Imad A; Majdalawieh, Amin F; Rethavathi, Janarthanam; Das, Prince Edwin; Poltronieri, Palmiro

2017-02-12

The microbial contamination in food packaging has been a major concern that has paved the way to search for novel, natural anti-microbial agents, such as modified α-mangostin. In the present study, twelve synthetic analogs were obtained through semi-synthetic modification of α-mangostin by Ritter reaction, reduction by palladium-carbon (Pd-C), alkylation, and acetylation. The evaluation of the anti-microbial potential of the synthetic analogs showed higher bactericidal activity than the parent molecule. The anti-microbial studies proved that I E showed high anti-bacterial activity whereas I I showed the highest anti-fungal activity. Due to their microbicidal potential, modified α-mangostin derivatives could be utilized as active anti-microbial agents in materials for the biomedical and food industry.

Incorporation of hydrophobized mineral particles in activated sludge flocs: a way to assess ballasting efficiency.

PubMed

Defontaine, G; Thormann, J; Lartiges, B S; El Samrani, A G; Barrs, O

2005-01-01

The role of mineral surface hydrophobicity in attachment to activated sludge flocs was investigated. Fluorite and quartz particles of similar granulometry were hydrophobized by adsorbing sodium oleate and dodecylamine chloride, respectively. Mineral hydrophobicity was assessed by flotation expriments. The attachment of particles to microbial flocs was determined by optical microscopy. The results indicate that hydrophobized particles are always better incorporated within activated sludge flocs than non-coated particles. A comparison with Aquatal particles used as sludge ballast reveals that hydrophobized minerals are associated with microbial flocs to the same extent.

Biofilm-induced bioclogging produces sharp interfaces in hyporheic flow, redox conditions, and microbial community structure

NASA Astrophysics Data System (ADS)

Caruso, Alice; Boano, Fulvio; Ridolfi, Luca; Chopp, David L.; Packman, Aaron

2017-05-01

Riverbed sediments host important biogeochemical processes that play a key role in nutrient dynamics. Sedimentary nutrient transformations are mediated by bacteria in the form of attached biofilms. The influence of microbial metabolic activity on the hydrochemical conditions within the hyporheic zone is poorly understood. We present a hydrobiogeochemical model to assess how the growth of heterotrophic and autotrophic biomass affects the transport and transformation of dissolved nitrogen compounds in bed form-induced hyporheic zones. Coupling between hyporheic exchange, nitrogen metabolism, and biomass growth leads to an equilibrium between permeability reduction and microbial metabolism that yields shallow hyporheic flows in a region with low permeability and high rates of microbial metabolism near the stream-sediment interface. The results show that the bioclogging caused by microbial growth can constrain rates and patterns of hyporheic fluxes and microbial transformation rate in many streams.

In situ Detection of Microbial Life in the Deep Biosphere in Igneous Ocean Crust.

PubMed

Salas, Everett C; Bhartia, Rohit; Anderson, Louise; Hug, William F; Reid, Ray D; Iturrino, Gerardo; Edwards, Katrina J

2015-01-01

The deep biosphere is a major frontier to science. Recent studies have shown the presence and activity of cells in deep marine sediments and in the continental deep biosphere. Volcanic lavas in the deep ocean subsurface, through which substantial fluid flow occurs, present another potentially massive deep biosphere. We present results from the deployment of a novel in situ logging tool designed to detect microbial life harbored in a deep, native, borehole environment within igneous oceanic crust, using deep ultraviolet native fluorescence spectroscopy. Results demonstrate the predominance of microbial-like signatures within the borehole environment, with densities in the range of 10(5) cells/mL. Based on transport and flux models, we estimate that such a concentration of microbial cells could not be supported by transport through the crust, suggesting in situ growth of these communities.

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.

[Soil biological activities at maize seedling stage under application of slow/controlled release nitrogen fertilizers].

PubMed

Li, Dongpo; Wu, Zhijie; Chen, Lijun; Liang, Chenghua; Zhang, Lili; Wang, Weicheng; Yang, Defu

2006-06-01

With pot experiment and simulating field ecological environment, this paper studied the effects of different slow/ controlled release N fertilizers on the soil nitrate - reductase and urease activities and microbial biomass C and N at maize seedling stage. The results showed that granular urea amended with dicyandiamide (DCD) and N-(n-bultyl) thiophosphoric triamide (NBPT) induced the highest soil nitrate-reductase activity, granular urea brought about the highest soil urease activity and microbial biomass C and N, while starch acetate (SA)-coated granular urea, SA-coated granular urea amended with DCD, methyl methacrylate (MMA) -coated granular urea amended with DCD, and no N fertilization gave a higher soil urease activity. Soil microbial C and N had a similar variation trend after applying various kinds of test slow/controlled release N fertilizers, and were the lowest after applying SA-coated granular urea amended with DCD and NBPT. Coated granular urea amended with inhibitors had a stronger effect on soil biological activities than coated granular urea, and MMA-coating had a better effect than SA-coating.

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.

Preliminary screening of some traditional zulu medicinal plants for anti-inflammatory and anti-microbial activities.

PubMed

Lin, J; Opoku, A R; Geheeb-Keller, M; Hutchings, A D; Terblanche, S E; Jäger, A K; van Staden, J

1999-12-15

Aqueous and methanolic extracts from different parts of nine traditional Zulu medicinal plants, of the Vitaceae from KwaZulu-Natal, South Africa were evaluated for therapeutic potential as anti-inflammatory and anti-microbial agents. Of the twenty-nine crude extracts assayed for prostaglandin synthesis inhibitors, only five methanolic extracts of Cyphostemma natalitium-root, Rhoicissus digitata-leaf, R. rhomboidea-root, R. tomentosa-leaf/stem and R. tridentata-root showed significant inhibition of cyclo-oxygenase (COX-1). The extracts of R. digitata-leaf and of R. rhomboidea-root exhibited the highest inhibition of prostaglandin synthesis with 53 and 56%, respectively. The results suggest that Rhoicissus digitata leaves and of Rhoicissus rhomboidea roots may have the potential to be used as anti-inflammatory agents. All the screened plant extracts showed some degrees of anti-microbial activity against gram-positive and gram-negative microorganisms. The methanolic extracts of C. natalitium-stem and root, R. rhomboidea-root, and R. tomentosa-leaf/stem, showed different anti-microbial activities against almost all micro-organisms tested. Generally, these plant extracts inhibited the gram-positive micro-organisms more than the gram-negative ones. Several plant extracts inhibited the growth of Candida albicans while only one plant extract showed inhibitory activity against Saccharomyces cerevisiae. All the plant extracts which demonstrated good anti-inflammatory activities also showed better inhibitory activity against Candida albicans.

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.

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.

Site- and horizon-specific patterns of microbial community structure and enzyme activities in permafrost-affected soils of Greenland

PubMed Central

Gittel, Antje; Bárta, Jiří; Kohoutová, Iva; Schnecker, Jörg; Wild, Birgit; Čapek, Petr; Kaiser, Christina; Torsvik, Vigdis L.; Richter, Andreas; Schleper, Christa; Urich, Tim

2014-01-01

Permafrost-affected soils in the Northern latitudes store huge amounts of organic carbon (OC) that is prone to microbial degradation and subsequent release of greenhouse gasses to the atmosphere. In Greenland, the consequences of permafrost thaw have only recently been addressed, and predictions on its impact on the carbon budget are thus still highly uncertain. However, the fate of OC is not only determined by abiotic factors, but closely tied to microbial activity. We investigated eight soil profiles in northeast Greenland comprising two sites with typical tundra vegetation and one wet fen site. We assessed microbial community structure and diversity (SSU rRNA gene tag sequencing, quantification of bacteria, archaea and fungi), and measured hydrolytic and oxidative enzyme activities. Sampling site and thus abiotic factors had a significant impact on microbial community structure, diversity and activity, the wet fen site exhibiting higher potential enzyme activities and presumably being a hot spot for anaerobic degradation processes such as fermentation and methanogenesis. Lowest fungal to bacterial ratios were found in topsoils that had been relocated by cryoturbation (“buried topsoils”), resulting from a decrease in fungal abundance compared to recent (“unburied”) topsoils. Actinobacteria (in particular Intrasporangiaceae) accounted for a major fraction of the microbial community in buried topsoils, but were only of minor abundance in all other soil horizons. It was indicated that the distribution pattern of Actinobacteria and a variety of other bacterial classes was related to the activity of phenol oxidases and peroxidases supporting the hypothesis that bacteria might resume the role of fungi in oxidative enzyme production and degradation of phenolic and other complex substrates in these soils. Our study sheds light on the highly diverse, but poorly-studied communities in permafrost-affected soils in Greenland and their role in OC degradation. PMID:25360132

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.

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.

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.

Biological versus mineralogical chromium reduction: potential for reoxidation by manganese oxide.

PubMed

Butler, Elizabeth C; Chen, Lixia; Hansel, Colleen M; Krumholz, Lee R; Elwood Madden, Andrew S; Lan, Ying

2015-11-01

Hexavalent chromium (Cr(vi), present predominantly as CrO4(2-) in water at neutral pH) is a common ground water pollutant, and reductive immobilization is a frequent remediation alternative. The Cr(iii) that forms upon microbial or abiotic reduction often co-precipitates with naturally present or added iron (Fe), and the stability of the resulting Fe-Cr precipitate is a function of its mineral properties. In this study, Fe-Cr solids were formed by microbial Cr(vi) reduction using Desulfovibrio vulgaris strain RCH1 in the presence of the Fe-bearing minerals hematite, aluminum substituted goethite (Al-goethite), and nontronite (NAu-2, Clay Minerals Society), or by abiotic Cr(vi) reduction by dithionite reduced NAu-2 or iron sulfide (FeS). The properties of the resulting Fe-Cr solids and their behavior upon exposure to the oxidant manganese (Mn) oxide (birnessite) differed significantly. In microcosms containing strain RCH1 and hematite or Al-goethite, there was significant initial loss of Cr(vi) in a pattern consistent with adsorption, and significant Cr(vi) was found in the resulting solids. The solid formed when Cr(vi) was reduced by FeS contained a high proportion of Cr(iii) and was poorly crystalline. In microcosms with strain RCH1 and hematite, Cr precipitates appeared to be concentrated in organic biofilms. Reaction between birnessite and the abiotically formed Cr(iii) solids led to production of significant dissolved Cr(vi) compared to the no-birnessite controls. This pattern was not observed in the solids generated by microbial Cr(vi) reduction, possibly due to re-reduction of any Cr(vi) generated upon oxidation by birnessite by active bacteria or microbial enzymes. The results of this study suggest that Fe-Cr precipitates formed in groundwater remediation may remain stable only in the presence of active anaerobic microbial reduction. If exposed to environmentally common Mn oxides such as birnessite in the absence of microbial activity, there is the potential for rapid (re)formation of dissolved Cr(vi) above regulatory levels.

Effect of Soil Amendments on Microbial Resilience Capacity of Acid Soil Under Copper Stress.

PubMed

Mounissamy, Vassanda Coumar; Kundu, Samaresh; Selladurai, Rajendiran; Saha, Jayanta Kumar; Biswas, Ashish Kumar; Adhikari, Tapan; Patra, Ashok Kumar

2017-11-01

An incubation study was undertaken to study microbial resilience capacity of acid soil amended with farmyard manure (FYM), charcoal and lime under copper (Cu) perturbation. Copper stress significantly reduced enzymatic activities and microbial biomass carbon (MBC) in soil. Percent reduction in microbial activity of soil due to Cu stress was 74.7% in dehydrogenase activity, 59.9% in MBC, 48.2% in alkaline phosphatase activity and 15.1% in acid phosphatase activity. Soil treated with FYM + charcoal showed highest resistance index for enzymatic activities and MBC. Similarly, the highest resilience index for acid phosphatase activity was observed in soil amended with FYM (0.40), whereas FYM + charcoal-treated soil showed the highest resilience indices for alkaline, dehydrogenase activity and MBC: 0.50, 0.22 and 0.25, respectively. This investigation showed that FYM and charcoal application, either alone or in combination, proved to be better than lime with respect to microbial functional resistance and resilience of acid soil under Cu perturbation.

Does iron inhibit cryptoendolithic microbial communities?

NASA Technical Reports Server (NTRS)

Johnston, C. G.; Vestal, J. R.; Friedmann, E. I. (Principal Investigator)

1988-01-01

Photosynthetic activity of three cryptoendolithic microbial communities was studied under controlled conditions in the laboratory. In two of these communities, the dominant organisms were lichens, collected from Linnaeus Terrace and from Battleship Promontory. The third community, dominated by cyanobacteria, was collected from Battleship Promontory. Both sites are in the ice-free valleys of southern Victoria Land. Previous efforts have shown how physical conditions can influence metabolic activity in endolithic communities (Kappen and Friedmann 1983; Kappen, Friedmann, and Garty 1981; Vestal, Federle, and Friedmann 1984). Biological activity can also be strongly influenced by the chemical environment. Inorganic nutrients such as nitrate, ammonia, and phosphate are often limiting factors, so their effects on photosynthetic carbon-14 bicarbonate incorporation were investigated. Iron and manganese are two metals present in Linnaeus Terrace and Battleship Promontory sandstones, and their effects on photosynthesis were also studied. The results may add to our understanding of biogeochemical interactions within this unique microbial community.

Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest.

PubMed

Taş, Neslihan; Prestat, Emmanuel; McFarland, Jack W; Wickland, Kimberley P; Knight, Rob; Berhe, Asmeret Asefaw; Jorgenson, Torre; Waldrop, Mark P; Jansson, Janet K

2014-09-01

Permafrost soils are large reservoirs of potentially labile carbon (C). Understanding the dynamics of C release from these soils requires us to account for the impact of wildfires, which are increasing in frequency as the climate changes. Boreal wildfires contribute to global emission of greenhouse gases (GHG-CO2, CH4 and N2O) and indirectly result in the thawing of near-surface permafrost. In this study, we aimed to define the impact of fire on soil microbial communities and metabolic potential for GHG fluxes in samples collected up to 1 m depth from an upland black spruce forest near Nome Creek, Alaska. We measured geochemistry, GHG fluxes, potential soil enzyme activities and microbial community structure via 16SrRNA gene and metagenome sequencing. We found that soil moisture, C content and the potential for respiration were reduced by fire, as were microbial community diversity and metabolic potential. There were shifts in dominance of several microbial community members, including a higher abundance of candidate phylum AD3 after fire. The metagenome data showed that fire had a pervasive impact on genes involved in carbohydrate metabolism, methanogenesis and the nitrogen cycle. Although fire resulted in an immediate release of CO2 from surface soils, our results suggest that the potential for emission of GHG was ultimately reduced at all soil depths over the longer term. Because of the size of the permafrost C reservoir, these results are crucial for understanding whether fire produces a positive or negative feedback loop contributing to the global C cycle.

Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest

PubMed Central

Taş, Neslihan; Prestat, Emmanuel; McFarland, Jack W; Wickland, Kimberley P; Knight, Rob; Berhe, Asmeret Asefaw; Jorgenson, Torre; Waldrop, Mark P; Jansson, Janet K

2014-01-01

Permafrost soils are large reservoirs of potentially labile carbon (C). Understanding the dynamics of C release from these soils requires us to account for the impact of wildfires, which are increasing in frequency as the climate changes. Boreal wildfires contribute to global emission of greenhouse gases (GHG—CO2, CH4 and N2O) and indirectly result in the thawing of near-surface permafrost. In this study, we aimed to define the impact of fire on soil microbial communities and metabolic potential for GHG fluxes in samples collected up to 1 m depth from an upland black spruce forest near Nome Creek, Alaska. We measured geochemistry, GHG fluxes, potential soil enzyme activities and microbial community structure via 16SrRNA gene and metagenome sequencing. We found that soil moisture, C content and the potential for respiration were reduced by fire, as were microbial community diversity and metabolic potential. There were shifts in dominance of several microbial community members, including a higher abundance of candidate phylum AD3 after fire. The metagenome data showed that fire had a pervasive impact on genes involved in carbohydrate metabolism, methanogenesis and the nitrogen cycle. Although fire resulted in an immediate release of CO2 from surface soils, our results suggest that the potential for emission of GHG was ultimately reduced at all soil depths over the longer term. Because of the size of the permafrost C reservoir, these results are crucial for understanding whether fire produces a positive or negative feedback loop contributing to the global C cycle. PMID:24722629

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.

Interactions between extracellular polymeric substances and clay minerals affect soil aggregation

NASA Astrophysics Data System (ADS)

Vogel, Cordula; Rehschuh, Stephanie; Kemi Olagoke, Folasade; Redmile Gordon, Marc; Kalbiltz, Karsten

2017-04-01

Soil aggregation is crucial for carbon (C) sequestration and microbial processes have been recognised as important control of aggregate turnover (formation, stability, and destruction). However, how microorganisms contribute to these processes is still a matter of debate. An enthralling mechanism determining aggregate turnover and therefore C sequestration may be the excretion of extracellular polymeric substances (EPS) as microbial glue, but effects of EPS on aggregation is largely unknown. Moreover, interdependencies between important aggregation factors like the amount of fine-sized particles (clay content), the decomposability of organic matter and the microbial community (size and composition, as well as the excretion of EPS) are still poorly understood. Therefore, we studied the complex interactions between these factors and their role in aggregate turnover. It was hypothesized that an increase in microbial activity, induced by the input of organic substrates, will stimulate EPS production and therefore the formation and stability of aggregates. To test this hypothesis, an incubation experiment has been conducted across a gradient of clay content (montmorillonite) and substrate decomposability (starch and glucose) as main drivers of the microbial activity. A combination of aggregate separation and stability tests were applied. This results will be examined with respect to the obtained microbial parameters (amount and composition of EPS, CO2 emission, microbial biomass, phospholipid fatty acid), to disentangle the mechanisms and factors controlling aggregate turnover affected by soil microorganisms. This study is expected to provide insights on the role of EPS in the stability of aggregates. Thus, the results of this study will provide an improved understanding of the underlying processes of aggregate turnover in soils, which is necessary to implement strategies for enhanced C sequestration in agricultural soils.

Linking geology and microbiology: inactive pockmarks affect sediment microbial community structure.

PubMed

Haverkamp, Thomas H A; Hammer, Øyvind; Jakobsen, Kjetill S

2014-01-01

Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm) sediment communities are affected by local conditions within the sediment.

Microbial trace-fossil formation, biogenous, and abiotic weathering in the Antarctic cold desert

NASA Technical Reports Server (NTRS)

Friedmann, E. Imre; Weed, Rebecca

1987-01-01

In the Antarctic cold desert (Ross Desert), the survival of the cryptoendolithic microorganisms that colonize the near-surface layer of porous sandstone rocks depends on a precarious equilibrium of biological and geological factors. An unfavorable shift of this equilibrium results in death, and this may be followed by formation of trace fossils that preserve the characteristic iron-leaching pattern caused by microbial activity. Similar microbial trace fossils may exist in the geological record. If life ever arose on early Mars, similar processes may have occurred there and left recognizable traces.

[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.

Mapping and determinism of soil microbial community distribution across an agricultural landscape

PubMed Central

Constancias, Florentin; Terrat, Sébastien; Saby, Nicolas P A; Horrigue, Walid; Villerd, Jean; Guillemin, Jean-Philippe; Biju-Duval, Luc; Nowak, Virginie; Dequiedt, Samuel; Ranjard, Lionel; Chemidlin Prévost-Bouré, Nicolas

2015-01-01

Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13 km². Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured distribution of microbial biomass and diversity with patches of several hundreds of meters. Variance partitioning revealed that both microbial abundance and bacterial diversity distribution were highly dependent of soil properties and land use (total variance explained ranged between 55% and 78%). Microbial biomass and bacterial richness distributions were mainly explained by soil pH and texture whereas bacterial evenness distribution was mainly related to land management. Bacterial diversity (richness, evenness, and Shannon index) was positively influenced by cropping intensity and especially by soil tillage, resulting in spots of low microbial diversity in soils under forest management. Spatial descriptors also explained a small but significant portion of the microbial distribution suggesting that landscape configuration also shapes microbial biomass and bacterial diversity. PMID:25833770

Active and total microbial communities in forest soil are largely different and highly stratified during decomposition.

PubMed

Baldrian, Petr; Kolařík, Miroslav; Stursová, Martina; Kopecký, Jan; Valášková, Vendula; Větrovský, Tomáš; Zifčáková, Lucia; Snajdr, Jaroslav; Rídl, Jakub; Vlček, Cestmír; Voříšková, Jana

2012-02-01

Soils of coniferous forest ecosystems are important for the global carbon cycle, and the identification of active microbial decomposers is essential for understanding organic matter transformation in these ecosystems. By the independent analysis of DNA and RNA, whole communities of bacteria and fungi and its active members were compared in topsoil of a Picea abies forest during a period of organic matter decomposition. Fungi quantitatively dominate the microbial community in the litter horizon, while the organic horizon shows comparable amount of fungal and bacterial biomasses. Active microbial populations obtained by RNA analysis exhibit similar diversity as DNA-derived populations, but significantly differ in the composition of microbial taxa. Several highly active taxa, especially fungal ones, show low abundance or even absence in the DNA pool. Bacteria and especially fungi are often distinctly associated with a particular soil horizon. Fungal communities are less even than bacterial ones and show higher relative abundances of dominant species. While dominant bacterial species are distributed across the studied ecosystem, distribution of dominant fungi is often spatially restricted as they are only recovered at some locations. The sequences of cbhI gene encoding for cellobiohydrolase (exocellulase), an essential enzyme for cellulose decomposition, were compared in soil metagenome and metatranscriptome and assigned to their producers. Litter horizon exhibits higher diversity and higher proportion of expressed sequences than organic horizon. Cellulose decomposition is mediated by highly diverse fungal populations largely distinct between soil horizons. The results indicate that low-abundance species make an important contribution to decomposition processes in soils.

Successional and seasonal variations in soil and litter microbial community structure and function during tropical postagricultural forest regeneration: a multiyear study.

PubMed

Smith, A Peyton; Marín-Spiotta, Erika; Balser, Teri

2015-09-01

Soil microorganisms regulate fundamental biochemical processes in plant litter decomposition and soil organic matter (SOM) transformations. Understanding how microbial communities respond to changes in vegetation is critical for improving predictions of how land-cover change affects belowground carbon storage and nutrient availability. We measured intra- and interannual variability in soil and forest litter microbial community composition and activity via phospholipid fatty acid analysis (PLFA) and extracellular enzyme activity across a well-replicated, long-term chronosequence of secondary forests growing on abandoned pastures in the wet subtropical forest life zone of Puerto Rico. Microbial community PLFA structure differed between young secondary forests and older secondary and primary forests, following successional shifts in tree species composition. These successional patterns held across seasons, but the microbial groups driving these patterns differed over time. Microbial community composition from the forest litter differed greatly from those in the soil, but did not show the same successional trends. Extracellular enzyme activity did not differ with forest succession, but varied by season with greater rates of potential activity in the dry seasons. We found few robust significant relationships among microbial community parameters and soil pH, moisture, carbon, and nitrogen concentrations. Observed inter- and intrannual variability in microbial community structure and activity reveal the importance of a multiple, temporal sampling strategy when investigating microbial community dynamics with land-use change. Successional control over microbial composition with forest recovery suggests strong links between above and belowground communities. © 2015 John Wiley & Sons Ltd.

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

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

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

Geochemical and iron isotopic insights into hydrothermal iron oxyhydroxide deposit formation at Loihi Seamount

NASA Astrophysics Data System (ADS)

Rouxel, Olivier; Toner, Brandy; Germain, Yoan; Glazer, Brian

2018-01-01

Low-temperature hydrothermal vents, such as those encountered at Loihi Seamount, harbor abundant microbial communities and provide ideal systems to test hypotheses on biotic versus abiotic formation of hydrous ferric oxide (FeOx) deposits at the seafloor. Hydrothermal activity at Loihi Seamount produces abundant microbial mats associated with rust-colored FeOx deposits and variably encrusted with Mn-oxyhydroxides. Here, we applied Fe isotope systematics together with major and trace element geochemistry to study the formation mechanisms and preservation of such mineralized microbial mats. Iron isotope composition of warm (<60 °C), Fe-rich and H2S-depleted hydrothermal fluids yielded δ56Fe values near +0.1‰, indistinguishable from basalt values. Suspended particles in the vent fluids and FeOx deposits recovered nearby active vents yielded systematically positive δ56Fe values. The enrichment in heavy Fe isotopes between +1.05‰ and +1.43‰ relative to Fe(II) in vent fluids suggest partial oxidation of Fe(II) during mixing of the hydrothermal fluid with seawater. By comparing the results with experimentally determined Fe isotope fractionation factors, we determined that less than 20% of Fe(II) is oxidized within active microbial mats, although this number may reach 80% in aged or less active deposits. These results are consistent with Fe(II) oxidation mediated by microbial processes considering the expected slow kinetics of abiotic Fe oxidation in low oxygen bottom water at Loihi Seamount. In contrast, FeOx deposits recovered at extinct sites have distinctly negative Fe-isotope values down to -1.77‰ together with significant enrichment in Mn and occurrence of negative Ce anomalies. These results are best explained by the near-complete oxidation of an isotopically light Fe(II) source produced during the waning stage of hydrothermal activity under more oxidizing conditions. Light Fe isotope values of FeOx are therefore generated by subsurface precipitation of isotopically heavy Fe-oxides rather than by the activity of dissimilatory Fe reduction in the subsurface. Overall, Fe-isotope compositions of microbial mats at Loihi Seamount display a remarkable range between -1.2‰ and +1.6‰ which indicate that Fe isotope compositions of hydrothermal Fe-oxide precipitates are particularly sensitive to local environmental conditions where they form, and are less sensitive to abiotic versus biotic origins. It follows that FeOx deposits at Loihi Seamount provides important modern analogues for ancient seafloor Fe-rich deposits allowing for testing hypotheses about the biogeochemical cycling of Fe isotopes on early Earth.

The role of microbial low-molecular-weight autoregulatory factors (alkylhydroxybenzenes) in resistance of microorganisms to radiation

NASA Astrophysics Data System (ADS)

El-Registan, G. I.; Mulyukin, A. L.; Nikolaev, Yu. A.; Stepanenko, I. Yu.; Shanenko, E. A.; Strakhovskaya, M. G.; Revina, A. A.

Low-molecular-weight cell-to-cell communication factors are produced by various pro- and eukaryotes and involved in autoregulation of the growth and development of microbial cultures. As for some bacterial and yeast species, these factors were identified as isomers and homologs of alkylhydroxybenzenes (AHBs). Depending on the concentration, they participate in controlling the transition to stationary phase, entering the resting state, and stress resistance of vegetative cells to gamma-irradiation, photooxidation (singlet oxygen), heat shock. Chemical analogs of microbial AHBs protected microbial cultures from stressful situations and prolonged starvation and exerted (1) the stabilizing activity toward biomacromolecules and supermolecular structures (cell membranes) and (2) the ability to scavenge active oxygen species. The stabilizing effect of AHBs as chemical chaperones resulted from their complex formation with protected macromolecules due to intermolecular hydrogen bonds, hydrophobic and electrostatic interactions and was demonstrated on models of individual enzymes (trypsin, amylase, etc.). The action of AHBs as active oxygen species scavengers was related to their oxidative conversion to water-insoluble polymeric products. Particularly, AHBs protected the yeast from the action of (a) active oxygen species formed during gamma-irradiation (50 krad, 196 rad/sec) or (b) singlet oxygen generated in cells photosensitized by chlorin e6 (10 mkg/L). It is important that microbial AHBs were not species-specific and defended cultured animal cells (ras-transformed fibroblasts) from the action of organic toxicants. The use of AHBs as protectants and adaptogens will be discussed as well as perspectives of further investigations.

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

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.

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

The coupling of the plant and microbial catabolisms of phenanthrene in the rhizosphere of Medicago sativa.

PubMed

Muratova, Anna; Dubrovskaya, Ekaterina; Golubev, Sergey; Grinev, Vyacheslav; Chernyshova, Marina; Turkovskaya, Olga

2015-09-01

We studied the catabolism of the polycyclic aromatic hydrocarbon phenanthrene by four rhizobacterial strains and the possibility of enzymatic oxidation of this compound and its microbial metabolites by the root exudates of alfalfa (Medicago sativa L.) in order to detect the possible coupling of the plant and microbial metabolisms under the rhizospheric degradation of the organic pollutant. A comparative study of phenanthrene degradation pathways in the PAH-degrading rhizobacteria Ensifer meliloti, Pseudomonas kunmingensis, Rhizobium petrolearium, and Stenotrophomonas sp. allowed us to identify the key metabolites from the microbial transformation of phenanthrene, including 9,10-phenanthrenequinone, 2-carboxybenzaldehyde, and 1-hydroxy-2-naphthoic, salicylic, and o-phthalic acids. Sterile alfalfa plants were grown in the presence and absence of phenanthrene (0.03 g kg(-1)) in quartz sand under controlled environmental conditions to obtain plant root exudates. The root exudates were collected, concentrated by ultrafiltration, and the activity of oxidoreductases was detected spectrophotometrically by the oxidation rate for various substrates. The most marked activity was that of peroxidase, whereas the presence of oxidase and tyrosinase was detected on the verge of the assay sensitivity. Using alfalfa root exudates as a crude enzyme preparation, we found that in the presence of the synthetic mediator, the plant peroxidase could oxidize phenanthrene and its microbial metabolites. The results indicate the possibility of active participation of plants in the rhizospheric degradation of polycyclic aromatic hydrocarbons and their microbial metabolites, which makes it possible to speak about the coupling of the plant and microbial catabolisms of these contaminants in the rhizosphere. Copyright © 2015 Elsevier GmbH. All rights reserved.

Biogeochemistry of Produced Water from Unconventional Wells in the Powder River Basin, Wyoming

NASA Astrophysics Data System (ADS)

Drogos, D. L.; Nye, C.; Quillinan, S.; Urynowicz, M. A.; Wawrousek, K.

2017-12-01

Microbial activity in waters associated with unconventional oil and gas reservoirs is poorly described but can profoundly affect management strategies for produced water (PW), frac fluids, and biocides. Improved identification of microbial communities is required to develop targeted solutions for detrimental microbial activity such as biofouling and to exploit favorable activity such as microbial induced gas production. We quantified the microbial communities and inorganic chemistry in PW samples from cretaceous formations in six unconventional oil and gas wells in the Powder River Basin in northeast Wyoming. The wells are horizontal completions in the Frontier, Niobrara, Shannon, and Turner formations at depths of 10,000 to 12,000 feet, with PW temperatures ranging from 93oF to 130oF. Biocides utilized in frac fluids primarily included glutaraldehyde and Alkyl Dimethyl Benzyl Ammonium Chloride (ADBAC), with first production occurring in 2013. Geochemical results for PW are: pH 6.5 to 6.9; alkalinity (as CaCO3) 219 to 519 ppm; salinity 13,200 to 22,300 ppm; and TDS 39,364 to 62,725 ppm. Illumina MiSeq 16S rRNA sequencing identified the majority of communities in PW are related to anaerobic, thermophilic, halophilic, chemoheterotrophic, and chemoorganotrophic bacteria, including Thermotoga, Clostridiaceae, Thermoanaerobacter, Petrotoga, Anaerobaculum, Clostridiales, Desulfomicrobium, and Halanaerobiaceae. These findings are important for identification of biogeochemical reactions that affect the organic-inorganic-microbial interactions among reservoir rocks, formation waters, and frac fluids. Better understanding of these biogeochemical reactions would allow producers to formulate frac fluids and biocides to encourage beneficial microbial phenomena such as biogenic gas production while discouraging detrimental effects such as biofouling.

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.

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

Innate and cytokine-driven signals, rather than microbial antigens, dominate in natural killer T cell activation during microbial infection.

PubMed

Brigl, Manfred; Tatituri, Raju V V; Watts, Gerald F M; Bhowruth, Veemal; Leadbetter, Elizabeth A; Barton, Nathaniel; Cohen, Nadia R; Hsu, Fong-Fu; Besra, Gurdyal S; Brenner, Michael B

2011-06-06

Invariant natural killer T cells (iNKT cells) are critical for host defense against a variety of microbial pathogens. However, the central question of how iNKT cells are activated by microbes has not been fully explained. The example of adaptive MHC-restricted T cells, studies using synthetic pharmacological α-galactosylceramides, and the recent discovery of microbial iNKT cell ligands have all suggested that recognition of foreign lipid antigens is the main driver for iNKT cell activation during infection. However, when we compared the role of microbial antigens versus innate cytokine-driven mechanisms, we found that iNKT cell interferon-γ production after in vitro stimulation or infection with diverse bacteria overwhelmingly depended on toll-like receptor-driven IL-12. Importantly, activation of iNKT cells in vivo during infection with Sphingomonas yanoikuyae or Streptococcus pneumoniae, pathogens which are known to express iNKT cell antigens and which require iNKT cells for effective protection, also predominantly depended on IL-12. Constitutive expression of high levels of IL-12 receptor by iNKT cells enabled instant IL-12-induced STAT4 activation, demonstrating that among T cells, iNKT cells are uniquely equipped for immediate, cytokine-driven activation. These findings reveal that innate and cytokine-driven signals, rather than cognate microbial antigen, dominate in iNKT cell activation during microbial infections.

Microbial Interactions Associated with Biofilms Attached to Trichodesmium spp. and Detrital Particles in the Ocean

DTIC Science & Technology

2010-06-01

AHLs enhanced certain organic-matter degrading hydrolytic enzyme activities. My results suggest that AHL-QS is a factor regulating...biogeochemically relevant enzyme activities on sinking POC and within the biofilms attached to Trichodesmium colonies and thereby may impact the timing and... Enzyme activity assays ......................................................................................................................232 RESULTS

Diversity of proteolytic microbes isolated from Antarctic freshwater lakes and characteristics of their cold-active proteases

NASA Astrophysics Data System (ADS)

Matsui, Mihoko; Kawamata, Akinori; Kosugi, Makiko; Imura, Satoshi; Kurosawa, Norio

2017-09-01

Despite being an extreme environment, the water temperature of freshwater lakes in Antarctica reaches 10 °C in summer, accelerating biological activity. In these environments, proteolytic microbial decomposers may play a large role in protein hydrolysis. We isolated 71 microbial strains showing proteolytic activity at 4 °C from three Antarctic freshwater lakes. They were classified as bacteria (63 isolates) and eukaryotes (8 isolates). The bacterial isolates were classified into the genera Flavobacterium (28 isolates), Pseudomonas (14 isolates), Arthrobacter (10 isolates), Psychrobacter (7 isolates), Cryobacterium (2 isolates), Hymenobacter (1 isolate), and Polaromonas (1 isolate). Five isolates of Flavobacterium and one of Hymenobacter seemed to belong to novel species. All eukaryotic isolates belonged to Glaciozyma antarctica, a psychrophilic yeast species originally isolated from the Weddell Sea near the Joinville Island, Antarctica. A half of representative strains were psychrophilic and did not grow at temperatures above 25 °C. The protease secreted by Pseudomonas prosekii strain ANS4-1 showed the highest activity among all proteases from representative isolates. The results of inhibitor tests indicated that nearly all the isolates secreted metalloproteases. Proteases from four representative isolates retained more than 30% maximal activity at 0 °C. These results expand our knowledge about microbial protein degradation in Antarctic freshwater lakes.

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.

Ex situ bioremediation of oil-contaminated soil.

PubMed

Lin, Ta-Chen; Pan, Po-Tsen; Cheng, Sheng-Shung

2010-04-15

An innovative bioprocess method, Systematic Environmental Molecular Bioremediation Technology (SEMBT) that combines bioaugmentation and biostimulation with a molecular monitoring microarray biochip, was developed as an integrated bioremediation technology to treat S- and T-series biopiles by using the landfarming operation and reseeding process to enhance the bioremediation efficiency. After 28 days of the bioremediation process, diesel oil (TPH(C10-C28)) and fuel oil (TPH(C10-C40)) were degraded up to approximately 70% and 63% respectively in the S-series biopiles. When the bioaugmentation and biostimulation were applied in the beginning of bioremediation, the microbial concentration increased from approximately 10(5) to 10(6) CFU/g dry soil along with the TPH biodegradation. Analysis of microbial diversity in the contaminated soils by microarray biochips revealed that Acinetobacter sp. and Pseudomonas aeruginosa were the predominant groups in indigenous consortia, while the augmented consortia were Gordonia alkanivorans and Rhodococcus erythropolis in both series of biopiles during bioremediation. Microbial respiration as influenced by the microbial activity reflected directly the active microbial population and indirectly the biodegradation of TPH. Field experimental results showed that the residual TPH concentration in the complex biopile was reduced to less than 500 mg TPH/kg dry soil. The above results demonstrated that the SEMBT technology is a feasible alternative to bioremediate the oil-contaminated soil. Crown Copyright 2009. Published by Elsevier B.V. All rights reserved.

[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.

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

Construction and Characterization of a Cellulolytic Consortium Enriched from the Hindgut of Holotrichia parallela Larvae.

PubMed

Sheng, Ping; Huang, Jiangli; Zhang, Zhihong; Wang, Dongsheng; Tian, Xiaojuan; Ding, Jiannan

2016-09-30

Degradation of rice straw by cooperative microbial activities is at present the most attractive alternative to fuels and provides a basis for biomass conversion. The use of microbial consortia in the biodegradation of lignocelluloses could reduce problems such as incomplete synergistic enzymes, end-product inhibition, and so on. In this study, a cellulolytic microbial consortium was enriched from the hindgut of Holotrichia parallela larvae via continuous subcultivation (20 subcultures in total) under static conditions. The degradation ratio for rice straw was about 83.1% after three days of cultivation, indicating its strong cellulolytic activity. The diversity analysis results showed that the bacterial diversity and richness decreased during the consortium enrichment process, and the consortium enrichment process could lead to a significant enrichment of phyla Proteobacteria and Spirochaetes, classes Clostridia, Epsilonproteobacteria, and Betaproteobacteria, and genera Arcobacter , Treponema , Comamonas , and Clostridium . Some of these are well known as typical cellulolytic and hemicellulolytic microorganisms. Our results revealed that the microbial consortium identified herein is a potential candidate for use in the degradation of waste lignocellulosic biomass and further highlights the hindgut of the larvae as a reservoir of extensive and specific cellulolytic and hemicellulolytic microbes.

Investigations of the microbial transformation of cortisol to prednisolone in urine samples.

PubMed

Bredehöft, Michael; Baginski, Rainer; Parr, Maria-Kristina; Thevis, Mario; Schänzer, Wilhelm

2012-03-01

Doping control samples are normally collected under non-sterile conditions and sometimes, storage and transportation are influenced by parameters such as the temperature. Therefore, microbial contamination and subsequent alteration of a sample's composition are possible. Studies regarding sample collection in cattle breeding have already shown enzymatic transformation of endogenous testosterone to boldenone causing false-positive findings. The aim of the present study was to investigate whether positive doping cases with the synthetic corticosteroids prednisolone and prednisone may result from microbial transformation of the endogenous corticosteroids cortisol and cortisone, respectively. A method comprising parameters such as pH values and screening results for synthetic glucocorticosteroids as well as incubation experiments followed by liquid chromatographic and mass spectrometric analysis was employed to test for contaminating germs with Δ(1)-dehydrogenase activity. Over 700 urine samples comprising inpatient and doping control specimens were investigated. In none of them, 1,2-dehydrogenating activity was confirmed. These findings are in accordance with other studies. However, the problem of microbial alteration of doping control specimens with special respect to 1,2-dehydrogenation must not be underestimated. Article from a special issue on steroids and microorganisms. Copyright © 2010 Elsevier Ltd. All rights reserved.

Microbial physiology-based model of ethanol metabolism in subsurface sediments

NASA Astrophysics Data System (ADS)

Jin, Qusheng; Roden, Eric E.

2011-07-01

A biogeochemical reaction model was developed based on microbial physiology to simulate ethanol metabolism and its influence on the chemistry of anoxic subsurface environments. The model accounts for potential microbial metabolisms that degrade ethanol, including those that oxidize ethanol directly or syntrophically by reducing different electron acceptors. Out of the potential metabolisms, those that are active in the environment can be inferred by fitting the model to experimental observations. This approach was applied to a batch sediment slurry experiment that examined ethanol metabolism in uranium-contaminated aquifer sediments from Area 2 at the U.S. Department of Energy Field Research Center in Oak Ridge, TN. According to the simulation results, complete ethanol oxidation by denitrification, incomplete ethanol oxidation by ferric iron reduction, ethanol fermentation to acetate and H 2, hydrogenotrophic sulfate reduction, and acetoclastic methanogenesis: all contributed significantly to the degradation of ethanol in the aquifer sediments. The assemblage of the active metabolisms provides a frame work to explore how ethanol amendment impacts the chemistry of the environment, including the occurrence and levels of uranium. The results can also be applied to explore how diverse microbial metabolisms impact the progress and efficacy of bioremediation strategies.

Snow Surface Microbiome on the High Antarctic Plateau (DOME C)

PubMed Central

Michaud, Luigi; Lo Giudice, Angelina; Mysara, Mohamed; Monsieurs, Pieter; Raffa, Carmela; Leys, Natalie; Amalfitano, Stefano; Van Houdt, Rob

2014-01-01

The cryosphere is an integral part of the global climate system and one of the major habitable ecosystems of Earth's biosphere. These permanently frozen environments harbor diverse, viable and metabolically active microbial populations that represent almost all the major phylogenetic groups. In this study, we investigated the microbial diversity in the surface snow surrounding the Concordia Research Station on the High Antarctic Plateau through a polyphasic approach, including direct prokaryotic quantification by flow cytometry and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH), and phylogenetic identification by 16S RNA gene clone library sequencing and 454 16S amplicon pyrosequencing. Although the microbial abundance was low (<103 cells/ml of snowmelt), concordant results were obtained with the different techniques. The microbial community was mainly composed of members of the Alpha-proteobacteria class (e.g. Kiloniellaceae and Rhodobacteraceae), which is one of the most well-represented bacterial groups in marine habitats, Bacteroidetes (e.g. Cryomorphaceae and Flavobacteriaceae) and Cyanobacteria. Based on our results, polar microorganisms could not only be considered as deposited airborne particles, but as an active component of the snowpack ecology of the High Antarctic Plateau. PMID:25101779

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.

[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.

Changing bacterial profile of Sundarbans, the world heritage mangrove: impact of anthropogenic interventions.

PubMed

Chakraborty, Arpita; Bera, Amit; Mukherjee, Arghya; Basak, Pijush; Khan, Imroze; Mondal, Arindam; Roy, Arunava; Bhattacharyya, Anish; SenGupta, Sohan; Roy, Debojyoti; Nag, Sudip; Ghosh, Abhrajyoti; Chattopadhyay, Dhrubajyoti; Bhattacharyya, Maitree

2015-04-01

Mangrove microbial communities and their associated activities have profound impact on biogeochemical cycles. Although microbial composition and structure are known to be influenced by biotic and abiotic factors in the mangrove sediments, finding direct correlations between them remains a challenge. In this study we have explored sediment bacterial diversity of the Sundarbans, a world heritage site using a culture-independent molecular approach. Bacterial diversity was analyzed from three different locations with a history of exposure to differential anthropogenic activities. 16S rRNA gene libraries were constructed and partial sequencing of the clones was performed to identify the microbial strains. We identified bacterial strains known to be involved in a variety of biodegradation/biotransformation processes including hydrocarbon degradation, and heavy metal resistance. Canonical Correspondence Analysis of the environmental and exploratory datasets revealed correlations between the ecological indices associated with pollutant levels and bacterial diversity across the sites. Our results indicate that sites with similar exposure of anthropogenic intervention reflect similar patterns of microbial diversity besides spatial commonalities.

New insight into the environmental impact of two imidazolium ionic liquids. Effects on seed germination and soil microbial activity.

PubMed

Salgado, J; Parajó, J J; Teijeira, T; Cruz, O; Proupín, J; Villanueva, M; Rodríguez-Añón, J A; Verdes, P V; Reyes, O

2017-10-01

The next generation of ionic liquids must be synthetized taking into account structures that guarantee the suitable properties for a defined application as well as ecological data. Thus, searching of the right methodologies to know, quickly and efficiently, the ecological effects of these compounds is a preliminary task. The effects of two imidazolium based ionic liquids with different anions, 1-butyl-3-methylimidazolium tetrafluoroborate, [C 4 C 1 Im][BF 4 ], and 1-propyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, [C 3 C 1 Im][NTf 2 ], on seedling emergence of six tree species and on the microbial behaviour of two soils were determined in this work. Results showed that the highest doses of both ionic liquids caused the total inhibition of germination for almost all the species studied and that the seeds are more sensitive to the presence of these compounds than soil microbial activity. Nevertheless, signals of stress and death are observed from the results of heat released by microorganisms after the addition of the highest doses of both ionic liquids. The novelty of this work resides in the enlargement of knowledge of toxicity of ILs on complex organisms such as arboreal species and microbial activity of soils studied for the first time through a microcalorimetric technique. Copyright © 2017 Elsevier Ltd. All rights reserved.

Effects of Flavonoids on Rumen Fermentation Activity, Methane Production, and Microbial Population

PubMed Central

Abdullah, Norhani; Oskoueian, Armin

2013-01-01

This research was carried out to evaluate the effects of flavone, myricetin, naringin, catechin, rutin, quercetin, and kaempferol at the concentration of 4.5% of the substrate (dry matter basis) on the rumen microbial activity in vitro. Mixture of guinea grass and concentrate (60 : 40) was used as the substrate. The results showed that all the flavonoids except naringin and quercetin significantly (P < 0.05) decreased the dry matter degradability. The gas production significantly (P < 0.05) decreased by flavone, myricetin, and kaempferol, whereas naringin, rutin, and quercetin significantly (P < 0.05) increased the gas production. The flavonoids suppressed methane production significantly (P < 0.05). The total VFA concentration significantly (P < 0.05) decreased in the presence of flavone, myricetin, and kaempferol. All flavonoids except naringin and quercetin significantly (P < 0.05) reduced the carboxymethyl cellulase, filter paperase, xylanase, and β-glucosidase activities, purine content, and the efficiency of microbial protein synthesis. Flavone, myricetin, catechin, rutin, and kaempferol significantly (P < 0.05) reduced the population of rumen microbes. Total populations of protozoa and methanogens were significantly (P < 0.05) suppressed by naringin and quercetin. The results of this research demonstrated that naringin and quercetin at the concentration of 4.5% of the substrate (dry matter basis) were potential metabolites to suppress methane production without any negative effects on rumen microbial fermentation. PMID:24175289

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

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.

Mercury behaviour and C, N, and P biogeochemical cycles during ecological restoration processes of old mining sites in French Guiana.

PubMed

Couic, Ewan; Grimaldi, Michel; Alphonse, Vanessa; Balland-Bolou-Bi, Clarisse; Livet, Alexandre; Giusti-Miller, Stéphanie; Sarrazin, Max; Bousserrhine, Noureddine

2018-04-25

Several decades of gold mining extraction activities in the Amazonian rainforest have caused deforestation and pollution. While ecological rehabilitation is essential for restoring biodiversity and decreasing erosion on deforested lands, few studies note the behaviour or toxicity of trace elements during the rehabilitation process. Our original study focused on the potential use of microbial activity and Hg speciation and compared them with As, Cu, Zn and Cr speciation in assessing the chemical and biological quality of ecological restoration efforts. We sampled two sites in French Guyana 17 years after rehabilitation efforts began. The former site was actively regenerated (R) with the leguminous species Clitoria racemosa and Acacia mangium, and the second site was passively regenerated with spontaneous vegetation (Sv). We also sampled soil from a control site without a history of gold mining (F). We performed microcosm soil experiments for 30 days, where trace element speciation and enzyme activities (i.e., FDA, dehydrogenase, β-glucosidase, urease, alkaline and acid phosphatase) were estimated to characterise the behaviour of trace elements and the soil microbial activity. As bioindicators, the use of soil microbial carbon biomass and soil enzyme activities related to the carbon and phosphorus cycles seems to be relevant for assessing soil quality in rehabilitated and regenerated old mining sites. Our results showed that restoration with leguminous species had a positive effect on soil chemical quality and on soil microbial bioindicators, with activities that tended toward natural non-degraded soil (F). Active restoration processes also had a positive effect on Hg speciation by reducing its mobility. While in Sv we found more exchangeable and soluble mercury, in regenerated sites, Hg was mostly bound to organic matter. These results also suggested that enzyme activities and mercury cycles are sensitive to land restoration and must be considered when evaluating the efficiency of restoration processes.

Effects of temperature on microbial transformation of organic matter - comparing stories told by purified enzyme assays, chemostat experiments and soils

NASA Astrophysics Data System (ADS)

Lehmeier, C.; Min, K.; Good, H. J.; Billings, S. A.

2015-12-01

Temperature (T) is a major determinant of microbial decomposition of soil organic matter (SOM). Quantifying T responses of microbial C fluxes is crucial to improve predictions of SOM dynamics and atmospheric CO2 concentrations, but interpretation of experimental data is complicated by many properties inherent to soils. Comparing such data with complementary, reductionist experiments can help to identify basic mechanisms and interpret soil measurements. We quantified T effects on activity levels (i.e., rates of substrate cleavage) of microbial extracellular enzymes β-glucosidase (BGase) and β-N-acetyl glucosaminidase (NAGase), and on rates of CO2 efflux in soil incubations. We compare the results to those derived from purified enzyme assays, and to measurements of microbial respiration rates in continuous-flow chemostat culture in which a population of the soil bacterium Pseudomonas fluorescens was grown on medium with similar C:N ratio as the incubated SOM (10:1). Activity levels of both BGase and NAGase decreased by 80% between 25 and 5 °C. These T responses were higher than predictions from intrinsic (i.e., maximum) T responses in purified assays of BGase (minus 50%) and NAGase (minus 67%). This suggests that factors like physical access to substrate or reduced microbial production of enzymes constrained substrate decomposition rates in the soils relatively more at low than at high T. In chemostats, (mass-)specific bacterial respiration rate at T 14.5 °C was 50% of the rate observed at 26.5 °C; in contrast, CO2 efflux from the soil incubations decreased by only ~25% from 25 to 15 °C. The reason for this discrepancy can be manifold, including changes in microbial community composition, but results from ongoing measurements of microbial biomass in the soil samples will allow a closer comparison of these respiration rate responses. Our efforts highlight the significance of experimenting across scales and complexity for a better understanding of SOM dynamics.

Mining of Microbial Genomes for the Novel Sources of Nitrilases.

PubMed

Sharma, Nikhil; Thakur, Neerja; Raj, Tilak; Savitri; Bhalla, Tek Chand

2017-01-01

Next-generation DNA sequencing (NGS) has made it feasible to sequence large number of microbial genomes and advancements in computational biology have opened enormous opportunities to mine genome sequence data for novel genes and enzymes or their sources. In the present communication in silico mining of microbial genomes has been carried out to find novel sources of nitrilases. The sequences selected were analyzed for homology and considered for designing motifs. The manually designed motifs based on amino acid sequences of nitrilases were used to screen 2000 microbial genomes (translated to proteomes). This resulted in identification of one hundred thirty-eight putative/hypothetical sequences which could potentially code for nitrilase activity. In vitro validation of nine predicted sources of nitrilases was done for nitrile/cyanide hydrolyzing activity. Out of nine predicted nitrilases, Gluconacetobacter diazotrophicus , Sphingopyxis alaskensis , Saccharomonospora viridis , and Shimwellia blattae were specific for aliphatic nitriles, whereas nitrilases from Geodermatophilus obscurus , Nocardiopsis dassonvillei , Runella slithyformis , and Streptomyces albus possessed activity for aromatic nitriles. Flavobacterium indicum was specific towards potassium cyanide (KCN) which revealed the presence of nitrilase homolog, that is, cyanide dihydratase with no activity for either aliphatic, aromatic, or aryl nitriles. The present study reports the novel sources of nitrilases and cyanide dihydratase which were not reported hitherto by in silico or in vitro studies.

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

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

Relative changes in phosphatase activities as influenced by source and application rate of organic composts in field crops.

PubMed

Saha, Supradip; Mina, B L; Gopinath, K A; Kundu, S; Gupta, H S

2008-04-01

Potential impact of different levels and sources of organic composts on activities of phosphatases (acid and alkaline phosphatase, phosphodiesterase, and inorganic pyrophosphatase) was studied after three years of continuous application. Enzyme activities were compared with microbial biomass P and available P. Experimental plots were divided based on the organic source into three groups: those receiving farmyard manure (FYM), vermicompost (VC) and Lantana compost (LC). Microbial biomass P (11.7 g kg(-1) soil), available P (24.0 g kg(-1) soil) and acid phosphatase (1.3 mg g(-1) p-NP g(-1) soil h(-1)) was highest in highest dose of VC. Acid phosphatase activity was high in all plots, including those where microbial biomass P levels were low. Most of the phosphatase activities were significantly correlated with available P in FYM and VC. These relationships were negative for LC treatments. Results showed that application of earthworm casts is helpful in faster transformation of organic P by facilitating better environment to microbes and plant roots.

Climate shapes the protein abundance of dominant soil bacteria.

PubMed

Bastida, Felipe; Crowther, Tom W; Prieto, Iván; Routh, Devin; García, Carlos; Jehmlich, Nico

2018-05-28

Sensitive models of climate change impacts would require a better integration of multi-omics approaches that connect the abundance and activity of microbial populations. Here, we show that climate is a fundamental driver of the protein abundance of Actinobacteria, Planctomycetes and Proteobacteria, supporting the hypothesis that metabolic activity of some dominant phyla may be closely linked to climate. These results may improve our capacity to construct microbial models that better predict the impact of climate change in ecosystem processes. Copyright © 2018 Elsevier B.V. All rights reserved.

Processes of carbonate precipitation in modern microbial mats

NASA Astrophysics Data System (ADS)

Dupraz, Christophe; Reid, R. Pamela; Braissant, Olivier; Decho, Alan W.; Norman, R. Sean; Visscher, Pieter T.

2009-10-01

Microbial mats are ecosystems that arguably greatly affected the conditions of the biosphere on Earth through geological time. These laminated organosedimentary systems, which date back to > 3.4 Ga bp, are characterized by high metabolic rates, and coupled to this, rapid cycling of major elements on very small (mm-µm) scales. The activity of the mat communities has changed Earth's redox conditions (i.e. oxidation state) through oxygen and hydrogen production. Interpretation of fossil microbial mats and their potential role in alteration of the Earth's geochemical environment is challenging because these mats are generally not well preserved. Preservation of microbial mats in the fossil record can be enhanced through carbonate precipitation, resulting in the formation of lithified mats, or microbialites. Several types of microbially-mediated mineralization can be distinguished, including biologically-induced and biologically influenced mineralization. Biologically-induced mineralization results from the interaction between biological activity and the environment. Biologically-influenced mineralization is defined as passive mineralization of organic matter (biogenic or abiogenic in origin), whose properties influence crystal morphology and composition. We propose to use the term organomineralization sensu lato as an umbrella term encompassing biologically influenced and biologically induced mineralization. Key components of organomineralization sensu lato are the "alkalinity" engine (microbial metabolism and environmental conditions impacting the calcium carbonate saturation index) and an organic matrix comprised of extracellular polymeric substances (EPS), which may provide a template for carbonate nucleation. Here we review the specific role of microbes and the EPS matrix in various mineralization processes and discuss examples of modern aquatic (freshwater, marine and hypersaline) and terrestrial microbialites.

A trait-based framework for predicting when and where microbial adaptation to climate change will affect ecosystem functioning

USGS Publications Warehouse

Wallenstein, Matthew D.; Hall, Edward K.

2012-01-01

As the earth system changes in response to human activities, a critical objective is to predict how biogeochemical process rates (e.g. nitrification, decomposition) and ecosystem function (e.g. net ecosystem productivity) will change under future conditions. A particular challenge is that the microbial communities that drive many of these processes are capable of adapting to environmental change in ways that alter ecosystem functioning. Despite evidence that microbes can adapt to temperature, precipitation regimes, and redox fluctuations, microbial communities are typically not optimally adapted to their local environment. For example, temperature optima for growth and enzyme activity are often greater than in situ temperatures in their environment. Here we discuss fundamental constraints on microbial adaptation and suggest specific environments where microbial adaptation to climate change (or lack thereof) is most likely to alter ecosystem functioning. Our framework is based on two principal assumptions. First, there are fundamental ecological trade-offs in microbial community traits that occur across environmental gradients (in time and space). These trade-offs result in shifting of microbial function (e.g. ability to take up resources at low temperature) in response to adaptation of another trait (e.g. limiting maintenance respiration at high temperature). Second, the mechanism and level of microbial community adaptation to changing environmental parameters is a function of the potential rate of change in community composition relative to the rate of environmental change. Together, this framework provides a basis for developing testable predictions about how the rate and degree of microbial adaptation to climate change will alter biogeochemical processes in aquatic and terrestrial ecosystems across the planet.

Deterministic mechanisms define the long-term anaerobic digestion microbiome and its functionality regardless of the initial microbial community.

PubMed

Peces, M; Astals, S; Jensen, P D; Clarke, W P

2018-05-17

The impact of the starting inoculum on long-term anaerobic digestion performance, process functionality and microbial community composition remains unclear. To understand the impact of starting inoculum, active microbial communities from four different full-scale anaerobic digesters were each used to inoculate four continuous lab-scale anaerobic digesters, which were operated identically for 295 days. Digesters were operated at 15 days solid retention time, an organic loading rate of 1 g COD L r -1 d -1 (75:25 - cellulose:casein) and 37 °C. Results showed that long-term process performance, metabolic rates (hydrolytic, acetogenic, and methanogenic) and microbial community are independent of the inoculum source. Digesters process performance converged after 80 days, while metabolic rates and microbial communities converged after 120-145 days. The convergence of the different microbial communities towards a core-community proves that the deterministic factors (process operational conditions) were a stronger driver than the initial microbial community composition. Indeed, the core-community represented 72% of the relative abundance among the four digesters. Moreover, a number of positive correlations were observed between higher metabolic rates and the relative abundance of specific microbial groups. These correlations showed that both substrate consumers and suppliers trigger higher metabolic rates, expanding the knowledge of the nexus between microorganisms and functionality. Overall, these results support that deterministic factors control microbial communities in bioreactors independently of the inoculum source. Hence, it seems plausible that a desired microbial composition and functionality can be achieved by tuning process operational conditions. Copyright © 2018. Published by Elsevier Ltd.

Phosphorus cycling in natural and low input soil/plant systems: the role of soil microorganisms

NASA Astrophysics Data System (ADS)

Tamburini, F.; Bünemann, E. K.; Oberson, A.; Bernasconi, S. M.; Frossard, E.

2011-12-01

Availability of phosphorus (as orthophosphate, Pi) limits biological production in many terrestrial ecosystems. During the first phase of soil development, weathering of minerals and leaching of Pi are the processes controlling Pi concentrations in the soil solution, while in mature soils, Pi is made available by desorption of mineral Pi and mineralization of organic compounds. In agricultural soils additional Pi is supplied by fertilization, either with mineral P and/or organic inputs (animal manure or plant residues). Soil microorganisms (bacteria and fungi) mediate several processes, which are central to the availability of Pi to plants. They play a role in the initial release of Pi from the mineral phase, and through extracellular phosphatase enzymes, they decompose and mineralize organic compounds, releasing Pi. On the other hand, microbial immobilization and internal turnover of Pi can decrease the soil available Pi pool, competing in this way with plants. Using radio- and stable isotopic approaches, we show evidence from different soil/plant systems which points to the central role of the microbial activity. In the presented case studies, P contained in the soil microbial biomass is a larger pool than available Pi. In a soil chronosequence after deglaciation, stable isotopes of oxygen associated to phosphate showed that even in the youngest soils microbial activity highly impacted the isotopic signature of available Pi. These results suggested that microorganisms were rapidly taking up and cycling Pi, using it to sustain their community. Microbial P turnover time was faster in the young (about 20 days) than in older soils (about 120 days), reflecting a different functioning of the microbial community. Microbial community crashes, caused by drying/rewetting and freezing/thawing cycles, were most likely responsible for microbial P release to the available P pool. In grassland fertilization experiments with mineral NK and NPK amendments, microbial P turnover was faster in the P-free treatment. Laboratory incubation also showed a more rapid P uptake by microbial biomass in the NK than in the NPK treatment (37% and 6% of added 33P recovered in microbial P after 100 minutes in NK and NPK, respectively). The seasonal microbial P flux in both treatments was 1.5-4 times larger than the annual plant P uptake. In field studies carried out on highly weathered low P soils in Colombia, the comparison between grass-legume and grass-only pastures showed that the presence of legumes had an impact on the overall biological activity. In fact, microbial biomass and phosphatase activity were significantly larger in grass-legume pastures than in the legume-free experiments. Larger release of Pi from the organic P pool improved P availability to plants and pointed at a modified C:N:P stoichiometry along pathways of the nutrient cycle in the soil/plant system. All these data are evidence of a highly dynamic microbial P pool, which controls Pi concentration and, hence, availability for plants in natural and low input agricultural ecosystems.

Representation of Dormant and Active Microbial Dynamics for Ecosystem Modeling

NASA Astrophysics Data System (ADS)

Wang, G.; Mayes, M. A.; Gu, L.; Schadt, C. W.

2013-12-01

Experimental observations and modeling efforts have shown that dormancy is likely a common strategy for microorganisms to contend with environmental stress. We review the state-of-the-art in modeling approaches for microbial dormancy and discuss the rationales of these models. We proved that the physiological state index model is not appropriate for describing transformation between active and dormant states. Based on the generally accepted assumptions summarized from ten existing models, we postulated a new synthetic microbial physiology component within the Microbial-ENzyme-mediated Decomposition (MEND) model. Both the steady state active fraction (rss) and substrate saturation level (Øss) positively depend on two physiological indices: α and β. The index α = mR /(μG+ mR), where μG and mR represent the maximum specific growth and maintenance rates, respectively, for active microbes. β denotes the ratio of dormant to active maintenance rate. The rss equals to Øss only under the condition of β→0, and they are identical to α. When substrate availability is the only limiting factor, the maximum rss is ca. 0.5 with α≤0.5 and β ≤0.01. This threshold value (0.5) of rss (not dynamic r) can explain the low active microbial fractions observed in undisturbed soils. The applications of the improved model to a 14C-labeled glucose induced respiration dataset and a batch experimental dataset show satisfactory model performance. We found that the exponential growth respiration rates can only be used to determine μG and initial active microbial biomass (Ba0), thus we suggest using respiration data representing both exponential growth and non-accelerating phases to robustly determine other important parameters such as initial total live microbial biomass (B0), initial active fraction (r0), μG, α, and the half-saturation constant (Ks). Similar improved representations of microbial physiology should be incorporated into existing ecosystem models in order to account for the significance of dormancy in microbially-mediated processes.

In situ Detection of Microbial Life in the Deep Biosphere in Igneous Ocean Crust

PubMed Central

Salas, Everett C.; Bhartia, Rohit; Anderson, Louise; Hug, William F.; Reid, Ray D.; Iturrino, Gerardo; Edwards, Katrina J.

2015-01-01

The deep biosphere is a major frontier to science. Recent studies have shown the presence and activity of cells in deep marine sediments and in the continental deep biosphere. Volcanic lavas in the deep ocean subsurface, through which substantial fluid flow occurs, present another potentially massive deep biosphere. We present results from the deployment of a novel in situ logging tool designed to detect microbial life harbored in a deep, native, borehole environment within igneous oceanic crust, using deep ultraviolet native fluorescence spectroscopy. Results demonstrate the predominance of microbial-like signatures within the borehole environment, with densities in the range of 105 cells/mL. Based on transport and flux models, we estimate that such a concentration of microbial cells could not be supported by transport through the crust, suggesting in situ growth of these communities. PMID:26617595

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

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.

Active Microbial Communities Inhabit Sulphate-Methane Interphase in Deep Bedrock Fracture Fluids in Olkiluoto, Finland

PubMed Central

Bomberg, Malin; Nyyssönen, Mari; Pitkänen, Petteri; Lehtinen, Anne; Itävaara, Merja

2015-01-01

Active microbial communities of deep crystalline bedrock fracture water were investigated from seven different boreholes in Olkiluoto (Western Finland) using bacterial and archaeal 16S rRNA, dsrB, and mcrA gene transcript targeted 454 pyrosequencing. Over a depth range of 296–798 m below ground surface the microbial communities changed according to depth, salinity gradient, and sulphate and methane concentrations. The highest bacterial diversity was observed in the sulphate-methane mixing zone (SMMZ) at 250–350 m depth, whereas archaeal diversity was highest in the lowest boundaries of the SMMZ. Sulphide-oxidizing ε-proteobacteria (Sulfurimonas sp.) dominated in the SMMZ and γ-proteobacteria (Pseudomonas spp.) below the SMMZ. The active archaeal communities consisted mostly of ANME-2D and Thermoplasmatales groups, although Methermicoccaceae, Methanobacteriaceae, and Thermoplasmatales (SAGMEG, TMG) were more common at 415–559 m depth. Typical indicator microorganisms for sulphate-methane transition zones in marine sediments, such as ANME-1 archaea, α-, β- and δ-proteobacteria, JS1, Actinomycetes, Planctomycetes, Chloroflexi, and MBGB Crenarchaeota were detected at specific depths. DsrB genes were most numerous and most actively transcribed in the SMMZ while the mcrA gene concentration was highest in the deep methane rich groundwater. Our results demonstrate that active and highly diverse but sparse and stratified microbial communities inhabit the Fennoscandian deep bedrock ecosystems. PMID:26425566

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

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.

Microbial community functional structures in wastewater treatment plants as characterized by GeoChip.

PubMed

Wang, Xiaohui; Xia, Yu; Wen, Xianghua; Yang, Yunfeng; Zhou, Jizhong

2014-01-01

Biological WWTPs must be functionally stable to continuously and steadily remove contaminants which rely upon the activity of complex microbial communities. However, knowledge is still lacking in regard to microbial community functional structures and their linkages to environmental variables. To investigate microbial community functional structures of activated sludge in wastewater treatment plants (WWTPs) and to understand the effects of environmental factors on their structure. 12 activated sludge samples were collected from four WWTPs in Beijing. A comprehensive functional gene array named GeoChip 4.2 was used to determine the microbial functional genes involved in a variety of biogeochemical processes such as carbon, nitrogen, phosphorous and sulfur cycles, metal resistance, antibiotic resistance and organic contaminant degradation. High similarities of the microbial community functional structures were found among activated sludge samples from the four WWTPs, as shown by both diversity indices and the overlapped genes. For individual gene category, such as egl, amyA, lip, nirS, nirK, nosZ, ureC, ppx, ppk, aprA, dsrA, sox and benAB, there were a number of microorganisms shared by all 12 samples. Canonical correspondence analysis (CCA) showed that the microbial functional patterns were highly correlated with water temperature, dissolved oxygen (DO), ammonia concentrations and loading rate of chemical oxygen demand (COD). Based on the variance partitioning analyses (VPA), a total of 53% of microbial community variation from GeoChip data can be explained by wastewater characteristics (25%) and operational parameters (23%), respectively. This study provided an overall picture of microbial community functional structures of activated sludge in WWTPs and discerned the linkages between microbial communities and environmental variables in WWTPs.

Towards a rapid and comprehensive microbial detection and identification system for life support and planetary protection applications

NASA Astrophysics Data System (ADS)

Lasseur, Christophe

Long term manned missions of our Russian colleagues have demonstrated the risks associated with microbial contamination. These risks concern both crew health via the metabolic consumables contamination (water, air,.) but and also the hardware degradation. In parallel to these life support issues, planetary protection experts have agreed to place clear specifications of the microbial quality of future hardware landing on extraterrestrial planets as well as elaborate the requirements of contamination for manned missions on surface. For these activities, it is necessary to have a better understanding of microbial activity, to create culture collections and to develop on-line detection tools. . In this respect, over the last 6 years , ESA has supported active scientific research on the choice of critical genes and functions, including those linked to horizontal gene pool of bacteria and its dissemination. In parallel, ESA and European industries have been developing an automated instrument for rapid microbial detection on air and surface samples. Within this paper, we first present the life support and planetary protection requirements, and the state of the art of the instrument development. Preliminary results at breadboard level, including a mock-up view of the final instrument are also presented. Finally, the remaining steps required to reach a functional instrument for planetary hardware integration and life support flight hardware are also presented.

Tracking Dynamics of Plant Biomass Composting by Changes in Substrate Structure, Microbial Community, and Enzyme Activity

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

Wei, H.; Tucker, M. P.; Baker, J. O.

2012-04-01

Understanding the dynamics of the microbial communities that, along with their secreted enzymes, are involved in the natural process of biomass composting may hold the key to breaking the major bottleneck in biomass-to-biofuels conversion technology, which is the still-costly deconstruction of polymeric biomass carbohydrates to fermentable sugars. However, the complexity of both the structure of plant biomass and its counterpart microbial degradation communities makes it difficult to investigate the composting process. In this study, a composter was set up with a mix of yellow poplar (Liriodendron tulipifera) wood-chips and mown lawn grass clippings (85:15 in dry-weight) and used as amore » model system. The microbial rDNA abundance data obtained from analyzing weekly-withdrawn composted samples suggested population-shifts from bacteria-dominated to fungus-dominated communities. Further analyses by an array of optical microscopic, transcriptional and enzyme-activity techniques yielded correlated results, suggesting that such population shifts occurred along with early removal of hemicellulose followed by attack on the consequently uncovered cellulose as the composting progressed. The observed shifts in dominance by representative microbial groups, along with the observed different patterns in the gene expression and enzymatic activities between cellulases, hemicellulases, and ligninases during the composting process, provide new perspectives for biomass-derived biotechnology such as consolidated bioprocessing (CBP) and solid-state fermentation for the production of cellulolytic enzymes and biofuels.« less

[Effects of intercropping Chinese milk vetch on functional characteristics of soil microbial community in rape rhizosphere].

PubMed

Zhou, Quan; Wang, Long Chang; Xing, Yi; Ma, Shu Min; Zhang, Xiao Duan; Chen, Jiao; Shi, Chao

2018-03-01

The application of green manure is facing serious problems in purple soil region of southwest China. With the aim to explore the potential application of green manure, we examined the functional characteristics of soil microbial community in a system of Chinese milk vetch intercropped with rape. The innovations are the application of Chinese milk vetch in dry land of the southwest China and the establishment of new planting pattern of rape by providing empirical data. Results showed that the intercropping with Chinese milk vetch decreased the carbon resource use efficiency of microbial community in rape rhizosphere, especially for the utilization of carbohydrates. At the same time, Shannon index, Simpson index, and richness were reduced, but evenness index was increased by intercropping. Those results from cluster analysis and principal component analysis suggest that the soil microbial community composition was significantly different between monocropping and intercropping. The carbohydrates, amino acids and carboxylic acids were the sensitive carbon sources for differentiating the changes of the microbial community induced by monocropping and intercropping. Intercropping Chinese milk vetch could decrease functional activity, change community composition, and reduce diversity of soil microbial community in rape rhizosphere.

Conversion of Uric Acid into Ammonium in Oil-Degrading Marine Microbial Communities: a Possible Role of Halomonads.

PubMed

Gertler, Christoph; Bargiela, Rafael; Mapelli, Francesca; Han, Xifang; Chen, Jianwei; Hai, Tran; Amer, Ranya A; Mahjoubi, Mouna; Malkawi, Hanan; Magagnini, Mirko; Cherif, Ameur; Abdel-Fattah, Yasser R; Kalogerakis, Nicolas; Daffonchio, Daniele; Ferrer, Manuel; Golyshin, Peter N

2015-10-01

Uric acid is a promising hydrophobic nitrogen source for biostimulation of microbial activities in oil-impacted marine environments. This study investigated metabolic processes and microbial community changes in a series of microcosms using sediment from the Mediterranean and the Red Sea amended with ammonium and uric acid. Respiration, emulsification, ammonium and protein concentration measurements suggested a rapid production of ammonium from uric acid accompanied by the development of microbial communities containing hydrocarbonoclastic bacteria after 3 weeks of incubation. About 80 % of uric acid was converted to ammonium within the first few days of the experiment. Microbial population dynamics were investigated by Ribosomal Intergenic Spacer Analysis and Illumina sequencing as well as by culture-based techniques. Resulting data indicated that strains related to Halomonas spp. converted uric acid into ammonium, which stimulated growth of microbial consortia dominated by Alcanivorax spp. and Pseudomonas spp. Several strains of Halomonas spp. were isolated on uric acid as the sole carbon source showed location specificity. These results point towards a possible role of halomonads in the conversion of uric acid to ammonium utilized by hydrocarbonoclastic bacteria.

Changes in land use driven by urbanization impact nitrogen cycling and the microbial community composition in soils

NASA Astrophysics Data System (ADS)

Wang, Haitao; Marshall, Christopher W.; Cheng, Minying; Xu, Huijuan; Li, Hu; Yang, Xiaoru; Zheng, Tianling

2017-03-01

Transition of populations from rural to urban living causes landscape changes and alters the functionality of soil ecosystems. It is unclear how this urbanization disturbs the microbial ecology of soils and how the disruption influences nitrogen cycling. In this study, microbial communities in turfgrass-grown soils from urban and suburban areas around Xiamen City were compared to microbial communities in the soils from rural farmlands. The potential N2O emissions, potential denitrification activity, and abundances of denitrifiers were higher in the rural farmland soils compared with the turfgrass soils. Ammonia oxidizing archaea (AOA) were more abundant than ammonia oxidizing bacteria (AOB) in turfgrass soils. Within turfgrass soils, the potential nitrification activities and AOA abundances were higher in the urban than in the suburban soils. These results indicate a more pivotal role of AOA in nitrification, especially in urban soils. Microbial community composition was distinctly grouped along urbanization categories (urban, suburban, and rural) classified according to the population density, which can in part be attributed to the differences in soil properties. These observed changes could potentially have a broader impact on soil nutrient availability and greenhouse gas emissions.

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

Input related microbial carbon dynamic of soil organic matter in particle size fractions

NASA Astrophysics Data System (ADS)

Gude, A.; Kandeler, E.; Gleixner, G.

2012-04-01

This paper investigated the flow of carbon into different groups of soil microorganisms isolated from different particle size fractions. Two agricultural sites of contrasting organic matter input were compared. Both soils had been submitted to vegetation change from C3 (Rye/Wheat) to C4 (Maize) plants, 25 and 45 years ago. Soil carbon was separated into one fast-degrading particulate organic matter fraction (POM) and one slow-degrading organo-mineral fraction (OMF). The structure of the soil microbial community were investigated using phospholipid fatty acids (PLFA), and turnover of single PLFAs was calculated from the changes in their 13C content. Soil enzyme activities involved in the degradation of carbohydrates was determined using fluorogenic MUF (methyl-umbelliferryl phosphate) substrates. We found that fresh organic matter input drives soil organic matter dynamic. Higher annual input of fresh organic matter resulted in a higher amount of fungal biomass in the POM-fraction and shorter mean residence times. Fungal activity therefore seems essential for the decomposition and incorporation of organic matter input into the soil. As a consequence, limited litter input changed especially the fungal community favouring arbuscular mycorrhizal fungi. Altogether, supply and availability of fresh plant carbon changed the distribution of microbial biomass, the microbial community structure and enzyme activities and resulted in different priming of soil organic matter. Most interestingly we found that only at low input the OMF fraction had significantly higher calculated MRT for Gram-positive and Gram-negative bacteria suggesting high recycling of soil carbon or the use of other carbon sources. But on average all microbial groups had nearly similar carbon uptake rates in all fractions and both soils, which contrasted the turnover times of bulk carbon. Hereby the microbial carbon turnover was always faster than the soil organic carbon turnover and higher carbon input reduced the carbon storage efficiency from 51 % in the low input to 20 %. These findings suggest that microbial community preferentially assimilated fresh carbon sources but also used recycled existing soil carbon. However, the priming rate was drastically reduced under carbon limitation. In consequence at high carbon availability more carbon was respired to activate the existing soil carbon (priming) whereas at low carbon availability new soil carbon was formed at higher efficiencies.

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.

Effect of salinity tolerant PDH45 transgenic rice on physicochemical properties, enzymatic activities and microbial communities of rhizosphere soils

PubMed Central

Sahoo, Ranjan Kumar; Tuteja, Narendra

2013-01-01

The effect of genetically modified (GM) plants on environment is now major concern worldwide. The plant roots of rhizosphere soil interact with variety of bacteria which could be influenced by the transgene in GM plants. The antibiotic resistance genes in GM plants may be transferred to soil microbes. In this study we have examined the effect of overexpression of salinity tolerant pea DNA helicase 45 (PDH45) gene on microbes and enzymatic activities in the rhizosphere soil of transgenic rice IR64 in presence and absence of salt stress in two different rhizospheric soils (New Delhi and Odisha, India). The diversity of the microbial community and soil enzymes viz., dehydrogenase, alkaline phosphatase, urease and nitrate reductase was assessed. The results revealed that there was no significant effect of transgene expression on rhizosphere soil of the rice plants. The isolated bacteria were phenotyped both in absence and presence of salt and no significant changes were found in their phenotypic characters as well as in their population. Overall, the overexpression of PDH45 in rice did not cause detectable changes in the microbial population, soil enzymatic activities and functional diversity of the rhizosphere soil microbial community. PMID:23733066

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.

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 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

Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions.

PubMed

Yu, Chaowei; Reddy, Amitha P; Simmons, Christopher W; Simmons, Blake A; Singer, Steven W; VanderGheynst, Jean S

2015-01-01

Microbial communities enriched from diverse environments have shown considerable promise for the targeted discovery of microorganisms and enzymes for bioconversion of lignocellulose to liquid fuels. While preservation of microbial communities is important for commercialization and research, few studies have examined storage conditions ideal for preservation. The goal of this study was to evaluate the impact of preservation method on composition of microbial communities enriched on switchgrass before and after storage. The enrichments were completed in a high-solid and aerobic environment at 55 °C. Community composition was examined for each enrichment to determine when a stable community was achieved. Preservation methods included cryopreservation with the cryoprotective agents DMSO and glycerol, and cryopreservation without cryoprotective agents. Revived communities were examined for their ability to decompose switchgrass under high-solid and thermophilic conditions. High-throughput 16S rRNA gene sequencing of DNA extracted from enrichment samples showed that the majority of the shift in composition of the switchgrass-degrading community occurred during the initial three 2-week enrichments. Shifts in community structure upon storage occurred in all cryopreserved samples. Storage in liquid nitrogen in the absence of cryoprotectant resulted in variable preservation of dominant microorganisms in enriched samples. Cryopreservation with either DMSO or glycerol provided consistent and equivalent preservation of dominant organisms. A stable switchgrass-degrading microbial community was achieved after three 2-week enrichments. Dominant microorganisms were preserved equally well with DMSO and glycerol. DMSO-preserved communities required more incubation time upon revival to achieve pre-storage activity levels during high-solid thermophilic cultivation on switchgrass. Despite shifts in the community with storage, the samples were active upon revival under thermophilic and high-solid conditions. The results suggest that the presence of microorganisms may be more important than their relative abundance in retaining an active microbial community.

Relative contributions of mercury bioavailability and microbial growth rate on net methylmercury production by anaerobic mixed cultures

DOE PAGES

Kucharzyk, Katarzyna H.; Deshusses, Marc A.; Porter, Kaitlyn A.; ...

2015-07-17

Monomethylmercury (MeHg) is produced in many aquatic environments by anaerobic microorganisms that take up and methylate inorganic forms of Hg(II). Net methylation of Hg(II) appears to be correlated with factors that affect the activity of the anaerobic microbial community and factors that increase the bioavailability of Hg(II) to these organisms. However, the relative importance of one versus the other is difficult to elucidate even though this information can greatly assist remediation efforts and risk assessments. Here in this study, we investigated the effects of Hg speciation (dissolved Hg and nanoparticulate HgS) and microbial activity on the net production of MeHgmore » using two mixed microbial cultures that were enriched from marine sediments under sulfate reducing conditions. The cultures were amended with dissolved Hg (added as a dissolved nitrate salt) and nanoparticulate HgS, and grown under different carbon substrate concentrations. The results indicated that net mercury methylation was the highest for cultures incubated in the greatest carbon substrate concentration (60 mM) compared to incubations with less carbon (0.6 and 6 mM), regardless of the form of mercury amended. Net MeHg production in cultures exposed to HgS nanoparticles was significantly slower than in cultures exposed to dissolved Hg; however, the difference diminished with slower growing cultures with low carbon addition (0.6 mM). The net Hg methylation rate was found to correlate with sulfate reduction rate in cultures exposed to dissolved Hg, while methylation rate was roughly constant for cultures exposed to nanoparticulate HgS. These results indicated a potential threshold of microbial productivity: below this point net MeHg production was limited by microbial activity, regardless of Hg bioavailability. Lastly, above this threshold of productivity, Hg speciation became a contributing factor towards net MeHg production.« less

Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions

DOE PAGES

Yu, Chaowei; Reddy, Amitha P.; Simmons, Christopher W.; ...

2015-12-02

Microbial communities enriched from diverse environments have shown considerable promise for the targeted discovery of microorganisms and enzymes for bioconversion of lignocellulose to liquid fuels. While preservation of microbial communities is important for commercialization and research, few studies have examined storage conditions ideal for preservation. The goal of this study was to evaluate the impact of preservation method on composition of microbial communities enriched on switchgrass before and after storage. The enrichments were completed in a high-solid and aerobic environment at 55 °C. Community composition was examined for each enrichment to determine when a stable community was achieved. Preservation methodsmore » included cryopreservation with the cryoprotective agents DMSO and glycerol, and cryopreservation without cryoprotective agents. Revived communities were examined for their ability to decompose switchgrass under high-solid and thermophilic conditions. High-throughput 16S rRNA gene sequencing of DNA extracted from enrichment samples showed that the majority of the shift in composition of the switchgrass-degrading community occurred during the initial three 2-week enrichments. Shifts in community structure upon storage occurred in all cryopreserved samples. Storage in liquid nitrogen in the absence of cryoprotectant resulted in variable preservation of dominant microorganisms in enriched samples. Cryopreservation with either DMSO or glycerol provided consistent and equivalent preservation of dominant organisms. In conclusion, a stable switchgrass-degrading microbial community was achieved after three 2-week enrichments. Dominant microorganisms were preserved equally well with DMSO and glycerol. DMSO-preserved communities required more incubation time upon revival to achieve pre-storage activity levels during high-solid thermophilic cultivation on switchgrass. Despite shifts in the community with storage, the samples were active upon revival under thermophilic and high-solid conditions. The results suggest that the presence of microorganisms may be more important than their relative abundance in retaining an active microbial community.« less

Physiological Ecology of Microorganisms in Subglacial Lake Whillans

PubMed Central

Vick-Majors, Trista J.; Mitchell, Andrew C.; Achberger, Amanda M.; Christner, Brent C.; Dore, John E.; Michaud, Alexander B.; Mikucki, Jill A.; Purcell, Alicia M.; Skidmore, Mark L.; Priscu, John C.

2016-01-01

Subglacial microbial habitats are widespread in glaciated regions of our planet. Some of these environments have been isolated from the atmosphere and from sunlight for many thousands of years. Consequently, ecosystem processes must rely on energy gained from the oxidation of inorganic substrates or detrital organic matter. Subglacial Lake Whillans (SLW) is one of more than 400 subglacial lakes known to exist under the Antarctic ice sheet; however, little is known about microbial physiology and energetics in these systems. When it was sampled through its 800 m thick ice cover in 2013, the SLW water column was shallow (~2 m deep), oxygenated, and possessed sufficient concentrations of C, N, and P substrates to support microbial growth. Here, we use a combination of physiological assays and models to assess the energetics of microbial life in SLW. In general, SLW microorganisms grew slowly in this energy-limited environment. Heterotrophic cellular carbon turnover times, calculated from 3H-thymidine and 3H-leucine incorporation rates, were long (60 to 500 days) while cellular doubling times averaged 196 days. Inferred growth rates (average ~0.006 d−1) obtained from the same incubations were at least an order of magnitude lower than those measured in Antarctic surface lakes and oligotrophic areas of the ocean. Low growth efficiency (8%) indicated that heterotrophic populations in SLW partition a majority of their carbon demand to cellular maintenance rather than growth. Chemoautotrophic CO2-fixation exceeded heterotrophic organic C-demand by a factor of ~1.5. Aerobic respiratory activity associated with heterotrophic and chemoautotrophic metabolism surpassed the estimated supply of oxygen to SLW, implying that microbial activity could deplete the oxygenated waters, resulting in anoxia. We used thermodynamic calculations to examine the biogeochemical and energetic consequences of environmentally imposed switching between aerobic and anaerobic metabolisms in the SLW water column. Heterotrophic metabolisms utilizing acetate and formate as electron donors yielded less energy than chemolithotrophic metabolisms when calculated in terms of energy density, which supports experimental results that showed chemoautotrophic activity in excess of heterotrophic activity. The microbial communities of subglacial lake ecosystems provide important natural laboratories to study the physiological and biogeochemical behavior of microorganisms inhabiting cold, dark environments. PMID:27833599

Geochemical bioenergetics during low-temperature serpentinization: An example from the Samail ophiolite, Sultanate of Oman

NASA Astrophysics Data System (ADS)

Canovas, Peter A.; Hoehler, Tori; Shock, Everett L.

2017-07-01

Various classes of microbial and biomolecular evidence from global studies in marine and continental settings are used to identify a set of reactions that appear to support microbial metabolism during serpentinization of ultramafic rocks. Geochemical data from serpentinizing ecosystems in the Samail ophiolite of Oman are used to evaluate the extent of disequilibria that can support this set of microbial metabolisms and to provide a ranking of potential metabolic energy sources in hyperalkaline fluids that are direct products of serpentinization. Results are used to construct hypotheses for how microbial metabolism may be supported in the subsurface for two cases: ecosystems hosted in rocks that have already undergone significant serpentinization and those hosted by deeper, active serpentinization processes.

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.

Microbial Source Tracking: Current and Future Molecular Tools in Microbial Water Quality Forensics

EPA Science Inventory

Current regulations in the United States stipulate that the microbial quality of waters used for consumption and recreational activities should be determined regularly by measuring microbial indicators of fecal pollution. Hence, the microbial risk associated with these waters is...

Comparative Evaluation of Raw and Ripe Fruits of Forsythia suspensa by HPLC-ESI-MS/MS Analysis and Anti-Microbial Assay.

PubMed

Qu, Jialin; Yan, Xinjia; Li, Chunyan; Wen, Jing; Lu, Chongning; Ren, Jungang; Peng, Ying; Song, Shaojiang

2017-04-01

A multi-component quantification fingerprint based on high-performance liquid chromatography coupled with electrospray ionization tandem mass spectrometry technique has been established for the comparative analysis of raw and ripe fruits of Forsythia suspensa originated from different provinces. Eighteen bioactive constituents including three phenylethanoid glycosides derivatives, six phenolic acids, three flavonoids, four phenylpropanoids, one fatty acid and one terpenoid were identified and quantified. Total contents of phenylethanoid glycosides, phenylpropanoids and flavonoids from raw samples were found much higher than those from ripe samples, while total content of phenolic acids showed a contrary tendency. Moreover, the anti-microbial activities were comparatively assayed for the first time using five different bacterial strains. Results revealed a positive relationship between contents of total phenolic and anti-microbial activity. The results obtained in the present study may provide useful information for future utilization of F. suspensa. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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

Mapping and determinism of soil microbial community distribution across an agricultural landscape.

PubMed

Constancias, Florentin; Terrat, Sébastien; Saby, Nicolas P A; Horrigue, Walid; Villerd, Jean; Guillemin, Jean-Philippe; Biju-Duval, Luc; Nowak, Virginie; Dequiedt, Samuel; Ranjard, Lionel; Chemidlin Prévost-Bouré, Nicolas

2015-06-01

Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13 km². Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured distribution of microbial biomass and diversity with patches of several hundreds of meters. Variance partitioning revealed that both microbial abundance and bacterial diversity distribution were highly dependent of soil properties and land use (total variance explained ranged between 55% and 78%). Microbial biomass and bacterial richness distributions were mainly explained by soil pH and texture whereas bacterial evenness distribution was mainly related to land management. Bacterial diversity (richness, evenness, and Shannon index) was positively influenced by cropping intensity and especially by soil tillage, resulting in spots of low microbial diversity in soils under forest management. Spatial descriptors also explained a small but significant portion of the microbial distribution suggesting that landscape configuration also shapes microbial biomass and bacterial diversity. © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Microbial community structure and activity in a Colorado Rocky Mountain forest soil scarred by slash pile burning

Treesearch

Aida E. Jimenez Esquilin; Mary E. Stromberger; William J. Massman; John M. Frank; Wayne D. Shepperd

2007-01-01

Tree thinning and harvesting produces large amounts of slash material which are typically disposed of by burning, often resulting in severe soil heating. We measured soil chemical properties and microbial community structure and function over time to determine effects of slash pile burning in a ponderosa pine forest soil. Real time data were collected for soil...

Microbial production of epoxides

DOEpatents

Clark, Thomas R.; Roberto, Francisco F.

2003-06-10

A method for microbial production of epoxides and other oxygenated products is disclosed. The method uses a biocatalyst of methanotrophic bacteria cultured in a biphasic medium containing a major amount of a non-aqueous polar solvent. Regeneration of reducing equivalents is carried out by using endogenous hydrogenase activity together with supplied hydrogen gas. This method is especially effective with gaseous substrates and cofactors that result in liquid products.

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.

Methanogenic community composition in an organic waste mixture in an anaerobic bioreactor

NASA Astrophysics Data System (ADS)

Gryta, Agata; Oszust, Karolina; Brzezińska, Małgorzata; Ziemiński, Krzysztof; Bilińska-Wielgus, Nina; Frąc, Magdalena

2017-07-01

The aim of the study was to elucidate the substantial relationship between the compositions of methanogen community that assembles in the anaerobic digester mass and link it to methane production activity. The results of the metagenomic studies were used to evaluate how the methanogen structure changes during an anaerobic digestion process under various waste retention times (21, 23, 25, 29, 33, 39, 47 and 61 days). Phylogenetically coherent populations of methanogens were assessed by 16S rRNA gene next-generation sequencing and terminal restriction fragment length polymorphism fingerprinting of a specific molecular marker, the mcrA gene. The results indicated multiple phylogenetically diverse methanogen populations associated with the various steps of anaerobic digestion. The stages of the anaerobic digestion process and waste retention times determine the microbial composition. The most dominant and acclimated microbial communities in all samples belonged to the genera Methanosaeta and Methanobacterium. The methane yield was consistent with the results of the microbial community structure, which indicated that acetotrophic Methanosaeta was the most active and most important during the methanogenic stage.

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.

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.

[The relationship between abiotic factors and microbial activities of microbial eco-system in contaminated soil with petroleum hydrocarbons].

PubMed

Jia, Jian-li; Li, Guang-he; Zhong, Yi

2004-05-01

By means of the biostimulation and bioaugmentation in the micro-ecological environment of contaminated soil with petrochemical hydrocarbons, the biodegradation rates and mode of the contaminants were significantly improved. Based on the investigations carried out in some oilfields and petrochemical industrial area of Northern China, the relationship between the abiotic factors such as nutrient, pH, contaminants, water content, alkalinity, etc., and microbial activities was interpreted and identified in this paper. The results from the investigations and indoor and in-situ experiments conducted recent years indicated that the soils in the areas, to the extent, have been polluted by the different kinds of organic compounds composed of monoaromatic benzene, PAHs, chlorinated solvent, and alkanes, and the concentrations of the compounds mostly were elevated as compared to the background, with the highest 34,000 mg/kg dry soil. The column chromatography analysis results showed that the alkyl and aromatic compounds were accounted for more than 50% of the total hydrocarbon contents, which was readily degraded by degrading bacteria and improved the degrading microbe activities. The effective nitrogen and phosphorus encountered in the soil was less than 30 mg/kg dry soil and 10 mg/kg dry soil, only about 5% of total contents of them respectively. Based on the stoichiometric calculation and reasonable ratio of carbon to nutrient content regarding the biodegradation of organic compounds, the nutrient levels mainly composed of nitrogen and phosphorus in polluted soil as importantly limiting factors to degrading bacterial growth and activity were insufficient to the biodegradation of petrochemicals, and it is needed to add the nutrient for the bioremediation of contaminated soil. It is undoubted that the optimization of abiotic factors play significant role in increasing the microbial activity and improving the biodegradation rates.

Using Nitrogen Limiting Growth Conditions to Remove Atrazine from Groundwater: Laboratory Studies

USDA-ARS?s Scientific Manuscript database

In the past microbial redox reactions have been the driving mechanism behind in situ bioremediations that use a carbon substrate. This is because subsurface microbial activity is generally restricted by electron (e-) donor availability and microbial activity, growth and respiration, can be stimulat...

Solar energy powered microbial fuel cell with a reversible bioelectrode.

PubMed

Strik, David P B T B; Hamelers, Hubertus V M; Buisman, Cees J N

2010-01-01

The solar energy powered microbial fuel cell is an emerging technology for electricity generation via electrochemically active microorganisms fueled by solar energy via in situ photosynthesized metabolites from algae, cyanobacteria, or living higher plants. A general problem with microbial fuel cells is the pH membrane gradient which reduces cell voltage and power output. This problem is caused by acid production at the anode, alkaline production at the cathode, and the nonspecific proton exchange through the membrane. Here we report a solution for a new kind of solar energy powered microbial fuel cell via development of a reversible bioelectrode responsible for both biocatalyzed anodic and cathodic electron transfer. Anodic produced protons were used for the cathodic reduction reaction which held the formation of a pH membrane gradient. The microbial fuel cell continuously generated electricity and repeatedly reversed polarity dependent on aeration or solar energy exposure. Identified organisms within biocatalyzing biofilm of the reversible bioelectrode were algae, (cyano)bacteria and protozoa. These results encourage application of solar energy powered microbial fuel cells.

Bacterial density and community structure associated with aggregate size fractions of soil-feeding termite mounds.

PubMed

Fall, S; Nazaret, S; Chotte, J L; Brauman, A

2004-08-01

The building and foraging activities of termites are known to modify soil characteristics such as the heterogeneity. In tropical savannas the impact of the activity of soil-feeding termites ( Cubitermes niokoloensis) has been shown to affect the properties of the soil at the aggregate level by creating new soil microenvironments (aggregate size fractions) [13]. These changes were investigated in greater depth by looking at the microbial density (AODC) and the genetic structure (automated rRNA intergenic spacer analysis: ARISA) of the communities in the different aggregate size fractions (i.e., coarse sand, fine sand, coarse silt, fine silt, and dispersible clays) separated from compartments (internal and external wall) of three Cubitermes niokoloensis mounds. The bacterial density of the mounds was significantly higher (1.5 to 3 times) than that of the surrounding soil. Within the aggregate size fractions, the termite building activity resulted in a significant increase in bacterial density within the coarser fractions (>20 mum). Multivariate analysis of the ARISA profiles revealed that the bacterial genetic structures of unfractionated soil and soil aggregate size fractions of the three mounds was noticeably different from the savanna soil used as a reference. Moreover, the microbial community associated with the different microenvironments in the three termite mounds revealed three distinct clusters formed by the aggregate size fractions of each mound. Except for the 2-20 mum fraction, these results suggest that the mound microbial genetic structure is more dependent upon microbial pool affiliation (the termite mound) than on the soil location (aggregate size fraction). The causes of the specificity of the microbial community structure of termite mound aggregate size fractions are discussed.

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

Yu, Chaowei; Reddy, Amitha P.; Simmons, Christopher W.

Microbial communities enriched from diverse environments have shown considerable promise for the targeted discovery of microorganisms and enzymes for bioconversion of lignocellulose to liquid fuels. While preservation of microbial communities is important for commercialization and research, few studies have examined storage conditions ideal for preservation. The goal of this study was to evaluate the impact of preservation method on composition of microbial communities enriched on switchgrass before and after storage. The enrichments were completed in a high-solid and aerobic environment at 55 °C. Community composition was examined for each enrichment to determine when a stable community was achieved. Preservation methodsmore » included cryopreservation with the cryoprotective agents DMSO and glycerol, and cryopreservation without cryoprotective agents. Revived communities were examined for their ability to decompose switchgrass under high-solid and thermophilic conditions. High-throughput 16S rRNA gene sequencing of DNA extracted from enrichment samples showed that the majority of the shift in composition of the switchgrass-degrading community occurred during the initial three 2-week enrichments. Shifts in community structure upon storage occurred in all cryopreserved samples. Storage in liquid nitrogen in the absence of cryoprotectant resulted in variable preservation of dominant microorganisms in enriched samples. Cryopreservation with either DMSO or glycerol provided consistent and equivalent preservation of dominant organisms. In conclusion, a stable switchgrass-degrading microbial community was achieved after three 2-week enrichments. Dominant microorganisms were preserved equally well with DMSO and glycerol. DMSO-preserved communities required more incubation time upon revival to achieve pre-storage activity levels during high-solid thermophilic cultivation on switchgrass. Despite shifts in the community with storage, the samples were active upon revival under thermophilic and high-solid conditions. The results suggest that the presence of microorganisms may be more important than their relative abundance in retaining an active microbial community.« less

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

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.

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.

Microbial Condition of Water Samples from Foreign Fuel Storage Facilities

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

Berry, C.J.; Fliermans, C.B.; Santo Domingo, J.

1997-10-30

In order to assess the microbial condition of foreign nuclear fuel storage facilities, fourteen different water samples were received from facilities outside the United States that have sent spent nuclear fuel to SRS for wet storage. Each water sample was analyzed for microbial content and activity as determined by total bacteria, viable aerobic bacteria, viable anaerobic bacteria, viable sulfate- reducing bacteria, viable acid-producing bacteria and enzyme diversity. The results for each water sample were then compared to other foreign samples and to data from the receiving basin for off- site fuel (RBOF) at SRS.

Lectins of beneficial microbes: system organisation, functioning and functional superfamily.

PubMed

Lakhtin, M; Lakhtin, V; Alyoshkin, V; Afanasyev, S

2011-06-01

In this review our last results and proposals with respect to general aspects of lectin studies are summarised and compared. System presence, organisation and functioning of lectins are proposed, and accents on beneficial symbiotic microbial lectins studies are presented. The proposed general principles of lectin functioning allows for a comparison of lectins with other carbohydrate-recognition systems. A new structure-functional superfamily of symbiotic microbial lectins is proposed and its main properties are described. The proposed superfamily allows for extended searches of the biological activities of any microbial member. Prospects of lectins of beneficial symbiotic microorganisms are discussed.

The Impact of Human Activities on Microbial Quality of Rivers in the Vhembe District, South Africa

PubMed Central

Traoré, Afsatou N.; Mulaudzi, Khodani; Chari, Gamuchirai J.E.; Foord, Stefan H.; Mudau, Lutendo S.; Barnard, Tobias G.; Potgieter, Natasha

2016-01-01

Background: Water quality testing is dictated by microbial agents found at the time of sampling in reference to their acceptable risk levels. Human activities might contaminate valuable water resources and add to the microbial load present in water bodies. Therefore, the effects of human activities on the microbial quality of rivers collected from twelve catchments in the Vhembe District in South Africa were investigated, with samples analyzed for total coliform (TC) and Eschericha coli (E. coli) contents. Methods: Physical parameters and various human activities were recorded for each sampling site. The Quanti-Tray® method was adopted for the assessment of TC and E. coli contents in the rivers over a two-year period. A multiplex polymerase chain (PCR) method was used to characterize the strains of E. coli found. Results: The microbial quality of the rivers was poor with both TC and E. coli contents found to be over acceptable limits set by the South African Department of Water and Sanitation (DWS). No significant difference (p > 0.05) was detected between TC and E. coli risks in dry and wet seasons. All six pathogenic E. coli strains were identified and Enteroaggregative E. coli (EAEC), atypical Enteropathogenic E. coli (a-EPEC) and Enterotoxigenic E. coli (ETEC) were the most prevalent E. coli strains detected (respectively, 87%, 86% and 83%). Conclusions: The study indicated that contamination in the majority of sampling sites, due to human activities such as car wash, animal grazing and farming, poses health risks to communities using the rivers for various domestic chores. It is therefore recommended that more education by the respective departments is done to avert pollution of rivers and prevent health risks to the communities in the Vhembe District. PMID:27529265

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.

Response of microbial community composition and function to soil climate change

USGS Publications Warehouse

Waldrop, M.P.; Firestone, M.K.

2006-01-01

Soil microbial communities mediate critical ecosystem carbon and nutrient cycles. How microbial communities will respond to changes in vegetation and climate, however, are not well understood. We reciprocally transplanted soil cores from under oak canopies and adjacent open grasslands in a California oak-grassland ecosystem to determine how microbial communities respond to changes in the soil environment and the potential consequences for the cycling of carbon. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid analysis (PLFA), microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups by quantifying 13C uptake from a universal substrate (pyruvate) into PLFA biomarkers. Soil in the open grassland experienced higher maximum temperatures and lower soil water content than soil under the oak canopies. Soil microbial communities in soil under oak canopies were more sensitive to environmental change than those in adjacent soil from the open grassland. Oak canopy soil communities changed rapidly when cores were transplanted into the open grassland soil environment, but grassland soil communities did not change when transplanted into the oak canopy environment. Similarly, microbial biomass, enzyme activities, and microbial respiration decreased when microbial communities were transplanted from the oak canopy soils to the grassland environment, but not when the grassland communities were transplanted to the oak canopy environment. These data support the hypothesis that microbial community composition and function is altered when microbes are exposed to new extremes in environmental conditions; that is, environmental conditions outside of their "life history" envelopes. ?? 2006 Springer Science+Business Media, Inc.

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.

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.

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.

Opening the black box of spring water microbiology from alpine karst aquifers to support proactive drinking water resource management.

PubMed

Savio, Domenico; Stadler, Philipp; Reischer, Georg H; Kirschner, Alexander K T; Demeter, Katalin; Linke, Rita; Blaschke, Alfred P; Sommer, Regina; Szewzyk, Ulrich; Wilhartitz, Inés C; Mach, Robert L; Stadler, Hermann; Farnleitner, Andreas H

2018-01-01

Over the past 15 years, pioneering interdisciplinary research has been performed on the microbiology of hydrogeologically well-defined alpine karst springs located in the Northern Calcareous Alps (NCA) of Austria. This article gives an overview on these activities and links them to other relevant research. Results from the NCA springs and comparable sites revealed that spring water harbors abundant natural microbial communities even in aquifers with high water residence times and the absence of immediate surface influence. Apparently, hydrogeology has a strong impact on the concentration and size of the observed microbes, and total cell counts (TCC) were suggested as a useful means for spring type classification. Measurement of microbial activities at the NCA springs revealed extremely low microbial growth rates in the base flow component of the studied spring waters and indicated the importance of biofilm-associated microbial activities in sediments and on rock surfaces. Based on genetic analysis, the autochthonous microbial endokarst community (AMEC) versus transient microbial endokarst community (TMEC) concept was proposed for the NCA springs, and further details within this overview article are given to prompt its future evaluation. In this regard, it is well known that during high-discharge situations, surface-associated microbes and nutrients such as from soil habitats or human settlements-potentially containing fecal-associated pathogens as the most critical water-quality hazard-may be rapidly flushed into vulnerable karst aquifers. In this context, a framework for the comprehensive analysis of microbial pollution has been proposed for the NCA springs to support the sustainable management of drinking water safety in accordance with recent World Health Organization guidelines. Near-real-time online water quality monitoring, microbial source tracking (MST) and MST-guided quantitative microbial-risk assessment (QMRA) are examples of the proposed analytical tools. In this context, this overview article also provides a short introduction to recently emerging methodologies in microbiological diagnostics to support reading for the practitioner. Finally, the article highlights future research and development needs. This article is categorized under: 1Engineering Water > Water, Health, and Sanitation2Science of Water > Water Extremes3Water and Life > Nature of Freshwater Ecosystems.

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.

Effects of soil water repellency on microbial community structure and functions in Mediterranean pine forests

NASA Astrophysics Data System (ADS)

Lozano, Elena; Grayston, Sue J.; Mataix-Solera, Jorge; Arcenegui, Victoria; Jimenez-Pinilla, Patricia; Mataix-Beneyto, Jorge

2015-04-01

Soil water repellency (SWR) is a property commonly observed in forest areas showing wettable and water repellent patches with high spatial variability. SWR can greatly influence the hydrology and the ecology of forest soils. The capacity of soil microorganisms to degrade different organic compounds depends upon species composition, so this may affect changes in SWR on the microsite scale (such as the presence of soil water repellent patches; Mülleret al., 2010). In the Mediterranean forest context, SWR has been found to be related to microbial community composition. The accumulation of different hydrophobic compounds might be causing the shifts in microbial community structure (Lozano et al., 2014). In this study we investigated the effects of SWR persistence on soil microbial community structure and enzyme activity under Pinus halepensis forest in three different sites: Petrer, Gorga and Jávea (Alicante, E Spain). Soil samples were classified into three different water repellency classes (wettable, slight or strongly water repellent samples) depending on the SWR persistence. The soil microbial community was determined through phospholipid fatty acids (PLFAs). Enzyme activities chosen for this study were cellulase, β-glucosidase and N-acetyl-β-glucosaminide (NAG). The relationships between microbiological community structure and some soil properties such as pH, Glomalin Related Soil Protein, soil organic matter content and soil respiration were also studied. Redundancy analyses and decomposition of the variances were performed to clarify how microbial community composition and enzyme activities are affected by SWR and soil properties. The effect of SWR on microbial community composition differed between locations. This effect was clearer in the Petrer site. Enzyme activity varied considerably depending on SWR persistence. The highest activities were found in slightly SWR samples and the lowest mostly in the strongly water repellent ones. These preliminary results suggest a possible influence of SWR on microbial structure and its activity in soils. References: Lozano, E., García-Orenes, F., Bárcenas-Moreno, G., Jiménez-Pinilla, P., Mataix-Solera, J., Arcenegui, V., Morugán-Coronado, A., Mataix-Beneyto, J., 2014. Relationships between soil water repellency and microbial community composition under different plant species in a Mediterranean semiarid forest. J. Hydrol. Hydromech., 62, 101-107 Müller, K., Deurer, M., Newton, P.C.D., 2010. Is there a link between elevated atmospheric carbon dioxide concentration, soil water repellency and soil carbon mineralization? Agric. Ecosyst. Environ., 139, 98-109. Acknowledgements: to the "Ministerio de Economía and Competitividad" of Spanish Government for finance the POSTFIRE project (CGL2013- 47862-C2-1-R), Generalitat Valenciana for PhD grant, and Spanish Soil Science Society and FUEGORED for their support.

The relief of microtherm inhibition for p-fluoronitrobenzene mineralization using electrical stimulation at low temperatures.

PubMed

Zhang, Xueqin; Feng, Huajun; Liang, Yuxiang; Zhao, Zhiqing; Long, Yuyang; Fang, Yuan; Wang, Meizhen; Yin, Jun; Shen, Dongsheng

2015-05-01

Low temperature aggravates biological treatment of refractory p-fluoronitrobenzene (p-FNB) because of microtherm inhibition of microbial activity. Considering the potential characterization of energy supply for microbial metabolism and spurring microbial activity by electrical stimulation, a bioelectrochemical system (BES) was established to provide sustaining electrical stimulation for p-FNB mineralization at a low temperature. Electrical stimulation facilitated p-FNB treatment and bioelectrochemical reaction rate constants for the removal and defluorination of p-FNB at 10 °C were 0.0931 and 0.0054 h(-1), which were higher than the sums of the rates found using a biological system and an electrocatalytic system by 62.8 and 64.8%, respectively. At a low temperature, microbial activity in terms of dehydrogenase and ATPase was found to be higher with electrical stimulation, being 121.1 and 100.1% more active than that in the biological system. Moreover, stronger antioxidant ability was observed in the BES, which implied a better cold-resistance and relief of microtherm inhibition by electrical stimulation. Bacterial diversity analysis revealed a significant evolution of microbial community by electrical stimulation, and Clostridia was uniquely enriched. One bacterial sequence close to Pseudomonas became uniquely predominant, which appeared to be crucial for excellent p-FNB treatment performance in the BES at a low temperature. Economic evaluation revealed that the energy required to mineralize an extra mole of p-FNB was found to be 247 times higher by heating the system than by application of electrical stimulation. These results indicated that application of electrical stimulation is extremely promising for treating refractory waste at low temperatures.

Earth's Earliest Ecosystems in the C: The Use of Microbial Mats to Demonstrate General Principles of Scientific Inquiry and Microbial Ecology

NASA Technical Reports Server (NTRS)

Bebout, Brad M.; Bucaria, Robin

2006-01-01

Microbial mats are living examples of the most ancient biological communities on Earth. As Earth's earliest ecosystems, they are centrally important to understanding the history of life on our planet and are useful models for the search for life elsewhere. As relatively compact (but complete) ecosystems, microbial mats are also extremely useful for educational activities. Mats may be used to demonstrate a wide variety of concepts in general and microbial ecology, including the biogeochemical cycling of elements, photosynthesis and respiration, and the origin of the Earth's present oxygen containing atmosphere. Microbial mats can be found in a number of common environments accessible to teachers, and laboratory microbial mats can be constructed using materials purchased from biological supply houses. With funding from NASA's Exobiology program, we have developed curriculum and web-based activities centered on the use of microbial mats as tools for demonstrating general principles in ecology, and the scientific process. Our web site (http://microbes.arc.nasa.gov) includes reference materials, lesson plans, and a "Web Lab", featuring living mats maintained in a mini-aquarium. The site also provides information as to how research on microbial mats supports NASA's goals, and various NASA missions. A photo gallery contains images of mats, microscopic views of the organisms that form them, and our own research activities. An animated educational video on the web site uses computer graphic and video microscopy to take students on a journey into a microbial mat. These activities are targeted to a middle school audience and are aligned with the National Science Standards.

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

Microbial contributions to the Precambrian Earth

NASA Technical Reports Server (NTRS)

Margulis, L.; Bermudes, D.; Obar, R.

1986-01-01

Life has existed on Earth for approximately 3.5 billion years. For most of this time, prokaryotic communities provided the major biological forces changing the Earth. Many changes in atmospheric gas composition occurred during the Archean and Proterozoic eons as a result of microbial activity. Extant microbial communities were used to help understand the dynamics which contributed to these atmospheric changes. The microbial mat communities were characterized according to the organismic constituents. Symbiosis in microbial communities is recognized as a major force in cell evolution. Among the evolutinary enigmas investigated is the problem of the origin of the undulipodia. Undulipodial microtubules are still deployed for major cellular processes such as mitosis and meiosis. Several prokaryotes were tested for the presence of the S1-type protein, so far only spirochetes were found to possess it. The S1-type protein is being sought in cyanobacteria reported to contain microtubules.

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.

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.

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.

Application of RNA Stable Isotope Probing (SIP) to Link Community Activity with Microorganisms Responsible for Autotrophy in the Subseafloor at Axial Seamount

NASA Astrophysics Data System (ADS)

Huber, J. A.; Fortunato, C. S.

2014-12-01

The global ocean comprises the Earth's largest biome, with microorganisms playing a dominant biogeochemical role. However, the potential for production of new microbial biomass within the subseafloor is rarely considered in traditional oceanographic paradigms of carbon cycling or microbial food webs. In this study, we used RNA Stable Isotope Probing (RNA SIP) to determine the microbial community composition and genetic repertoire of active subseafloor autotrophs in warm venting fluids from Axial Seamount. RNA is a responsive biomarker because it is a reflection of cellular activity independent of replication, and RNA SIP thus provides access to both the function of a microbial community and the phylogeny of the organisms accountable for key functions. Diffuse fluids were incubated shipboard at 30°C, 55°C, and 80°C with 13DIC and H2. Metatranscriptomic sequencing of both the enriched and non-enriched RNA was carried out from 13C and 12C controls. In addition, filtered fluid samples were preserved in situ for comparative meta -transcriptomic and -genomic analyses. Diverse lineages of bacteria and archaea and accompanying metabolisms were detected in situ, but RNA SIP results show dominance of three different groups of autotrophs active under each experimental condition. At 30°C, members of the Sulfurimonas genus dominated, with genes for hydrogen oxidation, nitrate reduction, and carbon fixation via the rTCA cycle highly expressed. At 55°C, both Caminibacter and Nautilia transcripts were detected for rTCA cycle, hydrogen oxidation, and nitrate reduction. At 80°C, transcripts for hydrogenotrophic methanogenesis mediated by members of Methanocaldococcus were detected. These results suggest the subseafloor hosts various anaerobic chemolithoautotrophs that span a wide temperature range, with hydrogen playing a key role in microbial metabolism. Complementary experiments are currently being carried out on the seafloor with a novel in situ incubator unit to provide further insights to primary productivity in the subseafloor.

Bacterial genome replication at subzero temperatures in permafrost

PubMed Central

Tuorto, Steven J; Darias, Phillip; McGuinness, Lora R; Panikov, Nicolai; Zhang, Tingjun; Häggblom, Max M; Kerkhof, Lee J

2014-01-01

Microbial metabolic activity occurs at subzero temperatures in permafrost, an environment representing ∼25% of the global soil organic matter. Although much of the observed subzero microbial activity may be due to basal metabolism or macromolecular repair, there is also ample evidence for cellular growth. Unfortunately, most metabolic measurements or culture-based laboratory experiments cannot elucidate the specific microorganisms responsible for metabolic activities in native permafrost, nor, can bulk approaches determine whether different members of the microbial community modulate their responses as a function of changing subzero temperatures. Here, we report on the use of stable isotope probing with 13C-acetate to demonstrate bacterial genome replication in Alaskan permafrost at temperatures of 0 to −20 °C. We found that the majority (80%) of operational taxonomic units detected in permafrost microcosms were active and could synthesize 13C-labeled DNA when supplemented with 13C-acetate at temperatures of 0 to −20 °C during a 6-month incubation. The data indicated that some members of the bacterial community were active across all of the experimental temperatures, whereas many others only synthesized DNA within a narrow subzero temperature range. Phylogenetic analysis of 13C-labeled 16S rRNA genes revealed that the subzero active bacteria were members of the Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes and Proteobacteria phyla and were distantly related to currently cultivated psychrophiles. These results imply that small subzero temperature changes may lead to changes in the active microbial community, which could have consequences for biogeochemical cycling in permanently frozen systems. PMID:23985750

Toxic industrial deposit remediation by ant activity

NASA Astrophysics Data System (ADS)

Jilkova, Veronika; Frouz, Jan

2016-04-01

Toxic industrial deposits are often contaminated by heavy metals and the substrates have low pH values. In such systems, soil development is thus slowed down by high toxicity and acidic conditions which are unfavourable to soil fauna. Ants (Hymenoptera, Formicidae) are considered tolerant to heavy metal pollution and are known to increase organic matter content and microbial activity in their nests. Here, we focused on soil remediation caused by three ant species (Formica sanguinea, Lasius niger, and Tetramorium sp.) in an ore-washery sedimentation basin near Chvaletice (Czech Republic). Soil samples were taken from the centre of ant nests and from the nest surroundings (>3 m from nests). Samples were then analyzed for microbial activity and biomass and contents of organic matter and nutrients. As a result, ant species that most influenced soil properties was F. sanguinea as there were higher microbial activity and total nitrogen and ammonia contents in ant nests than in the surrounding soil. We expected such a result because F. sanguinea builds conspicuous large nests and is a carnivorous species that brings substantial amounts of nitrogen in insect prey to their nests. Effects of the other two ant species might be lower because of smaller nests and different feeding habits as they rely mainly on honeydew from aphids or on plant seeds that do not contain much nutrients.

Deep sea microbial fuel cell output as a proxy for microbial activity

NASA Astrophysics Data System (ADS)

Richter, K.; George, R.; Hardy, K. R.

2016-02-01

Abstract: Microbial fuel cells (MFCs) work by providing bacteria in anaerobic sediments with an electron acceptor (anode) that stimulates metabolism of organic matter. The buried anode is connected via control circuitry to a cathode exposed to oxygen in the overlying water. During metabolism, bacteria release hydrogen ions into the sediment and transfer electrons extra-cellularly to the anode, which eventually reduce dissolved oxygen at the cathode, forming water. The current is chiefly limited by the rate of microbial metabolism at the anode and serves as a proxy for microbial activity. The Office of Naval Research has encouraged development of microbial fuel cells in the marine environment at a number of academic and naval institutions and studies of important environmental parameters that affect fuel cell performance. Earlier work in shallow sediments of San Diego Bay showed that the most important environmental parameters that control fuel cell power output in San Diego Bay were total organic carbon in the sediment and seasonal water temperature. Current MFC work at SPAWAR includes extension of microbial fuel cell tests to the deep sea environment (>4000 m) and, in parallel, testing microbial fuel cells in the laboratory under deep sea conditions. We are pursuing a field efforts to deploy a microbial fuel cell in progressively deeper water, record in situ power and temperature over several weeks, and retrieve the fuel cell along with sediment samples for analysis. We are also pursuing a laboratory effort to build a matching microbial fuel cell in a pressure vessel capable of matching the pressure and temperature of deep water, and stocking the pressure vessel with deep water sediment in order to take measurements analogous to those in the field. We also hope to determine whether bacteria growing on the anode are different from bacteria growing in the bulk sediment via DNA analysis. The current progress and results from this work at SPAWAR will be presented.

Colonization Habitat Controls Biomass, Composition, and Metabolic Activity of Attached Microbial Communities in the Columbia River Hyporheic Corridor

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

Stern, Noah; Ginder-Vogel, Matthew; Stegen, James C.

Hydrologic exchange plays a critical role in biogeochemical cycling within the hyporheic zone (the interface between river water and groundwater) of riverine ecosystems. Such exchange may set limits on the rates of microbial metabolism and impose deterministic selection on microbial communities that adapt to dynamically changing dissolved organic carbon (DOC) sources. This study examined the response of attached microbial communities (in situcolonized sand packs) from groundwater, hyporheic, and riverbed habitats within the Columbia River hyporheic corridor to “cross-feeding” with either groundwater, river water, or DOC-free artificial fluids. Our working hypothesis was that deterministic selection duringin situcolonization would dictate the responsemore » to cross-feeding, with communities displaying maximal biomass and respiration when supplied with their native fluid source. In contrast to expectations, the major observation was that the riverbed colonized sand had much higher biomass and respiratory activity, as well as a distinct community structure, compared with those of the hyporheic and groundwater colonized sands. 16S rRNA gene amplicon sequencing revealed a much higher proportion of certain heterotrophic taxa as well as significant numbers of eukaryotic algal chloroplasts in the riverbed colonized sand. Significant quantities of DOC were released from riverbed sediment and colonized sand, and separate experiments showed that the released DOC stimulated respiration in the groundwater and piezometer colonized sand. These results suggest that the accumulation and degradation of labile particulate organic carbon (POC) within the riverbed are likely to release DOC, which may enter the hyporheic corridor during hydrologic exchange, thereby stimulating microbial activity and imposing deterministic selective pressure on the microbial community composition. IMPORTANCEThe influence of river water-groundwater mixing on hyporheic zone microbial community structure and function is an important but poorly understood component of riverine biogeochemistry. This study employed an experimental approach to gain insight into how such mixing might be expected to influence the biomass, respiration, and composition of hyporheic zone microbial communities. Colonized sands from three different habitats (groundwater, river water, and hyporheic) were “cross-fed” with either groundwater, river water, or DOC-free artificial fluids. We expected that the colonization history would dictate the response to cross-feeding, with communities displaying maximal biomass and respiration when supplied with their native fluid source. By contrast, the major observation was that the riverbed communities had much higher biomass and respiration, as well as a distinct community structure compared with those of the hyporheic and groundwater colonized sands. These results highlight the importance of riverbed microbial metabolism in organic carbon processing in hyporheic corridors.« less

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

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.

Seasonal and spatial variations in microbial activity at various phylogenetic resolutions at a groundwater - surface water interface.

PubMed

Yu, Ran; Smets, Barth F; Gan, Ping; MacKay, Allison A; Graf, Joerg

2014-05-01

We investigated the seasonal and spatial variation in activity and density of the metabolically active in situ microbial community (AIMC) at a landfill leachate-impacted groundwater - surface water interface (GSI). A series of AIMC traps were designed and implemented for AIMC sampling and microbial activity and density examinations. Measurements were made not only at the level of bacterial domain but also at the levels of alphaproteobacterial Rhizobiales order and gammaproteobacterial Pseudomonas genus, both of which included a large number of iron-oxidizing bacteria as revealed from previous analysis. Consistently higher microbial activities with less variation in depth were measured in the AIMC traps than in the ambient sediments. Flood disturbance appeared to control AIMC activity distributions at the gradually elevated GSI. The highest AIMC activities were generally obtained from locations closest to the free surface water boundary except during the dry season when microbial activities were similar across the entire GSI. A clone library of AIMC 16S rRNA genes was constructed, and it confirmed the predominant role of the targeted alphaproteobacterial group in AIMC activity and composition. This taxon constituted 2%-14% of all bacteria with similar activity distribution profiles. The Pseudomonas group occupied only 0.1‰-0.5‰ of the total bacterial density, but its activity was 27 times higher than the bacterial average. Of the 16S rRNA sequences in the AIMC clone library, 7.5% were phylogenetically related to putative IOB, supporting the occurrence and persistence of active microbial iron oxidation across the studied iron-rich GSI ecosystem.

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.

The interacting roles of climate, soils, and plant production on soil microbial communities at a continental scale

USGS Publications Warehouse

Waldrop, Mark P.; Holloway, JoAnn M.; Smith, David; Goldhaber, Martin B.; Drenovsky, R.E.; Scow, K.M.; Dick, R.; Howard, Daniel M.; Wylie, Bruce K.; Grace, James B.

2017-01-01

Soil microbial communities control critical ecosystem processes such as decomposition, nutrient cycling, and soil organic matter formation. Continental scale patterns in the composition and functioning of microbial communities are related to climatic, biotic, and edaphic factors such as temperature and precipitation, plant community composition, and soil carbon, nitrogen, and pH. Although these relationships have been well explored individually, the examination of the factors that may act directly on microbial communities vs. those that may act indirectly through other ecosystem properties has not been well developed. To further such understanding, we utilized structural equation modeling (SEM) to evaluate a set of hypotheses about the direct and indirect effects of climatic, biotic, and edaphic variables on microbial communities across the continental United States. The primary goals of this work were to test our current understanding of the interactions among climate, soils, and plants in affecting microbial community composition, and to examine whether variation in the composition of the microbial community affects potential rates of soil enzymatic activities. A model of interacting factors created through SEM shows several expected patterns. Distal factors such as climate had indirect effects on microbial communities by influencing plant productivity, soil mineralogy, and soil pH, but factors related to soil organic matter chemistry had the most direct influence on community composition. We observed that both plant productivity and soil mineral composition were important indirect influences on community composition at the continental scale, both interacting to affect organic matter content and microbial biomass and ultimately community composition. Although soil hydrolytic enzymes were related to the moisture regime and soil carbon, oxidative enzymes were also affected by community composition, reflected in the abundance of soil fungi. These results highlight that soil microbial communities can be modeled within the context of multiple interacting ecosystem properties acting both directly and indirectly on their composition and function, and this provides a rich and informative context with which to examine communities. This work also highlights that variation in climate, microbial biomass, and microbial community composition can affect maximum rates of soil enzyme activities, potentially influencing rates of decomposition and nutrient mineralization in soils.

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.

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.

The effects of grazing intensity on soil processes in a Mediterranean protected area.

PubMed

Panayiotou, Evaggelia; Dimou, Maria; Monokrousos, Nikolaos

2017-08-08

We investigated the temporal and among-site differentiation of soil functionality properties in fields under different grazing intensities (heavy and light) and compared them to those found in their adjacent hedgerows, consisting either of wooden shrubs (Rubus canescens) or of high trees (Populus sp.), during the cold and humid seasons of the year. We hypothesized that greater intensity of grazing would result in higher degradation of the soil system. The grazing factor had a significant effect on soil organic C and N, microbial biomass C, microbial biomass N, microbial activity, and β-glucosidase, while acid phosphatase and urease activity were not found to differ significantly among the management systems. The intensity of grazing affected mostly the chemical properties of soil (organic C and N) and altered significantly the composition of the soil microbial community, as lower C:N ratio of the microbial biomass indicates the dominance of bacteria over fungi in the heavily grazed fields. All estimated biological variables presented higher values in the humid period, although the pattern of differentiation was similar at both sampling times, revealing that site-specific variations were more pronounced than the time-specific ones. Our results indicate that not all C, N, and P dynamics were equally affected by grazing. Management plans applied to pastures, in order to improve soil quality properties and accelerate passive reforestation, should aim at the improvement of soil parameters related primarily to C and secondly to N cycle.

Effect of land management on soil properties in flood irrigated citrus orchards in Eastern Spain

NASA Astrophysics Data System (ADS)

Morugán-Coronado, A.; García-Orenes, F.; Cerdà, A.

2015-01-01

Agricultural land management greatly affects soil properties. Microbial soil communities are the most sensitive and rapid indicators of perturbations in land use and soil enzyme activities are sensitive biological indicators of the effects of soil management practices. Citrus orchards frequently have degraded soils and this paper evaluates how land management in citrus orchards can improve soil quality. A field experiment was performed in an orchard of orange trees (Citrus Sinensis) in the Alcoleja Experimental Station (Eastern Spain) with clay-loam agricultural soils to assess the long-term effects of herbicides with inorganic fertilizers (H), intensive ploughing and inorganic fertilizers (P) and organic farming (O) on the soil microbial properties, and to study the relationship between them. Nine soil samples were taken from each agricultural management plot. In all the samples the basal soil respiration, soil microbial biomass carbon, water holding capacity, electrical conductivity, soil organic matter, total nitrogen, available phosphorus, available potassium, aggregate stability, cation exchange capacity, pH, texture, macronutrients (Na, Ca and Mg), micronutrients (Fe, Mn, Zn and Cu), calcium carbonate equivalent, calcium carbonate content of limestone and enzimatic activities (urease, dehydrogenase, β-glucosidase and acid phosphatase) were determined. The results showed a substantial level of differentiation in the microbial properties, which were highly associated with soil organic matter content. The management practices including herbicides and intensive ploughing had similar results on microbial soil properties. O management contributed to an increase in the soil biology quality, aggregate stability and organic matter content.

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.

A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge

PubMed Central

Meyer, Julie L.; Jaekel, Ulrike; Tully, Benjamin J.; Glazer, Brian T.; Wheat, C. Geoffrey; Lin, Huei-Ting; Hsieh, Chih-Chiang; Cowen, James P.; Hulme, Samuel M.; Girguis, Peter R.; Huber, Julie A.

2016-01-01

The rock-hosted, oceanic crustal aquifer is one of the largest ecosystems on Earth, yet little is known about its indigenous microorganisms. Here we provide the first phylogenetic and functional description of an active microbial community residing in the cold oxic crustal aquifer. Using subseafloor observatories, we recovered crustal fluids and found that the geochemical composition is similar to bottom seawater, as are cell abundances. However, based on relative abundances and functional potential of key bacterial groups, the crustal fluid microbial community is heterogeneous and markedly distinct from seawater. Potential rates of autotrophy and heterotrophy in the crust exceeded those of seawater, especially at elevated temperatures (25 °C) and deeper in the crust. Together, these results reveal an active, distinct, and diverse bacterial community engaged in both heterotrophy and autotrophy in the oxygenated crustal aquifer, providing key insight into the role of microbial communities in the ubiquitous cold dark subseafloor biosphere. PMID:26935537

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.

Dynamics of soil organic carbon and microbial activity in treated wastewater irrigated agricultural soils along soil profiles

NASA Astrophysics Data System (ADS)

Jüschke, Elisabeth; Marschner, Bernd; Chen, Yona; Tarchitzky, Jorge

2010-05-01

Treated wastewater (TWW) is an important source for irrigation water in arid and semiarid regions and already serves as an important water source in Jordan, the Palestinian Territories and Israel. Reclaimed water still contains organic matter (OM) and various compounds that may effect microbial activity and soil quality (Feigin et al. 1991). Natural soil organic carbon (SOC) may be altered by interactions between these compounds and the soil microorganisms. This study evaluates the effects of TWW irrigation on the quality, dynamics and microbial transformations of natural SOC. Priming effects (PE) and SOC mineralization were determined to estimate the influence of TWW irrigation on SOC along soil profiles of agricultural soils in Israel and the Westbank. The used soil material derived from three different sampling sites allocated in Israel and The Palestinian Authority. Soil samples were taken always from TWW irrigated sites and control fields from 6 different depths (0-10, 10-20, 20-30, 30-50, 50-70, 70-100 cm). Soil carbon content and microbiological parameters (microbial biomass, microbial activities and enzyme activities) were investigated. In several sites, subsoils (50-160 cm) from TWW irrigated plots were depleted in soil organic matter with the largest differences occurring in sites with the longest TWW irrigation history. Laboratory incubation experiments with additions of 14C-labelled compounds to the soils showed that microbial activity in freshwater irrigated soils was much more stimulated by sugars or amino acids than in TWW irrigated soils. The lack of such "priming effects" (Hamer & Marschner 2005) in the TWW irrigated soils indicates that here the microorganisms are already operating at their optimal metabolic activity due to the continuous substrate inputs with soluble organic compounds from the TWW. The fact that PE are triggered continuously due to TWW irrigation may result in a decrease of SOC over long term irrigation. Already now this could be detected at some agricultural fields by SOC measurements (Jüschke 2009). Therefore attention has to be drawn especially on the carbon content and quality of the used TWW for irrigation purposes.

Assessing Microbial Activity in Marcellus Shale Hydraulic Fracturing Fluids

NASA Astrophysics Data System (ADS)

Wishart, J. R.; Morono, Y.; Itoh, M.; Ijiri, A.; Hoshino, T.; Inagaki, F.; Verba, C.; Torres, M. E.; Colwell, F. S.

2014-12-01

Hydraulic fracturing (HF) produces millions of gallons of waste fluid which contains a microbial community adapted to harsh conditions such as high temperatures, high salinities and the presence of heavy metals and radionuclides. Here we present evidence for microbial activity in HF production fluids. Fluids collected from a Marcellus shale HF well were supplemented with 13C-labeled carbon sources and 15N-labeled ammonium at 25°C under aerobic or anaerobic conditions. Samples were analyzed for 13C and 15N incorporation at sub-micrometer scale by ion imaging with the JAMSTEC NanoSIMS to determine percent carbon and nitrogen assimilation in individual cells. Headspace CO2 and CH4 were analyzed for 13C enrichment using irm-GC/MS. At 32 days incubation carbon assimilation was observed in samples containing 1 mM 13C-labeled glucose under aerobic and anaerobic conditions with a maximum of 10.4 and 6.5% total carbon, respectively. Nitrogen assimilation of 15N ammonium observed in these samples were 0.3 and 0.8% of total nitrogen, respectively. Head space gas analysis showed 13C enrichment in CH4 in anaerobic samples incubated with 1mM 13C-labeled bicarbonate (2227 ‰) or methanol (98943 ‰). Lesser 13C enrichment of CO2 was observed in anaerobic samples containing 1 mM 13C-labeled acetate (13.7 ‰), methanol (29.9 ‰) or glucose (85.4 ‰). These results indicate metabolic activity and diversity in microbial communities present in HF flowback fluids. The assimilation of 13C-labeled glucose demonstrates the production of biomass, a critical part of cell replication. The production of 13CO2 and 13CH4 demonstrate microbial metabolism in the forms of respiration and methanogenesis, respectively. Methanogenesis additionally indicates the presence of an active archaeal community. This research shows that HF production fluid chemistry does not entirely inhibit microbial activity or growth and encourages further research regarding biogeochemical processes occurring in Marcellus shale HF wells. Biogeochemical activity may impact the efficacy of HF and natural gas production as well as the chemistry of produced fluids which have become an environmental and public health concern.

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.

Effects and mechanisms of biochar-microbe interactions in soil improvement and pollution remediation: A review.

PubMed

Zhu, Xiaomin; Chen, Baoliang; Zhu, Lizhong; Xing, Baoshan

2017-08-01

Biochars have attracted tremendous attention due to their effects on soil improvement; they enhance carbon storage, soil fertility and quality, and contaminant (organic and heavy metal) immobilization and transformation. These effects could be achieved by modifying soil microbial habitats and (or) directly influencing microbial metabolisms, which together induce changes in microbial activity and microbial community structures. This review links microbial responses, including microbial activity, community structures and soil enzyme activities, with changes in soil properties caused by biochars. In particular, we summarized possible mechanisms that are involved in the effects that biochar-microbe interactions have on soil carbon sequestration and pollution remediation. Special attention has been paid to biochar effects on the formation and protection of soil aggregates, biochar adsorption of contaminants, biochar-mediated transformation of soil contaminants by microorganisms, and biochar-facilitated electron transfer between microbial cells and contaminants and soil organic matter. Certain reactive organic compounds and heavy metals in biochar may induce toxicity to soil microorganisms. Adsorption and hydrolysis of signaling molecules by biochar interrupts microbial interspecific communications, potentially altering soil microbial community structures. Further research is urged to verify the proposed mechanisms involved in biochar-microbiota interactions for soil remediation and improvement. Copyright © 2017 Elsevier Ltd. All rights reserved.

Inhibition of microbial growth on air cathodes of single chamber microbial fuel cells by incorporating enrofloxacin into the catalyst layer.

PubMed

Liu, Weifeng; Cheng, Shaoan; Sun, Dan; Huang, Haobin; Chen, Jie; Cen, Kefa

2015-10-15

The inevitable growth of aerobic bacteria on the surface of air cathodes is an important factor reducing the performance stability of air cathode single-chamber membrane-free microbial fuel cells (MFCs). Thus searching for effective methods to inhibit the cathodic microbial growth is critical for the practical application of MFCs. In this study, enrofloxacin (ENR), a broad spectrum fluoroquinolone antibiotic, was incorporated into the catalyst layer of activated carbon air cathodes (ACACs) to inhibit the cathodic microbial growth. The biomass content on ACACs was substantially reduced by 60.2% with ENR treatment after 91 days of MFCs operation. As a result of the inhibited microbial growth, the oxygen reduction catalytic performance of the ENR treated ACACs was much stable compared to the fast performance decline of the untreated control. Consequently, a quite stable electricity production was obtained for the MFCs with the ENR treated ACACs, in contrast with a 22.5% decrease in maximum power density of the MFCs with the untreated cathode. ENR treatment of ACACs showed minimal effects on the anode performance. These results indicate that incorporating antibiotics into ACACs should be a simple and effective strategy to inhibit the microbial growth and improve the long-term stability of the performance of air cathode and the electricity production of MFCs. Copyright © 2015 Elsevier B.V. All rights reserved.

Microbial exposure early in life regulates airway inflammation in mice after infection with Streptococcus pneumoniae with enhancement of local resistance.

PubMed

Yasuda, Yasuki; Matsumura, Yoko; Kasahara, Kazuki; Ouji, Noriko; Sugiura, Shigeki; Mikasa, Keiichi; Kita, Eiji

2010-01-01

The immunological explanation for the "hygiene hypothesis" has been proposed to be induction of T helper 1 (Th1) responses by microbial products. However, the protective results of hygiene hypothesis-linked microbial exposures are currently shown to be unlikely to result from a Th1-skewed response. Until now, effect of microbial exposure early in life on airway innate resistance remained unclear. We examined the role of early life exposure to microbes in airway innate resistance to a respiratory pathogen. Specific pathogen-free weanling mice were nasally exposed to the mixture of microbial extracts or PBS (control) every other day for 28 days and intratracheally infected with Streptococcus pneumoniae 10 days after the last exposure. Exposure to microbial extracts facilitated colonization of aerobic gram-positive bacteria, anaerobic microorganisms, and Lactobacillus in the airway, compared with control exposure. In pneumococcal pneumonia, the exposure prolonged mouse survival days by suppressing bacterial growth and by retarding pneumococcal blood invasion, despite significantly low levels of leukocyte recruitment in the lung. Enhancement of airway resistance was associated with a significant decrease in production of leukocyte chemokine (KC) and TNFalpha, and suppression of matrix metalloproteinase (MMP-9) expression/activation with enhancement of tissue inhibitor of MMP (TIMP-3) activation. The exposure increased production of IFN-gamma, IL-4, and monocyte chemoattractant-1 following infection. Furthermore, expression of Toll-like receptor 2, 4, and 9 was promoted by the exposure but no longer upregulated upon pneumococcal infection. Thus, we suggest that hygiene hypothesis is more important in regulating the PMN-dominant inflammatory response than in inducing a Th1-dominant response.

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.

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

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.

Health benefits of fermented foods.

PubMed

Şanlier, Nevin; Gökcen, Büşra Başar; Sezgin, Aybüke Ceyhun

2017-09-25

In the past, the beneficial effects of fermented foods on health were unknown, and so people primarily used fermentation to preserve foods, enhance shelf life, and improve flavour. Fermented foods became an important part of the diet in many cultures, and over time fermentation has been associated with many health benefits. Because of this, the fermentation process and the resulting fermented products have recently attracted scientific interest. In addition, microorganisms contributing to the fermentation process have recently been associated with many health benefits, and so these microorganisms have become another focus of attention. Lactic acid bacteria (LAB) have been some of the most studied microorganisms. During fermentation, these bacteria synthesize vitamins and minerals, produce biologically active peptides with enzymes such as proteinase and peptidase, and remove some non-nutrients. Compounds known as biologically active peptides, which are produced by the bacteria responsible for fermentation, are also well known for their health benefits. Among these peptides, conjugated linoleic acids (CLA) have a blood pressure lowering effect, exopolysaccharides exhibit prebiotic properties, bacteriocins show anti-microbial effects, sphingolipids have anti-carcinogenic and anti-microbial properties, and bioactive peptides exhibit anti-oxidant, anti-microbial, opioid antagonist, anti-allergenic, and blood pressure lowering effects. As a result, fermented foods provide many health benefits such as anti-oxidant, anti-microbial, anti-fungal, anti-inflammatory, anti-diabetic and anti-atherosclerotic activity. However, some studies have shown no relationship between fermented foods and health benefits. Therefore, this paper aims to investigate the health effects of fermented foods.

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

Comparative characterization of digestate versus pig slurry and cow manure - Chemical composition and effects on soil microbial activity.

PubMed

Risberg, Kajsa; Cederlund, Harald; Pell, Mikael; Arthurson, Veronica; Schnürer, Anna

2017-03-01

The growing number of biogas plants in Europe has resulted in increased production of nutrient-rich digestate with great potential as fertilizer for arable land. The nutrient composition of digestate varies with the substrate treated in the biogas plant and may contain compounds that stimulate or inhibit soil microbial activity. This study compared 20 digestates (D) with 10 pig slurries (PS) and 10 cow manures (CM) regarding their chemical content and their effect on soil microbial activities, i.e. potential ammonia oxidation rate (PAO) and soil respiration. The results showed no significant differences within the D group when divided based on substrate type. i.e. manure dominated vs. other organic waste materials in any of the tests. In general D contained significantly higher concentrations of ammonium while the concentrations of total carbon and volatile fatty acids were higher in PS and CM than in D. The D showed both stimulating and inhibiting effects on PAO, while all CM and all PS except one showed inhibiting effects on PAO. However, PAO activity was negatively correlated with the content of volatile fatty acids in the residues indicating that these compounds may be the cause of the inhibition. The maximum respiration activity (h peakmax ) was lower and the time point for the maximum respiration activity (t peakmax ) occurred earlier for D compared with CM and PS. This earlier peak time could be indicative of a high proportion of easily degradable carbon in D compared with PS and CM. However, the utilization rate of carbon, i.e. the proportion of added organic C converted to CO 2 -C during 12days, did not differ significantly between D, PS and CM, indicating that overall carbon quality in the different fertilizers was still roughly comparable. In short, our results suggest that digestates were different compared with PS and CM but without posing a higher risk with respect to their impact on soil microbial activity. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Co-ordination of incoming and outgoing traffic in antigen-presenting cells by pattern recognition receptors and T cells.

PubMed

Nair, Priyanka; Amsen, Derk; Blander, J Magarian

2011-12-01

Dendritic cells are innate sentinels of the immune system and potent activators of naÏve T cells. Mechanisms must exist to enable these cells to achieve maximal activation of T cells specific for microbial antigens, while avoiding activation of T cells specific for self-antigens. Here we discuss how a combination of signals from pattern recognition receptors and T cells co-ordinates subcellular trafficking of antigen with both major histocompatibility complex class I and class II molecules and T-cell costimulatory molecules, resulting in the preferential presentation of microbial peptides within a stimulatory context. © 2011 John Wiley & Sons A/S.

Anti-Mycobacterium activity of microbial peptides in a silkworm infection model with Mycobacterium smegmatis.

PubMed

Yagi, Akiho; Uchida, Ryuji; Hamamoto, Hiroshi; Sekimizu, Kazuhisa; Kimura, Ken-Ichi; Tomoda, Hiroshi

2017-05-01

An in vivo-mimic silkworm infection model with Mycobacterium smegmatis was established. When silkworms were raised at 37 °C following an injection of M. smegmatis cells (1.25 × 10 7 CFU larva -1  g -1 ) into the silkworm hemolymph, they died within 48 h. Under these conditions, four microbial peptides with anti-M. smegmatis activity, lariatin A, calpinactam, lysocin E and propeptin, exerted therapeutic effects in a dose-dependent manner, and these are also clinically used agents that are active against Mycobacterium tuberculosis. These results indicate that the silkworm infection model with M. smegmatis is practically useful for the screening of therapeutically effective anti-M. tuberculosis antibiotics.

Microbial decomposers not constrained by climate history along a Mediterranean climate gradient in southern California.

PubMed

Baker, Nameer R; Khalili, Banafshe; Martiny, Jennifer B H; Allison, Steven D

2018-06-01

Microbial decomposers mediate the return of CO 2 to the atmosphere by producing extracellular enzymes to degrade complex plant polymers, making plant carbon available for metabolism. Determining if and how these decomposer communities are constrained in their ability to degrade plant litter is necessary for predicting how carbon cycling will be affected by future climate change. We analyzed mass loss, litter chemistry, microbial biomass, extracellular enzyme activities, and enzyme temperature sensitivities in grassland litter transplanted along a Mediterranean climate gradient in southern California. Microbial community composition was manipulated by caging litter within bags made of nylon membrane that prevent microbial immigration. To test whether grassland microbes were constrained by climate history, half of the bags were inoculated with local microbial communities native to each gradient site. We determined that temperature and precipitation likely interact to limit microbial decomposition in the extreme sites along our gradient. Despite their unique climate history, grassland microbial communities were not restricted in their ability to decompose litter under different climate conditions across the gradient, although microbial communities across our gradient may be restricted in their ability to degrade different types of litter. We did find some evidence that local microbial communities were optimized based on climate, but local microbial taxa that proliferated after inoculation into litterbags did not enhance litter decomposition. Our results suggest that microbial community composition does not constrain C-cycling rates under climate change in our system, but optimization to particular resource environments may act as more general constraints on microbial communities. © 2018 by the Ecological Society of America.

Susceptibility of green and conventional building materials to microbial growth.

PubMed

Mensah-Attipoe, J; Reponen, T; Salmela, A; Veijalainen, A-M; Pasanen, P

2015-06-01

Green building materials are becoming more popular. However, little is known about their ability to support or limit microbial growth. The growth of fungi was evaluated on five building materials. Two green, two conventional building materials and wood as a positive control were selected. The materials were inoculated with Aspergillus versicolor, Cladosporium cladosporioides and Penicillium brevicompactum, in the absence and presence of house dust. Microbial growth was assessed at four different time points by cultivation and determining fungal biomass using the N-acetylhexosaminidase (NAHA) enzyme assay. No clear differences were seen between green and conventional building materials in their susceptibility to support microbial growth. The presence of dust, an external source of nutrients, promoted growth of all the fungal species similarly on green and conventional materials. The results also showed a correlation coefficient ranging from 0.81 to 0.88 between NAHA activity and culturable counts. The results suggest that the growth of microbes on a material surface depends on the availability of organic matter rather than the classification of the material as green or conventional. NAHA activity and culturability correlated well indicating that the two methods used in the experiments gave similar trends for the growth of fungi on material surfaces. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Microbial minorities modulate methane consumption through niche partitioning

PubMed Central

Bodelier, Paul LE; Meima-Franke, Marion; Hordijk, Cornelis A; Steenbergh, Anne K; Hefting, Mariet M; Bodrossy, Levente; von Bergen, Martin; Seifert, Jana

2013-01-01

Microbes catalyze all major geochemical cycles on earth. However, the role of microbial traits and community composition in biogeochemical cycles is still poorly understood mainly due to the inability to assess the community members that are actually performing biogeochemical conversions in complex environmental samples. Here we applied a polyphasic approach to assess the role of microbial community composition in modulating methane emission from a riparian floodplain. We show that the dynamics and intensity of methane consumption in riparian wetlands coincide with relative abundance and activity of specific subgroups of methane-oxidizing bacteria (MOB), which can be considered as a minor component of the microbial community in this ecosystem. Microarray-based community composition analyses demonstrated linear relationships of MOB diversity parameters and in vitro methane consumption. Incubations using intact cores in combination with stable isotope labeling of lipids and proteins corroborated the correlative evidence from in vitro incubations demonstrating γ-proteobacterial MOB subgroups to be responsible for methane oxidation. The results obtained within the riparian flooding gradient collectively demonstrate that niche partitioning of MOB within a community comprised of a very limited amount of active species modulates methane consumption and emission from this wetland. The implications of the results obtained for biodiversity–ecosystem functioning are discussed with special reference to the role of spatial and temporal heterogeneity and functional redundancy. PMID:23788331

Air sampling methods to evaluate microbial contamination in operating theatres: results of a comparative study in an orthopaedics department.

PubMed

Napoli, C; Tafuri, S; Montenegro, L; Cassano, M; Notarnicola, A; Lattarulo, S; Montagna, M T; Moretti, B

2012-02-01

To evaluate the level of microbial contamination of air in operating theatres using active [i.e. surface air system (SAS)] and passive [i.e. index of microbial air contamination (IMA) and nitrocellulose membranes positioned near the wound] sampling systems. Sampling was performed between January 2010 and January 2011 in the operating theatre of the orthopaedics department in a university hospital in Southern Italy. During surgery, the mean bacterial loads recorded were 2232.9 colony-forming units (cfu)/m(2)/h with the IMA method, 123.2 cfu/m(3) with the SAS method and 2768.2 cfu/m(2)/h with the nitrocellulose membranes. Correlation was found between the results of the three methods. Staphylococcus aureus was detected in 12 of 60 operations (20%) with the membranes, five (8.3%) operations with the SAS method, and three operations (5%) with the IMA method. Use of nitrocellulose membranes placed near a wound is a valid method for measuring the microbial contamination of air. This method was more sensitive than the IMA method and was not subject to any calibration bias, unlike active air monitoring systems. Copyright © 2011 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

Microbial minorities modulate methane consumption through niche partitioning.

PubMed

Bodelier, Paul L E; Meima-Franke, Marion; Hordijk, Cornelis A; Steenbergh, Anne K; Hefting, Mariet M; Bodrossy, Levente; von Bergen, Martin; Seifert, Jana

2013-11-01

Microbes catalyze all major geochemical cycles on earth. However, the role of microbial traits and community composition in biogeochemical cycles is still poorly understood mainly due to the inability to assess the community members that are actually performing biogeochemical conversions in complex environmental samples. Here we applied a polyphasic approach to assess the role of microbial community composition in modulating methane emission from a riparian floodplain. We show that the dynamics and intensity of methane consumption in riparian wetlands coincide with relative abundance and activity of specific subgroups of methane-oxidizing bacteria (MOB), which can be considered as a minor component of the microbial community in this ecosystem. Microarray-based community composition analyses demonstrated linear relationships of MOB diversity parameters and in vitro methane consumption. Incubations using intact cores in combination with stable isotope labeling of lipids and proteins corroborated the correlative evidence from in vitro incubations demonstrating γ-proteobacterial MOB subgroups to be responsible for methane oxidation. The results obtained within the riparian flooding gradient collectively demonstrate that niche partitioning of MOB within a community comprised of a very limited amount of active species modulates methane consumption and emission from this wetland. The implications of the results obtained for biodiversity-ecosystem functioning are discussed with special reference to the role of spatial and temporal heterogeneity and functional redundancy.

Gene finding in metatranscriptomic sequences.

PubMed

Ismail, Wazim Mohammed; Ye, Yuzhen; Tang, Haixu

2014-01-01

Metatranscriptomic sequencing is a highly sensitive bioassay of functional activity in a microbial community, providing complementary information to the metagenomic sequencing of the community. The acquisition of the metatranscriptomic sequences will enable us to refine the annotations of the metagenomes, and to study the gene activities and their regulation in complex microbial communities and their dynamics. In this paper, we present TransGeneScan, a software tool for finding genes in assembled transcripts from metatranscriptomic sequences. By incorporating several features of metatranscriptomic sequencing, including strand-specificity, short intergenic regions, and putative antisense transcripts into a Hidden Markov Model, TranGeneScan can predict a sense transcript containing one or multiple genes (in an operon) or an antisense transcript. We tested TransGeneScan on a mock metatranscriptomic data set containing three known bacterial genomes. The results showed that TranGeneScan performs better than metagenomic gene finders (MetaGeneMark and FragGeneScan) on predicting protein coding genes in assembled transcripts, and achieves comparable or even higher accuracy than gene finders for microbial genomes (Glimmer and GeneMark). These results imply, with the assistance of metatranscriptomic sequencing, we can obtain a broad and precise picture about the genes (and their functions) in a microbial community. TransGeneScan is available as open-source software on SourceForge at https://sourceforge.net/projects/transgenescan/.

Assessing the impact of nano- and micro-scale zerovalent iron particles on soil microbial activities: particle reactivity interferes with assay conditions and interpretation of genuine microbial effects.

PubMed

Cullen, Laurence G; Tilston, Emma L; Mitchell, Geoff R; Collins, Chris D; Shaw, Liz J

2011-03-01

The effects of nano-scale and micro-scale zerovalent iron (nZVI and mZVI) particles on general (dehydrogenase and hydrolase) and specific (ammonia oxidation potential, AOP) activities mediated by the microbial community in an uncontaminated soil were examined. nZVI (diameter 12.5 nm; 10 mg g⁻¹ soil) apparently inhibited AOP and nZVI and mZVI apparently stimulated dehydrogenase activity but had minimal influence on hydrolase activity. Sterile experiments revealed that the apparent inhibition of AOP could not be interpreted as such due to the confounding action of the particles, whereas, the nZVI-enhanced dehydrogenase activity could represent the genuine response of a stimulated microbial population or an artifact of ZVI reactivity. Overall, there was no evidence for negative effects of nZVI or mZVI on the processes studied. When examining the impact of redox active particles such as ZVI on microbial oxidation-reduction reactions, potential confounding effects of the test particles on assay conditions should be considered. Copyright © 2010 Elsevier Ltd. All rights reserved.

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

The effects of plant nutritional strategy on soil microbial denitrification activity through rhizosphere primary metabolites.

PubMed

Guyonnet, Julien P; Vautrin, Florian; Meiffren, Guillaume; Labois, Clément; Cantarel, Amélie A M; Michalet, Serge; Comte, Gilles; Haichar, Feth El Zahar

2017-04-01

The aim of this study was to determine (i) whether plant nutritional strategy affects the composition of primary metabolites exuded into the rhizosphere and (ii) the impact of exuded metabolites on denitrification activity in soil. We answered this question by analysing primary metabolite content extracted from the root-adhering soil (RAS) and the roots of three grasses representing different nutrient management strategies: conservative (Festuca paniculata), intermediate (Bromus erectus) and exploitative (Dactylis glomerata). We also investigated the impact of primary metabolites on soil microbial denitrification enzyme activity without carbon addition, comparing for each plant RAS and bulk soils. Our data show that plant nutritional strategy impacts on primary metabolite composition of root extracts or RAS. Further we show, for the first time, that RAS-extracted primary metabolites are probably better indicators to explain plant nutrient strategy than root-extracted ones. In addition, our results show that some primary metabolites present in the RAS were well correlated with soil microbial denitrification activity with positive relationships found between denitrification and the presence of some organic acids and negative ones with the presence of xylose. We demonstrated that the analysis of primary metabolites extracted from the RAS is probably more pertinent to evaluate the impact of plant on soil microbial community functioning. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Are antimicrobial defences in bird eggs related to climatic conditions associated with risk of trans-shell microbial infection?

PubMed

Horrocks, Nicholas Pc; Hine, Kathryn; Hegemann, Arne; Ndithia, Henry K; Shobrak, Mohammed; Ostrowski, Stéphane; Williams, Joseph B; Matson, Kevin D; Tieleman, B Irene

2014-01-01

All bird eggs are exposed to microbes in the environment, which if transmitted to the developing embryo, could cause hatching failure. However, the risk of trans-shell infection varies with environmental conditions and is higher for eggs laid in wetter environments. This might relate to generally higher microbial abundances and diversity in more humid environments, including on the surface of eggshells, as well as the need for moisture to facilitate microbial penetration of the eggshell. To protect against microbial infection, the albumen of avian eggs contains antimicrobial proteins, including lysozyme and ovotransferrin. We tested whether lysozyme and ovotransferrin activities varied in eggs of larks (Alaudidae) living along an arid-mesic gradient of environmental aridity, which we used as a proxy for risk of trans-shell infection. Contrary to expectations, lysozyme activity was highest in eggs from hotter, more arid locations, where we predicted the risk of trans-shell infection would be lower. Ovotransferrin concentrations did not vary with climatic factors. Temperature was a much better predictor of antimicrobial protein activity than precipitation, a result inconsistent with studies stressing the importance of moisture for trans-shell infection. Our study raises interesting questions about the links between temperature and lysozyme activity in eggs, but we find no support for the hypothesis that antimicrobial protein deposition is higher in eggs laid in wetter environments.

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.

Disconnect of microbial structure and function: enzyme activities and bacterial communities in nascent stream corridors.

PubMed

Frossard, Aline; Gerull, Linda; Mutz, Michael; Gessner, Mark O

2012-03-01

A fundamental issue in microbial and general ecology is the question to what extent environmental conditions dictate the structure of communities and the linkages with functional properties of ecosystems (that is, ecosystem function). We approached this question by taking advantage of environmental gradients established in soil and sediments of small stream corridors in a recently created, early successional catchment. Specifically, we determined spatial and temporal patterns of bacterial community structure and their linkages with potential microbial enzyme activities along the hydrological flow paths of the catchment. Soil and sediments were sampled in a total of 15 sites on four occasions spread throughout a year. Denaturing gradient gel electrophoresis (DGGE) was used to characterize bacterial communities, and substrate analogs linked to fluorescent molecules served to track 10 different enzymes as specific measures of ecosystem function. Potential enzyme activities varied little among sites, despite contrasting environmental conditions, especially in terms of water availability. Temporal changes, in contrast, were pronounced and remarkably variable among the enzymes tested. This suggests much greater importance of temporal dynamics than spatial heterogeneity in affecting specific ecosystem functions. Most strikingly, bacterial community structure revealed neither temporal nor spatial patterns. The resulting disconnect between bacterial community structure and potential enzyme activities indicates high functional redundancy within microbial communities even in the physically and biologically simplified stream corridors of early successional landscapes.

Effects of enhanced UV-B radiation on the diversity and activity of soil microorganism of alpine meadow ecosystem in Qinghai-Tibet Plateau.

PubMed

Niu, Fujun; He, Junxia; Zhang, Gaosen; Liu, Xiaomei; Liu, Wei; Dong, Maoxing; Wu, Fasi; Liu, Yongjun; Ma, Xiaojun; An, Lizhe; Feng, Huyuan

2014-12-01

The effects of enhanced UV-B radiation on abundance, community composition and the total microbial activity of soil bacteria in alpine meadow ecosystem of Qinghai-Tibet Plateau were investigated. Traditional counting and 16S rRNA gene sequencing were used to investigate the culturable bacteria and their composition in soil, meanwhile the total microbial activity was measured by microcalorimetry. The population of soil culturable bacteria was slightly reduced with the enhanced UV-B radiation in both of the two depths, 2.46 × 10(6) CFU/g in upper layer (0-10 cm), 1.44 × 10(6) CFU/g in under layer (10-20 cm), comparing with the control (2.94 × 10(6) CFU/g in upper layer, 1.65 × 10(6) CFU/g in under layer), although the difference was not statistically significant (P > 0.05). However, the bacteria diversity decreased obviously due to enhanced UV-B, the number of species for upper layer was decreased from 20 to 13, and from 16 to 13 for the lower layer. The distribution of species was also quite different between the two layers. Another obvious decrease induced by enhanced UV-B radiation was in the total soil microbial activities, which was represented by the microbial growth rate constant (k) in this study. The results indicated that the culturable bacteria community composition and the total activity of soil microbes have been considerably changed by the enhanced UV-B radiation.

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.

Dynamics of microbial community composition and function during in-situ bioremediation of a uranium-contaminated aquifer

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

Nostrand, J.D. Van; Wu, L.; Wu, W.M.

2010-08-15

A pilot-scale system was established to examine the feasibility of in situ U(VI) immobilization at a highly contaminated aquifer (U.S. DOE Integrated Field Research Challenge site, Oak Ridge, TN). Ethanol was injected intermittently as an electron donor to stimulate microbial U(VI) reduction, and U(VI) concentrations fell to below the Environmental Protection Agency drinking water standard (0.03 mg liter{sup -1}). Microbial communities from three monitoring wells were examined during active U(VI) reduction and maintenance phases with GeoChip, a high-density, comprehensive functional gene array. The overall microbial community structure exhibited a considerable shift over the remediation phases examined. GeoChip-based analysis revealed thatmore » Fe(III)-reducing bacterial (FeRB), nitrate-reducing bacterial (NRB), and sulfate-reducing bacterial (SRB) functional populations reached their highest levels during the active U(VI) reduction phase (days 137 to 370), in which denitrification and Fe(III) and sulfate reduction occurred sequentially. A gradual decrease in these functional populations occurred when reduction reactions stabilized, suggesting that these functional populations could play an important role in both active U(VI) reduction and maintenance of the stability of reduced U(IV). These results suggest that addition of electron donors stimulated the microbial community to create biogeochemical conditions favorable to U(VI) reduction and prevent the reduced U(IV) from reoxidation and that functional FeRB, SRB, and NRB populations within this system played key roles in this process.« less

Dynamics of Microbial Community Composition and Function during In Situ Bioremediation of a Uranium-Contaminated Aquifer▿‡

PubMed Central

Van Nostrand, Joy D.; Wu, Liyou; Wu, Wei-Min; Huang, Zhijian; Gentry, Terry J.; Deng, Ye; Carley, Jack; Carroll, Sue; He, Zhili; Gu, Baohua; Luo, Jian; Criddle, Craig S.; Watson, David B.; Jardine, Philip M.; Marsh, Terence L.; Tiedje, James M.; Hazen, Terry C.; Zhou, Jizhong

2011-01-01

A pilot-scale system was established to examine the feasibility of in situ U(VI) immobilization at a highly contaminated aquifer (U.S. DOE Integrated Field Research Challenge site, Oak Ridge, TN). Ethanol was injected intermittently as an electron donor to stimulate microbial U(VI) reduction, and U(VI) concentrations fell to below the Environmental Protection Agency drinking water standard (0.03 mg liter−1). Microbial communities from three monitoring wells were examined during active U(VI) reduction and maintenance phases with GeoChip, a high-density, comprehensive functional gene array. The overall microbial community structure exhibited a considerable shift over the remediation phases examined. GeoChip-based analysis revealed that Fe(III)-reducing bacterial (FeRB), nitrate-reducing bacterial (NRB), and sulfate-reducing bacterial (SRB) functional populations reached their highest levels during the active U(VI) reduction phase (days 137 to 370), in which denitrification and Fe(III) and sulfate reduction occurred sequentially. A gradual decrease in these functional populations occurred when reduction reactions stabilized, suggesting that these functional populations could play an important role in both active U(VI) reduction and maintenance of the stability of reduced U(IV). These results suggest that addition of electron donors stimulated the microbial community to create biogeochemical conditions favorable to U(VI) reduction and prevent the reduced U(IV) from reoxidation and that functional FeRB, SRB, and NRB populations within this system played key roles in this process. PMID:21498771

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.

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.

An investigation into the effects of silver nanoparticles on natural microbial communities in two freshwater sediments.

PubMed

Bao, Shaopan; Wang, Han; Zhang, Weicheng; Xie, Zhicai; Fang, Tao

2016-12-01

The expanding production and usage of commercial silver nanoparticles (AgNPs) will inevitably increase their environmental release, with sediments as a substantial sink. However, little knowledge is available about the potential impacts of AgNPs on freshwater sediment microbial communities, as well as the interactions between microbial communities and biogeochemical factors in AgNPs polluted sediment. To address these issues, two different sediments: a eutrophic freshwater sediment and an oligotrophic freshwater sediment, were exposed to 1 mg/g of either AgNO 3 , uncoated AgNPs (35-nm and 75-nm), or polyvinylpyrrolidone coated AgNPs (PVP-AgNPs) (30-50 nm) for 45 days. High-throughput sequencing of 16S ribosomal ribonucleic acid (16S rRNA) genes using the Illumina MiSeq platform was conducted to evaluate the effects of Ag addition on bacterial community composition. Moreover, sediment microbial biomass and activity were assessed by counting cultivable bacterial number and determining enzyme activities. During the 45-day exposure, compared with no amendment control, some treatments had resulted in significant changes and alterations of sediment biomass or bacterial enzyme activities shortly. While the microbial components at phylum level were rarely affected by AgNPs addition, and as confirmed by the statistical analysis with two-factor analysis of similarities (ANOSIM), there were no significant differences on bacterial community structure across the amended treatments. Redundancy analysis further demonstrated that chemical parameters acid-volatile sulfide (AVS) and simultaneously extracted silver (SE-Ag) in sediment significantly structured the overall bacterial community in sediments spiked with various silver species. In summary, these findings suggested that the ecotoxicity of AgNPs may be attenuated by the transformation under complex environmental conditions and the self-adaption of sediment microbial communities. Copyright © 2016 Elsevier Ltd. All rights reserved.

Marine coastal sediments microbial hydrocarbon degradation processes: contribution of experimental ecology in the omics’era

PubMed Central

Cravo-Laureau, Cristiana; Duran, Robert

2014-01-01

Coastal marine sediments, where important biological processes take place, supply essential ecosystem services. By their location, such ecosystems are particularly exposed to human activities as evidenced by the recent Deepwater Horizon disaster. This catastrophe revealed the importance to better understand the microbial processes involved on hydrocarbon degradation in marine sediments raising strong interests of the scientific community. During the last decade, several studies have shown the key role played by microorganisms in determining the fate of hydrocarbons in oil-polluted sediments but only few have taken into consideration the whole sediment’s complexity. Marine coastal sediment ecosystems are characterized by remarkable heterogeneity, owning high biodiversity and are subjected to fluctuations in environmental conditions, especially to important oxygen oscillations due to tides. Thus, for understanding the fate of hydrocarbons in such environments, it is crucial to study microbial activities, taking into account sediment characteristics, physical-chemical factors (electron acceptors, temperature), nutrients, co-metabolites availability as well as sediment’s reworking due to bioturbation activities. Key information could be collected from in situ studies, which provide an overview of microbial processes, but it is difficult to integrate all parameters involved. Microcosm experiments allow to dissect in-depth some mechanisms involved in hydrocarbon degradation but exclude environmental complexity. To overcome these lacks, strategies have been developed, by creating experiments as close as possible to environmental conditions, for studying natural microbial communities subjected to oil pollution. We present here a review of these approaches, their results and limitation, as well as the promising future of applying “omics” approaches to characterize in-depth microbial communities and metabolic networks involved in hydrocarbon degradation. In addition, we present the main conclusions of our studies in this field. PMID:24575083

Metabolic activity of subterranean microbial communities in deep granitic groundwater supplemented with methane and H2

PubMed Central

Pedersen, Karsten

2013-01-01

It was previously concluded that opposing gradients of sulphate and methane, observations of 16S ribosomal DNA sequences displaying great similarity to those of anaerobic methane-oxidizing Archaea and a peak in sulphide concentration in groundwater from a depth of 250–350 m in Olkiluoto, Finland, indicated proper conditions for methane oxidation with sulphate. In the present research, pressure-resistant, gas-tight circulating systems were constructed to enable the investigation of attached and unattached anaerobic microbial populations from a depth of 327 m in Olkiluoto under in situ pressure (2.4 MPa), diversity, dissolved gas and chemistry conditions. Three parallel flow cell cabinets were configured to allow observation of the influence on microbial metabolic activity of 11 mℳ methane, 11 mℳ methane plus 10 mℳ H2 or 2.1 mℳ O2 plus 7.9 mℳ N2 (that is, air). The concentrations of these gases and of organic acids and carbon, sulphur chemistry, pH and Eh, ATP, numbers of cultivable micro-organisms, and total numbers of cells and bacteriophages were subsequently recorded under batch conditions for 105 days. The system containing H2 and methane displayed microbial reduction of 0.7 mℳ sulphate to sulphide, whereas the system containing only methane resulted in 0.2 mℳ reduced sulphate. The system containing added air became inhibited and displayed no signs of microbial activity. Added H2 and methane induced increasing numbers of lysogenic bacteriophages per cell. It appears likely that a microbial anaerobic methane-oxidizing process coupled to acetate formation and sulphate reduction may be ongoing in aquifers at a depth of 250–350 m in Olkiluoto. PMID:23235288

Organic layer serves as a hotspot of microbial activity and abundance in Arctic tundra soils.

PubMed

Lee, Seung-Hoon; Jang, Inyoung; Chae, Namyi; Choi, Taejin; Kang, Hojeong

2013-02-01

Tundra ecosystem is of importance for its high accumulation of organic carbon and vulnerability to future climate change. Microorganisms play a key role in carbon dynamics of the tundra ecosystem by mineralizing organic carbon. We assessed both ecosystem process rates and community structure of Bacteria, Archaea, and Fungi in different soil layers (surface organic layer and subsurface mineral soil) in an Arctic soil ecosystem located at Spitsbergen, Svalbard during the summer of 2008 by using biochemical and molecular analyses, such as enzymatic assay, terminal restriction fragment length polymorphism (T-RFLP), quantitative polymerase chain reaction (qPCR), and pyrosequencing. Activity of hydrolytic enzymes showed difference according to soil type. For all three microbial communities, the average gene copy number did not significantly differ between soil types. However, archaeal diversities appeared to differ according to soil type, whereas bacterial and fungal diversity indices did not show any variation. Correlation analysis between biogeochemical and microbial parameters exhibited a discriminating pattern according to microbial or soil types. Analysis of the microbial community structure showed that bacterial and archaeal communities have different profiles with unique phylotypes in terms of soil types. Water content and hydrolytic enzymes were found to be related with the structure of bacterial and archaeal communities, whereas soil organic matter (SOM) and total organic carbon (TOC) were related with bacterial communities. The overall results of this study indicate that microbial enzyme activity were generally higher in the organic layer than in mineral soils and that bacterial and archaeal communities differed between the organic layer and mineral soils in the Arctic region. Compared to mineral soil, peat-covered organic layer may represent a hotspot for secondary productivity and nutrient cycling in this ecosystem.

Microbial composition and diversity are associated with plant performance: a case study on long-term fertilization effect on wheat growth in an Ultisol.

PubMed

Li, Lihua; Fan, Fenliang; Song, Alin; Yin, Chang; Cui, Peiyuan; Li, Zhaojun; Liang, Yongchao

2017-06-01

The association between microbial communities and plant growth in long-term fertilization system has not been fully studied. In the present study, impacts of long-term fertilization have been determined on the size and activity of soil microbial communities and wheat performance in a red soil (Ultisol) collected from Qiyang Experimental Station, China. For this, different microbial communities originating from long-term fertilized pig manure (M), mineral fertilizer (NPK), pig manure plus mineral fertilizer (MNPK), and no fertilizer (CK) were used as inocula for the Ultisol tested. Changes in total bacterial and fungal community composition and structures using Ion Torrent sequencing were determined. The results show that the biomass of wheat was significantly higher in both sterilized soil inoculated with NPK (SNPK) and sterilized soil inoculated with MNPK (SMNPK) treatments than in other treatments (P < 0.05). The activities of β-1,4-N-acetylglucosaminidase (NAG) and cellobiohydrolase (CBH) were significantly correlated with wheat biomass. Among the microbial communities, the largest Ascomycota phylum in soils was negatively correlated with β-1,4-glucosidase (βG) (P < 0.05). The phylum Basidiomycota was negatively correlated with plant biomass (PB) and tillers per plant (TI) (P < 0.05). Nonmetric multidimensional scaling analysis shows that fungal community was strongly correlated with long-term fertilization strategy, while the bacterial community was strongly correlated with β-1,4-N-acetylglucosaminidase activity. According to the Mantel test, the growth of wheat was affected by fungal community. Taken together, microbial composition and diversity in soils could be a good player in predicting soil fertility and consequently plant growth.

The implications of microbial and substrate limitation for the fates of carbon in different organic soil horizon types of boreal forest ecosystems: a mechanistically based model analysis

USGS Publications Warehouse

He, Y.; Zhuang, Q.; Harden, Jennifer W.; McGuire, A. David; Fan, Z.; Liu, Y.; Wickland, Kimberly P.

2014-01-01

The large amount of soil carbon in boreal forest ecosystems has the potential to influence the climate system if released in large quantities in response to warming. Thus, there is a need to better understand and represent the environmental sensitivity of soil carbon decomposition. Most soil carbon decomposition models rely on empirical relationships omitting key biogeochemical mechanisms and their response to climate change is highly uncertain. In this study, we developed a multi-layer microbial explicit soil decomposition model framework for boreal forest ecosystems. A thorough sensitivity analysis was conducted to identify dominating biogeochemical processes and to highlight structural limitations. Our results indicate that substrate availability (limited by soil water diffusion and substrate quality) is likely to be a major constraint on soil decomposition in the fibrous horizon (40–60% of soil organic carbon (SOC) pool size variation), while energy limited microbial activity in the amorphous horizon exerts a predominant control on soil decomposition (>70% of SOC pool size variation). Elevated temperature alleviated the energy constraint of microbial activity most notably in amorphous soils, whereas moisture only exhibited a marginal effect on dissolved substrate supply and microbial activity. Our study highlights the different decomposition properties and underlying mechanisms of soil dynamics between fibrous and amorphous soil horizons. Soil decomposition models should consider explicitly representing different boreal soil horizons and soil–microbial interactions to better characterize biogeochemical processes in boreal forest ecosystems. A more comprehensive representation of critical biogeochemical mechanisms of soil moisture effects may be required to improve the performance of the soil model we analyzed in this study.

Gut barrier structure, mucosal immunity and intestinal microbiota in the pathogenesis and treatment of HIV infection.

PubMed

Tincati, Camilla; Douek, Daniel C; Marchetti, Giulia

2016-01-01

Over the past 10 years, extensive work has been carried out in the field of microbial translocation in HIV infection, ranging from studies on its clinical significance to investigations on its pathogenic features. In the present work, we review the most recent findings on this phenomenon, focusing on the predictive role of microbial translocation in HIV-related morbidity and mortality, the mechanisms by which it arises and potential therapeutic approaches. From a clinical perspective, current work has shown that markers of microbial translocation may be useful in predicting clinical events in untreated HIV infection, while conflicting data exist on their role in cART-experienced subjects, possibly due to the inclusion of extremely varied patient populations in cohort studies. Results from studies addressing the pathogenesis of microbial translocation have improved our knowledge of the damage of the gastrointestinal epithelial barrier occurring in HIV infection. However, the extent to which mucosal impairment translates directly to increased gastrointestinal permeability remains an open issue. In this respect, novel work has established a role for IL-17 and IL-22-secreting T cell populations in limiting microbial translocation and systemic T-cell activation/inflammation, thus representing a possible target of immune-therapeutic interventions shown to be promising in the animal model. Further, recent reports have not only confirmed the presence of a dysbiotic intestinal community in the course of HIV infection but have also shown that it may be linked to mucosal damage, microbial translocation and peripheral immune activation. Importantly, technical advances have also shed light on the metabolic activity of gut microbes, highlighting the need for novel therapeutic approaches to correct the function, as well as the composition, of the gastrointestinal microbiota.

TBK1-targeted suppression of TRIF-dependent signaling pathway of Toll-like receptors by 6-shogaol, an active component of ginger.

PubMed

Park, Se-Jeong; Lee, Mi-Young; Son, Bu-Soon; Youn, Hyung-Sun

2009-07-01

Toll-like receptors (TLRs) are primary sensors that detect a wide variety of microbial components involving induction of innate immune responses. After recognition of microbial components, TLRs trigger the activation of myeloid differential factor 88 (MyD88) and Toll-interleukin-1 (IL-1) receptor domain-containing adapter inducing interferon-beta (TRIF)-dependent downstream signaling pathways. 6-Shoagol, an active ingredient of ginger, inhibits the MyD88-dependent signaling pathway by inhibiting inhibitor-kappaB kinase activity. Inhibitor-kappaB kinase is a key kinase in nuclear factor kappaB (NF-kappaB) activation. However, it is not known whether 6-shogaol inhibits the TRIF-dependent signaling pathway. Our goal was to identify the molecular target of 6-shogaol in the TRIF-dependent pathway of TLRs. 6-Shogaol inhibited the activation of interferon-regulatory factor 3 (IRF3) induced by lipopolysaccharide (LPS) and by polyriboinosinic polyribocytidylic acid (poly[I:C]), overexpression of TRIF, TANK-binding kinase1 (TBK1), and IRF3. Furthermore, 6-shogaol inhibited TBK1 activity in vitro. Together, these results suggest that 6-shogaol inhibits the TRIF-dependent signaling pathway of TLRs by targeting TBK1, and, they imply that 6-shogaol can modulate TLR-derived immune/inflammatory target gene expression induced by microbial infection.

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.

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.

Evaluation of the factors governing metal biosorption and metal toxicity in acidic soil isolates

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

Pradhan, A.A.

1992-06-09

This research project was designed to determine the feasibility of microbial biosorption processes for removing metal ions from aqueous systems. A culture of acidic soil actinomycetes, grown in an aerobic environment in a completely mixed, semibatch culture reactor, was used for the study. The experiments were based on removal of copper and lead from test solutions. The anionic systems tested were nitrate, sulfate, and chloride. To determine the factors influencing biosorption and to characterize metal uptake by cellular and extracellular components of the microbial system, a dialysis testing procedure was developed. The effectiveness of biosorption was influenced by pH, initialmore » concentration of metals, type of anionic system, and organic content of the system. respirometric runs were carried out to identify potential inhibitory effects of metal accumulation on microbial activities. In general, metal accumulation resulted in a decrease in the microbial oxygen uptake rate. Also, a lag phase was observed before the onset of the respiratory activity particularly at concentrations of copper and lead greater than 100 ppM.« less

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.

Morphology and ultrastructure of epilithic versus cryptic, microbial growth in lower Cambrian phosphorites from the Montagne Noire, France.

PubMed

Alvaro, J J; Clausen, S

2010-03-01

The lower Cambrian grainy phosphorites of the northern Montagne Noire occur interbedded with grey to black, laminated to massive shales and limestones deposited along the edge of a continental shelf, associated with slope-related facies and unstable substrates. The concentration of phosphate took place by repeated alternations of low sedimentation rates and condensation (hardgrounds), in situ early-diagenetic precipitation of fluorapatite, winnowing and polyphase reworking of previously phosphatized skeletons and hardground-derived clasts. The succession of repeated cycles of sedimentation, phosphate concentration, and reworking led to multi-event phosphate deposits rich in allochthonous particles. Phosphogenesis was primarily mediated by microbial activity, which is evidenced by the abundance of phosphatized putative microbial remains. These occur as smooth and segmented filaments, sheaths, and ovoid-shaped coccoids. These simple morphologies commonly form composite frameworks as a result of their aggregation and entanglement, leading to the record of biofilms, microbial mats, and complex networks. These infested the calcitic skeletonized microfossils that littered the substrate. Microbial activity evidences epilithic (anisotropic coatings on skeletons), euendolithic (perforating skeletal walls), and cryptoendolithic (lining inter- and intraparticulate pores) strategies, the latter dominated by bundles of filaments and globular clusters that grew along the cavities of helcionellids and hyoliths. According to their epilithic versus cryptic strategies, microbial populations that penetrated and dwelled inside hard skeletal substrates show different network and colonial morphologies. These early Cambrian shell concentrations were the loci of a stepwise colonization made by saprophytic to mutualistic, cyanobacterial-fungal consortia. Their euendolithic and cryptoendolithic ecological niches provided microbial refugia to manage the grazing impact mainly led by metazoans.