Stoichiometry of microbial carbon use efficiency in soils

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

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

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

Stoichiometry of microbial carbon use efficiency in soils

DOE PAGES

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

2016-03-23

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

Biofiltration of airborne VOCs with green wall systems-Microbial and chemical dynamics.

PubMed

Mikkonen, A; Li, T; Vesala, M; Saarenheimo, J; Ahonen, V; Kärenlampi, S; Blande, J D; Tiirola, M; Tervahauta, A

2018-05-06

Botanical air filtration is a promising technology for reducing indoor air contaminants, but the underlying mechanisms need better understanding. Here, we made a set of chamber fumigation experiments of up to 16 weeks of duration, to study the filtration efficiencies for seven volatile organic compounds (VOCs; decane, toluene, 2-ethylhexanol, α-pinene, octane, benzene, and xylene) and to monitor microbial dynamics in simulated green wall systems. Biofiltration functioned on sub-ppm VOC levels without concentration-dependence. Airflow through the growth medium was needed for efficient removal of chemically diverse VOCs, and the use of optimized commercial growth medium further improved the efficiency compared with soil and Leca granules. Experimental green wall simulations using these components were immediately effective, indicating that initial VOC removal was largely abiotic. Golden pothos plants had a small additional positive impact on VOC filtration and bacterial diversity in the green wall system. Proteobacteria dominated the microbiota of rhizosphere and irrigation water. Airborne VOCs shaped the microbial communities, enriching potential VOC-utilizing bacteria (especially Nevskiaceae and Patulibacteraceae) in the irrigation water, where much of the VOC degradation capacity of the biofiltration systems resided. These results clearly show the benefits of active air circulation and optimized growth media in modern green wall systems. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Innovative strategies to overcome biofilm resistance.

PubMed

Taraszkiewicz, Aleksandra; Fila, Grzegorz; Grinholc, Mariusz; Nakonieczna, Joanna

2013-01-01

We review the recent literature concerning the efficiency of antimicrobial photodynamic inactivation toward various microbial species in planktonic and biofilm cultures. The review is mainly focused on biofilm-growing microrganisms because this form of growth poses a threat to chronically infected or immunocompromised patients and is difficult to eradicate from medical devices. We discuss the biofilm formation process and mechanisms of its increased resistance to various antimicrobials. We present, based on data in the literature, strategies for overcoming the problem of biofilm resistance. Factors that have potential for use in increasing the efficiency of the killing of biofilm-forming bacteria include plant extracts, enzymes that disturb the biofilm structure, and other nonenzymatic molecules. We propose combining antimicrobial photodynamic therapy with various antimicrobial and antibiofilm approaches to obtain a synergistic effect to permit efficient microbial growth control at low photosensitizer doses.

[Characteristics of microbial community and operation efficiency in biofilter process for drinking water purification].

PubMed

Xiang, Hong; Lü, Xi-Wu; Yang, Fei; Yin, Li-Hong; Zhu, Guang-Can

2011-04-01

In order to explore characteristics of microbial community and operation efficiency in biofilter (biologically-enhanced active filter and biological activated carbon filter) process for drinking water purification, Biolog and polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) techniques were applied to analyze the metabolic function and structure of microbial community developing in biofilters. Water quality parameters, such as NH; -N, NO; -N, permanganate index, UV254 and BDOC etc, were determined in inflow and outflow of biofilters for investigation of operation efficiency of the biofilters. The results show that metabolic capacity of microbial community of the raw water is reduced after the biofilters, which reflect that metabolically active microbial communities in the raw water can be intercepted by biofilters. After 6 months operation of biofilters, the metabolic profiles of microbial communities are similar between two kinds of biologically-enhanced active filters, and utilization of carbon sources of microbial communities in the two filters are 73.4% and 75.5%, respectively. The metabolic profiles of microbial communities in two biological activated carbon filters showed significant difference. The carbon source utilization rate of microbial community in granule-activated carbon filter is 79.6%, which is obviously higher than 53.8% of the rate in the columnar activated carbon filter (p < 0.01). The analysis results of PCR-SSCP indicate that microbial communities in each biofilter are variety, but the structure of dominant microorganisms is similar among different biofilters. The results also show that the packing materials had little effect on the structure and metabolic function of microbial community in biologically-enhanced active filters, and the difference between two biofilters for the water purification efficiency was not significant (p > 0.05). However, in biological activated carbon filters, granule-activated carbon is conducive to microbial growth and reproduction, and the microbial communities in the biofilter present high metabolic activities, and the removal efficiency for NH4(+)-N, permanganate index and BDOC is better than the columnar activated carbon filter(p < 0.05). The results also suggest that operation efficiency of biofilter is related to the metabolic capacity of microbial community in biofilter.

Warm-adapted microbial communities enhance their carbon-use efficiency in warmed soils

NASA Astrophysics Data System (ADS)

Rousk, Johannes; Frey, Serita

2017-04-01

Ecosystem models predict that climate warming will stimulate microbial decomposition of soil carbon (C), resulting in a positive feedback to increasing temperatures. The current generation of models assume that the temperature sensitivities of microbial processes do not respond to warming. However, recent studies have suggested that the ability of microbial communities to adapt to warming can lead both strengthened and weakened feedbacks. A further complication is that the balance between microbial C used for growth to that used for respiration - the microbial carbon-use efficiency (CUE) - also has been shown through both modelling and empirical study to respond to warming. In our study, we set out to assess how chronic warming (+5°C over ambient during 9 years) of a temperate hardwood forest floor (Harvard Forest LTER, USA) affected temperature sensitivities of microbial processes in soil. To do this, we first determined the temperature relationships for bacterial growth, fungal growth, and respiration in plots exposed to warmed or ambient conditions. Secondly, we parametrised the established temperature functions microbial growth and respiration with plot-specific measured soil temperature data at a hourly time-resolution over the course of 3 years to estimate the real-time variation of in situ microbial C production and respiration. To estimate the microbial CUE, we also divided the microbial C production with the sum of microbial C production and respiration as a proxy for substrate use. We found that warm-adapted bacterial and fungal communities both shifted their temperature relationships to grow at higher rates in warm conditions which coincided with reduced rates at cool conditions. As such, their optimal temperature (Topt), minimum temperature (Tmin) and temperature sensitivity (Q10) were all increased. The temperature relationship for temperature, in contrast, was only marginally shifted in the same direction, but at a much smaller effect size, with negligible changes in Topt, Tmin and Q10 for respiration. When these physiological changes were scaled with soil temperature data to estimate real-time variation in situ during three years, the warm-adaptation resulted in elevated microbial CUEs during summer temperatures in warm-adapted communities and reduced microbial CUEs during winter temperatures. By comparing simulated microbial CUEs in cold-adapted communities exposed to warmed conditions to microbial CUEs in the warm-adapted communities exposed to those temperatures, we could demonstrate that the shifts towards warm-adapted microbial communities had selected for elevated microbial CUEs for the full range of in situ soil temperatures during three years. Our results suggest that microbial adaptation to warming will enhance microbial CUEs, shifting their balance of C use from respiration to biomass production. If our estimates scale to ecosystem level, this would imply that warm-adapted microbial communities will ultimately have the potential to store more C in soil than their cold-adapted counter parts could when exposed to warmer temperatures.

Microbial Growth and Metabolism in Soil - Refining the Interpretation of Carbon Use Efficiency

NASA Astrophysics Data System (ADS)

Geyer, K.; Frey, S. D.

2016-12-01

Carbon use efficiency (CUE) describes a critical step in the terrestrial carbon cycle where microorganisms partition organic carbon (C) between stabilized organic forms and CO2. Application of this concept, however, begins with accurate measurements of CUE. Both traditional and developing approaches still depend on numerous assumptions that render them difficult to interpret and potentially incompatible with one another. Here we explore the soil processes inherent to traditional (e.g., substrate-based, biomass-based) and emerging (e.g., growth rate-based, calorimetry) CUE techniques in order to better understand the information they provide. Soil from the Harvard Forest Long Term Ecological Research (LTER) site in Massachusetts, USA, was amended with both 13C-glucose and 18O-water and monitored over 72 h for changes in dissolved organic carbon (DOC), respiration (R), microbial biomass (MB), DNA synthesis, and heat flux (Q). Four different CUE estimates were calculated: 1) (ΔDOC - R)/ΔDOC (substrate-based), 2) Δ13C-MB/(Δ13C-MB + R) (biomass-based), 3) Δ18O-DNA/(Δ18O-DNA + R) (growth rate-based), 4) Q/R (energy-based). Our results indicate that microbial growth (estimated by both 13C and 18O techniques) was delayed for 40 h after amendment even though DOC had declined to pre-amendment levels within 48 h. Respiration and heat flux also peaked after 40 h. Although these soils have a relatively high organic C content (5% C), respired CO2 was greater than 88% glucose-derived throughout the experiment. All estimates of microbial growth (Spearman's ρ >0.83, p<0.01) and efficiency (Spearman's ρ >0.65, p<0.05) were positively correlated, but strong differences in the magnitude of CUE suggest incomplete C accounting. This work increases the transparency of CUE techniques for researchers looking to choose the most appropriate measure for their scale of inquiry or to use CUE estimates in modeling applications.

Maximizing efficiency of rumen microbial protein production

PubMed Central

Hackmann, Timothy J.; Firkins, Jeffrey L.

2015-01-01

Rumen microbes produce cellular protein inefficiently partly because they do not direct all ATP toward growth. They direct some ATP toward maintenance functions, as long-recognized, but they also direct ATP toward reserve carbohydrate synthesis and energy spilling (futile cycles that dissipate heat). Rumen microbes expend ATP by vacillating between (1) accumulation of reserve carbohydrate after feeding (during carbohydrate excess) and (2) mobilization of that carbohydrate thereafter (during carbohydrate limitation). Protozoa account for most accumulation of reserve carbohydrate, and in competition experiments, protozoa accumulated nearly 35-fold more reserve carbohydrate than bacteria. Some pure cultures of bacteria spill energy, but only recently have mixed rumen communities been recognized as capable of the same. When these communities were dosed glucose in vitro, energy spilling could account for nearly 40% of heat production. We suspect that cycling of glycogen (a major reserve carbohydrate) is a major mechanism of spilling; such cycling has already been observed in single-species cultures of protozoa and bacteria. Interconversions of short-chain fatty acids (SCFA) may also expend ATP and depress efficiency of microbial protein production. These interconversions may involve extensive cycling of intermediates, such as cycling of acetate during butyrate production in certain butyrivibrios. We speculate this cycling may expend ATP directly or indirectly. By further quantifying the impact of reserve carbohydrate accumulation, energy spilling, and SCFA interconversions on growth efficiency, we can improve prediction of microbial protein production and guide efforts to improve efficiency of microbial protein production in the rumen. PMID:26029197

An Exogenous Surfactant-Producing Bacillus subtilis Facilitates Indigenous Microbial Enhanced Oil Recovery

PubMed Central

Gao, Peike; Li, Guoqiang; Li, Yanshu; Li, Yan; Tian, Huimei; Wang, Yansen; Zhou, Jiefang; Ma, Ting

2016-01-01

This study used an exogenous lipopeptide-producing Bacillus subtilis to strengthen the indigenous microbial enhanced oil recovery (IMEOR) process in a water-flooded reservoir in the laboratory. The microbial processes and driving mechanisms were investigated in terms of the changes in oil properties and the interplay between the exogenous B. subtilis and indigenous microbial populations. The exogenous B. subtilis is a lipopeptide producer, with a short growth cycle and no oil-degrading ability. The B. subtilis facilitates the IMEOR process through improving oil emulsification and accelerating microbial growth with oil as the carbon source. Microbial community studies using quantitative PCR and high-throughput sequencing revealed that the exogenous B. subtilis could live together with reservoir microbial populations, and did not exert an observable inhibitory effect on the indigenous microbial populations during nutrient stimulation. Core-flooding tests showed that the combined exogenous and indigenous microbial flooding increased oil displacement efficiency by 16.71%, compared with 7.59% in the control where only nutrients were added, demonstrating the application potential in enhanced oil recovery in water-flooded reservoirs, in particular, for reservoirs where IMEOR treatment cannot effectively improve oil recovery. PMID:26925051

An Exogenous Surfactant-Producing Bacillus subtilis Facilitates Indigenous Microbial Enhanced Oil Recovery.

PubMed

Gao, Peike; Li, Guoqiang; Li, Yanshu; Li, Yan; Tian, Huimei; Wang, Yansen; Zhou, Jiefang; Ma, Ting

2016-01-01

This study used an exogenous lipopeptide-producing Bacillus subtilis to strengthen the indigenous microbial enhanced oil recovery (IMEOR) process in a water-flooded reservoir in the laboratory. The microbial processes and driving mechanisms were investigated in terms of the changes in oil properties and the interplay between the exogenous B. subtilis and indigenous microbial populations. The exogenous B. subtilis is a lipopeptide producer, with a short growth cycle and no oil-degrading ability. The B. subtilis facilitates the IMEOR process through improving oil emulsification and accelerating microbial growth with oil as the carbon source. Microbial community studies using quantitative PCR and high-throughput sequencing revealed that the exogenous B. subtilis could live together with reservoir microbial populations, and did not exert an observable inhibitory effect on the indigenous microbial populations during nutrient stimulation. Core-flooding tests showed that the combined exogenous and indigenous microbial flooding increased oil displacement efficiency by 16.71%, compared with 7.59% in the control where only nutrients were added, demonstrating the application potential in enhanced oil recovery in water-flooded reservoirs, in particular, for reservoirs where IMEOR treatment cannot effectively improve oil recovery.

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

NASA Astrophysics Data System (ADS)

Hofmann, Roland; Griebler, Christian

2017-04-01

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

Roof-harvested rainwater for potable purposes: application of solar disinfection (SODIS) and limitations.

PubMed

Amin, Muhammad Tahir; Han, Mooyoung

2009-01-01

Efficiency of solar disinfection (SODIS) was evaluated for the potability of rainwater in view of the increasing water and energy crises especially in developing countries. Rainwater samples were collected from an underground storage tank in 2 L polyethylene terephthalate (PET) bottles and SODIS efficiency was evaluated at different weather conditions. For optimizing SODIS, PET bottles with different backing surfaces to enhance the optical and thermal effects of SODIS were used and different physicochemical parameters were selected and evaluated along with microbial re-growth observations and calculating microbial decay constants. Total and fecal coliforms were used along with Escherichia Coli and Heterotrophic Plate Counts (HPC) as basic microbial and indicator organisms of water quality. For irradiance less than 600 W/m(2), reflective type PET bottles were best types while for radiations greater than 700 W/m(2), absorptive type PET bottles offered best solution due to the synergistic effects of both thermal and UV radiations. Microbial inactivation did not improve significantly by changing the initial pH and turbidity values but optimum SODIS efficiency is achieved for rainwater with acidic pH and low initial turbidity values by keeping air-spaced PET bottles in undisturbed conditions. Microbial re-growth occurred after one day only at higher turbidity values and with basic pH values. First-order reaction rate constant was in accordance with recent findings for TC but contradicted with previous researches for E. coli. No microbial parameter met drinking water guidelines even under strong experimental weather conditions rendering SODIS ineffective for complete disinfection and hence needed more exposure time or stronger sunlight radiations. With maximum possible storage of rainwater, however, and by using some means for accelerating SODIS process, rainwater can be disinfected and used for potable purposes.

Nitrogen distribution within the soil-plant-microbial system in response to pre-thinning fertilization treatments in Louisiana

Treesearch

Michael A. Blazier; D. Andrew Scott

2006-01-01

Improvements in nitrogen (N) uptake efficiency and plantation growth require refined silvicultural systems that consider soil type, stand development, ecology, and their interactions. On four unthinned, mid-rotation loblolly pine plantations in Louisiana located on a gradient of soil drainage classes, soil, plant, and microbial N dynamics were measured in response to...

Effect of some biotic factors on microbially-induced calcite precipitation in cement mortar.

PubMed

Al-Salloum, Yousef; Abbas, H; Sheikh, Q I; Hadi, S; Alsayed, Saleh; Almusallam, Tarek

2017-02-01

Sporosarcina pasteurii , a common soil bacterium has been tested for microbial treatment of cement mortar. The present study also seeks to investigate the effects of growth medium, bacterial concentration and different buffers concerning the preparation of bacterial suspensions on the compressive strength of cement mortar. Two growth media, six different suspensions and two bacterial concentrations were used in the study. The influence of growth medium on calcification efficiency of S. pasteurii was insignificant. Significant improvement in the compressive as well as the tensile strength of cement mortar was observed. Microbial mineral precipitation visualized by Scanning Electron Microscopy (SEM) shows fibrous material that increased the strength of cement mortar. Formation of thin strands of fillers observed through SEM micrographs improves the pore structure, impermeability and thus the compressive as well as the tensile strengths of the cement mortar. The type of substrate and its molarity have a significant influence on the strength of cement mortar.

Global microbialization of coral reefs.

PubMed

Haas, Andreas F; Fairoz, Mohamed F M; Kelly, Linda W; Nelson, Craig E; Dinsdale, Elizabeth A; Edwards, Robert A; Giles, Steve; Hatay, Mark; Hisakawa, Nao; Knowles, Ben; Lim, Yan Wei; Maughan, Heather; Pantos, Olga; Roach, Ty N F; Sanchez, Savannah E; Silveira, Cynthia B; Sandin, Stuart; Smith, Jennifer E; Rohwer, Forest

2016-04-25

Microbialization refers to the observed shift in ecosystem trophic structure towards higher microbial biomass and energy use. On coral reefs, the proximal causes of microbialization are overfishing and eutrophication, both of which facilitate enhanced growth of fleshy algae, conferring a competitive advantage over calcifying corals and coralline algae. The proposed mechanism for this competitive advantage is the DDAM positive feedback loop (dissolved organic carbon (DOC), disease, algae, microorganism), where DOC released by ungrazed fleshy algae supports copiotrophic, potentially pathogenic bacterial communities, ultimately harming corals and maintaining algal competitive dominance. Using an unprecedented data set of >400 samples from 60 coral reef sites, we show that the central DDAM predictions are consistent across three ocean basins. Reef algal cover is positively correlated with lower concentrations of DOC and higher microbial abundances. On turf and fleshy macroalgal-rich reefs, higher relative abundances of copiotrophic microbial taxa were identified. These microbial communities shift their metabolic potential for carbohydrate degradation from the more energy efficient Embden-Meyerhof-Parnas pathway on coral-dominated reefs to the less efficient Entner-Doudoroff and pentose phosphate pathways on algal-dominated reefs. This 'yield-to-power' switch by microorganism directly threatens reefs via increased hypoxia and greater CO2 release from the microbial respiration of DOC.

Introducing a novel interaction model structure for the combined effect of temperature and pH on the microbial growth rate.

PubMed

Akkermans, Simen; Noriega Fernandez, Estefanía; Logist, Filip; Van Impe, Jan F

2017-01-02

Efficient modelling of the microbial growth rate can be performed by combining the effects of individual conditions in a multiplicative way, known as the gamma concept. However, several studies have illustrated that interactions between different effects should be taken into account at stressing environmental conditions to achieve a more accurate description of the growth rate. In this research, a novel approach for modeling the interactions between the effects of environmental conditions on the microbial growth rate is introduced. As a case study, the effect of temperature and pH on the growth rate of Escherichia coli K12 is modeled, based on a set of computer controlled bioreactor experiments performed under static environmental conditions. The models compared in this case study are the gamma model, the model of Augustin and Carlier (2000), the model of Le Marc et al. (2002) and the novel multiplicative interaction model, developed in this paper. This novel model enables the separate identification of interactions between the effects of two (or more) environmental conditions. The comparison of these models focuses on the accuracy, interpretability and compatibility with efficient modeling approaches. Moreover, for the separate effects of temperature and pH, new cardinal parameter model structures are proposed. The novel interaction model contributes to a generic modeling approach, resulting in predictive models that are (i) accurate, (ii) easily identifiable with a limited work load, (iii) modular, and (iv) biologically interpretable. Copyright © 2016. Published by Elsevier B.V.

Understanding Mechanism of Photocatalytic Microbial Decontamination of Environmental Wastewater

PubMed Central

Regmi, Chhabilal; Joshi, Bhupendra; Ray, Schindra K.; Gyawali, Gobinda; Pandey, Ramesh P.

2018-01-01

Several photocatalytic nanoparticles are synthesized and studied for potential application for the degradation of organic and biological wastes. Although these materials degrade organic compounds by advance oxidation process, the exact mechanisms of microbial decontamination remains partially known. Understanding the real mechanisms of these materials for microbial cell death and growth inhibition helps to fabricate more efficient semiconductor photocatalyst for large-scale decontamination of environmental wastewater or industries and hospitals/biomedical labs generating highly pathogenic bacteria and toxic molecules containing liquid waste by designing a reactor. Recent studies on microbial decontamination by photocatalytic nanoparticles and their possible mechanisms of action is highlighted with examples in this mini review. PMID:29541632

Respiration-to-DNA ratio reflects physiological state of microorganisms in root-free and rhizosphere soil

NASA Astrophysics Data System (ADS)

Blagodatskaya, E.; Blagodatsky, S.; Kuzyakov, Y.

2009-04-01

The double-stranded DNA (dsDNA) content in soil can serve as a measure of microbial biomass under near steady-state conditions and quantitatively reflect the exponential microbial growth initiated by substrate addition. The yield of respired CO2 per microbial biomass unit (expressed as DNA content) could be a valuable physiological indicator reflecting state of soil microbial community. Therefore, investigations combining both analyses of DNA content and respiration of soil microorganisms under steady-state and during periods of rapid growth are needed. We studied the relationship between CO2 evolution and microbial dsDNA content in native and glucose-amended samples of root-free and rhizosphere soil under Beta vulgaris (Cambisol, loamy sand from the field experiment of the Institute of Agroecology FAL, Braunschweig, Germany). Quantity of dsDNA was determined by direct DNA isolation from soil with mechanic and enzymatic disruption of microbial cell walls with following spectrofluorimetric detection with PicoGreen (Blagodatskaya et al., 2003). Microbial biomass and the kinetic parameters of microbial growth were estimated by dynamics of the CO2 emission from soil amended with glucose and nutrients (Blagodatsky et al., 2000). The CO2 production rate was measured hourly at 22оС using an automated infrared-gas analyzer system. The overall increase in microbial biomass, DNA content, maximal specific growth rate and therefore, in the fraction of microorganisms with r-strategy were observed in rhizosphere as compared to bulk soil. The rhizosphere effect for microbial respiration, biomass and specific growth rate was more pronounced for plots with half-rate of N fertilizer compared to full N addition. The DNA content was significantly lower in bulk compared to rhizosphere soil both before and during microbial growth initiated by glucose amendment. Addition of glucose to the soil strongly increased the amount of CO2 respired per DNA unit. Without substrate addition the VCO2-to-total DNA ratios were lower than 0.1 µg CO2-C µg-1 total DNA h-1 whereas during exponential microbial growth these values increased consistently and exceeded 1 µg CO2-C µg-1 DNA h-1. Thus, the VCO2-to-total DNA ratio strongly changes along with the physiological state of soil microorganisms and can be used as valuable physiological parameter. In growing microorganisms the quantity of CO2 evolved per unit of newly formed DNA was identical in rhizosphere and root free soil and averaged for 13.5 ± 1.1 µg CO2-C µg-1 newly formed DNA. The CO2 yield per unit of newly formed DNA allows the estimation of microbial growth efficiency and validation of specific growth rates obtained during kinetic analysis of respiration curves. The study was supported by European Commission (Marie Curie IIF program, project MICROSOM) and by Alexander von Humboldt Foundation. References: Blagodatskaya EV, Blagodatskii SA, Anderson TH. 2003. Quantitative Isolation of Microbial DNA from Different Types of Soils of Natural and Agricultural Ecosystems. Microbiology 72(6):744-749. Blagodatsky SA, Heinemeyer O, Richter J. 2000. Estimating the active and total soil microbial biomass by kinetic respiration analysis. Biology and Fertility of Soils 32(1):73-81.

Adaptation of the autotrophic acetogen Sporomusa ovata to methanol accelerates the conversion of CO2 to organic products.

PubMed

Tremblay, Pier-Luc; Höglund, Daniel; Koza, Anna; Bonde, Ida; Zhang, Tian

2015-11-04

Acetogens are efficient microbial catalysts for bioprocesses converting C1 compounds into organic products. Here, an adaptive laboratory evolution approach was implemented to adapt Sporomusa ovata for faster autotrophic metabolism and CO2 conversion to organic chemicals. S. ovata was first adapted to grow quicker autotrophically with methanol, a toxic C1 compound, as the sole substrate. Better growth on different concentrations of methanol and with H2-CO2 indicated the adapted strain had a more efficient autotrophic metabolism and a higher tolerance to solvent. The growth rate on methanol was increased 5-fold. Furthermore, acetate production rate from CO2 with an electrode serving as the electron donor was increased 6.5-fold confirming that the acceleration of the autotrophic metabolism of the adapted strain is independent of the electron donor provided. Whole-genome sequencing, transcriptomic, and biochemical studies revealed that the molecular mechanisms responsible for the novel characteristics of the adapted strain were associated with the methanol oxidation pathway and the Wood-Ljungdahl pathway of acetogens along with biosynthetic pathways, cell wall components, and protein chaperones. The results demonstrate that an efficient strategy to increase rates of CO2 conversion in bioprocesses like microbial electrosynthesis is to evolve the microbial catalyst by adaptive laboratory evolution to optimize its autotrophic metabolism.

Microbial hotspots and hot moments in soil

NASA Astrophysics Data System (ADS)

Kuzyakov, Yakov; Blagodatskaya, Evgenia

2015-04-01

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

Electricity generation in microbial fuel cells using neutral red as an electronophore

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

Park, D.H.; Zeikus, J.G.

2000-04-01

Neutral red (NR) was utilized as an electron mediator in microbial fuel cells consuming glucose to study both its efficiency during electricity generation and its role in altering anaerobic growth and metabolism of Escherichia coli and Actinobacillus succinogenes. A study of chemical fuel cells in which NADH, NR, and ferricyanide were the electron donor, the electronophore, and the electron acceptor, respectively, showed that electrical current produced from NADH was proportional to the concentration of NADH. Fourfold more current was produced from NADH in chemical fuel cells when NR was the electron mediator than when thionin was the electron mediator. Inmore » microbial fuel cells in which E. coli resting cells were used the amount of current produced from glucose when NR was the electron mediator was 10-fold more than the amount produced when thionin was the electron mediator. The amount of electrical energy generated and the amount of current produced from glucose in NR-mediated microbial fuel cells containing either E. coli or A. succinogenes were about 10- and 2-fold greater, respectively, when resting cells were used than when growing cells were used. Cell growth was inhibited substantially when these microbial fuel cells were making current, and more oxidized end products were formed under these conditions. When sewage sludge was used in the fuel cell, stable and equivalent levels of current were obtained with glucose, as observed in the pure-culture experiments. These results suggest that NR is better than other electron mediators used in microbial fuel cells and that sludge production can be decreased while electricity is produced in fuel cells. Their results are discussed in relation to factors that may improve the relatively low electrical efficiencies obtained with microbial fuel cells.« less

Supplementation of direct-fed microbial as an alternative to antibiotic on growth performance, intestinal immune status and epithelial barrier integrity in broiler chicken

USDA-ARS?s Scientific Manuscript database

The objective of this study was to investigate the effects of supplementation of broiler diets with Bacillus subtilis-based probiotics on growth performance, feed efficiency, intestinal cytokine and tight junction (TJ) protein mRNA expression. Day-old broiler chicks (n = 140) were randomly assigned...

Use of natural compounds to improve the microbial stability of Amaranth-based homemade fresh pasta.

PubMed

Del Nobile, M A; Di Benedetto, N; Suriano, N; Conte, A; Lamacchia, C; Corbo, M R; Sinigaglia, M

2009-04-01

A study on the use of natural antimicrobial compounds to improve the microbiological stability of refrigerated amaranth-based homemade fresh pasta is presented in this work. In particular, the antimicrobial activity of thymol, lemon extract, chitosan and grapefruit seed extract (GFSE) has been tested against mesophilic and psychrotrophic bacteria, total coliforms, Staphylococcus spp., yeasts and moulds. A sensory analysis on both fresh and cooked pasta was also run. Results suggest that chitosan and GFSE strongly increase the microbial acceptability limit of the investigated spoilage microorganisms, being the former the most effective. Thymol efficiently reduces the growth of mesophilic bacteria, psychrotrophic bacteria and Staphylococcus spp., whereas it does not affect, substantially, the growth cycle of total coliforms. Lemon extract is the less effective in preventing microbial growth. In fact, it is able to delay only total mesophilic and psychrotrophic bacterial evolution. From a sensorial point of view no significant differences were recorded between the control samples and all the types of loaded amaranth-based pasta.

Strength and stability of microbial plugs in porous media

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

Sarkar, A.K.; Sharma, M.M.; Georgiou, G.

1995-12-31

Mobility reduction induced by the growth and metabolism of bacteria in high-permeability layers of heterogeneous reservoirs is an economically attractive technique to improve sweep efficiency. This paper describes an experimental study conducted in sandpacks using an injected bacterium to investigate the strength and stability of microbial plugs in porous media. Successful convective transport of bacteria is important for achieving sufficient initial bacteria distribution. The chemotactic and diffusive fluxes are probably not significant even under static conditions. Mobility reduction depends upon the initial cell concentrations and increase in cell mass. For single or multiple static or dynamic growth techniques, permeability reductionmore » was approximately 70% of the original permeability. The stability of these microbial plugs to increases in pressure gradient and changes in cell physiology in a nutrient-depleted environment needs to be improved.« less

Isolation and characterization of phosphofungi, and screening of their plant growth-promoting activities.

PubMed

Wang, Xiaohui; Wang, Changdong; Sui, Junkang; Liu, Zhaoyang; Li, Qian; Ji, Chao; Song, Xin; Hu, Yurong; Wang, Changqian; Sa, Rongbo; Zhang, Jiamiao; Du, Jianfeng; Liu, Xunli

2018-04-20

Rhizospheric microorganisms can increase phosphorus availability in the soil. In this regard, the ability of phosphofungi to dissolve insoluble phosphorus compounds is greater than that of phosphate-solubilizing bacteria. The aim of the current study was to identify efficient phosphofungi that could be developed as commercial microbial agents. Among several phosphate-solubilizing fungal isolates screened, strain CS-1 showed the highest phosphorus-solubilization ability. Based on phylogenetic analysis of the internal transcribed spacer region sequence, it was identified as Aspergillus niger. High-performance liquid chromatography analysis revealed that the mechanism of phosphorus solubilization by CS-1 involved the synthesis and secretion of organic acids, mainly oxalic, tartaric, and citric acids. Furthermore, strain CS-1 exhibited other growth-promoting abilities, including efficient potassium release and degradation of crop straw cellulose. These properties help to returning crop residues to the soil, thereby increasing nutrient availability and sustaining organic matter concentration therein. A pot experiment revealed that CS-1 apparently increased the assessed biometric parameters of wheat seedlings, implying the potential of this strain to be developed as a commercial microbial agent. We used Illumina MiSeq sequencing to investigate the microbial community composition in the rhizosphere of uninoculated wheat plants and wheat plants inoculated with the CS-1 strain to obtain insight into the effect of the CS-1 strain inoculation. The data clearly demonstrated that CS-1 significantly reduced the content of pathogenic fungi, including Gibberella, Fusarium, Monographella, Bipolaris, and Volutella, which cause soil-borne diseases in various crops. Strain CS-1 may hence be developed into a microbial agent for plant growth improvement.

Methodology for modeling the microbial contamination of air filters.

PubMed

Joe, Yun Haeng; Yoon, Ki Young; Hwang, Jungho

2014-01-01

In this paper, we propose a theoretical model to simulate microbial growth on contaminated air filters and entrainment of bioaerosols from the filters to an indoor environment. Air filter filtration and antimicrobial efficiencies, and effects of dust particles on these efficiencies, were evaluated. The number of bioaerosols downstream of the filter could be characterized according to three phases: initial, transitional, and stationary. In the initial phase, the number was determined by filtration efficiency, the concentration of dust particles entering the filter, and the flow rate. During the transitional phase, the number of bioaerosols gradually increased up to the stationary phase, at which point no further increase was observed. The antimicrobial efficiency and flow rate were the dominant parameters affecting the number of bioaerosols downstream of the filter in the transitional and stationary phase, respectively. It was found that the nutrient fraction of dust particles entering the filter caused a significant change in the number of bioaerosols in both the transitional and stationary phases. The proposed model would be a solution for predicting the air filter life cycle in terms of microbiological activity by simulating the microbial contamination of the filter.

Biopolymer system for permeability modification in porous media

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

Stepp, A.K.; Bryant, R.S.; Llave, F.M.

1995-12-31

New technologies are needed to reduce the current high rate of well abandonment. Improved sweep efficiency, reservoir conformance, and permeability modification can have a significant impact on oil recovery processes. Microorganisms can be used to selectively plug high-permeability zones to improve sweep efficiency and impart conformance control. Studies of a promising microbial system for polymer production were conducted to evaluate reservoir conditions in which this system would be effective. Factors which can affect microbial growth and polymer production include salinity, pH, temperature, divalent ions, presence of residual oil, and rock matrix. Flask tests and coreflooding experiments were conducted to optimizemore » and evaluate the effectiveness of this system. Nuclear magnetic resonance imaging (NMRI) was used to visualize microbial polymer production in porous media. Changes in fluid distribution within the pore system of the core were detected.« less

Enhanced bioremediation of lead-contaminated soil by Solanum nigrum L. with Mucor circinelloides.

PubMed

Sun, Liqun; Cao, Xiufeng; Li, Min; Zhang, Xu; Li, Xinxin; Cui, Zhaojie

2017-04-01

Strain selected from mine tailings in Anshan for Pb bioremediation was characterized at the genetic level by internal transcribed spacer (ITS) sequencing. Results revealed that the strain belongs to Mucor circinelloides. Bioremediation of lead-contaminated soil was conducted using Solanum nigrum L. combined with M. circinelloides. The removal efficacy was in the order microbial/phytoremediation > phytoremediation > microbial remediation > control. The bioremediation rates were 58.6, 47.2, and 40.2% in microbial/phytoremediation, microbial remediation, and phytoremediation groups, respectively. Inoculating soil with M. circinelloides enhanced Pb removal and S. nigrum L. growth. The bioaccumulation factor (BF, 1.43), enrichment factor (EF, 1.56), and translocation factor (TF, 1.35) were higher than unit, suggesting an efficient ability of S. nigrum L. in Pb bioremediation. Soil fertility was increased after bioremediation according to change in enzyme activities. The results indicated that inoculating S. nigrum L. with M. circinelloides enhanced its efficiency for phytoremediation of soil contaminated with Pb.

The effect of direct-fed microbial supplementation, as an alternative to antibiotics, on growth performance, intestinal immune status and epithelial barrier protein expression in broiler chickens

USDA-ARS?s Scientific Manuscript database

The objective of this study was to investigate the effects of Bacillus subtilis-based probiotic supplementation in broiler chicken diets on growth performance, feed efficiency, intestinal cytokine and tight junction (TJ) protein mRNA expression. Day-old broiler chicks (n = 140) were randomly assigne...

The effects of direct-fed microbial supplementation, as alternative to antibiotics, on growth performance, intestinal immune status and epithelial barrier protein expression in broiler chickens

USDA-ARS?s Scientific Manuscript database

This study was conducted to investigate the effects of Bacillus subtilis supplementation in broiler chicken diets on growth performance, feed efficiency, intestinal cytokine and tight junction (TJ) protein mRNA expression. Day-old broiler chicks (n = 140) were assigned five dietary treatments: basal...

Molecular imprinted hydrogel polymer (MIHP) as microbial immobilization media in artificial produced water treatment

NASA Astrophysics Data System (ADS)

Kardena, E.; Ridhati, S. L.; Helmy, Q.

2018-01-01

Produced water generated during oil and gas exploration and drilling, consists of many chemicals which used in drilling process. The production of produced water is over three fold of the oil production. The water-cut has increased over time and continues to do so because the fraction of oil in the reservoir decreases and it is more difficult to get the oil out from an old oil-field. It therefore requires more sea water to be injected in order to force the oil out; hence more produced water is generated. Produced water can pollute the environment if it is not treated properly. In this research, produced water will be treated biologically using bacterial consortium which is isolated from petroleum processing facility with Molecular Imprinted Hydrogel Polymer (MIHP) for microbial immobilization media. Microbial growth rate is determined by measuring the MLVSS and hydrogel mass, also by SEM-EDS analysis. SEM-EDS analysis is an analysis to evidence the presence of microbe trapped in hydrogel, and also to determine the types and weight of the molecules of hydrogel. From this research, suspended microbial growth rate was found at 0.1532/days and attached microbial growth rate was 0.3322/days. Furthermore, based on SEM analysis, microbe is entrapped inside the hydrogel. Effectiveness of microbial degradation activity was determined by measuring organic materials as COD. Based on COD measurement, degradation rate of organic materials in wastewater is 0.3089/days, with maximum COD removal efficiency of 76.67%.

Adaptation of the autotrophic acetogen Sporomusa ovata to methanol accelerates the conversion of CO2 to organic products

PubMed Central

Tremblay, Pier-Luc; Höglund, Daniel; Koza, Anna; Bonde, Ida; Zhang, Tian

2015-01-01

Acetogens are efficient microbial catalysts for bioprocesses converting C1 compounds into organic products. Here, an adaptive laboratory evolution approach was implemented to adapt Sporomusa ovata for faster autotrophic metabolism and CO2 conversion to organic chemicals. S. ovata was first adapted to grow quicker autotrophically with methanol, a toxic C1 compound, as the sole substrate. Better growth on different concentrations of methanol and with H2-CO2 indicated the adapted strain had a more efficient autotrophic metabolism and a higher tolerance to solvent. The growth rate on methanol was increased 5-fold. Furthermore, acetate production rate from CO2 with an electrode serving as the electron donor was increased 6.5-fold confirming that the acceleration of the autotrophic metabolism of the adapted strain is independent of the electron donor provided. Whole-genome sequencing, transcriptomic, and biochemical studies revealed that the molecular mechanisms responsible for the novel characteristics of the adapted strain were associated with the methanol oxidation pathway and the Wood-Ljungdahl pathway of acetogens along with biosynthetic pathways, cell wall components, and protein chaperones. The results demonstrate that an efficient strategy to increase rates of CO2 conversion in bioprocesses like microbial electrosynthesis is to evolve the microbial catalyst by adaptive laboratory evolution to optimize its autotrophic metabolism. PMID:26530351

Effects of plant diversity on microbial nitrogen and phosphorus dynamics in soil

NASA Astrophysics Data System (ADS)

Prommer, Judith; Braun, Judith; Daly, Amanda; Gorka, Stefan; Hu, Yuntao; Kaiser, Christina; Martin, Victoria; Meyerhofer, Werner; Walker, Tom W. N.; Wanek, Wolfgang; Wasner, Daniel; Wiesenbauer, Julia; Zezula, David; Zheng, Qing; Richter, Andreas

2017-04-01

There is a general consensus that plant diversity affects many ecosystem functions. One example of such an effect is the enhanced aboveground and belowground plant biomass production with increasing species richness, with implications for carbon and nutrient distribution in soil. The Jena Experiment (http://www.the-jena-experiment.de/), a grassland biodiversity experiment established in 2002 in Germany, comprises different levels of plant species richness and different numbers of plant functional groups. It provides the opportunity to examine how changes in biodiversity impact on microbially-mediated nutrient cycling processes. We here report on plant diversity and plant functional composition effects on growth and nitrogen and phosphorus transformation rates, including nitrogen use efficiency, of microbial communities. Microbial growth rates and microbial biomass were positively affected by increasing plant species richness. Amino acid and ammonium concentrations in soil were also positively affected by plant species richness, while phosphate concentrations in contrast were negatively affected. The cycling of organic N in soils (estimated as gross protein depolymerization rates) increased about threefold with plant diversity, while gross N and P mineralization were not significantly affected by either species or functional richness. Microbial nitrogen use efficiency did not respond to different levels of plant diversity but was very high (0.96 and 0.98) across all levels of plant species richness, demonstrating a low N availability for microbes. Taken together this indicates that soil microbial communities were able to meet the well-documented increase in plant N content with species richness, and also the higher N demand of the microbial community by increasing the recycling of organic N such as proteins. In fact, the microbial community even overcompensated the increased plant and microbial N demand, as evidenced by increased levels of free amino acids and ammonium in the soil solution at higher species richness. A possible explanation for increased organic nitrogen transformation rates is the increased microbial biomass, which has previously been related to higher quantity and variety of plant derived compounds that are available to the microbial communities at higher plant diversity. Given that this explanation is right, it is interesting to note that the additional (plant-derived) microbial biomass at higher species richness, did not translate in higher soil P mineralization rates or phosphate availability.

Effect of Agricultural Amendments on Cajanus cajan (Pigeon Pea) and Its Rhizospheric Microbial Communities – A Comparison between Chemical Fertilizers and Bioinoculants

PubMed Central

Gupta, Rashi; Bisaria, V. S.; Sharma, Shilpi

2015-01-01

Inoculation of leguminous seeds with bioinoculants has been practiced in agriculture for decades to ameliorate grain yield by enhanced growth parameters and soil fertility. However, effective enhancement of plant growth parameters results not only from the direct effects these bioinoculants impose on them but also from their non-target effects. The ability of bioinoculants to reduce the application of chemicals for obtaining optimum yield of legume appears to be of great ecological and economic importance. In the present study, we compared the influence of seed inoculation of Cajanus cajan with a microbial consortium, comprising Bacillus megaterium, Pseudomonas fluorescens and Trichoderma harzianum, with that of application of chemical fertilizers on plant’s growth parameters and its rhizospheric microbial communities. Real-time PCR assay was carried out to target the structure (16S rRNA) and function (nitrogen cycle) of rhizospheric microbiota, using both DNA and RNA as markers. The results showed that the microbial consortium was the most efficient in increasing grain yield (2.5-fold), even better than the recommended dose of chemical fertilizers (by 1.2-fold) and showed enhancement in nifH and amoA transcripts by 2.7- and 2.0-fold, respectively. No adverse effects of bioinoculants' application were observed over the rhizospheric microbial community, rendering the consortium to be safe for release in agricultural fields. PMID:26231030

Effect of Agricultural Amendments on Cajanus cajan (Pigeon Pea) and Its Rhizospheric Microbial Communities--A Comparison between Chemical Fertilizers and Bioinoculants.

PubMed

Gupta, Rashi; Bisaria, V S; Sharma, Shilpi

2015-01-01

Inoculation of leguminous seeds with bioinoculants has been practiced in agriculture for decades to ameliorate grain yield by enhanced growth parameters and soil fertility. However, effective enhancement of plant growth parameters results not only from the direct effects these bioinoculants impose on them but also from their non-target effects. The ability of bioinoculants to reduce the application of chemicals for obtaining optimum yield of legume appears to be of great ecological and economic importance. In the present study, we compared the influence of seed inoculation of Cajanus cajan with a microbial consortium, comprising Bacillus megaterium, Pseudomonas fluorescens and Trichoderma harzianum, with that of application of chemical fertilizers on plant's growth parameters and its rhizospheric microbial communities. Real-time PCR assay was carried out to target the structure (16S rRNA) and function (nitrogen cycle) of rhizospheric microbiota, using both DNA and RNA as markers. The results showed that the microbial consortium was the most efficient in increasing grain yield (2.5-fold), even better than the recommended dose of chemical fertilizers (by 1.2-fold) and showed enhancement in nifH and amoA transcripts by 2.7- and 2.0-fold, respectively. No adverse effects of bioinoculants' application were observed over the rhizospheric microbial community, rendering the consortium to be safe for release in agricultural fields.

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.

Organic and inorganic fertilizer effect on soil CO2 flux, microbial biomass, and growth of Nigella sativa L.

NASA Astrophysics Data System (ADS)

Salehi, Aliyeh; Fallah, Seyfollah; Sourki, Ali Abasi

2017-01-01

Cattle manure has a high carbon/nitrogen ratio and may not decompose; therefore, full-dose application of urea fertilizer might improve biological properties by increasing manure decomposition. This study aimed to investigate the effect of combining cattle manure and urea fertilizer on soil CO2 flux, microbial biomass carbon, and dry matter accumulation during Nigella sativa L. (black cumin) growth under field conditions. The treatments were control, cattle manure, urea, different levels of split and full-dose integrated fertilizer. The results showed that integrated application of cattle manure and chemical fertilizer significantly increased microbial biomass carbon by 10%, soil organic carbon by 2.45%, total N by 3.27%, mineral N at the flowering stage by 7.57%, and CO2 flux by 9% over solitary urea application. Integrated application increased microbial biomass carbon by 10% over the solitary application and the full-dose application by 5% over the split application. The soil properties and growth parameters of N. sativa L. benefited more from the full-dose application than the split application of urea. Cattle manure combined with chemical fertilizer and the full-dose application of urea increased fertilizer efficiency and improved biological soil parameters and plant growth. This method decreased the cost of top dressing urea fertilizer and proved beneficial for the environment and medicinal plant health.

Pathophysiology of avian intestinal ion transport.

PubMed

Nighot, Meghali; Nighot, Prashant

2018-06-01

The gut has great importance for the commercial success of poultry production. Numerous ion transporters, exchangers, and channels are present on both the apical and the basolateral membrane of intestinal epithelial cells, and their differential expression along the crypt-villus axis within the various intestinal segments ensures efficient intestinal absorption and effective barrier function. Recent studies have shown that intensive production systems, microbial exposure, and nutritional management significantly affect intestinal physiology and intestinal ion transport. Dysregulation of normal intestinal ion transport is manifested as diarrhoea, malabsorption, and intestinal inflammation resulting into poor production efficiency. This review discusses the basic mechanisms involved in avian intestinal ion transport and the impact of development during growth, nutritional and environmental alterations, and intestinal microbial infections on it. The effect of intestinal microbial infections on avian intestinal ion transport depends on factors such as host immunity, pathogen virulence, and the mucosal organisation of the particular intestinal segment.

Effects of coral-derived organic matter on the growth of bacterioplankton and heterotrophic nanoflagellates

NASA Astrophysics Data System (ADS)

Nakajima, Ryota; Tanaka, Yasuaki; Guillemette, Ryan; Kurihara, Haruko

2017-12-01

Exudates derived from hermatypic corals were incubated with <2 µm filtered seawater containing heterotrophic bacteria and <10 µm filtered seawater containing bacteria and nanoflagellates (HNF) under dark conditions for 96 h to quantify the growth of both bacteria and HNF in response to coral-derived dissolved organic matter (DOM). The addition of coral-derived DOM caused significantly higher growth rates and production of bacteria and HNF compared to those in control seawater without coral exudates. During the incubation, HNF exhibited their peak in abundance 24-48 h after the peak abundance of bacteria. The growth efficiencies of both bacteria and HNF were significantly higher with coral-derived DOM, suggesting higher transfer efficiency from bacteria that is fueled by coral organic matter to HNF. Therefore, trophic transfer of coral-derived DOM from bacteria to HNF can contribute to efficient carbon flow through the microbial food web.

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

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

Investigating substrate use efficiency across different microbial physiologies in soil-extracted, solubilized organic matter (SESOM)

NASA Astrophysics Data System (ADS)

Cyle, K. T.; Martinez, C. E.

2017-12-01

Recent experimental work has elevated the importance of microbial processing for the stabilization of fresh carbon inputs within the soil mineral matrix. Enhancing our understanding of soil carbon and nitrogen dynamics therefore requires a better understanding of how efficiently microbial metabolism can process low molecular weight carbon substrates (carbon use efficiency, CUE) under environmentally relevant conditions. One approach to better understanding microbial uptake rates and CUE is the ecophysiological study of soil isolates in liquid media culture consisting of soil-extracted solubilized organic matter (SESOM). We are using SESOM from an Oa horizon under hemlock hardwood vegetation in upstate New York as liquid media for the growth of 12 isolates from the Oa and B horizon of the same site. Here we seek to test the uptake rates as well as CUE of 5 different low molecular weight substrates spanning compound class and nominal oxidation state (glucose, acetate, formate, glycine, valine) by isolates differing in phylogeny and physiology. The use of a spike of each of the 13C-labeled substrates into SESOM, along with a 0.2 μm filtration step, allows accurate partitioning of labeled carbon between biomass, gaseous CO2 as well as the exometabolome. Coupled UHPLC-MS measurements are being used to identify and determine uptake rates of over 80 potential C substrates present in the extract as well as our labeled substrate of interest along the course of the isolate growth curve. This work seeks to utilize a gradient in substrate class as well as microbial physiologies to inform our understanding of C and N cycling under relevant soil solution conditions. Future experiments may also use labeled biomass from stationary phase to investigate the stabilization potential of anabolic products formed from each substrate with a clay fraction isolated from the same site.

Electricity Generation in Microbial Fuel Cells Using Neutral Red as an Electronophore

PubMed Central

Park, Doo Hyun; Zeikus, J. Gregory

2000-01-01

Neutral red (NR) was utilized as an electron mediator in microbial fuel cells consuming glucose to study both its efficiency during electricity generation and its role in altering anaerobic growth and metabolism of Escherichia coli and Actinobacillus succinogenes. A study of chemical fuel cells in which NADH, NR, and ferricyanide were the electron donor, the electronophore, and the electron acceptor, respectively, showed that electrical current produced from NADH was proportional to the concentration of NADH. Fourfold more current was produced from NADH in chemical fuel cells when NR was the electron mediator than when thionin was the electron mediator. In microbial fuel cells in which E. coli resting cells were used the amount of current produced from glucose when NR was the electron mediator (3.5 mA) was 10-fold more than the amount produced when thionin was the electron mediator (0.4 mA). The amount of electrical energy generated (expressed in joules per mole of substrate) and the amount of current produced from glucose (expressed in milliamperes) in NR-mediated microbial fuel cells containing either E. coli or A. succinogenes were about 10- and 2-fold greater, respectively, when resting cells were used than when growing cells were used. Cell growth was inhibited substantially when these microbial fuel cells were making current, and more oxidized end products were formed under these conditions. When sewage sludge (i.e., a mixed culture of anaerobic bacteria) was used in the fuel cell, stable (for 120 h) and equivalent levels of current were obtained with glucose, as observed in the pure-culture experiments. These results suggest that NR is better than other electron mediators used in microbial fuel cells and that sludge production can be decreased while electricity is produced in fuel cells. Our results are discussed in relation to factors that may improve the relatively low electrical efficiencies (1.2 kJ/mol) obtained with microbial fuel cells. PMID:10742202

Comparison of fermentation of diets of variable composition and microbial populations in the rumen of sheep and Rusitec fermenters. I. Digestibility, fermentation parameters, and microbial growth.

PubMed

Martínez, M E; Ranilla, M J; Tejido, M L; Ramos, S; Carro, M D

2010-08-01

Four ruminally and duodenally cannulated sheep and 8 Rusitec fermenters were used to determine the effects of forage to concentrate (F:C) ratio and type of forage in the diet on ruminal fermentation and microbial protein synthesis. The purpose of the study was to assess how closely fermenters can mimic the dietary differences found in vivo. The 4 experimental diets contained F:C ratios of 70:30 or 30:70 with either alfalfa hay or grass hay as the forage. Microbial growth was determined in both systems using (15)N as a microbial marker. Rusitec fermenters detected differences between diets similar to those observed in sheep by changing F:C ratio on pH; neutral detergent fiber digestibility; total volatile fatty acid concentrations; molar proportions of acetate, propionate, butyrate, isovalerate, and caproate; and amylase activity. In contrast, Rusitec fermenters did not reproduce the dietary differences found in sheep for NH(3)-N and lactate concentrations, dry matter (DM) digestibility, proportions of isobutyrate and valerate, carboxymethylcellulase and xylanase activities, and microbial growth and its efficiency. Regarding the effect of the type of forage in the diet, Rusitec fermenters detected differences between diets similar to those found in sheep for most determined parameters, with the exception of pH, DM digestibility, butyrate proportion, and carboxymethylcellulase activity. Minimum pH and maximal volatile fatty acid concentrations were reached at 2h and at 6 to 8h postfeeding in sheep and fermenters, respectively, indicating that feed fermentation was slower in fermenters compared with that in sheep. There were differences between systems in the magnitude of most determined parameters. In general, fermenters showed lower lactate concentrations, neutral detergent fiber digestibility, acetate:propionate ratios, and enzymatic activities. On the contrary, fermenters showed greater NH(3)-N concentrations, DM digestibility, and proportions of propionate, butyrate, isovalerate, valerate, and caproate. Values of efficiency of microbial growth were greater in fermenters compared with sheep for 70:30 diets, but they were lower for 30:70 diets. Differences between fermentation in sheep and fermenters can be mainly attributed to the lack of absorption in fermenters, differences in solid retention time, and compartmentalization in the Rusitec system. In general, the Rusitec system simulated more closely the in vivo fermentation of high-forage diets compared with high-concentrate diets. Copyright (c) 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Methodology for Modeling the Microbial Contamination of Air Filters

PubMed Central

Joe, Yun Haeng; Yoon, Ki Young; Hwang, Jungho

2014-01-01

In this paper, we propose a theoretical model to simulate microbial growth on contaminated air filters and entrainment of bioaerosols from the filters to an indoor environment. Air filter filtration and antimicrobial efficiencies, and effects of dust particles on these efficiencies, were evaluated. The number of bioaerosols downstream of the filter could be characterized according to three phases: initial, transitional, and stationary. In the initial phase, the number was determined by filtration efficiency, the concentration of dust particles entering the filter, and the flow rate. During the transitional phase, the number of bioaerosols gradually increased up to the stationary phase, at which point no further increase was observed. The antimicrobial efficiency and flow rate were the dominant parameters affecting the number of bioaerosols downstream of the filter in the transitional and stationary phase, respectively. It was found that the nutrient fraction of dust particles entering the filter caused a significant change in the number of bioaerosols in both the transitional and stationary phases. The proposed model would be a solution for predicting the air filter life cycle in terms of microbiological activity by simulating the microbial contamination of the filter. PMID:24523908

Biodegradation of crude oil using an efficient microbial consortium in a simulated marine environment.

PubMed

Bao, Mu-tai; Wang, Li-na; Sun, Pei-yan; Cao, Li-xin; Zou, Jie; Li, Yi-ming

2012-06-01

Ochrobactrum sp. N1, Brevibacillus parabrevis N2, B. parabrevis N3 and B. parabrevis N4 were selected when preparing a mixed bacterial consortium based on the efficiency of crude oil utilization. A crude oil degradation rate of the N-series microbial consortium reached upwards of 79% at a temperature of 25 °C in a 3.0% NaCl solution in the shake flask trial. In the mesocosm experiment, a specially designed device was used to simulate the marine environment. The internal tank size was 1.5 m (L)×0.8 m (W)×0.7 m (H). The microbial growth conditions, nutrient utilization and environmental factors were thoroughly investigated. Over 51.1% of the crude oil was effectively removed from the simulated water body. The escalation process (from flask trials to the mesocosm experiment), which sought to represent removal under conditions more similar to the field, proved the high efficiency of using N-series bacteria in crude oil degradation. Copyright © 2012 Elsevier Ltd. All rights reserved.

Microbially Mediated Plant Salt Tolerance and Microbiome-based Solutions for Saline Agriculture.

PubMed

Qin, Yuan; Druzhinina, Irina S; Pan, Xueyu; Yuan, Zhilin

2016-11-15

Soil salinization adversely affects plant growth and has become one of the major limiting factors for crop productivity worldwide. The conventional approach, breeding salt-tolerant plant cultivars, has often failed to efficiently alleviate the situation. In contrast, the use of a diverse array of microorganisms harbored by plants has attracted increasing attention because of the remarkable beneficial effects of microorganisms on plants. Multiple advanced '-omics' technologies have enabled us to gain insights into the structure and function of plant-associated microbes. In this review, we first focus on microbe-mediated plant salt tolerance, in particular on the physiological and molecular mechanisms underlying root-microbe symbiosis. Unfortunately, when introducing such microbes as single strains to soils, they are often ineffective in improving plant growth and stress tolerance, largely due to competition with native soil microbial communities and limited colonization efficiency. Rapid progress in rhizosphere microbiome research has revived the belief that plants may benefit more from association with interacting, diverse microbial communities (microbiome) than from individual members in a community. Understanding how a microbiome assembles in the continuous compartments (endosphere, rhizoplane, and rhizosphere) will assist in predicting a subset of core or minimal microbiome and thus facilitate synthetic re-construction of microbial communities and their functional complementarity and synergistic effects. These developments will open a new avenue for capitalizing on the cultivable microbiome to strengthen plant salt tolerance and thus to refine agricultural practices and production under saline conditions. Copyright © 2016 Elsevier Inc. All rights reserved.

Contaminant concentration versus flow velocity: drivers of biodegradation and microbial growth in groundwater model systems.

PubMed

Grösbacher, Michael; Eckert, Dominik; Cirpka, Olaf A; Griebler, Christian

2018-06-01

Aromatic hydrocarbons belong to the most abundant contaminants in groundwater systems. They can serve as carbon and energy source for a multitude of indigenous microorganisms. Predictions of contaminant biodegradation and microbial growth in contaminated aquifers are often vague because the parameters of microbial activity in the mathematical models used for predictions are typically derived from batch experiments, which don't represent conditions in the field. In order to improve our understanding of key drivers of natural attenuation and the accuracy of predictive models, we conducted comparative experiments in batch and sediment flow-through systems with varying concentrations of contaminant in the inflow and flow velocities applying the aerobic Pseudomonas putida strain F1 and the denitrifying Aromatoleum aromaticum strain EbN1. We followed toluene degradation and bacterial growth by measuring toluene and oxygen concentrations and by direct cell counts. In the sediment columns, the total amount of toluene degraded by P. putida F1 increased with increasing source concentration and flow velocity, while toluene removal efficiency gradually decreased. Results point at mass transfer limitation being an important process controlling toluene biodegradation that cannot be assessed with batch experiments. We also observed a decrease in the maximum specific growth rate with increasing source concentration and flow velocity. At low toluene concentrations, the efficiencies in carbon assimilation within the flow-through systems exceeded those in the batch systems. In all column experiments the number of attached cells plateaued after an initial growth phase indicating a specific "carrying capacity" depending on contaminant concentration and flow velocity. Moreover, in all cases, cells attached to the sediment dominated over those in suspension, and toluene degradation was performed practically by attached cells only. The observed effects of varying contaminant inflow concentration and flow velocity on biodegradation could be captured by a reactive-transport model. By monitoring both attached and suspended cells we could quantify the release of new-grown cells from the sediments to the mobile aqueous phase. Studying flow velocity and contaminant concentrations as key drivers of contaminant transformation in sediment flow-through microcosms improves our system understanding and eventually the prediction of microbial biodegradation at contaminated sites.

Influence of SiO2 and graphene oxide nanoparticles on efficiency of biological removal process.

PubMed

Esmaeili-Faraj, Seyyed Hamid; Nasr Esfahany, Mohsen

2017-11-01

The effects of the presence of synthesized silica (SS) and exfoliated graphene oxide (EGO) on the removal of sulfide ion with activated sludge (AS) are experimentally investigated. The maximum removal efficiency of sulfide ion for AS without nanoparticles, and the samples with SS and EGO nanoparticles were 81%, 88% and 79%, respectively. Moreover, the maximum elimination capacity (EC max ) for the bioreactor with SS-nanoparticles is 7542 mg/L s, while the EC max of AS and EGO samples were 7075 and 6625 mg/L s, respectively. Two filamentous microbial strains as Gram-negative and Gram-positive bacteria are discerned that removed sulfide ion in the presence of nanoparticles. The measurement of mixture liquor volatile suspended solid that indicates the biomass growth rate during the test shows that the bioreactor containing SS-nanoparticles has more biomass content than the other samples. Our findings indicate that SS-nanoparticles with 0.1% wt. concentration in the bioreactor have no negative effects on the efficiency of the biological removal of sulfide and the presence of SS-nanoparticles even enhances the performance of the bioreactor. On the other side, a bioreactor with EGO nanosheets, as highly antibacterial nanoparticles, with 0.02% wt. concentration significantly influences the microbial growth and reduces sulfide removal efficiency.

Depth dependent microbial carbon use efficiency in the capillary fringe as affected by water table fluctuations in a column incubation experiment

NASA Astrophysics Data System (ADS)

Pronk, G. J.; Mellage, A.; Milojevic, T.; Smeaton, C. M.; Rezanezhad, F.; Van Cappellen, P.

2017-12-01

Microbial growth and turnover of soil organic carbon (SOC) depend on the availability of electron donors and acceptors. The steep geochemical gradients in the capillary fringe between the saturated and unsaturated zones provide hotspots of soil microbial activity. Water table fluctuations and the associated drying and wetting cycles within these zones have been observed to lead to enhanced turnover of SOC and adaptation of the local microbial communities. To improve our understanding of SOC degradation under changing moisture conditions, we carried out an automated soil column experiment with integrated of hydro-bio-geophysical monitoring under both constant and oscillating water table conditions. An artificial soil mixture composed of quartz sand, montmorillonite, goethite and humus was used to provide a well-defined system. This material was inoculated with a microbial community extracted from a forested riparian zone. The soils were packed into 6 columns (60 cm length and 7.5 cm inner diameter) to a height of 45 cm; and three replicate columns were incubated under constant water table while another three were saturated and drained monthly. The initial soil development, carbon cycling and microbial community development were then characterized during 10 months of incubation. This system provides an ideal artificial gradient from the saturated to the unsaturated zone to study soil development from initially homogeneous materials and the same microbial community composition under controlled conditions. Depth profiles of SOC and microbial biomass after 329 days of incubation showed a depletion of carbon in the transition drying and wetting zone that was not associated with higher accumulation of microbial biomass, indicating a lower carbon use efficiency of the microbial community established within the water table fluctuation zone. This was supported by a higher ATP to microbial biomass carbon ratio within the same zone. The findings from this study highlight the importance of considering the effects of transient soil moisture and oxygen availability on microbial mediated SOC transformations. The effects of these changes in carbon use efficiency need to be included in soil models in order to accurately predict SOC turnover.

Combination of bioremediation and electrokinetics for the in-situ treatment of diesel polluted soil: A comparison of strategies.

PubMed

Mena Ramírez, Esperanza; Villaseñor Camacho, José; Rodrigo, Manuel A; Cañizares, Pablo

2015-11-15

The aim of this work is to compare different strategies based on electrokinetic soil flushing and bioremediation for the remediation of diesel-polluted soil. Four options were tested at the laboratory scale: single bioremediation (Bio), performed as a control test; a direct combination of electrokinetic soil flushing and biological technologies (EKSF-Bio); EKSF-Bio with daily polarity reversal of the electric field (PR-EKSF-Bio); and a combination of electrokinetic soil flushing and a permeable reactive biological barrier (EKSF-BioPRB). Four batch experiments of 14 days duration were carried out for comparing technologies at room temperature with an electric field of 1.0 V cm(-1) (in EKSF). A diesel degrading microbial consortium was used. The experimental procedure and some specific details, such as the flushing fluids used, varied depending on the strategy. When using the EKSF-Bio option, a high buffer concentration was required to control the pH, causing soil heating, which negatively affected the biological growth and thus the diesel removal. The PR-EKSF-Bio and the EKSF-BioPRB options attained suitable operating conditions and improved the transport processes for biological growth. Polarity reversal was an efficient option for pH, moisture and temperature control. Homogeneous microbial growth was observed, and approximately 20% of the diesel was removed. The BioPRB option was not as efficient as PR-EKSF-Bio in controlling the operating conditions, but the central biobarrier protected the biological activity. Microbial growth was observed not only in the biobarrier but also in a large portion of the soil, and 29% of the diesel was removed in the short remediation test. Copyright © 2015 Elsevier B.V. All rights reserved.

Study of the diversity of microbial communities in a sequencing batch reactor oxic-settling-anaerobic process and its modified process.

PubMed

Sun, Lianpeng; Chen, Jianfan; Wei, Xiange; Guo, Wuzhen; Lin, Meishan; Yu, Xiaoyu

2016-05-01

To further reveal the mechanism of sludge reduction in the oxic-settling-anaerobic (OSA) process, the polymerase chain reaction - denaturing gradient gel electrophoresis protocol was used to study the possible difference in the microbial communities between a sequencing batch reactor (SBR)-OSA process and its modified process, by analyzing the change in the diversity of the microbial communities in each reactor of both systems. The results indicated that the structure of the microbial communities in aerobic reactors of the 2 processes was very different, but the predominant microbial populations in anaerobic reactors were similar. The predominant microbial population in the aerobic reactor of the SBR-OSA belonged to Burkholderia cepacia, class Betaproteobacteria, while those of the modified process belonged to the classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. These 3 types of microbes had a cryptic growth characteristic, which was the main cause of a greater sludge reduction efficiency achieved by the modified process.

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

PubMed

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

2011-09-01

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

Validation of a predictive model coupling gas transfer and microbial growth in fresh food packed under modified atmosphere.

PubMed

Guillard, V; Couvert, O; Stahl, V; Hanin, A; Denis, C; Huchet, V; Chaix, E; Loriot, C; Vincelot, T; Thuault, D

2016-09-01

Predicting microbial safety of fresh products in modified atmosphere packaging implies to take into account the dynamic of O2, CO2 and N2 exchanges in the system and its effect on microbial growth. In this paper a mechanistic model coupling gas transfer and predictive microbiology was validated using dedicated challenge-tests performed on poultry meat, fresh salmon and processed cheese, inoculated with either Listeria monocytogenes or Pseudomonas fluorescens and packed in commercially used packaging materials (tray + lid films). The model succeeded in predicting the relative variation of O2, CO2 and N2 partial pressure in headspace and the growth of the studied microorganisms without any parameter identification. This work highlighted that the respiration of the targeted microorganism itself and/or that of the naturally present microflora could not be neglected in most of the cases, and could, in the particular case of aerobic microbes contribute to limit the growth by removing all residual O2 in the package. This work also confirmed the low sensitivity of L. monocytogenes toward CO2 while that of P. fluorescens permitted to efficiently prevent its growth by choosing the right combination of packaging gas permeability value and initial % of CO2 initially flushed in the pack. Copyright © 2016 Elsevier Ltd. All rights reserved.

Chemical diversity of microbial volatiles and their potential for plant growth and productivity

PubMed Central

Kanchiswamy, Chidananda Nagamangala; Malnoy, Mickael; Maffei, Massimo E.

2015-01-01

Microbial volatile organic compounds (MVOCs) are produced by a wide array of microorganisms ranging from bacteria to fungi. A growing body of evidence indicates that MVOCs are ecofriendly and can be exploited as a cost-effective sustainable strategy for use in agricultural practice as agents that enhance plant growth, productivity, and disease resistance. As naturally occurring chemicals, MVOCs have potential as possible alternatives to harmful pesticides, fungicides, and bactericides as well as genetic modification. Recent studies performed under open field conditions demonstrate that efficiently adopting MVOCs may contribute to sustainable crop protection and production. We review here the chemical diversity of MVOCs by describing microbial–plants and microbial–microbial interactions. Furthermore, we discuss MVOCs role in inducing phenotypic plant responses and their potential physiological effects on crops. Finally, we analyze potential and actual limitations for MVOC use and deployment in field conditions as a sustainable strategy for improving productivity and reducing pesticide use. PMID:25821453

Effects of encapsulated Lactobacillus acidophilus along with pasteurized longan juice on the colon microbiota residing in a dynamic simulator of the human intestinal microbial ecosystem.

PubMed

Chaikham, Pittaya; Apichartsrangkoon, Arunee

2014-01-01

The effect of encapsulated Lactobacillus acidophilus LA5 along with pasteurized longan juice on the colon microbiota was investigated by applying a dynamic model of the human gastrointestinal tract. Encapsulated L. acidophilus LA5 in pasteurized longan juice or sole encapsulated L. acidophilus LA5 exhibited the efficiency of colonizing the colon and enabling the growth of colon lactobacilli as well as beneficial bifidobacteria but inhibited the growth of fecal coliforms and clostridia. Moreover, these treatments gave rise to a significant increase of lactic acid and short-chain fatty acids such as acetate, propionate, and butyrate. Although acetate displayed the highest quantity, it was likely that after incorporating encapsulated L. acidophilus LA5 plus pasteurized longan juice, quantity of butyrate exceed propionate, and acetate in comparison with their controls. Denaturant gradient gel electrophoresis patterns confirmed that various treatments affected the alteration of microbial community within the simulator of the human intestinal microbial ecosystem.

Impact of electro-stimulation on denitrifying bacterial growth and analysis of bacterial growth kinetics using a modified Gompertz model in a bio-electrochemical denitrification reactor.

PubMed

Liu, Hengyuan; Chen, Nan; Feng, Chuanping; Tong, Shuang; Li, Rui

2017-05-01

This study aimed to investigate the effect of electro-stimulation on denitrifying bacterial growth in a bio-electrochemical reactor, and the growth were modeled using modified Gompertz model under different current densities at three C/Ns. It was found that the similar optimum current density of 250mA/m 2 was obtained at C/N=0.75, 1.00 and 1.25, correspondingly the maximum nitrate removal efficiencies were 98.0%, 99.2% and 99.9%. Moreover, ATP content and cell membrane permeability of denitrifying bacteria were significantly increased at optimum current density. Furthermore, modified Gompertz model fitted well with the microbial growth curves, and the highest maximum growth rates (µ max ) and shorter lag time were obtained at the optimum current density for all C/Ns. This study demonstrated that the modified Gompertz model could be used for describing microbial growth under different current densities and C/Ns in a bio-electrochemical denitrification reactor, and it provided an alternative for improving the performance of denitrification process. Copyright © 2017 Elsevier Ltd. All rights reserved.

Lysing bloom-causing alga Phaeocystis globosa with microbial algicide: An efficient process that decreases the toxicity of algal exudates

PubMed Central

Cai, Guanjing; Yang, Xujun; Lai, Qiliang; Yu, Xiaoqi; Zhang, Huajun; Li, Yi; Chen, Zhangran; Lei, Xueqian; Zheng, Wei; Xu, Hong; Zheng, Tianling

2016-01-01

Algicidal microbes could effectively remove the harmful algae from the waters. In this study, we were concerned with the ecological influence of an algicide extracted from Streptomyces alboflavus RPS, which could completely lyse the Phaeocystis globosa cells within two days. In microcosms, 4 μg/mL of the microbial algicide could efficiently remove P. globosa cells without suppressing other aquatic organisms. Bioluminescent assays confirmed that the toxicity of microbial algicide at this concentration was negligible. Interestingly, the toxicity of P. globosa exudates was also significantly reduced after being treated with the algicide. Further experiments revealed that the microbial algicide could instantly increase the permeability of the plasma membrane and disturb the photosynthetic system, followed by the deformation of organelles, vacuolization and increasing oxidative stress. The pre-incubation of N-acetyl cysteine (NAC) verified that the rapid damages to the plasma membrane and photosynthetic system caused the algal death in the early phase, and the increasing oxidative stress killed the rest. The late accumulation and possible release of CAT also explained the decreasing toxicity of the algal culture. These results indicated that this microbial algicide has great potential in controlling the growth of P. globosa on site. PMID:26847810

Recycling of treated domestic effluent from an on-site wastewater treatment system for hydroponics.

PubMed

Oyama, N; Nair, J; Ho, G E

2005-01-01

An alternative method to conserve water and produce crops in arid regions is through hydroponics. Application of treated wastewater for hydroponics will help in stripping off nutrients from wastewater, maximising reuse through reduced evaporation losses, increasing control on quality of water and reducing risk of pathogen contamination. This study focuses on the efficiency of treated wastewater from an on-site aerobic wastewater treatment unit. The experiment aimed to investigate 1) nutrient reduction 2) microbial reduction and 3) growth rate of plants fed on wastewater compared to a commercial hydroponics medium. The study revealed that the chemical and microbial quality of wastewater after hydroponics was safe and satisfactory for irrigation and plant growth rate in wastewater hydroponics was similar to those grown in a commercial medium.

Quantitative exploration of the contribution of settlement, growth, dispersal and grazing to the accumulation of natural marine biofilms on antifouling and fouling-release coatings

PubMed Central

Van Mooy, Benjamin A. S.; Hmelo, Laura R.; Fredricks, Helen F.; Ossolinski, Justin E.; Pedler, Byron E.; Bogorff, Daniel J.; Smith, Peter J.S.

2014-01-01

The accumulation of microbial biofilms on ships' hulls negatively affects ships' performance and efficiency while also moderating the establishment of even more detrimental hard-fouling communities. However, there is little quantitative information on how the accumulation rate of microbial biofilms is impacted by the balance of the rates of cell settlement, in situ production (ie growth), dispersal to surrounding waters and mortality induced by grazers. These rates were quantified on test panels coated with copper-based antifouling or polymer-based fouling-release coatings by using phospholipids as molecular proxies for microbial biomass. The results confirmed the accepted modes of efficacy of these two types of coatings. In a more extensive set of experiments with only the fouling-release coatings, it was found that seasonally averaged cellular production rates were 1.5 ± 0.5 times greater than settlement and the dispersal rates were 2.7 ± 0.8 greater than grazing. The results of this study quantitatively describe the dynamic balance of processes leading to microbial biofilm accumulation on coatings designed for ships' hulls. PMID:24417212

Effects of proton exchange membrane on the performance and microbial community composition of air-cathode microbial fuel cells.

PubMed

Lee, Yun-Yeong; Kim, Tae Gwan; Cho, Kyung-Suk

2015-10-10

This study investigated the effects of proton exchange membranes (PEMs) on performance and microbial community of air-cathode microbial fuel cells (MFCs). Air-cathode MFCs with reactor volume of 1L were constructed in duplicate with or without PEM (designated as ACM-MFC and AC-MFC, respectively) and fed with a mixture of glucose and acetate (1:1, w:w). The maximum power density and coulombic efficiency did not differ between MFCs in the absence or presence of a PEM. However, PEM use adversely affected maximum voltage production and the rate of organic compound removal (p<0.05). Quantitative droplet digital PCR indicated that AC-MFCs had a greater bacterial population than ACM-MFCs (p<0.05). Likewise, ribosomal tag pyrosequencing revealed that the diversity index of bacterial communities was greater for AC-MFCs (p<0.05). Network analysis revealed that the most abundant genus was Enterococcus, which comprised ≥62% of the community and was positively associated with PEM and negatively associated with the rate of chemical oxygen demand (COD) removal (Pearson correlation>0.9 and p<0.05). Geobacter, which is known as an exoelectrogen, was positively associated with maximum power density and negatively associated with PEM. Thus, these results suggest that the absence of PEM favored the growth of Geobacter, a key player for electricity generation in MFC systems. Taken together, these findings demonstrate that MFC systems without PEM are more efficient with respect to power production and COD removal as well as exoelectrogen growth. Copyright © 2015 Elsevier B.V. All rights reserved.

Controlling Microbial Byproducts using Model-Based Substrate Monitoring and Control Strategies

NASA Technical Reports Server (NTRS)

Smernoff, David T.; Blackwell, Charles; Mancinelli, Rocco L.; DeVincenzi, Donald (Technical Monitor)

2000-01-01

We have developed a computer-controlled bioreactor system to study various aspects of microbially-mediated nitrogen cycling. The system has been used to investigate methods for controlling microbial denitrification (the dissimilatory reduction of nitrate to N2O and N2) in hydroponic plant growth chambers. Such chambers are key elements of advanced life support systems being designed for use on long duration space missions, but nitrogen use efficiency in them is reduced by denitrification. Control software architecture was designed which permits the heterogeneous control of system hardware using traditional feedback control, and quantitative and qualitative models of various system features. Model-based feed forward control entails prediction of future systems in states and automated regulation of system parameters to achieve desired and avoid undesirable system states. A bacterial growth rate model based on the classic Monod model of saturation kinetics was used to evaluate the response of several individual denitrifying species to varying environmental conditions. The system and models are now being applied to mixed microbial communities harvested from the root zone of a hydroponic growth chamber. The use of a modified Monod organism interaction model was evaluated as a means of achieving more accurate description of the dynamic behavior of the communities. A minimum variance parameter estimation routine was also' used to calibrate the constant parameters in the model by iterative evaluation of substrate (nitrate) uptake and growth kinetics. This representation of processes and interactions aids in the formulation of control laws. The feed forward control strategy being developed will increase system autonomy, reduce crew intervention and limit the accumulation of undesirable waste products (NOx).

Impact of fouling on the decline of aeration efficiency under different operational conditions at WRRFs.

PubMed

Garrido-Baserba, Manel; Asvapathanagul, Pitiporn; Park, Hee-Deung; Kim, Taek-Seung; Baquero-Rodriguez, G Andres; Olson, Betty H; Rosso, Diego

2018-10-15

Biofilm formation influences the most energy-demanding process in the waste water treatment cycle. Biofilm growth on the surface of wastewater aeration diffusers in water resource recovery facilities (WRRFs) can increase the energy requirements up to 50% in less than 2 years. The impact of biofilms in aeration diffusers was quantified and assessed for first time using molecular tools (i.e., Energy-dispersive X-ray, Ra and RMS and Pyrosequencing) and state-of-the-art techniques (i.e., EPS quantification, Hydrophobicity and DNA quantification). To provide a better understanding and quantitative connections between biological activity and aeration energy efficiency, two replicates of the most common diffusers were installed and tested in two different operational conditions (higher and lower organic loading rate processes) during 15 months. Different scenarios and conditions provided for first time comprehensive understanding of the major factors contributing to diffuser fouling. The array of analysis suggested that higher loading conditions can promote specialized microbial populations to halve aeration efficiency parameters (i.e., αF) in comparison to lower loading conditions. Biofilms adapted to certain operational conditions can trigger changes in diffuser membrane properties (i.e., biological enhanced roughness and hydrophobicity) and enhance EPS growth rates. Improved understanding of the effects of scaling, biofouling, aging and microbial population shifts on the decrease in aeration efficiency is provided. Copyright © 2018 Elsevier B.V. All rights reserved.

Electricity generation through a photo sediment microbial fuel cell using algae at the cathode.

PubMed

Neethu, B; Ghangrekar, M M

2017-12-01

Sediment microbial fuel cells (SMFCs) are bio-electrochemical devices generating electricity from redox gradients occurring across the sediment-water interface. Sediment microbial carbon-capture cell (SMCC), a modified SMFC, uses algae grown in the overlying water of sediment and is considered as a promising system for power generation along with algal cultivation. In this study, the performance of SMCC and SMFC was evaluated in terms of power generation, dissolved oxygen variations, sediment organic matter removal and algal growth. SMCC gave a maximum power density of 22.19 mW/m 2 , which was 3.65 times higher than the SMFC operated under similar conditions. Sediment organic matter removal efficiencies of 77.6 ± 2.1% and 61.0 ± 1.3% were obtained in SMCC and SMFC, respectively. With presence of algae at the cathode, a maximum chemical oxygen demand and total nitrogen removal efficiencies of 63.3 ± 2.3% (8th day) and 81.6 ± 1.2% (10th day), respectively, were observed. The system appears to be favorable from a resources utilization perspective as it does not depend on external aeration or membranes and utilizes algae and organic matter present in sediment for power generation. Thus, SMCC has proven its applicability for installation in an existing oxidation pond for sediment remediation, algae growth, carbon conversion and power generation, simultaneously.

The engineered biofiltration system

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

Pisotti, D.A.

1997-12-31

For years, biofiltration has meant compost, peat, bark, leave mulch, or any combination of these as the substrate to house microorganisms. This has lead to a number of operational and maintenance problems, including: compaction, channeling, anaerobic zones, dry spots, pressure drop, and media degradation. All of these cause reduced efficiency and increased maintenance and increased operational costs. For these reasons inert media, including plastic beads and low grade carbons have been added to the media for buffering capacity, resists compaction, channeling and to increase efficiency. This has led to search for a more reliable and sturdy media. The media themore » authors chose was activated carbon. Pelletized activated carbon was the ideal candidate due to its uniform size and shape, its inherent hardness, adsorptive capacity, and its ability to withstand microbial degradation. The pressure drop of the system will remain constant after microbial growth occurs, due to the ability to wash the media bed. Carbon allows for the removal of excess biomass which can not be performed on organic media, this is one of the problems leading to media degradation, too many microbes and not enough food (i.e. VOCs). Carbon also allows for spike or increased loads to be treated without performance suffering. Carbon also has tremendous surface area, which allows more microorganisms to be present in a smaller volume, therefore reducing the overall size of the biofilter vessel. This paper will discuss further the findings of a pilot test that was performed using activated carbon as the media for microbial growth. This paper will show the performance of the carbon based biofilter system with respect to pressure drop, residence time, removal efficiency, microbial populations, temperature, moisture, and water requirements. The pilot unit is 350 acfm and operated for 4 months on an air stream in which the contaminant concentrations varied greatly every few minutes.« less

Development of a program to fit data to a new logistic model for microbial growth.

PubMed

Fujikawa, Hiroshi; Kano, Yoshihiro

2009-06-01

Recently we developed a mathematical model for microbial growth in food. The model successfully predicted microbial growth at various patterns of temperature. In this study, we developed a program to fit data to the model with a spread sheet program, Microsoft Excel. Users can instantly get curves fitted to the model by inputting growth data and choosing the slope portion of a curve. The program also could estimate growth parameters including the rate constant of growth and the lag period. This program would be a useful tool for analyzing growth data and further predicting microbial growth.

Microbial mineral illization of montmorillonite in low-permeability oil reservoirs for microbial enhanced oil recovery.

PubMed

Cui, Kai; Sun, Shanshan; Xiao, Meng; Liu, Tongjing; Xu, Quanshu; Dong, Honghong; Wang, Di; Gong, Yejing; Sha, Te; Hou, Jirui; Zhang, Zhongzhi; Fu, Pengcheng

2018-05-11

Microbial mineral illization has been investigated for its role in the extraction and recovery of metals from ores. Here we report our application of mineral bioillization for the microbial enhanced oil recovery in low-permeability oil reservoirs. It aimed to reveal the etching mechanism of the four Fe (III)-reducing microbial strains under anaerobic growth conditions on the Ca-montmorillonite. The mineralogical characterization of the Ca-montmorillonite was performed by Fourier transform infrared spectroscopy, X-ray powder diffraction, scanning electron microscopy and energy dispersive spectrometer. Results showed that the microbial strains could efficiently reduce Fe (III) at an optimal rate of 71 %, and alter the crystal lattice structure of the lamella to promote the interlayer cation exchange, and to efficiently inhibit the Ca-montmorillonite swelling at an inhibitory rate of 48.9 %. Importance Microbial mineral illization is ubiquitous in the natural environment. Microbes in low-permeability reservoirs are able to enable the alteration of the structure and phase of the Fe-poor minerals by reducing Fe (III) and inhibiting clay swelling which is still poorly studied. This study aimed to reveal the interaction mechanism between Fe (III)-reducing bacterial strains and Ca-montmorillonite under anaerobic atmosphere, and to investigate the extent and rates of Fe (III) reduction and phase changes with their activities. Application of Fe (III)-reducing bacteria will provide a new way to inhibit clay swelling, to elevate reservoir permeability, and to reduce pore throat resistance after water flooding for enhanced oil recovery in low-permeability reservoirs. Copyright © 2018 American Society for Microbiology.

Mining the Volatilomes of Plant-Associated Microbiota for New Biocontrol Solutions

PubMed Central

Bailly, Aurélien; Weisskopf, Laure

2017-01-01

Microbial lifeforms associated with land plants represent a rich source for crop growth- and health-promoting microorganisms and biocontrol agents. Volatile organic compounds (VOCs) produced by the plant microbiota have been demonstrated to elicit plant defenses and inhibit the growth and development of numerous plant pathogens. Therefore, these molecules are prospective alternatives to synthetic pesticides and the determination of their bioactivities against plant threats could contribute to the development of control strategies for sustainable agriculture. In our previous study we investigated the inhibitory impact of volatiles emitted by Pseudomonas species isolated from a potato field against the late blight-causing agent Phytophthora infestans. Besides the well-documented emission of hydrogen cyanide, other Pseudomonas VOCs impeded P. infestans mycelial growth and sporangia germination. Current advances in the field support the emerging concept that the microbial volatilome contains unexploited, eco-friendly chemical resources that could help select for efficient biocontrol strategies and lead to a greener chemical disease management in the field. PMID:28890716

Mining the Volatilomes of Plant-Associated Microbiota for New Biocontrol Solutions.

PubMed

Bailly, Aurélien; Weisskopf, Laure

2017-01-01

Microbial lifeforms associated with land plants represent a rich source for crop growth- and health-promoting microorganisms and biocontrol agents. Volatile organic compounds (VOCs) produced by the plant microbiota have been demonstrated to elicit plant defenses and inhibit the growth and development of numerous plant pathogens. Therefore, these molecules are prospective alternatives to synthetic pesticides and the determination of their bioactivities against plant threats could contribute to the development of control strategies for sustainable agriculture. In our previous study we investigated the inhibitory impact of volatiles emitted by Pseudomonas species isolated from a potato field against the late blight-causing agent Phytophthora infestans . Besides the well-documented emission of hydrogen cyanide, other Pseudomonas VOCs impeded P. infestans mycelial growth and sporangia germination. Current advances in the field support the emerging concept that the microbial volatilome contains unexploited, eco-friendly chemical resources that could help select for efficient biocontrol strategies and lead to a greener chemical disease management in the field.

Evaluation of food storage racks available on the Polish market in the hygienic context

PubMed

Grzesińska, Wiesława; Tomaszewska, Marzena; Bilska, Beata; Trafiałek, Joanna; Dziadek, Michał

Providing safe food products to the consumer depends on the material and technology used and adherence to hygienic practices, throughout the production process. The degree of microbial contamination of a surface is an important indicator of equipment cleanliness and effectiveness of cleaning and disinfection. Used material, construction solutions and quality of the applied devices also have an effect on hygienic status. The objective of the present study was to evaluate the influence of the design and construction material of selected food storage racks, available on the Polish market, on their hygienic status. The study was based on determination of the capability of microbial growth on the surface of the racks and the effectiveness of their cleaning. Microbiological cleanliness on the surface of the racks was monitored by the contact plates which are able to estimate the total number of icroorganisms. Examination of effectiveness of cleaning was conducted by the use of ATP bioluminescence method. This experiment has proven a significant influence of adopted construction solutions on the hygienic status of the examined racks. Presence of antibacterial layer and a choice of the appropriate construction material characterized by a low surface roughness impedes the microbial growth and increases the effectiveness of cleaning. Design solutions have significant impact on the hygienic status of shelves. Selection of a suitable material for the construction of racks can greatly reduce the possibility of the development of microorganism, despite the low efficiency of the cleaning. The application of antimicrobial coatings inhibits microbial growth.

Analysis of the gut microbiome in beef cattle and its association with feed intake, growth, and efficiency

USDA-ARS?s Scientific Manuscript database

Next-generation sequencing has taken a central role in studies of microbial ecology, especially with regard to culture-independent methods based on molecular phylogenies of the small-subunit ribosomal RNA gene (16S rRNA gene). The ability to relate trends at the species or genus level to host/envir...

An efficient nonlinear finite-difference approach in the computational modeling of the dynamics of a nonlinear diffusion-reaction equation in microbial ecology.

PubMed

Macías-Díaz, J E; Macías, Siegfried; Medina-Ramírez, I E

2013-12-01

In this manuscript, we present a computational model to approximate the solutions of a partial differential equation which describes the growth dynamics of microbial films. The numerical technique reported in this work is an explicit, nonlinear finite-difference methodology which is computationally implemented using Newton's method. Our scheme is compared numerically against an implicit, linear finite-difference discretization of the same partial differential equation, whose computer coding requires an implementation of the stabilized bi-conjugate gradient method. Our numerical results evince that the nonlinear approach results in a more efficient approximation to the solutions of the biofilm model considered, and demands less computer memory. Moreover, the positivity of initial profiles is preserved in the practice by the nonlinear scheme proposed. Copyright © 2013 Elsevier Ltd. All rights reserved.

Effects of concentrate replacement by feed blocks on ruminal fermentation and microbial growth in goats and single-flow continuous-culture fermenters.

PubMed

Molina-Alcaide, E; Pascual, M R; Cantalapiedra-Hijar, G; Morales-García, E Y; Martín-García, A I

2009-04-01

The effect of replacing concentrate with 2 different feed blocks (FB) on ruminal fermentation and microbial growth was evaluated in goats and in single-flow continuous-culture fermenters. Diets consisted of alfalfa hay plus concentrate and alfalfa hay plus concentrate with 1 of the 2 studied FB. Three trials were carried out with 6 rumen-fistulated Granadina goats and 3 incubation runs in 6 single-flow continuous-culture fermenters. Experimental treatments were assigned randomly within each run, with 2 repetitions for each diet. At the end of each in vivo trial, the rumen contents were obtained for inoculating the fermenters. For each incubation run, the fermenters were inoculated with ruminal fluid from goats fed the same diet supplied to the corresponding fermenter flask. The average pH values, total and individual VFA, and NH(3)-N concentrations, and acetate:propionate ratios in the rumen of goats were not affected (P >or= 0.10) by diet, whereas the microbial N flow (MNF) and efficiency were affected (P or= 0.05), and total (P=0.02), NH(3) (P=0.005), and non-NH(3) (P=0.02) N flows, whereas the efficiency of VFA production was not affected (P=0.75). The effect of diet on MNF and efficiency depended on the bacterial pellet used as a reference. An effect (P<0.05) of diet on the composition of solid- and liquid-associated bacteria was observed. The compositions of liquid-associated bacteria in the fermenter contents and effluent were similar (P=0.05). Differences (P<0.001) between in vivo and in vitro values for most fermentation variables and bacterial pellet compositions were found. Partial replacement of the concentrate with FB did not greatly compromise carbohydrate fermentation in unproductive goats. However, this was not the case for MNF and efficiency. Differences between the results obtained in vivo and in vitro indicate a need to identify conditions in fermenters that allow better simulation of fermentation, microbial growth, and bacterial pellet composition in vivo. Reduced feeding cost could be achieved with the inclusion of FB in the diets of unproductive goats without altering rumen fermentation.

Validation Study of Rapid Assays of Bioburden, Endotoxins and Other Contamination.

PubMed

Shintani, Hideharu

2016-01-01

Microbial testing performed in support of pharmaceutical and biopharmaceutical production falls into three main categories: detection (qualitative), enumeration (quantitative), and characterization/identification. Traditional microbiological methods are listed in the compendia and discussed by using the conventional growth-based techniques, which are labor intensive and time consuming. In general, such tests require several days of incubation for microbial contamination (bioburden) to be detected, and therefore management seldom is able to take proactive corrective measures. In addition, microbial growth is limited by the growth medium used and incubation conditions, thus impacting testing sensitivity, accuracy, and reproducibility. 　For more than 20 years various technology platforms for rapid microbiological methods (RMM) have been developed, and many have been readily adopted by the food industry and clinical microbiology laboratories. Their use would certainly offer drug companies faster test turnaround times to accommodate the aggressive deadlines for manufacturing processes and product release. Some rapid methods also offer the possibility for real-time microbial analyses, enabling management to respond to microbial contamination events in a more timely fashion, and can provide cost savings and higher efficiencies in quality control testing laboratories. Despite the many proven business and quality benefits and the fact that the FDA's initiative to promote the use of process analytical technology (PAT) includes rapid microbial methods, pharmaceutical and biopharmaceutical industries have been somewhat slow to embrace alternative microbial methodologies for several reasons. The major reason is that the bioburden counts detected by the incubation method and rapid assay are greatly divergent. 　The use of rapid methods is a dynamic field in applied microbiology and one that has gained increased attention nationally and internationally over time. This topic has been extensively addressed at conferences and in published documents around the world. More recently, the use of alternative methods for control of the microbiological quality of pharmaceutical products and materials used in pharmaceutical production has been addressed by the compendia in an attempt to facilitate implementation of these technologies by pharmaceutical companies. The author presents some of the rapid method technologies under evaluation or in use by pharmaceutical microbiologists and the current status of the implementation of alternative microbial methods.

Remediation aspect of microbial changes of plant rhizosphere in mercury contaminated soil.

PubMed

Sas-Nowosielska, Aleksandra; Galimska-Stypa, Regina; Kucharski, Rafał; Zielonka, Urszula; Małkowski, Eugeniusz; Gray, Laymon

2008-02-01

Phytoremediation, an approach that uses plants to remediate contaminated soil through degradation, stabilization or accumulation, may provide an efficient solution to some mercury contamination problems. This paper presents growth chamber experiments that tested the ability of plant species to stabilize mercury in soil. Several indigenous herbaceous species and Salix viminalis were grown in soil collected from a mercury-contaminated site in southern Poland. The uptake and distribution of mercury by these plants were investigated, and the growth and vitality of the plants through a part of one vegetative cycle were assessed. The highest concentrations of mercury were found at the roots, but translocation to the aerial part also occurred. Most of the plant species tested displayed good growth on mercury contaminated soil and sustained a rich microbial population in the rhizosphere. The microbial populations of root-free soil and rhizosphere soil from all species were also examined. An inverse correlation between the number of sulfur amino acid decomposing bacteria and root mercury content was observed. These results indicate the potential for using some species of plants to treat mercury contaminated soil through stabilization rather than extraction. The present investigation proposes a practical cost-effective temporary solution for phytostabilization of soil with moderate mercury contamination as well as the basis for plant selection.

Rhizosphere Microbial Community Composition Affects Cadmium and Zinc Uptake by the Metal-Hyperaccumulating Plant Arabidopsis halleri

PubMed Central

Muehe, E. Marie; Weigold, Pascal; Adaktylou, Irini J.; Planer-Friedrich, Britta; Kraemer, Ute; Kappler, Andreas

2015-01-01

The remediation of metal-contaminated soils by phytoextraction depends on plant growth and plant metal accessibility. Soil microorganisms can affect the accumulation of metals by plants either by directly or indirectly stimulating plant growth and activity or by (im)mobilizing and/or complexing metals. Understanding the intricate interplay of metal-accumulating plants with their rhizosphere microbiome is an important step toward the application and optimization of phytoremediation. We compared the effects of a “native” and a strongly disturbed (gamma-irradiated) soil microbial communities on cadmium and zinc accumulation by the plant Arabidopsis halleri in soil microcosm experiments. A. halleri accumulated 100% more cadmium and 15% more zinc when grown on the untreated than on the gamma-irradiated soil. Gamma irradiation affected neither plant growth nor the 1 M HCl-extractable metal content of the soil. However, it strongly altered the soil microbial community composition and overall cell numbers. Pyrosequencing of 16S rRNA gene amplicons of DNA extracted from rhizosphere samples of A. halleri identified microbial taxa (Lysobacter, Streptomyces, Agromyces, Nitrospira, “Candidatus Chloracidobacterium”) of higher relative sequence abundance in the rhizospheres of A. halleri plants grown on untreated than on gamma-irradiated soil, leading to hypotheses on their potential effect on plant metal uptake. However, further experimental evidence is required, and wherefore we discuss different mechanisms of interaction of A. halleri with its rhizosphere microbiome that might have directly or indirectly affected plant metal accumulation. Deciphering the complex interactions between A. halleri and individual microbial taxa will help to further develop soil metal phytoextraction as an efficient and sustainable remediation strategy. PMID:25595759

Ex-situ biogas upgrading and enhancement in different reactor systems.

PubMed

Kougias, Panagiotis G; Treu, Laura; Benavente, Daniela Peñailillo; Boe, Kanokwan; Campanaro, Stefano; Angelidaki, Irini

2017-02-01

Biogas upgrading is envisioned as a key process for clean energy production. The current study evaluates the efficiency of different reactor configurations for ex-situ biogas upgrading and enhancement, in which externally provided hydrogen and carbon dioxide were biologically converted to methane by the action of hydrogenotrophic methanogens. The methane content in the output gas of the most efficient configuration was >98%, allowing its exploitation as substitute to natural gas. Additionally, use of digestate from biogas plants as a cost efficient method to provide all the necessary nutrients for microbial growth was successful. High-throughput 16S rRNA sequencing revealed that the microbial community was resided by novel phylotypes belonging to the uncultured order MBA08 and to Bacteroidales. Moreover, only hydrogenotrophic methanogens were identified belonging to Methanothermobacter and Methanoculleus genera. Methanothermobacter thermautotrophicus was the predominant methanogen in the biofilm formed on top of the diffuser surface in the bubble column reactor. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evaluation of the effects of different liquid inoculant formulations on the survival and plant-growth-promoting efficiency of Rhodopseudomonas palustris strain PS3.

PubMed

Lee, Sook-Kuan; Lur, Huu-Sheng; Lo, Kai-Jiun; Cheng, Kuan-Chen; Chuang, Chun-Chao; Tang, Shiueh-Jung; Yang, Zhi-Wei; Liu, Chi-Te

2016-09-01

Biofertilizers can help improve soil quality, promote crop growth, and sustain soil health. The photosynthetic bacterium Rhodopseudomonas palustris strain PS3 (hereafter, PS3), which was isolated from Taiwanese paddy soil, can not only exert beneficial effects on plant growth but also enhance the efficiency of nutrient uptake from applied fertilizer. To produce this elite microbial isolate for practical use, product development and formulation are needed to permit the maintenance of the high quality of the inoculant during storage. The aim of this study was to select a suitable formulation that improves the survival and maintains the beneficial effects of the PS3 inoculant. Six additives (alginate, polyethylene glycol [PEG], polyvinylpyrrolidone-40 [PVP], glycerol, glucose, and horticultural oil) were used in liquid-based formulations, and their capacities for maintaining PS3 cell viability during storage in low, medium, and high temperature ranges were evaluated. Horticultural oil (0.5 %) was chosen as a potential additive because it could maintain a relatively high population and conferred greater microbial vitality under various storage conditions. Furthermore, the growth-promoting effects exerted on Chinese cabbage by the formulated inoculants were significantly greater than those of the unformulated treatments. The fresh and dry weights of the shoots were significantly increased, by 10-27 and 22-40 %, respectively. Horticultural oil is considered a safe, low-cost, and easy-to-process material, and this formulation would facilitate the practical use of strain PS3 in agriculture.

Novel optimization strategy for tannase production through a modified solid-state fermentation system.

PubMed

Wu, Changzheng; Zhang, Feng; Li, Lijun; Jiang, Zhedong; Ni, Hui; Xiao, Anfeng

2018-01-01

High amounts of insoluble substrates exist in the traditional solid-state fermentation (SSF) system. The presence of these substrates complicates the determination of microbial biomass. Thus, enzyme activity is used as the sole index for the optimization of the traditional SSF system, and the relationship between microbial growth and enzyme synthesis is always ignored. This study was conducted to address this deficiency. All soluble nutrients from tea stalk were extracted using water. The aqueous extract was then mixed with polyurethane sponge to establish a modified SSF system, which was then used to conduct tannase production. With this system, biomass, enzyme activity, and enzyme productivity could be measured rationally and accurately. Thus, the association between biomass and enzyme activity could be easily identified, and the shortcomings of traditional SSF could be addressed. Different carbon and nitrogen sources exerted different effects on microbial growth and enzyme production. Single-factor experiments showed that glucose and yeast extract greatly improved microbial biomass accumulation and that tannin and (NH 4 ) 2 SO 4 efficiently promoted enzyme productivity. Then, these four factors were optimized through response surface methodology. Tannase activity reached 19.22 U/gds when the added amounts of tannin, glucose, (NH 4 ) 2 SO 4 , and yeast extract were 7.49, 8.11, 9.26, and 2.25%, respectively. Tannase activity under the optimized process conditions was 6.36 times higher than that under the initial process conditions. The optimized parameters were directly applied to the traditional tea stalk SSF system. Tannase activity reached 245 U/gds, which is 2.9 times higher than our previously reported value. In this study, a modified SSF system was established to address the shortcomings of the traditional SSF system. Analysis revealed that enzymatic activity and microbial biomass are closely related, and different carbon and nitrogen sources have different effects on microbial growth and enzyme production. The maximal tannase activity was obtained under the optimal combination of nutrient sources that enhances cell growth and tannase accumulation. Moreover, tannase production through the traditional tea stalk SSF was markedly improved when the optimized parameters were applied. This work provides an innovative approach to bioproduction research through SSF.

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

Molecular characterization of microbial population dynamics during sildenafil citrate degradation.

PubMed

De Felice, Bruna; Argenziano, Carolina; Guida, Marco; Trifuoggi, Marco; Russo, Francesca; Condorelli, Valerio; Inglese, Mafalda

2009-02-01

Little is known about pharmaceutical and personal care products pollutants (PPCPs), but there is a growing interest in how they might impact the environment and microbial communities. The widespread use of Viagra (sildenafil citrate) has attracted great attention because of the high usage rate, the unpredictable disposal and the unknown potential effects on wildlife and the environment. Until now information regarding the impact of Viagra on microbial community in water environment has not been reported. In this research, for the first time, the genetic profile of the microbial community, developing in a Viagra polluted water environment, was evaluated by means of the 16S and 18S rRNA genes, for bacteria and fungi, respectively, amplified by polymerase chain reaction (PCR) and separated using the denaturing gradient gel electrophoresis (DGGE) technique. The DGGE results revealed a complex microbial community structure with most of the population persisting throughout the experimental period. DNA sequences from bands observed in the different denaturing gradient gel electrophoresis profiles exhibited the highest degree of identity to uncultured bacteria and fungi found previously mainly in polluted environmental and treating bioreactors. Biotransformation ability of sildenafil citrate by the microbial pool was studied and the capability of these microorganisms to detoxify a polluted water ecosystem was assessed. The bacterial and fungal population was able to degrade sildenafil citrate entirely. Additionally, assays conducted on Daphnia magna, algal growth inhibition assay and cell viability determination on HepG2 human cells showed that biotransformation products obtained from the bacterial growth was not toxic. The higher removal efficiency for sildenafil citrate and the lack of toxicity by the biotransformation products obtained showed that the microbial community identified here represented a composite population that might have biotechnological relevance to retrieve sildenafil citrate contaminated sites.

Thermodynamic analysis of fermentation and anaerobic growth of baker's yeast for ethanol production.

PubMed

Teh, Kwee-Yan; Lutz, Andrew E

2010-05-17

Thermodynamic concepts have been used in the past to predict microbial growth yield. This may be the key consideration in many industrial biotechnology applications. It is not the case, however, in the context of ethanol fuel production. In this paper, we examine the thermodynamics of fermentation and concomitant growth of baker's yeast in continuous culture experiments under anaerobic, glucose-limited conditions, with emphasis on the yield and efficiency of bio-ethanol production. We find that anaerobic metabolism of yeast is very efficient; the process retains more than 90% of the maximum work that could be extracted from the growth medium supplied to the chemostat reactor. Yeast cells and other metabolic by-products are also formed, which reduces the glucose-to-ethanol conversion efficiency to less than 75%. Varying the specific ATP consumption rate, which is the fundamental parameter in this paper for modeling the energy demands of cell growth, shows the usual trade-off between ethanol production and biomass yield. The minimum ATP consumption rate required for synthesizing cell materials leads to biomass yield and Gibbs energy dissipation limits that are much more severe than those imposed by mass balance and thermodynamic equilibrium constraints. 2010 Elsevier B.V. All rights reserved.

Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield

PubMed Central

Ferris, Michael; Bruggeman, Frank J.

2018-01-01

Microbes may maximize the number of daughter cells per time or per amount of nutrients consumed. These two strategies correspond, respectively, to the use of enzyme-efficient or substrate-efficient metabolic pathways. In reality, fast growth is often associated with wasteful, yield-inefficient metabolism, and a general thermodynamic trade-off between growth rate and biomass yield has been proposed to explain this. We studied growth rate/yield trade-offs by using a novel modeling framework, Enzyme-Flux Cost Minimization (EFCM) and by assuming that the growth rate depends directly on the enzyme investment per rate of biomass production. In a comprehensive mathematical model of core metabolism in E. coli, we screened all elementary flux modes leading to cell synthesis, characterized them by the growth rates and yields they provide, and studied the shape of the resulting rate/yield Pareto front. By varying the model parameters, we found that the rate/yield trade-off is not universal, but depends on metabolic kinetics and environmental conditions. A prominent trade-off emerges under oxygen-limited growth, where yield-inefficient pathways support a 2-to-3 times higher growth rate than yield-efficient pathways. EFCM can be widely used to predict optimal metabolic states and growth rates under varying nutrient levels, perturbations of enzyme parameters, and single or multiple gene knockouts. PMID:29451895

The microbial community structure in petroleum-contaminated sediments corresponds to geophysical signatures

USGS Publications Warehouse

Allen, J.P.; Atekwana, E.A.; Duris, J.W.; Werkema, D.D.; Rossbach, S.

2007-01-01

The interdependence between geoelectrical signatures at underground petroleum plumes and the structures of subsurface microbial communities was investigated. For sediments contaminated with light non-aqueousphase liquids, anomalous high conductivity values have been observed. Vertical changes in the geoelectrical properties of the sediments were concomitant with significant changes in the microbial community structures as determined by the construction and evaluation of 16S rRNA gene libraries. DNA sequencing of clones from four 16S rRNA gene libraries from different depths of a contaminated field site and two libraries from an uncontaminated background site revealed spatial heterogeneity in the microbial community structures. Correspondence analysis showed that the presence of distinct microbial populations, including the various hydrocarbon-degrading, syntrophic, sulfate-reducing, and dissimilatory-iron-reducing populations, was a contributing factor to the elevated geoelectrical measurements. Thus, through their growth and metabolic activities, microbial populations that have adapted to the use of petroleum as a carbon source can strongly influence their geophysical surroundings. Since changes in the geophysical properties of contaminated sediments parallel changes in the microbial community compositions, it is suggested that geoelectrical measurements can be a cost-efficient tool to guide microbiological sampling for microbial ecology studies during the monitoring of natural or engineered bioremediation processes. Copyright ?? 2007, American Society for Microbiology. All Rights Reserved.

Plant, microbial and ecosystem carbon use efficiencies interact to stabilize microbial growth as a fraction of gross primary production.

PubMed

Sinsabaugh, Robert L; Moorhead, Daryl L; Xu, Xiaofeng; Litvak, Marcy E

2017-06-01

The carbon use efficiency of plants (CUE a ) and microorganisms (CUE h ) determines rates of biomass turnover and soil carbon sequestration. We evaluated the hypothesis that CUE a and CUE h counterbalance at a large scale, stabilizing microbial growth (μ) as a fraction of gross primary production (GPP). Collating data from published studies, we correlated annual CUE a , estimated from satellite imagery, with locally determined soil CUE h for 100 globally distributed sites. Ecosystem CUE e , the ratio of net ecosystem production (NEP) to GPP, was estimated for each site using published models. At the ecosystem scale, CUE a and CUE h were inversely related. At the global scale, the apparent temperature sensitivity of CUE h with respect to mean annual temperature (MAT) was similar for organic and mineral soils (0.029°C -1 ). CUE a and CUE e were inversely related to MAT, with apparent sensitivities of -0.009 and -0.032°C -1 , respectively. These trends constrain the ratio μ : GPP (= (CUE a  × CUE h )/(1 - CUE e )) with respect to MAT by counterbalancing the apparent temperature sensitivities of the component processes. At the ecosystem scale, the counterbalance is effected by modulating soil organic matter stocks. The results suggest that a μ : GPP value of c. 0.13 is a homeostatic steady state for ecosystem carbon fluxes at a large scale. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Advanced Chemical Design for Efficient Lignin Bioconversion

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

Xie, Shangxian; Sun, Qining; Pu, Yunqiao

Here, lignin depolymerization mainly involves redox reactions relying on the effective electron transfer. Even though electron mediators were previously used for delignification of paper pulp, no study has established a bioprocess to fragment and solubilize the lignin with an effective laccase–mediator system, in particular, for subsequent microbial bioconversion. Efficient lignin depolymerization was achieved by screening proper electron mediators with laccase to attain a nearly 6-fold increase of kraft lignin solubility compared to the control kraft lignin without laccase treatment. Chemical analysis suggested the release of a low molecular weight fraction of kraft lignin into the solution phase. Moreover, NMR analysismore » revealed that an efficient enzyme–mediator system can promote the lignin degradation. More importantly, the fundamental mechanisms guided the development of an efficient lignin bioconversion process, where solubilized lignin from laccase–HBT treatment served as a superior substrate for bioconversion by Rhodococcus opacus PD630. The cell growth was increased by 10 6 fold, and the lipid titer reached 1.02 g/L. Overall, the study has manifested that an efficient enzyme–mediator–microbial system can be exploited to establish a bioprocess to solubilize lignin, cleave lignin linkages, modify the structure, and produce substrates amenable to bioconversion.« less

Advanced Chemical Design for Efficient Lignin Bioconversion

DOE PAGES

Xie, Shangxian; Sun, Qining; Pu, Yunqiao; ...

2017-01-30

Here, lignin depolymerization mainly involves redox reactions relying on the effective electron transfer. Even though electron mediators were previously used for delignification of paper pulp, no study has established a bioprocess to fragment and solubilize the lignin with an effective laccase–mediator system, in particular, for subsequent microbial bioconversion. Efficient lignin depolymerization was achieved by screening proper electron mediators with laccase to attain a nearly 6-fold increase of kraft lignin solubility compared to the control kraft lignin without laccase treatment. Chemical analysis suggested the release of a low molecular weight fraction of kraft lignin into the solution phase. Moreover, NMR analysismore » revealed that an efficient enzyme–mediator system can promote the lignin degradation. More importantly, the fundamental mechanisms guided the development of an efficient lignin bioconversion process, where solubilized lignin from laccase–HBT treatment served as a superior substrate for bioconversion by Rhodococcus opacus PD630. The cell growth was increased by 10 6 fold, and the lipid titer reached 1.02 g/L. Overall, the study has manifested that an efficient enzyme–mediator–microbial system can be exploited to establish a bioprocess to solubilize lignin, cleave lignin linkages, modify the structure, and produce substrates amenable to bioconversion.« less

Injectable Self-Healing Hydrogel with Antimicrobial and Antifouling Properties.

PubMed

Li, Lin; Yan, Bin; Yang, Jingqi; Huang, Weijuan; Chen, Lingyun; Zeng, Hongbo

2017-03-22

Microbial adhesion, biofilm formation and associated microbial infection are common challenges faced by implanted biomaterials (e.g., hydrogels) in bioengineering applications. In this work, an injectable self-healing hydrogel with antimicrobial and antifouling properties was prepared through self-assembly of an ABA triblock copolymer employing catechol functionalized polyethylene glycol (PEG) as A block and poly{[2-(methacryloyloxy)-ethyl] trimethylammonium iodide}(PMETA) as B block. This hydrogel exhibits excellent thermosensitivity, and can effectively inhibit the growth of E. coli (>99.8% killing efficiency) and prevent cell attachment. It can also heal autonomously from repeated damage, through mussel-inspired catechol-mediated hydrogen bonding and aromatic interactions, exhibiting great potential in bioengineering applications.

Evaluation of bacterial diversity recovered from petroleum samples using different physical matrices.

PubMed

Dellagnezze, Bruna Martins; Vasconcellos, Suzan Pantaroto de; Melo, Itamar Soares de; Santos Neto, Eugênio Vaz Dos; Oliveira, Valéria Maia de

2016-01-01

Unraveling the microbial diversity and its complexity in petroleum reservoir environments has been a challenge throughout the years. Despite the techniques developed in order to improve methodologies involving DNA extraction from crude oil, microbial enrichments using different culture conditions can be applied as a way to increase the recovery of DNA from environments with low cellular density for further microbiological analyses. This work aimed at the evaluation of different matrices (arenite, shale and polyurethane foam) as support materials for microbial growth and biofilm formation in enrichments using a biodegraded petroleum sample as inoculum in sulfate reducing condition. Subsequent microbial diversity characterization was carried out using Scanning Electronic Microscopy (SEM), Denaturing Gradient Gel Electrophoresis (DGGE) and 16S rRNA gene libraries in order to compare the microbial biomass yield, DNA recovery efficiency and diversity among the enrichments. The DNA from microbial communities in petroleum enrichments was purified according to a protocol established in this work and used for 16S rRNA amplification with bacterial generic primers. The PCR products were cloned, and positive clones were screened by Amplified Ribosomal DNA Restriction Analysis (ARDRA). Sequencing and phylogenetic analyses revealed that the bacterial community was mostly represented by members of the genera Petrotoga, Bacillus, Pseudomonas, Geobacillus and Rahnella. The use of different support materials in the enrichments yielded an increase in microbial biomass and biofilm formation, indicating that these materials may be employed for efficient biomass recovery from petroleum reservoir samples. Nonetheless, the most diverse microbiota were recovered from the biodegraded petroleum sample using polyurethane foam cubes as support material. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

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.

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.

Sterilization of rotary NiTi instruments within endodontic sponges.

PubMed

Chan, H W A; Tan, K H; Dashper, S G; Reynolds, E C; Parashos, P

2015-08-17

To determine whether the following can be sterilized by autoclaving - endodontic sponges, rotary nickel-titanium (NiTi) instruments within endodontic sponges, and rotary NiTi instruments with rubber stoppers. Sixty-four samples of eight different endodontic sponges (n = 512) were placed into brain heart infusion broth (BHI) for 72 h. An aliquot of this was then spread onto horse blood agar and cultured aerobically and anaerobically to test sterility at purchase. Bacterial suspensions of Enterococcus faecalis, Porphyromonas gingivalis and Geobacillus stearothermophilus in BHI were used to contaminate sterile sponges and rotary NiTi instruments (with and without rubber stoppers) inserted into sponges. The various samples were autoclaved and then cultured aerobically and anaerobically. Success of sterilization was measured qualitatively as no growth. The experiment was repeated with clinically used rotary NiTi instruments (n = 512). All experiments were conducted in quadruplicate. No sponges on purchase had microbial growth when anaerobically cultured but some did when aerobically cultured. All autoclaved sponges and instruments (within or without sponges, and with or without rubber stoppers) were associated with no microbial growth. All nonautoclaved positive control samples showed microbial growth. Autoclaving was effective in the sterilization of sponges and endodontic instruments. Endodontic sponges should be autoclaved before clinical use. For clinical efficiency and cost-effectiveness, rotary NiTi instruments can be sterilized in endodontic sponges without removal of rubber stoppers. © 2015 International Endodontic Journal. Published by John Wiley & Sons Ltd.

Growth rates of rhizosphere microorganisms depend on competitive abilities of plants for nitrogen

NASA Astrophysics Data System (ADS)

Blagodatskaya, Evgenia; Littschwager, Johanna; Lauerer, Marianna; Kuzyakov, Yakov

2010-05-01

Rhizosphere - one of the most important ‘hot spots' in soil - is characterized not only by accelerated turnover of microbial biomass and nutrients but also by strong intra- and inter-specific competition. Intra-specific competition occurs between individual plants of the same species, while inter-specific competition can occur both at population level (plant species-specific, microbial species-specific interactions) and at community level (plant - microbial interactions). Such plant - microbial interactions are mainly governed by competition for available N sources, since N is one of the main growth limiting nutrients in natural ecosystems. Functional structure and activity of microbial community in rhizosphere is not uniform and is dependent on quantity and quality of root exudates which are plant specific. It is still unclear how microbial growth and turnover in the rhizosphere are dependent on the features and competitive abilities of plants for N. Depending on C and N availability, acceleration and even retardation of microbial activity and carbon mineralization can be expected in the rhizosphere of plants with high competitive abilities for N. We hypothesized slower microbial growth rates in the rhizosphere of plants with smaller roots, as they usually produce less exudates compared to plants with small shoot-to-root ratio. As the first hypothesis is based solely on C availability, we also expected the greater effect of N availability on microbial growth in rhizosphere of plants with smaller root mass. These hypothesis were tested for two plant species of strawberry: Fragaria vesca L. (native species), and Duchesnea indica (Andrews) Focke (an invasive plant in central Europe) growing in intraspecific and interspecific competition. Microbial biomass and the kinetic parameters of microbial growth in the rhizosphere were estimated by dynamics of CO2 emission from the soil amended with glucose and nutrients. Specific growth rate (µ) of soil microorganisms was estimated by fitting the parameters of the equation: CO2(t) = A + B × exp(µ×t), to the measured CO2 production rate (CO2(t)) after glucose addition, where A is the initial respiration rate uncoupled from ATP production, B the initial rate of the growing fraction of total respiration coupled with ATP generation and cell growth, and t time. Our study revealed the linkage between growth strategies of rhizosphere microorganisms and different adaptation strategies of F. vesca and D. indica to N limitation. Plant - strong competitor for N (D. indica) did not change root mass under N limitation causing the deficit of N in the rhizosphere and altering the structure of rhizosphere microbial community. Benefiting of slow growing microorganisms with K-strategy under N limiting conditions was indicated by strong decrease in specific microbial growth rates in the rhizosphere of D. indica. Root mass of the plant with weak competitive abilities for N (F. vesca) increased under lack of N to compensate the lack of nutrients. The increase in root mass and possible increase in amount of root exudates coincided with no structural changes in microbial community in rhizosphere of F. vesca. By intraspecific competition at low N level a 2.4-fold slower microbial specific growth rates were observed under D. indica (0.09 h-1) characterized by smaller root biomass and lower N content in roots compared with F. vesca. The generation time of actively growing microbial biomass was for the 6 hours longer in rhizosphere of D. indica than under F. vesca (10.7 to 4.6 h, respectively). Thus, under N limitation the strong competition for N between plant and microorganisms decreased microbial growth rates and carbon turnover in rhizosphere. By interspecific competition of both plants at low N level, microbial growth rates were similar to those for D. indica indicating that plant with stronger competitive abilities for N controls microbial community in the rhizosphere. At high N availability the root biomass did not differ significantly between both plants. This resulted in similar microbial growth rates for intra- and interspecific plant competition. Since high N level smoothed the differences between plant species in root and microbial biomass as well as in microbial growth rates, we conclude that competitive abilities of plant species were responsible for microbial growth in rhizosphere only under N imitation. As it is common that fine root proliferation and root exudation decrease at high N level, N addition smoothed the differences in microbial growth independently on plant competitive abilities.

Profiling of Indigenous Microbial Community Dynamics and Metabolic Activity During Enrichment in Molasses-Supplemented Crude Oil-Brine Mixtures for Improved Understanding of Microbial Enhanced Oil Recovery.

PubMed

Halim, Amalia Yunita; Pedersen, Dorthe Skou; Nielsen, Sidsel Marie; Lantz, Anna Eliasson

2015-06-01

Anaerobic incubations using crude oil and brine from a North Sea reservoir were conducted to gain increased understanding of indigenous microbial community development, metabolite production, and the effects on the oil-brine system after addition of a complex carbon source, molasses, with or without nitrate to boost microbial growth. Growth of the indigenous microbes was stimulated by addition of molasses. Pyrosequencing showed that specifically Anaerobaculum, Petrotoga, and Methanothermococcus were enriched. Addition of nitrate favored the growth of Petrotoga over Anaerobaculum. The microbial growth caused changes in the crude oil-brine system: formation of oil emulsions, and reduction of interfacial tension (IFT). Reduction in IFT was associated with microbes being present at the oil-brine interphase. These findings suggest that stimulation of indigenous microbial growth by addition of molasses has potential as microbial enhanced oil recovery (MEOR) strategy in North Sea oil reservoirs.

A phosphorus-free anolyte to enhance coulombic efficiency of microbial fuel cells

NASA Astrophysics Data System (ADS)

Tang, Xinhua; Li, Haoran; Du, Zhuwei; Ng, How Yong

2014-12-01

In this study, a phosphorus-free anolyte is prepared by using bicarbonate to replace phosphate buffer for application in two chamber microbial fuel cells (MFCs). Optical density test and Bradford protein assay shows that this phosphorus-free anolyte effectively inhibits the growth and reproduction of microorganisms suspended in the solution and greatly reduces the suspended cell mass. As a result, it considerably enhances the coulombic efficiency (CE) of MFCs. When the acetate concentration is 11 mM, the CE of the MFC using the pH 7 phosphate-containing anolyte is 9.7% and the CE with the pH 8.3 phosphate-containing anolyte is 9.1%, while the CE of the MFC using the phosphorus-free anolyte (pH 8.3) achieves 26.6%. This study demonstrates that this phosphorus-free anolyte holds the potential to enhance the feasibility for practical applications of MFCs.

Efficiency of repeated phytoextraction of cadmium and zinc from an agricultural soil contaminated with sewage sludge.

PubMed

Luo, Kai; Ma, Tingting; Liu, Hongyan; Wu, Longhua; Ren, Jing; Nai, Fengjiao; Li, Rui; Chen, Like; Luo, Yongming; Christie, Peter

2015-01-01

Long-term application of sewage sludge resulted in soil cadmium (Cd) and zinc (Zn) contamination in a pot experiment conducted to phytoextract Cd/Zn repeatedly using Sedum plumbizincicola and Apium graceolens in monoculture or intercropping mode eight times. Shoot yields and soil physicochemical properties changed markedly with increasing number of remediation crops when the two plant species were intercropped compared with the unplanted control soil and the two monoculture treatments. Changes in soil microbial indices such as average well colour development, soil enzyme activity and soil microbial counts were also significantly affected by the growth of the remediation plants, especially intercropping with S. plumbizincicola and A. graveolens. The higher yields and amounts of Cd taken up indicated that intercropping of the hyperaccumulator and the vegetable species may be suitable for simultaneous agricultural production and soil remediation, with larger crop yields and higher phytoremediation efficiencies than under monoculture conditions.

Response of microbial growth to orthophosphate and organic carbon influx in copper and plastic based plumbing water systems.

PubMed

Park, Se-Keun; Kim, Yeong-Kwan; Choi, Sung-Chan

2008-07-01

Consequences of orthophosphate addition for corrosion control in water distribution pipes with respect to microbial growth were investigated using batch and dynamic tests. Batch tests showed that the release of copper in either low or high organic carbon content water was decreased by 69% and 56% with addition 206 microg PO(4)-P, respectively. Dosing of orthophosphate against corrosion did not increase microbial growth potential in the water and in the biofilm in both corroded and uncorroded systems receiving tap water with a low content of organic carbon and of biodegradable organic fraction. However, in tap water having a high concentration of organic carbon from acetate addition, orthophosphate addition promoted the growth of bacteria, allowed more bacteria to assemble on corroded and uncorroded surfaces, and increased the consumption of organic carbon. Orthophosphate consumption did not exceed 1% of the amount of easily biodegradable organic carbon required for microbial growth, and the orthophosphate demand for corrosion control greatly exceeded the nutritional requirement of microbial growth. The results of the dynamic tests demonstrated that there was a significant effect of interaction between biodegradable organic carbon and orthophosphate on biofilm growth, whereby the effect of orthophosphate flux on microbial growth was dependent on the levels of biodegradable organic carbon. Controlling an easily biodegradable organic carbon would be therefore necessary to minimize the microbial growth potential induced by orthophosphate-based anticorrosion treatment.

Metabolic engineering of microbial competitive advantage for industrial fermentation processes.

PubMed

Shaw, A Joe; Lam, Felix H; Hamilton, Maureen; Consiglio, Andrew; MacEwen, Kyle; Brevnova, Elena E; Greenhagen, Emily; LaTouf, W Greg; South, Colin R; van Dijken, Hans; Stephanopoulos, Gregory

2016-08-05

Microbial contamination is an obstacle to widespread production of advanced biofuels and chemicals. Current practices such as process sterilization or antibiotic dosage carry excess costs or encourage the development of antibiotic resistance. We engineered Escherichia coli to assimilate melamine, a xenobiotic compound containing nitrogen. After adaptive laboratory evolution to improve pathway efficiency, the engineered strain rapidly outcompeted a control strain when melamine was supplied as the nitrogen source. We additionally engineered the yeasts Saccharomyces cerevisiae and Yarrowia lipolytica to assimilate nitrogen from cyanamide and phosphorus from potassium phosphite, and they outcompeted contaminating strains in several low-cost feedstocks. Supplying essential growth nutrients through xenobiotic or ecologically rare chemicals provides microbial competitive advantage with minimal external risks, given that engineered biocatalysts only have improved fitness within the customized fermentation environment. Copyright © 2016, American Association for the Advancement of Science.

The micro-Petri dish, a million-well growth chip for the culture and high-throughput screening of microorganisms.

PubMed

Ingham, Colin J; Sprenkels, Ad; Bomer, Johan; Molenaar, Douwe; van den Berg, Albert; van Hylckama Vlieg, Johan E T; de Vos, Willem M

2007-11-13

A miniaturized, disposable microbial culture chip has been fabricated by microengineering a highly porous ceramic sheet with up to one million growth compartments. This versatile culture format, with discrete compartments as small as 7 x 7 mum, allowed the growth of segregated microbial samples at an unprecedented density. The chip has been used for four complementary applications in microbiology. (i) As a fast viable counting system that showed a dynamic range of over 10,000, a low degree of bias, and a high culturing efficiency. (ii) In high-throughput screening, with the recovery of 1 fluorescent microcolony in 10,000. (iii) In screening for an enzyme-based, nondominant phenotype by the targeted recovery of Escherichia coli transformed with the plasmid pUC18, based on expression of the lacZ reporter gene without antibiotic-resistance selection. The ease of rapid, successive changes in the environment of the organisms on the chip, needed for detection of beta-galactosidase activity, highlights an advantageous feature that was also used to screen a metagenomic library for the same activity. (iv) In high-throughput screening of >200,000 isolates from Rhine water based on metabolism of a fluorogenic organophosphate compound, resulting in the recovery of 22 microcolonies with the desired phenotype. These isolates were predicted, on the basis of rRNA sequence, to include six new species. These four applications suggest that the potential for such simple, readily manufactured chips to impact microbial culture is extensive and may facilitate the full automation and multiplexing of microbial culturing, screening, counting, and selection.

Microbe observation and cultivation array (MOCA) for cultivating and analyzing environmental microbiota.

PubMed

Gao, Weimin; Navarroli, Dena; Naimark, Jared; Zhang, Weiwen; Chao, Shih-Hui; Meldrum, Deirdre R

2013-01-09

The use of culture-independent nucleic acid techniques, such as ribosomal RNA gene cloning library analysis, has unveiled the tremendous microbial diversity that exists in natural environments. In sharp contrast to this great achievement is the current difficulty in cultivating the majority of bacterial species or phylotypes revealed by molecular approaches. Although recent new technologies such as metagenomics and metatranscriptomics can provide more functionality information about the microbial communities, it is still important to develop the capacity to isolate and cultivate individual microbial species or strains in order to gain a better understanding of microbial physiology and to apply isolates for various biotechnological applications. We have developed a new system to cultivate bacteria in an array of droplets. The key component of the system is the microbe observation and cultivation array (MOCA), which consists of a Petri dish that contains an array of droplets as cultivation chambers. MOCA exploits the dominance of surface tension in small amounts of liquid to spontaneously trap cells in well-defined droplets on hydrophilic patterns. During cultivation, the growth of the bacterial cells across the droplet array can be monitored using an automated microscope, which can produce a real-time record of the growth. When bacterial cells grow to a visible microcolony level in the system, they can be transferred using a micropipette for further cultivation or analysis. MOCA is a flexible system that is easy to set up, and provides the sensitivity to monitor growth of single bacterial cells. It is a cost-efficient technical platform for bioassay screening and for cultivation and isolation of bacteria from natural environments.

Prediction of microbial growth in fresh-cut vegetables treated with acidic electrolyzed water during storage under various temperature conditions.

PubMed

Koseki, S; Itoh, K

2001-12-01

Effects of storage temperature (1, 5, and 10 degrees C) on growth of microbial populations (total aerobic bacteria, coliform bacteria, Bacillus cereus, and psychrotrophic bacteria) on acidic electrolyzed water (AcEW)-treated fresh-cut lettuce and cabbage were determined. A modified Gompertz function was used to describe the kinetics of microbial growth. Growth data were analyzed using regression analysis to generate "best-fit" modified Gompertz equations, which were subsequently used to calculate lag time, exponential growth rate, and generation time. The data indicated that the growth kinetics of each bacterium were dependent on storage temperature, except at 1 degrees C storage. At 1 degrees C storage, no increases were observed in bacterial populations. Treatment of vegetables with AcEW produced a decrease in initial microbial populations. However, subsequent growth rates were higher than on nontreated vegetables. The recovery time required by the reduced microbial population to reach the initial (treated with tap water [TW]) population was also determined in this study, with the recovery time of the microbial population at 10 degrees C being <3 days. The benefits of reducing the initial microbial populations on fresh-cut vegetables were greatly affected by storage temperature. Results from this study could be used to predict microbial quality of fresh-cut lettuce and cabbage throughout their distribution.

21 CFR 866.2560 - Microbial growth monitor.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Microbial growth monitor. 866.2560 Section 866.2560 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices § 866.2560 Microbial growth...

21 CFR 866.2560 - Microbial growth monitor.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Microbial growth monitor. 866.2560 Section 866.2560 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices § 866.2560 Microbial growth...

21 CFR 866.2560 - Microbial growth monitor.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Microbial growth monitor. 866.2560 Section 866.2560 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices § 866.2560 Microbial growth...

Acoustic and Electrical Property Changes Due to Microbial Growth and Biofilm Formation in Porous Media

EPA Science Inventory

A laboratory study was conducted to investigate the effect of microbial growth and biofilm formation on compressional waves, and complex conductivity during stimulated microbial growth. Over the 29 day duration of the experiment, compressional wave amplitudes and arrival times f...

Direct Growth of Bacteria in Headspace Vials Allows for Screening of Volatiles by Gas Chromatography Mass Spectrometry.

PubMed

Timm, Collin M; Lloyd, Evan P; Egan, Amanda; Mariner, Ray; Karig, David

2018-01-01

Bacterially produced volatile organic compounds (VOCs) can modify growth patterns of eukaryotic hosts and competing/cohabiting microbes. These compounds have been implicated in skin disorders and attraction of biting pests. Current methods to detect and characterize VOCs from microbial cultures can be laborious and low-throughput, making it difficult to understand the behavior of microbial populations. In this work we present an efficient method employing gas chromatography/mass spectrometry with autosampling to characterize VOC profiles from solid-phase bacterial cultures. We compare this method to complementary plate-based assays and measure the effects of growth media and incubation temperature on the VOC profiles from a well-studied Pseudomonas aeruginosa PAO1 system. We observe that P. aeruginosa produces longer chain VOCs, such as 2-undecanone and 2-undecanol in higher amounts at 37°C than 30°C. We demonstrate the throughput of this method by studying VOC profiles from a representative collection of skin bacterial isolates under three parallel growth conditions. We observe differential production of various aldehydes and ketones depending on bacterial strain. This generalizable method will support screening of bacterial populations in a variety of research areas.

Optimal Resting-Growth Strategies of Microbial Populations in Fluctuating Environments

PubMed Central

Geisel, Nico; Vilar, Jose M. G.; Rubi, J. Miguel

2011-01-01

Bacteria spend most of their lifetime in non-growing states which allow them to survive extended periods of stress and starvation. When environments improve, they must quickly resume growth to maximize their share of limited nutrients. Cells with higher stress resistance often survive longer stress durations at the cost of needing more time to resume growth, a strong disadvantage in competitive environments. Here we analyze the basis of optimal strategies that microorganisms can use to cope with this tradeoff. We explicitly show that the prototypical inverse relation between stress resistance and growth rate can explain much of the different types of behavior observed in stressed microbial populations. Using analytical mathematical methods, we determine the environmental parameters that decide whether cells should remain vegetative upon stress exposure, downregulate their metabolism to an intermediate optimum level, or become dormant. We find that cell-cell variability, or intercellular noise, is consistently beneficial in the presence of extreme environmental fluctuations, and that it provides an efficient population-level mechanism for adaption in a deteriorating environment. Our results reveal key novel aspects of responsive phenotype switching and its role as an adaptive strategy in changing environments. PMID:21525975

Direct Growth of Bacteria in Headspace Vials Allows for Screening of Volatiles by Gas Chromatography Mass Spectrometry

PubMed Central

Timm, Collin M.; Lloyd, Evan P.; Egan, Amanda; Mariner, Ray; Karig, David

2018-01-01

Bacterially produced volatile organic compounds (VOCs) can modify growth patterns of eukaryotic hosts and competing/cohabiting microbes. These compounds have been implicated in skin disorders and attraction of biting pests. Current methods to detect and characterize VOCs from microbial cultures can be laborious and low-throughput, making it difficult to understand the behavior of microbial populations. In this work we present an efficient method employing gas chromatography/mass spectrometry with autosampling to characterize VOC profiles from solid-phase bacterial cultures. We compare this method to complementary plate-based assays and measure the effects of growth media and incubation temperature on the VOC profiles from a well-studied Pseudomonas aeruginosa PAO1 system. We observe that P. aeruginosa produces longer chain VOCs, such as 2-undecanone and 2-undecanol in higher amounts at 37°C than 30°C. We demonstrate the throughput of this method by studying VOC profiles from a representative collection of skin bacterial isolates under three parallel growth conditions. We observe differential production of various aldehydes and ketones depending on bacterial strain. This generalizable method will support screening of bacterial populations in a variety of research areas. PMID:29662472

Plant Growth Promoting and Biocontrol Activity of Streptomyces spp. as Endophytes.

PubMed

Vurukonda, Sai Shiva Krishna Prasad; Giovanardi, Davide; Stefani, Emilio

2018-03-22

There has been many recent studies on the use of microbial antagonists to control diseases incited by soilborne and airborne plant pathogenic bacteria and fungi, in an attempt to replace existing methods of chemical control and avoid extensive use of fungicides, which often lead to resistance in plant pathogens. In agriculture, plant growth-promoting and biocontrol microorganisms have emerged as safe alternatives to chemical pesticides. Streptomyces spp. and their metabolites may have great potential as excellent agents for controlling various fungal and bacterial phytopathogens. Streptomycetes belong to the rhizosoil microbial communities and are efficient colonizers of plant tissues, from roots to the aerial parts. They are active producers of antibiotics and volatile organic compounds, both in soil and in planta , and this feature is helpful for identifying active antagonists of plant pathogens and can be used in several cropping systems as biocontrol agents. Additionally, their ability to promote plant growth has been demonstrated in a number of crops, thus inspiring the wide application of streptomycetes as biofertilizers to increase plant productivity. The present review highlights Streptomyces spp.-mediated functional traits, such as enhancement of plant growth and biocontrol of phytopathogens.

Microbial respiration, but not biomass, responded linearly to increasing light fraction organic matter input: Consequences for carbon sequestration.

PubMed

Rui, Yichao; Murphy, Daniel V; Wang, Xiaoli; Hoyle, Frances C

2016-10-18

Rebuilding 'lost' soil carbon (C) is a priority in mitigating climate change and underpinning key soil functions that support ecosystem services. Microorganisms determine if fresh C input is converted into stable soil organic matter (SOM) or lost as CO 2 . Here we quantified if microbial biomass and respiration responded positively to addition of light fraction organic matter (LFOM, representing recent inputs of plant residue) in an infertile semi-arid agricultural soil. Field trial soil with different historical plant residue inputs [soil C content: control (tilled) = 9.6 t C ha -1 versus tilled + plant residue treatment (tilled + OM) = 18.0 t C ha -1 ] were incubated in the laboratory with a gradient of LFOM equivalent to 0 to 3.8 t C ha -1 (0 to 500% LFOM). Microbial biomass C significantly declined under increased rates of LFOM addition while microbial respiration increased linearly, leading to a decrease in the microbial C use efficiency. We hypothesise this was due to insufficient nutrients to form new microbial biomass as LFOM input increased the ratio of C to nitrogen, phosphorus and sulphur of soil. Increased CO 2 efflux but constrained microbial growth in response to LFOM input demonstrated the difficulty for C storage in this environment.

Exploring a microbial ecosystem approach to modeling deep ocean biogeochemical cycles

NASA Astrophysics Data System (ADS)

Zakem, E.; Follows, M. J.

2014-12-01

Though microbial respiration of organic matter in the deep ocean governs ocean and atmosphere biogeochemistry, it is not represented mechanistically in current global biogeochemical models. We seek approaches that are feasible for a global resolution, yet still reflect the enormous biodiversity of the deep microbial community and its associated metabolic pathways. We present a modeling framework grounded in thermodynamics and redox reaction stoichiometry that represents diverse microbial metabolisms explicitly. We describe a bacterial/archaeal functional type with two parameters: a growth efficiency representing the chemistry underlying a bacterial metabolism, and a rate limitation given by the rate of uptake of each of the necessary substrates for that metabolism. We then apply this approach to answer questions about microbial ecology. As a start, we resolve two dominant heterotrophic respiratory pathways- reduction of oxygen and nitrate- and associated microbial functional types. We combine these into an ecological model and a two-dimensional ocean circulation model to explore the organization, biogeochemistry, and ecology of oxygen minimum zones. Intensified upwelling and lateral transport conspire to produce an oxygen minimum at mid-depth, populated by anaerobic denitrifiers. This modeling approach should ultimately allow for the emergence of bacterial biogeography from competition of metabolisms and for the incorporation of microbial feedbacks to the climate system.

Teaching the Microbial Growth Curve Concept Using Microalgal Cultures and Flow Cytometry

ERIC Educational Resources Information Center

Forget, Nathalie; Belzile, Claude; Rioux, Pierre; Nozais, Christian

2010-01-01

The microbial growth curve is widely studied within microbiology classes and bacteria are usually the microbial model used. Here, we describe a novel laboratory protocol involving flow cytometry to assess the growth dynamics of the unicellular microalgae "Isochrysis galbana." The algal model represents an appropriate alternative to…

40 CFR Appendix B to Subpart Q of... - Standard Health Effects Language for Public Notification

Code of Federal Regulations, 2014 CFR

2014-07-01

... microbial growth. Turbidity may indicate the presence of disease-causing organisms. These organisms include... interfere with disinfection and provide a medium for microbial growth. Turbidity may indicate the presence... provide a medium for microbial growth. Turbidity may indicate the presence of disease-causing organisms...

40 CFR Appendix B to Subpart Q of... - Standard Health Effects Language for Public Notification

Code of Federal Regulations, 2012 CFR

2012-07-01

... interfere with disinfection and provide a medium for microbial growth. Turbidity may indicate the presence... microbial growth. Turbidity may indicate the presence of disease-causing organisms. These organisms include..., turbidity can interfere with disinfection and provide a medium for microbial growth. Turbidity may indicate...

Effects of spaceflight and simulated microgravity on microbial growth and secondary metabolism.

PubMed

Huang, Bing; Li, Dian-Geng; Huang, Ying; Liu, Chang-Ting

2018-05-14

Spaceflight and ground-based microgravity analog experiments have suggested that microgravity can affect microbial growth and metabolism. Although the effects of microgravity and its analogs on microorganisms have been studied for more than 50 years, plausible conflicting and diverse results have frequently been reported in different experiments, especially regarding microbial growth and secondary metabolism. Until now, only the responses of a few typical microbes to microgravity have been investigated; systematic studies of the genetic and phenotypic responses of these microorganisms to microgravity in space are still insufficient due to technological and logistical hurdles. The use of different test strains and secondary metabolites in these studies appears to have caused diverse and conflicting results. Moreover, subtle changes in the extracellular microenvironments around microbial cells play a key role in the diverse responses of microbial growth and secondary metabolisms. Therefore, "indirect" effects represent a reasonable pathway to explain the occurrence of these phenomena in microorganisms. This review summarizes current knowledge on the changes in microbial growth and secondary metabolism in response to spaceflight and its analogs and discusses the diverse and conflicting results. In addition, recommendations are given for future studies on the effects of microgravity in space on microbial growth and secondary metabolism.

Surpassing the current limitations of high purity H2 production in microbial electrolysis cell (MECs): Strategies for inhibiting growth of methanogens.

PubMed

Kadier, Abudukeremu; Kalil, Mohd Sahaid; Chandrasekhar, Kuppam; Mohanakrishna, Gunda; Saratale, Ganesh Dattatraya; Saratale, Rijuta Ganesh; Kumar, Gopalakrishnan; Pugazhendhi, Arivalagan; Sivagurunathan, Periyasamy

2018-02-01

Microbial electrolysis cells (MECs) are perceived as a potential and promising innovative biotechnological tool that can convert carbon-rich waste biomass or wastewater into hydrogen (H 2 ) or other value-added chemicals. Undesired methane (CH 4 ) producing H 2 sinks, including methanogens, is a serious challenge faced by MECs to achieve high-rate H 2 production. Methanogens can consume H 2 to produce CH 4 in MECs, which has led to a drop of H 2 production efficiency, H 2 production rate (HPR) and also a low percentage of H 2 in the produced biogas. Organized inference related to the interactions of microbes and potential processes has assisted in understanding approaches and concepts for inhibiting the growth of methanogens and profitable scale up design. Thus, here in we review the current developments and also the improvements constituted for the reduction of microbial H 2 losses to methanogens. Firstly, the greatest challenge in achieving practical applications of MECs; undesirable microorganisms (methanogens) growth and various studied techniques for eliminating and reducing methanogens activities in MECs were discussed. Additionally, this extensive review also considers prospects for stimulating future research that could help to achieve more information and would provide the focus and path towards MECs as well as their possibilities for simultaneously generating H 2 and waste remediation. Copyright © 2017 Elsevier B.V. All rights reserved.

Bacterial and fungal growth for monitoring the impact of wildfire combined or not with different soil stabilization treatments

NASA Astrophysics Data System (ADS)

Barreiro, Ana; Baath, Erland; Díaz-Raviña, Montserrat

2015-04-01

Soil stabilization techniques are rapidly gaining acceptance as efficient tool for reducing post-fire erosion. However, despite its interest, information concerning their impact on soil biota is scarce. We examined, under field conditions, the bacterial and fungal medium-term responses in a hillslope area located in Laza (NW Spain) affected by a high severity wildfire with the following treatments established by triplicate (4 x 20 m plots): unburnt control soil, burnt control soil, burnt soil with rye seeding and burnt soil with straw mulch. The bacterial and fungal growth, as well as respiration, were measured 4 years after fire and application of treatments using leucine incorporation for bacterial growth and acetate-in-ergosterol incorporation for fungal growth. The results showed that soil respiration and fungal biomass were negatively affected by fire, in the top layer (0-5 cm), while bacterial and fungal growth was stimulated. These microbial changes induced by fire were associated with modifications in organic matter (50% reduction in C content) and soil pH (increase of 0.5-0.9 units). Thus, the results suggested that under acid environment (pH in water 3.5) post-fire conditions might have favoured both microbial groups, which is supported by the fact that estimated bacterial and fungal growth were positive and significant correlated with soil pH (range of 3.5-4.5). This contrast with the well-known reported investigations showing that bacteria rather than fungi proliferation occurred after prescribed fire or wildfire; it should be noticed, however, that soils with a higher pH than that in the present study were used. Our data also indicated that bacterial and fungal communities were not significantly affected by seeding and mulching treatments. The results highlighted the importance of pre-fire soil pH as key factor in determining the microbial response after fire. Acknowledgements. A. Barreiro is recipient of FPU grant from Spanish Ministry of Education. Keywords: wildfire, seeding, mulching, bacterial growth, fungal growth

Selective cathodic microbial biofilm retention allows a high current-to-sulfide efficiency in sulfate-reducing microbial electrolysis cells.

PubMed

Pozo, Guillermo; Lu, Yang; Pongy, Sebastien; Keller, Jürg; Ledezma, Pablo; Freguia, Stefano

2017-12-01

Selective microbial retention is of paramount importance for the long-term performance of cathodic sulfate reduction in microbial electrolysis cells (MECs) due to the slow growth rate of autotrophic sulfate-reducing bacteria. In this work, we investigate the biofilm retention and current-to-sulfide conversion efficiency using carbon granules (CG) or multi-wall carbon nanotubes deposited on reticulated vitreous carbon (MWCNT-RVC) as electrode materials. For ~2months, the MECs were operated at sulfate loading rates of 21 to 309gSO 4 -S/m 2 /d. Although MWCNT-RVC achieved a current density of 57±11A/m 2 , greater than the 32±9A/m 2 observed using CG, both materials exhibited similar sulfate reduction rates (SRR), with MWCNT-RVC reaching 104±16gSO 4 -S/m 2 /d while 110±13gSO 4 -S/m 2 /d were achieved with CG. Pyrosequencing analysis of the 16S rRNA at the end of experimentation revealed a core community dominated by Desulfovibrio (28%), Methanobacterium (19%) and Desulfomicrobium (14%), on the MWCNT-RVC electrodes. While a similar Desulfovibrio relative abundance of 29% was found in CG-biofilms, Desulfomicrobium was found to be significantly less abundant (4%) and Methanobacterium practically absent (0.2%) on CG electrodes. Surprisingly, our results show that CG can achieve higher current-to-sulfide efficiencies at lower power consumption than the nano-modified three-dimensional MWCNT-RVC. Copyright © 2017 Elsevier B.V. All rights reserved.

Combining microbial cultures for efficient production of electricity from butyrate in a microbial electrochemical cell.

PubMed

Miceli, Joseph F; Garcia-Peña, Ines; Parameswaran, Prathap; Torres, César I; Krajmalnik-Brown, Rosa

2014-10-01

Butyrate is an important product of anaerobic fermentation; however, it is not directly used by characterized strains of the highly efficient anode respiring bacteria (ARB) Geobacter sulfurreducens in microbial electrochemical cells. By combining a butyrate-oxidizing community with a Geobacter rich culture, we generated a microbial community which outperformed many naturally derived communities found in the literature for current production from butyrate and rivaled the highest performing natural cultures in terms of current density (∼ 11A/m(2)) and Coulombic efficiency (∼ 70%). Microbial community analyses support the shift in the microbial community from one lacking efficient ARB in the marine hydrothermal vent community to a community consisting of ∼ 80% Geobacter in the anode biofilm. This demonstrates the successful production and adaptation of a novel microbial culture for generating electrical current from butyrate with high current density and high Coulombic efficiency, by combining two mixed microbial cultures containing complementing biochemical pathways. Copyright © 2014 Elsevier Ltd. All rights reserved.

Chlorobaculum tepidum Modulates Amino Acid Composition in Response to Energy Availability, as Revealed by a Systematic Exploration of the Energy Landscape of Phototrophic Sulfur Oxidation.

PubMed

Levy, Amalie T; Lee, Kelvin H; Hanson, Thomas E

2016-11-01

Microbial sulfur metabolism, particularly the formation and consumption of insoluble elemental sulfur (S 0 ), is an important biogeochemical engine that has been harnessed for applications ranging from bioleaching and biomining to remediation of waste streams. Chlorobaculum tepidum, a low-light-adapted photoautolithotrophic sulfur-oxidizing bacterium, oxidizes multiple sulfur species and displays a preference for more reduced electron donors: sulfide > S 0 > thiosulfate. To understand this preference in the context of light energy availability, an "energy landscape" of phototrophic sulfur oxidation was constructed by varying electron donor identity, light flux, and culture duration. Biomass and cellular parameters of C. tepidum cultures grown across this landscape were analyzed. From these data, a correction factor for colorimetric protein assays was developed, enabling more accurate biomass measurements for C. tepidum, as well as other organisms. C. tepidum's bulk amino acid composition correlated with energy landscape parameters, including a tendency toward less energetically expensive amino acids under reduced light flux. This correlation, paired with an observation of increased cell size and storage carbon production under electron-rich growth conditions, suggests that C. tepidum has evolved to cope with changing energy availability by tuning its proteome for energetic efficiency and storing compounds for leaner times. How microbes cope with and adapt to varying energy availability is an important factor in understanding microbial ecology and in designing efficient biotechnological processes. We explored the response of a model phototrophic organism, Chlorobaculum tepidum, across a factorial experimental design that enabled simultaneous variation and analysis of multiple growth conditions, what we term the "energy landscape." C. tepidum biomass composition shifted toward less energetically expensive amino acids at low light levels. This observation provides experimental evidence for evolved efficiencies in microbial proteomes and emphasizes the role that energy flux may play in the adaptive responses of organisms. From a practical standpoint, our data suggest that bulk biomass amino acid composition could provide a simple proxy to monitor and identify energy stress in microbial systems. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Chlorobaculum tepidum Modulates Amino Acid Composition in Response to Energy Availability, as Revealed by a Systematic Exploration of the Energy Landscape of Phototrophic Sulfur Oxidation

PubMed Central

2016-01-01

ABSTRACT Microbial sulfur metabolism, particularly the formation and consumption of insoluble elemental sulfur (S0), is an important biogeochemical engine that has been harnessed for applications ranging from bioleaching and biomining to remediation of waste streams. Chlorobaculum tepidum, a low-light-adapted photoautolithotrophic sulfur-oxidizing bacterium, oxidizes multiple sulfur species and displays a preference for more reduced electron donors: sulfide > S0 > thiosulfate. To understand this preference in the context of light energy availability, an “energy landscape” of phototrophic sulfur oxidation was constructed by varying electron donor identity, light flux, and culture duration. Biomass and cellular parameters of C. tepidum cultures grown across this landscape were analyzed. From these data, a correction factor for colorimetric protein assays was developed, enabling more accurate biomass measurements for C. tepidum, as well as other organisms. C. tepidum's bulk amino acid composition correlated with energy landscape parameters, including a tendency toward less energetically expensive amino acids under reduced light flux. This correlation, paired with an observation of increased cell size and storage carbon production under electron-rich growth conditions, suggests that C. tepidum has evolved to cope with changing energy availability by tuning its proteome for energetic efficiency and storing compounds for leaner times. IMPORTANCE How microbes cope with and adapt to varying energy availability is an important factor in understanding microbial ecology and in designing efficient biotechnological processes. We explored the response of a model phototrophic organism, Chlorobaculum tepidum, across a factorial experimental design that enabled simultaneous variation and analysis of multiple growth conditions, what we term the “energy landscape.” C. tepidum biomass composition shifted toward less energetically expensive amino acids at low light levels. This observation provides experimental evidence for evolved efficiencies in microbial proteomes and emphasizes the role that energy flux may play in the adaptive responses of organisms. From a practical standpoint, our data suggest that bulk biomass amino acid composition could provide a simple proxy to monitor and identify energy stress in microbial systems. PMID:27565613

The Influence of Chitosan Substrate and Its Nanometric Form Toward the Green Power Generation in Sediment Microbial Fuel Cell.

PubMed

Karthikeyan, C; Sathishkumar, Y; Lee, Yang Soo; Kim, Ae Rhan; Yoo, Dong Jin; Kumar, G Gnana

2017-01-01

A simple, environmental friendly and biologically important sediment interfaced fuel cell was developed for the green energy generation. The soil sediment used for the study is enriched of rich anthropogenic free organic carbon, sufficient manganese and high level potassium contents as evidenced from the geochemical characterizations. The saccharides produced by the catalytic reaction of substrate chitosan were utilized for the growth of microorganisms and electron shuttling processes. Chitosan substrate influenced sediment microbial fuel cells exhibited the nearly two fold power increment over the substrate free fuel cells. The fuel cell efficiencies were further increased by bringing the substrate chitosan at nanometric level, which is nearly three and two fold higher than that of substrate free and chitosan influenced sediment microbial fuel cells, respectively, and the influential parameters involved in the power and longevity issues were addressed with different perspectives.

An improved biofilter to control the dissolved organic nitrogen concentration during drinking water treatment.

PubMed

Zhang, Huining; Gu, Li; Liu, Bing; Gan, Huihui; Zhang, Kefeng; Jin, Huixia; Yu, Xin

2016-09-01

Dissolved organic nitrogen (DON) is a key precursor of numerous disinfection by-products (DBPs), especially nitrogenous DBPs (N-DBPs) formed during disinfection in drinking water treatment. To effectively control DBPs, reduction of the DON concentration before the disinfection process is critical. Traditional biofilters can increase the DON concentration in the effluent, so an improved biofilter is needed. In this study, an improved biofilter was set up with two-layer columns using activated carbon and quartz sand under different influent patterns. Compared with the single-layer filter, the two-layer biofilter controlled the DON concentration more efficiently. The two-point influent biofilter controlled the DON concentration more effectively than the single-point influent biofilter. The improved biofilter resulted in an environment (including matrix, DO, and pH) suitable for microbial growth. Along the depth of the biofilter column, the environment affected the microbial biomass and microbial activity and thus affected the DON concentration.

[Biogas production from cellulose-containing substrates: a review].

PubMed

Tsavkelova, E A; Netrusov, A I

2012-01-01

Anaerobic microbial conversion of organic substrates to various biofuels is one of the alternative energy sources attracting the greatest attention of scientists. The advantages of biogas production over other technologies are the ability of methanogenic communities to degrade a broad range of substrates and concomitant benefits: neutralization of organic waste, reduction of greenhouse gas emission, and fertilizer production. Cellulose-containing materials are a good substrate, but their full-scale utilization encounters a number of problems, including improvement of the quality and amount ofbiogas produced and maintenance of the stability and high efficiency of microbial communities. We review data on microorganisms that form methanogenic cellulolytic communities, enzyme complexes of anaerobes essential for cellulose fiber degradation, and feedstock pretreatment, as biodegradation is hindered in the presence of lignin. Methods for improving biogas production by optimization of microbial growth conditions are considered on the examples of biogas formation from various types of plant and paper materials: writing paper and cardboard.

A Theoretical Reassessment of Microbial Maintenance and Implications for Microbial Ecology Modeling

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

Wang, Gangsheng; Post, Wilfred M

We attempted to reconcile three microbial maintenance models (Herbert, Pirt, and Compromise) through a critical reassessment. We provided a rigorous proof that the true growth yield coefficient (YG) is the ratio of the specific maintenance rate (a in Herbert) to the maintenance coefficient (m in Pirt). Other findings from this study include: (1) the Compromise model is identical to the Herbert for computing microbial growth and substrate consumption, but it expresses the dependence of maintenance on both microbial biomass and substrate; (2) the maximum specific growth rate in the Herbert ( max,H) is higher than those in the other twomore » models ( max,P and max,C), and the difference is the physiological maintenance factor (mq = a); and (3) the overall maintenance coefficient (mT) is more sensitive to mq than to the specific growth rate ( G) and YG. Our critical reassessment of microbial maintenance provides a new approach for quantifying some important components in soil microbial ecology models.« 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.

A Simulator-Assisted Workshop for Teaching Chemostat Cultivation in Academic Classes on Microbial Physiology.

PubMed

Hakkaart, Xavier D V; Pronk, Jack T; van Maris, Antonius J A

2017-01-01

Understanding microbial growth and metabolism is a key learning objective of microbiology and biotechnology courses, essential for understanding microbial ecology, microbial biotechnology and medical microbiology. Chemostat cultivation, a key research tool in microbial physiology that enables quantitative analysis of growth and metabolism under tightly defined conditions, provides a powerful platform to teach key features of microbial growth and metabolism. Substrate-limited chemostat cultivation can be mathematically described by four equations. These encompass mass balances for biomass and substrate, an empirical relation that describes distribution of consumed substrate over growth and maintenance energy requirements (Pirt equation), and a Monod-type equation that describes the relation between substrate concentration and substrate-consumption rate. The authors felt that the abstract nature of these mathematical equations and a lack of visualization contributed to a suboptimal operative understanding of quantitative microbial physiology among students who followed their Microbial Physiology B.Sc. courses. The studio-classroom workshop presented here was developed to improve student understanding of quantitative physiology by a set of question-guided simulations. Simulations are run on Chemostatus, a specially developed MATLAB-based program, which visualizes key parameters of simulated chemostat cultures as they proceed from dynamic growth conditions to steady state. In practice, the workshop stimulated active discussion between students and with their teachers. Moreover, its introduction coincided with increased average exam scores for questions on quantitative microbial physiology. The workshop can be easily implemented in formal microbial physiology courses or used by individuals seeking to test and improve their understanding of quantitative microbial physiology and/or chemostat cultivation.

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

Diflerent formulations of microbial respiratory losses and microbial efficiency have pronounced short and long term consequences for soil C dynamics and soil respiration

NASA Astrophysics Data System (ADS)

Ballantyne, F.; Billings, S. A.

2016-12-01

Much of the variability in projections of Earth's future C balance derives from uncertainty in how to formulate and parameterize models of biologically mediated transformations of soil organic C (SOC). Over the past decade, models of belowground decomposition have incorporated more realism, namely microbial biomass and exoenzyme pools, but it remains unclear whether microbially mediated decomposition is accurately formulated. Different models and different assumptions about how microbial efficiency, defined in terms of respiratory losses, varies with temperature exert great influence on SOC and CO2 flux projections for the future. Here, we incorporate a physiologically realistic formulation of CO2 loss from microbes, distinct from extant formulations and logically consistent with microbial C uptake and losses, into belowground dynamics and contrast its projections for SOC pools and CO2 flux from soils to those from the phenomenological formulations of efficiency in current models. We quantitatively describe how short and long term SOC dynamics are influenced by different mathematical formulations of efficiency, and that our lack of knowledge regarding loss rates from SOC and microbial biomass pools, specific respiration rate and maximum substrate uptake rate severely constrains our ability to confidently parameterize microbial SOC modules in Earth System Models. Both steady-state SOC and microbial biomass C pools, as well as transient responses to perturbations, can differ substantially depending on how microbial efficiency is derived. In particular, the discrepancy between SOC stocks for different formulations of efficiency varies from negligible to more than two orders of magnitude, depending on the relative values of respiratory versus non-respiratory losses from microbial biomass. Mass-specific respiration and proportional loss rates from soil microbes emerge as key determinants of the consequences of different formulations of efficiency for C flux in soils.

Phytoremediation: State-of-the-art and a key role for the plant microbiome in future trends and research prospects.

PubMed

Thijs, Sofie; Sillen, Wouter; Weyens, Nele; Vangronsveld, Jaco

2017-01-02

Phytoremediation is increasingly adopted as a more sustainable approach for soil remediation. However, significant advances in efficiency are still necessary to attain higher levels of environmental and economic sustainability. Current interventions do not always give the expected outcomes in field settings due to an incomplete understanding of the multicomponent biological interactions. New advances in -omics are gradually implemented for studying microbial communities of polluted land in situ. This opens new perspectives for the discovery of biodegradative strains and provides us new ways of interfering with microbial communities to enhance bioremediation rates. This review presents retrospectives and future perspectives for plant microbiome studies relevant to phytoremediation, as well as some knowledge gaps in this promising research field. The implementation of phytoremediation in soil clean-up management systems is discussed, and an overview of the promoting factors that determine the growth of the phytoremediation market is given. Continuous growth is expected since elimination of contaminants from the environment is demanded. The evolution of scientific thought from a reductionist view to a more holistic approach will boost phytoremediation as an efficient and reliable phytotechnology. It is anticipated that phytoremediation will prove the most promising for organic contaminant degradation and bioenergy crop production on marginal land.

Assessment of microbial contamination of radiographic equipment and materials during intraoral imaging procedures.

PubMed

Pinheiro, S L; Martoni, S C; Ogera, R R

2012-05-01

Aim of the present study was to assess microbial contamination of radiology procedures. Patients who needed radiographic exams were selected and the bisecting technique was used: G1 - (control): absence of plastic barrier and overgloving or disinfectant solutions; G2 - alcohol spraying; G3 - protection of the film with a plastic barrier and alcohol spray; G4 - protection of film with plastic barrier, use of overgloving and alcohol spray. The following regions were assessed: trigger switch, X-ray tube, sleeve of the portable dark chamber, water, developer and fixer. The areas for microbiological sample collection were standardized with a label cut internally so that the hollow area was 5 cm long and 2 cm wide. One mL of the developer, water and fixer were also collected before and after developing the films. The samples were incubated under anaerobiosis and aerobiosis. The results were submitted to the Cochran's Q and Mann-Whitney tests. The sleeve of the developing chamber showed greater anaerobic contamination followed by the X-ray tube and only the use of alcohol associated with mechanical barriers was efficient to control this microbiota. The trigger showed higher aerobic microbial contamination and the use of alcohol or alcohol associated with mechanical barriers was efficient to control this microbiota. The developing solutions presented no significant growth of anaerobic and aerobic bacteria. The characteristic of an aerobic or anaerobic microbial strain influences microbial contamination while radiographic projections are being taken and the use of alcohol associated with a plastic barrier and overgloving is indicated to reduce this microbiota.

Quantifying condition-dependent intracellular protein levels enables high-precision fitness estimates.

PubMed

Geiler-Samerotte, Kerry A; Hashimoto, Tatsunori; Dion, Michael F; Budnik, Bogdan A; Airoldi, Edoardo M; Drummond, D Allan

2013-01-01

Countless studies monitor the growth rate of microbial populations as a measure of fitness. However, an enormous gap separates growth-rate differences measurable in the laboratory from those that natural selection can distinguish efficiently. Taking advantage of the recent discovery that transcript and protein levels in budding yeast closely track growth rate, we explore the possibility that growth rate can be more sensitively inferred by monitoring the proteomic response to growth, rather than growth itself. We find a set of proteins whose levels, in aggregate, enable prediction of growth rate to a higher precision than direct measurements. However, we find little overlap between these proteins and those that closely track growth rate in other studies. These results suggest that, in yeast, the pathways that set the pace of cell division can differ depending on the growth-altering stimulus. Still, with proper validation, protein measurements can provide high-precision growth estimates that allow extension of phenotypic growth-based assays closer to the limits of evolutionary selection.

Nanoporous Mo2C functionalized 3D carbon architecture anode for boosting flavins mediated interfacial bioelectrocatalysis in microbial fuel cells

NASA Astrophysics Data System (ADS)

Zou, Long; Lu, Zhisong; Huang, Yunhong; Long, Zhong-er; Qiao, Yan

2017-08-01

An efficient microbial electrocatalysis in microbial fuel cells (MFCs) needs both high loading of microbes (biocatalysts) and robust interfacial electron transfer from microbes to electrode. Herein a nanoporous molybdenum carbide (Mo2C) functionalized carbon felt electrode with rich 3D hierarchical porous architecture is applied as MFC anode to achieve superior electrocatalytic performance. The nanoporous Mo2C functionalized anode exhibits strikingly improved microbial electrocatalysis in MFCs with 5-fold higher power density and long-term stability of electricity production. The great enhancement is attributed to the introduction of rough Mo2C nanostructural interface into macroporous carbon architecture for promoting microbial growth with great excretion of endogenous electron shuttles (flavins) and rich available nanopores for enlarging electrochemically active surface area. Importantly, the nanoporous Mo2C functionalized anode is revealed for the first time to have unique electrocatalytic activity towards redox reaction of flavins with more negative redox potential, indicating a more favourable thermodynamic driving force for anodic electron transfer. This work not only provides a promising electrode for high performance MFCs but also brings up a new insight into the effect of nanostructured materials on interfacial bioelectrocatalysis.

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

A review on the bioenergetics of anaerobic microbial metabolism close to the thermodynamic limits and its implications for digestion applications.

PubMed

Leng, Ling; Yang, Peixian; Singh, Shubham; Zhuang, Huichuan; Xu, Linji; Chen, Wen-Hsing; Dolfing, Jan; Li, Dong; Zhang, Yan; Zeng, Huiping; Chu, Wei; Lee, Po-Heng

2018-01-01

The exploration of the energetics of anaerobic digestion systems can reveal how microorganisms cooperate efficiently for cell growth and methane production, especially under low-substrate conditions. The establishment of a thermodynamically interdependent partnership, called anaerobic syntrophy, allows unfavorable reactions to proceed. Interspecies electron transfer and the concentrations of electron carriers are crucial for maintaining this mutualistic activity. This critical review summarizes the functional microorganisms and syntroph partners, particularly in the metabolic pathways and energy conservation of syntrophs. The kinetics and thermodynamics of propionate degradation to methane, reversibility of the acetate oxidation process, and estimation of microbial growth are summarized. The various routes of interspecies electron transfer, reverse electron transfer, and Poly-β-hydroxyalkanoate formation in the syntrophic community are also reviewed. Finally, promising and critical directions of future research are proposed. Fundamental insight in the activities and interactions involved in AD systems could serve as a guidance for engineered systems optimization and upgrade. Copyright © 2017 Elsevier Ltd. All rights reserved.

Connecting Taxon-Specific Microbial Activities to Carbon Cycling in the Rhizosphere

NASA Astrophysics Data System (ADS)

Hungate, B. A.; Morrissey, E.; Schwartz, E.; Dijkstra, P.; Blazewicz, S.; Pett-Ridge, J.; Koch, G. W.; Marks, J.; Koch, B.; McHugh, T. A.; Mau, R. L.; Hayer, M.

2016-12-01

Plant carbon inputs influence microbial growth in the rhizosphere, but the quantitative details of these effects are not well understood, nor are their consequences for carbon cycling in the rhizosphere. With a new pulse of carbon input to soil, which microbial taxa increase their growth rates, and by how much? Do any microbial taxa respond negatively? And how does the extra carbon addition alter the utilization of other resources, including other carbon sources, as well as inorganic nitrogen? This talk will present new research using quantitative stable isotope probing that reveals the distribution of growth responses among microbial taxa, from positive to neutral to negative, and how these growth responses are associated with various substrates. For example, decomposition of soil C in response to added labile carbon occurred as a phylogenetically-diverse majority of taxa shifted toward soil C use for growth. In contrast, bacteria with suppressed growth or that relied directly on glucose for growth clustered strongly by phylogeny. These results suggest that priming is a prototypical response of bacteria to sustained labile C addition, consistent with the widespread occurrence of the priming effect in nature. These results also illustrate the potential power of molecular tools and models that seek to estimate metrics directly relevant to quantitative ecology and biogeochemistry, moreso than is the standard currently in microbial ecology. Tools that estimate growth rate, mortality rate, and rates of substrate use - all quantified with the taxonomic precision afforded by modern sequencing - provide a foundation for quantifying the biogeochemical significance of microbial biodiversity, and a more complete understanding of the rich ecosystem of the rhizosphere.

Microbial respiration, but not biomass, responded linearly to increasing light fraction organic matter input: Consequences for carbon sequestration

PubMed Central

Rui, Yichao; Murphy, Daniel V.; Wang, Xiaoli; Hoyle, Frances C.

2016-01-01

Rebuilding ‘lost’ soil carbon (C) is a priority in mitigating climate change and underpinning key soil functions that support ecosystem services. Microorganisms determine if fresh C input is converted into stable soil organic matter (SOM) or lost as CO2. Here we quantified if microbial biomass and respiration responded positively to addition of light fraction organic matter (LFOM, representing recent inputs of plant residue) in an infertile semi-arid agricultural soil. Field trial soil with different historical plant residue inputs [soil C content: control (tilled) = 9.6 t C ha−1 versus tilled + plant residue treatment (tilled + OM) = 18.0 t C ha−1] were incubated in the laboratory with a gradient of LFOM equivalent to 0 to 3.8 t C ha−1 (0 to 500% LFOM). Microbial biomass C significantly declined under increased rates of LFOM addition while microbial respiration increased linearly, leading to a decrease in the microbial C use efficiency. We hypothesise this was due to insufficient nutrients to form new microbial biomass as LFOM input increased the ratio of C to nitrogen, phosphorus and sulphur of soil. Increased CO2 efflux but constrained microbial growth in response to LFOM input demonstrated the difficulty for C storage in this environment. PMID:27752083

Nitrogen availability drives priming effect by altering microbial carbon-use efficiency after permafrost thaw

NASA Astrophysics Data System (ADS)

Chen, L.; Liu, L.; Zhang, Q.; Mao, C.; Liu, F.; Yang, Y.

2017-12-01

Enhanced vegetation growth can potentially aggravate soil C loss by accelerating the decomposition of soil organic matter (SOM) ("priming effect"), thereby reinforcing the positive C-climate feedback in permafrost ecosystems. However, the degree to which priming effect alters permafrost C dynamics is expected to be modified by nitrogen (N) availability after permafrost thaw. Despite this recognition, experimental evidence for the linkage between priming effect and post-thaw N availability is still lacking. Particularly, the microbial mechanisms involved remain unknown. Here, using a thermokarst-induced natural N gradient combined with an isotope-labeled glucose and N addition experiment, we presented a strong linkage between soil N availability and priming effect in Tibetan permafrost. We observed that the magnitude of priming effect along the thaw gradient was negatively associated with soil total dissolved nitrogen (TDN) concentration. This negative effect of post-thaw N availability was further proved by a sharply reduced priming effect following mineral N supply. These two lines of evidence jointly illustrated that the priming effect along the thaw chronosequence was controlled by N availability, supporting the `N mining theory'. In contrast to the prevailing assumption, this N-regulated priming effect was independent from changes in C- or N-acquiring enzyme activities, but positively associated with the change in metabolic quotients (△SOM-qCO2), highlighting that decreased microbial metabolism efficiency rather than increased enzyme activities account for greater priming effect under reduced N availability. Taken together, these findings demonstrate that C dynamics in melting permafrost largely depends on post-thaw N availability due to its effect of retarding SOM mineralization. This C-N interaction and the relevant microbial metabolic efficiency should be considered in Earth System Models for a better understanding of soil C dynamics after permafrost thaw.

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.

A simple microbial fuel cell model for improvement of biomedical device powering times.

PubMed

Roxby, Daniel N; Tran, Nham; Nguyen, Hung T

2014-01-01

This study describes a Matlab based Microbial Fuel Cell (MFC) model for a suspended microbial population, in the anode chamber for the use of the MFC in powering biomedical devices. The model contains three main sections including microbial growth, microbial chemical uptake and secretion and electrochemical modeling. The microbial growth portion is based on a Continuously Stirred Tank Reactor (CSTR) model for the microbial growth with substrate and electron acceptors. Microbial stoichiometry is used to determine chemical concentrations and their rates of change and transfer within the MFC. These parameters are then used in the electrochemical modeling for calculating current, voltage and power. The model was tested for typically exhibited MFC characteristics including increased electrode distances and surface areas, overpotentials and operating temperatures. Implantable biomedical devices require long term powering which is the main objective for MFCs. Towards this end, our model was tested with different initial substrate and electron acceptor concentrations, revealing a four-fold increase in concentrations decreased the power output time by 50%. Additionally, the model also predicts that for a 35.7% decrease in specific growth rate, a 50% increase in power longevity is possible.

INVESTIGATING THE EFFECT OF MICROBIAL GROWTH AND BIOFILM FORMATION ON SEISMIC WAVE PROPAGATION IN SEDIMENT

EPA Science Inventory

Previous laboratory investigations have demonstrated that the seismic methods are sensitive to microbially-induced changes in porous media through the generation of biogenic gases and biomineralization. The seismic signatures associated with microbial growth and biofilm formation...

The Research and Application of Microbial Degradation Technology on Heavy Oil Reservoir in Huabei Oilfield

NASA Astrophysics Data System (ADS)

Wang, Guan; Wang, Rui; Fu, Yaxiu; Duan, Lisha; Yuan, Xizhi; Zheng, Ya; Wang, Ai; Huo, Ran; Su, Na

2018-06-01

Mengulin sandstone reservoir in Huabei oilfield is low- temperature heavy oil reservoir. Recently, it is at later stage of waterflooding development. The producing degree of water flooding is poor, and it is difficult to keep yield stable. To improve oilfield development effect, according to the characteristics of reservoir geology, microbial enhanced oil recovery to improve oil displacement efficiency is researched. 2 microbial strains suitable for the reservoir conditions were screened indoor. The growth characteristics of strains, compatibility and function mechanism with crude oil were studied. Results show that the screened strains have very strong ability to utilize petroleum hydrocarbon to grow and metabolize, can achieve the purpose of reducing oil viscosity, and can also produce biological molecules with high surface activity to reduce the oil-water interfacial tension. 9 oil wells had been chosen to carry on the pilot test of microbial stimulation, of which 7 wells became effective with better experiment results. The measures effective rate is 77.8%, the increased oil is 1,093.5 tons and the valid is up to 190 days.

A theoretical reassessment of microbial maintenance and implications for microbial ecology modeling.

PubMed

Wang, Gangsheng; Post, Wilfred M

2012-09-01

We attempted to reconcile three microbial maintenance models (Herbert, Pirt, and Compromise) through a theoretical reassessment. We provided a rigorous proof that the true growth yield coefficient (Y(G)) is the ratio of the specific maintenance rate (a in Herbert) to the maintenance coefficient (m in Pirt). Other findings from this study include: (1) the Compromise model is identical to the Herbert for computing microbial growth and substrate consumption, but it expresses the dependence of maintenance on both microbial biomass and substrate; (2) the maximum specific growth rate in the Herbert (μ(max,H)) is higher than those in the other two models (μ(max,P) and μ(max,C)), and the difference is the physiological maintenance factor (m(q) = a); and (3) the overall maintenance coefficient (m(T)) is more sensitive to m(q) than to the specific growth rate (μ(G)) and Y(G). Our critical reassessment of microbial maintenance provides a new approach for quantifying some important components in soil microbial ecology models. © This article is a US government work and is in the public domain in the USA.

Methanogenic burst in the end-Permian carbon cycle.

PubMed

Rothman, Daniel H; Fournier, Gregory P; French, Katherine L; Alm, Eric J; Boyle, Edward A; Cao, Changqun; Summons, Roger E

2014-04-15

The end-Permian extinction is associated with a mysterious disruption to Earth's carbon cycle. Here we identify causal mechanisms via three observations. First, we show that geochemical signals indicate superexponential growth of the marine inorganic carbon reservoir, coincident with the extinction and consistent with the expansion of a new microbial metabolic pathway. Second, we show that the efficient acetoclastic pathway in Methanosarcina emerged at a time statistically indistinguishable from the extinction. Finally, we show that nickel concentrations in South China sediments increased sharply at the extinction, probably as a consequence of massive Siberian volcanism, enabling a methanogenic expansion by removal of nickel limitation. Collectively, these results are consistent with the instigation of Earth's greatest mass extinction by a specific microbial innovation.

Are Uncultivated Bacteria Really Uncultivable?

PubMed Central

Puspita, Indun Dewi; Kamagata, Yoichi; Tanaka, Michiko; Asano, Kozo; Nakatsu, Cindy H.

2012-01-01

Many strategies have been used to increase the number of bacterial cells that can be grown from environmental samples but cultivation efficiency remains a challenge for microbial ecologists. The difficulty of cultivating a fraction of bacteria in environmental samples can be classified into two non-exclusive categories. Bacterial taxa with no cultivated representatives for which appropriate laboratory conditions necessary for growth are yet to be identified. The other class is cells in a non-dividing state (also known as dormant or viable but not culturable cells) that require the removal or addition of certain factors to re-initiate growth. A number of strategies, from simple to high throughput techniques, are reviewed that have been used to increase the cultivation efficiency of environmental samples. Some of the underlying mechanisms that contribute to the success of these cultivation strategies are described. Overall this review emphasizes the need of researchers to first understand the factors that are hindering cultivation to identify the best strategies to improve cultivation efficiency. PMID:23059723

Growth and element flux at fine taxonomic resolution in natural microbial communities

NASA Astrophysics Data System (ADS)

Hungate, Bruce; Mau, Rebecca; Schwartz, Egbert; Caporaso, J. Gregory; Dijkstra, Paul; van Gestel, Natasja; Koch, Benjamin J.; Liu, Cindy M.; McHugh, Theresa; Marks, Jane C.; Morrissey, Ember; Price, Lance B.

2015-04-01

Microorganisms are the engines of global biogeochemical cycles, driving half of all photosynthesis and nearly all decomposition. Yet, quantifying the rates at which uncultured microbial taxa grow and transform elements in intact and highly diverse natural communities in the environment remains among the most pressing challenges in microbial ecology today. Here, we show how shifts in the density of DNA caused by stable isotope incorporation can be used to estimate the growth rates of individual bacterial taxa in intact soil communities. We found that the distribution of growth rates followed the familiar lognormal distribution observed for the abundances, biomasses, and traits of many organisms. Growth rates of most bacterial taxa increased in response to glucose amendment, though the increase in growth observed for many taxa was larger than could be explained by direct utilization of the added glucose for growth, illustrating that glucose addition indirectly stimulated the utilization of other substrates. Variation in growth rates and phylogenetic distances were quantitatively related, connecting evolutionary history and biogeochemical function in intact soil microbial communities. Our approach has the potential to identify biogeochemically significant taxa in the microbial community and quantify their contributions to element transformations and ecosystem processes.

Comparison of Primary Models to Predict Microbial Growth by the Plate Count and Absorbance Methods.

PubMed

Pla, María-Leonor; Oltra, Sandra; Esteban, María-Dolores; Andreu, Santiago; Palop, Alfredo

2015-01-01

The selection of a primary model to describe microbial growth in predictive food microbiology often appears to be subjective. The objective of this research was to check the performance of different mathematical models in predicting growth parameters, both by absorbance and plate count methods. For this purpose, growth curves of three different microorganisms (Bacillus cereus, Listeria monocytogenes, and Escherichia coli) grown under the same conditions, but with different initial concentrations each, were analysed. When measuring the microbial growth of each microorganism by optical density, almost all models provided quite high goodness of fit (r(2) > 0.93) for all growth curves. The growth rate remained approximately constant for all growth curves of each microorganism, when considering one growth model, but differences were found among models. Three-phase linear model provided the lowest variation for growth rate values for all three microorganisms. Baranyi model gave a variation marginally higher, despite a much better overall fitting. When measuring the microbial growth by plate count, similar results were obtained. These results provide insight into predictive microbiology and will help food microbiologists and researchers to choose the proper primary growth predictive model.

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...

Investigating the initial stages of soil formation in glacier forefields using the new biogeochemical model: SHIMMER

NASA Astrophysics Data System (ADS)

Bradley, James; Anesio, Alexandre; Arndt, Sandra; Sabacka, Marie; Barker, Gary; Benning, Liane; Blacker, Joshua; Singarayer, Joy; Tranter, Martyn; Yallop, Marian

2016-04-01

Glaciers and ice sheets in Polar and alpine regions are retreating in response to recent climate warming, exposing terrestrial ecosystems that have been locked under the ice for thousands of years. Exposed soils exhibit successional characteristics that can be characterised using a chronosequence approach. Decades of empirical research in glacier forefields has shown that soils are quickly colonised by microbes which drive biogeochemical cycling of elements and affect soil properties including nutrient concentrations, carbon fluxes and soil stability (Bradley et al, 2014). The characterisation of these soils is important for our understanding of the cycling of organic matter under extreme environmental and nutrient limiting conditions, and their potential contribution to global biogeochemical cycles. This is particularly important as these new areas will become more geographically expansive with continued ice retreat. SHIMMER (Soil biogeocHemIcal Model of Microbial Ecosystem Response) (Bradley et al, 2015) is a new mathematical model that simulates biogeochemical and microbial dynamics in glacier forefields. The model captures, explores and predicts the growth of different microbial groups (classified by function), and the associated cycling of carbon, nitrogen and phosphorus along a chronosequence. SHIMMER improves typical soil model formulations by including explicit representation of microbial dynamics, and those processes which are shown to be important for glacier forefields. For example, we categorise microbial groups by function to represent the diversity of soil microbial communities, and include the different metabolic needs and physiological pathways of microbial organisms commonly found in glacier forefields (e.g. microbes derived from underneath the glacier, typical soil bacteria, and microbes that can fix atmospheric nitrogen and assimilate soil nitrogen). Here, we present data from a study where we integrated modelling using SHIMMER with empirical observations from chronosequences from the forefield of Midtre Lovénbreen, Svalbard (78°N), to investigate the first 120 years of soil development. We carried out an in depth analysis of the model dynamics and determined the most sensitive parameters. We then used laboratory measurements to derive values for those parameters: bacterial growth rate, growth efficiency and temperature dependency. By applying the model to the High-Arctic forefield and integrating the measured parameter values, we could refine the model and easily predict the rapid accumulation of microbial biomass that was observed in our field data. Furthermore, we show that the bacterial production is dominated by autotrophy (rather than heterotrophy). Heterotrophic production in young soils (0-20 years) is supported by labile substrate, whereas carbon stocks in older soils (60-120 years) are more refractory. Nitrogen fixing organisms are responsible for the initial accumulation of available nitrates in the soil. However, microbial processes alone do not explain the build-up of organic matter observed in the field data record. Consequently, the model infers that allochthonous deposition of organic material may play a significant contributory role that could accelerate or facilitate further microbial growth. SHIMMER provides a quantitative evaluation on the dynamics of glacier forefield systems that have previously largely been explored through qualitative interpretation of datasets. References Bradley J.A., Singarayer J.S., Anesio A.M. (2014) Microbial community dynamics in the forefield of glaciers. Proceedings Biological sciences / The Royal Society 281(1795), 2793-2802. (doi:10.1098/rspb.2014.0882). Bradley J.A., Anesio A.M., Singarayer J.S., Heath M.R., Arndt S. (2015) SHIMMER (1.0): a novel mathematical model for microbial and biogeochemical dynamics in glacier forefield ecosystems. Geosci Model Dev 8(10), 3441-3470. (doi:10.5194/gmd-8-3441-2015).

Divergence of compost extract and bio-organic manure effects on lucerne plant and soil

PubMed Central

Hu, Jian; Hu, Yifei; Yang, Gaowen; Zhang, Yingjun

2017-01-01

Aim Application of organic materials into agricultural systems enhances plant growth and yields, and improves soil fertility and structure. This study aimed to examine the effects of “compost extract (CE)”, a soil conditioner, and bio-organic manure (BOM) on the growth of lucerne (Medicago sativa), and compare the efficiency between BOM (including numbers of microorganisms) and CE (including no added microorganisms). Method A greenhouse experiment was conducted with four soil amendment treatments (control, BOM, CE and CEBOM), and was arranged in a completely randomized design with 10 replicates for each treatment. Plant biomass, nutritive value and rhizobia efficacy as well as soil characteristics were monitored. Result CE rather than BOM application showed a positive effect on plant growth and soil properties when compared with the control. Lucerne nodulation responded equally to CE addition and rhizobium inoculation. CE alone and in combination with BOM significantly increased plant growth and soil microbial activities and improved soil structure. The synergistic effects of CE and BOM indicate that applying CE and BOM together could increase their efficiency, leading to higher economic returns and improved soil health. However, CE alone is more effective for legume growth since nodulation was suppressed by nitrogen input from BOM. CE had a higher efficiency than BOM for enriching soil indigenous microorganisms instead of adding microorganisms and favouring plant nodulation. PMID:28894647

Optimized Extraction Method To Remove Humic Acid Interferences from Soil Samples Prior to Microbial Proteome Measurements

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

Qian, Chen; Hettich, Robert L.

The microbial composition and their activities in soil environments play a critical role in organic matter transformation and nutrient cycling, perhaps most specifically with respect to impact on plant growth but also more broadly to global impact on carbon and nitrogen-cycling. Liquid chromatography coupled to high performance mass spectrometry provides a powerful approach to characterize soil microbiomes; however, the limited microbial biomass and the presence of abundant interferences in soil samples present major challenges to soil proteome extraction and subsequent MS measurement. To address some of the major issues, we have designed and optimized an experimental method to enhance microbialmore » proteome extraction concomitant with minimizing the soil-borne humic substances co-extraction from soils. Among the range of interferences, humic substances are often the worst in terms of adversely impacting proteome extraction and mass spectrometry measurement. Our approach employs an in-situ detergent-based microbial lysis / TCA precipitation coupled with an additional acidification precipitation step at the peptide level which efficiently removes humic acids. By combing filtration and pH adjustment of the final peptide solution, the remaining humic acids can be differentially precipitated and removed with a membrane filter, thereby leaving much cleaner proteolytic peptide samples for MS measurement. As a result, this modified method is a reliable and straight-forward protein extraction method that efficiently removes soil-borne humic substances without inducing proteome sample loss or reducing or biasing protein identification in mass spectrometry.« less

Optimized Extraction Method To Remove Humic Acid Interferences from Soil Samples Prior to Microbial Proteome Measurements

DOE PAGES

Qian, Chen; Hettich, Robert L.

2017-05-24

The microbial composition and their activities in soil environments play a critical role in organic matter transformation and nutrient cycling, perhaps most specifically with respect to impact on plant growth but also more broadly to global impact on carbon and nitrogen-cycling. Liquid chromatography coupled to high performance mass spectrometry provides a powerful approach to characterize soil microbiomes; however, the limited microbial biomass and the presence of abundant interferences in soil samples present major challenges to soil proteome extraction and subsequent MS measurement. To address some of the major issues, we have designed and optimized an experimental method to enhance microbialmore » proteome extraction concomitant with minimizing the soil-borne humic substances co-extraction from soils. Among the range of interferences, humic substances are often the worst in terms of adversely impacting proteome extraction and mass spectrometry measurement. Our approach employs an in-situ detergent-based microbial lysis / TCA precipitation coupled with an additional acidification precipitation step at the peptide level which efficiently removes humic acids. By combing filtration and pH adjustment of the final peptide solution, the remaining humic acids can be differentially precipitated and removed with a membrane filter, thereby leaving much cleaner proteolytic peptide samples for MS measurement. As a result, this modified method is a reliable and straight-forward protein extraction method that efficiently removes soil-borne humic substances without inducing proteome sample loss or reducing or biasing protein identification in mass spectrometry.« less

Energy Efficiency and Productivity Enhancement of Microbial Electrosynthesis of Acetate

PubMed Central

LaBelle, Edward V.; May, Harold D.

2017-01-01

It was hypothesized that a lack of acetogenic biomass (biocatalyst) at the cathode of a microbial electrosynthesis system, due to electron and nutrient limitations, has prevented further improvement in acetate productivity and efficiency. In order to increase the biomass at the cathode and thereby performance, a bioelectrochemical system with this acetogenic community was operated under galvanostatic control and continuous media flow through a reticulated vitreous carbon (RVC) foam cathode. The combination of galvanostatic control and the high surface area cathode reduced the electron limitation and the continuous flow overcame the nutrient limitation while avoiding the accumulation of products and potential inhibitors. These conditions were set with the intention of operating the biocathode through the production of H2. Biofilm growth occurred on and within the unmodified RVC foam regardless of vigorous H2 generation on the cathode surface. A maximum volumetric rate or space time yield for acetate production of 0.78 g/Lcatholyte/h was achieved with 8 A/Lcatholyte (83.3 A/m2projected surface area of cathode) supplied to the continuous flow/culture bioelectrochemical reactors. The total Coulombic efficiency in H2 and acetate ranged from approximately 80–100%, with a maximum of 35% in acetate. The overall energy efficiency ranged from approximately 35–42% with a maximum to acetate of 12%. PMID:28515713

Energy Efficiency and Productivity Enhancement of Microbial Electrosynthesis of Acetate.

PubMed

LaBelle, Edward V; May, Harold D

2017-01-01

It was hypothesized that a lack of acetogenic biomass (biocatalyst) at the cathode of a microbial electrosynthesis system, due to electron and nutrient limitations, has prevented further improvement in acetate productivity and efficiency. In order to increase the biomass at the cathode and thereby performance, a bioelectrochemical system with this acetogenic community was operated under galvanostatic control and continuous media flow through a reticulated vitreous carbon (RVC) foam cathode. The combination of galvanostatic control and the high surface area cathode reduced the electron limitation and the continuous flow overcame the nutrient limitation while avoiding the accumulation of products and potential inhibitors. These conditions were set with the intention of operating the biocathode through the production of H 2 . Biofilm growth occurred on and within the unmodified RVC foam regardless of vigorous H 2 generation on the cathode surface. A maximum volumetric rate or space time yield for acetate production of 0.78 g/L catholyte /h was achieved with 8 A/L catholyte (83.3 A/m 2 projected surface area of cathode) supplied to the continuous flow/culture bioelectrochemical reactors. The total Coulombic efficiency in H 2 and acetate ranged from approximately 80-100%, with a maximum of 35% in acetate. The overall energy efficiency ranged from approximately 35-42% with a maximum to acetate of 12%.

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

PubMed Central

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

1983-01-01

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

Spotsizer: High-throughput quantitative analysis of microbial growth.

PubMed

Bischof, Leanne; Převorovský, Martin; Rallis, Charalampos; Jeffares, Daniel C; Arzhaeva, Yulia; Bähler, Jürg

2016-10-01

Microbial colony growth can serve as a useful readout in assays for studying complex genetic interactions or the effects of chemical compounds. Although computational tools for acquiring quantitative measurements of microbial colonies have been developed, their utility can be compromised by inflexible input image requirements, non-trivial installation procedures, or complicated operation. Here, we present the Spotsizer software tool for automated colony size measurements in images of robotically arrayed microbial colonies. Spotsizer features a convenient graphical user interface (GUI), has both single-image and batch-processing capabilities, and works with multiple input image formats and different colony grid types. We demonstrate how Spotsizer can be used for high-throughput quantitative analysis of fission yeast growth. The user-friendly Spotsizer tool provides rapid, accurate, and robust quantitative analyses of microbial growth in a high-throughput format. Spotsizer is freely available at https://data.csiro.au/dap/landingpage?pid=csiro:15330 under a proprietary CSIRO license.

Comparison of Different Strategies for Selection/Adaptation of Mixed Microbial Cultures Able to Ferment Crude Glycerol Derived from Second-Generation Biodiesel.

PubMed

Varrone, C; Heggeset, T M B; Le, S B; Haugen, T; Markussen, S; Skiadas, I V; Gavala, H N

2015-01-01

Objective of this study was the selection and adaptation of mixed microbial cultures (MMCs), able to ferment crude glycerol generated from animal fat-based biodiesel and produce building-blocks and green chemicals. Various adaptation strategies have been investigated for the enrichment of suitable and stable MMC, trying to overcome inhibition problems and enhance substrate degradation efficiency, as well as generation of soluble fermentation products. Repeated transfers in small batches and fed-batch conditions have been applied, comparing the use of different inoculum, growth media, and Kinetic Control. The adaptation of activated sludge inoculum was performed successfully and continued unhindered for several months. The best results showed a substrate degradation efficiency of almost 100% (about 10 g/L glycerol in 21 h) and different dominant metabolic products were obtained, depending on the selection strategy (mainly 1,3-propanediol, ethanol, or butyrate). On the other hand, anaerobic sludge exhibited inactivation after a few transfers. To circumvent this problem, fed-batch mode was used as an alternative adaptation strategy, which led to effective substrate degradation and high 1,3-propanediol and butyrate production. Changes in microbial composition were monitored by means of Next Generation Sequencing, revealing a dominance of glycerol consuming species, such as Clostridium, Klebsiella, and Escherichia.

Indirect microbial detection

NASA Technical Reports Server (NTRS)

Wilkins, J. R. (Inventor)

1981-01-01

The growth of microorganisms in a sample is detected and monitored by culturing microorganisms in a growth medium and detecting a change in potential between two electrodes, separated from the microbial growth by a barrier which is permeable to charged paticles but microorganism impermeable.

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.

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

PubMed

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

2015-12-01

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

Biochar-enhanced composts reduce the potential leaching of nutrients and heavy metals and suppress plant-parasitic nematodes in excessively fertilized cucumber soils.

PubMed

Cao, Yune; Gao, Yanming; Qi, Yanbin; Li, Jianshe

2018-03-01

Excessive fertilization is a common agricultural practice that has largely reduced soil nutrient retention capacity and led to nutrient leaching in China. To reduce nutrient leaching, in this study, we evaluated the application of biochar, compost, and biochar-compost on soil properties, leaching water quality, and cucumber plant growth in soils with different nutrient levels. In general, the concentrations of nutrients and heavy metals in leaching water were higher under high-nutrient conditions than under low-nutrient conditions. Both biochar and compost efficiently enhanced soil cation exchange capacity (CEC), water holding capacity (WHC), and microbial biomass carbon (MBC), nitrogen (MBN), and phosphorus (MBP), reduced the potential leaching of nutrients and heavy metals, and improved plant growth. The efficiency of biochar and compost in soil CEC, WHC, MBC, MBN, and MBP and plant growth was enhanced when applied jointly. In addition, biochar and biochar-enhanced compost efficiently suppressed plant-parasitic nematode infestation in a soil with high levels of both N and P. Our results suggest that biochar-enhanced compost can reduce the potential environmental risks in excessively fertilized vegetable soils.

Exploiting rRNA operon copy number to investigate bacterial reproductive strategies.

PubMed

Roller, Benjamin R K; Stoddard, Steven F; Schmidt, Thomas M

2016-09-12

The potential for rapid reproduction is a hallmark of microbial life, but microbes in nature must also survive and compete when growth is constrained by resource availability. Successful reproduction requires different strategies when resources are scarce and when they are abundant 1,2 , but a systematic framework for predicting these reproductive strategies in bacteria has not been available. Here, we show that the number of ribosomal RNA operons (rrn) in bacterial genomes predicts two important components of reproduction-growth rate and growth efficiency-which are favoured under contrasting regimes of resource availability 3,4 . We find that the maximum reproductive rate of bacteria doubles with a doubling of rrn copy number, and the efficiency of carbon use is inversely related to maximal growth rate and rrn copy number. We also identify a feasible explanation for these patterns: the rate and yield of protein synthesis mirror the overall pattern in maximum growth rate and growth efficiency. Furthermore, comparative analysis of genomes from 1,167 bacterial species reveals that rrn copy number predicts traits associated with resource availability, including chemotaxis and genome streamlining. Genome-wide patterns of orthologous gene content covary with rrn copy number, suggesting convergent evolution in response to resource availability. Our findings imply that basic cellular processes adapt in contrasting ways to long-term differences in resource availability. They also establish a basis for predicting changes in bacterial community composition in response to resource perturbations using rrn copy number measurements 5 or inferences 6,7 .

Biomass production from electricity using ammonia as an electron carrier in a reverse microbial fuel cell.

PubMed

Khunjar, Wendell O; Sahin, Asli; West, Alan C; Chandran, Kartik; Banta, Scott

2012-01-01

The storage of renewable electrical energy within chemical bonds of biofuels and other chemicals is a route to decreasing petroleum usage. A critical challenge is the efficient transfer of electrons into a biological host that can covert this energy into high energy organic compounds. In this paper, we describe an approach whereby biomass is grown using energy obtained from a soluble mediator that is regenerated electrochemically. The net result is a separate-stage reverse microbial fuel cell (rMFC) that fixes CO₂ into biomass using electrical energy. We selected ammonia as a low cost, abundant, safe, and soluble redox mediator that facilitated energy transfer to biomass. Nitrosomonas europaea, a chemolithoautotroph, was used as the biocatalyst due to its inherent capability to utilize ammonia as its sole energy source for growth. An electrochemical reactor was designed for the regeneration of ammonia from nitrite, and current efficiencies of 100% were achieved. Calculations indicated that overall bioproduction efficiency could approach 2.7±0.2% under optimal electrolysis conditions. The application of chemolithoautotrophy for industrial bioproduction has been largely unexplored, and results suggest that this and related rMFC platforms may enable biofuel and related biochemical production.

Biomass Production from Electricity Using Ammonia as an Electron Carrier in a Reverse Microbial Fuel Cell

PubMed Central

West, Alan C.; Chandran, Kartik; Banta, Scott

2012-01-01

The storage of renewable electrical energy within chemical bonds of biofuels and other chemicals is a route to decreasing petroleum usage. A critical challenge is the efficient transfer of electrons into a biological host that can covert this energy into high energy organic compounds. In this paper, we describe an approach whereby biomass is grown using energy obtained from a soluble mediator that is regenerated electrochemically. The net result is a separate-stage reverse microbial fuel cell (rMFC) that fixes CO2 into biomass using electrical energy. We selected ammonia as a low cost, abundant, safe, and soluble redox mediator that facilitated energy transfer to biomass. Nitrosomonas europaea, a chemolithoautotroph, was used as the biocatalyst due to its inherent capability to utilize ammonia as its sole energy source for growth. An electrochemical reactor was designed for the regeneration of ammonia from nitrite, and current efficiencies of 100% were achieved. Calculations indicated that overall bioproduction efficiency could approach 2.7±0.2% under optimal electrolysis conditions. The application of chemolithoautotrophy for industrial bioproduction has been largely unexplored, and results suggest that this and related rMFC platforms may enable biofuel and related biochemical production. PMID:23028643

[Promoting efficiency of microbial extracellular electron transfer by synthetic biology].

PubMed

Li, Feng; Song, Hao

2017-03-25

Electroactive bacteria, including electrigenic bacteria (exoelectrogens) and electroautotrophic bacteria, implement microbial bioelectrocatalysis processes via bi-directional exchange of electrons and energy with environments, enabling a wide array of applications in environmental and energy fields, including microbial fuel cells (MFC), microbial electrolysis cells (MEC), microbial electrosynthesis (MES) to produce electricity and bulk fine chemicals. However, the low efficiency in the extracellular electron transfer (EET) of exoelectrogens and electrotrophic microbes limited their industrial applications. Here, we reviewed synthetic biology approaches to engineer electroactive microorganisms to break the bottleneck of their EET pathways, to achieve higher efficiency of EET of a number of electroactive microorganisms. Such efforts will lead to a breakthrough in the applications of these electroactive microorganisms and microbial electrocatalysis systems.

Modelling coupled microbial processes in the subsurface: Model development, verification, evaluation and application

NASA Astrophysics Data System (ADS)

Masum, Shakil A.; Thomas, Hywel R.

2018-06-01

To study subsurface microbial processes, a coupled model which has been developed within a Thermal-Hydraulic-Chemical-Mechanical (THCM) framework is presented. The work presented here, focuses on microbial transport, growth and decay mechanisms under the influence of multiphase flow and bio-geochemical reactions. In this paper, theoretical formulations and numerical implementations of the microbial model are presented. The model has been verified and also evaluated against relevant experimental results. Simulated results show that the microbial processes have been accurately implemented and their impacts on porous media properties can be predicted either qualitatively or quantitatively or both. The model has been applied to investigate biofilm growth in a sandstone core that is subjected to a two-phase flow and variable pH conditions. The results indicate that biofilm growth (if not limited by substrates) in a multiphase system largely depends on the hydraulic properties of the medium. When the change in porewater pH which occurred due to dissolution of carbon dioxide gas is considered, growth processes are affected. For the given parameter regime, it has been shown that the net biofilm growth is favoured by higher pH; whilst the processes are considerably retarded at lower pH values. The capabilities of the model to predict microbial respiration in a fully coupled multiphase flow condition and microbial fermentation leading to production of a gas phase are also demonstrated.

Anoxic conditions drive phosphorus limitation in humid tropical forest soil microorganisms

NASA Astrophysics Data System (ADS)

Gross, A.; Pett-Ridge, J.; Weber, P. K.; Blazewicz, S.; Silver, W. L.

2017-12-01

The elemental stoichiometry of carbon (C), nitrogen (N) and phosphorus (P) of soil microorganisms (C:N:P ratios) regulates transfers of energy and nutrients to higher trophic levels. In humid tropical forests that grow on P-depleted soils, the ability of microbes to concentrate P from their surroundings likely plays a critical role in P-retention and ultimately in forest productivity. Models predict that climate change will cause dramatic changes in rainfall patterns in the humid tropics and field studies have shown these changes can affect the redox state of tropical forest soils, influencing soil respiration and biogeochemical cycling. However, the responses of soil microorganisms to changing environmental conditions are not well known. Here, we incubated humid tropical soils under oxic or anoxic conditions with substrates differing in both C:P stoichiometry and lability, to assess how soil microorganisms respond to different redox regimes. We found that under oxic conditions, microbial C:P ratios were similar to the global optimal ratio (55:1), indicating most microbial cells can adapt to persistent aerated conditions in these soils. However, under anoxic conditions, the ability of soil microbes to acquire soil P declined and their C:P ratios shifted away from the optimal ratio. NanoSIMS elemental imaging of single cells extracted from soil revealed that under anoxic conditions, C:P ratios were above the microbial optimal value in 83% of the cells, in comparison to 41% under oxic conditions. These data suggest microbial growth efficiency switched from being energy limited under oxic conditions to P-limited under anoxic conditions, indicating that, microbial growth in low P humid tropical forests soils may be most constrained by P-limitation when conditions are oxygen-limited. We suggest that differential microbial responses to soil redox states could have important implications for productivity of humid tropical forests under future climate scenarios.

Cooperative role of electrical stimulation on microbial metabolism and selection of thermophilic communities for p-fluoronitrobenzene treatment.

PubMed

Zhang, Xueqin; Shen, Dongsheng; Feng, Huajun; Wang, Yanfeng; Li, Na; Han, Jingyi; Long, Yuyang

2015-01-01

A novel thermophilic bioelectrochemical system (TBES) based on electrical stimulation was established for the enhanced treatment of p-fluoronitrobenzene (p-FNB) wastewater. p-FNB removal rate constant in the TBES was 78.6% higher than that of the mesophilic BES (MBES), the elevation of which owing to high-temperature overtook the rate improvement of 50.8% in the electrocatalytic system (ECS). Additionally, an overwhelming mineralization efficiency of 91.96% ± 5.70% was obtained in the TBES. The superiority of TBES was attributed to the integrated role of electrical stimulation and high-temperature. Electrical stimulation provided an alternative for the microbial growth independent energy requirements, compensating insufficient energy support from p-FNB metabolism under the high-temperature stress. Besides, electrical stimulation facilitated microbial community evolution to form specific thermophilic biocatalysis. The uniquely selected thermophilic microorganisms including Coprothermobacter sp. and other ones cooperated to enhance p-FNB mineralization. Copyright © 2015 Elsevier Ltd. All rights reserved.

Comparison of DNA extraction protocols for microbial communities from soil treated with biochar

PubMed Central

Leite, D.C.A.; Balieiro, F.C.; Pires, C.A.; Madari, B.E.; Rosado, A.S.; Coutinho, H.L.C.; Peixoto, R.S.

2014-01-01

Many studies have evaluated the effects of biochar application on soil structure and plant growth. However, there are very few studies describing the effect of biochar on native soil microbial communities. Microbial analysis of environmental samples requires accurate and reproducible methods for the extraction of DNA from samples. Because of the variety among microbial species and the strong adsorption of the phosphate backbone of the DNA molecule to biochar, extracting and purifying high quality microbial DNA from biochar-amended soil is not a trivial process and can be considerably more difficult than the extraction of DNA from other environmental samples. The aim of this study was to compare the relative efficacies of three commercial DNA extraction kits, the FastDNA® SPIN Kit for Soil (FD kit), the PowerSoil® DNA Isolation Kit (PS kit) and the ZR Soil Microbe DNA Kit Miniprep™ (ZR kit), for extracting microbial genomic DNA from sand treated with different types of biochar. The methods were evaluated by comparing the DNA yields and purity and by analysing the bacterial and fungal community profiles generated by PCR-DGGE. Our results showed that the PCR-DGGE profiles for bacterial and fungal communities were highly affected by the purity and yield of the different DNA extracts. Among the tested kits, the PS kit was the most efficient with respect to the amount and purity of recovered DNA and considering the complexity of the generated DGGE microbial fingerprint from the sand-biochar samples. PMID:24948928

Comparison of DNA extraction protocols for microbial communities from soil treated with biochar.

PubMed

Leite, D C A; Balieiro, F C; Pires, C A; Madari, B E; Rosado, A S; Coutinho, H L C; Peixoto, R S

2014-01-01

Many studies have evaluated the effects of biochar application on soil structure and plant growth. However, there are very few studies describing the effect of biochar on native soil microbial communities. Microbial analysis of environmental samples requires accurate and reproducible methods for the extraction of DNA from samples. Because of the variety among microbial species and the strong adsorption of the phosphate backbone of the DNA molecule to biochar, extracting and purifying high quality microbial DNA from biochar-amended soil is not a trivial process and can be considerably more difficult than the extraction of DNA from other environmental samples. The aim of this study was to compare the relative efficacies of three commercial DNA extraction kits, the FastDNA® SPIN Kit for Soil (FD kit), the PowerSoil® DNA Isolation Kit (PS kit) and the ZR Soil Microbe DNA Kit Miniprep™ (ZR kit), for extracting microbial genomic DNA from sand treated with different types of biochar. The methods were evaluated by comparing the DNA yields and purity and by analysing the bacterial and fungal community profiles generated by PCR-DGGE. Our results showed that the PCR-DGGE profiles for bacterial and fungal communities were highly affected by the purity and yield of the different DNA extracts. Among the tested kits, the PS kit was the most efficient with respect to the amount and purity of recovered DNA and considering the complexity of the generated DGGE microbial fingerprint from the sand-biochar samples.

Biodegradation of Jet Fuel in Vented Columns of Water-Unsaturated Sandy Soil

DTIC Science & Technology

1990-01-01

phosphorus, sulfur, iron, magnesium, calcium, sodium and other elements are required for microbial growth ( Atlas , 1977). Dibble and Bartha (1979b...371-386. Bartha , R. 1986. Biotechnology of Petroleum Pollutant Biodegradation. Microbial Ecology . v.12, p.155-172. Batchelder, G.V., W.A. Panzeri...E.L. Schmidt. 1978. Limiting Factors for Microbial Growth and Activity in Soil, in Advances in Microbial Ecology , v.2, Plenum Press, New York. p.49

Effect of microbial-based inoculants on nutrient concentrations and early root morphology of corn (Zea mays)

USDA-ARS?s Scientific Manuscript database

Microbial-based inoculants have been reported to stimulate plant growth and nutrient uptake. However, their effect may vary depending on the growth stage when evaluated and on the chemical fertilizer applied. Thus, the objective of this study was to test the hypothesis that microbial-based inoculant...

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.

Uranium removal from a contaminated effluent using a combined microbial and nanoparticle system.

PubMed

Baiget, Mar; Constantí, Magda; López, M Teresa; Medina, Francesc

2013-09-25

Reduction of soluble uranium(VI) to insoluble uranium(IV) for remediating a uranium-contaminated effluent (EF-03) was examined using a biotic and abiotic integrated system. Shewanella putrefaciens was first used and reduced U(VI) in a synthetic medium but not in the EF-03 effluent sample. Subsequently the growth of autochthonous microorganisms was stimulated with lactate. When lactate was supported on active carbon 77% U(VI) was removed in 4 days. Separately, iron nanoparticles that were 50 nm in diameter reduced U(VI) by 60% in 4 hours. The efficiency of uranium(VI) removal was improved to 96% in 30 min by using a system consisting of lactate and iron nanoparticles immobilized on active carbon. Lactate also stimulated the growth of potential uranium-reducing microorganisms in the EF-03 sample. This system can be efficiently used for the bioremediation of uranium-contaminated effluents. Copyright © 2013 Elsevier B.V. All rights reserved.

Effects of storage environment on the moisture content and microbial growth of food waste.

PubMed

Chen, Ying-Chu; Hsu, Yi-Cheng; Wang, Chung-Ting

2018-05-15

Food waste (FW) has become a critical issue in sustainable development as the world's population has increased. Direct incineration of FW remains the primary treatment option. The moisture content of FW may affect the energy efficiency of incineration. In Taiwan, FW, which includes raw (r-FW) and post-consumer (p-FW) waste, is often stored in freezers before pretreatment. This study evaluated the effects of storage environment on the moisture content and microbial growth of FW. Storage at 263 K was associated with the largest reduction in moisture content in both r-FW and p-FW. At 263 K, the moisture content of r-FW and p-FW was lowest at 96 and 72 h, respectively. The E.coli and total bacteria counts were steady over 120 h when stored at 263 K. Storage at 253 K required the greatest electricity consumption, followed by 263 K and 258 K. Based on the reduction of moisture content and increase in energy efficiency, it is suggested that FW is placed in temporary storage at 263 K before (pre)treatment. The results of this study will help waste-to-energy plants, incinerators, and waste management enterprises to implement proper (pre)treatment of FW for sustainable waste management. Copyright © 2018 Elsevier Ltd. All rights reserved.

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.

Final Report for Project "A high-throughput pipeline for mapping inter-species interactions and metabolic synergy relevant to next-generation biofuel production"

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

Segre, Daniel; Marx, Christopher J.; Northen, Trent

The goal of our project was to implement a pipeline for the systematic, computationally-driven study and optimization of microbial interactions and their effect on lignocellulose degradation and biofuel production. We specifically sought to design and construct artificial microbial consortia that could collectively degrade lignocellulose from plant biomass, and produce precursors of energy-rich biofuels. This project fits into the bigger picture goal of helping identify a sustainable strategy for the production of energy-rich biofuels that would satisfy the existing energy constraints and demand of our society. Based on the observation that complex natural microbial communities tend to be metabolically efficient andmore » ecologically robust, we pursued the study of a microbial system in which the desired engineering function is achieved through division of labor across multiple microbial species. Our approach was aimed at bypassing the complexity of natural communities by establishing a rational approach to design small synthetic microbial consortia. Towards this goal, we combined multiple approaches, including computer modeling of ecosystem-level microbial metabolism, mass spectrometry of metabolites, genetic engineering, and experimental evolution. The microbial production of biofuels from lignocellulose is a complex, multi-step process. Microbial consortia are an ideal approach to consolidated bioprocessing: a community of microorganisms performs a wide variety of functions more efficiently and is more resilient to environmental perturbations than a microbial monoculture. Each organism we chose for this project addresses a specific challenge: lignin degradation (Pseudomonas putida); (hemi)cellulose degradation (Cellulomonas fimi); lignin degradation product demethoxylation (Methylobacterium spp); generation of biofuel lipid precursors (Yarrowia lipolytica). These organisms are genetically tractable, aerobic, and have been used in biotechnological applications. Throughout the project, we have used mass spectrometry to characterize and measure the metabolic inputs and outputs of each of these consortium members, providing valuable information for model refinement, and enabling the establishment of metabolism-mediated interactions. In addition to lignocellulose degradation, we have started addressing the challenge of removing metabolites (e.g. formaldehyde) produced by the demethoxylation of lignin monomers, which can otherwise inhibit microbial growth due to their toxicity. On the computational side, we have implemented genome-scale models for all consortium members, based on KBase reconstructions and literature curation, and we studied small consortia and their properties. Overall, our project has identified a complex landscape of interactions types and metabolic processes relevant to community-level functions, illustrating the challenges and opportunities of microbial community engineering for the transformation of biomass into bioproducts.« less

Effect of gamma irradiation and storage time on microbial growth and physicochemical characteristics of pumpkin (Cucurbita Moschata Duchesne ex Poiret) puree.

PubMed

Gliemmo, María F; Latorre, María E; Narvaiz, Patricia; Campos, Carmen A; Gerschenson, Lía N

2014-01-01

The effect of gamma irradiation (0-2 kGy) and storage time (0-28 days) on microbial growth and physicochemical characteristics of a packed pumpkin puree was studied. For that purpose, a factorial design was applied. The puree contained potassium sorbate, glucose and vanillin was stored at 25°C . Gamma irradiation diminished and storage time increased microbial growth. A synergistic effect between both variables on microbial growth was observed. Storage time decreased pH and color of purees. Sorbate content decreased with storage time and gamma irradiation. Mathematical models of microbial growth generated by the factorial design allowed estimating that a puree absorbing 1.63 kGy would have a shelf-life of 4 days. In order to improve this time, some changes in the applied hurdles were assayed. These included a thermal treatment before irradiation, a reduction of irradiation dose to 0.75 kGy and a decrease in storage temperature at 20°C . As a result, the shelf-life of purees increased to 28 days.

Synthesis of novel bioactive lactose-derived oligosaccharides by microbial glycoside hydrolases

PubMed Central

Díez-Municio, Marina; Herrero, Miguel; Olano, Agustín; Moreno, F Javier

2014-01-01

Prebiotic oligosaccharides are increasingly demanded within the Food Science domain because of the interesting healthy properties that these compounds may induce to the organism, thanks to their beneficial intestinal microbiota growth promotion ability. In this regard, the development of new efficient, convenient and affordable methods to obtain this class of compounds might expand even further their use as functional ingredients. This review presents an overview on the most recent interesting approaches to synthesize lactose-derived oligosaccharides with potential prebiotic activity paying special focus on the microbial glycoside hydrolases that can be effectively employed to obtain these prebiotic compounds. The most notable advantages of using lactose-derived carbohydrates such as lactosucrose, galactooligosaccharides from lactulose, lactulosucrose and 2-α-glucosyl-lactose are also described and commented. PMID:24690139

Electro-Fermentation - Merging Electrochemistry with Fermentation in Industrial Applications.

PubMed

Schievano, Andrea; Pepé Sciarria, Tommy; Vanbroekhoven, Karolien; De Wever, Heleen; Puig, Sebastià; Andersen, Stephen J; Rabaey, Korneel; Pant, Deepak

2016-11-01

Electro-fermentation (EF) merges traditional industrial fermentation with electrochemistry. An imposed electrical field influences the fermentation environment and microbial metabolism in either a reductive or oxidative manner. The benefit of this approach is to produce target biochemicals with improved selectivity, increase carbon efficiency, limit the use of additives for redox balance or pH control, enhance microbial growth, or in some cases enhance product recovery. We discuss the principles of electrically driven fermentations and how EF can be used to steer both pure culture and microbiota-based fermentations. An overview is given on which advantages EF may bring to both existing and innovative industrial fermentation processes, and which doors might be opened in waste biomass utilization towards added-value biorefineries. Copyright © 2016 Elsevier Ltd. All rights reserved.

[Development of a predictive program for microbial growth under various temperature conditions].

PubMed

Fujikawa, Hiroshi; Yano, Kazuyoshi; Morozumi, Satoshi; Kimura, Bon; Fujii, Tateo

2006-12-01

A predictive program for microbial growth under various temperature conditions was developed with a mathematical model. The model was a new logistic model recently developed by us. The program predicts Escherichia coli growth in broth, Staphylococcus aureus growth and its enterotoxin production in milk, and Vibrio parahaemolyticus growth in broth at various temperature patterns. The program, which was built with Microsoft Excel (Visual Basic Application), is user-friendly; users can easily input the temperature history of a test food and obtain the prediction instantly on the computer screen. The predicted growth and toxin production can be important indices to determine whether a food is microbiologically safe or not. This program should be a useful tool to confirm the microbial safety of commercial foods.

Trichoderma reesei FS10-C enhances phytoremediation of Cd-contaminated soil by Sedum plumbizincicola and associated soil microbial activities

PubMed Central

Teng, Ying; Luo, Yang; Ma, Wenting; Zhu, Lingjia; Ren, Wenjie; Luo, Yongming; Christie, Peter; Li, Zhengao

2015-01-01

This study aimed to explore the effects of Trichoderma reesei FS10-C on the phytoremediation of Cd-contaminated soil by the hyperaccumulator Sedum plumbizincicola and on soil fertility. The Cd tolerance of T. reesei FS10-C was characterized and then a pot experiment was conducted to investigate the growth and Cd uptake of S. plumbizincicola with the addition of inoculation agents in the presence and absence of T. reesei FS10-C. The results indicated that FS10-C possessed high Cd resistance (up to 300 mg L-1). All inoculation agents investigated enhanced plant shoot biomass by 6–53% of fresh weight and 16–61% of dry weight and Cd uptake by the shoots by 10–53% compared with the control. All inoculation agents also played critical roles in increasing soil microbial biomass and microbial activities (such as biomass C, dehydrogenase activity and fluorescein diacetate hydrolysis activity). Two inoculation agents accompanied by FS10-C were also superior to the inoculation agents, indicating that T. reesei FS10-C was effective in enhancing both Cd phytoremediation by S. plumbizincicola and soil fertility. Furthermore, solid fermentation powder of FS10-C showed the greatest capacity to enhance plant growth, Cd uptake, nutrient release, microbial biomass and activities, as indicated by its superior ability to promote colonization by Trichoderma. The solid fermentation powder of FS10-C might serve as a suitable inoculation agent for T. reesei FS10-C to enhance both the phytoremediation efficiency of Cd-contaminated soil and soil fertility. PMID:26113858

[Abnormal bacterial colonisation of the vagina and implantation during assisted reproduction].

PubMed

Wittemer, C; Bettahar-Lebugle, K; Ohl, J; Rongières, C; Viville, S; Nisand, I

2004-02-01

To evaluate the efficiency of our treatment of vaginal infection for couples included in an IVF program. Microbiologic screening of vaginal flora and semen has been performed one month prior to in vitro fertilization for 951 couples in 2000. Antibiotic treatment was prescribed in case of positive culture. Positive microbial growths were observed from endocervical and vaginal cultures in 218 women (22.9%). The clinical pregnancy rate was 30.29% in the group of patients without growth and 30.27% in the group with positive microbial growth. The implantation rate was significantly diminished in case of bacterial growth: 14.6 compared to 19.3% (P <0.02) for sterile endocervical culture. Five main bacterial species were found at the cervical level: Candida albicans (69 cases), Ureaplasma urealyticum (49 cases), Gardnerella vaginalis (43 cases), Streptococcus B or D (24 cases) and Escherichia coli (22 cases). Positive cultures from both vagina and semen were observed for 77 couples whose clinical pregnancy rate was 19.5 vs 36.2% in case of vaginal infection alone (P <0.01) with a spontaneous miscarriage rate of 46.7 compared to 17.6% (P <0.01). Endocervical microorganisms, even treated with adapted antibiotics, may affect embryonic implantation. Positive culture from both female and male partner may enhance this negative effect. In this case, the best strategy would be to cancel the IVF treatment.

Microbial Anomalies Encountered on the International Space Station

NASA Technical Reports Server (NTRS)

Bruce, Rebekah J.; Wong, Wing; Pierson, Duane; Castro, Victoria

2010-01-01

Microorganisms in our living environments are unavoidable. A community of microbes arrived in space with the delivery of the first element of the International Space Station (ISS), attached to hardware and on the bodies of the humans tasked with the initial assembly missions. The risk that microorganisms could cause adverse effects in the health of both the human occupants of the ISS as well as the physical integrity of the station environment and life support systems has been both a driver and a function of engineering and operational controls. Scientists and engineers at NASA have gone to extensive measures to control microbial growth at levels safe for the crewmembers and the spacecraft environment. Many of these measures were initiated with the design of the spacecraft and its systems. Materials used in the ISS were tested for resistance to fungi, such as mold and a paint with a fungus-killing chemical was also used. Controlling the humidity of the air in the Station is also an effective way of discouraging microbe growth. The breathing air is reconditioned by the Environmental Control Life Support System (ECLSS) prior to distribution, utilizing High Efficiency Particulate Air (HEPA) filtration. Requirements restricting the accumulation of water condensate in the air handlers and habitable volume of the ISS were other safeguards added. Water for drinking and food rehydration is disinfected or filtered. A robust in-flight housekeeping regimen for the ISS significantly reduces inappropriate growth of microorganisms and includes a regular cleaning of accessible surfaces with disinfectant wipes. Most of these requirements were suggested by microbiologists to mitigate and possibly prevent many microbiological risks. In addition to these controls, before flight monitoring and analyses of the cabin air, exposed surfaces, water and food, consumables, and crew members are conducted to mitigate microbial risk to the crew and spacecraft. Many microbial risks are much easier to identify and resolve before launch than during space flight. Although the focus has been on prevention of microbiologically related, not all problems can be anticipated. A number of microbial anomalies have occurred on ISS. This paper will discuss the occurrences, root-cause investigations, and mitigation steps taken to remediate the contamination.

Bio-control and plant growth promotion potential of Salicaceae endophytes

USDA-ARS?s Scientific Manuscript database

Microbial endophytes are important for growth benefits in a variety of plant species. Microbial communities of the poplar (Populus sp.) and willow (Salix sp.) endosphere have been demonstrated to be important for plant growth promotion, protection from abiotic stresses, and degradation of toxic subs...

Microbial analysis of meatballs cooled with vacuum and conventional cooling.

PubMed

Ozturk, Hande Mutlu; Ozturk, Harun Kemal; Koçar, Gunnur

2017-08-01

Vacuum cooling is a rapid evaporative cooling technique and can be used for pre-cooling of leafy vegetables, mushroom, bakery, fishery, sauces, cooked food, meat and particulate foods. The aim of this study was to apply the vacuum cooling and the conventional cooling techniques for the cooling of the meatball and to show the vacuum pressure effect on the cooling time, the temperature decrease and microbial growth rate. The results of the vacuum cooling and the conventional cooling (cooling in the refrigerator) were compared with each other for different temperatures. The study shows that the conventional cooling was much slower than the vacuum cooling. Moreover, the microbial growth rate of the vacuum cooling was extremely low compared with the conventional cooling. Thus, the lowest microbial growth occurred at 0.7 kPa and the highest microbial growth was observed at 1.5 kPa for the vacuum cooling. The mass loss ratio for the conventional cooling and vacuum cooling was about 5 and 9% respectively.

Microbial shifts in the swine distal gut in response to the treatment with antimicrobial growth promoter, tylosin

PubMed Central

Kim, Hyeun Bum; Borewicz, Klaudyna; White, Bryan A.; Singer, Randall S.; Sreevatsan, Srinand; Tu, Zheng Jin; Isaacson, Richard E.

2012-01-01

Antimicrobials have been used extensively as growth promoters (AGPs) in agricultural animal production. However, the specific mechanism of action for AGPs has not yet been determined. The work presented here was to determine and characterize the microbiome of pigs receiving one AGP, tylosin, compared with untreated pigs. We hypothesized that AGPs exerted their growth promoting effect by altering gut microbial population composition. We determined the fecal microbiome of pigs receiving tylosin compared with untreated pigs using pyrosequencing of 16S rRNA gene libraries. The data showed microbial population shifts representing both microbial succession and changes in response to the use of tylosin. Quantitative and qualitative analyses of sequences showed that tylosin caused microbial population shifts in both abundant and less abundant species. Our results established a baseline upon which mechanisms of AGPs in regulation of health and growth of animals can be investigated. Furthermore, the data will aid in the identification of alternative strategies to improve animal health and consequently production. PMID:22955886

Biodegradation of commercial gasoline (24% ethanol added) in liquid medium by microorganisms isolated from a landfarming site.

PubMed

Oliveira, Núbia M; Bento, Fátima M; Camargo, Flávio A O; Knorst, Aline Jéssica; Dos Santos, Anai Loreiro; Pizzolato, Tania M; Peralba, Maria do Carmo R

2011-01-01

Isolation of soil microorganisms from a landfarming site with a 19-year history of petrochemical residues disposal was carried out. After isolation, the bacteria behavior in mineral medium with 1% commercial gasoline (24% ethanol) was evaluated. Parameters employed for microorganism evaluation and selection of those with the greatest degradation potential were: microbial growth; biosurfactant generation and compound reduction in commercial gasoline. Starting from bacteria that presented the best degradation results, consortiums formed by 4 distinct microorganisms were formed. A microbial growth in the presence of commercial gasoline was observed and, for most of the bacteria, degradations of compounds such as benzene, toluene and xylenes (BTX) as well as biosurfactant production was observed. Ethanol was partially degraded by the bacterial isolates although the data does not allow affirming that it was degraded preferentially to the aromatic hydrocarbons investigated. The analyzed consortiums present an efficiency of 95% to 98% for most of the commercial gasoline compounds and a preferential attack to ethanol under the essay condition was not observed within 72 h.

Sustainable water desalination and electricity generation in a separator coupled stacked microbial desalination cell with buffer free electrolyte circulation.

PubMed

Chen, Xi; Liang, Peng; Wei, Zhimou; Zhang, Xiaoyuan; Huang, Xia

2012-09-01

A separator coupled circulation stacked microbial desalination cell (c-SMDC-S) was constructed to stabilize the pH imbalances in MDCs without buffer solution and achieved the stable desalination. The long-term operation of c-SMDC-S, regular stacked MDC (SMDC) and no separator coupled circulation SMDC (c-SMDC) were tested. The SMDC and c-SMDC could only stably operate for 1 week and 1 month owing to dramatic anolyte pH decrease and serious biofilm growth on the air cathode, respectively. The c-SMDC-S gained in anolyte alkalinity and operated stably for about 60 days without the thick biofilm growth on cathode. Besides, the chemical oxygen demand removal and coulombic efficiency were 64 ± 6% and 30 ± 2%, higher than that of SMDC and c-SMDC, respectively. It was concluded that the circulation of alkalinity could remove pH imbalance while the separator could expand the operation period and promote the conversion of organic matter to electricity. Copyright © 2012 Elsevier Ltd. All rights reserved.

Microbial volatile organic compounds in moldy interiors: a long-term climate chamber study.

PubMed

Schuchardt, Sven; Strube, Andrea

2013-06-01

The present study simulated large-scale indoor mold damage in order to test the efficiency of air sampling for the detection of microbial volatile organic compounds (MVOCs). To do this, a wallpaper damaged by condensation was stored in a climate chamber (representing a hypothetical test room of 40 m(3) volume) and was inoculated with 14 typical indoor fungal strains. The chamber ventilation conditions were adjusted to common values found in moldy homes, and the mold growth was allowed to continue to higher than average values. The MVOC content of the chamber air was analyzed daily for a period of 105 days using coupled gas chromatography/mass spectrometry (GC-MS). This procedure guarantees MVOC profiling without external factors such as outdoor air, building materials, furniture, and occupants. However, only nine MVOCs could be detected during the sampling period, which indicates that the very low concentrated MVOCs are hardly accessible, even under these favorable conditions. Furthermore, most of the MVOCs that were detected cannot be considered as reliable indicators of mold growth in indoor environments. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Pelagic photoferrotrophy and iron cycling in a modern ferruginous basin.

PubMed

Llirós, Marc; García-Armisen, Tamara; Darchambeau, François; Morana, Cédric; Triadó-Margarit, Xavier; Inceoğlu, Özgül; Borrego, Carles M; Bouillon, Steven; Servais, Pierre; Borges, Alberto V; Descy, Jean-Pierre; Canfield, Don E; Crowe, Sean A

2015-09-08

Iron-rich (ferruginous) ocean chemistry prevailed throughout most of Earth's early history. Before the evolution and proliferation of oxygenic photosynthesis, biological production in the ferruginous oceans was likely driven by photoferrotrophic bacteria that oxidize ferrous iron {Fe(II)} to harness energy from sunlight, and fix inorganic carbon into biomass. Photoferrotrophs may thus have fuelled Earth's early biosphere providing energy to drive microbial growth and evolution over billions of years. Yet, photoferrotrophic activity has remained largely elusive on the modern Earth, leaving models for early biological production untested and imperative ecological context for the evolution of life missing. Here, we show that an active community of pelagic photoferrotrophs comprises up to 30% of the total microbial community in illuminated ferruginous waters of Kabuno Bay (KB), East Africa (DR Congo). These photoferrotrophs produce oxidized iron {Fe(III)} and biomass, and support a diverse pelagic microbial community including heterotrophic Fe(III)-reducers, sulfate reducers, fermenters and methanogens. At modest light levels, rates of photoferrotrophy in KB exceed those predicted for early Earth primary production, and are sufficient to generate Earth's largest sedimentary iron ore deposits. Fe cycling, however, is efficient, and complex microbial community interactions likely regulate Fe(III) and organic matter export from the photic zone.

Stimulation effect of electric current density (ECD) on microbial community of a three dimensional particle electrode coupled with biological aerated filter reactor (TDE-BAF).

PubMed

Feng, Yan; Li, Xing; Song, Ting; Yu, Yanzhen; Qi, Jingyao

2017-11-01

Improving the stimulation effect of electric current density (ECD) on microbial community is critical in designing and operating TDE-BAF. This study investigated the effect of ECD at 0.00, 4.08, 6.12, 12.20, 14.25, 16.30 and 20.20A·m -2 on the removal performance, diversity and structure of microbial community in TDE-BAF. Results indicated that the ECD of 14.25A·m -2 exhibited the highest COD, TOC and NH 4 + -N average removal rates with 93.33%, 91.26% and 93.87%, respectively; Under high ECD, especially exceeding 14.25A·m -2 , the inhibition of growth and activity because of plasmatorrhexis was in agreement with the sharp biomass decline; there was no significant relation between community richness and diversity and removal efficiency below optimum ECD, while above optimal ECD, it was just the opposite; Microbial communities mainly including Hydrogenophaga, Saprospiraceae_uncultured, Delftia, Enterobacter, Pseudomonas, Pseudoxanthomonas, and Nitrosospira and physicochemical properties well explained the excellent removal performance at the optimum ECD. Copyright © 2017 Elsevier Ltd. All rights reserved.

MBGD update 2013: the microbial genome database for exploring the diversity of microbial world.

PubMed

Uchiyama, Ikuo; Mihara, Motohiro; Nishide, Hiroyo; Chiba, Hirokazu

2013-01-01

The microbial genome database for comparative analysis (MBGD, available at http://mbgd.genome.ad.jp/) is a platform for microbial genome comparison based on orthology analysis. As its unique feature, MBGD allows users to conduct orthology analysis among any specified set of organisms; this flexibility allows MBGD to adapt to a variety of microbial genomic study. Reflecting the huge diversity of microbial world, the number of microbial genome projects now becomes several thousands. To efficiently explore the diversity of the entire microbial genomic data, MBGD now provides summary pages for pre-calculated ortholog tables among various taxonomic groups. For some closely related taxa, MBGD also provides the conserved synteny information (core genome alignment) pre-calculated using the CoreAligner program. In addition, efficient incremental updating procedure can create extended ortholog table by adding additional genomes to the default ortholog table generated from the representative set of genomes. Combining with the functionalities of the dynamic orthology calculation of any specified set of organisms, MBGD is an efficient and flexible tool for exploring the microbial genome diversity.

Electron Donors Supporting Growth and Electroactivity of Geobacter sulfurreducens Anode Biofilms

PubMed Central

Speers, Allison M.

2012-01-01

Geobacter bacteria efficiently oxidize acetate into electricity in bioelectrochemical systems, yet the range of fermentation products that support the growth of anode biofilms and electricity production has not been thoroughly investigated. Here, we show that Geobacter sulfurreducens oxidized formate and lactate with electrodes and Fe(III) as terminal electron acceptors, though with reduced efficiency compared to acetate. The structure of the formate and lactate biofilms increased in roughness, and the substratum coverage decreased, to alleviate the metabolic constraints derived from the assimilation of carbon from the substrates. Low levels of acetate promoted formate carbon assimilation and biofilm growth and increased the system's performance to levels comparable to those with acetate only. Lactate carbon assimilation also limited biofilm growth and led to the partial oxidization of lactate to acetate. However, lactate was fully oxidized in the presence of fumarate, which redirected carbon fluxes into the tricarboxylic acid (TCA) cycle, and by acetate-grown biofilms. These results expand the known ranges of electron donors for Geobacter-driven fuel cells and identify microbial constraints that can be targeted to develop better-performing strains and increase the performance of bioelectrochemical systems. PMID:22101036

Characterization of tobermolite as a bed material for selective growth of methanotrophs in biofiltration.

PubMed

Kim, Tae Gwan; Jeong, So-Yeon; Cho, Kyung-Suk

2014-03-10

Tobermolite was characterized as a bed material for methanotrophic biofiltration. A lab-scale biofilter packed with tobermolite was operated for different operation times under identical conditions. The three different runs showed similar acclimation patterns of methane oxidation, with methane removal efficiency increasing rapidly for the first few days and peaking within three weeks, after which the efficiency remained stable. The mean methane removal capacities ranged from 766gm(-3)d(-1) to 974gm(-3)d(-1) after acclimation. Pyrosequencing indicated that the methanotrophic proportion (methanotroph/bacteria) increased to 71-94% within three weeks. Type I methanotrophs Methylocaldum and Methylosarcina were dominant during the initial growth period, then Methylocaldum alone dominated the methanotrophic community. A community comparison showed that total bacterial and methanotrophic communities were temporally stable after the initial growth period. Quantitative PCR showed that methanotrophic density increased during the first 3-4 weeks, then remained stable over 120 days. Tobermolite can provide a special habitat for the selective growth of methanotrophs, resulting in rapid acclimation. Tobermolite also allows the microbial community and methanotrophic density to remain stable, resulting in stable methane biofiltration. Copyright © 2014 Elsevier B.V. All rights reserved.

Membrane Fatty Acid Composition and Cell Surface Hydrophobicity of Marine Hydrocarbonoclastic Alcanivorax borkumensis SK2 Grown on Diesel, Biodiesel and Rapeseed Oil as Carbon Sources.

PubMed

Konieczna, Maria; Olzog, Martin; Naether, Daniela J; Chrzanowski, Łukasz; Heipieper, Hermann J

2018-06-13

The marine hydrocarbonoclastic bacterium Alcanivorax borkumensis is well known for its ability to successfully degrade various mixtures of n -alkanes occurring in marine oil spills. For effective growth on these compounds, the bacteria possess the unique capability not only to incorporate but also to modify fatty intermediates derived from the alkane degradation pathway. High efficiency of both these processes provides better competitiveness for a single bacteria species among hydrocarbon degraders. To examine the efficiency of A. borkumensis to cope with different sources of fatty acid intermediates, we studied the growth rates and membrane fatty acid patterns of this bacterium cultivated on diesel, biodiesel and rapeseed oil as carbon and energy source. Obtained results revealed significant differences in both parameters depending on growth substrate. Highest growth rates were observed with biodiesel, while growth rates on rapeseed oil and diesel were lower than on the standard reference compound (hexadecane). The most remarkable observation is that cells grown on rapeseed oil, biodiesel, and diesel showed significant amounts of the two polyunsaturated fatty acids linoleic acid and linolenic acid in their membrane. By direct incorporation of these external fatty acids, the bacteria save energy allowing them to degrade those pollutants in a more efficient way. Such fast adaptation may increase resilience of A. borkumensis and allow them to strive and maintain populations in more complex hydrocarbon degrading microbial communities.

Modelling the competition of planktonic and sessile aerobic heterotrophs for complementary nutrients in biofilm reactor.

PubMed

Lu, T; Saikaly, P E; Oerther, D B

2007-01-01

A comprehensive, simplified microbial biofilm model was developed to evaluate the impact of bioreactor operating parameters on changes in microbial population abundance. Biofilm simulations were conducted using three special cases: fully penetrated, internal mass transfer resistance and external mass transfer resistance. The results of model simulations showed that for certain operating conditions, competition for growth limiting nutrients generated oscillations in the abundance of planktonic and sessile microbial populations. These oscillations resulted in the violation of the competitive exclusion principle where the number of microbial populations was greater than the number of growth limiting nutrients. However, the operating conditions which impacted microbial community diversity were different for the three special cases. Comparing the results of model simulations for dispersed-growth, biofilms and bioflocs showed that oscillations and microbial community diversity were a function of competition as well as other key features of the ecosystem. The significance of the current study is that it is the first to examine competition as a mechanism for controlling microbial community diversity in biofilm reactors.

Valorization of pyrolysis water: a biorefinery side stream, for 1,2-propanediol production with engineered Corynebacterium glutamicum.

PubMed

Lange, Julian; Müller, Felix; Bernecker, Kerstin; Dahmen, Nicolaus; Takors, Ralf; Blombach, Bastian

2017-01-01

A future bioeconomy relies on the efficient use of renewable resources for energy and material product supply. In this context, biorefineries have been developed and play a key role in converting lignocellulosic residues. Although a holistic use of the biomass feed is desired, side streams evoke in current biorefinery approaches. To ensure profitability, efficiency, and sustainability of the overall conversion process, a meaningful valorization of these materials is needed. Here, a so far unexploited side stream derived from fast pyrolysis of wheat straw-pyrolysis water-was used for production of 1,2-propanediol in microbial fermentation with engineered Corynebacterium glutamicum . A protocol for pretreatment of pyrolysis water was established and enabled growth on its major constituents, acetate and acetol, with rates up to 0.36 ± 0.04 h -1 . To convert acetol to 1,2-propanediol, the plasmid pJUL gldA expressing the glycerol dehydrogenase from Escherichia coli was introduced into C. glutamicum . 1,2-propanediol was formed in a growth-coupled biotransformation and production was further increased by construction of C. glutamicum Δ pqo Δ aceE Δ ldhA Δ mdh pJUL gldA . In a two-phase aerobic/microaerobic fed-batch process with pyrolysis water as substrate, this strain produced 18.3 ± 1.2 mM 1,2-propanediol with a yield of 0.96 ± 0.05 mol 1,2-propanediol per mol acetol and showed an overall volumetric productivity of 1.4 ± 0.1 mmol 1,2-propanediol L -1  h -1 . This study implements microbial fermentation into a biorefinery based on pyrolytic liquefaction of lignocellulosic biomass and accesses a novel value chain by valorizing the side stream pyrolysis water for 1,2-PDO production with engineered C. glutamicum . The established bioprocess operated at maximal product yield and accomplished the so far highest overall volumetric productivity for microbial 1,2-PDO production with an engineered producer strain. Besides, the results highlight the potential of microbial conversion of this biorefinery side stream to other valuable products.

Microbial community and removal of nitrogen via the addition of a carrier in a pilot-scale duckweed-based wastewater treatment system.

PubMed

Zhao, Yonggui; Fang, Yang; Jin, Yanling; Huang, Jun; Ma, Xinrong; He, Kaize; He, Zhiming; Wang, Feng; Zhao, Hai

2015-03-01

Carriers were added to a pilot-scale duckweed-based (Lemna japonica 0223) wastewater treatment system to immobilize and enhance microorganisms. This system and another parallel duckweed system without carriers were operated for 1.5 years. The results indicated the addition of the carrier did not significantly affect the growth and composition of duckweed, the recovery of total nitrogen (TN), total phosphorus (TP) and CO2 or the removal of TP. However, it significantly improved the removal efficiency of TN and NH4(+)-N (by 19.97% and 15.02%, respectively). The use of 454 pyrosequencing revealed large differences of the microbial communities between the different components within a system and similarities within the same components between the two systems. The carrier biofilm had the highest bacterial diversity and relative abundance of nitrifying bacteria (3%) and denitrifying bacteria (24% of Rhodocyclaceae), which improved nitrogen removal of the system. An efficient N-removal duckweed system with enhanced microorganisms was established. Copyright © 2014 Elsevier Ltd. All rights reserved.

Beyond Agar: Gel Substrates with Improved Optical Clarity and Drug Efficiency and Reduced Autofluorescence for Microbial Growth Experiments

PubMed Central

McElfresh, Cameron; Wong, Lily R.

2015-01-01

Agar, a seaweed extract, has been the standard support matrix for microbial experiments for over a century. Recent developments in high-throughput genetic screens have created a need to reevaluate the suitability of agar for use as colony support, as modern robotic printing systems now routinely spot thousands of colonies within the area of a single microtiter plate. Identifying optimal biophysical, biochemical, and biological properties of the gel support matrix in these extreme experimental conditions is instrumental to achieving the best possible reproducibility and sensitivity. Here we systematically evaluate a range of gelling agents by using the yeast Saccharomyces cerevisiae as a model microbe. We find that carrageenan and Phytagel have superior optical clarity and reduced autofluorescence, crucial for high-resolution imaging and fluorescent reporter screens. Nutrient choice and use of refined Noble agar or pure agarose reduce the effective dose of numerous selective drugs by >50%, potentially enabling large cost savings in genetic screens. Using thousands of mutant yeast strains to compare colony growth between substrates, we found no evidence of significant growth or nutrient biases between gel substrates, indicating that researchers could freely pick and choose the optimal gel for their respective application and experimental condition. PMID:26070672

Beyond Agar: Gel Substrates with Improved Optical Clarity and Drug Efficiency and Reduced Autofluorescence for Microbial Growth Experiments.

PubMed

Jaeger, Philipp A; McElfresh, Cameron; Wong, Lily R; Ideker, Trey

2015-08-15

Agar, a seaweed extract, has been the standard support matrix for microbial experiments for over a century. Recent developments in high-throughput genetic screens have created a need to reevaluate the suitability of agar for use as colony support, as modern robotic printing systems now routinely spot thousands of colonies within the area of a single microtiter plate. Identifying optimal biophysical, biochemical, and biological properties of the gel support matrix in these extreme experimental conditions is instrumental to achieving the best possible reproducibility and sensitivity. Here we systematically evaluate a range of gelling agents by using the yeast Saccharomyces cerevisiae as a model microbe. We find that carrageenan and Phytagel have superior optical clarity and reduced autofluorescence, crucial for high-resolution imaging and fluorescent reporter screens. Nutrient choice and use of refined Noble agar or pure agarose reduce the effective dose of numerous selective drugs by >50%, potentially enabling large cost savings in genetic screens. Using thousands of mutant yeast strains to compare colony growth between substrates, we found no evidence of significant growth or nutrient biases between gel substrates, indicating that researchers could freely pick and choose the optimal gel for their respective application and experimental condition. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Microbial community profiles of the colon from steers differing in feed efficiency

USDA-ARS?s Scientific Manuscript database

Ruminal microbial fermentation plays an essential role in host nutrition, and as a result, the rumen microbiota have been a major focus of research examining bovine feed efficiency. Microbial communities within other sections of the gastrointestinal tract may also be important with regard to feed ef...

Investigating the legacy effect of drought on microbial responses to drying and rewetting along a Texan precipitation gradient

NASA Astrophysics Data System (ADS)

Hicks, Lettice; Leizeaga, Ainara; Hawkes, Christine; Rousk, Johannes

2017-04-01

Hydrological regimes will intensify due to climate change, thus increasing the duration and intensity of drought and rainfall events. Rewetting of dry soil is known to stimulate dramatic CO2 releases. A clear understanding of the mechanisms that determine the dynamics of CO2 loss upon rewetting is therefore required to characterise ecosystem C-budgets and predict responses to climate change. Laboratory studies have identified two distinct responses upon rewetting; bacterial growth either increases linearly immediately, with maximal respiration also occurring immediately and decreasing exponentially with time ("Type 1"), or bacterial growth increases exponentially after a period of near-zero growth, with a sustained period of elevated respiration, sometimes followed by a secondary increase in respiration coinciding with the onset of bacterial growth ("Type 2"). A shift from a Type 1 to a Type 2 response has been observed with increasing duration and intensity of drying prior to rewetting. The size of the surviving microbial community after drying, relative to resources available after rewetting, is suggested to dictate whether a Type 1 or 2 response occurs, with more 'harsh' (i.e. longer or more severe) drying reducing microbial biomass such that carbon available upon rewetting is sufficient to support exponential growth (leading to Type 2 response). However, this is yet to be tested in intact ecosystems. We investigated the legacy of drought on microbial responses to drying and rewetting using grassland soils from a natural precipitation gradient in Texas. Mean annual precipitation spanned a 500 mm range (400-900 mm year-1) across the 400 km gradient, while mean annual temperature was constant. Soil properties (pH, SOM) did not vary systematically across the gradient, with differences reflecting land-use history rather than rainfall. Air dried soils from 18 sites were rewetted to 50 % water holding capacity with bacterial growth, fungal growth and respiration measured at high temporal resolution over 7 days. We predicted that there would be a shift in the type of response to rewetting (Type 1 to Type 2) across the gradient, as a consequence of exposure to harsher drying. Further, given the lack of systematic variation in other factors with rainfall, we expected levels of maximal growth and respiration as well as the level of steady state growth and respiration to be similar across the gradient. All soils exhibited a Type 1 response, with respiration, bacterial and fungal growth increasing immediately upon rewetting and typically stabilising after c. 20 hours. There were, however, differences in the magnitude of CO2 release and microbial growth among soils, whereby rewetting of historically wetter soils stimulated higher rates of microbial growth and a greater release of CO2, compared to rewetting of historically drier soils. Contrary to expectations, there was no difference in the type of microbial response to rewetting, but instead a systematic dependence of overall microbial rates, depending on the legacy of drought. This contrasted with previous laboratory studies, suggesting that exposure to drought across the natural gradient was not perceived as 'harsh' by the microbial communities. This may be explained by either (i) differences in resource availability (i.e. plant input) mitigating the microbial susceptibility to drought in intact ecosystems or (ii) microbial tolerance to drought.

Teaching Microbial Growth by Simulation.

ERIC Educational Resources Information Center

Ruiz, A. Fernandez; And Others

1989-01-01

Presented is a simulation program for Apple II computer which assays the effects of a series of variables on bacterial growth and interactions between microbial populations. Results of evaluation of the program with students are summarized. (CW)

Modeling the impact of the indigenous microbial population on the maximum population density of Salmonella on alfalfa.

PubMed

Rijgersberg, Hajo; Franz, Eelco; Nierop Groot, Masja; Tromp, Seth-Oscar

2013-07-01

Within a microbial risk assessment framework, modeling the maximum population density (MPD) of a pathogenic microorganism is important but often not considered. This paper describes a model predicting the MPD of Salmonella on alfalfa as a function of the initial contamination level, the total count of the indigenous microbial population, the maximum pathogen growth rate and the maximum population density of the indigenous microbial population. The model is parameterized by experimental data describing growth of Salmonella on sprouting alfalfa seeds at inoculum size, native microbial load and Pseudomonas fluorescens 2-79. The obtained model fits well to the experimental data, with standard errors less than ten percent of the fitted average values. The results show that the MPD of Salmonella is not only dictated by performance characteristics of Salmonella but depends on the characteristics of the indigenous microbial population like total number of cells and its growth rate. The model can improve the predictions of microbiological growth in quantitative microbial risk assessments. Using this model, the effects of preventive measures to reduce pathogenic load and a concurrent effect on the background population can be better evaluated. If competing microorganisms are more sensitive to a particular decontamination method, a pathogenic microorganism may grow faster and reach a higher level. More knowledge regarding the effect of the indigenous microbial population (size, diversity, composition) of food products on pathogen dynamics is needed in order to make adequate predictions of pathogen dynamics on various food products.

Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves.

PubMed

Sprouffske, Kathleen; Wagner, Andreas

2016-04-19

Plate readers can measure the growth curves of many microbial strains in a high-throughput fashion. The hundreds of absorbance readings collected simultaneously for hundreds of samples create technical hurdles for data analysis. Growthcurver summarizes the growth characteristics of microbial growth curve experiments conducted in a plate reader. The data are fitted to a standard form of the logistic equation, and the parameters have clear interpretations on population-level characteristics, like doubling time, carrying capacity, and growth rate. Growthcurver is an easy-to-use R package available for installation from the Comprehensive R Archive Network (CRAN). The source code is available under the GNU General Public License and can be obtained from Github (Sprouffske K, Growthcurver sourcecode, 2016).

Microbial Ecology Assessment of Mixed Copper Oxide/Sulfide Dump Leach Operation

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

Bruhn, D F; Thompson, D N; Noah, K S

1999-06-01

Microbial consortia composed of complex mixtures of autotrophic and heterotrophic bacteria are responsible for the dissolution of metals from sulfide minerals. Thus, an efficient copper bioleaching operation depends on the microbial ecology of the system. A microbial ecology study of a mixed oxide/sulfide copper leaching operation was conducted using an "overlay" plating technique to differentiate and identify various bacterial consortium members of the genera Thiobacillus, Leptospirillum, Ferromicrobium, and Acidiphilium. Two temperatures (30C and 45C) were used to select for mesophilic and moderately thermophilic bacteria. Cell numbers varied from 0-106 cells/g dry ore, depending on the sample location and depth. Aftermore » acid curing for oxide leaching, no viable bacteria were recovered, although inoculation of cells from raffinate re-established a microbial population after three months. Due to the low pH of the operation, very few non-iron-oxidizing acidophilic heterotrophs were recovered. Moderate thermophiles were isolated from the ore samples. Pregnant liquor solutions (PLS) and raffinate both contained a diversity of bacteria. In addition, an intermittently applied waste stream that contained high levels of arsenic and fluoride was tested for toxicity. Twenty vol% waste stream in PLS killed 100% of the cells in 48 hours, indicating substantial toxicity and/or growth inhibition. The data indicate that bacteria populations can recover after acid curing, and that application of the waste stream to the dump should be avoided. Monitoring the microbial ecology of the leaching operation provided significant information that improved copper recovery.« less

[Mechanisms for the increased fertilizer nitrogen use efficiency of rice in wheat-rice rotation system under combined application of inorganic and organic fertilizers].

PubMed

Liu, Yi-Ren; Li, Xiang; Yu, Jie; Shen, Qi-Rong; Xu, Yang-Chun

2012-01-01

A pot experiment was conducted to study the effects of combined application of organic and inorganic fertilizers on the nitrogen uptake by rice and the nitrogen supply by soil in a wheat-rice rotation system, and approach the mechanisms for the increased fertilizer nitrogen use efficiency of rice under the combined fertilization from the viewpoint of microbiology. Comparing with applying inorganic fertilizers, combined application of organic and inorganic fertilizers decreased the soil microbial biomass carbon and nitrogen and soil mineral nitrogen contents before tillering stage, but increased them significantly from heading to filling stage. Under the combined fertilization, the dynamics of soil nitrogen supply matched best the dynamics of rice nitrogen uptake and utilization, which promoted the nitrogen accumulation in rice plant and the increase of rice yield and biomass, and increased the fertilizer nitrogen use efficiency of rice significantly. Combined application of inorganic and organic fertilizers also promoted the propagation of soil microbes, and consequently, more mineral nitrogen in soil was immobilized by the microbes at rice early growth stage, and the immobilized nitrogen was gradually released at the mid and late growth stages of rice, being able to better satisfy the nitrogen demand of rice in its various growth and development stages.

BioMig--A Method to Evaluate the Potential Release of Compounds from and the Formation of Biofilms on Polymeric Materials in Contact with Drinking Water.

PubMed

Wen, Gang; Kötzsch, Stefan; Vital, Marius; Egli, Thomas; Ma, Jun

2015-10-06

In contact with water, polymeric materials (plastics) release compounds that can support suspended microbial growth and/or biofilm formation. The different methods presently used in the European Union to test plastics take 7-16 weeks to obtain a result. In industry, this delays material and product development as well as quality testing. Therefore, we developed a method package (BioMig) that allows testing of plastic materials with high reproducibility in 2 weeks for their potential biofilm (or biomass) formation and release of carbonaceous migration products when in contact with water. BioMig consists of (i) an extended migration potential test (seven times for 24 h at 60 °C), based on the European norm EN 12873-1 and the German UBA (Umweltbundesamt) guideline, and (ii) a biomass formation potential (BFP) test (14 days at 30 °C), which is a modified version of the Dutch biofilm production potential test. In the migration potential test, the amount of carbon released into water by the specimen is quantified by monitoring total and assimilable organic carbon over time; furthermore, the modular design of the test also allows one to assess additional parameters such as pathogen growth potential on the migration water or toxic effects on microbial growth. Flow cytometry (FCM)-based total cell counting (TCC) is used to quantify microbial growth in suspension and on surfaces after removal with mild sonication without affecting cell integrity. The BFP test allows one to determine both the planktonic (pBFP) and the sessile (sBFP) cell fractions. The sBFP consists of surface-attached cells after removal (>90% efficiency). Results for four standard test materials (PE-Xa, PE-Xc, EPDM 2%, and EPDM 20%), plus positive (PVC-P) and negative (glass) controls are presented. FCM-based TCC demonstrates that the release of growth-supporting carbon and proliferation of surface-attached cells stops increasing and stabilizes after 14 days of incubation; this allows for faster assessment of growth-supporting properties of plastics with BioMig compared to established tests.

An Economic Framework of Microbial Trade

PubMed Central

Mee, Michael T.

2015-01-01

A large fraction of microbial life on earth exists in complex communities where metabolic exchange is vital. Microbes trade essential resources to promote their own growth in an analogous way to countries that exchange goods in modern economic markets. Inspired by these similarities, we developed a framework based on general equilibrium theory (GET) from economics to predict the population dynamics of trading microbial communities. Our biotic GET (BGET) model provides an a priori theory of the growth benefits of microbial trade, yielding several novel insights relevant to understanding microbial ecology and engineering synthetic communities. We find that the economic concept of comparative advantage is a necessary condition for mutualistic trade. Our model suggests that microbial communities can grow faster when species are unable to produce essential resources that are obtained through trade, thereby promoting metabolic specialization and increased intercellular exchange. Furthermore, we find that species engaged in trade exhibit a fundamental tradeoff between growth rate and relative population abundance, and that different environments that put greater pressure on group selection versus individual selection will promote varying strategies along this growth-abundance spectrum. We experimentally tested this tradeoff using a synthetic consortium of Escherichia coli cells and found the results match the predictions of the model. This framework provides a foundation to study natural and engineered microbial communities through a new lens based on economic theories developed over the past century. PMID:26222307

Estimating phosphorus availability for microbial growth in an emerging landscape

USGS Publications Warehouse

Schmidt, S.K.; Cleveland, C.C.; Nemergut, D.R.; Reed, S.C.; King, A.J.; Sowell, P.

2011-01-01

Estimating phosphorus (P) availability is difficult—particularly in infertile soils such as those exposed after glacial recession—because standard P extraction methods may not mimic biological acquisition pathways. We developed an approach, based on microbial CO2 production kinetics and conserved carbon:phosphorus (C:P) ratios, to estimate the amount of P available for microbial growth in soils and compared this method to traditional, operationally-defined indicators of P availability. Along a primary succession gradient in the High Andes of Perú, P additions stimulated the growth-related (logistic) kinetics of glutamate mineralization in soils that had been deglaciated from 0 to 5 years suggesting that microbial growth was limited by soil P availability. We then used a logistic model to estimate the amount of C incorporated into biomass in P-limited soils, allowing us to estimate total microbial P uptake based on a conservative C:P ratio of 28:1 (mass:mass). Using this approach, we estimated that there was < 1 μg/g of microbial-available P in recently de-glaciated soils in both years of this study. These estimates fell well below estimates of available soil P obtained using traditional extraction procedures. Our results give both theoretical and practical insights into the kinetics of C and P utilization in young soils, as well as show changes in microbial P availability during early stages of soil development.

Biochar increases plant growth and alters microbial communities via regulating the moisture and temperature of green roof substrates.

PubMed

Chen, Haoming; Ma, Jinyi; Wei, Jiaxing; Gong, Xin; Yu, Xichen; Guo, Hui; Zhao, Yanwen

2018-09-01

Green roofs have increasingly been designed and applied to relieve environmental problems, such as water loss, air pollution as well as heat island effect. Substrate and vegetation are important components of green roofs providing ecosystem services and benefiting the urban development. Biochar made from sewage sludge could be potentially used as the substrate amendment for green roofs, however, the effects of biochar on substrate quality and plant performance in green roofs are still unclear. We evaluated the effects of adding sludge biochar (0, 5, 10, 15 and 20%, v/v) to natural soil planted with three types of plant species (ryegrass, Sedum lineare and cucumber) on soil properties, plant growth and microbial communities in both green roof and ground ecosystems. Our results showed that sludge biochar addition significantly increased substrate moisture, adjusted substrate temperature, altered microbial community structure and increased plant growth. The application rate of 10-15% sludge biochar on the green roof exerted the most significant effects on both microbial and plant biomass by 63.9-89.6% and 54.0-54.2% respectively. Path analysis showed that biochar addition had a strong effect on microbial biomass via changing the soil air-filled porosity, soil moisture and temperature, and promoted plant growth through the positive effects on microbial biomass. These results suggest that the applications of biochar at an appropriate rate can significantly alter plant growth and microbial community structure, and increase the ecological benefits of green roofs via exerting effects on the moisture, temperature and nutrients of roof substrates. Copyright © 2018 Elsevier B.V. All rights reserved.

Physiological and Transcriptional Responses of Different Industrial Microbes at Near-Zero Specific Growth Rates.

PubMed

Ercan, Onur; Bisschops, Markus M M; Overkamp, Wout; Jørgensen, Thomas R; Ram, Arthur F; Smid, Eddy J; Pronk, Jack T; Kuipers, Oscar P; Daran-Lapujade, Pascale; Kleerebezem, Michiel

2015-09-01

The current knowledge of the physiology and gene expression of industrially relevant microorganisms is largely based on laboratory studies under conditions of rapid growth and high metabolic activity. However, in natural ecosystems and industrial processes, microbes frequently encounter severe calorie restriction. As a consequence, microbial growth rates in such settings can be extremely slow and even approach zero. Furthermore, uncoupling microbial growth from product formation, while cellular integrity and activity are maintained, offers perspectives that are economically highly interesting. Retentostat cultures have been employed to investigate microbial physiology at (near-)zero growth rates. This minireview compares information from recent physiological and gene expression studies on retentostat cultures of the industrially relevant microorganisms Lactobacillus plantarum, Lactococcus lactis, Bacillus subtilis, Saccharomyces cerevisiae, and Aspergillus niger. Shared responses of these organisms to (near-)zero growth rates include increased stress tolerance and a downregulation of genes involved in protein synthesis. Other adaptations, such as changes in morphology and (secondary) metabolite production, were species specific. This comparison underlines the industrial and scientific significance of further research on microbial (near-)zero growth physiology. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Coupling plant growth and waste recycling systems in a controlled life support system (CELSS)

NASA Technical Reports Server (NTRS)

Garland, Jay L.

1992-01-01

The development of bioregenerative systems as part of the Controlled Ecological Life Support System (CELSS) program depends, in large part, on the ability to recycle inorganic nutrients, contained in waste material, into plant growth systems. One significant waste (resource) stream is inedible plant material. This research compared wheat growth in hydroponic solutions based on inorganic salts (modified Hoagland's) with solutions based on the soluble fraction of inedible wheat biomass (leachate). Recycled nutrients in leachate solutions provided the majority of mineral nutrients for plant growth, although additions of inorganic nutrients to leachate solutions were necessary. Results indicate that plant growth and waste recyling systems can be effectively coupled within CELSS based on equivalent wheat yield in leachate and Hoagland solutions, and the rapid mineralization of waste organic material in the hydroponic systems. Selective enrichment for microbial communities able to mineralize organic material within the leachate was necessary to prevent accumulation of dissolved organic matter in leachate-based solutions. Extensive analysis of microbial abundance, growth, and activity in the hydroponic systems indicated that addition of soluble organic material from plants does not cause excessive microbial growth or 'biofouling', and helped define the microbially-mediated flux of carbon in hydroponic solutions.

Mechanistic modelling of the inhibitory effect of pH on microbial growth.

PubMed

Akkermans, Simen; Van Impe, Jan F

2018-06-01

Modelling and simulation of microbial dynamics as a function of processing, transportation and storage conditions is a useful tool to improve microbial food safety and quality. The goal of this research is to improve an existing methodology for building mechanistic predictive models based on the environmental conditions. The effect of environmental conditions on microbial dynamics is often described by combining the separate effects in a multiplicative way (gamma concept). This idea was extended further in this work by including the effects of the lag and stationary growth phases on microbial growth rate as independent gamma factors. A mechanistic description of the stationary phase as a function of pH was included, based on a novel class of models that consider product inhibition. Experimental results on Escherichia coli growth dynamics indicated that also the parameters of the product inhibition equations can be modelled with the gamma approach. This work has extended a modelling methodology, resulting in predictive models that are (i) mechanistically inspired, (ii) easily identifiable with a limited work load and (iii) easily extended to additional environmental conditions. Copyright © 2017. Published by Elsevier Ltd.

Division of Energy Biosciences annual report and summaries of FY 1996 activities

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

NONE

1997-04-01

The mission of the Division of Energy Biosciences is to support research that advances the fundamental knowledge necessary for the future development of biotechnologies related to the Department of Energy`s mission. The departmental civilian objectives include effective and efficient energy production, energy conservation, environmental restoration, and waste management. The Energy Biosciences program emphasizes research in the microbiological and plant sciences, as these understudied areas offer numerous scientific opportunities to dramatically influence environmentally sensible energy production and conservation. The research supported is focused on the basic mechanism affecting plant productivity, conversion of biomass and other organic materials into fuels and chemicalsmore » by microbial systems, and the ability of biological systems to replace energy-intensive or pollutant-producing processes. The Division also addresses the increasing number of new opportunities arising at the interface of biology with other basic energy-related sciences such as biosynthesis of novel materials and the influence of soil organisms on geological processes. This report gives summaries on 225 projects on photosynthesis, membrane or ion transport, plant metabolism and biosynthesis, carbohydrate metabolism lipid metabolism, plant growth and development, plant genetic regulation and genetic mechanisms, plant cell wall development, lignin-polysaccharide breakdown, nitrogen fixation and plant-microbial symbiosis, mechanism for plant adaptation, fermentative microbial metabolism, one and two carbon microbial metabolism, extremophilic microbes, microbial respiration, nutrition and metal metabolism, and materials biosynthesis.« less

Field studies on two rock phosphate solubilizing actinomycete isolates as biofertilizer sources

NASA Astrophysics Data System (ADS)

Mba, Caroline C.

1994-03-01

Recently biotechnology is focusing attention on utilization of biological resources to solve a number of environmental problems such as soil fertility management. Results of microbial studies on earthworm compost in the University of Nigeria farm identified a number of rock phosphate solubilizing actinomycetes. Two of these, isclates 02 and 13, were found to be efficient rock phosphate (RP) solubilizers and fast-growing cellulolytic microbes producing extracellular hydrolase enzymes. In this preliminary field study the two microbial isolates were investigated with respect to their effects on the growth of soybean and egusi as well as their effect on the incidence of toxicity of poultry droppings. Application of these isolates in poultry manure-treated field plots, as microbial fertilizers, brought about yield increases of 43% and 17% with soybeans and 19% and 33% with egusi, respectively. Soil properties were also improved. With isolates 02 and 13, the soil available phosphorus increased at the five-leaf stage, while N-fixation in the soil increased by 45% or 11% relative to control. It was further observed that air-dried poultry manure after four days of incubation was still toxic to soybean. The toxic effect of the applied poultry manure was reduced or eliminated with microbial fertilizers 02 or 13, respectively. The beneficial effects of the microbial organic fertilizer are discussed. Justification for more intensive research on rock phosphate organic fertilizer is highlighted.

Nanoscale zero-valent iron/persulfate enhanced upflow anaerobic sludge blanket reactor for dye removal: Insight into microbial metabolism and microbial community

PubMed Central

Pan, Fei; Zhong, Xiaohan; Xia, Dongsheng; Yin, Xianze; Li, Fan; Zhao, Dongye; Ji, Haodong; Liu, Wen

2017-01-01

This study investigated the efficiency of nanoscale zero-valent iron combined with persulfate (NZVI/PS) for enhanced degradation of brilliant red X-3B in an upflow anaerobic sludge blanket (UASB) reactor, and examined the effects of NZVI/PS on anaerobic microbial communities during the treatment process. The addition of NZVI (0.5 g/L) greatly enhanced the decolourization rate of X-3B from 63.8% to 98.4%. The Biolog EcoPlateTM technique was utilized to examine microbial metabolism in the reactor, and the Illumina MiSeq high-throughput sequencing revealed 22 phyla and 88 genera of the bacteria. The largest genera (Lactococcus) decreased from 33.03% to 7.94%, while the Akkermansia genera increased from 1.69% to 20.23% according to the abundance in the presence of 0.2 g/L NZVI during the biological treatment process. Meanwhile, three strains were isolated from the sludge in the UASB reactors and identified by 16 S rRNA analysis. The distribution of three strains was consistent with the results from the Illumina MiSeq high throughput sequencing. The X-ray photoelectron spectroscopy results indicated that Fe(0) was transformed into Fe(II)/Fe(III) during the treatment process, which are beneficial for the microorganism growth, and thus promoting their metabolic processes and microbial community. PMID:28300176

Microbes in the upper atmosphere and unique opportunities for astrobiology research.

PubMed

Smith, David J

2013-10-01

Microbial taxa from every major biological lineage have been detected in Earth's upper atmosphere. The goal of this review is to communicate (1) relevant astrobiology questions that can be addressed with upper atmosphere microbiology studies and (2) available sampling methods for collecting microbes at extreme altitudes. Precipitation, mountain stations, airplanes, balloons, rockets, and satellites are all feasible routes for conducting aerobiology research. However, more efficient air samplers are needed, and contamination is also a pervasive problem in the field. Measuring microbial signatures without false positives in the upper atmosphere might contribute to sterilization and bioburden reduction methods for proposed astrobiology missions. Intriguingly, environmental conditions in the upper atmosphere resemble the surface conditions of Mars (extreme cold, hypobaria, desiccation, and irradiation). Whether terrestrial microbes are active in the upper atmosphere is an area of intense research interest. If, in fact, microbial metabolism, growth, or replication is achievable independent of Earth's surface, then the search for habitable zones on other worlds should be broadened to include atmospheres (e.g., the high-altitude clouds of Venus). Furthermore, viable cells in the heavily irradiated upper atmosphere of Earth could help identify microbial genes or enzymes that bestow radiation resistance. Compelling astrobiology questions on the origin of life (if the atmosphere synthesized organic aerosols), evolution (if airborne transport influenced microbial mutation rates and speciation), and panspermia (outbound or inbound) are also testable in Earth's upper atmosphere.

Nanoscale zero-valent iron/persulfate enhanced upflow anaerobic sludge blanket reactor for dye removal: Insight into microbial metabolism and microbial community

NASA Astrophysics Data System (ADS)

Pan, Fei; Zhong, Xiaohan; Xia, Dongsheng; Yin, Xianze; Li, Fan; Zhao, Dongye; Ji, Haodong; Liu, Wen

2017-03-01

This study investigated the efficiency of nanoscale zero-valent iron combined with persulfate (NZVI/PS) for enhanced degradation of brilliant red X-3B in an upflow anaerobic sludge blanket (UASB) reactor, and examined the effects of NZVI/PS on anaerobic microbial communities during the treatment process. The addition of NZVI (0.5 g/L) greatly enhanced the decolourization rate of X-3B from 63.8% to 98.4%. The Biolog EcoPlateTM technique was utilized to examine microbial metabolism in the reactor, and the Illumina MiSeq high-throughput sequencing revealed 22 phyla and 88 genera of the bacteria. The largest genera (Lactococcus) decreased from 33.03% to 7.94%, while the Akkermansia genera increased from 1.69% to 20.23% according to the abundance in the presence of 0.2 g/L NZVI during the biological treatment process. Meanwhile, three strains were isolated from the sludge in the UASB reactors and identified by 16 S rRNA analysis. The distribution of three strains was consistent with the results from the Illumina MiSeq high throughput sequencing. The X-ray photoelectron spectroscopy results indicated that Fe(0) was transformed into Fe(II)/Fe(III) during the treatment process, which are beneficial for the microorganism growth, and thus promoting their metabolic processes and microbial community.

Effect of temperature on microbial growth rate-mathematical analysis: the Arrhenius and Eyring-Polanyi connections.

PubMed

Huang, Lihan; Hwang, Andy; Phillips, John

2011-10-01

The objective of this work is to develop a mathematical model for evaluating the effect of temperature on the rate of microbial growth. The new mathematical model is derived by combination and modification of the Arrhenius equation and the Eyring-Polanyi transition theory. The new model, suitable for both suboptimal and the entire growth temperature ranges, was validated using a collection of 23 selected temperature-growth rate curves belonging to 5 groups of microorganisms, including Pseudomonas spp., Listeria monocytogenes, Salmonella spp., Clostridium perfringens, and Escherichia coli, from the published literature. The curve fitting is accomplished by nonlinear regression using the Levenberg-Marquardt algorithm. The resulting estimated growth rate (μ) values are highly correlated to the data collected from the literature (R(2) = 0.985, slope = 1.0, intercept = 0.0). The bias factor (B(f) ) of the new model is very close to 1.0, while the accuracy factor (A(f) ) ranges from 1.0 to 1.22 for most data sets. The new model is compared favorably with the Ratkowsky square root model and the Eyring equation. Even with more parameters, the Akaike information criterion, Bayesian information criterion, and mean square errors of the new model are not statistically different from the square root model and the Eyring equation, suggesting that the model can be used to describe the inherent relationship between temperature and microbial growth rates. The results of this work show that the new growth rate model is suitable for describing the effect of temperature on microbial growth rate. Practical Application:  Temperature is one of the most significant factors affecting the growth of microorganisms in foods. This study attempts to develop and validate a mathematical model to describe the temperature dependence of microbial growth rate. The findings show that the new model is accurate and can be used to describe the effect of temperature on microbial growth rate in foods. Journal of Food Science © 2011 Institute of Food Technologists® No claim to original US government works.

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.

A quasi-chemical model for the growth and death of microorganisms in foods by non-thermal and high-pressure processing.

PubMed

Doona, Christopher J; Feeherry, Florence E; Ross, Edward W

2005-04-15

Predictive microbial models generally rely on the growth of bacteria in laboratory broth to approximate the microbial growth kinetics expected to take place in actual foods under identical environmental conditions. Sigmoidal functions such as the Gompertz or logistics equation accurately model the typical microbial growth curve from the lag to the stationary phase and provide the mathematical basis for estimating parameters such as the maximum growth rate (MGR). Stationary phase data can begin to show a decline and make it difficult to discern which data to include in the analysis of the growth curve, a factor that influences the calculated values of the growth parameters. In contradistinction, the quasi-chemical kinetics model provides additional capabilities in microbial modelling and fits growth-death kinetics (all four phases of the microbial lifecycle continuously) for a general set of microorganisms in a variety of actual food substrates. The quasi-chemical model is differential equations (ODEs) that derives from a hypothetical four-step chemical mechanism involving an antagonistic metabolite (quorum sensing) and successfully fits the kinetics of pathogens (Staphylococcus aureus, Escherichia coli and Listeria monocytogenes) in various foods (bread, turkey meat, ham and cheese) as functions of different hurdles (a(w), pH, temperature and anti-microbial lactate). The calculated value of the MGR depends on whether growth-death data or only growth data are used in the fitting procedure. The quasi-chemical kinetics model is also exploited for use with the novel food processing technology of high-pressure processing. The high-pressure inactivation kinetics of E. coli are explored in a model food system over the pressure (P) range of 207-345 MPa (30,000-50,000 psi) and the temperature (T) range of 30-50 degrees C. In relatively low combinations of P and T, the inactivation curves are non-linear and exhibit a shoulder prior to a more rapid rate of microbial destruction. In the higher P, T regime, the inactivation plots tend to be linear. In all cases, the quasi-chemical model successfully fit the linear and curvi-linear inactivation plots for E. coli in model food systems. The experimental data and the quasi-chemical mathematical model described herein are candidates for inclusion in ComBase, the developing database that combines data and models from the USDA Pathogen Modeling Program and the UK Food MicroModel.

Analysis of a novel class of predictive microbial growth models and application to coculture growth.

PubMed

Poschet, F; Vereecken, K M; Geeraerd, A H; Nicolaï, B M; Van Impe, J F

2005-04-15

In this paper, a novel class of microbial growth models is analysed. In contrast with the currently used logistic type models (e.g., the model of Baranyi and Roberts [Baranyi, J., Roberts, T.A., 1994. A dynamic approach to predicting bacterial growth in food. International Journal of Food Microbiology 23, 277-294]), the novel model class, presented in Van Impe et al. (Van Impe, J.F., Poschet, F., Geeraerd, A.H., Vereecken, K.M., 2004. Towards a novel class of predictive microbial growth models. International Journal of Food Microbiology, this issue), explicitly incorporates nutrient exhaustion and/or metabolic waste product effects inducing stationary phase behaviour. As such, these novel model types can be extended in a natural way towards microbial interactions in cocultures and microbial growth in structured foods. Two illustrative case studies of the novel model types are thoroughly analysed and compared to the widely used model of Baranyi and Roberts. In a first case study, the stationary phase is assumed to be solely resulting from toxic product inhibition and is described as a function of the pH-evolution. In the second case study, substrate exhaustion is the sole cause of the stationary phase. Finally, a more complex case study of a so-called P-model is presented, dealing with a coculture inhibition of Listeria innocua mediated by lactic acid production of Lactococcus lactis.

Microbial enhanced heavy crude oil recovery through biodegradation using bacterial isolates from an Omani oil field.

PubMed

Al-Sayegh, Abdullah; Al-Wahaibi, Yahya; Al-Bahry, Saif; Elshafie, Abdulkadir; Al-Bemani, Ali; Joshi, Sanket

2015-09-16

Biodegradation is a cheap and environmentally friendly process that could breakdown and utilizes heavy crude oil (HCO) resources. Numerous bacteria are able to grow using hydrocarbons as a carbon source; however, bacteria that are able to grow using HCO hydrocarbons are limited. In this study, HCO degrading bacteria were isolated from an Omani heavy crude oil field. They were then identified and assessed for their biodegradation and biotransformation abilities under aerobic and anaerobic conditions. Bacteria were grown in five different minimum salts media. The isolates were identified by MALDI biotyper and 16S rRNA sequencing. The nucleotide sequences were submitted to GenBank (NCBI) database. The bacteria were identified as Bacillus subtilis and B. licheniformis. To assess microbial growth and biodegradation of HCO by well-assay on agar plates, samples were collected at different intervals. The HCO biodegradation and biotransformation were determined using GC-FID, which showed direct correlation of microbial growth with an increased biotransformation of light hydrocarbons (C12 and C14). Among the isolates, B. licheniformis AS5 was the most efficient isolate in biodegradation and biotransformation of the HCO. Therefore, isolate AS5 was used for heavy crude oil recovery experiments, in core flooding experiments using Berea core plugs, where an additional 16 % of oil initially in place was recovered. This is the first report from Oman for bacteria isolated from an oil field that were able to degrade and transform HCO to lighter components, illustrating the potential use in HCO recovery. The data suggested that biodegradation and biotransformation processes may lead to additional oil recovery from heavy oil fields, if bacteria are grown in suitable medium under optimum growth conditions.

Spatial variation in edaphic characteristics is a stronger control than nitrogen inputs in regulating soil microbial effects on a desert grass

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

Chung, Y. Anny; Sinsabaugh, Robert L.; Kuske, Cheryl Rae

Increased atmospheric nitrogen (N) deposition can have wide-ranging effects on plant community structure and ecosystem function, some of which may be indirectly mediated by soil microbial responses to an altered biogeochemical environment. In this study, soils from a field N fertilization experiment that spanned a soil texture gradient were used as inocula in the greenhouse to assess the indirect effects of soil microbial communities on growth of a desert grass. Plant performance and interaction with soil microbiota were evaluated via plant above- and belowground biomass, leaf N concentration, and root fungal colonization. Nitrogen fertilization in the field increased the benefitsmore » of soil microbial inoculation to plant leaf N concentration, but did not alter the effect of soil microbes on plant growth. Plant-microbe interaction outcomes differed most strongly among sites with different soil textures, where the soil microbial community from the sandiest site was most beneficial to host plant growth. In conclusion, the findings of this study suggest that in a desert grassland, increases in atmospheric N deposition may exert a more subtle influence on plant-microbe interactions by altering plant nutrient status, whereas edaphic factors can alter the whole-plant growth response to soil microbial associates.« less

The effect of dosages of microbial consortia formulation and synthetic fertilizer on the growth and yield of field-grown chili

NASA Astrophysics Data System (ADS)

Istifadah, N.; Sapta, D.; Krestini, H.; Natalie, B.; Suryatmana, P.; Nurbaity, A.; Hidersah, R.

2018-03-01

Chili (Capsicum annuum, L) is one of important horticultural crop in Indonesia. Formulation of microbial consortia containing Bacillus subtilis, Pseudomonas sp., Azotobacter chroococcum and Trichoderma harzianum has been developed. This study evaluated the effects of dosage of the microbial formulation combined with NPK fertilizer on growth and yield of chili plants in the field experiment. The experiment was arranged in completely randomized design of factorial, in which the first factor was dosage of formulation (0, 2.5, 5.0, 7.5, 10 g per plant) and the second factor was NPK fertilizer dosage (0, 25, 50 and 75% of the standard dosage). The treatments were replicated three times. For application, the formulation was mixed with chicken manure 1:10 (w/v). The results showed that application of microbial formulation solely improved the chili growth. There was interaction between dosages of the microbial formulation and NPK fertilizer in improving plant height, nitrogen availability and the chili yield, while there was no interaction between those dosages in improving the root length. Combination between microbial formulation at the dosage of 5.0-7.5 g per plant combined with NPK fertilizer with the dosage 50 or 75% of the standard dosage support relatively better growth and the chili yield.

Spatial variation in edaphic characteristics is a stronger control than nitrogen inputs in regulating soil microbial effects on a desert grass

DOE PAGES

Chung, Y. Anny; Sinsabaugh, Robert L.; Kuske, Cheryl Rae; ...

2017-03-22

Increased atmospheric nitrogen (N) deposition can have wide-ranging effects on plant community structure and ecosystem function, some of which may be indirectly mediated by soil microbial responses to an altered biogeochemical environment. In this study, soils from a field N fertilization experiment that spanned a soil texture gradient were used as inocula in the greenhouse to assess the indirect effects of soil microbial communities on growth of a desert grass. Plant performance and interaction with soil microbiota were evaluated via plant above- and belowground biomass, leaf N concentration, and root fungal colonization. Nitrogen fertilization in the field increased the benefitsmore » of soil microbial inoculation to plant leaf N concentration, but did not alter the effect of soil microbes on plant growth. Plant-microbe interaction outcomes differed most strongly among sites with different soil textures, where the soil microbial community from the sandiest site was most beneficial to host plant growth. In conclusion, the findings of this study suggest that in a desert grassland, increases in atmospheric N deposition may exert a more subtle influence on plant-microbe interactions by altering plant nutrient status, whereas edaphic factors can alter the whole-plant growth response to soil microbial associates.« less

Spatial variation in edaphic characteristics is a stronger control than nitrogen inputs in regulating soil microbial effects on a desert grass

USGS Publications Warehouse

Chung, Y. Anny; Sinsabaugh, Robert L; Kuske, Cheryl R.; Reed, Sasha C.; Rudgers, Jennifer A.

2017-01-01

Increased atmospheric nitrogen (N) deposition can have wide-ranging effects on plant community structure and ecosystem function, some of which may be indirectly mediated by soil microbial responses to an altered biogeochemical environment. In this study, soils from a field N fertilization experiment that spanned a soil texture gradient were used as inocula in the greenhouse to assess the indirect effects of soil microbial communities on growth of a desert grass. Plant performance and interaction with soil microbiota were evaluated via plant above- and belowground biomass, leaf N concentration, and root fungal colonization. Nitrogen fertilization in the field increased the benefits of soil microbial inoculation to plant leaf N concentration, but did not alter the effect of soil microbes on plant growth. Plant-microbe interaction outcomes differed most strongly among sites with different soil textures, where the soil microbial community from the sandiest site was most beneficial to host plant growth. The findings of this study suggest that in a desert grassland, increases in atmospheric N deposition may exert a more subtle influence on plant-microbe interactions by altering plant nutrient status, whereas edaphic factors can alter the whole-plant growth response to soil microbial associates.

RESISTANCE OF MICROBIAL COMMUNITIES FROM ECUADOR ECOSYSTEMS TO REPRESENTATIVE TOXIC METALS - CrO4(2-), Co2+, Ni2+, Cu2+, Hg2+.

PubMed

Tashyrev, O B; Prekrasna, Ie P; Tashyreva, G O; Bielikova, O Iu

2015-01-01

Microbial communities of the Ecuadorian Andes and volcano Tungurahua were shown to be super resistant to representative toxic metals. Maximum permissible concentrations of toxic metals were 100 ppm of Hg2+, 500 ppm of Co2+ and Ni2+, 1000 and 1500 ppm of Cr(VI), 10000 and 20000 ppm of Cu2+. The effect of metal concentration increasing on the biomass growth, CO2 and H2 synthesis was investigated. Two types of response of microbial communities on the increasing of toxic metals concentrations were discovered. The first type of response is the catastrophic inhibition of microbial growth. The second type of response is the absence of microbial growth inhibition at certain metal concentration gradient. The succession of qualitative structure of Ecuadorian microbial communities was shown for the first time. Bacteria, yeasts and finally fungi consistently dominate in the microbial community at the Cu2+ concentration raising. Microorganisms resistant to ultra-high concentrations of toxic metals (e.g., 3000 ... 20000 ppm of Cu2+) were isolated from Ecuadorian ecosystems. These microorganisms are able to accumulate toxic metals.

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.

Mechanisms of microbial destabilization of soil C shifts over decades of warming

NASA Astrophysics Data System (ADS)

DeAngelis, K.; Pold, G.; Chowdhury, P. R.; Schnabel, J.; Grandy, S.; Melillo, J. M.

2017-12-01

Microbes are major actors in regulating the earth's biogeochemical cycles, with temperature-sensitive microbial tradeoffs improving ecosystem biogeochemical models. Meanwhile, the Earth's climate is changing, with decades of warming undercutting the ability of soil to store carbon. Our work explores trends of 26 years of experimental warming in temperate deciduous forest soils, which is associated with cycles of soil carbon degradation punctuated by periods of changes in soil microbial dynamics. Using a combination of biogeochemistry and molecular analytical methods, we explore the hypotheses that substrate availability, community structure, altered temperature sensitivity of microbial turnover-growth efficiency tradeoff, and microbial evolution are responsible for observations of accelerated degradation of soil carbon over time. Amplicon sequencing of microbial communities suggests a small role of changing microbial community composition over decades of warming, but a sustained suppression of fungal biomass is accompanied by increased biomass of Actinobacteria, Actinobacteria, Alphaproteobacteria, Verrucomicrobia and Planctomycetes. Substrate availability plays an important role in microbial dynamics, with depleted labile carbon in the first decade and depleted lignin in the second decade. Increased lignin-degrading enzyme activity supports the suggestion that lignin-like organic matter is an important substrate in chronically warmed soils. Metatranscriptomics data support the suggestion that increased turnover is associated with long-term warming, with metagenomic signals of increased carbohydrate-degrading enzymes in the organic horizon but decreased in the mineral soils. Finally, traits analysis of over 200 cultivated isolates of bacterial species from heated and control soils suggests an expanded ability for degradation of cellulose and hemicellulose but not chitin, supporting the hypothesis that long-term warming is exerting evolutionary pressure on microbial species. Together, these data suggest that after decades of warming both direct kinetic effects and indirect effects of altered substrate availability are affecting microbial ecology and evolution in ways that conspire to destabilize soil organic matter.

Growth of Aerobic Ripening Bacteria at the Cheese Surface Is Limited by the Availability of Iron

PubMed Central

Back, Alexandre; Irlinger, Françoise

2012-01-01

The microflora on the surface of smear-ripened cheeses is composed of various species of bacteria and yeasts that contribute to the production of the desired organoleptic properties. The objective of the present study was to show that iron availability is a limiting factor in the growth of typical aerobic ripening bacteria in cheese. For that purpose, we investigated the effect of iron or siderophore addition in model cheeses that were coinoculated with a yeast and a ripening bacterium. Both iron and the siderophore desferrioxamine B stimulated the growth of ripening bacteria belonging to the genera Arthrobacter, Corynebacterium, and Brevibacterium. The extent of stimulation was strain dependent, and generally, the effect of desferrioxamine B was greater than that of iron. Measurements of the expression of genes related to the metabolism of iron by Arthrobacter arilaitensis Re117 by real-time reverse transcription-PCR showed that these genes were transcribed during growth in cheese. The addition of desferrioxamine B increased the expression of two genes encoding iron-siderophore ABC transport binding proteins. The addition of iron decreased the expression of siderophore biosynthesis genes and of part of the genes encoding iron-siderophore ABC transport components. It was concluded that iron availability is a limiting factor in the growth of typical cheese surface bacteria. The selection of strains with efficient iron acquisition systems may be useful for the development of defined-strain surface cultures. Furthermore, the importance of iron metabolism in the microbial ecology of cheeses should be investigated since it may result in positive or negative microbial interactions. PMID:22367081

Decoupling production from growth by magnesium sulfate limitation boosts de novo limonene production.

PubMed

Willrodt, Christian; Hoschek, Anna; Bühler, Bruno; Schmid, Andreas; Julsing, Mattijs K

2016-06-01

The microbial production of isoprenoids has recently developed into a prime example for successful bottom-up synthetic biology or top-down systems biology strategies. Respective fermentation processes typically rely on growing recombinant microorganisms. However, the fermentative production of isoprenoids has to compete with cellular maintenance and growth for carbon and energy. Non-growing but metabolically active E. coli cells were evaluated in this study as alternative biocatalyst configurations to reduce energy and carbon loss towards biomass formation. The use of non-growing cells in an optimized fermentation medium resulted in more than fivefold increased specific limonene yields on cell dry weight and glucose, as compared to the traditional growing-cell-approach. Initially, the stability of the resting-cell activity was limited. This instability was overcome via the optimization of the minimal fermentation medium enabling high and stable limonene production rates for up to 8 h and a high specific yield of ≥50 mg limonene per gram cell dry weight. Omitting MgSO4 from the fermentation medium was very promising to prohibit growth and allow high productivities. Applying a MgSO4 -limitation also improved limonene formation by growing cells during non-exponential growth involving a reduced biomass yield on glucose and a fourfold increase in specific limonene yields on biomass as compared to non-limited cultures. The control of microbial growth via the medium composition was identified as a key but yet underrated strategy for efficient isoprenoid production. Biotechnol. Bioeng. 2016;113: 1305-1314. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

The role of microbial signals in plant growth and development

PubMed Central

Ortíz-Castro, Randy; Contreras-Cornejo, Hexon Angel; Macías-Rodríguez, Lourdes

2009-01-01

Plant growth and development involves a tight coordination of the spatial and temporal organization of cell division, cell expansion and cell differentiation. Orchestration of these events requires the exchange of signaling molecules between the root and shoot, which can be affected by both biotic and abiotic factors. The interactions that occur between plants and their associated microorganisms have long been of interest, as knowledge of these processes could lead to the development of novel agricultural applications. Plants produce a wide range of organic compounds including sugars, organic acids and vitamins, which can be used as nutrients or signals by microbial populations. On the other hand, microorganisms release phytohormones, small molecules or volatile compounds, which may act directly or indirectly to activate plant immunity or regulate plant growth and morphogenesis. In this review, we focus on recent developments in the identification of signals from free-living bacteria and fungi that interact with plants in a beneficial way. Evidence has accumulated indicating that classic plant signals such as auxins and cytokinins can be produced by microorganisms to efficiently colonize the root and modulate root system architecture. Other classes of signals, including N-acyl-L-homoserine lactones, which are used by bacteria for cell-to-cell communication, can be perceived by plants to modulate gene expression, metabolism and growth. Finally, we discuss the role played by volatile organic compounds released by certain plant growth-promoting rhizobacteria in plant immunity and developmental processes. The picture that emerges is one in which plants and microbes communicate themselves through transkingdom signaling systems involving classic and novel signals. PMID:19820333

Microbial transformation of citral by Penicillium sp..

PubMed

Esmaeili, Akbar; Tavassoli, Afsaneh

2010-01-01

Thymol is present in the essential oils from herbs and spices, such as thyme. It is produced by these plant species as a chemical defense against phytopathogenic microorganisms. Therefore, this compound has attracted great attention in food industry, i.e., it has been used as a natural preservative in foods such as cheese to prevent fungal growth. Previous studies concerning the biotransformation of nerol by Penicillium sp. and microbial transformation of citral by sporulated surface cultures method (SSCM) of Penicillium digitatum have been reported. The objective of this research was to study the pathway involved during biotransformation of citral by Penicillium sp. using two methods. The culture preparation was done using different microbial methods and incubation periods to obtain Penicillium for citral biotransformation. The biotransformation products were identified by gas chromatography (GC) and gas chromatography/mass spectroscopy (GC/MS). A comparison of the two methods showed that SSCM was more effective, its major products were thymol (21.5 %), geranial (18.6 %) and nerol (13.7 %). LM produced only one compound — thymol — with a low efficiency.

Graphene/Fe3 O4 Nanocomposites as Efficient Anodes to Boost the Lifetime and Current Output of Microbial Fuel Cells.

PubMed

Song, Rong-Bin; Zhao, Cui-E; Gai, Pan-Pan; Guo, Dan; Jiang, Li-Ping; Zhang, Qichun; Zhang, Jian-Rong; Zhu, Jun-Jie

2017-02-01

The enhancement of microbial activity and electrocatalysis through the design of new anode materials is essential to develop microbial fuel cells (MFCs) with longer lifetimes and higher output. In this research, a novel anode material, graphene/Fe 3 O 4 (G/Fe 3 O 4 ) composite, has been designed for Shewanella-inoculated MFCs. Because the Shewanella species could bind to Fe 3 O 4 with high affinity and their growth could be supported by Fe 3 O 4 , the bacterial cells attached quickly onto the anode surface and their long-term activity improved. As a result, MFCs with reduced startup time and improved stability were obtained. Additionally, the introduction of graphene not only provided a large surface area for bacterial attachment, but also offered high electrical conductivity to facilitate extracellular electron transfer (EET). The results showed that the current and power densities of a G/Fe 3 O 4 anode were much higher than those of each individual component as an anode. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ecological plasticity of Trichoderma fungi in leached chernozem

NASA Astrophysics Data System (ADS)

Svistova, I. D.; Senchakova, T. Yu.

2010-03-01

The autecological properties of Trichoderma fungi ecotypes isolated from the leached chernozem of the forest-steppe zone of the European part of Russia have been studied. We were the first who carried out the complex study of the synecological relations of micromycetes of such kinds in a system including the soil, microbial community, and plants, i.e., their relations with soil saprotrophic fungi, bacteria, actinomycetes, plants, and pathogenic fungi. It was shown that the ecological plasticity of the Trichoderma genus in the soil of this zone is determined by its growth rate, the optimum pH and temperature, the biosynthesis of extracellular hydrolytic enzymes, the biological action of mycotoxins, and the ability for parasitism. The efficiency of the introduction of Trichoderma species typical and atypical for the leached chernozem into this soil and their influence on the structure of the microbial community were evaluated. The T. pseudokoningii ecotype, which produces cellulolytic enzymes, is very promising for industrial biotechnology, and the T. harzianum ecotype can be used in soil biotechnology for the biocontrol of chernozem. The addition of a commercial trichodermin preparation into the chernozem damages the structure of its microbial community.

Biodegradable nanostructures with selective lysis of microbial membranes

NASA Astrophysics Data System (ADS)

Nederberg, Fredrik; Zhang, Ying; Tan, Jeremy P. K.; Xu, Kaijin; Wang, Huaying; Yang, Chuan; Gao, Shujun; Guo, Xin Dong; Fukushima, Kazuki; Li, Lanjuan; Hedrick, James L.; Yang, Yi-Yan

2011-05-01

Macromolecular antimicrobial agents such as cationic polymers and peptides have recently been under an increased level of scrutiny because they can combat multi-drug-resistant microbes. Most of these polymers are non-biodegradable and are designed to mimic the facially amphiphilic structure of peptides so that they may form a secondary structure on interaction with negatively charged microbial membranes. The resulting secondary structure can insert into and disintegrate the cell membrane after recruiting additional polymer molecules. Here, we report the first biodegradable and in vivo applicable antimicrobial polymer nanoparticles synthesized by metal-free organocatalytic ring-opening polymerization of functional cyclic carbonate. We demonstrate that the nanoparticles disrupt microbial walls/membranes selectively and efficiently, thus inhibiting the growth of Gram-positive bacteria, methicillin-resistant Staphylococcus aureus (MRSA) and fungi, without inducing significant haemolysis over a wide range of concentrations. These biodegradable nanoparticles, which can be synthesized in large quantities and at low cost, are promising as antimicrobial drugs, and can be used to treat various infectious diseases such as MRSA-associated infections, which are often linked with high mortality.

Use of an uncertainty analysis for genome-scale models as a prediction tool for microbial growth processes in subsurface environments.

PubMed

Klier, Christine

2012-03-06

The integration of genome-scale, constraint-based models of microbial cell function into simulations of contaminant transport and fate in complex groundwater systems is a promising approach to help characterize the metabolic activities of microorganisms in natural environments. In constraint-based modeling, the specific uptake flux rates of external metabolites are usually determined by Michaelis-Menten kinetic theory. However, extensive data sets based on experimentally measured values are not always available. In this study, a genome-scale model of Pseudomonas putida was used to study the key issue of uncertainty arising from the parametrization of the influx of two growth-limiting substrates: oxygen and toluene. The results showed that simulated growth rates are highly sensitive to substrate affinity constants and that uncertainties in specific substrate uptake rates have a significant influence on the variability of simulated microbial growth. Michaelis-Menten kinetic theory does not, therefore, seem to be appropriate for descriptions of substrate uptake processes in the genome-scale model of P. putida. Microbial growth rates of P. putida in subsurface environments can only be accurately predicted if the processes of complex substrate transport and microbial uptake regulation are sufficiently understood in natural environments and if data-driven uptake flux constraints can be applied.

Anaerobic Degradation of Phthalate Isomers by Methanogenic Consortia

PubMed Central

Kleerebezem, Robbert; Pol, Look W. Hulshoff; Lettinga, Gatze

1999-01-01

Three methanogenic enrichment cultures, grown on ortho-phthalate, iso-phthalate, or terephthalate were obtained from digested sewage sludge or methanogenic granular sludge. Cultures grown on one of the phthalate isomers were not capable of degrading the other phthalate isomers. All three cultures had the ability to degrade benzoate. Maximum specific growth rates (μSmax) and biomass yields (YXtotS) of the mixed cultures were determined by using both the phthalate isomers and benzoate as substrates. Comparable values for these parameters were found for all three cultures. Values for μSmax and YXtotS were higher for growth on benzoate compared to the phthalate isomers. Based on measured and estimated values for the microbial yield of the methanogens in the mixed culture, specific yields for the phthalate and benzoate fermenting organisms were calculated. A kinetic model, involving three microbial species, was developed to predict intermediate acetate and hydrogen accumulation and the final production of methane. Values for the ratio of the concentrations of methanogenic organisms, versus the phthalate isomer and benzoate fermenting organisms, and apparent half-saturation constants (KS) for the methanogens were calculated. By using this combination of measured and estimated parameter values, a reasonable description of intermediate accumulation and methane formation was obtained, with the initial concentration of phthalate fermenting organisms being the only variable. The energetic efficiency for growth of the fermenting organisms on the phthalate isomers was calculated to be significantly smaller than for growth on benzoate. PMID:10049876

Colonization strategy of the endophytic plant growth-promoting strains of Pseudomonas fluorescens and Klebsiella oxytoca on the seeds, seedlings and roots of the epiphytic orchid, Dendrobium nobile Lindl.

PubMed

Pavlova, A S; Leontieva, M R; Smirnova, T A; Kolomeitseva, G L; Netrusov, A I; Tsavkelova, E A

2017-04-29

Orchids form strong mycorrhizal associations, but their interactions with bacteria are poorly understood. We aimed to investigate the distribution of plant growth promoting rhizobacteria (PGPR) at different stages of orchid development and to study if there is any selective specificity in choosing PGPR partners. Colonization patterns of gfp-tagged Pseudomonas fluorescens and Klebsiella oxytoca were studied on roots, seeds, and seedlings of Dendrobium nobile. Endophytic rhizobacteria rapidly colonized velamen and core parenchyma entering through exodermis and the passage cells, whereas at the early stages, they stayed restricted to the surface and the outer layers of the protocorms and rhizoids. The highest amounts of auxin (indole-3-acetic acid) were produced by K. oxytoca and P. fluorescens in the nitrogen-limiting and NO 3 -containing media respectively. Bacterization of D. nobile seeds resulted in promotion of their in vitro germination. The plant showed no selective specificity to the tested strains. Klebsiella oxytoca demonstrated more intense colonization activity and more efficient growth promoting impact under tryptophan supplementation, while P. fluorescens revealed its growth-promoting capacity without tryptophan. Both strategies are regarded as complementary, improving adaptive potentials of the orchid when different microbial populations colonize the plant. This study enlarges our knowledge on orchid-microbial interactions, and provides new features on application of the nonorchid PGPR in orchid seed germination and conservation. © 2017 The Society for Applied Microbiology.

Microbial resource management of one-stage partial nitritation/anammox.

PubMed

Vlaeminck, S E; De Clippeleir, H; Verstraete, W

2012-05-01

About 30 full-scale partial nitritation/anammox plants are established, treating mostly sewage sludge reject water, landfill leachate or food processing digestate. Although two-stage and one-stage processes each have their advantages, the one-stage configuration is mostly applied, termed here as oxygen-limited autotrophic nitrification/denitrification (OLAND), and is the focus of this review. The OLAND application domain is gradually expanding, with technical-scale plants on source-separated domestic wastewater, pre-treated manure and sewage, and liquors from organic waste bioenergy plants. A 'microbial resource management' (MRM) OLAND framework was elaborated, showing how the OLAND engineer/operator (1: input) can design/steer the microbial community (2: biocatalyst) to obtain optimal functionality (3: output). In the physicochemical toolbox (1), design guidelines are provided, as well as advantages of different reactor technologies. Particularly the desirable aeration regime, feeding regime and shear forces are not clear yet. The development of OLAND trickling filters, membrane bioreactors and systems with immobilized biomass is awaited. The biocatalyst box (2) considers 'Who': biodiversity and its dynamic patterns, 'What': physiology, and 'Where': architecture creating substrate gradients. Particularly community dynamics and extracellular polymeric substances (EPS) still require insights. Performant OLAND (3) comprises fast start-up (storage possibility; fast growth of anammox bacteria), process stability (endured biomass retention; stress resilience), reasonable overall costs, high nitrogen removal efficiency and a low environmental footprint. Three important OLAND challenges are elaborated in detailed frameworks, demonstrating how to maximize nitrogen removal efficiency, minimize NO and N(2)O emissions and obtain through OLAND a plant-wide net energy gain from sewage treatment. © 2012 The Authors. Microbial Biotechnology © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Spatial & Temporal Geophysical Monitoring of Microbial Growth and Biofilm Formation

EPA Science Inventory

Previous studies have examined the effect of biogenic gases and biomineralization on the acoustic properties of porous media. In this study, we investigated the spatiotemporal effect of microbial growth and biofilm formation on compressional waves and complex conductivity in sand...

Biotic interactions reduce microbial carbon use efficiency

NASA Astrophysics Data System (ADS)

Bradford, M.; Maynard, D. S.

2017-12-01

The efficiency by which microbes decompose organic matter governs the amount of carbon that is retained in microbial biomass versus lost to the atmosphere as respiration. This carbon use efficiency (CUE) is affected by various abiotic conditions, such as temperature and nutrient availability. In biogeochemical model simulations, CUE is a key variable regulating how much soil carbon is stored or lost from ecosystems under simulated global changes, such as climate warming. Theoretically, the physiological costs of biotic interactions such as competition should likewise alter CUE, yet the direction and magnitude of these costs are untested. Here we conduct a microcosm experiment to quantify how competitive interactions among saprotrophic fungi alter growth, respiration, and CUE. Free-living decomposer fungi representing a broad range of traits and phylogenies were grown alone, in pairwise competition, and in multi-species (up to 15) communities. By combing culturing and stable carbon isotope approaches, we could resolve the amount of carbon substrate allocated to fungal biomass versus respiration, and so estimate CUE. By then comparing individual performance to community-level outcomes, we show that species interactions induce consistent declines in CUE, regardless of abiotic conditions. Pairwise competition lowers CUE by as much as 25%, with the magnitude of these costs equal to or greater than the observed variation across abiotic conditions. However, depending on the competitive network structure, increasing species richness led to consistent gains or declines in CUE. Our results suggest that the extent to which microbial-mediated carbon fluxes respond to environmental change may be influenced strongly by competitive interactions. As such, knowledge of abiotic conditions and community composition is necessary to confidently project CUE and hence ecosystem carbon dynamics.

A Broader View: Microbial Enzymes and Their Relevance in Industries, Medicine, and Beyond

PubMed Central

Bose, Sutapa; Rai, Vivek

2013-01-01

Enzymes are the large biomolecules that are required for the numerous chemical interconversions that sustain life. They accelerate all the metabolic processes in the body and carry out a specific task. Enzymes are highly efficient, which can increase reaction rates by 100 million to 10 billion times faster than any normal chemical reaction. Due to development in recombinant technology and protein engineering, enzymes have evolved as an important molecule that has been widely used in different industrial and therapeutical purposes. Microbial enzymes are currently acquiring much attention with rapid development of enzyme technology. Microbial enzymes are preferred due to their economic feasibility, high yields, consistency, ease of product modification and optimization, regular supply due to absence of seasonal fluctuations, rapid growth of microbes on inexpensive media, stability, and greater catalytic activity. Microbial enzymes play a major role in the diagnosis, treatment, biochemical investigation, and monitoring of various dreaded diseases. Amylase and lipase are two very important enzymes that have been vastly studied and have great importance in different industries and therapeutic industry. In this review, an approach has been made to highlight the importance of different enzymes with special emphasis on amylase and lipase in the different industrial and medical fields. PMID:24106701

Carbonate fabrics in the modern microbialites of Pavilion Lake: two suites of microfabrics that reflect variation in microbial community morphology, growth habit, and lithification.

PubMed

Theisen, C Harwood; Sumner, D Y; Mackey, T J; Lim, D S S; Brady, A L; Slater, G F

2015-07-01

Modern microbialites in Pavilion Lake, BC, provide an analog for ancient non-stromatolitic microbialites that formed from in situ mineralization. Because Pavilion microbialites are mineralizing under the influence of microbial communities, they provide insights into how biological processes influence microbialite microfabrics and mesostructures. Hemispherical nodules and micrite-microbial crusts are two mesostructures within Pavilion microbialites that are directly associated with photosynthetic communities. Both filamentous cyanobacteria in hemispherical nodules and branching filamentous green algae in micrite-microbial crusts were associated with calcite precipitation at microbialite surfaces and with characteristic microfabrics in the lithified microbialite. Hemispherical nodules formed at microbialite surfaces when calcite precipitated around filamentous cyanobacteria with a radial growth habit. The radial filament pattern was preserved within the microbialite to varying degrees. Some subsurface nodules contained well-defined filaments, whereas others contained only dispersed organic inclusions. Variation in filament preservation is interpreted to reflect differences in timing and amount of carbonate precipitation relative to heterotrophic decay, with more defined filaments reflecting greater lithification prior to degradation than more diffuse filaments. Micrite-microbial crusts produce the second suite of microfabrics and form in association with filamentous green algae oriented perpendicular to the microbialite surface. Some crusts include calcified filaments, whereas others contained voids that reflect the filamentous community in shape, size, and distribution. Pavilion microbialites demonstrate that microfabric variation can reflect differences in lithification processes and microbial metabolisms as well as microbial community morphology and organization. Even when the morphology of individual filaments or cells is not well preserved, the microbial growth habit can be captured in mesoscale microbialite structures. These results suggest that when petrographic preservation is extremely good, ancient microbialite growth structures and microfabrics can be interpreted in the context of variation in community organization, community composition, and lithification history. Even in the absence of distinct microbial microfabrics, mesostructures can capture microbial community morphology. © 2015 John Wiley & Sons Ltd.

Divergence in plant and microbial allocation strategies explains continental patterns in microbial allocation and biogeochemical fluxes.

PubMed

Averill, Colin

2014-10-01

Allocation trade-offs shape ecological and biogeochemical phenomena at local to global scale. Plant allocation strategies drive major changes in ecosystem carbon cycling. Microbial allocation to enzymes that decompose carbon vs. organic nutrients may similarly affect ecosystem carbon cycling. Current solutions to this allocation problem prioritise stoichiometric tradeoffs implemented in plant ecology. These solutions may not maximise microbial growth and fitness under all conditions, because organic nutrients are also a significant carbon resource for microbes. I created multiple allocation frameworks and simulated microbial growth using a microbial explicit biogeochemical model. I demonstrate that prioritising stoichiometric trade-offs does not optimise microbial allocation, while exploiting organic nutrients as carbon resources does. Analysis of continental-scale enzyme data supports the allocation patterns predicted by this framework, and modelling suggests large deviations in soil C loss based on which strategy is implemented. Therefore, understanding microbial allocation strategies will likely improve our understanding of carbon cycling and climate. © 2014 John Wiley & Sons Ltd/CNRS.

PRECOG: a tool for automated extraction and visualization of fitness components in microbial growth phenomics.

PubMed

Fernandez-Ricaud, Luciano; Kourtchenko, Olga; Zackrisson, Martin; Warringer, Jonas; Blomberg, Anders

2016-06-23

Phenomics is a field in functional genomics that records variation in organismal phenotypes in the genetic, epigenetic or environmental context at a massive scale. For microbes, the key phenotype is the growth in population size because it contains information that is directly linked to fitness. Due to technical innovations and extensive automation our capacity to record complex and dynamic microbial growth data is rapidly outpacing our capacity to dissect and visualize this data and extract the fitness components it contains, hampering progress in all fields of microbiology. To automate visualization, analysis and exploration of complex and highly resolved microbial growth data as well as standardized extraction of the fitness components it contains, we developed the software PRECOG (PREsentation and Characterization Of Growth-data). PRECOG allows the user to quality control, interact with and evaluate microbial growth data with ease, speed and accuracy, also in cases of non-standard growth dynamics. Quality indices filter high- from low-quality growth experiments, reducing false positives. The pre-processing filters in PRECOG are computationally inexpensive and yet functionally comparable to more complex neural network procedures. We provide examples where data calibration, project design and feature extraction methodologies have a clear impact on the estimated growth traits, emphasising the need for proper standardization in data analysis. PRECOG is a tool that streamlines growth data pre-processing, phenotypic trait extraction, visualization, distribution and the creation of vast and informative phenomics databases.

High throughput automated microbial bioreactor system used for clone selection and rapid scale‐down process optimization

PubMed Central

Velez‐Suberbie, M. Lourdes; Betts, John P. J.; Walker, Kelly L.; Robinson, Colin; Zoro, Barney

2017-01-01

High throughput automated fermentation systems have become a useful tool in early bioprocess development. In this study, we investigated a 24 x 15 mL single use microbioreactor system, ambr 15f, designed for microbial culture. We compared the fed‐batch growth and production capabilities of this system for two Escherichia coli strains, BL21 (DE3) and MC4100, and two industrially relevant molecules, hGH and scFv. In addition, different carbon sources were tested using bolus, linear or exponential feeding strategies, showing the capacity of the ambr 15f system to handle automated feeding. We used power per unit volume (P/V) as a scale criterion to compare the ambr 15f with 1 L stirred bioreactors which were previously scaled‐up to 20 L with a different biological system, thus showing a potential 1,300 fold scale comparability in terms of both growth and product yield. By exposing the cells grown in the ambr 15f system to a level of shear expected in an industrial centrifuge, we determined that the cells are as robust as those from a bench scale bioreactor. These results provide evidence that the ambr 15f system is an efficient high throughput microbial system that can be used for strain and molecule selection as well as rapid scale‐up. © 2017 The Authors Biotechnology Progress published by Wiley Periodicals, Inc. on behalf of American Institute of Chemical Engineers Biotechnol. Prog., 34:58–68, 2018 PMID:28748655

Determination of Microbial Growth by Protein Assay in an Air-Cathode Single Chamber Microbial Fuel Cell.

PubMed

Li, Na; Kakarla, Ramesh; Moon, Jung Mi; Min, Booki

2015-07-01

Microbial fuel cells (MFCs) have gathered attention as a novel bioenergy technology to simultaneously treat wastewater with less sludge production than the conventional activated sludge system. In two different operations of the MFC and aerobic process, microbial growth was determined by the protein assay method and their biomass yields using real wastewater were compared. The biomass yield on the anode electrode of the MFC was 0.02 g-COD-cell/g- COD-substrate and the anolyte planktonic biomass was 0.14 g-COD-cell/g-COD-substrate. An MFC without anode electrode resulted in the biomass yield of 0.07 ± 0.03 g-COD-cell/g-COD-substrate, suggesting that oxygen diffusion from the cathode possibly supported the microbial growth. In a comparative test, the biomass yield under aerobic environment was 0.46 ± 0.07 g-COD-cell/g-COD-substrate, which was about 3 times higher than the total biomass value in the MFC operation.

Effect of sulfur supplements on cellulolytic rumen micro-organisms and microbial protein synthesis in cattle fed a high fibre diet.

PubMed

McSweeney, C S; Denman, S E

2007-11-01

To examine the effect of sulfur-containing compounds on the growth of anaerobic rumen fungi and the fibrolytic rumen bacteria Ruminococcus albus, Ruminococcus flavefaciens and Fibrobacter succinogenes in pure culture and within the cattle rumen. The effect of two reduced sulfur compounds, 3-mercaptopropionic acid (MPA) or 3-mercapto-1-propanesulfonic acid as the sole S source on growth of pure fibroyltic fungal and bacterial cultures showed that these compounds were capable of sustaining growth. An in vivo trial was then conducted to determine the effect of sulfur supplements (MPA and sodium sulfate) on microbial population dynamics in cattle fed the roughage Dichanthium aristatum. Real-time PCR showed significant increases in fibrolytic bacterial and fungal populations when cattle were supplemented with these compounds. Sulfate supplementation leads to an increase in dry matter intake without a change in whole tract dry matter digestibility. Supplementation of low S-containing diets with either sodium sulfate or MPA stimulates microbial growth with an increase in rumen microbial protein supply to the animal. Through the use of real-time PCR monitoring, a better understanding of the effect of S supplementation on discrete microbial populations within the rumen is provided.

Using N-Limiting Growth Conditions to Remove Atrazine from Groundwater: Laboratory Studies.

USDA-ARS?s Scientific Manuscript database

Typically, respiratory redox reactions are the driving mechanism behind in situ bioremediations that use a carbon substrate. This is because electron (e-) donor availability generally restricts subsurface microbial activity. Thus, microbial growth and respiration can be greatly stimulated by the a...

Assessment of microbial growth on the surface of materials in contact with water intended for human consumption using ATP method.

PubMed

Szczotko, Maciej; Krogulski, Adam

2010-01-01

Elaboration of an assessment method for plumbing materials contacting drinking water was the main purpose of this study. The investigation was conducted in 8 week cycles in dynamic conditions using a continuous flow reactor. Microbial growth was measured indirectly by a bioluminescence technique (ATP assay). Every week swabs from the surface of tested materials (polypropylene and different types of polyethylene), from the domestic market were collected and the level of bioluminescence was examined. The results obtained from the surface of tested materials were repeatable and clearly approximated those obtained from the surface of a negative control (stainless steel, low susceptibility for microbial growth). The level of bioluminescence (ATP) on the surface of positive control (paraffin, high susceptibility for microbial growth) was many times higher than that observed on other materials. The presented investigation was the main part of a validation process, which in short time will serve to initiate a complete assessment system for organic materials contacting drinking water.

New plant-growth medium for increased power output of the Plant-Microbial Fuel Cell.

PubMed

Helder, M; Strik, D P B T B; Hamelers, H V M; Kuijken, R C P; Buisman, C J N

2012-01-01

In a Plant-Microbial Fuel Cell anode-conditions must be created that are favorable for plant growth and electricity production. One of the major aspects in this is the composition of the plant-growth medium. Hoagland medium has been used until now, with added phosphate buffer to reduce potential losses over the membrane because of differences in pH between anode and cathode. We developed a new, improved plant-growth medium that improves current production, while the plant keeps growing. This medium is a nitrate-less, ammonium-rich medium that contains all macro- and micro-nutrients necessary for plant growth, with a balanced amount of bicarbonate buffer. Sulphate presence in the plant-growth medium helps to keep a low anode-potential. With the new plant-growth medium the maximum current production of the Plant-Microbial Fuel Cell increased from 186 mA/m(2) to 469 mA/m(2). Copyright © 2011 Elsevier Ltd. All rights reserved.

Cultivation of high-biomass crops on coal mine spoil banks: can microbial inoculation compensate for high doses of organic matter?

PubMed

Gryndler, Milan; Sudová, Radka; Püschel, David; Rydlová, Jana; Janousková, Martina; Vosátka, Miroslav

2008-09-01

Two greenhouse experiments were focused on the application of arbuscular mycorrhizal fungi (AMF) and plant growth promoting rhizobacteria (PGPR) in planting of high-biomass crops on reclaimed spoil banks. In the first experiment, we tested the effects of different organic amendments on growth of alfalfa and on the introduced microorganisms. While growth of plants was supported in substrate with compost amendment, mycorrhizal colonization was suppressed. Lignocellulose papermill waste had no negative effects on AMF, but did not positively affect growth of plants. The mixture of these two amendments was found to be optimal in both respects, plant growth and mycorrhizal development. Decreasing doses of this mixture amendment were used in the second experiment, where the effects of microbial inoculation (assumed to compensate for reduced doses of organic matter) on growth of two high-biomass crops, hemp and reed canarygrass, were studied. Plant growth response to microbial inoculation was either positive or negative, depending on the dose of the applied amendment and plant species.

Nitrogen recycling through the gut and the nitrogen economy of ruminants: an asynchronous symbiosis.

PubMed

Reynolds, C K; Kristensen, N B

2008-04-01

The extensive development of the ruminant forestomach sets apart their N economy from that of nonruminants in a number of respects. Extensive pregastric fermentation alters the profile of protein reaching the small intestine, largely through the transformation of nitrogenous compounds into microbial protein. This process is fueled primarily by carbohydrate fermentation and includes extensive recycling of N between the body and gut lumen pools. Nitrogen recycling occurs via blood and gut lumen exchanges of urea and NH(3), as well as endogenous gut and secretory N entry into the gut lumen, and the subsequent digestion and absorption of microbial and endogenous protein. Factors controlling urea transfer to the gut from blood, including the contributions of urea transporters, remain equivocal. Ammonia produced by microbial degradation of urea and dietary and endogenous AA is utilized by microbial fermentation or absorbed and primarily converted to urea. Therefore, microbial growth and carbohydrate fermentation affect the extent of NH(3) absorption and urea N recycling and excretion. The extensive recycling of N to the rumen represents an evolutionary advantage of the ruminant in terms of absorbable protein supply during periods of dietary protein deficiency, or asynchronous carbohydrate and protein supply, but incurs a cost of greater N intakes, especially in terms of excess N excretion. Efforts to improve the efficiency of N utilization in ruminants by synchronizing fermentable energy and N availability have generally met with limited success with regards to production responses. In contrast, imposing asynchrony through oscillating dietary protein concentration, or infrequent supplementation, surprisingly has not negatively affected production responses unless the frequency of supplementation is less than once every 3 d. In some cases, oscillation of dietary protein concentration has improved N retention compared with animals fed an equal amount of dietary protein on a daily basis. This may reflect benefits of Orn cycle adaptations and sustained recycling of urea to the gut. The microbial symbiosis of the ruminant is inherently adaptable to asynchronous N and energy supply. Recycling of urea to the gut buffers the effect of irregular dietary N supply such that intuitive benefits of rumen synchrony in terms of the efficiency of N utilization are typically not observed in practice.

Electrokinetic-Enhanced Remediation of Phenanthrene-Contaminated Soil Combined with Sphingomonas sp. GY2B and Biosurfactant.

PubMed

Lin, Weijia; Guo, Chuling; Zhang, Hui; Liang, Xujun; Wei, Yanfu; Lu, Guining; Dang, Zhi

2016-04-01

Electrokinetic-microbial remediation (EMR) has emerged as a promising option for the removal of polycyclic aromatic hydrocarbons (PAHs) from contaminated soils. The aim of this study was to enhance degradation of phenanthrene (Phe)-contaminated soils using EMR combined with biosurfactants. The electrokinetic (EK) remediation, combined with Phe-degrading Sphingomonas sp. GY2B, and biosurfactant obtained by fermentation of Pseudomonas sp. MZ01, degraded Phe in the soil with an efficiency of up to 65.1 % at the anode, 49.9 % at the cathode after 5 days of the treatment. The presence of biosurfactants, electricity, and a neutral electrolyte stimulated the growth of the degrading bacteria as shown by a rapid increase in microbial biomass with time. The electrical conductivity and pH changed little during the course of the treatment, which benefitted the growth of microorganisms and the remediation of Phe-contaminated soil. The EMR system with the addition of biosurfactant had the highest Phe removal, demonstrating the biosurfactant may enhance the bioavailability of Phe and the interaction with the microorganism. This study suggests that the EMR combined with biosurfactants can be used to enhance in situ bioremediation of PAH-contaminated soils.

Isolation and characterization of a plant growth-promoting rhizobacterium, Serratia sp. SY5.

PubMed

Koo, So-Yeon; Cho, Kyung-Suk

2009-11-01

The role of plant growth-promoting rhizobacteria (PGPR) in the phytoremediation of heavy-metal-contaminated soils is important in overcoming its limitations for field application. A plant growth-promoting rhizobacterium, Serratia sp. SY5, was isolated from the rhizoplane of barnyard grass (Echinochloa crus-galli) grown in petroleum and heavy-metal-contaminated soil. This isolate has shown capacities for indole acetic acid production and siderophores synthesis. Compared with a non-inoculated control, the radicular root growth of Zea mays seedlings inoculated with SY5 can be increased by 27- or 15.4-fold in the presence of 15 mg-Cd/l or 15 mg-Cu/l, respectively. The results from hydroponic cultures showed that inoculation of Serratia sp. SY5 had a favorable influence on the initial shoot growth and biomass of Zea mays under noncontaminated conditions. However, under Cd-contaminated conditions, the inoculation of SY5 significantly increased the root biomass of Zea mays. These results indicate that Serratia sp. SY5 can serve as a promising microbial inoculant for increased plant growth in heavy-metal-contaminated soils to improve the phytoremediation efficiency.

Spatio-seasonal variability in dissolved organic matter optical properties and its bioavailability in a subalpine lake

NASA Astrophysics Data System (ADS)

Stadler, Masumi; Ejarque, Elisabet; Kainz, Martin J.

2017-04-01

Allochthonous and autochothonous dissolved organic matter (DOM) in lakes mainly originate from terrestrial and aquatic primary production, respectively. Due to their differing biochemical composition the degradability of DOM by microorganisms is expected to vary. The carbon use efficiency of bacteria and DOM biodegradability determine whether the consumed DOM is incorporated into microbial biomass or respired to CO2 and ultimately emitted into the atmosphere. Thus, understanding the interaction of biodegradable DOM and its consumers is crucial to increase our knowledge on the role of lakes in the global carbon cycling. However, interactions of specific aquatic DOM signatures and the microbial population still remain widely debated. The aim of this study was to explore how DOM biodegradability changes along a stream-lake continuum at different seasons of the year. We monitored DOM quantity and its optical properties, inorganic nutrients, CO2 and bacterial growth over 20 days in dark bioassays with water from the inflow, outflow and at three layers of an oligotrophic subalpine lake. Preliminary results reveal highest microbial abundance in the metalimnion in winter and summer (0.7 106 and 2.5 106 cells mL-1, respectively) and the inflow in spring and autumn (1 106 and 1.4 106 cells mL-1, respectively) after 20 days. Surprisingly, with the exception of winter samples final inflow bacterial abundance results high, despite its lowest initial natural cell concentration, providing evidence for effective utilisation of terrestrial DOM, even with its high humic signature as indicated by the humification index (HIX). Nonetheless, after a microbial biomass peak with the inflow yielding mostly highest after three days, at the final experimental stage microbial biomass does only marginally differ between all sites with the exception of autumn samples where outflow and metalimnion turn out most productive. Even though the DOM of all lake sites and the lake outflow were characterised by lower molecular weight (indicated by the slope ratio (SR)) and a higher autochthonous signature (BIX) in all seasons, rapid growth of inflow bacteria highlight the potential of terrestrially-derived DOM to support bacterial growth, and challenge previous ideas that autchthonously-produced DOM would be more labile than DOM of terrestrial origin.

Microbial Ecology Assessment of Mixed Copper Oxide/Sulfide Dump Leach Operation

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

Bruhn, Debby Fox; Thompson, David Neal; Noah, Karl Scott

1999-06-01

Microbial consortia composed of complex mixtures of autotrophic and heterotrophic bacteria are responsible for the dissolution of metals from sulfide minerals. Thus, an efficient copper bioleaching operation depends on the microbial ecology of the system. A microbial ecology study of a mixed oxide/sulfide copper leaching operation was conducted using an "overlay" plating technique to differentiate and identify various bacterial consortium members of the genera Thiobacillus, “Leptospirillum”, “Ferromicrobium”, and Acidiphilium. Two temperatures (30°C and 45°C) were used to select for mesophilic and moderately thermophilic bacteria. Cell numbers varied from 0-106 cells/g dry ore, depending on the sample location and depth. Aftermore » acid curing for oxide leaching, no viable bacteria were recovered, although inoculation of cells from raffinate re-established a microbial population after three months. Due to low the pH of the operation, very few non-iron-oxidizing acidophilic heterotrophs were recovered. Moderate thermophiles were isolated from the ore samples. Pregnant liquor solutions (PLS) and raffinate both contained a diversity of bacteria. In addition, an intermittently applied waste stream that contained high levels of arsenic and fluoride was tested for toxicity. Twenty vol% waste stream in PLS killed 100% of the cells in 48 hours, indicating substantial toxicity and/or growth inhibition. The data indicate that bacteria populations can recover after acid curing, and that application of the waste stream to the dump should be avoided. Monitoring the microbial ecology of the leaching operation provided significant information that improved copper recovery.« less

Long-Term Enrichment on Cellulose or Xylan Causes Functional and Taxonomic Convergence of Microbial Communities from Anaerobic Digesters

PubMed Central

Jia, Yangyang; Wilkins, David; Lu, Hongyuan; Cai, Mingwei

2015-01-01

Cellulose and xylan are two major components of lignocellulosic biomass, which represents a potentially important energy source, as it is abundant and can be converted to methane by microbial action. However, it is recalcitrant to hydrolysis, and the establishment of a complete anaerobic digestion system requires a specific repertoire of microbial functions. In this study, we maintained 2-year enrichment cultures of anaerobic digestion sludge amended with cellulose or xylan to investigate whether a cellulose- or xylan-digesting microbial system could be assembled from sludge previously used to treat neither of them. While efficient methane-producing communities developed under mesophilic (35°C) incubation, they did not under thermophilic (55°C) conditions. Illumina amplicon sequencing results of the archaeal and bacterial 16S rRNA genes revealed that the mature cultures were much lower in richness than the inocula and were dominated by single archaeal (genus Methanobacterium) and bacterial (order Clostridiales) groups, although at finer taxonomic levels the bacteria were differentiated by substrates. Methanogenesis was primarily via the hydrogenotrophic pathway under all conditions, although the identity and growth requirements of syntrophic acetate-oxidizing bacteria were unclear. Incubation conditions (substrate and temperature) had a much greater effect than inoculum source in shaping the mature microbial community, although analysis based on unweighted UniFrac distance found that the inoculum still determined the pool from which microbes could be enriched. Overall, this study confirmed that anaerobic digestion sludge treating nonlignocellulosic material is a potential source of microbial cellulose- and xylan-digesting functions given appropriate enrichment conditions. PMID:26712547

Biological potential of extraterrestrial materials. 2. Microbial and plant responses to nutrients in the Murchison carbonaceous meteorite

NASA Technical Reports Server (NTRS)

Mautner, M. N.; Conner, A. J.; Killham, K.; Deamer, D. W.

1997-01-01

Meteoritic materials are investigated as potential early planetary nutrients. Aqueous extracts of the Murchison C2 carbonaceous meteorite are utilized as a sole carbon source by microorganisms, as demonstrated by the genetically modified Pseudomonas fluorescence equipped with the lux gene. Nutrient effects are observed also with the soil microorganisms Nocardia asteroides and Arthrobacter pascens that reach populations up to 5 x 10(7) CFU/ml in meteorite extracts, similar to populations in terrestrial soil extracts. Plant tissue cultures of Asparagus officinalis and Solanum tuberosum (potato) exhibit enhanced pigmentation and some enhanced growth when meteorite extracts are added to partial nutrient media, but inhibited growth when added to full nutrient solution. The meteorite extracts lead to large increases in S, Ca, Mg, and Fe plant tissue contents as shown by X-ray fluorescence, while P, K, and Cl contents show mixed effects. In both microbiological and plant tissue experiments, the nutrient and inhibitory effects appear to be best balanced for growth at about 1:20 (extracted solid : H2O) ratios. The results suggest that solutions in cavities in meteorites can provide efficient concentrated biogenic and early nutrient environments, including high phosphate levels, which may be the limiting nutrient. The results also suggest that carbonaceous asteroid resources can sustain soil microbial activity and provide essential macronutrients for future space-based ecosystems.

DNA Isolation of Microbial Contaminants in Aviation Turbine Fuel via Traditional Polymerase Chain Reaction (PCR) and Direct PCR. Preliminary Results

DTIC Science & Technology

2005-11-01

fuel gauge malfunctions, fuel line and filter plugging, and corrosion. As a result, there is considerable interest in identifying microbial growth ...corrosion. As a result, there is considerable interest in identifying microbial growth and finding strategies to mitigate it. Previous research to... Rhodotorula sp. Yes Yes Trichosporium sp. Yes Trichoderma sp. (viride + others) Yes Yes 4 Table 2. Culturability Determined as a Percentage of

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

Downstream reactions and engineering in the microbially reconstituted pathway for Taxol.

PubMed

Jiang, Ming; Stephanopoulos, Gregory; Pfeifer, Blaine A

2012-05-01

Taxol (a trademarked product of Bristol-Myers Squibb) is a complex isoprenoid natural product which has displayed potent anticancer activity. Originally isolated from the Pacific yew tree (Taxus brevifolia), Taxol has been mass-produced through processes reliant on plant-derived biosynthesis. Recently, there have been alternative efforts to reconstitute the biosynthetic process through technically convenient microbial hosts, which offer unmatched growth kinetics and engineering potential. Such an approach is made challenging by the need to successfully introduce the significantly foreign enzymatic steps responsible for eventual biosynthesis. Doing so, however, offers the potential to engineer more efficient and economical production processes and the opportunity to design and produce tailored analog compounds with enhanced properties. This mini review will specifically focus on heterologous biosynthesis as it applies to Taxol with an emphasis on the challenges associated with introducing and reconstituting the downstream reaction steps needed for final bioactivity.

Sustainable power generation in continuous flow microbial fuel cell treating actual wastewater: influence of biocatalyst type on electricity production.

PubMed

Ismail, Zainab Z; Jaeel, Ali Jwied

2013-01-01

Microbial fuel cells (MFCs) have the potential to simultaneously treat wastewater for reuse and to generate electricity. This study mainly considers the performance of an upflow dual-chambered MFC continuously fueled with actual domestic wastewater and alternatively biocatalyzed with aerobic activated sludge and strain of Bacillus Subtilis. The behavior of MFCs during initial biofilm growth and characterization of anodic biofilm were studied. After 45 days of continuous operation, the biofilms on the anodic electrode were well developed. The performance of MFCs was mainly evaluated in terms of COD reductions and electrical power output. Results revealed that the COD removal efficiency was 84% and 90% and the stabilized power outputs were clearly observed achieving a maximum value of 120 and 270 mW/m(2) obtained for MFCs inoculated with mixed cultures and Bacillus Subtilis strain, respectively.

Recent advances of microbial breeding via heavy-ion mutagenesis at IMP.

PubMed

Hu, W; Li, W; Chen, J

2017-10-01

Nowadays, the value of heavy-ion mutagenesis has been accepted as a novel powerful mutagen technique to generate new microbial mutants due to its high linear energy transfer and high relative biological effectiveness. This paper briefly reviews recent progress in developing a more efficient mutagenesis technique for microbial breeding using heavy-ion mutagenesis, and also presents the outline of the beam line for microbial breeding in Heavy Ion Research Facility of Lanzhou. Then, new insights into microbial biotechnology via heavy-ion mutagenesis are also further explored. We hope that our concerns will give deep insight into microbial breeding biotechnology via heavy-ion mutagenesis. We also believe that heavy-ion mutagenesis breeding will greatly contribute to the progress of a comprehensive study industrial strain engineering for bioindustry in the future. There is currently a great interest in developing rapid and diverse microbial mutation tool for strain modification. Heavy-ion mutagenesis has been proved as a powerful technology for microbial breeding due to its broad spectrum of mutation phenotypes with high efficiency. In order to deeply understand heavy-ion mutagenesis technology, this paper briefly reviews recent progress in microbial breeding using heavy-ion mutagenesis at IMP, and also presents the outline of the beam line for microbial breeding in Heavy Ion Research Facility of Lanzhou (HIRFL) as well as new insights into microbial biotechnology via heavy-ion mutagenesis. Thus, this work can provide the guidelines to promote the development of novel microbial biotechnology cross-linking heavy-ion mutagenesis breeding that could make breeding process more efficiently in the future. © 2017 The Society for Applied Microbiology.

Fertilizer efficiency and environmental risk of irrigating Impatiens with composting leachate in decentralized solid waste management.

PubMed

Zhou, Chuanbin; Wang, Rusong; Zhang, Yishan

2010-06-01

The reduction and reuse of composting leachate is an issue of importance in the field of decentralized solid waste management. In this study, composting leachate from source-separated food waste was treated and subsequently used as liquid fertilizer to irrigate Impatiens (Impatiens balsamina). The leachate was altered by adjusting storage time and dilution, and through addition of microbial inocula. For each test case, the effects of irrigation were monitored by analyzing the Impatiens extension degree, numbers of leaves and flowers, dry weight, and photosynthetic pigment content to assess fertilizer efficiency. The main results obtained revealed that the addition of microbial inocula and lengthening of storage times may lower COD concentrations, adjust pH value and maintain a comparatively high level of nutrient contents. By adding microbial inocula, a COD concentration of 9.6% and BOD(5) concentration of 6.7% were obtained for non-treated leachate with the same storage time. COD concentrations in leachate decreased to 69.4% after 36weeks storage. Moreover, composting leachate promoted growth of Impatiens. The dry weight biomass of Impatiens irrigated using treated diluted leachate was 1.15-2.94 times that obtained for Impatiens irrigated using tap water. Lastly, following the irrigation of Impatiens over a short period, soil did not accumulate VOCs and heavy metals to levels exceeding relative standards. Further research on heavy metal and salinity accumulation in plants should be undertaken to meet the needs of large-scale applications. Copyright 2010 Elsevier Ltd. All rights reserved.

Growth of Aureobasidium pullulans on straw hydrolysate.

PubMed Central

Han, Y W; Cheeke, P R; Anderson, A W; Lekprayoon, C

1976-01-01

Growth characteristics and cell properties of Aureobasidium (Pullularia) pullulans were studied. The organism grew well on an acid hydrolysate of ryegrass straw over a wide range of pH and temperature. The optimum temperature and pH for the growth of the organism were 32 degrees C and 5.5, respectively. A cell yield of 1.5 g/liter of straw hydrolysate was obtained. The dried cell mass contained 42.6% crude protein, 0.4% crude fat, and 6.4% nucleic acids. The essential amino acid profile of the microbial protein was comparable to that of Candida utilis. A rat feeding study indicated that the A. pullulans cells were not toxic and that the feed intake, weight gain, and protein efficiency ratio values were superior to those obtained with C. utilis. Once the question of mathogenicity is resolved, A. pullulans could be useful for production of single-cell protein from cellulosic wastes. PMID:12721

Natural attenuation, biostimulation and bioaugmentation of landfill leachate management

NASA Astrophysics Data System (ADS)

Er, X. Y.; Seow, T. W.; Lim, C. K.; Ibrahim, Z.

2018-04-01

Landfills used for solid waste management will lead to leachate production. Proper leachate management is highly essential to be paid attention to protect the environment and living organisms’ health and safety. In this study, the remedial strategies used for leachate management were natural attenuation, biostimulation and bioaugmentation. All treatment samples were treated via 42-days combined anaerobic-aerobic treatment and the treatment efficiency was studied by measuring the removal rate of COD and ammonia nitrogen. In this study, all remedial strategies showed different degrees of contaminants removal. Lowest contaminants removal rate was achieved via bioaugmentation of B. panacihumi strain ZB1, which were 39.4% of COD and 37.6% of ammonia nitrogen removed from the leachate sample. Higher contaminants removal rate was achieved via natural attenuation and biostimulation. Native microbial population was able to remove 41% of COD and 59% of ammonia nitrogen from the leachate sample. The removal efficiency could be further improved via biostimulation to trigger microbial growth and decontamination rate. Through biostimulation, 58% of COD and 51.8% of ammonia nitrogen were removed from the leachate sample. In conclusion, natural attenuation and biostimulation should be the main choice for leachate management to avoid any unexpected impacts due to introduction of exogenous species.

The Microbial Efficiency-Matrix Stabilization (MEMS) framework integrates plant litter decomposition with soil organic matter stabilization: do labile plant inputs form stable soil organic matter?

PubMed

Cotrufo, M Francesca; Wallenstein, Matthew D; Boot, Claudia M; Denef, Karolien; Paul, Eldor

2013-04-01

The decomposition and transformation of above- and below-ground plant detritus (litter) is the main process by which soil organic matter (SOM) is formed. Yet, research on litter decay and SOM formation has been largely uncoupled, failing to provide an effective nexus between these two fundamental processes for carbon (C) and nitrogen (N) cycling and storage. We present the current understanding of the importance of microbial substrate use efficiency and C and N allocation in controlling the proportion of plant-derived C and N that is incorporated into SOM, and of soil matrix interactions in controlling SOM stabilization. We synthesize this understanding into the Microbial Efficiency-Matrix Stabilization (MEMS) framework. This framework leads to the hypothesis that labile plant constituents are the dominant source of microbial products, relative to input rates, because they are utilized more efficiently by microbes. These microbial products of decomposition would thus become the main precursors of stable SOM by promoting aggregation and through strong chemical bonding to the mineral soil matrix. © 2012 Blackwell Publishing Ltd.

Microbial growth and physiology in space - A review

NASA Technical Reports Server (NTRS)

Cioletti, Louis A.; Mishra, S. K.; Pierson, Duane L.

1991-01-01

An overview of microbial behavior in closed environments is given with attention to data related to simulated microgravity and actual space flight. Microbes are described in terms of antibiotic sensitivity, subcellular structure, and physiology, and the combined effects are considered of weightlessness and cosmic radiation on human immunity to such microorganisms. Space flight results report such effects as increased phage induction, accelerated microbial growth rates, and the increased risk of disease communication and microbial exchange aboard confining spacecraft. Ultrastructural changes are also noted in the nuclei, cell membranes, and cytoplasmic streaming, and it appears that antibiotic sensitivity is reduced under both actual and simulated conditions of spaceflight.

Mineral solubility and free energy controls on microbial reaction kinetics: Application to contaminant transport in the subsurface

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

Taillefert, Martial; Van Cappellen, Philippe

Recent developments in the theoretical treatment of geomicrobial reaction processes have resulted in the formulation of kinetic models that directly link the rates of microbial respiration and growth to the corresponding thermodynamic driving forces. The overall objective of this project was to verify and calibrate these kinetic models for the microbial reduction of uranium(VI) in geochemical conditions that mimic as much as possible field conditions. The approach combined modeling of bacterial processes using new bioenergetic rate laws, laboratory experiments to determine the bioavailability of uranium during uranium bioreduction, evaluation of microbial growth yield under energy-limited conditions using bioreactor experiments, competitionmore » experiments between metabolic processes in environmentally relevant conditions, and model applications at the field scale. The new kinetic descriptions of microbial U(VI) and Fe(III) reduction should replace those currently used in reactive transport models that couple catabolic energy generation and growth of microbial populations to the rates of biogeochemical redox processes. The above work was carried out in collaboration between the groups of Taillefert (batch reactor experiments and reaction modeling) at Georgia Tech and Van Cappellen (retentostat experiments and reactive transport modeling) at University of Waterloo (Canada).« less

Comprehensive Evaluation of Biological Growth Control by Chlorine-Based Biocides in Power Plant Cooling Systems Using Tertiary Effluent

PubMed Central

Chien, Shih-Hsiang; Dzombak, David A.; Vidic, Radisav D.

2013-01-01

Abstract Recent studies have shown that treated municipal wastewater can be a reliable cooling water alternative to fresh water. However, elevated nutrient concentration and microbial population in wastewater lead to aggressive biological proliferation in the cooling system. Three chlorine-based biocides were evaluated for the control of biological growth in cooling systems using tertiary treated wastewater as makeup, based on their biocidal efficiency and cost-effectiveness. Optimal chemical regimens for achieving successful biological growth control were elucidated based on batch-, bench-, and pilot-scale experiments. Biocide usage and biological activity in planktonic and sessile phases were carefully monitored to understand biological growth potential and biocidal efficiency of the three disinfectants in this particular environment. Water parameters, such as temperature, cycles of concentration, and ammonia concentration in recirculating water, critically affected the biocide performance in recirculating cooling systems. Bench-scale recirculating tests were shown to adequately predict the biocide residual required for a pilot-scale cooling system. Optimal residuals needed for proper biological growth control were 1, 2–3, and 0.5–1 mg/L as Cl2 for NaOCl, preformed NH2Cl, and ClO2, respectively. Pilot-scale tests also revealed that Legionella pneumophila was absent from these cooling systems when using the disinfectants evaluated in this study. Cost analysis showed that NaOCl is the most cost-effective for controlling biological growth in power plant recirculating cooling systems using tertiary-treated wastewater as makeup. PMID:23781129

Comprehensive Evaluation of Biological Growth Control by Chlorine-Based Biocides in Power Plant Cooling Systems Using Tertiary Effluent.

PubMed

Chien, Shih-Hsiang; Dzombak, David A; Vidic, Radisav D

2013-06-01

Recent studies have shown that treated municipal wastewater can be a reliable cooling water alternative to fresh water. However, elevated nutrient concentration and microbial population in wastewater lead to aggressive biological proliferation in the cooling system. Three chlorine-based biocides were evaluated for the control of biological growth in cooling systems using tertiary treated wastewater as makeup, based on their biocidal efficiency and cost-effectiveness. Optimal chemical regimens for achieving successful biological growth control were elucidated based on batch-, bench-, and pilot-scale experiments. Biocide usage and biological activity in planktonic and sessile phases were carefully monitored to understand biological growth potential and biocidal efficiency of the three disinfectants in this particular environment. Water parameters, such as temperature, cycles of concentration, and ammonia concentration in recirculating water, critically affected the biocide performance in recirculating cooling systems. Bench-scale recirculating tests were shown to adequately predict the biocide residual required for a pilot-scale cooling system. Optimal residuals needed for proper biological growth control were 1, 2-3, and 0.5-1 mg/L as Cl 2 for NaOCl, preformed NH 2 Cl, and ClO 2 , respectively. Pilot-scale tests also revealed that Legionella pneumophila was absent from these cooling systems when using the disinfectants evaluated in this study. Cost analysis showed that NaOCl is the most cost-effective for controlling biological growth in power plant recirculating cooling systems using tertiary-treated wastewater as makeup.

Automated Microorganism Detector

NASA Astrophysics Data System (ADS)

Keahey, Pelham; Hardy, Will; Cradit, Mason; Solis, Steven; Holland, Andrea; Wade, Gerry

2010-10-01

The detection and identification of bacteria in blood samples is crucial for treating patients suspected of having a blood infection. Current hospital methods for pathogen detection are time-consuming processes with multiple steps. This project's goal was to develop an efficient biomedical device to detect bacterial growth in blood samples, based on Gerald J. Wade's 1979 invention (US patents 4250266 and 4267276). Detection was accomplished using a system of electronics to examine the change in the electrochemical properties of a sample in response to bacterial growth, by measuring the sample's electrical charging and charge dispersion characteristics. After initial trials, it was found that a sample yielded consistent voltage measurements of approximately 200 millivolts prior to any detectable microbial growth. The first species tested, Escherichia coli (E. coli), was detected 11.7 hours after its inoculation in a culture bottle at a concentration of approximately 5-10 organisms per milliliter. In future tests, it is expected that detection times will vary in proportion to the growth rate of each species.

The contribution of microbial biotechnology to economic growth and employment creation.

PubMed

Timmis, Kenneth; de Lorenzo, Victor; Verstraete, Willy; Ramos, Juan Luis; Danchin, Antoine; Brüssow, Harald; Singh, Brajesh K; Timmis, James Kenneth

2017-09-01

Our communication discusses the profound impact of bio-based economies - in particular microbial biotechnologies - on SDG 8: Promote sustained, inclusive and sustainable economic growth, full and productive employment and decent work for all. A bio-based economy provides significant potential for improving labour supply, education and investment, and thereby for substantially increasing the demographic dividend. This, in turn, improves the sustainable development of economies. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

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

PubMed

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

2014-07-01

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

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

NASA Astrophysics Data System (ADS)

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

2014-05-01

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

GEOELECTRICAL EVIDENCE OF MICROBIAL DEGRADATION OF DIESEL CONTAMINATED SEDIMENTS

EPA Science Inventory

The alteration of physical properties by microbial activity in petroleum contaminated sediments was investigated using geophysical techniques in laboratory column experiments. Microbial population growth was determined by the Most Probable Number technique (MPN), community dynami...

Macrofaunal involvement in the sublittoral decay of kelp debris: The sea urchin Psammechinus miliaris (Gmelin) (Echinodermata: Echinoidea)

NASA Astrophysics Data System (ADS)

Bedford, A. P.; Moore, P. G.

1985-01-01

Psammechinus miliaris occurs in the Clyde Sea area in large numbers (<18 individuals per 100 g -1 weed dry wt) on sublittoral beds of detached Laminaria saccharina. Its rôle in weed decomposition has been examined by comparing its responses (behavioural choice, growth rate, absorption efficiencies of both carbon and protein, gut retention times and rate of faecal output) to fresh and rotting weed. Younger urchins grew faster than older individuals on a diet of rotting weed but not on fresh weed. Large seasonal variation existed, however, with fast growth occurring in June-August and little, or no, growth in December-February, irrespective of diet. Starved controls did not grow. Correcting for seasonality, rotting kelp still promoted faster growth of young urchins than did fresh weed. Larger (older) individuals showed no difference. Urchins fed fresh weed had significantly longer gut retention times. Protein absorption efficiency was higher on fresh than rotting weed, varying with weed protein content and size of urchin. Very young individuals can only digest high protein weed efficiently, eg. material derived from near the frond meristem. Organic carbon content of rotting weed was significantly lower than fresh weed. Carbon absorption efficiencies were significantly higher on fresh weed which related to organic carbon content. Standard-sized urchins fed rotting weed produced larger dry weights of faeces per day, reflecting increased ingestion rate. In closed-system choice experiments urchins preferred rotting weed kinetically. Size-frequency analysis of field populations suggested that weed beds are principally colonized by larval settlement from the plankton. Mature Psammechinus have evolved different 'strategies' for exploiting fresh and rotting weed. Fresh weed is relatively difficult to digest and long gut retention times allow high protein absorption efficiencies to be attained. Rotting weed has microbial protein in quantities and a lower organic carbon fraction. Some bacterial protein is seemingly unavailable though and lower protein absorption efficiencies result. Thus gut retention time is shortened and more food passed through the gut. Growth remains equivalent. Substratum digestion is of paramount importance for Psammechinus feeding on either fresh or rotting weed, cf. the 'classical' microbe-stripping detritivore of Fenchel.

Substrate growth dynamics and biomineralization of an Ediacaran encrusting poriferan.

PubMed

Wood, Rachel; Penny, Amelia

2018-01-10

The ability to encrust in order to secure and maintain growth on a substrate is a key competitive innovation in benthic metazoans. Here we describe the substrate growth dynamics, mode of biomineralization and possible affinity of Namapoikia rietoogensis , a large (up to 1 m), robustly skeletal, and modular Ediacaran metazoan which encrusted the walls of synsedimentary fissures within microbial-metazoan reefs. Namapoikia formed laminar or domal morphologies with an internal structure of open tubules and transverse elements, and had a very plastic, non-deterministic growth form which could encrust both fully lithified surfaces as well as living microbial substrates, the latter via modified skeletal holdfasts. Namapoikia shows complex growth interactions and substrate competition with contemporary living microbialites and thrombolites, including the production of plate-like dissepiments in response to microbial overgrowth which served to elevate soft tissue above the microbial surface. Namapoikia could also recover from partial mortality due to microbial fouling. We infer initial skeletal growth to have propagated via the rapid formation of an organic scaffold via a basal pinacoderm prior to calcification. This is likely an ancient mode of biomineralization with similarities to the living calcified demosponge Vaceletia. Namapoikia also shows inferred skeletal growth banding which, combined with its large size, implies notable individual longevity. In sum, Namapoikia was a large, relatively long-lived Ediacaran clonal skeletal metazoan that propagated via an organic scaffold prior to calcification, enabling rapid, effective and dynamic substrate occupation and competition in cryptic reef settings. The open tubular internal structure, highly flexible, non-deterministic skeletal organization, and inferred style of biomineralization of Namapoikia places probable affinity within total-group poriferans. © 2018 The Author(s).

Variable-Internal-Stores models of microbial growth and metabolism with dynamic allocation of cellular resources.

PubMed

Nev, Olga A; van den Berg, Hugo A

2017-01-01

Variable-Internal-Stores models of microbial metabolism and growth have proven to be invaluable in accounting for changes in cellular composition as microbial cells adapt to varying conditions of nutrient availability. Here, such a model is extended with explicit allocation of molecular building blocks among various types of catalytic machinery. Such an extension allows a reconstruction of the regulatory rules employed by the cell as it adapts its physiology to changing environmental conditions. Moreover, the extension proposed here creates a link between classic models of microbial growth and analyses based on detailed transcriptomics and proteomics data sets. We ascertain the compatibility between the extended Variable-Internal-Stores model and the classic models, demonstrate its behaviour by means of simulations, and provide a detailed treatment of the uniqueness and the stability of its equilibrium point as a function of the availabilities of the various nutrients.

Assessment of the probability of contaminating Mars

NASA Technical Reports Server (NTRS)

Judd, B. R.; North, D. W.; Pezier, J. P.

1974-01-01

New methodology is proposed to assess the probability that the planet Mars will by biologically contaminated by terrestrial microorganisms aboard a spacecraft. Present NASA methods are based on the Sagan-Coleman formula, which states that the probability of contamination is the product of the expected microbial release and a probability of growth. The proposed new methodology extends the Sagan-Coleman approach to permit utilization of detailed information on microbial characteristics, the lethality of release and transport mechanisms, and of other information about the Martian environment. Three different types of microbial release are distinguished in the model for assessing the probability of contamination. The number of viable microbes released by each mechanism depends on the bio-burden in various locations on the spacecraft and on whether the spacecraft landing is accomplished according to plan. For each of the three release mechanisms a probability of growth is computed, using a model for transport into an environment suited to microbial growth.

Influence of diet on growth yields of rumen micro-organisms in vitro and in vivo: influence on growth yield of variable carbon fluxes to fermentation products.

PubMed

Blümmel, M; Karsli, A; Russell, J R

2003-09-01

The efficiency of rumen microbial production (EMP) in vitro and in vivo was examined for three roughages (lucerne (Medicago sativa L.) hay, oat (Avenia sativa L.)-berseem clover (Trifolium alexandrinum cultivar BigBee) hay and maize (Zea mays L.) crop residue (MCR)) and for five isonitrogenous (106 g crude protein (Nx6.25)/kg) diets formulated from lucerne hay, oat-berseem clover hay, MCR, soybean meal and maize grain to provide degradable intake protein for the production of 130 g microbial protein/kg total digestible nutrients. EMP in vivo was determined by intestinal purine recovery in sheep and ranged from 240 to 360 g microbial biomass/kg organic matter truly degraded in MCR and in one of the diets respectively (P<0.05). EMP in vitro was estimated by the substrate degraded : gas volume produced thereby (termed partitioning factor, PF (mg/ml)) at times of estimated peak microbial production and after 16.0 and 24.0 h of incubation. For the diets, PF values were significantly related to EMP in vivo at peak microbial production (P=0.04), but not after 16.0 (P=0.08) and 24.0 h (P=0.66). For roughages, PF values were significantly related to EMP in vivo only when measured after 16.0 h (P=0.04). For MCR and diets, a close non-linear relationship was found between PF values at peak microbial production and EMP in vivo (R(2) 0.99, P<0.0001) suggesting a maximum EMP in vivo of 0.39. Low gas production per unit substrate degraded (high PF) was associated with high EMP in vivo. The in vitro study of the products of fermentation, short-chain fatty acids, gases and microbial biomass (by purine analysis) after 16.0 h of incubation showed very strong relationships (R(2)> or =0.89, P<0.0001) between short-chain fatty acids, gases and gravimetrically measured apparent degradability. Except for maize grain, the true degradability of organic matter estimated by neutral-detergent solution treatment agreed with the sum of the products of fermentation (R(2) 0.81, P=0.0004). After 16.0 h of incubation, the synergistic effects of diet ingredient on diets were greater for microbial biomass (18 %) than for short-chain fatty acids and gas production (7 %). It is concluded that measurement of gas production only gives incomplete information about fodder quality; complementation of gas measurements by true degradability measurements is recommended.

Effect of cassava starch coating on quality and shelf life of fresh-cut pineapple (Ananas comosus L. Merril cv "Pérola").

PubMed

Bierhals, Vânia S; Chiumarelli, Marcela; Hubinger, Miriam D

2011-01-01

This research studied the influence of treatment with ascorbic acid, citric acid, and calcium lactate dipping and cassava starch edible coatings on quality parameters and shelf life of fresh-cut pineapple in slices during 12 d at 5 °C. After previous tests, the treatments selected for this study were samples dipped into antibrowning solution with 0.5% of ascorbic acid and 1% of citric acid, with and without 2% of calcium lactate and coated with 2% of cassava starch suspensions. Changes in weight loss, juice leakage, mechanical properties (stress at failure), color parameters (L* and H*), ascorbic acid content, sensory acceptance, and microbial growth of fruits were evaluated. Samples only treated with antibrowning agents were used as control. Edible coatings with and without calcium lactate were efficient in reducing weight loss, juice leakage, and maintaining firmness during storage. However, these samples showed more browning and the ascorbic acid content was reduced. All treatments presented good sensory acceptance (scores above 6). The determining factor of shelf life of pineapple slices was the microbial spoilage. A shelf life of 8 d was obtained for pineapple slices only treated with antibrowning agents. On the other hand, coated samples showed a reduced shelf life of 7 d and higher yeast and mold growth. Thus, although cassava starch coatings were efficient in reducing respiration rate, weight loss, and juice leakage and maintained mechanical properties, these treatments were not able to increase the shelf life of minimally processed pineapple. Practical Application: Pineapple fruit is highly appreciated for its aroma, flavor, and juiciness, but its immediate consumption is difficult. Therefore, pineapple is a potential fruit for minimal processing. However, shelf life of fresh-cut pineapple is very limited by changes in color, texture, appearance, off-flavors, and microbial growth. The use of edible coatings as gas and water vapor barrier and antibrowning agents can extend the storage time and maintain the quality of fresh-cut produce. Cassava starch and alginate coatings are alternative to preserve minimally processed pineapples without changing the quality parameters of fresh fruit. Thus, this study is useful for consumers and fresh-cut industry interested in knowing factors affecting shelf life and quality of fresh-cut pineapple.

Distinct growth strategies of soil bacteria as revealed by large-scale colony tracking.

PubMed

Ernebjerg, Morten; Kishony, Roy

2012-03-01

Our understanding of microbial ecology has been significantly furthered in recent years by advances in sequencing techniques, but comprehensive surveys of the phenotypic characteristics of environmental bacteria remain rare. Such phenotypic data are crucial for understanding the microbial strategies for growth and the diversity of microbial ecosystems. Here, we describe a high-throughput measurement of the growth of thousands of bacterial colonies using an array of flat-bed scanners coupled with automated image analysis. We used this system to investigate the growth properties of members of a microbial community from untreated soil. The system provides high-quality measurements of the number of CFU, colony growth rates, and appearance times, allowing us to directly study the distribution of these properties in mixed environmental samples. We find that soil bacteria display a wide range of growth strategies which can be grouped into several clusters that cannot be reduced to any of the classical dichotomous divisions of soil bacteria, e.g., into copiotophs and oligotrophs. We also find that, at early times, cells are most likely to form colonies when other, nearby colonies are present but not too dense. This maximization of culturability at intermediate plating densities suggests that the previously observed tendency for high density to lead to fewer colonies is partly offset by the induction of colony formation caused by interactions between microbes. These results suggest new types of growth classification of soil bacteria and potential effects of species interactions on colony growth.

Microbial growth under a high-pressure CO2 environment

NASA Astrophysics Data System (ADS)

Thompson, J. R.; Hernandez, H. H.

2009-12-01

Carbon capture and storage (CCS) of CO2 has the potential to significantly reduce the emission of greenhouse gasses associated with fossil fuel combustion. The largest potential for storing captured CO2 in the United Sates is in deep geologic saline formations. Currently, little is known about the effects of CO2 storage on biologically active microbial communities found in the deep earth biosphere. Therefore, to investigate how deep earth microbial communities will be affected by the storage of CO2, we have built a high-pressure microbial growth system in which microbial samples are subjected to a supercritical CO2 (scCO2) environment. Recently we have isolated a microbial consortium that is capable of growth and extracellular matrix production in nutrient media under a supercritical CO2 headspace. This consortium was cultivated from hydrocarbon residues associated with saline formation waters and includes members of the gram-positive Bacillus genus. The cultivation of actively growing cells in an environment containing scCO2 is unexpected based on previous experimental evidence of microbial sterilization attributed to the acidic, desiccating, and solvent-like properties of scCO2. Such microbial consortia have potential for development as (i) biofilm barriers for geological carbon-dioxide sequestration, and as (ii) agents of biocatalysis in environmentally-friendly supercritical (sc) CO2 solvent systems. The discovery that microbes can remain biologically active, and grow, in these environments opens new frontiers for the use of self-regenerating biological systems in engineering applications.

Groundwater-fed Iron-rich Microbial Mats in a Freshwater Creek: Growth Cycles and Fossilization Potential of Microbial Features

NASA Astrophysics Data System (ADS)

Schieber, J.

2004-03-01

Study of modern microbial mats produced by iron precipitating microbes. Aging and compaction experiments to evaluate fossilization potential and likelihood to recognize these deposits in the rock record.

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 remediation amendments on vadose zone microorganisms

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

Miller, Hannah M.; Tilton, Fred A.

2012-08-10

Surfactant-based foam delivery technology has been studied to remediate Hanford 200 area deep vadose zone sediment. However, the surfactants and remediation amendments have an unknown effect on indigenous subsurface microorganisms. Microbial populations are important factors to consider in remediation efforts due to their potential to alter soil geochemistry. This project focuses on measuring microbial metabolic responses to remediation amendments in batch and column studies using Deep Vadose Zone Sediments. Initial studies of the microbes from Hanford 200 area deep vadose zone sediment showed surfactants sodium dodecyl sulfate (SDS) and cocamidopropyl betaine (CAPB) and remediation amendment calcium polysulfide (CPS) had nomore » affect on microbial growth using BiologTM Ecoplates. To move towards a more realistic field analog, soil columns were packed with Hanford 200 Area sediment. Once microbial growth in the column was verified by observing growth of the effluent solution on tryptic soy agar plates, remedial surfactants were injected into the columns, and the resulting metabolic diversity was measured. Results suggest surfactant sodium dodecyl sulfate (SDS) stimulates microbial growth. The soil columns were also visualized using X-ray microtomography to inspect soil packing and possibly probe for evidence of biofilms. Overall, BiologTM Ecoplates provide a rapid assay to predict effects of remediation amendments on Hanford 200 area deep vadose zone microorganisms.« less

The role of lactic acid bacteria (Lactobacillus sp yel133) from beef in inhibiting of microbial contaminants on various fillers of starter culture

NASA Astrophysics Data System (ADS)

Yunilas; Mirwandhono, E.

2018-02-01

The role of Lactic Acid Bacteria (LAB) on the starter culture can be seen from the ability to grow and suppress the growth of microbial contaminants (fungi). The research aimed to investigate the role of LAB (Lactobacillus sp YEL133) in inhibiting microbial contaminants (fungi) on starter cultures of various fillers. The materials used in this research was Lactobacillus sp YEL133 from beef and various fillers (rice flour, corn starch and wheat flour). The research methods used completely randomized design (CRD) with 3 treatments and 4 replications. The treatments of this research was P1(rice flour), P2 (corn starch) and P3 (wheat flour) that inoculated with Lactobacillus sp YEL133. Parameters which is observed such as: growth of lactic acid bacteria, total microbes and total fungi as microbial contaminants. The results showed that the starter culture with a filler material of rice flour produce lactic acid bacteria and microbes were highly significant (P <0.01) for corn starch and wheat flour, as well as able to suppress the growth of microbial contaminants (fungi). The conclusion of the research is the use Lactobacillus sp YEL133 can suppress the growth of fungi on the starter culture using rice flour.

Systems and Photosystems: Cellular Limits of Autotrophic Productivity in Cyanobacteria

PubMed Central

Burnap, Robert L.

2014-01-01

Recent advances in the modeling of microbial growth and metabolism have shown that growth rate critically depends upon the optimal allocation of finite proteomic resources among different cellular functions and that modeling growth rates becomes more realistic with the explicit accounting for the costs of macromolecular synthesis, most importantly, protein expression. The “proteomic constraint” is considered together with its application to understanding photosynthetic microbial growth. The central hypothesis is that physical limits of cellular space (and corresponding solvation capacity) in conjunction with cell surface-to-volume ratios represent the underlying constraints on the maximal rate of autotrophic microbial growth. The limitation of cellular space thus constrains the size the total complement of macromolecules, dissolved ions, and metabolites. To a first approximation, the upper limit in the cellular amount of the total proteome is bounded this space limit. This predicts that adaptation to osmotic stress will result in lower maximal growth rates due to decreased cellular concentrations of core metabolic proteins necessary for cell growth owing the accumulation of compatible osmolytes, as surmised previously. The finite capacity of membrane and cytoplasmic space also leads to the hypothesis that the species-specific differences in maximal growth rates likely reflect differences in the allocation of space to niche-specific proteins with the corresponding diminution of space devoted to other functions including proteins of core autotrophic metabolism, which drive cell reproduction. An optimization model for autotrophic microbial growth, the autotrophic replicator model, was developed based upon previous work investigating heterotrophic growth. The present model describes autotrophic growth in terms of the allocation protein resources among core functional groups including the photosynthetic electron transport chain, light-harvesting antennae, and the ribosome groups. PMID:25654078

The Underlying Ecological Processes of Gut Microbiota Among Cohabitating Retarded, Overgrown and Normal Shrimp.

PubMed

Xiong, Jinbo; Dai, Wenfang; Zhu, Jinyong; Liu, Keshao; Dong, Chunming; Qiu, Qiongfen

2017-05-01

Increasing evidence of tight links among the gut microbiota, obesity, and host health has emerged, but knowledge of the ecological processes that shape the variation in microbial assemblages across growth rates remains elusive. Moreover, inadequately control for differences in factors that profoundly affect the gut microbial community, hampers evaluation of the gut microbiota roles in regulating growth rates. To address this gap, we evaluated the composition and ecological processes of the gut bacterial community in cohabitating retarded, overgrown, and normal shrimps from identically managed ponds. Gut bacterial community structures were distinct (P = 0.0006) among the shrimp categories. Using a structural equation modeling (SEM), we found that changes in the gut bacterial community were positively related to digestive activities, which subsequently affected shrimp growth rate. This association was further supported by intensified interspecies interaction and enriched lineages with high nutrient intake efficiencies in overgrown shrimps. However, the less phylogenetic clustering of gut microbiota in overgrown and retarded subjects may offer empty niches for pathogens invasion, as evidenced by higher abundances of predicted functional pathways involved in disease infection. Given no differences in biotic and abiotic factors among the cohabitating shrimps, we speculated that the distinct gut community assembly could be attributed to random colonization in larval shrimp (e.g., priority effects) and that an altered microbiota could be a causative factor in overgrowth or retardation in shrimp. To our knowledge, this is the first study to provide an integrated overview of the direct roles of gut microbiota in shaping shrimp growth rate and the underlying ecological mechanisms.

Impacts of Microbial Growth on the Air Quality of the International Space Station

NASA Technical Reports Server (NTRS)

Macatangay, Ariel V.; Bruce, Rebekah J.

2009-01-01

An understanding of the various sources of non-methane volatile organic compounds (NMVOCs) is one facet to ensuring the habitability of crewed spacecraft. Even though the International Space Station (ISS) atmosphere is relatively well characterized in terms of what is in the atmosphere and approximately how much, linking the majority of these trace contaminants detected to their source is virtually impossible. Albeit a few of can be associated to a single source, the majority of these trace contaminants have their origins from multiple sources. On crewed spacecraft such as ISS, trace contaminants are broadly categorized as either coming from equipment, which includes systems and payloads, or from the metabolic processes of the crew members. Such widely encompassing categories clearly illustrate the difficulty in linking air contaminants to their source(s). It is well known that microbial growth in ISS can flourish if left unchecked. Although processes are in place to limit microbial growth, in reality, microbial growth has pervaded the habitable environment of ISS. This is simply a consequence of having crewed spacecraft, as humans are the largest contributor to the bioload. As with crew members, microbes also have metabolic processes which, in many ways, are comparable to human metabolism. As such, it can be expected that microbial growth can lead to the release of volatile organic compounds into the ISS atmosphere. Given a large enough microbial population, the impact to the air quality of ISS can be potentially large. A survey of the microbiology found in ISS will be presented as well as the possible types of volatile organic compounds that can result from such organisms. This will be correlated to the observations provided by ground-based analysis of ISS atmosphere samples.

Impacts of Microbial Growth on the Air Quality of the International Space Station

NASA Technical Reports Server (NTRS)

Macatangay, Ariel V.; Bruce, Rebekah J.

2010-01-01

An understanding of the various sources of non-methane volatile organic compounds (NMVOCs) is one facet to ensuring the habitability of crewed spacecraft. Even though the International Space Station (ISS) atmosphere is relatively well characterized in terms of what is in the atmosphere and approximately how much, linking the majority of these trace contaminants detected to their source is virtually impossible. Albeit a few of can be associated to a single source, the majority of these trace contaminants have their origins from multiple sources. On crewed spacecraft such as ISS, trace contaminants are broadly categorized as either coming from equipment, which includes systems and payloads, or from the metabolic processes of the crew members. Such widely encompassing categories clearly illustrate the difficulty in linking air contaminants to their source(s). It is well known that microbial growth in ISS can flourish if left unchecked. Although processes are in place to limit microbial growth, in reality, microbial growth has pervaded the habitable environment of ISS. This is simply a consequence of having crewed spacecraft, as humans are the largest contributor to the bioload. As with crew members, microbes also have metabolic processes which, in many ways, are comparable to human metabolism. As such, it can be expected that microbial growth can lead to the release of volatile organic compounds into the ISS atmosphere. Given a large enough microbial population, the impact to the air quality of ISS can be potentially large. A survey of the microbiology found in ISS will be presented as well as the possible types of volatile organic compounds that can result from such organisms. This will be correlated to the observations provided by ground-based analysis of ISS atmosphere samples

[Engineering photosynthetic cyanobacterial chassis: a review].

PubMed

Wu, Qin; Chen, Lei; Wang, Jiangxin; Zhang, Weiwen

2013-08-01

Photosynthetic cyanobacteria possess a series of good properties, such as their abilities to capture solar energy for CO2 fixation, low nutritional requirements for growth, high growth rate, and relatively simple genetic background. Due to the high oil price and increased concern of the global warming in recent years, cyanobacteria have attracted widespread attention because they can serve as an 'autotrophic microbial factory' for producing renewable biofuels and fine chemicals directly from CO2. Particularly, significant progress has been made in applying synthetic biology techniques and strategies to construct and optimize cyanobacteria chassis. In this article, we critically summarized recent advances in developing new methods to optimize cyanobacteria chassis, improving cyanobacteria photosynthetic efficiency, and in constructing cyanobacteria chassis tolerant to products or environmental stresses. In addition, various industrial applications of cyanobacteria chassis are also discussed.

Organophosphonates utilization by soil strains of Ochrobactrum anthropi and Achromobacter sp.

PubMed

Ermakova, Inna T; Shushkova, Tatyana V; Sviridov, Alexey V; Zelenkova, Nina F; Vinokurova, Natalya G; Baskunov, Boris P; Leontievsky, Alexey A

2017-07-01

Four bacterial strains from glyphosate- or alkylphosphonates-contaminated soils were tested for ability to utilize different organophosphonates. All studied strains readily utilized methylphosphonic acid and a number of other phosphonates, but differed in their ability to degrade glyphosate. Only strains Ochrobactrum anthropi GPK 3 and Achromobacter sp. Kg 16 utilized this compound after isolation from enrichment cultures with glyphosate. Achromobacter sp. MPK 7 from the same enrichment culture, similar to Achromobacter sp. MPS 12 from methylphosphonate-polluted source, required adaptation to growth on GP. Studied strains varied significantly in their growth parameters, efficiency of phosphonates degradation and characteristic products of this process, as well as in their energy metabolism. These differences give grounds to propose a possible model of interaction between these strains in microbial consortium in phosphonate-contaminated soils.

Better to light a candle than curse the darkness: illuminating spatial localization and temporal dynamics of rapid microbial growth in the rhizosphere

PubMed Central

Herron, Patrick M.; Gage, Daniel J.; Arango Pinedo, Catalina; Haider, Zane K.; Cardon, Zoe G.

2013-01-01

The rhizosphere is a hotbed of microbial activity in ecosystems, fueled by carbon compounds from plant roots. Basic questions about the location and dynamics of plant-spurred microbial growth in the rhizosphere are difficult to answer with standard, destructive soil assays mixing a multitude of microbe-scale microenvironments in a single, often sieved, sample. Soil microbial biosensors designed with the luxCDABE reporter genes fused to a promoter of interest enable continuous imaging of the microbial perception of (and response to) environmental conditions in soil. We used the common soil bacterium Pseudomonas putida KT2440 as host to plasmid pZKH2 containing a fusion between the strong constitutive promoter nptII and luxCDABE (coding for light-emitting proteins) from Vibrio fischeri. Experiments in liquid media demonstrated that high light production by KT2440/pZKH2 was associated with rapid microbial growth supported by high carbon availability. We applied the biosensors in microcosms filled with non-sterile soil in which corn (Zea mays L.), black poplar (Populus nigra L.), or tomato (Solanum lycopersicum L.) was growing. We detected minimal light production from microbiosensors in the bulk soil, but biosensors reported continuously from around roots for as long as six days. For corn, peaks of luminescence were detected 1–4 and 20–35 mm along the root axis behind growing root tips, with the location of maximum light production moving farther back from the tip as root growth rate increased. For poplar, luminescence around mature roots increased and decreased on a coordinated diel rhythm, but was not bright near root tips. For tomato, luminescence was dynamic, but did not exhibit a diel rhythm, appearing in acropetal waves along roots. KT2440/pZKH2 revealed that root tips are not always the only, or even the dominant, hotspots for rhizosphere microbial growth, and carbon availability is highly variable in space and time around roots. PMID:24032034

A synthetic microbial consortium of Shewanella and Bacillus for enhanced generation of bioelectricity.

PubMed

Liu, Ting; Yu, Yang-Yang; Chen, Tao; Chen, Wei Ning

2017-03-01

In this study, a synthetic microbial consortium containing exoelectrogen Shewanella oneidensis MR-1 and riboflavin-producing strain, Bacillus subtilis RH33, was rationally designed and successfully constructed, enabling a stable, multiple cycles of microbial fuel cells (MFCs) operation for more than 500 h. The maximum power density of MFCs with this synthetic microbial consortium was 277.4 mW/m 2 , which was 4.9 times of that with MR-1 (56.9 mW/m 2 ) and 40.2 times of RH33 (6.9 mW/m 2 ), separately. At the same time, the Coulombic efficiency of the synthetic microbial consortium (5.6%) was higher than MR-1 (4.1%) and RH33 (2.3%). Regardless the high concentration of riboflavin produced by RH33, the power density of RH33 was rather low. The low bioelectricity generation can be ascribed to the low efficiency of RH33 in utilizing riboflavin for extracellular electron transfer (EET). In the synthetic microbial consortium of MR-1 and RH33, it was found that both mediated and direct electron transfer efficiencies were enhanced. By exchanging the anolyte of MR-1 and RH33, it was confirmed that the improved MFC performance with the synthetic microbial consortium was because MR-1 could efficiently utilize the high concentration of riboflavin produced by RH33. Biotechnol. Bioeng. 2017;114: 526-532. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Increasing strawberry shelf-life with carvacrol and methyl cinnamate antimicrobial vapors released from edible films (abstract)

USDA-ARS?s Scientific Manuscript database

Shelf life of strawberries (Fragaria x ananassa) is limited by decay caused by microbial growth that negatively impacts their color, texture and weight. Plant natural volatile compounds, such as terpenoids and esters, have been reported to be effective against microbial pathogen growth. The advantag...

BIODEGRADATION DURING CONTAMINANT TRANSPORT IN POROUS MEDIA. 4. IMPACT OF MICROBIAL LAG AND BACTERIAL CELL GROWTH. (R825415)

EPA Science Inventory

Abstract

Miscible-displacement experiments were conducted to examine the impact of microbial lag and bacterial cell growth on the transport of salicylate, a model hydrocarbon compound. The impacts of these processes were examined separately, as well as jointly, to dete...

Effect of temperature on microbial growth rate - thermodynamic analysis, the arrhenius and eyring-polanyi connection

USDA-ARS?s Scientific Manuscript database

The objective of this work is to develop a new thermodynamic mathematical model for evaluating the effect of temperature on the rate of microbial growth. The new mathematical model is derived by combining the Arrhenius equation and the Eyring-Polanyi transition theory. The new model, suitable for ...

On Growth and Form of the Zebrafish Gut Microbiome

NASA Astrophysics Data System (ADS)

Jemielita, Matthew; Taormina, Michael; Rolig, Annah; Burns, Adam; Hampton, Jennifer; Guillemin, Karen; Parthasarathy, Raghuveer

2014-03-01

The vertebrate gut is home to a diverse microbial community whose composition has a strong influence on the development and health of the host organism. Researchers can identify the members of the microbiota, yet little is known about the spatial and temporal dynamics of these microbial communities, including the mechanisms guiding their nucleation, growth, and interactions. We address these issues using the larval zebrafish (Danio rerio) as a model organism, which are raised microbe-free and then inoculated with controlled compositions of fluorophore-expressing bacteria. Live imaging using light sheet fluorescence microscopy enables visualization of the gut's entire microbial population over the first 24 hours of colonization. Image analysis allows us to quantify microbial populations that range from a few individuals to tens of thousands of microbes, and analyze the structure and growth kinetics of gut bacterial communities. We find that genetically-identical microbes can show surprisingly different growth rates and colonization abilities depending on their order of arrival. This demonstrates that knowing only the constituents of the gut community is insufficient to determine their dynamics; rather, the history of colonization matters.

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

PubMed

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

2013-12-01

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

An investigation of the sensitivity of low-field nuclear magnetic resonance to microbial growth and activity

NASA Astrophysics Data System (ADS)

Zhang, C.; Keating, K.

2014-12-01

Microbes and microbial processes play a significant role in shaping subsurface environments and are involved in applications ranging from microbially enhanced oil recovery to soil and groundwater contaminant remediation. Stimulated microbial growth in such applications could cause wide variety of changes of physical/chemical properties in the subsurface; however, due to the complexity of subsurface systems,it is difficult to monitor the growth of microbes and microbial activity in porous media. The focus of this research is to determine if low-field nuclear magnetic resonance (NMR), a method used in well logging to characterize fluids in hydrocarbon reservoirs or water in aquifers, can be used to directly detect the presence and the growth of microbes in geologic media. In this laboratory study, low-field NMR (2 MHz) relaxation measurements were collected on microbial suspensions with measured densities (i.e. biomasses), microbial pellets (live and dead), and inoculated silica. We focus on the direct contribution of microbes to the NMR signals in the absence of biomineralization. Shewanella oneidensis (MR-1), a facultative metal reducer known to play an important role in subsurface environments, were used as a model organism and were inoculated under aerobic condition. Data were collected using a CPMG pulse sequence, which was to determine the T2-distribution, and using a gradient spin-echo (PGSE) plus CPMG pulse sequence, which was used to encode diffusion properties and determine the effective diffusion-spin-spin relaxation correlation (D-T2) plot. Our data show no obvious change in the T2-distribution as S. oneidensis density varied in suspension, but show a clear distinction in the T2-distribution and D-T2 plots between live and dead cell pellets. A decrease in the T2-distribution is observed in the inoculated sand column. These results will provide a basis for understanding the effect of microbes within geologic media on low-field NMR measurements. This research is necessary to determine if NMR measurements can ultimately to be used to monitor microbial growth and activity in oil reservoirs or contaminated aquifers.

Short- and long-term influence of stand density on soil microbial communities in ponderosa pine forests

Treesearch

Steven T. Overby

2009-01-01

Soil microbial communities process plant detritus and returns nutrients needed for plant growth. Increased knowledge of this intimate linkage between plant and soil microbial communities will provide a better understanding of ecosystem response to changing abiotic and biotic conditions. This dissertation consists of three studies to determine soil microbial community...

Sludge reduction and microbial community structure in an anaerobic/anoxic/oxic process coupled with potassium ferrate disintegration.

PubMed

An, Ying; Zhou, Zhen; Yao, Jie; Niu, Tianhao; Qiu, Zhan; Ruan, Danian; Wei, Haijuan

2017-12-01

An anaerobic/anoxic/oxic (AAO) wastewater treatment system combining with a potassium ferrate (K 2 FeO 4 ) oxidation side-stream reactor (SSR) was proposed for sludge reduction. Batch experiments showed that optimal K 2 FeO 4 dosage and reaction time for sludge disintegration was 100mg/g suspended solids (SS) and 24h, respectively. Subsequently, an AAO-SSR and a conventional AAO were operated in parallel to investigate effects of K 2 FeO 4 oxidation on process performance, sludge characteristics and microbial community structures. The AAO-SSR process operated under the optimized condition achieved efficient COD and NH 4 + -N removal, and reduced sludge by 47.5% with observed yield coefficient of 0.21gSS/g COD. K 2 FeO 4 addition broke sludge particles, increased dissolved organic matters in the mixed liquor, and improved sludge dewaterability. Illumina-MiSeq sequencing results showed that K 2 FeO 4 oxidation in the AAO-SSR decreased microbial richness and diversity, enriched slow growers (Dechloromonas), anaerobic fermentative bacteria (Azospira) and Fe(III)-reducing bacteria (Ferribacterium), but limited the growth of phosphate-accumulating organisms. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microbial interactions in building of communities

PubMed Central

Wright, Christopher J.; Burns, Logan H.; Jack, Alison A.; Back, Catherine R.; Dutton, Lindsay C.; Nobbs, Angela H.; Lamont, Richard J.; Jenkinson, Howard F.

2012-01-01

SUMMARY Establishment of a community is considered to be essential for microbial growth and survival in the human oral cavity. Biofilm communities have increased resilience to physical forces, antimicrobial agents, and nutritional variations. Specific cell-to-cell adherence processes, mediated by adhesin-receptor pairings on respective microbial surfaces, are able to direct community development. These interactions co-localize species in mutually beneficial relationships, such as streptococci, veillonellae, Porphyromonas gingivalis and Candida albicans. In transition from the planktonic mode of growth to a biofilm community, microorganisms undergo major transcriptional and proteomic changes. These occur in response to sensing of diffusible signals, such as autoinducer molecules, and to contact with host tissues or other microbial cells. Underpinning many of these processes are intracellular phosphorylation events that regulate a large number of microbial interactions relevant to community formation and development. PMID:23253299

A Community-Based Culture Collection for Targeting Novel Plant Growth-Promoting Bacteria from the Sugarcane Microbiome

PubMed Central

Armanhi, Jaderson Silveira Leite; de Souza, Rafael Soares Correa; Damasceno, Natália de Brito; de Araújo, Laura M.; Imperial, Juan; Arruda, Paulo

2018-01-01

The soil-plant ecosystem harbors an immense microbial diversity that challenges investigative approaches to study traits underlying plant-microbe association. Studies solely based on culture-dependent techniques have overlooked most microbial diversity. Here we describe the concomitant use of culture-dependent and -independent techniques to target plant-beneficial microbial groups from the sugarcane microbiome. The community-based culture collection (CBC) approach was used to access microbes from roots and stalks. The CBC recovered 399 unique bacteria representing 15.9% of the rhizosphere core microbiome and 61.6–65.3% of the endophytic core microbiomes of stalks. By cross-referencing the CBC (culture-dependent) with the sugarcane microbiome profile (culture-independent), we designed a synthetic community comprised of naturally occurring highly abundant bacterial groups from roots and stalks, most of which has been poorly explored so far. We then used maize as a model to probe the abundance-based synthetic inoculant. We show that when inoculated in maize plants, members of the synthetic community efficiently colonize plant organs, displace the natural microbiota and dominate at 53.9% of the rhizosphere microbial abundance. As a result, inoculated plants increased biomass by 3.4-fold as compared to uninoculated plants. The results demonstrate that abundance-based synthetic inoculants can be successfully applied to recover beneficial plant microbes from plant microbiota. PMID:29354144

Reproduction allocation and potential mechanism of individual allelopathic rice plants in the presence of competing barnyardgrass.

PubMed

Kong, Chui-Hua; Wang, Ming-Li; Wang, Peng; Ni, Han-Wen; Meng, Xiang-Rui

2013-01-01

In spite of increasing knowledge of allelopathic rice as an efficient component involved in paddy weed management, relatively little is known about its reproduction in response to competing weeds. Reproduction allocation of individual allelopathic rice plants in relation to monoculture and mixed culture with competing barnyardgrass in a paddy field was studied, along with analyses of soil nutrients and microbial communities to understand the potential mechanism. At a 1:1 barnyardgrass and rice mixture proportion identified from a replacement series study, biomass, grain yield and major parameters of individual allelopathic rice plants at the mature stage were increased by competing barnyardgrass. There was no difference in allelopathic rice root-zone soil ammonium N and Olsen P between monoculture and mixed culture. However, mixed culture altered soil microbial biomass C and communities. When mixed with barnyardgrass, allelopathic rice root zone had an 87% increase in soil microbial biomass C. Phospholipid fatty acid (PLFA) profiling indicated that the signature lipid biomarkers of bacteria, actinobacteria and fungi were affected by mixed culture. Principal component analysis clearly identified differences in the composition of PLFA in different soil samples. Allelopathic rice specific changes in soil microbial communities may generate a positive feedback on its own growth and reproduction in the presence of competing barnyardgrass in a given paddy system. Copyright © 2012 Society of Chemical Industry.

Linking biofilm growth to fouling and aeration performance of fine-pore diffuser in activated sludge.

PubMed

Garrido-Baserba, Manel; Asvapathanagul, Pitiporn; McCarthy, Graham W; Gocke, Thomas E; Olson, Betty H; Park, Hee-Deung; Al-Omari, Ahmed; Murthy, Sudhir; Bott, Charles B; Wett, Bernhard; Smeraldi, Joshua D; Shaw, Andrew R; Rosso, Diego

2016-03-01

Aeration is commonly identified as the largest contributor to process energy needs in the treatment of wastewater and therefore garners significant focus in reducing energy use. Fine-pore diffusers are the most common aeration system in municipal wastewater treatment. These diffusers are subject to fouling and scaling, resulting in loss in transfer efficiency as biofilms form and change material properties producing larger bubbles, hindering mass transfer and contributing to increased plant energy costs. This research establishes a direct correlation and apparent mechanistic link between biofilm DNA concentration and reduced aeration efficiency caused by biofilm fouling. Although the connection between biofilm growth and fouling has been implicit in discussions of diffuser fouling for many years, this research provides measured quantitative connection between the extent of biofouling and reduced diffuser efficiency. This was clearly established by studying systematically the deterioration of aeration diffusers efficiency during a 1.5 year period, concurrently with the microbiological study of the biofilm fouling in order to understand the major factors contributing to diffuser fouling. The six different diffuser technologies analyzed in this paper included four different materials which were ethylene-propylene-diene monomer (EPDM), polyurethane, silicone and ceramic. While all diffusers foul eventually, some novel materials exhibited fouling resistance. The material type played a major role in determining the biofilm characteristics (i.e., growth rate, composition, and microbial density) which directly affected the rate and intensity at what the diffusers were fouled, whereas diffuser geometry exerted little influence. Overall, a high correlation between the increase in biofilm DNA and the decrease in αF was evident (CV < 14.0 ± 2.0%). By linking bacterial growth with aeration efficiency, the research was able to show quantitatively the causal connection between bacterial fouling and energy wastage during aeration. Copyright © 2015 Elsevier Ltd. All rights reserved.

Interactions Between Mineral Surfaces, Substrates, Enzymes, and Microbes Result in Hysteretic Temperature Sensitivities and Microbial Carbon Use Efficiencies and Weaker Predicted Carbon-Climate Feedbacks

NASA Astrophysics Data System (ADS)

Riley, W. J.; Tang, J.

2014-12-01

We hypothesize that the large observed variability in decomposition temperature sensitivity and carbon use efficiency arises from interactions between temperature, microbial biogeochemistry, and mineral surface sorptive reactions. To test this hypothesis, we developed a numerical model that integrates the Dynamic Energy Budget concept for microbial physiology, microbial trait-based community structure and competition, process-specific thermodynamically ­­based temperature sensitivity, a non-linear mineral sorption isotherm, and enzyme dynamics. We show, because mineral surfaces interact with substrates, enzymes, and microbes, both temperature sensitivity and microbial carbon use efficiency are hysteretic and highly variable. Further, by mimicking the traditional approach to interpreting soil incubation observations, we demonstrate that the conventional labile and recalcitrant substrate characterization for temperature sensitivity is flawed. In a 4 K temperature perturbation experiment, our fully dynamic model predicted more variable but weaker carbon-climate feedbacks than did the static temperature sensitivity and carbon use efficiency model when forced with yearly, daily, and hourly variable temperatures. These results imply that current earth system models likely over-estimate the response of soil carbon stocks to global warming.

High throughput automated microbial bioreactor system used for clone selection and rapid scale-down process optimization.

PubMed

Velez-Suberbie, M Lourdes; Betts, John P J; Walker, Kelly L; Robinson, Colin; Zoro, Barney; Keshavarz-Moore, Eli

2018-01-01

High throughput automated fermentation systems have become a useful tool in early bioprocess development. In this study, we investigated a 24 x 15 mL single use microbioreactor system, ambr 15f, designed for microbial culture. We compared the fed-batch growth and production capabilities of this system for two Escherichia coli strains, BL21 (DE3) and MC4100, and two industrially relevant molecules, hGH and scFv. In addition, different carbon sources were tested using bolus, linear or exponential feeding strategies, showing the capacity of the ambr 15f system to handle automated feeding. We used power per unit volume (P/V) as a scale criterion to compare the ambr 15f with 1 L stirred bioreactors which were previously scaled-up to 20 L with a different biological system, thus showing a potential 1,300 fold scale comparability in terms of both growth and product yield. By exposing the cells grown in the ambr 15f system to a level of shear expected in an industrial centrifuge, we determined that the cells are as robust as those from a bench scale bioreactor. These results provide evidence that the ambr 15f system is an efficient high throughput microbial system that can be used for strain and molecule selection as well as rapid scale-up. © 2017 The Authors Biotechnology Progress published by Wiley Periodicals, Inc. on behalf of American Institute of Chemical Engineers Biotechnol. Prog., 34:58-68, 2018. © 2017 The Authors Biotechnology Progress published by Wiley Periodicals, Inc. on behalf of American Institute of Chemical Engineers.

Microbial carbon metabolism associated with electrogenic sulphur oxidation in coastal sediments.

PubMed

Vasquez-Cardenas, Diana; van de Vossenberg, Jack; Polerecky, Lubos; Malkin, Sairah Y; Schauer, Regina; Hidalgo-Martinez, Silvia; Confurius, Veronique; Middelburg, Jack J; Meysman, Filip J R; Boschker, Henricus T S

2015-09-01

Recently, a novel electrogenic type of sulphur oxidation was documented in marine sediments, whereby filamentous cable bacteria (Desulfobulbaceae) are mediating electron transport over cm-scale distances. These cable bacteria are capable of developing an extensive network within days, implying a highly efficient carbon acquisition strategy. Presently, the carbon metabolism of cable bacteria is unknown, and hence we adopted a multidisciplinary approach to study the carbon substrate utilization of both cable bacteria and associated microbial community in sediment incubations. Fluorescence in situ hybridization showed rapid downward growth of cable bacteria, concomitant with high rates of electrogenic sulphur oxidation, as quantified by microelectrode profiling. We studied heterotrophy and autotrophy by following (13)C-propionate and -bicarbonate incorporation into bacterial fatty acids. This biomarker analysis showed that propionate uptake was limited to fatty acid signatures typical for the genus Desulfobulbus. The nanoscale secondary ion mass spectrometry analysis confirmed heterotrophic rather than autotrophic growth of cable bacteria. Still, high bicarbonate uptake was observed in concert with the development of cable bacteria. Clone libraries of 16S complementary DNA showed numerous sequences associated to chemoautotrophic sulphur-oxidizing Epsilon- and Gammaproteobacteria, whereas (13)C-bicarbonate biomarker labelling suggested that these sulphur-oxidizing bacteria were active far below the oxygen penetration. A targeted manipulation experiment demonstrated that chemoautotrophic carbon fixation was tightly linked to the heterotrophic activity of the cable bacteria down to cm depth. Overall, the results suggest that electrogenic sulphur oxidation is performed by a microbial consortium, consisting of chemoorganotrophic cable bacteria and chemolithoautotrophic Epsilon- and Gammaproteobacteria. The metabolic linkage between these two groups is presently unknown and needs further study.

Effects of Supplementing Microbially-fermented Spent Mushroom Substrates on Growth Performance and Carcass Characteristics of Hanwoo Steers (a Field Study)

PubMed Central

Kim, Y. I.; Lee, Y. H.; Kim, K. H.; Oh, Y. K.; Moon, Y. H.; Kwak, W. S.

2012-01-01

This study evaluated the effect of dietary supplementation of microbially-fermented spent mushroom substrates (MFSMS) on weight gain, carcass characteristics, and economic efficiency of Hanwoo steers. Highly cellulolytic bacteria (Enterobacter spp. and Bacillus spp.) isolated from spent mushroom substrates (SMS) stacks were inoculated (1% v/v) into the SMS, which was anaerobically fermented and fed to the steers for 12.6 months during the growing and fattening periods. Growing Hanwoo steers were assigned to the control group without supplementation of Microbially-fermented SMS (MFSMS), to a treatment group with 50% of MFSMS (1/2 of the ad libitum group), and to a treatment group with ad libitum access to SMS (the ad libitum group). All the groups were fed the formulated feed and rice straw. The voluntary intake (DM basis) of MFSMS was 1.6 kg/d during the growing period and 1.4 kg/d during the fattening period. The voluntary rice straw intake decreased by 6 to 11%, but the total voluntary DMI increased by 7 to 15% with MFSMS fed. The increased DMI with MFSMS supplementation resulted in a tendency of increased (p = 0.055) live weight gain by 8 to 12% compared with the control group. At slaughtering, the supplementation of MFSMS increased (p<0.05) the ribeye area by an average of 10 cm2. In conclusion, feeding MFSMS improved growth performance and carcass traits of Hanwoo steers and could successfully replace a part of conventional roughage such as rice straw commonly used in Asian countries. PMID:25049519

[Microbial settlement of paint- and building-materials in the sphere of drinking water. 5. Communication: Macrocolonies on the cement mortar lining in a water main (author's transl)].

PubMed

Schoenen, D

1980-09-01

It is reported a microbial growth in form of macrocolonies on a cement mortar line in a potable water main. Simultaneously an increase of bacterial content in the water could be observed. The bacterial content could be reduced by chlorination, but the microbial growth on the surface of the lining was not suppressed. Macrocolonies could be observed the same as before at the last inspection 6 1/2 years after opening of the main.

The distinctive microbial community improves composting efficiency in a full-scale hyperthermophilic composting plant.

PubMed

Yu, Zhen; Tang, Jia; Liao, Hanpeng; Liu, Xiaoming; Zhou, Puxiong; Chen, Zhi; Rensing, Christopher; Zhou, Shungui

2018-06-07

The application of conventional thermophilic composting (TC) is limited by poor efficiency. Newly-developed hyperthermophilic composting (HTC) is expected to overcome this shortcoming. However, the characterization of microbial communities associated with HTC remains unclear. Here, we compared the performance of HTC and TC in a full-scale sludge composting plant, and found that HTC running at the hyperthermophilic and thermophilic phases for 21 days, led to higher composting efficiency and techno-economic advantages over TC. Results of high-throughput sequencing showed drastic changes in the microbial community during HTC. Thermaceae (35.5-41.7%) was the predominant family in the hyperthermophilic phase, while the thermophilic phase was dominated by both Thermaceae (28.0-53.3%) and Thermoactinomycetaceae (29.9-36.1%). The change of microbial community could be the cause of continuous high temperature in HTC, and thus improve composting efficiency by accelerating the maturation process. This work has provided theoretical and practical guidance for managing sewage sludge by HTC. Copyright © 2018 Elsevier Ltd. All rights reserved.

Efficient breaking of water/oil emulsions by a newly isolated de-emulsifying bacterium, Ochrobactrum anthropi strain RIPI5-1.

PubMed

Mohebali, Ghasemali; Kaytash, Ashk; Etemadi, Narges

2012-10-01

Water-oil emulsions occur throughout oil production, transportation, and processing. The breaking of the water/oil emulsion improves oil quality and as a consequence chemically synthesized de-emulsifiers are commonly used in the petroleum industries. Microbial de-emulsifiers represent potential alternatives to the chemicals and may become important products for petroleum industries. The main goal of this work was isolation, identification, and characterization of an efficient de-emulsifying bacterium. Following a multi-step enrichment programme a de-emulsifying bacterium, Ochrobactrum anthropi strain RIPI5-1was isolated from the oil-polluted sandy bank of Siri Island, Iran. The presence of an oil phase in growth medium was found to be unnecessary for production of the de-emulsifier. The de-emulsifying activity of both the whole culture and the cells of this strain was examined using a model multiple water-crude oil (w/o/w) emulsion. This w/o/w emulsion was used for the first time in microbial de-emulsification research. Whole cells of strain RIPI5-1 exhibited high de-emulsifying activity during the late-exponential growth and stationary phases; de-emulsifying activity of the whole culture was highest during the early-exponential growth phase. The time course of de-emulsification by whole culture and whole cells of strain RIPI5-1 was investigated; the initial rate (DeI(1)) of breaking of the multiple water-crude oil emulsion by whole culture and whole cells was calculated as 11% and 54%, respectively. However, overall de-emulsification (DeI(8.5)) for whole culture and whole cells was calculated as 63% and 72%, respectively. A clear correlation was observed between cell surface hydrophobicity and the de-emulsifying activity of whole cells. With the water/kerosene emulsion, emulsion half-life (t(1/2)) was found to be <0.5h. The potential activity of this strain was also explained using a complex oilfield emulsion. Copyright © 2012 Elsevier B.V. All rights reserved.

Importance of Soil Temperature for the Growth of Temperate Crops under a Tropical Climate and Functional Role of Soil Microbial Diversity.

PubMed

Sabri, Nurul Syazwani Ahmad; Zakaria, Zuriati; Mohamad, Shaza Eva; Jaafar, A Bakar; Hara, Hirofumi

2018-04-28

A soil cooling system that prepares soil for temperate soil temperatures for the growth of temperate crops under a tropical climate is described herein. Temperate agriculture has been threatened by the negative impact of temperature increases caused by climate change. Soil temperature closely correlates with the growth of temperate crops, and affects plant processes and soil microbial diversity. The present study focuses on the effects of soil temperatures on lettuce growth and soil microbial diversity that maintains the growth of lettuce at low soil temperatures. A model temperate crop, loose leaf lettuce, was grown on eutrophic soil under soil cooling and a number of parameters, such as fresh weight, height, the number of leaves, and root length, were evaluated upon harvest. Under soil cooling, significant differences were observed in the average fresh weight (P<0.05) and positive development of the roots, shoots, and leaves of lettuce. Janthinobacterium (8.142%), Rhodoplanes (1.991%), Arthrospira (1.138%), Flavobacterium (0.857%), Sphingomonas (0.790%), Mycoplana (0.726%), and Pseudomonas (0.688%) were the dominant bacterial genera present in cooled soil. Key soil fungal communities, including Pseudaleuria (18.307%), Phoma (9.968%), Eocronartium (3.527%), Trichosporon (1.791%), and Pyrenochaeta (0.171%), were also recovered from cooled soil. The present results demonstrate that the growth of temperate crops is dependent on soil temperature, which subsequently affects the abundance and diversity of soil microbial communities that maintain the growth of temperate crops at low soil temperatures.

Scan-o-matic: High-Resolution Microbial Phenomics at a Massive Scale

PubMed Central

Zackrisson, Martin; Hallin, Johan; Ottosson, Lars-Göran; Dahl, Peter; Fernandez-Parada, Esteban; Ländström, Erik; Fernandez-Ricaud, Luciano; Kaferle, Petra; Skyman, Andreas; Stenberg, Simon; Omholt, Stig; Petrovič, Uroš; Warringer, Jonas; Blomberg, Anders

2016-01-01

The capacity to map traits over large cohorts of individuals—phenomics—lags far behind the explosive development in genomics. For microbes, the estimation of growth is the key phenotype because of its link to fitness. We introduce an automated microbial phenomics framework that delivers accurate, precise, and highly resolved growth phenotypes at an unprecedented scale. Advancements were achieved through the introduction of transmissive scanning hardware and software technology, frequent acquisition of exact colony population size measurements, extraction of population growth rates from growth curves, and removal of spatial bias by reference-surface normalization. Our prototype arrangement automatically records and analyzes close to 100,000 growth curves in parallel. We demonstrate the power of the approach by extending and nuancing the known salt-defense biology in baker’s yeast. The introduced framework represents a major advance in microbial phenomics by providing high-quality data for extensive cohorts of individuals and generating well-populated and standardized phenomics databases PMID:27371952

Evaluation of indirect impedance for measuring microbial growth in complex food matrices.

PubMed

Johnson, N; Chang, Z; Bravo Almeida, C; Michel, M; Iversen, C; Callanan, M

2014-09-01

The suitability of indirect impedance to accurately measure microbial growth in real food matrices was investigated. A variety of semi-solid and liquid food products were inoculated with Bacillus cereus, Listeria monocytogenes, Staphylococcus aureus, Lactobacillus plantarum, Pseudomonas aeruginosa, Escherichia coli, Salmonella enteriditis, Candida tropicalis or Zygosaccharomyces rouxii and CO2 production was monitored using a conductimetric (Don Whitely R.A.B.I.T.) system. The majority (80%) of food and microbe combinations produced a detectable growth signal. The linearity of conductance responses in selected food products was investigated and a good correlation (R(2) ≥ 0.84) was observed between inoculum levels and times to detection. Specific growth rate estimations from the data were sufficiently accurate for predictive modeling in some cases. This initial evaluation of the suitability of indirect impedance to generate microbial growth data in complex food matrices indicates significant potential for the technology as an alternative to plating methods. Copyright © 2014 Elsevier Ltd. All rights reserved.

Bacteria with Phosphate Solubilizing Capacity Alter Mycorrhizal Fungal Growth Both Inside and Outside the Root and in the Presence of Native Microbial Communities.

PubMed

Ordoñez, Yuli Marcela; Fernandez, Belen Rocio; Lara, Lidia Susana; Rodriguez, Alia; Uribe-Vélez, Daniel; Sanders, Ian R

2016-01-01

Arbuscular mycorrhizal fungi (AMF) and phosphate solubilizing Pseudomonas bacteria (PSB) could potentially interact synergistically because PSB solubilize phosphate into a form that AMF can absorb and transport to the plant. However, very little is known about the interactions between these two groups of microorganisms and how they influence the growth of each other. We tested whether different strains of bacteria, that have the capacity to solubilize phosphate, are able to grow along AMF hyphae and differentially influence the growth of AMF both outside the roots of carrot in in vitro conditions and inside the roots of potato in the presence of a microbial community. We found strong effects of AMF on the growth of the different bacterial strains. Different bacterial strains also had very strong effects on the growth of AMF extraradical hyphae outside the roots of carrot and on colonization of potato roots by AMF. The differential effects on colonization occurred in the presence of a microbial community. Our results show that these two important groups of rhizosphere microorganisms indeed interact with each other. Such interactions could potentially lead to synergistic effects between the two groups but this could depend on whether the bacteria truly solubilize phosphate in the rhizosphere in the presence of microbial communities.

SHIMMER (1.0): a novel mathematical model for microbial and biogeochemical dynamics in glacier forefield ecosystems

NASA Astrophysics Data System (ADS)

Bradley, J. A.; Anesio, A. M.; Singarayer, J. S.; Heath, M. R.; Arndt, S.

2015-10-01

SHIMMER (Soil biogeocHemIcal Model for Microbial Ecosystem Response) is a new numerical modelling framework designed to simulate microbial dynamics and biogeochemical cycling during initial ecosystem development in glacier forefield soils. However, it is also transferable to other extreme ecosystem types (such as desert soils or the surface of glaciers). The rationale for model development arises from decades of empirical observations in glacier forefields, and enables a quantitative and process focussed approach. Here, we provide a detailed description of SHIMMER, test its performance in two case study forefields: the Damma Glacier (Switzerland) and the Athabasca Glacier (Canada) and analyse sensitivity to identify the most sensitive and unconstrained model parameters. Results show that the accumulation of microbial biomass is highly dependent on variation in microbial growth and death rate constants, Q10 values, the active fraction of microbial biomass and the reactivity of organic matter. The model correctly predicts the rapid accumulation of microbial biomass observed during the initial stages of succession in the forefields of both the case study systems. Primary production is responsible for the initial build-up of labile substrate that subsequently supports heterotrophic growth. However, allochthonous contributions of organic matter, and nitrogen fixation, are important in sustaining this productivity. The development and application of SHIMMER also highlights aspects of these systems that require further empirical research: quantifying nutrient budgets and biogeochemical rates, exploring seasonality and microbial growth and cell death. This will lead to increased understanding of how glacier forefields contribute to global biogeochemical cycling and climate under future ice retreat.

Microbial-Induced Heterogeneity in the Acoustic Properties of Porous Media

EPA Science Inventory

Acoustic wave data were acquired over a two-dimensional region of a microbial-stimulated sand column and an unstimulated sand column to assess the spatiotemporal changes in a porous medium caused by microbial growth and biofilm formation. The acoustic signals from the unstimulate...

Microbial resource management of one‐stage partial nitritation/anammox

PubMed Central

Vlaeminck, S. E.; De Clippeleir, H.; Verstraete, W.

2012-01-01

Summary About 30 full‐scale partial nitritation/anammox plants are established, treating mostly sewage sludge reject water, landfill leachate or food processing digestate. Although two‐stage and one‐stage processes each have their advantages, the one‐stage configuration is mostly applied, termed here as oxygen‐limited autotrophic nitrification/denitrification (OLAND), and is the focus of this review. The OLAND application domain is gradually expanding, with technical‐scale plants on source‐separated domestic wastewater, pre‐treated manure and sewage, and liquors from organic waste bioenergy plants. A ‘microbial resource management’ (MRM) OLAND framework was elaborated, showing how the OLAND engineer/operator (1: input) can design/steer the microbial community (2: biocatalyst) to obtain optimal functionality (3: output). In the physicochemical toolbox (1), design guidelines are provided, as well as advantages of different reactor technologies. Particularly the desirable aeration regime, feeding regime and shear forces are not clear yet. The development of OLAND trickling filters, membrane bioreactors and systems with immobilized biomass is awaited. The biocatalyst box (2) considers ‘Who’: biodiversity and its dynamic patterns, ‘What’: physiology, and ‘Where’: architecture creating substrate gradients. Particularly community dynamics and extracellular polymeric substances (EPS) still require insights. Performant OLAND (3) comprises fast start‐up (storage possibility; fast growth of anammox bacteria), process stability (endured biomass retention; stress resilience), reasonable overall costs, high nitrogen removal efficiency and a low environmental footprint. Three important OLAND challenges are elaborated in detailed frameworks, demonstrating how to maximize nitrogen removal efficiency, minimize NO and N2O emissions and obtain through OLAND a plant‐wide net energy gain from sewage treatment. PMID:22452819

Empirical evidence that soil carbon formation from plant inputs is positively related to microbial growth

Treesearch

Mark A. Bradford; Ashley D. Keiser; Christian A. Davies; Calley A. Mersmann; Michael S. Strickland

2012-01-01

Plant-carbon inputs to soils in the form of dissolved sugars, organic acids and amino acids fuel much of heterotrophic microbial activity belowground. Initial residence times of these compounds in the soil solution are on the order of hours, with microbial uptake a primary removal mechanism. Through microbial biosynthesis, the dissolved compounds become dominant...

Cell growth and protein expression of Shewanella oneidensis in biofilms and hydrogel-entrapped cultures.

PubMed

Zhang, Yingdan; Ng, Chun Kiat; Cohen, Yehuda; Cao, Bin

2014-05-01

The performance of biofilm-based bioprocesses is difficult to predict and control because of the intrinsic heterogeneous and dynamic properties of microbial biofilms. Biofilm mimics, such as microbial cells entrapped in polymeric scaffolds that are permeable for nutrients, have been proposed to replace real biofilms to achieve long-term robust performance in engineering applications. However, the physiological differences between cells that are physically entrapped in a synthetic polymeric matrix and biofilm cells that are encased in a self-produced polymeric matrix remain unknown. In this study, using Shewanella oneidensis as a model organism and alginate hydrogel as a model synthetic matrix, we compared the cell growth and protein expression in entrapped cultures and biofilms. The hydrogel-entrapped cultures were found to exhibit a growth rate comparable with biofilms. There was no substantial difference in cell viability, surface charge, as well as hydrophobicity between the cells grown in alginate hydrogel and those grown in biofilms. However, the gel-entrapped cultures were found to be physiologically different from biofilms. The gel-entrapped cultures had a higher demand for metabolic energy. The siderophore-mediated iron uptake was repressed in the gel-entrapped cells. The presence of the hydrogel matrix decreased the expression of proteins involved in biofilm formation, while inducing the production of extracellular DNA (eDNA) in the gel-entrapped cultures. These results advance the fundamental understanding of the physiology of hydrogel-entrapped cells, which can lead to more efficient biofilm mimic-based applications.

Priming alters soil carbon dynamics during forest succession

NASA Astrophysics Data System (ADS)

Qiao, Na; Xu, Xingliang; Wang, Juan; Kuzyakov, Yakov

2017-04-01

The mechanisms underlying soil carbon (C) dynamics during forest succession remain challenged. We examined priming of soil organic matter (SOM) decomposition along a vegetation succession: grassland, young and old-growth forests. Soil C was primed much more strongly in young secondary forest than in grassland or old-growth forest. Priming resulted in large C losses (negative net C balance) in young-forest soil, whereas C stocks increased in grassland and old-growth forest. Microbial composition assessed by phospholipid fatty acids (PLFA) and utilization of easily available organics (13C-PLFA) indicate that fungi were responsible for priming in young-forest soils. Consequently, labile C inputs released by litter decomposition and root exudation determine microbial functional groups that decompose SOM during forest succession. These findings provide novel insights into connections between SOM dynamics and stabilization with microbial functioning during forest succession and show that priming is an important mechanism for contrasting soil C dynamics in young and old-growth forests.

Controlling the Hydrolysis and Loss of Nitrogen Fertilizer (Urea) by using a Nanocomposite Favors Plant Growth.

PubMed

Zhou, Linglin; Zhao, Pan; Chi, Yu; Wang, Dongfang; Wang, Pan; Liu, Ning; Cai, Dongqing; Wu, Zhengyan; Zhong, Naiqin

2017-05-09

Urea tends to be hydrolyzed by urease and then migrate into the environment, which results in a low utilization efficiency and severe environmental contamination. To solve this problem, a network-structured nanocomposite (sodium humate-attapulgite-polyacrylamide) was fabricated and used as an excellent fertilizer synergist (FS) that could effectively inhibit the hydrolysis, reduce the loss, and enhance the utilization efficiency of nitrogen. Additionally, the FS exerted significant positive effects on the expression of several nitrogen-uptake-related genes, ion flux in maize roots, the growth of crops, and the organic matter in soil. The FS could modify the microbial community in the soil and increase the number of bacteria involved in nitrogen metabolism, organic matter degradation, the iron cycle, and photosynthesis. Importantly, this technology displayed a high biosafety and has a great potential to reduce nonpoint agricultural pollution. Therefore, this work provides a promising approach to manage nitrogen and to promote the sustainable development of agriculture and the environment. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantifying the effects of the division of labor in metabolic pathways

PubMed Central

Harvey, Emily; Heys, Jeffrey; Gedeon, TomáS̆

2014-01-01

Division of labor is commonly observed in nature. There are several theories that suggest diversification in a microbial community may enhance stability and robustness, decrease concentration of inhibitory intermediates, and increase efficiency. Theoretical studies to date have focused on proving when the stable co-existence of multiple strains occurs, but have not investigated the productivity or biomass production of these systems when compared to a single ‘super microbe’ which has the same metabolic capacity. In this work we prove that if there is no change in the growth kinetics or yield of the metabolic pathways when the metabolism is specialized into two separate microbes, the biomass (and productivity) of a binary consortia system is always less than that of the equivalent monoculture. Using a specific example of Escherichia coli growing on a glucose substrate, we find that increasing the growth rates or substrate affinities of the pathways is not sufficient to explain the experimentally observed productivity increase in a community. An increase in pathway efficiency (yield) in specialized organisms provides the best explanation of the observed increase in productivity. PMID:25038317

A novel process-based model of microbial growth: self-inhibition in Saccharomyces cerevisiae aerobic fed-batch cultures.

PubMed

Mazzoleni, Stefano; Landi, Carmine; Cartenì, Fabrizio; de Alteriis, Elisabetta; Giannino, Francesco; Paciello, Lucia; Parascandola, Palma

2015-07-30

Microbial population dynamics in bioreactors depend on both nutrients availability and changes in the growth environment. Research is still ongoing on the optimization of bioreactor yields focusing on the increase of the maximum achievable cell density. A new process-based model is proposed to describe the aerobic growth of Saccharomyces cerevisiae cultured on glucose as carbon and energy source. The model considers the main metabolic routes of glucose assimilation (fermentation to ethanol and respiration) and the occurrence of inhibition due to the accumulation of both ethanol and other self-produced toxic compounds in the medium. Model simulations reproduced data from classic and new experiments of yeast growth in batch and fed-batch cultures. Model and experimental results showed that the growth decline observed in prolonged fed-batch cultures had to be ascribed to self-produced inhibitory compounds other than ethanol. The presented results clarify the dynamics of microbial growth under different feeding conditions and highlight the relevance of the negative feedback by self-produced inhibitory compounds on the maximum cell densities achieved in a bioreactor.

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

PubMed

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

2016-03-15

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

Microbial Community Structure in the Rhizosphere of Rice Plants

PubMed Central

Breidenbach, Björn; Pump, Judith; Dumont, Marc G.

2016-01-01

The microbial community in the rhizosphere environment is critical for the health of land plants and the processing of soil organic matter. The objective of this study was to determine the extent to which rice plants shape the microbial community in rice field soil over the course of a growing season. Rice (Oryza sativa) was cultivated under greenhouse conditions in rice field soil from Vercelli, Italy and the microbial community in the rhizosphere of planted soil microcosms was characterized at four plant growth stages using quantitative PCR and 16S rRNA gene pyrotag analysis and compared to that of unplanted bulk soil. The abundances of 16S rRNA genes in the rice rhizosphere were on average twice that of unplanted bulk soil, indicating a stimulation of microbial growth in the rhizosphere. Soil environment type (i.e., rhizosphere versus bulk soil) had a greater effect on the community structure than did time (e.g., plant growth stage). Numerous phyla were affected by the presence of rice plants, but the strongest effects were observed for Gemmatimonadetes, Proteobacteria, and Verrucomicrobia. With respect to functional groups of microorganisms, potential iron reducers (e.g., Geobacter, Anaeromyxobacter) and fermenters (e.g., Clostridiaceae, Opitutaceae) were notably enriched in the rhizosphere environment. A Herbaspirillum species was always more abundant in the rhizosphere than bulk soil and was enriched in the rhizosphere during the early stage of plant growth. PMID:26793175

Antarctic strict anaerobic microbiota from Deschampsia antarctica vascular plants rhizosphere reveals high ecology and biotechnology relevance.

PubMed

Peixoto, Rafael José Marques; Miranda, Karla Rodrigues; Lobo, Leandro Araujo; Granato, Alessandra; de Carvalho Maalouf, Pedro; de Jesus, Hugo Emiliano; Rachid, Caio T C C; Moraes, Saulo Roni; Dos Santos, Henrique Fragoso; Peixoto, Raquel Silva; Rosado, Alexandre Soares; Domingues, Regina Maria Cavalcanti Pilotto

2016-11-01

The Antarctic soil microbial community has a crucial role in the growth and stabilization of higher organisms, such as vascular plants. Analysis of the soil microbiota composition in that extreme environmental condition is crucial to understand the ecological importance and biotechnological potential. We evaluated the efficiency of isolation and abundance of strict anaerobes in the vascular plant Deschampsia antarctica rhizosphere collected in the Antarctic's Admiralty Bay and associated biodiversity to metabolic perspective and enzymatic activity. Using anaerobic cultivation methods, we identified and isolated a range of microbial taxa whose abundance was associated with Plant Growth-Promoting Bacteria (PGPB) and presences were exclusively endemic to the Antarctic continent. Firmicutes was the most abundant phylum (73 %), with the genus Clostridium found as the most isolated taxa. Here, we describe two soil treatments (oxygen gradient and heat shock) and 27 physicochemical culture conditions were able to increase the diversity of anaerobic bacteria isolates. Heat shock treatment allowed to isolate a high percentage of new species (63.63 %), as well as isolation of species with high enzymatic activity (80.77 %), which would have potential industry application. Our findings contribute to the understanding of the role of anaerobic microbes regarding ecology, evolutionary, and biotechnological features essential to the Antarctic ecosystem.

Engineering strategies for the design of plant nutrient delivery systems for use in space: approaches to countering microbiological contamination

NASA Technical Reports Server (NTRS)

Gonzales, A. A.; Schuerger, A. C.; Barford, C.; Mitchell, R.

1996-01-01

Microbiological contamination of crops within space-based plant growth research chambers has been postulated as a potentially significant problem. Microbial infestations; fouling of Nutrient Delivery System (NDS) fluid loops; and the formation of biofilms have been suggested as the most obvious and important manifestations of the problem. Strict sanitation and quarantine procedures will reduce, but not eliminate, microbial species introduced into plant growth systems in space habitats. Microorganisms transported into space most likely will occur as surface contaminants on spacecraft components, equipment, the crew, and plant-propagative materials. Illustrations of the potential magnitude of the microbiological contamination issue will be drawn from the literature and from documentation of laboratory and commercial field experience. Engineering strategies for limiting contamination and for the development of countermeasures will be described. Microbiological control technologies and NDS hardware will be discussed. Configurations appropriate for microgravity research facilities, as well as anticipated bio-regenerative life support system implementations, will be explored. An efficiently designed NDS, capable of adequately meeting the environmental needs of crop plants in space, is considered to be critical in both the research and operational domains. Recommended experiments, tests, and technology developments, structured to allow the development of prudent engineering solutions also will be presented.

Cassava starch coating and citric acid to preserve quality parameters of fresh-cut "Tommy Atkins" mango.

PubMed

Chiumarelli, Marcela; Pereira, Leila M; Ferrari, Cristhiane C; Sarantópoulos, Claire I G L; Hubinger, Miriam D

2010-06-01

Combination of citric acid dipping (5 g/L) and cassava starch coating (10 g/L), with and without glycerol (10 g/L), was studied to verify the effectiveness of these treatments to inhibit enzymatic browning, to reduce respiration rate, and to preserve quality parameters of "Tommy Atkins" fresh-cut mangoes during storage at 5 degrees C. Color characteristics (L and C), mechanical properties (stress at failure), weight loss, beta-carotene content, sensory acceptance, and microbial growth of fruits were evaluated during 15 d. The respiration rate of fruit subjected to the treatments was also analyzed. Nontreated fresh-cut mango was used as a control sample. Cassava starch edible coatings and citric acid dipping promoted a decrease in respiration rate of mango slices, with values up to 41% lower than the control fruit. This treatment also promoted better preservation of texture and color characteristics of mangoes and delayed carotenoid formation and browning reactions during storage. Moreover, the treated fruit showed great sensory acceptance by consumers throughout the whole storage period. However, the use of glycerol in the coating formulation was not efficient in the maintenance of quality parameters of fresh-cut mangoes, promoting a higher weight loss of samples, impairing fruit texture characteristics, increasing carotenogenesis, and favoring microbial growth during storage.

Biohydrogen production in the suspended and attached microbial growth systems from waste pastry hydrolysate.

PubMed

Han, Wei; Hu, Yunyi; Li, Shiyi; Li, Feifei; Tang, Junhong

2016-10-01

Waste pastry was hydrolyzed by glucoamylase and protease which were obtained from solid state fermentation of Aspergillus awamori and Aspergillus oryzae to produce waste pastry hydrolysate. Then, the effects of hydraulic retention times (HRTs) (4-12h) on hydrogen production rate (HPR) in the suspended microbial growth system (continuous stirred tank reactor, CSTR) and attached microbial growth system (continuous mixed immobilized sludge reactor, CMISR) from waste pastry hydrolysate were investigated. The maximum HPRs of CSTR (201.8mL/(h·L)) and CMISR (255.3mL/(h·L)) were obtained at HRT of 6h and 4h, respectively. The first-order reaction could be used to describe the enzymatic hydrolysis of waste pastry. The carbon content of the waste pastry remained 22.8% in the undigested waste pastry and consumed 77.2% for carbon dioxide and soluble microbial products. To our knowledge, this is the first study which reports biohydrogen production from waste pastry. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

PubMed

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

2018-07-01

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

Rhizosphere effect of colonizer plant species on the development of soil microbial community during primary succession on postmining sites

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

Elhottova, D.; Kristufek, V.; Maly, S.

2009-07-01

The impact of pioneer plant species Tussilago farfara on structural, functional, and growth characterization of microbial community colonizing the spoil colliery substrate was studied in a laboratory microcosm experiment. Microcosms consisting of spoil substrate (0.7 dm{sup 3} of tertiary alkaline clay sediment from Sokolov brown-coal mine area) from a pioneer site (without vegetation, 5 years after heaping) were cultivated in a greenhouse with one plant of this species. Plant roots substantially increased microbial diversity and biomass after one season (7 months) of cultivation. Roots influenced the microbial community and had nearly twice the size, higher growth, and metabolic potential inmore » comparison to the control. The development of microbial specialists improves the plant nutrient status. Bacterial nitrogen (N{sub 2}) fixators (Bradyrhizobium japonicum, Rhizobium radiobacter) and arbuscular mycorrhizal fungi were confirmed in the rhizosphere of Tussilago farfara.« less

Study on distribution of reservoir endogenous microbe and oil displacement mechanism.

PubMed

Yue, Ming; Zhu, Weiyao; Song, Zhiyong; Long, Yunqian; Song, Hongqing

2017-02-01

In order to research oil displacement mechanism by indigenous microbial communities under reservoir conditions, indigenous microbial flooding experiments using the endogenous mixed bacterium from Shengli Oilfield were carried out. Through microscopic simulation visual model, observation and analysis of distribution and flow of the remaining oil in the process of water flooding and microbial oil displacement were conducted under high temperature and high pressure conditions. Research has shown that compared with atmospheric conditions, the growth of the microorganism metabolism and attenuation is slowly under high pressure conditions, and the existence of the porous medium for microbial provides good adhesion, also makes its growth cycle extension. The microbial activities can effectively launch all kinds of residual oil, and can together with metabolites, enter the blind holes off which water flooding, polymer flooding and gas flooding can't sweep, then swap out remaining oil, increase liquidity of the crude oil and remarkably improve oil displacement effect.

Community-level physiological profiling in microbial communities of broiler cecae

USDA-ARS?s Scientific Manuscript database

Poultry production constitutes one of important agricultural output worldwide. It is known that the gut health of broilers is essential for their growth and for providing wholesome products for human consumption. Previously, the microbial diversity of broiler cecae was studied at the microbial gen...

Cecum microbial communities from steers differing in feed efficiency

USDA-ARS?s Scientific Manuscript database

Aims: To characterize the microbial communities of the cecum among steers differing in feed efficiency. Methods and Results: Individual feed intake (FI) and body weight (BW) gain were determined from animals fed the same ration, within two contemporary groups of steers. BW gain was regressed on F...

Final Report: Development of Renewable Microbial Polyesters for Cost Effective and Energy- Efficient Wood-Plastic Composites

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

Thompson, David N.; Emerick, Robert W.; England, Alfred B.

In this project, we proposed to produce wood fiber reinforced thermoplastic composites (WFRTCs) using microbial thermoplastic polyesters in place of petroleum-derived plastic. WFRTCs are a rapidly growing product area, averaging a 38% growth rate since 1997. Their production is dependent on substantial quantities of petroleum based thermoplastics, increasing their overall energy costs by over 230% when compared to traditional Engineered Wood Products (EWP). Utilizing bio-based thermoplastics for these materials can reduce our dependence on foreign petroleum. We have demonstrated that biopolymers (polyhydroxyalkanoates, PHA) can be successfully produced from wood pulping waste streams and that viable wood fiber reinforced thermoplastic compositemore » products can be produced from these materials. The results show that microbial polyester (PHB in this study) can be extruded together with wastewater-derived cell mass and wood flour into deck products having performance properties comparable to existing commercial HDPE/WF composite products. This study has thus proven the underlying concept that the microbial polyesters produced from waste effluents can be used to make cost-effective and energy-efficient wood-plastic composites. The cost of purified microbial polyesters is about 5-20 times that of HDPE depending on the cost of crude oil, due to high purification (40%), carbon substrate (40%) and sterilized fermentation (20%) costs for the PHB. Hence, the ability to produce competitive and functional composites with unpurified PHA-biomass mixtures from waste carbon sources in unsterile systems—without cell debris removal—is a significant step forward in producing competitive value-added structural composites from forest products residuals using a biorefinery approach. As demonstrated in the energy and waste analysis for the project, significant energy savings and waste reductions can also be realized using this approach. We recommend that the next step for development of useful products using this technology is to scale the technology from the 700-L pilot reactor to a small-scale production facility, with dedicated operation staff and engineering controls. In addition, we recommend that a market study be conducted as well as further product development for construction products that will utilize the unique properties of this bio-based material.« less

Overproduction of laccase and pectinase by microbial associations in solid substrate fermentation.

PubMed

Stoilova, Ivanka; Krastanov, Albert

2008-04-01

The growth and the enzymatic production of two microbial fungal associations were studied: Aspergillus niger and Fusarium moniliforme and Trametes versicolor and Aspergillus niger. The synergistic interrelations between the species of the first mixed culture increased the biosynthesis of alpha-amylase and pectinase. T. versicolor and A. niger proved to be compatible partners in the overproduction of the enzyme laccase, whose synthesis surpassed 8.4 times the enzymatic level in the monoculture, with both of the mixed microbial populations cocultivation facilitating the amplified synthesis of enzymes rather than their growth acceleration. A further proof of the presence of synergism established by the cultures was the enzyme volumetric productivities in both of the mixed microbial cultures, which increased parallel to the rise in the combined biomass synthesis. The competent selection of compatible partners can adjust the desired enzymatic levels and compositions in mixed fungal systems aimed at a number of specified designations. Thus, a very high level of laccase production (97,600 IU/g dry weight) was achieved. The chosen fungal strains produce a variety of different enzymes, but first microbial association produces mainly amylase and pectinase, necessary for their growth, and second association produces mainly laccase and pectinase.

Comparison of heavy metal toxicity in continuous flow and batch reactors

NASA Astrophysics Data System (ADS)

Sengor, S. S.; Gikas, P.; Moberly, J. G.; Peyton, B. M.; Ginn, T. R.

2009-12-01

The presence of heavy metals may significantly affect microbial growth. In many cases, small amounts of particular heavy metals may stimulate microbial growth; however, larger quantities may result in microbial growth reduction. Environmental parameters, such as growth pattern may alter the critical heavy metal concentration, above which microbial growth stimulation turns to growth inhibition. Thus, it is important to quantify the effects of heavy metals on microbial activity for understanding natural or manmade biological reactors, either in situ or ex situ. Here we compare the toxicity of Zn and Cu on Arthrobacter sp., a heavy metal tolerant microorganism, under continuous flow versus batch reactor operations. Batch and continuous growth tests of Arthrobacter sp. were carried out at various individual and combined concentrations of Zn and Cu. Biomass concentration (OD) was measured for both the batch and continuous reactors, whereas ATP, oxygen uptake rates and substrate concentrations were additionally measured for the continuous system. Results indicated that Cu was more toxic than Zn under all conditions for both systems. In batch reactors, all tested Zn concentrations up to 150 uM showed a stimulatory effect on microbial growth. However, in the case of mixed Zn and Cu exposures, the presence of Zn either eliminated (at the 50 uM level both Zn and Cu) or reduced by ~25% (at the 100 and 150 uM levels both Zn and Cu) the Cu-induced inhibition. In the continuous system, only one test involved combined Cu (40uM) and Zn (125uM) and this test showed similar results to the 40uM Cu continuous test, i.e., no reduction in inhibition. The specific ATP concentration, i.e., ATP/OD, results for the continuous reactor showed an apparent recovery for both Cu-treated populations, although neither the OD nor glucose data showed any recovery. This may reflect that the individual microorganisms that survived after the addition of heavy metals, kept maintaining the usual ATP levels, as before metal addition. The last may imply a short of adaptation by some microorganisms to the presence of heavy metals. Overall, the batch reactor tests underestimated significantly the heavy metal inhibition, as compared to the continuous flow reactors. Therefore, the results of batch reactor tests should be used with some caution when heavy metal inhibition is to be interpreted for continuous flow natural environmental systems, such as rivers or wetlands.

Anaerobic Growth of Corynebacterium glutamicum via Mixed-Acid Fermentation

PubMed Central

Michel, Andrea; Koch-Koerfges, Abigail; Krumbach, Karin; Brocker, Melanie

2015-01-01

Corynebacterium glutamicum, a model organism in microbial biotechnology, is known to metabolize glucose under oxygen-deprived conditions to l-lactate, succinate, and acetate without significant growth. This property is exploited for efficient production of lactate and succinate. Our detailed analysis revealed that marginal growth takes place under anaerobic conditions with glucose, fructose, sucrose, or ribose as a carbon and energy source but not with gluconate, pyruvate, lactate, propionate, or acetate. Supplementation of glucose minimal medium with tryptone strongly enhanced growth up to a final optical density at 600 nm (OD600) of 12, whereas tryptone alone did not allow growth. Amino acids with a high ATP demand for biosynthesis and amino acids of the glutamate family were particularly important for growth stimulation, indicating ATP limitation and a restricted carbon flux into the oxidative tricarboxylic acid cycle toward 2-oxoglutarate. Anaerobic cultivation in a bioreactor with constant nitrogen flushing disclosed that CO2 is required to achieve maximal growth and that the pH tolerance is reduced compared to that under aerobic conditions, reflecting a decreased capability for pH homeostasis. Continued growth under anaerobic conditions indicated the absence of an oxygen-requiring reaction that is essential for biomass formation. The results provide an improved understanding of the physiology of C. glutamicum under anaerobic conditions. PMID:26276118

Biofilm growth on polyvinylchloride surface incubated in suboptimal microbial warm water and effect of sanitizers on biofilm removal post biofilm formation

USDA-ARS?s Scientific Manuscript database

An in vitro experiment was conducted to understand the nature of biofilm growth on polyvinyl chloride (PVC) surface when exposed to sub optimal quality microbial water (> 4 log10 cfu/ml) obtained from poultry drinking water source mimicking water in waterlines during the first week of poultry broodi...

Successional changes in the chicken cecal microbiome during 42 days of growth are independent of organic acid feed additives

USDA-ARS?s Scientific Manuscript database

Poultry remains a major source of foodborne infections in the U.S. and globally. A variety of additives with presumed anti-microbial and/or growth-promoting effects are commonly added to poultry feed, yet the effects of these additives on the ecology of the gastro-intestinal microbial community (th...

The relative importance of exogenous and substrate-derived nitrogen for microbial growth during leaf decomposition

Treesearch

B.M. Cheever; J. R. Webster; E. E. Bilger; S. A. Thomas

2013-01-01

Heterotrophic microbes colonizing detritus obtain nitrogen (N) for growth by assimilating N from their substrate or immobilizing exogenous inorganic N. Microbial use of these two pools has different implications for N cycling and organic matter decomposition in the face of the global increase in biologically available N. We used sugar maple leaves labeled with

Temperature control of microbial respiration and growth efficiency in the mesopelagic zone of the South Atlantic and Indian Oceans

NASA Astrophysics Data System (ADS)

Mazuecos, Ignacio P.; Arístegui, Javier; Vázquez-Domínguez, Evaristo; Ortega-Retuerta, Eva; Gasol, Josep M.; Reche, Isabel

2015-01-01

We have measured both prokaryotic heterotrophic production (PHP) and respiration (R), then providing direct estimates of prokaryotic growth efficiencies (PGE), in the upper mesopelagic zone (300-600 m) of the South Atlantic and Indian Oceans. Our results show that in situ R ranged 3-fold, from 87 to 238 μmol C m-3 d-1. In situ PHP rates were much lower but also more variable than R (ranging from 0.3 to 9.1 μmol C m-3 d-1). The derived in situ PGE values were on average ~1.4% (from 0.3% to 3.7%), indicating that most of the organic substrates incorporated by prokaryotes were respired instead of being used for growth. Together with the few previous studies on PGE published before for the Atlantic Ocean and Mediterranean Sea, our findings support the hypothesis that the global mesopelagic zone represents a key remineralization site for export production in the open ocean. We also found a strong correlation between R and PGE with temperature across a gradient ranging from 8.7 to 14.9 °C. The derived Q10 value of 3.7 suggests that temperature variability in the mesopelagic zone plays a significant role in the remineralization of organic matter.

Assessing an effective feeding strategy to optimize crude glycerol utilization as sustainable carbon source for lipid accumulation in oleaginous yeasts.

PubMed

Signori, Lorenzo; Ami, Diletta; Posteri, Riccardo; Giuzzi, Andrea; Mereghetti, Paolo; Porro, Danilo; Branduardi, Paola

2016-05-05

Microbial lipids can represent a valuable alternative feedstock for biodiesel production in the context of a viable bio-based economy. This production can be driven by cultivating some oleaginous microorganisms on crude-glycerol, a 10% (w/w) by-product produced during the transesterification process from oils into biodiesel. Despite attractive, the perspective is still economically unsustainable, mainly because impurities in crude glycerol can negatively affect microbial performances. In this view, the selection of the best cell factory, together with the development of a robust and effective production process are primary requirements. The present work compared crude versus pure glycerol as carbon sources for lipid production by three different oleaginous yeasts: Rhodosporidium toruloides (DSM 4444), Lipomyces starkeyi (DSM 70295) and Cryptococcus curvatus (DSM 70022). An efficient yet simple feeding strategy for avoiding the lag phase caused by growth on crude glycerol was developed, leading to high biomass and lipid production for all the tested yeasts. Flow-cytometry and fourier transform infrared (FTIR) microspectroscopy, supported by principal component analysis (PCA), were used as non-invasive and quick techniques to monitor, compare and analyze the lipid production over time. Gas chromatography (GC) analysis completed the quali-quantitative description. Under these operative conditions, the highest lipid content (up to 60.9% wt/wt) was measured in R. toruloides, while L. starkeyi showed the fastest glycerol consumption rate (1.05 g L(-1) h(-1)). Being productivity the most industrially relevant feature to be pursued, under the presented optimized conditions R. toruloides showed the best lipid productivity (0.13 and 0.15 g L(-1) h(-1) on pure and crude glycerol, respectively). Here we demonstrated that the development of an efficient feeding strategy is sufficient in preventing the inhibitory effect of crude glycerol, and robust enough to ensure high lipid accumulation by three different oleaginous yeasts. Single cell and in situ analyses allowed depicting and comparing the transition between growth and lipid accumulation occurring differently for the three different yeasts. These data provide novel information that can be exploited for screening the best cell factory, moving towards a sustainable microbial biodiesel production.

Hydrogen production from switchgrass via a hybrid pyrolysis-microbial electrolysis process

DOE PAGES

Lewis, Alex J.; Ren, Shoujie; Ye, Philip; ...

2015-06-30

A new approach to hydrogen production using a hybrid pyrolysis-microbial electrolysis process is described. The aqueous stream generated during pyrolysis of switchgrass was used as a substrate for hydrogen production in a microbial electrolysis cell, achieving a maximum hydrogen production rate of 4.3 L H2/L-day at a loading of 10 g COD/L-anode-day. Hydrogen yields ranged from 50 3.2% to76 0.5% while anode coulombic efficiency ranged from 54 6.5% to 96 0.21%, respectively. Significant conversion of furfural, organic acids and phenolic molecules was observed under both batch and continuous conditions. The electrical and overall energy efficiency ranged from 149-175% and 48-63%,more » respectively. The results demonstrate the potential of the pyrolysis-microbial electrolysis process as a sustainable and efficient route for production of renewable hydrogen with significant implications for hydrocarbon production from biomass.« less

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

PubMed

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

2018-01-01

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

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

The Effect of Plant Cultivar, Growth Media, Harvest Method and Post Harvest Treatment on the Microbiology of Edible Crops

NASA Technical Reports Server (NTRS)

Hummerick, Mary P.; Gates, Justin R.; Nguyen, Bao-Thang; Massa, Gioia D.; Wheeler, Raymond M.

2011-01-01

Systems for the growth of crops in closed environments are being developed and tested for potential use in space applications to provide a source of fresh food. Plant growth conditions, growth media composition and harvest methods can have an effect on the microbial population of the plant, and therefore should be considered along with the optimization of plant growth and harvest yields to ensure a safe and palatable food crop. This work examines the effect of plant cultivar, growth media, and harvest method on plant microbial populations. Twelve varieties of leafy greens and herbs were grown on a mixture of Fafard #2 and Arcillite in the pillow root containment system currently being considered for the VEGGIE plant growth unit developed by Orbitec. In addition, ,Sierra and Outredgeous lettuce varieties were grown in three different mixtures (Fafard #2, Ardllite, and Perlite/Vermiculite). The plants were analyzed for microbial density. Two harvest methods, "cut and come again" (CACA) and terminal harvest were also compared. In one set ofexpe'riments red leaf lettuce and mizuna were grown in pots in a Biomass Production System for education. Plants were harvested every two weeks by either method. Another set of experiments was performed using the rooting pillows to grow 5 varieties of leafy greens and cut harvesting at different intervals. Radishes were harvested and replanted at two-week intervals. Results indicate up to a 3 IOglO difference in microbial counts between some varieties of plants. Rooting medium resulted in an approximately 2 IOglO lower count in the lettuce grown in arscillite then those grown in the other mixtures. Harvest method and frequency had less impact on microbial counts only showing a significant increase in one variety of plant. Post harvest methods to decrease the bacterial counts on edible crops were investigated in these and other experiments. The effectiveness of PRO-SAN and UV-C radiation is compared.

Evaluation of polymeric adsorbent resins for efficient detoxification of liquor generated during acid pretreatment of lignocellulosic biomass.

PubMed

Sandhya, Soolamkandath Variem; Kiran, Kumar; Kuttiraja, Mathiyazhakan; Preeti, Varghese Elizabeth; Sindhu, Raveendran; Vani, Sankar; Kumar, Sukumaran Rajeev; Pandey, Ashok; Binod, Parameswaran

2013-11-01

Production of fuel ethanol from lignocellulosic biomass conventionally includes biomass pretreatment, hydrolysis, and fermentation. The liquor generated during dilute acid pretreatment of biomass contains considerable quantities of pentose sugars as well as various degradation products of sugars and lignin, like furfural, hydroxymethyl furfural (HMF), organic acids, aldehydes and others, which are known to be inhibitory for microbial growth. This pentose rich liquor is a potent resource which can be used to produce alcohol or other value added metabolites by microbial fermentation. However, the presence of these inhibitory compounds is a major hindrance and their removal is essential for efficient utilization of this byproduct stream. In the present work, the polymeric adsorbent resins, XAD-4, XAD-7 and XAD-16 were evaluated for their ability to adsorb fermentation inhibitors like furfural and HMF from the acid pretreated liquor. These resins could remove 55-75% of furfural and 100% of HMF and more than 90% sugar remained un-adsorbed in the pretreated liquor. Desorption of furfural from stationary phase was evaluated by using ethanol and hot water. The results suggest that these polymeric resins may be used for detoxification of acid pretreatment liquor with selective removal of sugar degradation products without affecting the sugar content in the solution.

Effective production of biologically active water-soluble β-1,3-glucan by a coupled system of Agrobacterium sp. and Trichoderma harzianum.

PubMed

Liang, Ying; Zhu, Li; Gao, Minjie; Wu, Jianrong; Zhan, Xiaobei

2018-05-28

Water-soluble β-1,3-glucan (w-glucan) prepared from curdlan is reported to possess various bioactive and medicinal properties. To develop an efficient and cost-effective microbial fermentation method for the direct production of w-glucan, a coupled fermentation system of Agrobacterium sp. and Trichoderma harzianum (CFS-AT) was established. The effects of Tween-80, glucose flow rate, and the use of a dissolved oxygen (DO) control strategy on w-glucan production were assessed. The addition of 10 g L -1 Tween-80 to the CFS-AT enhanced w-glucan production, presumably by loosening the curdlan ultrastructure and increasing the efficiency of curdlan hydrolysis. A two-stage glucose and DO control strategy was optimal for w-glucan production. At the T. harzianum cell growth stage, the optimal glucose flow rate and agitation speed were 2.0 g L -1 hr -1 and 600 rpm, respectively, and at the w-glucan production stage, they were 0.5 g L -1 hr -1 and 400 rpm, respectively. W-glucan production reached 17.31 g L -1 , with a degree of polymerization of 19-25. Furthermore, w-glucan at high concentrations exhibited anti-tumor activity against MCF-7, HepG2, and Hela cancer cells in vitro. This study provides a novel, cost-effective, eco-friendly, and efficient microbial fermentation method for the direct production of biologically active w-glucan.

Experiment Research of Microbial Flooding Injected Capacity and Injected Volume

NASA Astrophysics Data System (ADS)

Shi, Fang; Zhao, Yang; Tang, Qinghua; Xie, Ximing

2018-01-01

Strains of microbial enhanced oil recovery technology is the use of crude oil directly in growth and the same time the metabolites of itself, so as to enhance oil recovery. Experimental study on paper through a number of data analysis. The growth and metabolism of three kinds of oil producing bacteria in the core are determined, and the corresponding growth curve is obtained. The parameter sensitivity analysis of the microorganism flooding process by homogeneous core is studied, and the influence of injection capacity and injection volume on the oil displacement effect is studied. The same permeability, water, temperature and other conditions, microbial injection pressure has a certain degree of increase than water flooding. Injection volume depends on the actual input-output ratio, quantity is 0.3PV is more reasonable.

Quantitative Modeling of Microbial Population Responses to Chronic Irradiation Combined with Other Stressors

PubMed Central

Shuryak, Igor; Dadachova, Ekaterina

2016-01-01

Microbial population responses to combined effects of chronic irradiation and other stressors (chemical contaminants, other sub-optimal conditions) are important for ecosystem functioning and bioremediation in radionuclide-contaminated areas. Quantitative mathematical modeling can improve our understanding of these phenomena. To identify general patterns of microbial responses to multiple stressors in radioactive environments, we analyzed three data sets on: (1) bacteria isolated from soil contaminated by nuclear waste at the Hanford site (USA); (2) fungi isolated from the Chernobyl nuclear-power plant (Ukraine) buildings after the accident; (3) yeast subjected to continuous γ-irradiation in the laboratory, where radiation dose rate and cell removal rate were independently varied. We applied generalized linear mixed-effects models to describe the first two data sets, whereas the third data set was amenable to mechanistic modeling using differential equations. Machine learning and information-theoretic approaches were used to select the best-supported formalism(s) among biologically-plausible alternatives. Our analysis suggests the following: (1) Both radionuclides and co-occurring chemical contaminants (e.g. NO2) are important for explaining microbial responses to radioactive contamination. (2) Radionuclides may produce non-monotonic dose responses: stimulation of microbial growth at low concentrations vs. inhibition at higher ones. (3) The extinction-defining critical radiation dose rate is dramatically lowered by additional stressors. (4) Reproduction suppression by radiation can be more important for determining the critical dose rate, than radiation-induced cell mortality. In conclusion, the modeling approaches used here on three diverse data sets provide insight into explaining and predicting multi-stressor effects on microbial communities: (1) the most severe effects (e.g. extinction) on microbial populations may occur when unfavorable environmental conditions (e.g. fluctuations of temperature and/or nutrient levels) coincide with radioactive contamination; (2) an organism’s radioresistance and bioremediation efficiency in rich laboratory media may be insufficient to carry out radionuclide bioremediation in the field—robustness against multiple stressors is needed. PMID:26808049

Pore-scale simulation of microbial growth using a genome-scale metabolic model: Implications for Darcy-scale reactive transport

NASA Astrophysics Data System (ADS)

Tartakovsky, G. D.; Tartakovsky, A. M.; Scheibe, T. D.; Fang, Y.; Mahadevan, R.; Lovley, D. R.

2013-09-01

Recent advances in microbiology have enabled the quantitative simulation of microbial metabolism and growth based on genome-scale characterization of metabolic pathways and fluxes. We have incorporated a genome-scale metabolic model of the iron-reducing bacteria Geobacter sulfurreducens into a pore-scale simulation of microbial growth based on coupling of iron reduction to oxidation of a soluble electron donor (acetate). In our model, fluid flow and solute transport is governed by a combination of the Navier-Stokes and advection-diffusion-reaction equations. Microbial growth occurs only on the surface of soil grains where solid-phase mineral iron oxides are available. Mass fluxes of chemical species associated with microbial growth are described by the genome-scale microbial model, implemented using a constraint-based metabolic model, and provide the Robin-type boundary condition for the advection-diffusion equation at soil grain surfaces. Conventional models of microbially-mediated subsurface reactions use a lumped reaction model that does not consider individual microbial reaction pathways, and describe reactions rates using empirically-derived rate formulations such as the Monod-type kinetics. We have used our pore-scale model to explore the relationship between genome-scale metabolic models and Monod-type formulations, and to assess the manifestation of pore-scale variability (microenvironments) in terms of apparent Darcy-scale microbial reaction rates. The genome-scale model predicted lower biomass yield, and different stoichiometry for iron consumption, in comparison to prior Monod formulations based on energetics considerations. We were able to fit an equivalent Monod model, by modifying the reaction stoichiometry and biomass yield coefficient, that could effectively match results of the genome-scale simulation of microbial behaviors under excess nutrient conditions, but predictions of the fitted Monod model deviated from those of the genome-scale model under conditions in which one or more nutrients were limiting. The fitted Monod kinetic model was also applied at the Darcy scale; that is, to simulate average reaction processes at the scale of the entire pore-scale model domain. As we expected, even under excess nutrient conditions for which the Monod and genome-scale models predicted equal reaction rates at the pore scale, the Monod model over-predicted the rates of biomass growth and iron and acetate utilization when applied at the Darcy scale. This discrepancy is caused by an inherent assumption of perfect mixing over the Darcy-scale domain, which is clearly violated in the pore-scale models. These results help to explain the need to modify the flux constraint parameters in order to match observations in previous applications of the genome-scale model at larger scales. These results also motivate further investigation of quantitative multi-scale relationships between fundamental behavior at the pore scale (where genome-scale models are appropriately applied) and observed behavior at larger scales (where predictions of reactive transport phenomena are needed).

Pore-scale simulation of microbial growth using a genome-scale metabolic model: Implications for Darcy-scale reactive transport

NASA Astrophysics Data System (ADS)

Scheibe, T. D.; Tartakovsky, G.; Tartakovsky, A. M.; Fang, Y.; Mahadevan, R.; Lovley, D. R.

2012-12-01

Recent advances in microbiology have enabled the quantitative simulation of microbial metabolism and growth based on genome-scale characterization of metabolic pathways and fluxes. We have incorporated a genome-scale metabolic model of the iron-reducing bacteria Geobacter sulfurreducens into a pore-scale simulation of microbial growth based on coupling of iron reduction to oxidation of a soluble electron donor (acetate). In our model, fluid flow and solute transport is governed by a combination of the Navier-Stokes and advection-diffusion-reaction equations. Microbial growth occurs only on the surface of soil grains where solid-phase mineral iron oxides are available. Mass fluxes of chemical species associated with microbial growth are described by the genome-scale microbial model, implemented using a constraint-based metabolic model, and provide the Robin-type boundary condition for the advection-diffusion equation at soil grain surfaces. Conventional models of microbially-mediated subsurface reactions use a lumped reaction model that does not consider individual microbial reaction pathways, and describe reactions rates using empirically-derived rate formulations such as the Monod-type kinetics. We have used our pore-scale model to explore the relationship between genome-scale metabolic models and Monod-type formulations, and to assess the manifestation of pore-scale variability (microenvironments) in terms of apparent Darcy-scale microbial reaction rates. The genome-scale model predicted lower biomass yield, and different stoichiometry for iron consumption, in comparison to prior Monod formulations based on energetics considerations. We were able to fit an equivalent Monod model, by modifying the reaction stoichiometry and biomass yield coefficient, that could effectively match results of the genome-scale simulation of microbial behaviors under excess nutrient conditions, but predictions of the fitted Monod model deviated from those of the genome-scale model under conditions in which one or more nutrients were limiting. The fitted Monod kinetic model was also applied at the Darcy scale; that is, to simulate average reaction processes at the scale of the entire pore-scale model domain. As we expected, even under excess nutrient conditions for which the Monod and genome-scale models predicted equal reaction rates at the pore scale, the Monod model over-predicted the rates of biomass growth and iron and acetate utilization when applied at the Darcy scale. This discrepancy is caused by an inherent assumption of perfect mixing over the Darcy-scale domain, which is clearly violated in the pore-scale models. These results help to explain the need to modify the flux constraint parameters in order to match observations in previous applications of the genome-scale model at larger scales. These results also motivate further investigation of quantitative multi-scale relationships between fundamental behavior at the pore scale (where genome-scale models are appropriately applied) and observed behavior at larger scales (where predictions of reactive transport phenomena are needed).

Pore-scale simulation of microbial growth using a genome-scale metabolic model: Implications for Darcy-scale reactive transport

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

Tartakovsky, Guzel D.; Tartakovsky, Alexandre M.; Scheibe, Timothy D.

2013-09-07

Recent advances in microbiology have enabled the quantitative simulation of microbial metabolism and growth based on genome-scale characterization of metabolic pathways and fluxes. We have incorporated a genome-scale metabolic model of the iron-reducing bacteria Geobacter sulfurreducens into a pore-scale simulation of microbial growth based on coupling of iron reduction to oxidation of a soluble electron donor (acetate). In our model, fluid flow and solute transport is governed by a combination of the Navier-Stokes and advection-diffusion-reaction equations. Microbial growth occurs only on the surface of soil grains where solid-phase mineral iron oxides are available. Mass fluxes of chemical species associated withmore » microbial growth are described by the genome-scale microbial model, implemented using a constraint-based metabolic model, and provide the Robin-type boundary condition for the advection-diffusion equation at soil grain surfaces. Conventional models of microbially-mediated subsurface reactions use a lumped reaction model that does not consider individual microbial reaction pathways, and describe reactions rates using empirically-derived rate formulations such as the Monod-type kinetics. We have used our pore-scale model to explore the relationship between genome-scale metabolic models and Monod-type formulations, and to assess the manifestation of pore-scale variability (microenvironments) in terms of apparent Darcy-scale microbial reaction rates. The genome-scale model predicted lower biomass yield, and different stoichiometry for iron consumption, in comparisonto prior Monod formulations based on energetics considerations. We were able to fit an equivalent Monod model, by modifying the reaction stoichiometry and biomass yield coefficient, that could effectively match results of the genome-scale simulation of microbial behaviors under excess nutrient conditions, but predictions of the fitted Monod model deviated from those of the genome-scale model under conditions in which one or more nutrients were limiting. The fitted Monod kinetic model was also applied at the Darcy scale; that is, to simulate average reaction processes at the scale of the entire pore-scale model domain. As we expected, even under excess nutrient conditions for which the Monod and genome-scale models predicted equal reaction rates at the pore scale, the Monod model over-predicted the rates of biomass growth and iron and acetate utilization when applied at the Darcy scale. This discrepancy is caused by an inherent assumption of perfect mixing over the Darcy-scale domain, which is clearly violated in the pore-scale models. These results help to explain the need to modify the flux constraint parameters in order to match observations in previous applications of the genome-scale model at larger scales. These results also motivate further investigation of quantitative multi-scale relationships between fundamental behavior at the pore scale (where genome-scale models are appropriately applied) and observed behavior at larger scales (where predictions of reactive transport phenomena are needed).« less

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

NASA Astrophysics Data System (ADS)

Zhang, Chi; Keating, Kristina; Revil, Andre

2015-04-01

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

Treated Wastewater Effluent as a Source of Microbial Pollution of Surface Water Resources

PubMed Central

Naidoo, Shalinee; Olaniran, Ademola O.

2013-01-01

Since 1990, more than 1.8 billion people have gained access to potable water and improved sanitation worldwide. Whilst this represents a vital step towards improving global health and well-being, accelerated population growth coupled with rapid urbanization has further strained existing water supplies. Whilst South Africa aims at spending 0.5% of its GDP on improving sanitation, additional factors such as hydrological variability and growing agricultural needs have further increased dependence on this finite resource. Increasing pressure on existing wastewater treatment plants has led to the discharge of inadequately treated effluent, reinforcing the need to improve and adopt more stringent methods for monitoring discharged effluent and surrounding water sources. This review provides an overview of the relative efficiencies of the different steps involved in wastewater treatment as well as the commonly detected microbial indicators with their associated health implications. In addition, it highlights the need to enforce more stringent measures to ensure compliance of treated effluent quality to the existing guidelines. PMID:24366046

Mineral-microbe interactions: biotechnological potential of bioweathering.

PubMed

Mapelli, Francesca; Marasco, Ramona; Balloi, Annalisa; Rolli, Eleonora; Cappitelli, Francesca; Daffonchio, Daniele; Borin, Sara

2012-02-20

Mineral-microbe interaction has been a key factor shaping the lithosphere of our planet since the Precambrian. Detailed investigation has been mainly focused on the role of bioweathering in biomining processes, leading to the selection of highly efficient microbial inoculants for the recovery of metals. Here we expand this scenario, presenting additional applications of bacteria and fungi in mineral dissolution, a process with novel biotechnological potential that has been poorly investigated. The ability of microorganisms to trigger soil formation and to sustain plant establishment and growth are suggested as invaluable tools to counteract the expansion of arid lands and to increase crop productivity. Furthermore, interesting exploitations of mineral weathering microbes are represented by biorestoration and bioremediation technologies, innovative and competitive solutions characterized by economical and environmental advantages. Overall, in the future the study and application of the metabolic properties of microbial communities capable of weathering can represent a driving force in the expanding sector of environmental biotechnology. Copyright © 2011 Elsevier B.V. All rights reserved.

Ethanol prefermentation of food waste in sequencing batch methane fermentation for improved buffering capacity and microbial community analysis.

PubMed

Yu, Miao; Wu, Chuanfu; Wang, Qunhui; Sun, Xiaohong; Ren, Yuanyuan; Li, Yu-You

2018-01-01

This study investigates the effects of ethanol prefermentation (EP) on methane fermentation. Yeast was added to the substrate for EP in the sequencing batch methane fermentation of food waste. An Illumina MiSeq high-throughput sequencing system was used to analyze changes in the microbial community. Methane production in the EP group (254mL/g VS) was higher than in the control group (35mL/g VS) because EP not only increased the buffering capacity of the system, but also increased hydrolytic acidification. More carbon source was converted to ethanol in the EP group than in the control group, and neutral ethanol could be converted continuously to acetic acid, which promoted the growth of Methanobacterium and Methanosarcina. As a result, the relative abundance of methane-producing bacteria was significantly higher than that of the control group. Kinetic modeling indicated that the EP group had a higher hydrolysis efficiency and shorter lag phase. Copyright © 2017 Elsevier Ltd. All rights reserved.

Formate Assimilation: The Metabolic Architecture of Natural and Synthetic Pathways.

PubMed

Bar-Even, Arren

2016-07-19

Formate may become an ideal mediator between the physicochemical and biological realms, as it can be produced efficiently from multiple available sources, such as electricity and biomass, and serve as one of the simplest organic compounds for providing both carbon and energy to living cells. However, limiting the realization of formate as a microbial feedstock is the low diversity of formate-fixing enzymes and thereby the small number of naturally occurring formate-assimilation pathways. Here, the natural enzymes and pathways supporting formate assimilation are presented and discussed together with proposed synthetic routes that could permit growth on formate via existing as well as novel formate-fixing reactions. By considering such synthetic routes, the diversity of metabolic solutions for formate assimilation can be expanded dramatically, such that different host organisms, cultivation conditions, and desired products could be matched with the most suitable pathway. Astute application of old and new formate-assimilation pathways may thus become a cornerstone in the development of sustainable strategies for microbial production of value-added chemicals.

The effect of denture adhesives on Candida albicans growth in vitro.

PubMed

Sampaio-Maia, Benedita; Figueiral, Maria Helena; Sousa-Rodrigues, Patricia; Fernandes, Maria Helena; Scully, Crispian

2012-06-01

Denture-wearing favours the growth of Candida. In view of the fact that many denture wearers regularly use adhesives to enhance denture retention, stability and function, the aim of this work was to study the effect of denture adhesives on Candida albicans growth in vitro. The denture adhesives tested were Corega(®) cream, Kukident(®) cream, Novafix(®) cream, Polident(®) cream, Protefix(®) cream, Steradent(®) cream, Aderyn(®) powder, Corega(®) ultra powder, Protefix(®) powder and Corega(®) strip. C. albicans growth curves were obtained in the presence or absence of a 1% solution of the denture adhesive diluted in Sabouraud broth. Macro- and microscopic morphological changes in C. albicans were analysed, as was microbial contamination of the denture adhesive. Most of the denture adhesives studied induced morphological changes in C. albicans cells and colonies, but only two had any significant inhibitory effect on yeast growth. Kukident(®) cream markedly inhibited C. albicans growth in a concentration-dependent way, reducing the growth rate by 95%, whereas Corega(®) cream also inhibited C. albicans growth but in a non-concentration-dependent way, reducing the growth rate by 37%. In addition, denture adhesives available as powders had detectable microbial contamination. Some commercially available denture adhesives showed microbial contamination and some had significant inhibitory effect on C. albicans growth. © 2011 The Gerodontology Society and John Wiley & Sons A/S.

Responses of mixed methanotrophic consortia to variable Cu2+/Fe2+ ratios.

PubMed

Chidambarampadmavathy, Karthigeyan; Karthikeyan, Obulisamy Parthiba; Huerlimann, Roger; Maes, Gregory E; Heimann, Kirsten

2017-07-15

Methane mitigation in landfill top cover soils is mediated by methanotrophs whose optimal methane (CH 4 ) oxidation capacity is governed by environmental and complex microbial community interactions. Optimization of CH 4 remediating bio-filters need to take microbial responses into account. Divalent copper (Cu 2+ ) and iron (Fe 2+ ) are present in landfills at variable ratios and play a vital role in methane oxidation capacity and growth of methanotrophs. This study, as a first of its kind, therefore quantified effects of variable Cu 2+ and Fe 2+ (5:5, 5:25 and 5:50 μM) ratios on mixed methanotrophic communities enriched from landfill top cover (LB) and compost soils (CB). CH 4 oxidation capacity, CH 4 removal efficiencies, fatty acids content/profiles and polyhydroxybutyrate (PHB; a biopolymer) contents were also analysed to quantify performance and potential co-product development. Mixed methanotroph cultures were raised in 10 L continuous stirred tank reactors (CSTRs, Bioflo ® & Celligen ® 310 Fermentor/Bioreactor; John Morris Scientific, Chatswood, NSW, Australia). Community structure was determined by amplifying the V3-V4 region of 16s rRNA gene. Community structure and, consequently, fatty acid-profiles changed significantly with increasing Cu 2+ /Fe 2+ ratios, and responses were different for LB and CB. Effects on methane oxidation capacities and PHB content were similar in the LB- and CB-CSTR, decreasing with increasing Cu 2+ /Fe 2+ ratios, while biomass growth was unaffected. In general, high Fe 2+ concentration favored growth of the type -II methanotroph Methylosinus in the CB-CSTR, but methanotroph abundances decreased in the LB-CSTR. Increase in Cu 2+ /Fe 2+ ratio increased the growth of Sphingopyxis in both systems, while Azospirllum was co-dominant in the LB- but absent in the CB-CSTR. After 13 days, methane oxidation capacities and PHB content decreased by ∼50% and more in response to increasing Fe 2+ concentrations. Although methanotroph abundance was ∼2% in the LB- (compared to >50% in CB-CSTR), methane oxidation capacities were comparable in the two systems, suggesting that methane oxidation capacity was maintained by the dominant Azospirllum and Sphingopyxis in the LB-CSTR. Despite similar methanotroph inoculum community composition and controlled environmental variables, increasing Cu 2+ /Fe 2+ ratios resulted in significantly different microbial community structures in the LB- and CB-CSTR, indicative of complex microbial interactions. In summary, our results suggest that a detailed understanding of allelopathic interactions in mixed methanotrophic consortia is vital for constructing robust bio-filters for CH 4 emission abatement. Copyright © 2017 Elsevier Ltd. All rights reserved.

Nitrogen controls spatial and temporal variability of substrate-induced respiration within seven years of bare fallow

NASA Astrophysics Data System (ADS)

Meyer, Nele; Bornemann, Ludger; Welp, Gerhard; Amelung, Wulf

2015-04-01

Bare fallow management goes along with lacking supply of new C sources; yet, little is known on the spatio-temporal controls of microbial adaptation processes. Here we hypothesized that microbial activity parameters decline upon bare fallow but that their spatial patterns are increasingly controlled by nutrient status as fallow management proceeds. To test these hypotheses, we investigated spatial and temporal patterns of substrate-induced respiration (SIR) and basal respiration curves in an arable field after 1, 3, and 7 years of bare fallow but with large within-field heterogeneity of physicochemical soil parameters. The analyses comprised the contents of SOC, mineral nitrogen (Nmin), particulate organic matter (POM), texture of the fine earth, and the proportion of rock fragments as well as basal respiration and several SIR fitting parameters (microbial biomass, microbial growth rates, peak respiration rates, cumulative CO2 release) each with and without additions of mineral N and P. We also repeated substrate (i.e. glucose) additions following the first SIR measurement. The results revealed that most respiration parameters like basal respiration, microbial biomass, and growth rates showed no or inconsistent responses to spatial and temporal patterns of basic soil properties like SOC, Nmin or texture. However, bare fallow changed the shape of the SIR curves; it developed two distinct microbial growth peaks at advanced stages of fallow, i.e. a delayed CO2 release. Likewise, the maximum respiration rate during the first growth phase declined during 7 years of fallow by 47% but its spatial distribution was always correlated with Nmin contents (r = 0.43 - 0.79). The nutrient additions suggested that these changes in SIR curves were caused by N deficiency; the first peak increased after N additions while the second growth phase diminished. Intriguingly, a repeated glucose addition had a similar effect on the SIR curves as the glucose+N addition. Thus, N deficiency apparently subsided during SIR. The results suggested that soil microbes acquire nitrogen from refractory SOM pools (i.e. microbial nitrogen mining). Hence, there was no significant decrease in cumulative CO2 evolution with proceeding time of fallow. As soil microorganisms maintained their functionality there was no overall loss in potential microbial activity, irrespective of the spatial patterns of other soil properties.

Microbial community profiles of the jejunum from steers differing in feed efficiency

USDA-ARS?s Scientific Manuscript database

Research regarding the association between the microbiome and host feed efficiency in cattle has primarily focused on the rumen. However, the various microbial populations within the gastrointestinal tract as a whole are critical to the overall well-being of the host and need to be examined when de...

Changes in Bacterial Composition of Zucchini Flowers Exposed to Refrigeration Temperatures

PubMed Central

Baruzzi, F.; Cefola, M.; Carito, A.; Vanadia, S.; Calabrese, N.

2012-01-01

Microbial spoilage is one of the main factors affecting the quality of fresh fruits and vegetables, leading to off-flavor, fermented aroma, and tissue decay. The knowledge of microbial growth kinetics is essential for estimating a correct risk assessment associated with consuming raw vegetables and better managing the development of spoilage microorganisms. This study shows, for the first time, that only a part of total microbial community, originally present on fresh harvested female zucchini flowers, was able to adapt itself to refrigerated conditions. Through the study of microbial growth kinetics it was possible to isolate forty-four strains belonging to twenty-two species of the genera Acinetobacter, Arthrobacter, Bacillus, Enterobacter, Erwinia, Klebsiella, Pantoea, Pseudoclavibacter, Pseudomonas, Serratia, Staphylococcus, and Weissella, suggesting Enterobacteriaceae as potentially responsible for pistil spoilage. PMID:22566759

Effects of exotic plantation forests on soil edaphon and organic matter fractions.

PubMed

Xu, Gang; Liu, Yao; Long, Zhijian; Hu, Shanglian; Zhang, Yuanbin; Jiang, Hao

2018-06-01

There is uncertainty and limited knowledge regarding soil microbial properties and organic matter fractions of natural secondary forest accompanying chemical environmental changes of replacement by pure alien plantation forests in a hilly area of southwest of Sichuan province China. The aim of this study was to evaluate the impact of natural secondary forest (NSF) to pure Cryptomeria fortunei forest (CFF) and Cunninghamia lanceolata forest (CLF) on soil organic fractions and microbial communities. The results showed that the soil total phospholipid fatty acids (PLFAs), total bacteria and fungi, microbial carbon pool, organic recalcitrant carbon (C) and (N) fractions, soil microbial quotient and labile and recalcitrant C use efficiencies in each pure plantation were significantly decreased, but their microbial N pool, labile C and N pools, soil carbon dioxide efflux, soil respiratory quotient and recalcitrant N use efficiency were increased. An RDA analysis revealed that soil total PLFAs, total bacteria and fungi and total Gram-positive and Gram-negative bacteria were significantly associated with exchangeable Al 3+ , exchangeable acid, Al 3+ , available P and Mg 2+ and pH, which resulted into microbial functional changes of soil labile and recalcitrant substrate use efficiencies. Modified microbial C- and N-use efficiency due to forest conversion ultimately meets those of rapidly growing trees in plantation forests. Enlarged soil labile fractions and soil respiratory quotients in plantation forests would be a potential positive effect for C source in the future forest management. Altogether, pure plantation practices could provoke regulatory networks and functions of soil microbes and enzyme activities, consequently leading to differentiated utilization of soil organic matter fractions accompanying the change in environmental factors. Copyright © 2018 Elsevier B.V. All rights reserved.

Biogeochemistry of Stinking Springs, Utah. Part II: Microbial Diversity and Photo- and Chemo-Autotrophic Growth Rates in a Layered Microbial Mat

NASA Astrophysics Data System (ADS)

Monteverde, D.; Metzger, J. G.; Bournod, C.; Kelly, H.; Johnson, H.; Sessions, A. L.; Osburn, M.; Shapiro, R. S.; Rideout, J.; Johnston, D. T.; Stevenson, B.; Stamps, B. W.; Vuono, D.; Hanselmann, K.; Spear, J. R.

2013-12-01

Layered microbial mats have garnered attention for their high phylogenetic diversity and exploitation of geochemical gradients often on the mm scale. However, despite their novelty and implications for early life diversification, little is known about layered microbial mat growth rates or the interdependence of the microbial communities within the system. Stinking Springs, a warm, sulfidic, saline spring northeast of the Great Salt Lake, serves as our test-site to investigate some of these questions. Stinking Springs undergoes downstream changes in pH (6.59-8.14), sulfide (527μM - below detection), sulfate (13-600μM), TCO2 (7.77-3.71mM), and temperature (40-21°C) along its ~150m flow path. The first 10m of discharge is channelized, beyond that, the spring supports a 10 to 40mm-thick layered microbial mat covering ~40% of the total spring runoff area. The mat was divided into four texturally-distinct layers which were each analyzed for 16S rRNA, lipid abundance, and bicarbonate and acetate uptake rates in addition to standard microscopy analyses. 16S rRNA analyses confirmed high taxa diversity within each layer, which varied significantly in taxa makeup such that no single phylum dominated the abundance (>33%) in more than one mat layer. The taxonomic diversity tended to increase with mat depth, a similar finding to other studies on layered microbial mats. A mat sampling transect across 16 meters showed that layer taxonomic diversity was conserved horizontally for all four mat layers, which implies mat depth has a larger control on diversity than physical or chemical parameters. Microscopy indicated the presence of diatoms in all layers which was confirmed by lipid abundance of sterols and long-branch fatty acid methyl esters. Incubation experiments were conducted in light and dark conditions over 24 hours with separate 13C-tagged bicarbonate and acetate additions. Heterotrophic growth rates (acetate uptake; 0.03-0.65%/day) were higher than autotrophic growth rates (bicarbonate uptake; 0-0.16%/day) under both dark and light conditions. Light conditions yielded higher growth rates for both heterotrophs and autotrophs and the highest rates were consistently found in the top mat layer and decreased with depth. The addition of 13C-acetate and concomitant high uptake is a measure of potential heterotrophy since in situ acetate concentrations are unlikely to be as high. 13C-bicarbonate uptake, on the other hand, should quantitatively represent the autotrophic growth rate. The Stinking Spring layered microbial mats display high taxonomic diversity, which is conserved horizontally across distances of meters and varies significantly with depth. Mats experience highest growth in the surface layer likely driven by phototrophs; high rates of bicarbonate uptake in the dark indicate considerable chemoautotrophy. Covariation in the heterotroph growth rates and 16S rRNA heterotroph abundance with mat depth indicates that heterotrophy may play an important role in the growth of these layered mats.

Situ microbial plugging process for subterranean formations

DOEpatents

McInerney, Michael J.; Jenneman, Gary E.; Knapp, Roy M.; Menzie, Donald E.

1985-12-17

Subterranean paths of water flow are impeded or changed by the facilitation of microbial growth therein. Either indigenous bacterial growth may be stimulated with nutrients or the formation may be first seeded with bacteria or their spores which inhibit fluid flow after proliferation. These methods and bacteria are usable to alter the flow of water in a waterflooded oil formation and to impede the outflow of contaminated water.

Insights into environmental controls on microbial communities in a continental serpentinite aquifer using a microcosm-based approach

PubMed Central

Crespo-Medina, Melitza; Twing, Katrina I.; Kubo, Michael D. Y.; Hoehler, Tori M.; Cardace, Dawn; McCollom, Tom; Schrenk, Matthew O.

2014-01-01

Geochemical reactions associated with serpentinization alter the composition of dissolved organic compounds in circulating fluids and potentially liberate mantle-derived carbon and reducing power to support subsurface microbial communities. Previous studies have identified Betaproteobacteria from the order Burkholderiales and bacteria from the order Clostridiales as key components of the serpentinite–hosted microbiome, however there is limited knowledge of their metabolic capabilities or growth characteristics. In an effort to better characterize microbial communities, their metabolism, and factors limiting their activities, microcosm experiments were designed with fluids collected from several monitoring wells at the Coast Range Ophiolite Microbial Observatory (CROMO) in northern California during expeditions in March and August 2013. The incubations were initiated with a hydrogen atmosphere and a variety of carbon sources (carbon dioxide, methane, acetate, and formate), with and without the addition of nutrients and electron acceptors. Growth was monitored by direct microscopic counts; DNA yield and community composition was assessed at the end of the 3 month incubation. For the most part, results indicate that bacterial growth was favored by the addition of acetate and methane, and that the addition of nutrients and electron acceptors had no significant effect on microbial growth, suggesting no nutrient- or oxidant-limitation. However, the addition of sulfur amendments led to different community compositions. The dominant organisms at the end of the incubations were closely related to Dethiobacter sp. and to the family Comamonadaceae, which are also prominent in culture-independent gene sequencing surveys. These experiments provide one of first insights into the biogeochemical dynamics of the serpentinite subsurface environment and will facilitate experiments to trace microbial activities in serpentinizing ecosystems. PMID:25452748

Spatial patterns of cyanobacterial mat growth on sand ripples

NASA Astrophysics Data System (ADS)

Mariotti, G.; Klepac-Ceraj, V.; Perron, J. T.; Bosak, T.

2016-02-01

Photosynthetic microbial mats produce organic matter, cycle nutrients, bind pollutants and stabilize sediment in sandy marine environments. Here, we investigate the influence of bedforms and wave motion on the growth rate, composition and spatial variability of microbial mats by growing cyanobacterial mats on a rippled bed of carbonate sand in a wave tank. The tank was forced with an oscillatory flow with velocities below the threshold for sediment motion yet able to induce a porewater flow within the sediment. Different spatial patterns developed in mats depending on the initial biochemistry of the water medium. When growing in a medium rich in nitrogen, phosphorous and micronutrients, mats grew faster on ripple troughs than on ripple crests. After two months, mats covered the bed surface uniformly, and the microbial communities on the crests and in the troughs had similar compositions. Differences in bed shear stress and nutrient availability between crests and troughs were not able to explain the faster growth in the troughs. We hypothesize that this growth pattern is due to a "strainer" effect, i.e. the suspended bacteria from the inoculum were preferentially delivered to troughs by the wave-induced porewater flow. In the experiments initiated in a medium previously used up by a microbial mat and thus depleted in nutrients, mats grew preferentially on the ripple crests. This spatial pattern persisted for nearly two years, and the microbial composition on troughs and crests was different. We attribute this pattern to the upwelling of porewater in the crests, which increased the delivery of nutrients from sediment to the cyanobacteria on the bed surface. Thus, the macroscopic patterns formed by photosynthetic microbial mats on sand ripples may be used to infer whether mats are nutrient-limited and whether they are recently colonized or older than a month.

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.

Insights into environmental controls on microbial communities in a continental serpentinite aquifer using a microcosm-based approach.

PubMed

Crespo-Medina, Melitza; Twing, Katrina I; Kubo, Michael D Y; Hoehler, Tori M; Cardace, Dawn; McCollom, Tom; Schrenk, Matthew O

2014-01-01

Geochemical reactions associated with serpentinization alter the composition of dissolved organic compounds in circulating fluids and potentially liberate mantle-derived carbon and reducing power to support subsurface microbial communities. Previous studies have identified Betaproteobacteria from the order Burkholderiales and bacteria from the order Clostridiales as key components of the serpentinite-hosted microbiome, however there is limited knowledge of their metabolic capabilities or growth characteristics. In an effort to better characterize microbial communities, their metabolism, and factors limiting their activities, microcosm experiments were designed with fluids collected from several monitoring wells at the Coast Range Ophiolite Microbial Observatory (CROMO) in northern California during expeditions in March and August 2013. The incubations were initiated with a hydrogen atmosphere and a variety of carbon sources (carbon dioxide, methane, acetate, and formate), with and without the addition of nutrients and electron acceptors. Growth was monitored by direct microscopic counts; DNA yield and community composition was assessed at the end of the 3 month incubation. For the most part, results indicate that bacterial growth was favored by the addition of acetate and methane, and that the addition of nutrients and electron acceptors had no significant effect on microbial growth, suggesting no nutrient- or oxidant-limitation. However, the addition of sulfur amendments led to different community compositions. The dominant organisms at the end of the incubations were closely related to Dethiobacter sp. and to the family Comamonadaceae, which are also prominent in culture-independent gene sequencing surveys. These experiments provide one of first insights into the biogeochemical dynamics of the serpentinite subsurface environment and will facilitate experiments to trace microbial activities in serpentinizing ecosystems.

Effects of iron and calcium carbonate on contaminant removal efficiencies and microbial communities in integrated wastewater treatment systems.

PubMed

Zhao, Zhimiao; Song, Xinshan; Zhang, Yinjiang; Zhao, Yufeng; Wang, Bodi; Wang, Yuhui

2017-12-01

In the paper, we explored the influences of different dosages of iron and calcium carbonate on contaminant removal efficiencies and microbial communities in algal ponds combined with constructed wetlands. After 1-year operation of treatment systems, based on the high-throughput pyrosequencing analysis of microbial communities, the optimal operating conditions were obtained as follows: the ACW10 system with Fe 3+ (5.6 mg L -1 ), iron powder (2.8 mg L -1 ), and CaCO 3 powder (0.2 mg L -1 ) in influent as the adjusting agents, initial phosphorus source (PO 4 3- ) in influent, the ratio of nitrogen to phosphorus (N/P) of 30 in influent, and hydraulic retention time (HRT) of 1 day. Total nitrogen (TN) removal efficiency and total phosphorus (TP) removal efficiency were improved significantly. The hydrolysis of CaCO 3 promoted the physicochemical precipitation in contaminant removal. Meanwhile, Fe 3+ and iron powder produced Fe 2+ , which improved contaminant removal. Iron ion improved the diversity, distribution, and metabolic functions of microbial communities in integrated treatment systems. In the treatment ACW10, the dominant phylum in the microbial community was PLANCTOMYCETES, which positively promoted nitrogen removal. After 5 consecutive treatments in ACW10, contaminant removal efficiencies for TN and TP respectively reached 80.6% and 57.3% and total iron concentration in effluent was 0.042 mg L -1 . Copyright © 2017 Elsevier Ltd. All rights reserved.

Guiding bioprocess design by microbial ecology.

PubMed

Volmer, Jan; Schmid, Andreas; Bühler, Bruno

2015-06-01

Industrial bioprocess development is driven by profitability and eco-efficiency. It profits from an early stage definition of process and biocatalyst design objectives. Microbial bioprocess environments can be considered as synthetic technical microbial ecosystems. Natural systems follow Darwinian evolution principles aiming at survival and reproduction. Technical systems objectives are eco-efficiency, productivity, and profitable production. Deciphering technical microbial ecology reveals differences and similarities of natural and technical systems objectives, which are discussed in this review in view of biocatalyst and process design and engineering strategies. Strategies for handling opposing objectives of natural and technical systems and for exploiting and engineering natural properties of microorganisms for technical systems are reviewed based on examples. This illustrates the relevance of considering microbial ecology for bioprocess design and the potential for exploitation by synthetic biology strategies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Bio-Contamination Control for Spacesuit Garments - A Preliminary Study

NASA Technical Reports Server (NTRS)

Rhodes, Richard; Korona, Adam; Orndoff, Evelyn; Ott, Mark; Poritz, Darwin

2010-01-01

This paper outlines a preliminary study to review, test, and improve upon the current state of spacesuit bio-contamination control. The study includes an evaluation of current and advanced suit materials, ground and on-orbit cleaning methods, and microbial test and analysis methods. The first aspect of this study was to identify potential anti-microbial textiles and cleaning agents, and to review current microbial test methods. The anti-microbial cleaning agent and textile market survey included a review of current commercial-off-the-shelf (COTS) products that could potentially be used as future space flight hardware. This review included replacements for any of the softgood layers that may become contaminated during an extravehicular activity (EVA), including the pressure bladder, liquid cooling garment, and ancillary comfort undergarment. After a series of COTS anti-microbial textiles and clean ing agents were identified, a series of four tests were conducted: (1) a stacked configuration test that was conducted in order to review how bio-contamination would propagate through the various suit layers, (2) a individual materials test that evaluated how well each softgood layer either promoted or repressed growth, (3) a cleaning agent test that evaluated the efficacy on each of the baseline bladders, and (4) an evaluation of various COTS anti-microbial textiles. All antimicrobial COTS materials tested appeared to control bacteria colony forming unit (CFU) growth better than the Thermal Comfort Undergarment (TCU) and ACES Liquid Cooling Garment (LCG)/EMU Liquid Cooling Ventilation Garment (LCVG) materials currently in use. However, a comparison of fungi CFU growth in COTS to current suit materials appeared to vary per material. All cleaning agents tested in this study appeared to inhibit the level of bacteria and fungi growth to acceptable levels for short duration tests. While several trends can be obtained from the current analysis, a series of test improvements are described for future microbial testing.

Fetal Tissue Procurement for Karyotype Analysis: Clinician or Pathologist - Which is Better?

PubMed

Conant, Joanna L; Tang, Mary E; Waters, Brenda L

2016-01-01

Chromosomal abnormalities are detected in up to 13% of stillbirths and over 20% of those with developmental anomalies. These estimates may be low since up to 50% of samples fail to achieve a result due to microbial overgrowth or nonviability. Tissue for cytogenetics can be procured at bedside by the clinician or by the pathologist in the laboratory. With clinical collection, tissue is placed into culture media immediately, increasing chances of growth. However, collection competes for attention with other activities, which may result in microbial overgrowth or selection of maternal rather than fetal tissue. Laboratory procurement occurs in a controlled environment using sterile technique, but delay in collection may decrease viability. Our goal was to determine which collection method yields better results. We reviewed cases from 2007-2013 that had two samples submitted for cytogenetics, one from the clinician and one from the pathologist. Specimen source, delivery, collection, and culture setup times, harvest date, cell growth, microbial overgrowth, maternal contamination and final result were obtained from medical records and cytogenetic culture sheets. There was no difference in growth rate, maternal cell contamination, or reporting time between clinician- and pathologist-procured samples despite delay in collection time for laboratory samples. Clinical samples had more microbial overgrowth. Compared to samples collected at bedside, samples collected in the laboratory had a lower rate of microbial contamination with similar growth and maternal cell contamination rates, despite prolonged time to collection. Collecting samples both at bedside and in the laboratory is unnecessary.

Microbial Community Profiles in Wastewaters from Onsite Wastewater Treatment Systems Technology

PubMed Central

Jałowiecki, Łukasz; Chojniak, Joanna Małgorzata; Dorgeloh, Elmar; Hegedusova, Berta; Ejhed, Helene; Magnér, Jörgen; Płaza, Grażyna Anna

2016-01-01

The aim of the study was to determine the potential of community-level physiological profiles (CLPPs) methodology as an assay for characterization of the metabolic diversity of wastewater samples and to link the metabolic diversity patterns to efficiency of select onsite biological wastewater facilities. Metabolic fingerprints obtained from the selected samples were used to understand functional diversity implied by the carbon substrate shifts. Three different biological facilities of onsite wastewater treatment were evaluated: fixed bed reactor (technology A), trickling filter/biofilter system (technology B), and aerated filter system (the fluidized bed reactor, technology C). High similarities of the microbial community functional structures were found among the samples from the three onsite wastewater treatment plants (WWTPs), as shown by the diversity indices. Principal components analysis (PCA) showed that the diversity and CLPPs of microbial communities depended on the working efficiency of the wastewater treatment technologies. This study provided an overall picture of microbial community functional structures of investigated samples in WWTPs and discerned the linkages between microbial communities and technologies of onsite WWTPs used. The results obtained confirmed that metabolic profiles could be used to monitor treatment processes as valuable biological indicators of onsite wastewater treatment technologies efficiency. This is the first step toward understanding relations of technology types with microbial community patterns in raw and treated wastewaters. PMID:26807728

Genes Required for Growth at High Hydrostatic Pressure in Escherichia coli K-12 Identified by Genome-Wide Screening

PubMed Central

Black, S. Lucas; Dawson, Angela; Ward, F. Bruce; Allen, Rosalind J.

2013-01-01

Despite the fact that much of the global microbial biosphere is believed to exist in high pressure environments, the effects of hydrostatic pressure on microbial physiology remain poorly understood. We use a genome-wide screening approach, combined with a novel high-throughput high-pressure cell culture method, to investigate the effects of hydrostatic pressure on microbial physiology in vivo. The Keio collection of single-gene deletion mutants in Escherichia coli K-12 was screened for growth at a range of pressures from 0.1 MPa to 60 MPa. This led to the identification of 6 genes, rodZ, holC, priA, dnaT, dedD and tatC, whose products were required for growth at 30 MPa and a further 3 genes, tolB, rffT and iscS, whose products were required for growth at 40 MPa. Our results support the view that the effects of pressure on cell physiology are pleiotropic, with DNA replication, cell division, the cytoskeleton and cell envelope physiology all being potential failure points for cell physiology during growth at elevated pressure. PMID:24040140

A first study comparing preservation of a ready-to-eat soup under pressure (hyperbaric storage) at 25°C and 30°C with refrigeration.

PubMed

Moreira, Sílvia A; Fernandes, Pedro A R; Duarte, Ricardo; Santos, Diana I; Fidalgo, Liliana G; Santos, Mauro D; Queirós, Rui P; Delgadillo, Ivonne; Saraiva, Jorge A

2015-11-01

Hyperbaric storage (HS), storage under pressure at 25°C and 30°C, of a ready-to-eat (RTE) soup was studied and compared with refrigeration. Soup was stored at different time (4 and 8 h), temperature (4°C, 25°C, and 30°C), and pressure (0.1, 100, and 150 MPa) conditions, to compare microbial loads and physicochemical parameters. HS resulted in similar (microbial growth inhibition) to better (microbial inactivation) results compared to refrigeration, leading to equal and lower microbial loads, respectively, at the end of storage. Lower/higher pressure (100 vs. 150 MPa) and shorter/longer storage times (4 vs. 8 h) resulted in more pronounced microbial growth inhibition/microbial inactivation. Aerobic mesophiles showed less susceptibility to HS, compared to Enterobacteriaceae and yeast and molds. HS maintained generally the physicochemical parameters at values similar to refrigeration. Thus, HS with no need for temperature control throughout storage and so basically energetically costless, is a potential alternative to refrigeration.

Influence of mechanical disintegration on the microbial growth of aerobic sludge biomass: A comparative study of ultrasonic and shear gap homogenizers by oxygen uptake measurements.

PubMed

Divyalakshmi, P; Murugan, D; Sivarajan, M; Saravanan, P; Lajapathi Rai, C

2015-11-01

Wastewater treatment plant incorporates physical, chemical and biological processes to treat and remove the contaminants. The main drawback of conventional activated sludge process is the huge production of excess sludge, which is an unavoidable byproduct. The treatment and disposal of excess sludge costs about 60% of the total operating cost. The ideal way to reduce excess sludge production during wastewater treatment is by preventing biomass formation within the aerobic treatment train rather than post treatment of the generated sludge. In the present investigation two different mechanical devices namely, Ultrasonic and Shear Gap homogenizers have been employed to disintegrate the aerobic biomass. This study is intended to restrict the multiplication of microbial biomass and at the same time degrade the organics present in wastewater by increasing the oxidative capacity of microorganisms. The disintegrability on biomass was determined by biochemical methods. Degree of inactivation provides the information on inability of microorganisms to consume oxygen upon disruption. The soluble COD quantifies the extent of release of intra cellular compounds. The participation of disintegrated microorganism in wastewater treatment process was carried out in two identical respirometeric reactors. The results show that Ultrasonic homogenizer is very effective in the disruption of microorganisms leading to a maximum microbial growth reduction of 27%. On the other hand, Shear gap homogenizer does not favor the sludge growth reduction rather it facilitates the growth. This study also shows that for better microbial growth reduction, floc size reduction alone is not sufficient but also microbial disruption is essential. Copyright © 2015 Elsevier Inc. All rights reserved.

Plant-Microbe and Abiotic Factors Influencing Salmonella Survival and Growth on Alfalfa Sprouts and Swiss Chard Microgreens

PubMed Central

Reed, Elizabeth; Ferreira, Christina M.; Bell, Rebecca; Brown, Eric W.

2018-01-01

ABSTRACT Microgreens, like sprouts, are relatively fast-growing products and are generally consumed raw. Moreover, as observed for sprouts, microbial contamination from preharvest sources may also be present in the production of microgreens. In this study, two Salmonella enterica serovars (Hartford and Cubana), applied at multiple inoculation levels, were evaluated for survival and growth on alfalfa sprouts and Swiss chard microgreens by using the most-probable-number (MPN) method. Various abiotic factors were also examined for their effects on Salmonella survival and growth on sprouts and microgreens. Community-level physiological profiles (CLPPs) of sprout/microgreen rhizospheres with different levels of S. enterica inoculation at different growth stages were characterized by use of Biolog EcoPlates. In the seed contamination group, the ability of S. enterica to grow on sprouting alfalfa seeds was affected by both seed storage time and inoculation level but not by serovar. However, the growth of S. enterica on Swiss chard microgreens was affected by serovar and inoculation level. Seed storage time had little effect on the average level of Salmonella populations in microgreens. In the irrigation water contamination group, the growth of Salmonella on both alfalfa sprouts and microgreens was largely affected by inoculation level. Surprisingly, the growth medium was found to play an important role in Salmonella survival and growth on microgreens. CLPP analysis showed significant changes in the microbial community metabolic diversity during sprouting for alfalfa sprouts, but few temporal changes were seen with microgreens. The data suggest that the change in rhizosphere bacterial functional diversity was dependent on the host but independent of Salmonella contamination. IMPORTANCE Sprouts and microgreens are considered “functional foods,” i.e., foods containing health-promoting or disease-preventing properties in addition to normal nutritional values. However, the microbial risk associated with microgreens has not been well studied. This study evaluated Salmonella survival and growth on microgreens compared to those on sprouts, as well as other abiotic factors that could affect Salmonella survival and growth on microgreens. This work provides baseline data for risk assessment of microbial contamination of sprouts and microgreens. Understanding the risks of Salmonella contamination and its effects on rhizosphere microbial communities enables a better understanding of host-pathogen dynamics in sprouts and microgreens. The data also contribute to innovative preventive control strategies for Salmonella contamination of sprouts and microgreens. PMID:29453267

Plant-Microbe and Abiotic Factors Influencing Salmonella Survival and Growth on Alfalfa Sprouts and Swiss Chard Microgreens.

PubMed

Reed, Elizabeth; Ferreira, Christina M; Bell, Rebecca; Brown, Eric W; Zheng, Jie

2018-05-01

Microgreens, like sprouts, are relatively fast-growing products and are generally consumed raw. Moreover, as observed for sprouts, microbial contamination from preharvest sources may also be present in the production of microgreens. In this study, two Salmonella enterica serovars (Hartford and Cubana), applied at multiple inoculation levels, were evaluated for survival and growth on alfalfa sprouts and Swiss chard microgreens by using the most-probable-number (MPN) method. Various abiotic factors were also examined for their effects on Salmonella survival and growth on sprouts and microgreens. Community-level physiological profiles (CLPPs) of sprout/microgreen rhizospheres with different levels of S. enterica inoculation at different growth stages were characterized by use of Biolog EcoPlates. In the seed contamination group, the ability of S. enterica to grow on sprouting alfalfa seeds was affected by both seed storage time and inoculation level but not by serovar. However, the growth of S. enterica on Swiss chard microgreens was affected by serovar and inoculation level. Seed storage time had little effect on the average level of Salmonella populations in microgreens. In the irrigation water contamination group, the growth of Salmonella on both alfalfa sprouts and microgreens was largely affected by inoculation level. Surprisingly, the growth medium was found to play an important role in Salmonella survival and growth on microgreens. CLPP analysis showed significant changes in the microbial community metabolic diversity during sprouting for alfalfa sprouts, but few temporal changes were seen with microgreens. The data suggest that the change in rhizosphere bacterial functional diversity was dependent on the host but independent of Salmonella contamination. IMPORTANCE Sprouts and microgreens are considered "functional foods," i.e., foods containing health-promoting or disease-preventing properties in addition to normal nutritional values. However, the microbial risk associated with microgreens has not been well studied. This study evaluated Salmonella survival and growth on microgreens compared to those on sprouts, as well as other abiotic factors that could affect Salmonella survival and growth on microgreens. This work provides baseline data for risk assessment of microbial contamination of sprouts and microgreens. Understanding the risks of Salmonella contamination and its effects on rhizosphere microbial communities enables a better understanding of host-pathogen dynamics in sprouts and microgreens. The data also contribute to innovative preventive control strategies for Salmonella contamination of sprouts and microgreens.

Treatment impacts on temporal microbial community dynamics during phytostabilization of acid-generating mine tailings in semiarid regions.

PubMed

Valentín-Vargas, Alexis; Neilson, Julia W; Root, Robert A; Chorover, Jon; Maier, Raina M

2018-03-15

Direct revegetation, or phytostabilization, is a containment strategy for contaminant metals associated with mine tailings in semiarid regions. The weathering of sulfide ore-derived tailings frequently drives acidification that inhibits plant establishment resulting in materials prone to wind and water dispersal. The specific objective of this study was to associate pyritic mine waste acidification, characterized through pore-water chemistry analysis, with dynamic changes in microbial community diversity and phylogenetic composition, and to evaluate the influence of different treatment strategies on the control of acidification dynamics. Samples were collected from a highly instrumented one-year mesocosm study that included the following treatments: 1) unamended tailings control; 2) tailings amended with 15% compost; and 3) the 15% compost-amended tailings planted with Atriplex lentiformis. Tailings samples were collected at 0, 3, 6 and 12months and pore water chemistry was monitored as an indicator of acidification and weathering processes. Results confirmed that the acidification process for pyritic mine tailings is associated with a temporal progression of bacterial and archaeal phylotypes from pH sensitive Thiobacillus and Thiomonas to communities dominated by Leptospirillum and Ferroplasma. Pore-water chemistry indicated that weathering rates were highest when Leptospirillum was most abundant. The planted treatment was most successful in disrupting the successional evolution of the Fe/S-oxidizing community. Plant establishment stimulated growth of plant-growth-promoting heterotrophic phylotypes and controlled the proliferation of lithoautotrophic Fe/S-oxidizers. The results suggest the potential for eco-engineering a microbial inoculum to stimulate plant establishment and inhibit proliferation of the most efficient Fe/S-oxidizing phylotypes. Copyright © 2017 Elsevier B.V. All rights reserved.

Magnitude and Mechanism of Siderophore-Mediated Competition at Low Iron Solubility in the Pseudomonas aeruginosa Pyochelin System.

PubMed

Schiessl, Konstanze T; Janssen, Elisabeth M-L; Kraemer, Stephan M; McNeill, Kristopher; Ackermann, Martin

2017-01-01

A central question in microbial ecology is whether microbial interactions are predominantly cooperative or competitive. The secretion of siderophores, microbial iron chelators, is a model system for cooperative interactions. However, siderophores have also been shown to mediate competition by sequestering available iron and making it unavailable to competitors. The details of how siderophores mediate competition are not well understood, especially considering the complex distribution of iron phases in the environment. One pertinent question is whether sequestering iron through siderophores can indeed be effective in natural conditions; many natural environments are characterized by large pools of precipitated iron, and it is conceivable that any soluble iron that is sequestered by siderophores is replenished by the dissolution of these precipitated iron sources. Our goal here was to address this issue, and investigate the magnitude and mechanism of siderophore-mediated competition in the presence of precipitated iron. We combined experimental work with thermodynamic modeling, using Pseudomonas aeruginosa as a model system and ferrihydrite precipitates as the iron source with low solubility. Our experiments show that competitive growth inhibition by the siderophore pyochelin is indeed efficient, and that inhibition of a competitor can even have a stronger growth-promoting effect than solubilization of precipitated iron. Based on the results of our thermodynamic models we conclude that the observed inhibition of a competitor is effective because sequestered iron is only very slowly replenished by the dissolution of precipitated iron. Our research highlights the importance of competitive benefits mediated by siderophores, and underlines that the dynamics of siderophore production and uptake in environmental communities could be a signature of competitive, not just cooperative, dynamics.

Belowground Microbiota and the Health of Tree Crops.

PubMed

Mercado-Blanco, Jesús; Abrantes, Isabel; Barra Caracciolo, Anna; Bevivino, Annamaria; Ciancio, Aurelio; Grenni, Paola; Hrynkiewicz, Katarzyna; Kredics, László; Proença, Diogo N

2018-01-01

Trees are crucial for sustaining life on our planet. Forests and land devoted to tree crops do not only supply essential edible products to humans and animals, but also additional goods such as paper or wood. They also prevent soil erosion, support microbial, animal, and plant biodiversity, play key roles in nutrient and water cycling processes, and mitigate the effects of climate change acting as carbon dioxide sinks. Hence, the health of forests and tree cropping systems is of particular significance. In particular, soil/rhizosphere/root-associated microbial communities (known as microbiota) are decisive to sustain the fitness, development, and productivity of trees. These benefits rely on processes aiming to enhance nutrient assimilation efficiency (plant growth promotion) and/or to protect against a number of (a)biotic constraints. Moreover, specific members of the microbial communities associated with perennial tree crops interact with soil invertebrate food webs, underpinning many density regulation mechanisms. This review discusses belowground microbiota interactions influencing the growth of tree crops. The study of tree-(micro)organism interactions taking place at the belowground level is crucial to understand how they contribute to processes like carbon sequestration, regulation of ecosystem functioning, and nutrient cycling. A comprehensive understanding of the relationship between roots and their associate microbiota can also facilitate the design of novel sustainable approaches for the benefit of these relevant agro-ecosystems. Here, we summarize the methodological approaches to unravel the composition and function of belowground microbiota, the factors influencing their interaction with tree crops, their benefits and harms, with a focus on representative examples of Biological Control Agents (BCA) used against relevant biotic constraints of tree crops. Finally, we add some concluding remarks and suggest future perspectives concerning the microbiota-assisted management strategies to sustain tree crops.

Belowground Microbiota and the Health of Tree Crops

PubMed Central

Mercado-Blanco, Jesús; Abrantes, Isabel; Barra Caracciolo, Anna; Bevivino, Annamaria; Ciancio, Aurelio; Grenni, Paola; Hrynkiewicz, Katarzyna; Kredics, László; Proença, Diogo N.

2018-01-01

Trees are crucial for sustaining life on our planet. Forests and land devoted to tree crops do not only supply essential edible products to humans and animals, but also additional goods such as paper or wood. They also prevent soil erosion, support microbial, animal, and plant biodiversity, play key roles in nutrient and water cycling processes, and mitigate the effects of climate change acting as carbon dioxide sinks. Hence, the health of forests and tree cropping systems is of particular significance. In particular, soil/rhizosphere/root-associated microbial communities (known as microbiota) are decisive to sustain the fitness, development, and productivity of trees. These benefits rely on processes aiming to enhance nutrient assimilation efficiency (plant growth promotion) and/or to protect against a number of (a)biotic constraints. Moreover, specific members of the microbial communities associated with perennial tree crops interact with soil invertebrate food webs, underpinning many density regulation mechanisms. This review discusses belowground microbiota interactions influencing the growth of tree crops. The study of tree-(micro)organism interactions taking place at the belowground level is crucial to understand how they contribute to processes like carbon sequestration, regulation of ecosystem functioning, and nutrient cycling. A comprehensive understanding of the relationship between roots and their associate microbiota can also facilitate the design of novel sustainable approaches for the benefit of these relevant agro-ecosystems. Here, we summarize the methodological approaches to unravel the composition and function of belowground microbiota, the factors influencing their interaction with tree crops, their benefits and harms, with a focus on representative examples of Biological Control Agents (BCA) used against relevant biotic constraints of tree crops. Finally, we add some concluding remarks and suggest future perspectives concerning the microbiota-assisted management strategies to sustain tree crops. PMID:29922245

Dynamics of bacterial and fungal communities associated with eggshells during incubation

PubMed Central

Grizard, Stéphanie; Dini-Andreote, Francisco; Tieleman, B Irene; Salles, Joana F

2014-01-01

Microorganisms are closely associated with eggs and may play a determinant role in embryo survival. Yet, the majority of studies focusing on this association relied on culture-based methodology, eventually leading to a skewed assessment of microbial communities. By targeting the 16S rRNA gene and internal transcribed spacer (ITS) region, we, respectively, described bacterial and fungal communities on eggshells of the homing pigeon Columba livia. We explored their structure, abundance, and composition. Firstly, we showed that sampling technique affected the outcome of the results. While broadly used, the egg swabbing procedure led to a lower DNA extraction efficiency and provided different profiles of bacterial communities than those based on crushed eggshell pieces. Secondly, we observed shifts in bacterial and fungal communities during incubation. At late incubation, bacterial communities showed a reduction in diversity, while their abundance increased, possibly due to the competitive advantage of some species. When compared to their bacterial counterparts, fungal communities also decreased in diversity at late incubation. In that case, however, the decline was associated with a diminution of their overall abundance. Conclusively, our results showed that although incubation might inhibit microbial growth when compared to unincubated eggs, we observed the selective growth of specific bacterial species during incubation. Moreover, we showed that fungi are a substantial component of the microbial communities associated with eggshells and require further investigations in avian ecology. Identifying the functional roles of these microorganisms is likely to provide news insights into the evolutionary strategies that control embryo survival. We aimed to describe the dynamics of bacterial and fungal communities on homing pigeon eggshell surfaces. We investigated these communities at early and late incubation stages. PMID:24772289

Nutrient Digestibility, Rumen Microbial Protein Synthesis, and Growth Performance in Sheep Consuming Rations Containing Sea Buckthorn Pomace.

PubMed

Hao, X Y; Diao, X G; Yu, S C; Ding, N; Mu, C T; Zhao, J X; Zhang, J X

2018-05-12

This experiment was conducted to investigate nutrient digestibility, rumen microbial protein synthesis, and growth performance when different proportions of sea buckthorn pomace (SBP) were included in the diet of sheep. A total of forty1/2 Dorper × 1/2 thin-tailed Han ram lambs (BW= 22.2 ± 0.92 kg, Age =120 ± 11 d; mean ± SD) were selected and divided into four groups in a randomized design, and were randomly allocated to 1 of 4 treatment diets. Diets were formulated isonitrogenously and contained different levels of SBP: 1) 0% SBP (control); 2) 7.8% of DM SBP (8SBP); 3)16.0% of DM SBP (16SBP); and 4) 23.5% of DM SBP (24SBP). A portion of corn and forages were replaced with SBP. Dry matter intake and average daily gain increased linearly (P=0.001), but feed efficiency was not affected (P≥0.460) by increasing SBP inclusion rate. As the SBP inclusion increased, organic matter, neutral detergent fiber, and acid detergent fiber digestibility decreased linearly (P≤0.005) and that crude protein increased linearly (P=0.012). Response to inclusion level of SBP was quadratic (P=0.003) for the estimated microbial crude protein yield with the greatest at intermediate SBP levels. For intestinally absorbable dietary protein, a quadratic (P=0.029) effects was observed among treatments. The metabolizable protein supplies was linearly (P<0.0001) improved with increasing SBP inclusion rate. The results indicated that sea buckthorn pomace can be incorporated in the ration of ram lambs and improve metabolizable protein supply and average daily gain. However, high content of it in the diet was adverse for nutrient digestibility. The optimal proportion was 16.0% under the condition of this experiment.

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

Li, Dongfang; Voigt, Thomas B.; Kent, Angela D.

Here, bacterial assemblages, especially diazotroph assemblages residing in the rhizomes and the rhizosphere soil of Miscanthus × giganteus, contribute to plant growth and nitrogen use efficiency. However, the composition of these microbial communities has not been adequately explored nor have the potential ecological drivers for these communities been sufficiently studied. This knowledge is needed for understanding and potentially improving M. × giganteus – microbe interactions, and further enhancing sustainability of M. × giganteus production. In this study, cultivated M. × giganteus from four sites in Illinois, Kentucky, Nebraska, and New Jersey were collected to examine the relative influences of soilmore » conditions and plant compartments on assembly of the M. × giganteus-associated microbiome. Automated ribosomal intergenic spacer (ARISA) and terminal restriction fragment length polymorphism (T-RFLP) targeting the nifH gene were applied to examine the total bacterial communities and diazotroph assemblages that reside in the rhizomes and the rhizosphere. Distinct microbial assemblages were detected in the endophytic and rhizosphere compartments. Site soil conditions had strong correlation with both total bacterial and diazotroph assemblages, but in different ways. Nitrogen treatments showed no significant effect on the composition of diazotroph assemblages in most sites. Endophytic compartments of different M. × giganteus plants tended to harbor similar microbial communities across all sites, whereas the rhizosphere soil of different plant tended to harbor diverse microbial assemblages that were distinct among sites. These observations offer insight into better understanding of the associative interactions between M. × giganteus and diazotrophs, and how this relationship is influenced by agronomic and edaphic factors.« less

Biodegradable alternative for removing toxic compounds from sugarcane bagasse hemicellulosic hydrolysates for valorization in biorefineries.

PubMed

Silva-Fernandes, T; Santos, J C; Hasmann, F; Rodrigues, R C L B; Izario Filho, H J; Felipe, M G A

2017-11-01

Among the major challenges for hemicellulosic hydrolysate application in fermentative processes, there is the presence of toxic compounds generated during the pretreatment of the biomass, which can inhibit microbial growth. Therefore, the development of efficient, biodegradable and cost-effective detoxification methods for lignocellulosic hydrolysates is crucial. In this work, two tannin-based biopolymers (called A and B) were tested in the detoxification of sugarcane bagasse hydrolysate for subsequent fermentation by Candida guilliermondii. The effects of biopolymer concentration, pH, temperature, and contact time were studied using a 2 4 experimental design for both biopolymers. Results revealed that the biopolymer concentration and the pH were the most significant factors in the detoxification step. Biopolymer A removed phenolics, 5-hydroxymethylfurfural, and nickel from the hydrolysate more efficiently than biopolymer B, while biopolymer B was efficient to remove chromium at 15% (v/v). Detoxification enhanced the fermentation of sugarcane bagasse hydrolysate, and the biopolymers showed different influences on the process. Copyright © 2017 Elsevier Ltd. All rights reserved.

Continuous monitoring of bacterial biofilm growth using uncoated Thickness-Shear Mode resonators

NASA Astrophysics Data System (ADS)

Castro, P.; Resa, P.; Durán, C.; Maestre, J. R.; Mateo, M.; Elvira, L.

2012-12-01

Quartz Crystal Microbalances (QCM) were used to nondestructively monitor in real time the microbial growth of the bacteria Staphylococcus epidermidis (S. epidermidis) in a liquid broth. QCM, sometimes referred to as Thickness-Shear Mode (TSM) resonators, are highly sensitive sensors not only able to measure very small mass, but also non-gravimetric contributions of viscoelastic media. These devices can be used as biosensors for bacterial detection and are employed in many applications including their use in the food industry, water and environment monitoring, pharmaceutical sciences and clinical diagnosis. In this work, three strains of S. epidermidis (which differ in the ability to produce biofilm) have been continuously monitored using an array of piezoelectric TSM resonators, at 37 °C in a selective culturing media. Microbial growth was followed by measuring the changes in the crystal resonant frequency and bandwidth at several harmonics. It was shown that microbial growth can be monitored in real time using multichannel and multiparametric QCM sensors.

The microbial temperature sensitivity to warming is controlled by thermal adaptation and is independent of C-quality across a pan-continental survey

NASA Astrophysics Data System (ADS)

Berglund, Eva; Rousk, Johannes

2017-04-01

Climate models predict that warming will result in an increased loss of soil organic matter (SOM). However, field experiments suggest that although warming results in an immediate increase in SOM turnover, the effect diminishes over time. Although the use and subsequent turnover of SOM is dominated by the soil microbial community, the underlying physiology underpinning warming responses are not considered in current climate models. It has been suggested that a reduction in the perceived quality of SOM to the microbial community, and changes in the microbial thermal adaptation, could be important feed-backs to soil warming. Thus, studies distinguishing between temperature relationships and how substrate quality influences microbial decomposition are a priority. We examined microbial communities and temperature sensitivities along a natural climate gradient including 56 independent samples from across Europe. The gradient included mean annual temperatures (MAT) from ca -4 to 18 ˚ C, along with wide spans of environmental factors known to influence microbial communities, such as pH (4.0 to 8.8), nutrients (C/N from 7 to 50), SOM (from 4 to 94%), and plant communities, etc. The extensive ranges of environmental conditions resulted in wide ranges of substrate quality, indexed as microbial respiration per unit SOM, from 5-150 μg CO2g-1 SOM g-1 h-1. We hypothesised microbial communities to (1) be adapted to the temperature of their climate, leading to warm adapted bacterial communities that were more temperature sensitive (higher Q10s) at higher MAT; (2) have temperature sensitivities affected by the quality of SOM, with higher Q10s for lower quality SOM. To determine the microbial use of SOM and its dependence on temperature, we characterized microbial temperature dependences of bacterial growth (leu inc), fungal growth (ac-in-erg) and soil respiration in all 56 sites. Temperature dependences were determined using brief (ca. 1-2 h at 25˚ C) laboratory incubation experiments including temperatures from 0 to 35˚ C. Temperature relationships were modelled using the Ratkowsky model, and cardinal points including minimum temperature (Tmin) for growth and respiration along with temperature sensitivity (Q10) values were used as indices to compare sites. Microbial communities were cold-adapted in cold sites and warm-adapted in warm sites, as shown by Tmin values ranging from ca. -20 ˚ C to 0 ˚ C. For every 1˚ C rise in MAT, Tmin increased by 0.22˚ C and 0.28˚ C for bacteria and fungi, respectively. Soil respiration was less dependent on MAT, increasing 0.16 ˚ C per 1˚ C. Temperature dependence analyses grew stronger when regressed against summer temperatures, and weaker when regressed against winter temperatures. Hence, microbial communities adjusted their temperature dependence for growth more than for respiration, and higher temperatures had more impact than low temperatures did. The correlation between Tmin and MAT resulted in Q10s increasing with MAT, showing that microorganisms from cold regions were less temperature sensitive than those from warmer regions. For every 1˚ C increase in MAT, Q10 increased with 0.04 and 0.03 units for bacterial and fungal growth respectively, and 0.08 units for soil respiration. In contrast to previous studies, we found no relationship between temperature sensitivity and substrate quality. We demonstrate that the strongest driver of variation in microbial temperatures sensitivities (Q10s) is the microbial adaptation to its thermal environment. Surprisingly, the quality of SOM had no influence on the temperature sensitivity. This calls for a revision of the understanding for how microbial decomposers feed-back to climate warming. Specifically, the thermal adaptation of microbial communities need to be incorporated into climate models to capture responses to warming, while the quality of SOM can be ignored.

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.

Microbial community in a precursory scenario of growing Tagetes patula in a lunar greenhouse

NASA Astrophysics Data System (ADS)

Kozyrovska, N. O.; Korniichuk, O. S.; Voznyuk, T. M.; Kovalchuk, M. V.; Lytvynenko, T. L.; Rogutskyy, I. S.; Mytrokhyn, O. V.; Estrella-Liopis, V. R.; Borodinova, T. I.; Mashkovska, S. P.; Foing, B. H.; Kordyum, V. A.

A confined prototype plant-microbial system is elaborated for demonstration of growing pioneer plants in a lunar greenhouse. A precursory scenario of growing Tagetes patula L. in a substrate anorthosite which is similar mineralogically and chemically to lunar silicate rocks includes the use of a microbial community. Microorganisms served for preventive substrate colonization to avoid infection by deleterious microorganisms as well as for bioleaching and delivering of nutritional elements from anorthosite to plants. A model consortium of a siliceous bacterium, biocontrol agents, and arbuscular mycorrhizal fungi provided an acceptable growth and blossoming of Tagetes patula L. under growth limiting factors in terrestrial conditions.

Effects of Bacterial Community Members on the Proteome of the Ammonia-Oxidizing Bacterium Nitrosomonas sp. Strain Is79

PubMed Central

Sedlacek, Christopher J.; Nielsen, Susanne; Greis, Kenneth D.; Haffey, Wendy D.; Revsbech, Niels Peter; Ticak, Tomislav; Laanbroek, Hendrikus J.

2016-01-01

ABSTRACT Microorganisms in the environment do not exist as the often-studied pure cultures but as members of complex microbial communities. Characterizing the interactions within microbial communities is essential to understand their function in both natural and engineered environments. In this study, we investigated how the presence of a nitrite-oxidizing bacterium (NOB) and heterotrophic bacteria affect the growth and proteome of the chemolithoautotrophic ammonia-oxidizing bacterium (AOB) Nitrosomonas sp. strain Is79. We investigated Nitrosomonas sp. Is79 in co-culture with Nitrobacter winogradskyi, in co-cultures with selected heterotrophic bacteria, and as a member of the nitrifying enrichment culture G5-7. In batch culture, N. winogradskyi and heterotrophic bacteria had positive effects on the growth of Nitrosomonas sp. Is79. An isobaric tag for relative and absolute quantification (iTRAQ) liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics approach was used to investigate the effect of N. winogradskyi and the co-cultured heterotrophic bacteria from G5-7 on the proteome of Nitrosomonas sp. Is79. In co-culture with N. winogradskyi, several Nitrosomonas sp. Is79 oxidative stress response proteins changed in abundance, with periplasmic proteins increasing and cytoplasmic proteins decreasing in abundance. In the presence of heterotrophic bacteria, the abundance of proteins directly related to the ammonia oxidation pathway increased, while the abundance of proteins related to amino acid synthesis and metabolism decreased. In summary, the proteome of Nitrosomonas sp. Is79 was differentially influenced by the presence of either N. winogradskyi or heterotrophic bacteria. Together, N. winogradskyi and heterotrophic bacteria reduced the oxidative stress for Nitrosomonas sp. Is79, which resulted in more efficient metabolism. IMPORTANCE Aerobic ammonia-oxidizing microorganisms play an important role in the global nitrogen cycle, converting ammonia to nitrite. In their natural environment, they coexist and interact with nitrite oxidizers, which convert nitrite to nitrate, and with heterotrophic microorganisms. The presence of nitrite oxidizers and heterotrophic bacteria has a positive influence on the growth of the ammonia oxidizers. Here, we present a study investigating the effect of nitrite oxidizers and heterotrophic bacteria on the proteome of a selected ammonia oxidizer in a defined culture to elucidate how these two groups improve the performance of the ammonia oxidizer. The results show that the presence of a nitrite oxidizer and heterotrophic bacteria reduced the stress for the ammonia oxidizer and resulted in more efficient energy generation. This study contributes to our understanding of microbe-microbe interactions, in particular between ammonia oxidizers and their neighboring microbial community. PMID:27235442

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

PubMed Central

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

2016-01-01

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

Physico-chemical parameters, bioactive compounds and microbial quality of thermo-sonicated carrot juice during storage.

PubMed

Martínez-Flores, Héctor E; Garnica-Romo, Ma Guadalupe; Bermúdez-Aguirre, Daniela; Pokhrel, Prashant Raj; Barbosa-Cánovas, Gustavo V

2015-04-01

Thermosonication has been successfully tested in food for microbial inactivation; however, changes in bioactive compounds and shelf-life of treated products have not been thoroughly investigated. Carrot juice was thermo-sonicated (24 kHz, 120 μm amplitude) at 50 °C, 54 °C and 58 °C for 10 min (acoustic power 2204.40, 2155.72, 2181.68 mW/mL, respectively). Quality parameters and microbial growth were evaluated after processing and during storage at 4 °C. Control and sonicated treatments at 50 °C and 54 °C had 10, 12 and 14 d of shelf-life, respectively. Samples sonicated at 58 °C had the best quality; microbial growth remained low at around 3-log for mesophiles, 4.5-log for yeasts and molds and 2-log for enterobacteria after 20 d of storage. Furthermore, thermo-sonicated juice at 58 °C retained >98% of carotenoids and 100% of ascorbic acid. Phenolic compounds increased in all stored, treated juices. Thermo-sonication is therefore a promising technology for preserving the quality of carrot juice by minimising the physicochemical changes during storage, retarding microbial growth and retaining the bioactive compounds. Copyright © 2014 Elsevier Ltd. All rights reserved.

One-step pyrolysis route to three dimensional nitrogen-doped porous carbon as anode materials for microbial fuel cells

NASA Astrophysics Data System (ADS)

Bi, Linlin; Ci, Suqin; Cai, Pingwei; Li, Hao; Wen, Zhenhai

2018-01-01

The design and synthesis of low-cost and favourable anode materials is crucial to both power production efficiency and overall performance of microbial fuel cells (MFCs). Herein, we reported the preparation of three dimensional (3D) nitrogen-doped porous carbons (N/PCs) by one-step pyrolysis of solid mixture of sodium citrate and melamine. a variety of techniques, including electron microscopy, X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), etc., were applied to characterize the surface physicochemical properties of the products, featuring macroporous structure with rich nitrogen doping on the as-prepared N/PCs. When applied as anode materials of MFC, the N/PCs exhibits a maximum power density of 2777.7 mW m-2, approximately twice higher than that of the MFCs with the commercial carbon cloth (CC) as anode. The significantly improved performance of the N/PCs was attributed to the unique structure and properties, such as favourable porous structure, good electrical conductivity, and large pore volume (0.7 cm3 g-1) in the present N/PCs. Nitrogen dopant on the surface of porous carbon contributed to an increasing in biocompatibility, resulting in a suitable micro-environment for microbial growth and thus helps to decrease charge transfer resistance at the electrode interface.

Hydrogen production in single chamber microbial electrolysis cells with different complex substrates.

PubMed

Montpart, Nuria; Rago, Laura; Baeza, Juan A; Guisasola, Albert

2015-01-01

The use of synthetic wastewater containing carbon sources of different complexity (glycerol, milk and starch) was evaluated in single chamber microbial electrolysis cell (MEC) for hydrogen production. The growth of an anodic syntrophic consortium between fermentative and anode respiring bacteria was operationally enhanced and increased the opportunities of these complex substrates to be treated with this technology. During inoculation, current intensities achieved in single chamber microbial fuel cells were 50, 62.5, and 9 A m⁻³ for glycerol, milk and starch respectively. Both current intensities and coulombic efficiencies were higher than other values reported in previous works. The simultaneous degradation of the three complex substrates favored power production and COD removal. After three months in MEC operation, hydrogen production was only sustained with milk as a single substrate and with the simultaneous degradation of the three substrates. The later had the best results in terms of current intensity (150 A m⁻³), hydrogen production (0.94 m³ m⁻³ d⁻¹) and cathodic gas recovery (91%) at an applied voltage of 0.8 V. Glycerol and starch as substrates in MEC could not avoid the complete proliferation of hydrogen scavengers, even under low hydrogen retention time conditions induced by continuous nitrogen sparging.

Success evaluation of the biological control of Fusarium wilts of cucumber, banana, and tomato since 2000 and future research strategies.

PubMed

Raza, Waseem; Ling, Ning; Zhang, Ruifu; Huang, Qiwei; Xu, Yangchun; Shen, Qirong

2017-03-01

The Fusarium wilt caused by Fusarium oxysporum strains is the most devastating disease of cucumber, banana, and tomato. The biological control of this disease has become an attractive alternative to the chemical fungicides and other conventional control methods. In this review, the research trends and biological control efficiencies (BCE) of different microbial strains since 2000 are reviewed in detail, considering types of microbial genera, inoculum application methods, plant growth medium and conditions, inoculum application with amendments, and co-inoculation of different microbial strains and how those affect the BCE of Fusarium wilt. The data evaluation showed that the BCE of biocontrol agents was higher against the Fusarium wilt of cucumber compared to the Fusarium wilts of banana and tomato. Several biocontrol agents mainly Bacillus, Trichoderma, Pseudomonas, nonpathogenic Fusarium, and Penicillium strains were evaluated to control Fusarium wilt, but still this lethal disease could not be controlled completely. We have discussed different reasons of inconsistent results and recommendations for the betterment of BCE in the future. This review provides knowledge of the biotechnology of biological control of Fusarium wilt of cucumber, banana, and tomato in a nut shell that will provide researchers a beginning line to start and to organize and plan research for the future studies.

Implications of streamlining theory for microbial ecology

PubMed Central

Giovannoni, Stephen J; Cameron Thrash, J; Temperton, Ben

2014-01-01

Whether a small cell, a small genome or a minimal set of chemical reactions with self-replicating properties, simplicity is beguiling. As Leonardo da Vinci reportedly said, ‘simplicity is the ultimate sophistication'. Two diverging views of simplicity have emerged in accounts of symbiotic and commensal bacteria and cosmopolitan free-living bacteria with small genomes. The small genomes of obligate insect endosymbionts have been attributed to genetic drift caused by small effective population sizes (Ne). In contrast, streamlining theory attributes small cells and genomes to selection for efficient use of nutrients in populations where Ne is large and nutrients limit growth. Regardless of the cause of genome reduction, lost coding potential eventually dictates loss of function. Consequences of reductive evolution in streamlined organisms include atypical patterns of prototrophy and the absence of common regulatory systems, which have been linked to difficulty in culturing these cells. Recent evidence from metagenomics suggests that streamlining is commonplace, may broadly explain the phenomenon of the uncultured microbial majority, and might also explain the highly interdependent (connected) behavior of many microbial ecosystems. Streamlining theory is belied by the observation that many successful bacteria are large cells with complex genomes. To fully appreciate streamlining, we must look to the life histories and adaptive strategies of cells, which impose minimum requirements for complexity that vary with niche. PMID:24739623

Particulate and Dissolved Organic Carbon Production by the Heterotrophic Nanoflagellate Pteridomonas danica Patterson and Fenchel.

PubMed

Pelegrí; Christaki; Dolan; Rassoulzadegan

1999-05-01

> Abstract We established a budget of organic carbon utilization of a starved heterotrophic nanoflagellate, Pteridomonas danica, incubated in batch cultures with Escherichia coli as model prey. The cultures were sampled periodically for biomass determinations and total organic carbon dynamics: total organic carbon, total organic carbon <1 µm, and dissolved organic carbon (DOC, <0.2 µm). During the 22 h incubation period, P. danica underwent biovolume variations of 3.2-fold. Gross growth efficiency was 22% and net growth efficiency 40%. P. danica respired 33% and egested 44% of the ingested E. coli carbon during lag and exponential growth phases. The form of the organic carbon egested varied. Of the total ingested carbon, 9% was egested in the form of DOC and occurred mainly during the exponential growth phase; 35% was egested in the form of particulate organic carbon (POC), ranging in size from 0.2 to 1 µm, and took place during the lag phase. P. danica could have reingested as much of 58% of this previously produced POC during the exponential growth phase as food scarcity increased. We concluded that POC egestion by flagellates could represent a significant source of submicrometric particles and colloidal organic matter. In addition, flagellate reingestion of egested POC could play a nonnegligible role in the microbial food web. Finally, the methodology reported in this study has proved to be a useful tool in the study of carbon metabolism in aquatic microorganisms.http://link.springer-ny.com/link/service/journals/00248/bibs/37n4p276.html

Density and composition of microorganisms during long-term (418 day) growth of potato using biologically reclaimed nutrients from inedible plant biomass

NASA Technical Reports Server (NTRS)

Garland, J. L.; Cook, K. L.; Johnson, M.; Sumner, R.; Fields, N.; Sager, J. C. (Principal Investigator)

1997-01-01

A study evaluating alternative methods for long term operation of biomass production systems was recently completed at the Kennedy Space Center (KSC). The 418-day study evaluated repeated batch versus mixed-aged production of potato grown on either standard 1/2-strength Hoagland's nutrient solution or solutions including nutrients recycled from inedible plant material. The long term effects of closure and recycling on microbial dynamics were evaluated by monitoring the microbial communities associated with various habitats within the plant growth system (i.e., plant roots, nutrient solution, biofilms within the hydroponic systems, atmosphere, and atmospheric condensate). Plate count methods were used to enumerate and characterize microorganisms. Microscopic staining methods were used to estunate total cell densities. The primary finding was that the density and composition of microbial communities associated with controlled environmental plant growth systems are stable during long term operation. Continuous production resulted in slightly greater stability. Nutrient recycling, despite the addition of soluble organic material from the waste processing system, did not significantly increase microbial density in any of the habitats.

Density and composition of microorganisms during long-term (418 day) growth of potato using biologically reclaimed nutrients from inedible plant biomass

NASA Astrophysics Data System (ADS)

Garland, J. L.; Cook, K. L.; Johnson, M.; Sumner, R.; Fields, N.

1997-01-01

A study evaluating alternative methods for long term operation of biomass production systems was recently completed at the Kennedy Space Center (KSC). The 418-day study evaluated repeated batch versus mixed-aged production of potato grown on either standard 1/2-strength Hoagland's nutrient solution or solutions including nutrients recycled from inedible plant material. The long term effects of closure and recycling on microbial dynamics were evaluated by monitoring the microbial communities associated with various habitats within the plant growth system (i.e., plant roots, nutrient solution, biofilms within the hydroponic systems, atmosphere, and atmospheric condensate). Plate count methods were used to enumerate and characterize microorganisms. Microscopic staining methods were used to estimate total cell densities. The primary finding was that the density and composition of microbial communities associated with controlled environmental plant growth systems are stable during long term operation. Continuous production resulted in slightly greater stability. Nutrient recycling, despite the addition of soluble organic material from the waste processing system, did not significantly increase microbial density in any of the habitats.

Density and composition of microorganisms during long-term (418 day) growth of potato using biologically reclaimed nutrients from inedible plant biomass

NASA Astrophysics Data System (ADS)

1997-01-01

A study evaluating alternative methods for long term operation of biomass production systems was recently completed at the Kennedy Space Center (KSC). The 418-day study evaluated repeated batch versus mixed-aged production of potato grown on either standard 12-strength Hoagland's nutrient solution or solutions including nutrients recycled from inedible plant material. The long term effects of closure and recycling on microbial dynamics were evaluated by monitoring the microbial communities associated with various habitats within the plant growth system (i.e., plant roots, nutrient solution, biofilms within the hydroponic systems, atmosphere, and atmospheric condensate). Plate count methods were used to enumerate and characterize microorganisms. Microscopic staining methods were used to estimate total cell densities. The primary finding was that the density and composition of microbial communities associated with controlled environmental plant growth systems are stable during long term operation. Continuous production resulted in slightly greater stability. Nutrient recycling, despite the addition of soluble organic material from the waste processing system, did not significantly increase microbial density in any of the habitats.

Effect of red blood cells on the growth of Porphyromonas endodontalis and microbial community development.

PubMed

Zerr, M A; Cox, C D; Johnson, W T; Drake, D R

1998-04-01

Establishment of a microbial community in the root canal system depends on numerous factors, of which nutrient availability may be one of the most important. We hypothesized that the presence of red blood cells or hemoglobin in this environment could cause shifts in microbial composition of communities, resulting in organisms such as Porphyromonas endodontalis becoming more dominant. An in vitro model system using mixed, batch cultures was performed with the bacteria P. endodontalis, Fusobacterium nucleatum, Peptostreptococcus micros and Campylobacter rectus. Bacteria were cultured in media with or without the addition of washed red blood cells, hemoglobin, or serum. Cyclic growth studies revealed that P. endodontalis was lost from the community of organisms after three cycles. However, inclusion of red blood cells resulted in establishment of this organism. Moreover, red blood cells added to pure cultures of P. endodontalis substantially enhanced growth and protected the organisms from oxygen. We conclude that the presence of red blood cells could result in shifts of microbial communities of organisms within the root canal system.

Phenotypic responses to interspecies competition and commensalism in a naturally-derived microbial co-culture.

PubMed

Khan, Nymul; Maezato, Yukari; McClure, Ryan S; Brislawn, Colin J; Mobberley, Jennifer M; Isern, Nancy; Chrisler, William B; Markillie, Lye Meng; Barney, Brett M; Song, Hyun-Seob; Nelson, William C; Bernstein, Hans C

2018-01-10

The fundamental question of whether different microbial species will co-exist or compete in a given environment depends on context, composition and environmental constraints. Model microbial systems can yield some general principles related to this question. In this study we employed a naturally occurring co-culture composed of heterotrophic bacteria, Halomonas sp. HL-48 and Marinobacter sp. HL-58, to ask two fundamental scientific questions: 1) how do the phenotypes of two naturally co-existing species respond to partnership as compared to axenic growth? and 2) how do growth and molecular phenotypes of these species change with respect to competitive and commensal interactions? We hypothesized - and confirmed - that co-cultivation under glucose as the sole carbon source would result in competitive interactions. Similarly, when glucose was swapped with xylose, the interactions became commensal because Marinobacter HL-58 was supported by metabolites derived from Halomonas HL-48. Each species responded to partnership by changing both its growth and molecular phenotype as assayed via batch growth kinetics and global transcriptomics. These phenotypic responses depended on nutrient availability and so the environment ultimately controlled how they responded to each other. This simplified model community revealed that microbial interactions are context-specific and different environmental conditions dictate how interspecies partnerships will unfold.

Phenotypic responses to interspecies competition and commensalism in a naturally-derived microbial co-culture

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

Khan, Nymul; Maezato, Yukari; McClure, Ryan S.

The fundamental question of whether different microbial species will co-exist or compete in a given environment depends on context, composition and environmental constraints. Model microbial systems can yield some general principles related to this question. In this study we employed a naturally occurring co-culture composed of heterotrophic bacteria, Halomonas sp. HL-48 and Marinobacter sp. HL-58, to ask two fundamental scientific questions: 1) how do the phenotypes of two naturally co-existing species respond to partnership as compared to axenic growth? and 2) how do growth and molecular phenotypes of these species change with respect to competitive and commensal interactions? We hypothesizedmore » – and confirmed – that co-cultivation under glucose as the sole carbon source would result in a competitive interactions. Similarly, when glucose was swapped with xylose, the interactions became commensal because Marinobacter HL-58 was supported by metabolites derived from Halomonas HL-48. Each species responded to partnership by changing both its growth and molecular phenotype as assayed via batch growth kinetics and global transcriptomics. These phenotypic responses depended nutrient availability and so the environment ultimately controlled how they responded to each other. This simplified model community revealed that microbial interactions are context-specific and different environmental conditions dictate how interspecies partnerships will unfold.« less

Stochastic Assembly of Bacteria in Microwell Arrays Reveals the Importance of Confinement in Community Development

PubMed Central

Hansen, Ryan H.; Timm, Andrea C.; Timm, Collin M.; Bible, Amber N.; Morrell-Falvey, Jennifer L.; Pelletier, Dale A.; Simpson, Michael L.; Doktycz, Mitchel J.; Retterer, Scott T.

2016-01-01

The structure and function of microbial communities is deeply influenced by the physical and chemical architecture of the local microenvironment and the abundance of its community members. The complexity of this natural parameter space has made characterization of the key drivers of community development difficult. In order to facilitate these characterizations, we have developed a microwell platform designed to screen microbial growth and interactions across a wide variety of physical and initial conditions. Assembly of microbial communities into microwells was achieved using a novel biofabrication method that exploits well feature sizes for control of innoculum levels. Wells with incrementally smaller size features created populations with increasingly larger variations in inoculum levels. This allowed for reproducible growth measurement in large (20 μm diameter) wells, and screening for favorable growth conditions in small (5, 10 μm diameter) wells. We demonstrate the utility of this approach for screening and discovery using 5 μm wells to assemble P. aeruginosa colonies across a broad distribution of innoculum levels, and identify those conditions that promote the highest probability of survivial and growth under spatial confinement. Multi-member community assembly was also characterized to demonstrate the broad potential of this platform for studying the role of member abundance on microbial competition, mutualism and community succession. PMID:27152511

Selenite resistant rhizobacteria stimulate SeO(3) (2-) phytoextraction by Brassica juncea in bioaugmented water-filtering artificial beds.

PubMed

Lampis, Silvia; Ferrari, Anita; Cunha-Queda, A Cristina F; Alvarenga, Paula; Di Gregorio, Simona; Vallini, Giovanni

2009-09-01

Selenium is a trace metalloid of global environmental concern. The boundary among its essentiality, deficiency, and toxicity is narrow and mainly depends on the chemical forms and concentrations in which this element occurs. Different plant species-including Brassica juncea-have been shown to play a significant role in Se removal from soil as well as water bodies. Furthermore, the interactions between such plants, showing natural capabilities of metal uptake and their rhizospheric microbial communities, might be exploited to increase both Se scavenging and vegetable biomass production in order to improve the whole phytoextraction efficiency. The aim of the present study was to evaluate the capability of selenite removal of B. juncea grown in hydroponic conditions on artificially spiked effluents. To optimize phytoextraction efficiency, interactions between B. juncea and rhizobacteria were designedly elicited. Firstly, B. juncea was grown on water-filtering agriperlite beds in the presence of three different selenite concentrations, namely, 0.2, 1.0, and 2.0 mM. Plant growth was measured after 3 and 6 weeks of incubation in order to establish the selenite concentration at which the best plant biomass production could be obtained. Afterwards, water-filtering agriperlite beds were inoculated either with a selenium-acclimated microbial community deriving from the rhizosphere of B. juncea grown, erstwhile, in a selenite-amended soil or with axenic cultures of two bacterial strains, vicelike Bacillus mycoides SeITE01 and Stenotrophomonas maltophilia SeITE02, previously isolated and described for their high resistance to selenite. These latter were seeded separately or as a dual consortium. Selenite was amended at a final concentration of 1.0 mM. Total Se content in plant tissues (both shoots and roots), plant biomass production, and persistence of bioaugmented microbial inocula during the experimental time were monitored. Moreover, parameters such as bioconcentration factor (BF) and phytoextraction efficiency (PE) were determined at the end of the testing run to evaluate the effects of the different bioaugmentation strategies adopted on selenite phytoextraction efficiency of B. juncea. A general but significant increase in capacity to extract and transport selenium to the epigeous plant compartments was recorded in B. juncea grown in beds augmented with microbial inocula, except for the treatment with B. mycoides SeITE01 alone. Nevertheless, a severe decrease in vegetable biomass production was observed after all microbial treatments with the exception of the plants that had received only S. maltophilia SeITE02. Actually, an increase in selenium phytoextraction efficiency up to 65% was observed in B. juncea, when this bacterial strain was inoculated. Emendation of B. juncea grown in water-filtering beds with a Se(IV)-acclimated microbial community caused a higher Se uptake along with a reduction of plant biomass yield with respect to plants grown without addition of the same bacterial inoculum. The increase of selenium BF in shoots suggests that the Se(IV)-acclimated microbial community not only elicited the plant capacity to absorb selenite, but also did improve the capacity to transport the metalloid to the epigeous compartments. On the other hand, the reduction in plant biomass yield might be related exactly to this improved capability of B. juncea to accumulate selenium at concentrations that are actually toxic for plants. Differently, addition of two selenite-resistant bacterial strains, namely, S. maltophilia SeITE02 and B. mycoides SEITE01, had weaker effects on plant biomass production when compared to those recorded in the presence of the Se(IV)-adapted microbial community. In particular, inoculation of water-filtering beds with the SeITE02 strain alone was the sole strategy resulting in a positive effect on both plant biomass production in stressful conditions and the capacity of shoots to accumulate selenium. In fact, its putative ability of reducing Se(IV) to organo-Se compounds significantly enhanced either selenium absorption by the plants or active metalloid translocation to epigeous parts. Bioaugmentation with the bacterial strain S. malthophila SeITE02 is suggested to elicit selenite phytoextraction efficiency in B. juncea. Manipulation of synergistic interactions between plants having phytoextraction capabilities and their associated rhizobacteria may enhance already consolidated treatment processes aimed to detoxify selenite laden wastewater.

Detection of a wide variety of human and veterinary fluoroquinolone antibiotics in municipal wastewater and wastewater-impacted surface water.

PubMed

He, Ke; Soares, Ana Dulce; Adejumo, Hollie; McDiarmid, Melissa; Squibb, Katherine; Blaney, Lee

2015-03-15

As annual sales of antibiotics continue to rise, the mass of these specially-designed compounds entering municipal wastewater treatment systems has also increased. Of primary concern here is that antibiotics can inhibit growth of specific microorganisms in biological processes of wastewater treatment plants (WWTPs) or in downstream ecosystems. Growth inhibition studies with Escherichia coli demonstrated that solutions containing 1-10 μg/L of fluoroquinolones can inhibit microbial growth. Wastewater samples were collected on a monthly basis from various treatment stages of a 30 million gallon per day WWTP in Maryland, USA. Samples were analyzed for the presence of 11 fluoroquinolone antibiotics. At least one fluoroquinolone was detected in every sample. Ofloxacin and ciprofloxacin exhibited detection frequencies of 100% and 98%, respectively, across all sampling sites. Concentrations of fluoroquinolones in raw wastewater were as high as 1900 ng/L for ciprofloxacin and 600 ng/L for ofloxacin. Difloxacin, enrofloxacin, fleroxacin, moxifloxacin, norfloxacin, and orbifloxacin were also detected at appreciable concentrations of 9-170 ng/L. The total mass concentration of fluoroquinolones in raw wastewater was in the range that inhibited E. coli growth, suggesting that concerns over antibiotic presence in wastewater and wastewater-impacted surface water are valid. The average removal efficiency of fluoroquinolones during wastewater treatment was approximately 65%; furthermore, the removal efficiency for fluoroquinolones was found to be negatively correlated to biochemical oxygen demand removal and positively correlated to phosphorus removal. Copyright © 2014 Elsevier B.V. All rights reserved.

Effect of phytase from Aspergillus niger on plant growth and mineral assimilation in wheat (Triticum aestivum Linn.) and its potential for use as a soil amendment.

PubMed

Gujar, Pradnya D; Bhavsar, Kavita P; Khire, Jayant M

2013-07-01

Extensive use of non-replenishable phosphate reserves as phosphate supplements in agriculture and animal feed poses a threat for environmental pollution and necessitated a search for alternative phosphate sources. Unlocking the phytate phosphorus using microbial phytase can provide an ecofriendly solution in agriculture. The aim of the present work was to evaluate the effect of phytase from Aspergillus niger NCIM 563 in degradation of phytate phosphorus to benefit plant nutrition and soil amendment in comparison with chemical fertilizers. An enzyme dose of 12 IU was sufficient to hydrolyze phytate and increase assimilation of phosphorus by about 74%. Phytase supplementation leads to increase in shoot:total length ratio by about 200%, indicating its growth-promoting effect. Consistency in phytase-induced growth was reflected at pot and tray levels, wherein shoot:total length ratio was observed to be 2.01 and 2.12 respectively. Mineral assimilation due to phytase was more efficient as compared to chemical fertilizers, thus overcoming the constraints of practicability and economics in the agriculture industry. Phytase was efficient in reducing the phytic acid content of soil by about 30% while simultaneously increasing the phytate phosphate availability by 1.18-fold. Phytase from A. niger showed improvement in phytate phosphorus and mineral availability. Besides a plant growth-promoting effect, reduction in use of chemical fertilizers and soil improvement could be achieved simultaneously for maintaining the sustainability of agriculture. © 2012 Society of Chemical Industry.

Evaluation of Time-Temperature Integrators (TTIs) with Microorganism-Entrapped Microbeads Produced Using Homogenization and SPG Membrane Emulsification Techniques.

PubMed

Rahman, A T M Mijanur; Lee, Seung Ju; Jung, Seung Won

2015-12-28

A comparative study was conducted to evaluate precision and accuracy in controlling the temperature dependence of encapsulated microbial time-temperature integrators (TTIs) developed using two different emulsification techniques. Weissela cibaria CIFP 009 cells, immobilized within 2% Na-alginate gel microbeads using homogenization (5,000, 7,000, and 10,000 rpm) and Shirasu porous glass (SPG) membrane technologies (10 μm), were applied to microbial TTIs. The prepared micobeads were characterized with respect to their size, size distribution, shape and morphology, entrapment efficiency, and bead production yield. Additionally, fermentation process parameters including growth rate were investigated. The TTI responses (changes in pH and titratable acidity (TA)) were evaluated as a function of temperature (20°C, 25°C, and 30°C). In comparison with conventional methods, SPG membrane technology was able not only to produce highly uniform, small-sized beads with the narrowest size distribution, but also the bead production yield was found to be nearly 3.0 to 4.5 times higher. However, among the TTIs produced using the homogenization technique, poor linearity (R(2)) in terms of TA was observed for the 5,000 and 7,000 rpm treatments. Consequently, microbeads produced by the SPG membrane and by homogenization at 10,000 rpm were selected for adjusting the temperature dependence. The Ea values of TTIs containing 0.5, 1.0, and 1.5 g microbeads, prepared by SPG membrane and conventional methods, were estimated to be 86.0, 83.5, and 76.6 kJ/mol, and 85.5, 73.5, and 62.2 kJ/mol, respectively. Therefore, microbial TTIs developed using SPG membrane technology are much more efficient in controlling temperature dependence.

Fungal bioremediation of the creosote-contaminated soil: influence of Pleurotus ostreatus and Irpex lacteus on polycyclic aromatic hydrocarbons removal and soil microbial community composition in the laboratory-scale study.

PubMed

Byss, Marius; Elhottová, Dana; Tříska, Jan; Baldrian, Petr

2008-11-01

The aim of this study was to determine the efficacy of selected basidiomycetes in the removing of polycyclic aromatic hydrocarbons (PAH) from the creosote-contaminated soil. Fungi Pleurotus ostreatus and Irpex lacteus were supplemented with creosote-contaminated (50-200 mg kg(-1) PAH) soil originating from a wood-preserving plant and incubated at 15 °C for 120 d. Either fungus degraded PAH with 4-6 aromatic rings more efficiently than the microbial community present initially in the soil. PAH removal was higher in P. ostreatus treatments (55-67%) than in I. lacteus treatments (27-36%) in general. P. ostreatus (respectively, I. lacteus) removed 86-96% (47-59%) of 2-rings PAH, 63-72% (33-45%) of 3-rings PAH, 32-49% (9-14%) of 4-rings PAH and 31-38% (11-13%) of 5-6-rings PAH. MIS (Microbial Identification System) Sherlock analysis of the bacterial community determined the presence of dominant Gram-negative bacteria (G-) Pseudomonas in the inoculated soil before the application of fungi. Complex soil microbial community was characterized by phospholipid fatty acids analysis followed by GC-MS/MS. Either fungus induced the decrease of bacterial biomass (G- bacteria in particular), but the soil microbial community was influenced by P. ostreatus in a different way than by I. lacteus. The bacterial community was stressed more by the presence of I. lacteus than P. ostreatus (as proved by the ratio of the fungal/bacterial markers and by the ratio of trans/cis mono-unsaturated fatty acids). Moreover, P. ostreatus stimulated the growth of Gram-positive bacteria (G+), especially actinobacteria and these results indicate the potential of the positive synergistic interaction of this fungus and actinobacteria in creosote biodegradation.

Removal Mechanisms of Para-nitrophenol in Reclaimed Water using SAT and its Bio-enhancement

NASA Astrophysics Data System (ADS)

Wen, Y. L.; Yang, Y.; Zhang, H.; Lou, B.

2017-12-01

Nowadays, we were facing with water resource shortage along with water pollution. It was important to undertake the cost effective technology to treat polluted water whilst encourage water reuse. Soil aquifer treatment (SAT) was an efficient technology, using the infiltration process of mediation, adsorption and biodegradation on the pollutants in the environment to achieve the goal of recycling water. For a better understanding of the transport and attenuation of para-nitrophenol (P-NP) and the change of microbial community at the stress of p-nitrophenol in soil aquifer treatment system, two column experiments were operated to investigate the physical, chemical, and microbial dynamics. At the same time, the bio-augment method was used to enhance the SAT biodegradation system. The SAT column experiment was operated about 38 days, which demonstrated that two reduction zones were revealed at the middle of the column and the biodiversity of the microbial community could be destroyed under the P-NP stress. Absorption was the main removal mechanism according to the obtained experimental data. By using the displacement method, the BIO-SAT system was operated about 36 days, which showed perfect outcome for the P-NP removal at a higher concentration. From the PCR-DGGE and high throughput sequencing study, enhanced bacteria could form a stable biological community with indigenous communities. Through the Canonical Correspondence Analysis (CCA) microbial degradation and environmental factors, the results showed that the pH was a very important parameter affects the degradation of nitrophenol degradation bacteria. The metal ions under the condition of low concentration can promote the growth of microbial degradation. This study provide valuable result on the attenuation potential of for the bio-enhanced SAT system (BIO-SAT). (No Image Selected)

Soil biota effects on clonal growth and flowering in the forest herb Stachys sylvatica

NASA Astrophysics Data System (ADS)

de la Peña, Eduardo; Bonte, Dries

2011-03-01

The composition of a soil community can vary drastically at extremely short distances. Therefore, plants from any given population can be expected to experience strong differences in belowground biotic interactions. Although it is well recognized that the soil biota plays a significant role in the structure and dynamics of plant communities, plastic responses in growth strategies as a function of soil biotic interactions have received little attention. In this study, we question whether the biotic soil context from two forest associated contrasting environments (the forest understory and the hedgerows) determines the balance between clonal growth and flowering of the perennial Stachys sylvatica. Using artificial soils, we compared the growth responses of this species following inoculation with the mycorrhizal and microbial community extracted either from rhizospheric soil of the forest understory or from the hedgerows. The microbial context had a strong effect on plant functional traits, determining the production of runners and inflorescences. Plants inoculated with the hedgerow community had a greater biomass, larger number of runners, and lower resource investment in flower production than was seen in plants inoculated with the understory microbial community. The obtained results illustrate that belowground biotic interactions are essential to understand basic plastic growth responses determinant for plant establishment and survival. The interactions with microbial communities from two contrasting habitats resulted in two different, and presumably adaptive, growth strategies that were optimal for the conditions prevalent in the environments compared; and they are as such an essential factor to understand plant-plant, plant-animal interactions and the dispersal capacities of clonal plants.

Effects of elevated CO2 and shade on the decomposition of senesced tree foliage: impacts on microbial activity

Treesearch

Michael G. Kaufman; R. Malcolm Strand; Mark E. Kubiske; William J. Mattson; Daniel A. Herms; Edward D. Walker; Kurt S. Pregitzer; Richard W. Merritt

1996-01-01

We examined microbial respiration and carbon/nitrogen content of decomposing leaf material in microcosms used for growth studies of the treehole mosquito, Aedes triseriatus. Leaf material originated from birch and oak trees exposed to conditions of shade/sun and elevated/ambient levels of CO2. Microbial respiration as measured...

Soil ecological interactions: comparisons between tropical and subalpine forests

Treesearch

Grizelle Gonzalez; Ruth E. Ley; Steven K. Schmidt; Xiaoming Zou; Timothy R. Seastedt

2001-01-01

Soil fauna can influence soil processes through interactions with the microbial community. Due to the complexity of the functional roles of fauna and their effects on microbes, little consensus has been reached on the extent to which soil fauna can regulate microbial activities. We quantified soil microbial biomass and maximum growth rates in control and fauna-excluded...

Combination of sodium chlorite and calcium propionate reduces enzymatic browning and microbial population of fresh-cut ‘Granny Smith’ apples

USDA-ARS?s Scientific Manuscript database

Tissue browning and microbial growth are the main concerns associated with fresh-cut apples. In this study, effects of sodium chlorite (SC) and calcium propionate (CP), individually and combined, on quality and microbial population of apple slices were investigated. ‘Granny Smith’ apple slices, dipp...

Biological treatment of steroidal drug industrial effluent and electricity generation in the microbial fuel cells.

PubMed

Liu, Ru; Gao, Chongyang; Zhao, Yang-Guo; Wang, Aijie; Lu, Shanshan; Wang, Min; Maqbool, Farhana; Huang, Qing

2012-11-01

The single chamber microbial fuel cells (MFCs) were used to treat steroidal drug production wastewater (SPW) and generate electricity simultaneously. The results indicated that the maximum COD removal efficiency reached 82%, total nitrogen and sulfate removal rate approached 62.47% and 26.46%, respectively. The maximum power density and the Coulombic efficiency reached to 22.3Wm(-3) and 30%, respectively. The scanning electron microscope showed that the dominant microbial populations were remarkably different in morphology on the surface of SPW and acetate-fed anodes. PCR-denaturing gradient gel electrophoresis profiles revealed that the microbial community structure fed with different concentrations of SPW presented a gradual succession and unique bacterial sequences were detected on the SPW and acetate-fed anodes. This research demonstrates that MFCs fed with SPW achieved a high efficiency of power density and simultaneous nutrient removal, and the dominant microorganisms on the anode were related to the types and the concentrations of substrates. Copyright © 2012 Elsevier Ltd. All rights reserved.

Hydrogen production from switchgrass via an integrated pyrolysis-microbial electrolysis process.

PubMed

Lewis, A J; Ren, S; Ye, X; Kim, P; Labbe, N; Borole, A P

2015-11-01

A new approach to hydrogen production using an integrated pyrolysis-microbial electrolysis process is described. The aqueous stream generated during pyrolysis of switchgrass was used as a substrate for hydrogen production in a microbial electrolysis cell, achieving a maximum hydrogen production rate of 4.3 L H2/L anode-day at a loading of 10 g COD/L-anode-day. Hydrogen yields ranged from 50±3.2% to 76±0.5% while anode Coulombic efficiency ranged from 54±6.5% to 96±0.21%, respectively. Significant conversion of furfural, organic acids and phenolic molecules was observed under both batch and continuous conditions. The electrical and overall energy efficiency ranged from 149-175% and 48-63%, respectively. The results demonstrate the potential of the pyrolysis-microbial electrolysis process as a sustainable and efficient route for production of renewable hydrogen with significant implications for hydrocarbon production from biomass. Copyright © 2015 Elsevier Ltd. All rights reserved.

Bioremediation of PAHs and VOCs: Advances in clay mineral-microbial interaction.

PubMed

Biswas, Bhabananda; Sarkar, Binoy; Rusmin, Ruhaida; Naidu, Ravi

2015-12-01

Bioremediation is an effective strategy for cleaning up organic contaminants, such as polycyclic aromatic hydrocarbons (PAHs) and volatile organic compounds (VOCs). Advanced bioremediation implies that biotic agents are more efficient in degrading the contaminants completely. Bioremediation by microbial degradation is often employed and to make this process efficient, natural and cost-effective materials can serve as supportive matrices. Clay/modified clay minerals are effective adsorbents of PAHs/VOCs, and readily available substrate and habitat for microorganisms in the natural soil and sediment. However, the mechanism underpinning clay-mediated biodegradation of organic compounds is often unclear, and this requires critical investigation. This review describes the role of clay/modified clay minerals in hydrocarbon bioremediation through interaction with microbial agents in specific scenarios. The vision is on a faster, more efficient and cost-effective bioremediation technique using clay-based products. This review also proposes future research directions in the field of clay modulated microbial degradation of hydrocarbons. Copyright © 2015 Elsevier Ltd. All rights reserved.

Weaker soil carbon-climate feedbacks resulting from microbial and abiotic interactions

NASA Astrophysics Data System (ADS)

Tang, Jinyun; Riley, William J.

2015-01-01

The large uncertainty in soil carbon-climate feedback predictions has been attributed to the incorrect parameterization of decomposition temperature sensitivity (Q10; ref. ) and microbial carbon use efficiency. Empirical experiments have found that these parameters vary spatiotemporally, but such variability is not included in current ecosystem models. Here we use a thermodynamically based decomposition model to test the hypothesis that this observed variability arises from interactions between temperature, microbial biogeochemistry, and mineral surface sorptive reactions. We show that because mineral surfaces interact with substrates, enzymes and microbes, both Q10 and microbial carbon use efficiency are hysteretic (so that neither can be represented by a single static function) and the conventional labile and recalcitrant substrate characterization with static temperature sensitivity is flawed. In a 4-K temperature perturbation experiment, our fully dynamic model predicted more variable but weaker soil carbon-climate feedbacks than did the static Q10 and static carbon use efficiency model when forced with yearly, daily and hourly variable temperatures. These results imply that current Earth system models probably overestimate the response of soil carbon stocks to global warming. Future ecosystem models should therefore consider the dynamic interactions between sorptive mineral surfaces, substrates and microbial processes.

In vivo assimilation of one-carbon via a synthetic reductive glycine pathway in Escherichia coli.

PubMed

Yishai, Oren; Bouzon, Madeleine; Döring, Volker; Bar-Even, Arren

2018-05-15

Assimilation of one-carbon compounds presents a key biochemical challenge, which limits their use as sustainable feedstocks for microbial growth and production. The reductive glycine pathway is a synthetic metabolic route that could provide an optimal way for the aerobic assimilation of reduced C1 compounds. Here, we show that a rational integration of native and foreign enzymes enables the tetrahydrofolate and glycine cleavage/synthase systems to operate in the reductive direction, such that Escherichia coli satisfies all of its glycine and serine requirements from the assimilation of formate and CO2. Importantly, the biosynthesis of serine from formate and CO2 does not lower the growth rate, indicating high flux that is able to provide 10% of cellular carbon. Our findings assert that the reductive glycine pathway could support highly efficient aerobic assimilation of C1-feedstocks.

An Evaluation Method for Suppression of Pathogenic Fusarium oxysporum by Soil Microorganisms Using the Dilution Plate Technique.

PubMed

Mitsuboshi, Masahiro; Kioka, Yuuzou; Noguchi, Katsunori; Asakawa, Susumu

2017-01-01

Volume 31, No. 3, Page 307-313, 2016Page 310, Legend for Fig. 4 IncorrectFig. 4. Growth degree of Fusarium oxysporum f. sp. spinaciae for organic fertilizers at each dilution based on an estimation of the ellipse area (A) and extension length (B) of the colony. Cont, compound inorganic fertilizer; SBM, steamed bone meal; CDC, cow dung compost; MI, microbial inoculant. Values show mean of medians of degrees with SE (n=3). The ellipse area and extension length for control plates were 4,475 mm 2 and 36.5 mm, respectively. CorrectFig. 4. Growth degree of Fusarium oxysporum f. sp. spinaciae for organic fertilizers at each dilution based on an estimation of the ellipse area (A) and extension length (B) of the colony. Cont, compound inorganic fertilizer; SBM, steamed bone meal; CDC, cow dung compost; MI, microbial inoculant. Values show mean of growth degrees with SE (n=3). The ellipse area and extension length for control plates were 4,475 mm 2 and 36.5 mm, respectively. Page 311, Legend for Fig. 5 IncorrectFig. 5. Growth degree of Fusarium oxysporum f. sp. spinaciae for soil applied with organic fertilizers at each dilution based on an estimation of the ellipse area (A) and extension length (B) of the colony. Cont, compound inorganic fertilizer; SBM, steamed bone meal; CDC, cow dung compost; MI, microbial inoculant. Values show the mean of medians of degrees with SE (n=3). The ellipse area and extension length for control plates were 5,473 mm 2 and 40.5 mm, respectively. CorrectFig. 5. Growth degree of Fusarium oxysporum f. sp. spinaciae for soil applied with organic fertilizers at each dilution based on an estimation of the ellipse area (A) and extension length (B) of the colony. Cont, compound inorganic fertilizer; SBM, steamed bone meal; CDC, cow dung compost; MI, microbial inoculant. Values show the mean of growth degrees with SE (n=3). The ellipse area and extension length for control plates were 5,473 mm 2 and 40.5 mm, respectively. Page 312, Legend for Fig. 7 IncorrectFig. 7. Growth degree of Fusarium oxysporum f. sp. spinaciae at each dilution based on an estimation of the ellipse area (A) and extension length (B) of the colony. Cont, compound inorganic fertilizer; SBM, steamed bone meal; CDC, cow dung compost; MI2, microbial inoculant applied with 2,000 kg ha -1 ; MI10, microbial inoculant applied with 10,000 kg ha -1 . Values show the mean of medians of degrees with SE (n=3). The ellipse area and extension length for control plates were 3,404 mm 2 and 29.7 mm, respectively. CorrectFig. 7. Growth degree of Fusarium oxysporum f. sp. spinaciae at each dilution based on an estimation of the ellipse area (A) and extension length (B) of the colony. Cont, compound inorganic fertilizer; SBM, steamed bone meal; CDC, cow dung compost; MI2, microbial inoculant applied with 2,000 kg ha -1 ; MI10, microbial inoculant applied with 10,000 kg ha -1 . Values show the mean of growth degrees with SE (n=3). The ellipse area and extension length for control plates were 3,404 mm 2 and 29.7 mm, respectively. The authors would like to apologize for these corrections and any inconvenience caused.

Efficient synthesis, structural characterization and anti-microbial activity of chiral aryl boronate esters of 1,2-O-isopropylidene-α-D-xylofuranose.

PubMed

Trivedi, Rajiv; Rami Reddy, E; Kiran Kumar, Ch; Sridhar, B; Pranay Kumar, K; Srinivasa Rao, M

2011-07-01

A simple and efficient synthetic approach toward a series of chiral aryl boronate esters, starting from D-xylose, as anti-microbial agents, is described herein. Minimum inhibitory concentration and zone of inhibition revealed that these derivatives exhibit potent anti-bacterial and anti-fungal properties. Herein, we report the first anti-microbial activity of this class of compounds. All products have been characterized by NMR ((1)H, (13)C and (11)B), IR, elemental and mass spectral study. Copyright © 2011 Elsevier Ltd. All rights reserved.

Physical and ecological controllers of the microbial responses to drying and rewetting in soil

NASA Astrophysics Data System (ADS)

Leizeaga, Ainara; Meisner, Annelein; Bååth, Erland; Rousk, Johannes

2017-04-01

Soil moisture is one of the most powerful factors that regulate microbial activity in soil. The variation of moisture leads to drying-rewetting (DRW) events which are known to induce enormous dynamics in soil biogeochemistry; however, the microbial underpinnings are mostly unknown. Rewetting a dry soil can result in two response patterns of bacterial growth. In the Type 1 response, bacteria start growing immediately after rewetting with rates that increase in a linear fashion to converge with those prior to the DRW within hours. This growth response coincides with respiration rates that peak immediately after rewetting to then exponentially decrease. In the Type 2 response, bacterial growth remains very low after rewetting during a lag period of up to 20 hours. Bacteria then increase their growth rates exponentially to much higher rates than those before the DRW event. This growth response coincides with respiration rates that increase to high rates immediately after rewetting that then remain elevated and sometimes even increase further in sync with the growth increase. Previous studies have shown that (i) extended drying (ii) starving before DRW and (iii) inhibitors combined with drought could change the bacterial response from Type 1 to Type 2. This suggested that the response of bacteria upon rewetting could be related to the harshness of the disturbance as experienced by the microbes. In the present study, we set out to study if reduced harshness could change a Type 2 response into a Type 1 response. We hypothesized that (1) a reduced physical harshness of drying and (2) induced tolerance to drying in microbial communities could change a Type 2 response into a Type 1 growth response upon rewetting. To address this, two experiments were performed. First, soils were partially dried to different water contents and bacterial response upon rewetting was measured. Second, soils were exposed to repeated DRW cycles (< 9 cycles) and the bacterial response was followed after rewetting. A less harsh drying (partial drying) of a soil could change the growth responses to rewetting. The lag period decreased with less complete drying to eventually became 0, transitioning from a Type 2 to a Type 1. Even after a Type 1 response was induced, further reduction of harshness could also lead to a faster recovery of growth rates. Our results support the hypothesis: the physical harshness of drying can determine the microbial survival and thus the type of bacterial growth response. Subjecting soil to DRW cycles could also induce a change from a Type 2 to Type 1 growth response. This suggested that there was a community shift towards higher drought-tolerance. Thus, identical physical disturbance was less harsh for a community that has been subjected to more drying rewetting cycles. To predict how the microbial community's control of the soil C budget of ecosystems is affected warming-induced drought, our results demonstrate that both the physical characteristics of the disturbance and the community's tolerance to drought need to be considered.

Structural data and biological properties of almond gum oligosaccharide: application to beef meat preservation.

PubMed

Bouaziz, Fatma; Helbert, Claire Boisset; Romdhane, Molka Ben; Koubaa, Mohamed; Bhiri, Fatma; Kallel, Fatma; Chaari, Fatma; Driss, Dorra; Buon, Laurine; Chaabouni, Semia Ellouz

2015-01-01

Enzymatic hydrolysis of almond gum generates low molecular weight oligosaccharides (OAG) with a yield of 33.5%. The generated oligosaccharides were purified and identified. OAG analyses show that the most prominent residues were galactose and arabinose with traces of xylose, rhamnose, glucose and mannose. The glycosyl linkage positions were analyzed using gas chromatography-mass spectrometry showing a main chain composed of galactose units [ → 3)-Gal-(1 → ] branched mainly with arabinose residues [Ara-(1 → ]. The antioxidant and antimicrobial activities of OAG were investigated. As regards the in vitro antioxidant activities, the OAG showed a high total antioxidant activity (347 μg ascorbic acid equivalent/mL), an important DPPH (1,1-diphenyl-2-picrylhydrazyl) scavenging activity (IC50 = 0.64 mg/mL) and a high reducing capacity (RP0.5AU = 3.6 mg/mL). Furthermore, OAG had a high antimicrobial activity against Salmonella thyphimirium, Bacillus cereus, Actinomycetes sp, Klebsiella pneumoniae, Escherichia coli, Alternaria alternate and Candidat albicans. Finally, OAG efficiency was tested using 0.5%; 0.75% and 1% concentrations in beef meat preservation. Microbial growth and lipid oxidation were monitored during 9 days at 4 °C. The results showed significant inhibitions (p < 0.05) of lipid oxidation and microbial growth in ground beef meat containing OAG. Copyright © 2014 Elsevier B.V. All rights reserved.

[Microbial settlement of paint- and building-materials in the sphere of drinking water. 9. Communication: experimental examination of cement mortar for the lining with tiles (author's transl)].

PubMed

Schoenen, D; Thofern, E

1981-12-01

The observation of a microbial growth in form of macrocolonies upon the joints of a tiled drinking water reservoir caused the microbiological testing of different pure mineral and some plastic containing cement mortar. Besides the conditions allowing the growth of macrocolonies on tiled plates with a construction like in a reservoir were examined.

A simple laser-based device for simultaneous microbial culture and absorbance measurement

NASA Astrophysics Data System (ADS)

Abrevaya, X. C.; Cortón, E.; Areso, O.; Mauas, P. J. D.

2013-07-01

In this work we present a device specifically designed to study microbial growth with several applications related to environmental microbiology and other areas of research as astrobiology. The Automated Measuring and Cultivation device (AMC-d) enables semi-continuous absorbance measurements directly during cultivation. It can measure simultaneously up to 16 samples. Growth curves using low and fast growing microorganism were plotted, including Escherichia coli and Haloferax volcanii, a halophilic archaeon.

Microbial Flocculant for Nature Soda

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

Qin, Peiyong; Zhang, Tong; Chen, Cuixian

2004-03-31

Microbial flocculant for nature soda has been studied. Lactobacillus TRJ21, which was able to produce an excellent biopolymer flocculant for nature soda, was obtained in our lab. The microbial flocculant was mainly produced when the bacteria laid in stationary growth phase. Fructose or glucose, as carbon sources, were more favorable for the bacterial growth and flocculant production. The bacteria was able to use ammonium sulfate or Urea as nitrogen to produce flocculant, but was not able to use peptone effectively. High C/N ratio was more favorable to Lactobacillus TRJ21 growth and flocculant production than low C/N ratio. The biopolymer flocculantmore » was mainly composed of polysaccharide and protein with a molecular weight 1.38x106 by gel permeation chromatography. It was able to be easily purified from the culture medium by acetone. Protein in the flocculant was tested for the flocculating activity ingredient by heating the flocculant.« less

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

Growth Mechanism of Microbial Colonies

NASA Astrophysics Data System (ADS)

Zhu, Minhui; Martini, K. Michael; Kim, Neil H.; Sherer, Nicholas; Lee, Jia Gloria; Kuhlman, Thomas; Goldenfeld, Nigel

Experiments on nutrient-limited E. coli colonies, growing on agar gel from single cells reveal a power-law distribution of sizes, both during the growth process and in the final stage when growth has ceased. We developed a Python simulation to study the growth mechanism of the bacterial population and thus understand the broad details of the experimental findings. The simulation takes into account nutrient uptake, metabolic function, growth and cell division. Bacteria are modeled in two dimensions as hard circle-capped cylinders with steric interactions and elastic stress dependent growth characteristics. Nutrient is able to diffuse within and between the colonies. The mechanism of microbial colony growth involves reproduction of cells within the colonies and the merging of different colonies. We report results on the dynamic scaling laws and final state size distribution, that capture in semi-quantitative detail the trends observed in experiment. Supported by NSF Grant 0822613.

Viral effects on bacterial respiration, production and growth efficiency: Consistent trends in the Southern Ocean and the Mediterranean Sea

NASA Astrophysics Data System (ADS)

Bonilla-Findji, Osana; Malits, Andrea; Lefèvre, Dominique; Rochelle-Newall, Emma; Lemée, Rodolphe; Weinbauer, Markus G.; Gattuso, Jean-Pierre

2008-03-01

To investigate the potential effects of viruses on bacterial respiration (BR), production (BP) and growth efficiency (BGE), experiments were performed using natural microbial communities from the coastal Mediterranean Sea, from a typical high-nutrient low-chlorophyll (HNLC) region in the Southern Ocean and from a naturally iron (Fe)-fertilized algal bloom above the Kerguelen Plateau (Southern Ocean). Seawater was sequentially filtered and concentrated to produce a bacterial concentrate, a viral concentrate and a virus-free ultrafiltrate. The combination of all three fractions served as treatments with active viruses. Heating or microwaving was used to inactivate viruses for the control treatments. Despite the differences in the initial trophic state and community composition of the study sites, consistent trends were found. In the presence of active viruses, BR was stimulated (up to 113%), whereas BP and BGE were reduced (up to 51%). Our results suggest that viruses enhance the role of bacteria as oxidizers of organic matter, hence as producers of CO 2, and remineralizers of CO 2, N, P and Fe. In the context of Fe-fertilization, this has important implications for the final fate of organic carbon in marine systems.

Theory of a microfluidic serial dilution bioreactor for growth of planktonic and biofilm populations.

PubMed

Hsu, Sze-Bi; Yang, Ya-Tang

2016-04-01

We present the theory of a microfluidic bioreactor with a two-compartment growth chamber and periodic serial dilution. In the model, coexisting planktonic and biofilm populations exchange by adsorption and detachment. The criteria for coexistence and global extinction are determined by stability analysis of the global extinction state. Stability analysis yields the operating diagram in terms of the dilution and removal ratios, constrained by the plumbing action of the bioreactor. The special case of equal uptake function and logistic growth is analytically solved and explicit growth curves are plotted. The presented theory is applicable to generic microfluidic bioreactors with discrete growth chambers and periodic dilution at discrete time points. Therefore, the theory is expected to assist the design of microfluidic devices for investigating microbial competition and microbial biofilm growth under serial dilution conditions.

Breeding crops for improved mineral nutrition under climate change conditions.

PubMed

Pilbeam, David J

2015-06-01

Improvements in understanding how climate change may influence chemical and physical processes in soils, how this may affect nutrient availability, and how plants may respond to changed availability of nutrients will influence crop breeding programmes. The effects of increased atmospheric CO2 and warmer temperatures, both individually and combined, on soil microbial activity, including mycorrhizas and N-fixing organisms, are evaluated, together with their implications for nutrient availability. Potential changes to plant growth, and the combined effects of soil and plant changes on nutrient uptake, are discussed. The organization of research on the efficient use of macro- and micronutrients by crops under climate change conditions is outlined, including analysis of QTLs for nutrient efficiency. Suggestions for how the information gained can be used in plant breeding programmes are given. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

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

[Mycotrophic capacity and efficiency of microbial consortia of arbuscular mycorrhizal fungi native of soils from Buenos Aires province under contrasting management].

PubMed

Thougnon Islas, Andrea J; Eyherabide, Mercedes; Echeverría, Hernán E; Sainz Rozas, Hernán R; Covacevich, Fernanda

2014-01-01

We characterized the infective and sporulation capacities of microbial consortia of arbuscular mycorrhizal fungi (AMF) native of Buenos Aires province (Argentina) and determined if some soil characteristics and mycorrhizal parameters could allow to select potentially beneficial inocula. Soil samples were selected from seven locations in Buenos Aires province all under agricultural (A) and pristine (P) conditions. The AMF were multiplied and mycorrhizal root colonization of trap plants was observed at 10 weeks of growth. Spore number in field was low; however, after multiplication spore density accounted for 80-1175 spores per 100g of soil. The principal component analysis showed that the P and Fe soil contents are the main modulators of infectivity and sporulation capacity. The mycorrhizal potential was determined in three locations, being high in Pristine Lobería and Agricultural Trenque Lauquen and low in Junín. Agricultural Lobería (AL) and Pristine Lobería (PL) inocula were selected and their efficiency was evaluated under controlled conditions. Even though shoot dry matter increases after inoculation was not significant (p>0.05) mycorrhizal response was greater than 40% for tomato and 25% for corn, particularly after inoculation with inocula from the agricultural management. These results could be associated to the incipient development of mycorrhizae in both species. Additional research should be conducted to further develop our findings in order to determine the factors involved in the selection of efficient inocula. Copyright © 2014 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.

The responses of microbial temperature relationships to seasonal change and winter warming in a temperate grassland.

PubMed

Birgander, Johanna; Olsson, Pål Axel; Rousk, Johannes

2018-01-18

Microorganisms dominate the decomposition of organic matter and their activities are strongly influenced by temperature. As the carbon (C) flux from soil to the atmosphere due to microbial activity is substantial, understanding temperature relationships of microbial processes is critical. It has been shown that microbial temperature relationships in soil correlate with the climate, and microorganisms in field experiments become more warm-tolerant in response to chronic warming. It is also known that microbial temperature relationships reflect the seasons in aquatic ecosystems, but to date this has not been investigated in soil. Although climate change predictions suggest that temperatures will be mostly affected during winter in temperate ecosystems, no assessments exist of the responses of microbial temperature relationships to winter warming. We investigated the responses of the temperature relationships of bacterial growth, fungal growth, and respiration in a temperate grassland to seasonal change, and to 2 years' winter warming. The warming treatments increased winter soil temperatures by 5-6°C, corresponding to 3°C warming of the mean annual temperature. Microbial temperature relationships and temperature sensitivities (Q 10 ) could be accurately established, but did not respond to winter warming or to seasonal temperature change, despite significant shifts in the microbial community structure. The lack of response to winter warming that we demonstrate, and the strong response to chronic warming treatments previously shown, together suggest that it is the peak annual soil temperature that influences the microbial temperature relationships, and that temperatures during colder seasons will have little impact. Thus, mean annual temperatures are poor predictors for microbial temperature relationships. Instead, the intensity of summer heat-spells in temperate systems is likely to shape the microbial temperature relationships that govern the soil-atmosphere C exchange. © 2018 John Wiley & Sons Ltd.

Fluidized-bed bioreactor system for the microbial solubilization of coal

DOEpatents

Scott, C.D.; Strandberg, G.W.

1987-09-14

A fluidized-bed bioreactor system for the conversion of coal into microbially solubilized coal products. The fluidized-bed bioreactor continuously or periodically receives coal and bio-reactants and provides for the production of microbially solubilized coal products in an economical and efficient manner. An oxidation pretreatment process for rendering coal uniformly and more readily susceptible to microbial solubilization may be employed with the fluidized-bed bioreactor. 2 figs.

Microbial electrosynthetic cells

DOEpatents

May, Harold D.; Marshall, Christopher W.; Labelle, Edward V.

2018-01-30

Methods are provided for microbial electrosynthesis of H.sub.2 and organic compounds such as methane and acetate. Method of producing mature electrosynthetic microbial populations by continuous culture is also provided. Microbial populations produced in accordance with the embodiments as shown to efficiently synthesize H.sub.2, methane and acetate in the presence of CO.sub.2 and a voltage potential. The production of biodegradable and renewable plastics from electricity and carbon dioxide is also disclosed.

Fluidized-bed bioreactor process for the microbial solubiliztion of coal

DOEpatents

Scott, Charles D.; Strandberg, Gerald W.

1989-01-01

A fluidized-bed bioreactor system for the conversion of coal into microbially solubilized coal products. The fluidized-bed bioreactor continuously or periodically receives coal and bio-reactants and provides for the production of microbially solubilized coal products in an economical and efficient manner. An oxidation pretreatment process for rendering coal uniformly and more readily susceptible to microbial solubilization may be employed with the fluidized-bed bioreactor.

Statistical analysis and modeling of pelletized cultivation of Mucor circinelloides for microbial lipid accumulation.

PubMed

Xia, Chunjie; Wei, Wei; Hu, Bo

2014-04-01

Microbial oil accumulation via oleaginous fungi has some potential benefits because filamentous fungi can form pellets during cell growth and these pellets are easier to harvest from the culture broth than individual cells. This research studied the effect of various culture conditions on the pelletized cell growth of Mucor circinelloides and its lipid accumulation. The results showed that cell pelletization was positively correlated to biomass accumulation; however, pellet size was negatively correlated to the oil content of the fungal biomass, possibly due to the mass transfer barriers generated by the pellet structure. How to control the size of the pellet is the key to the success of the pelletized microbial oil accumulation process.

Extended duration orbiter medical project Microbial Air Sampler (STS-50/USML-1)

NASA Technical Reports Server (NTRS)

Pierson, Duane L.; Boettcher, Sheila W.

1994-01-01

The Microbial Air Sampler was used on mission days 1, 7, and 13 in the Spacelab during STS-50/USML-1. Microbial air samples were collected using two types of media strips containing agar (Rose Bengal for yeast and molds, TSA for bacteria). The bacterial level found on day 1 was lower than experienced on previous Spacelab missions. A high level of fungi was present on day 1, however subsequent samples on days 7 and 13 did not indicate fungal growth. Bacterial growth was also minimized in this microgravity environment as the mission progressed. No pathogenic microorganisms were isolated, and the health risk from airborne microbes was minimal throughout the mission.

Cesium-induced inhibition of bacterial growth of Pseudomonas aeruginosa PAO1 and their possible potential applications for bioremediation of wastewater.

PubMed

Kang, Sung-Min; Jang, Sung-Chan; Heo, Nam Su; Oh, Seo Yeong; Cho, Hye-Jin; Rethinasabapathy, Muruganantham; Vilian, A T Ezhil; Han, Young-Kyu; Roh, Changhyun; Huh, Yun Suk

2017-09-15

Radioactive isotopes and fission products have attracted considerable attention because of their long lasting serious damage to the health of humans and other organisms. This study examined the toxicity and accumulation behavior of cesium towards P. aeruginosa PAO1 and its capacity to remove cesium from waste water. Interestingly, the programmed bacterial growth inhibition occurred according to the cesium environment. The influence of cesium was analyzed using several optical methods for quantitative evaluation. Cesium plays vital role in the growth of microorganisms and functions as an anti-microbial agent. The toxicity of Cs to P. aeruginosa PAO1 increases as the concentration of cesium is increased in concentration-dependent manner. P. aeruginosa PAO1 shows excellent Cs removal efficiency of 76.1% from the contaminated water. The toxicity of cesium on the cell wall and in the cytoplasm were studied by transmission electron microscopy and electron dispersive X-ray analysis. Finally, the removal of cesium from wastewater using P. aeruginosa PAO1 as a potential biosorbent and the blocking of competitive interactions of other monovalent cation, such as potassium, were assessed. Overall, P. aeruginosa PAO1 can be used as a high efficient biomaterial in the field of radioactive waste disposal and management. Copyright © 2017 Elsevier B.V. All rights reserved.

Improved ethanol production from xylose in the presence of acetic acid by the overexpression of the HAA1 gene in Saccharomyces cerevisiae.

PubMed

Sakihama, Yuri; Hasunuma, Tomohisa; Kondo, Akihiko

2015-03-01

The hydrolysis of lignocellulosic biomass liberates sugars, primarily glucose and xylose, which are subsequently converted to ethanol by microbial fermentation. The rapid and efficient fermentation of xylose by recombinant Saccharomyces cerevisiae strains is limited by weak acids generated during biomass pretreatment processes. In particular, acetic acid negatively affects cell growth, xylose fermentation rate, and ethanol production. The ability of S. cerevisiae to efficiently utilize xylose in the presence of acetic acid is an essential requirement for the cost-effective production of ethanol from lignocellulosic hydrolysates. Here, an acetic acid-responsive transcriptional activator, HAA1, was overexpressed in a recombinant xylose-fermenting S. cerevisiae strain to yield BY4741X/HAA1. This strain exhibited improved cell growth and ethanol production from xylose under aerobic and oxygen limited conditions, respectively, in the presence of acetic acid. The HAA1p regulon enhanced transcript levels in BY4741X/HAA1. The disruption of PHO13, a p-nitrophenylphosphatase gene, in BY4741X/HAA1 led to further improvement in both yeast growth and the ability to ferment xylose, indicating that HAA1 overexpression and PHO13 deletion act by different mechanisms to enhance ethanol production. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Microbial Fuel Cells and Microbial Electrolyzers

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

Borole, Abhijeet P

2015-01-01

Microbial Fuel Cells and microbial electrolyzers represent an upcoming technology for production of electricity and hydrogen using a hybrid electrocatalytic-biocatalytic approach. The combined catalytic efficiency of these processes has potential to make this technology highly efficient among the various renewable energy production alternatives. This field has attracted electrochemists, biologists and many other disciplines due to its potential to contribute to the energy, water and environment sectors. A brief introduction to the technology is provided followed by current research needs from a bioelectrochemical perspective. Insights into the operation and limitations of these systems achieved via cyclic voltammetry and impedance spectroscopy aremore » discussed along with the power management needs to develop the application aspects. Besides energy production, other potential applications in bioenergy, bioelectronics, chemical production and remediation are also highlighted.« less

Assessment of Heterotrophic Growth Supported by Soluble Microbial Products in Anammox Biofilm using Multidimensional Modeling

PubMed Central

Liu, Yiwen; Sun, Jing; Peng, Lai; Wang, Dongbo; Dai, Xiaohu; Ni, Bing-Jie

2016-01-01

Anaerobic ammonium oxidation (anammox) is known to autotrophically convert ammonium to dinitrogen gas with nitrite as the electron acceptor, but little is known about their released microbial products and how these are relative to heterotrophic growth in anammox system. In this work, we applied a mathematical model to assess the heterotrophic growth supported by three key microbial products produced by bacteria in anammox biofilm (utilization associated products (UAP), biomass associated products (BAP), and decay released substrate). Both One-dimensional and two-dimensional numerical biofilm models were developed to describe the development of anammox biofilm as a function of the multiple bacteria–substrate interactions. Model simulations show that UAP of anammox is the main organic carbon source for heterotrophs. Heterotrophs are mainly dominant at the surface of the anammox biofilm with small fraction inside the biofilm. 1-D model is sufficient to describe the main substrate concentrations/fluxes within the anammox biofilm, while the 2-D model can give a more detailed biomass distribution. The heterotrophic growth on UAP is mainly present at the outside of anammox biofilm, their growth on BAP (HetB) are present throughout the biofilm, while the growth on decay released substrate (HetD) is mainly located in the inner layers of the biofilm. PMID:27273460

Quantum dots conjugated zinc oxide nanosheets: Impeder of microbial growth and biofilm

NASA Astrophysics Data System (ADS)

Patil, Rajendra; Gholap, Haribhau; Warule, Sambhaji; Banpurkar, Arun; Kulkarni, Gauri; Gade, Wasudeo

2015-01-01

The grieving problem of the 21st century has been the antimicrobial resistance in pathogenic microorganisms to conventional antibiotics. Therefore, developments of novel antibacterial materials which effectively inhibit or kill such resistant microorganisms have become the need of the hour. In the present study, we communicate the synthesis of quantum dots conjugated zinc oxide nanostructures (ZnO/CdTe) as an impeder of microbial growth and biofilm. The as-synthesized nanostructures were characterized by X-ray diffraction, ultraviolet-visible spectroscopy, photoluminescence spectroscopy, field emission scanning electron microscopy and high resolution transmission electron microscopy. The growth impedance property of ZnO and ZnO/CdTe on Gram positive organism, Bacillus subtilis NCIM 2063 and Gram negative, Escherichia coli NCIM 2931 and biofilm impedance activity in Pseudomonas aeruginosa O1 was found to occur due to photocatalytical action on the cell biofilm surfaces. The impedance in microbial growth and biofilm formation was further supported by ruptured appearances of cells and dettrered biofilm under field emission scanning electron and confocal laser scanning microscope. The ZnO/CdTe nanostructures array synthesized by hydrothermal method has an advantage of low growth temperature, and opportunity to fabricate inexpensive material for nano-biotechnological applications.

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.

Solar disinfection: an approach for low-cost household water treatment technology in Southwestern Ethiopia.

PubMed

Dessie, Awrajaw; Alemayehu, Esayas; Mekonen, Seblework; Legesse, Worku; Kloos, Helmut; Ambelu, Argaw

2014-01-10

Disinfection of contaminated water using solar radiation (SODIS) is known to inactivate bacteria. Its inactivation efficiency depends on local conditions where the disinfection is made. This study was aiming to test the efficiency of solar disinfection using different water parameters as low-cost household water treatment technology. Inactivation of microbes was tested using fecal coliform as test organism. The SODIS experiment was carried out at turbidity 2NTU, pH 7, and various water temperature (38.1°C, 41.8°C, 45.6°Cand 51.1°C) and solar intensities, using clear and black plastic bottles filled to different depths. The results show that the rate of microbial inactivation in relation to depth of water, turbidity, container type, intensity of light and color of container was statistically significant (p < 0.05). However, bottle placement, exposure and water pH were unrelated to microbial inactivation. Bacterial re-growth was not observed after solar disinfection. By adjusting the parameters, complete and irreversible fecal coliform inactivation was achieved within an exposure time of less than four hours in the areas where the solar irradiance is about 3.99 kW/m2 and above. Our results indicate that application of SODIS could play a significant role in the provision of safe water in rural communities of developing countries where there is ample sunshine, specifically in sub-Saharan African countries.

Isolation and bioelectrochemical characterization of novel fungal sources with oxidasic activity applied in situ for the cathodic oxygen reduction in microbial fuel cells.

PubMed

Morant, Kyriale Vasconcelos; da Silva, Paulo Henrique; de Campos-Takaki, Galba Maria; Hernández, Camilo Enrique La Rotta

2014-11-01

Brazilian filamentous fungi Rhizopus sp. (SIS-31), Aspergillus sp. (SIS-18) and Penicillium sp. (SIS-21), sources of oxidases were isolated from Caatinga's soils and applied during the in situ cathodic oxygen reduction in fuel cells. All strains were cultivated in submerged cultures using an optimized saline medium enriched with 10 g L(-1) of glucose, 3.0 g L(-1) of peptone and 0.0005 g L(-1) of CuSO4 as enzyme inducer. Parameters of oxidase activity, glucose consumption and microbial growth were evaluated. In-cell experiments evaluated by chronoamperometry were performed and two different electrode compositions were also compared. Maximum current densities of 125.7, 98.7 and 11.5 μA cm(-2) were observed before 24 h and coulombic efficiencies of 56.5, 46.5 and 23.8% were obtained for SIS-31, SIS-21 and SIS-18, respectively. Conversely, maximum power outputs of 328.73, 288.80 and 197.77 mW m(-3) were observed for SIS-18, SIS-21 and SIS-31, respectively. This work provides the primary experimental evidences that fungi isolated from the Caatinga region in Brazil can serve as efficient biocatalysts during the oxygen reduction in air-cathodes to improve electricity generation in MFCs. Copyright © 2014 Elsevier Inc. All rights reserved.

Solar disinfection: an approach for low-cost household water treatment technology in Southwestern Ethiopia

PubMed Central

2014-01-01

Disinfection of contaminated water using solar radiation (SODIS) is known to inactivate bacteria. Its inactivation efficiency depends on local conditions where the disinfection is made. This study was aiming to test the efficiency of solar disinfection using different water parameters as low-cost household water treatment technology. Inactivation of microbes was tested using fecal coliform as test organism. The SODIS experiment was carried out at turbidity 2NTU, pH 7, and various water temperature (38.1°C, 41.8°C, 45.6°Cand 51.1°C) and solar intensities, using clear and black plastic bottles filled to different depths. The results show that the rate of microbial inactivation in relation to depth of water, turbidity, container type, intensity of light and color of container was statistically significant (p < 0.05). However, bottle placement, exposure and water pH were unrelated to microbial inactivation. Bacterial re-growth was not observed after solar disinfection. By adjusting the parameters, complete and irreversible fecal coliform inactivation was achieved within an exposure time of less than four hours in the areas where the solar irradiance is about 3.99 kW/m2 and above. Our results indicate that application of SODIS could play a significant role in the provision of safe water in rural communities of developing countries where there is ample sunshine, specifically in sub-Saharan African countries. PMID:24410979

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.

Biochar modulates heavy metal toxicity and improves microbial carbon use efficiency in soil.

PubMed

Xu, Yilu; Seshadri, Balaji; Sarkar, Binoy; Wang, Hailong; Rumpel, Cornelia; Sparks, Donald; Farrell, Mark; Hall, Tony; Yang, Xiaodong; Bolan, Nanthi

2018-04-15

Soil organic carbon is essential to improve soil fertility and ecosystem functioning. Soil microorganisms contribute significantly to the carbon transformation and immobilisation processes. However, microorganisms are sensitive to environmental stresses such as heavy metals. Applying amendments, such as biochar, to contaminated soils can alleviate the metal toxicity and add carbon inputs. In this study, Cd and Pb spiked soils treated with macadamia nutshell biochar (5% w/w) were monitored during a 49days incubation period. Microbial phospholipid fatty acids (PLFAs) were extracted and analysed as biomarkers in order to identify the microbial community composition. Soil properties, metal bioavailability, microbial respiration, and microbial biomass carbon were measured after the incubation period. Microbial carbon use efficiency (CUE) was calculated from the ratio of carbon incorporated into microbial biomass to the carbon mineralised. Total PLFA concentration decreased to a greater extent in metal contaminated soils than uncontaminated soils. Microbial CUE also decreased due to metal toxicity. However, biochar addition alleviated the metal toxicity, and increased total PLFA concentration. Both microbial respiration and biomass carbon increased due to biochar application, and CUE was significantly (p<0.01) higher in biochar treated soils than untreated soils. Heavy metals reduced the microbial carbon sequestration in contaminated soils by negatively influencing the CUE. The improvement of CUE through biochar addition in the contaminated soils could be attributed to the decrease in metal bioavailability, thereby mitigating the biotoxicity to soil microorganisms. Copyright © 2017 Elsevier B.V. All rights reserved.

The effect of nitrate on ethylene biofiltration.

PubMed

Lee, Sang-Hun; Li, Congna; Heber, Albert J

2012-11-30

This study investigated the effects of filter media types and nitrate (NO(3)(-)) concentrations in nutrient solutions on C(2)H(4) biofiltration. A new nutrient solution with zero NO(3)(-) concentration was supplied to two perlite-bed biotrickling filters, two perlite-bed biofilters, and two GAC (Granular Activated Carbon)-bed biofilters, while the other with 2 g L(-1) of NO(3)(-) was used for the other two GAC biofilters. All reactors underwent a total test duration of over 175 days with an EBRT (Empty Bed Residence Time) of 30 s, inlet gas flow rate of 7 L min(-1), and inlet C(2)H(4) concentrations of 20-30 mg m(-3). NO(3)(-) concentration and media type significantly affected the C(2)H(4) removal efficiencies in all types of biofiltration. The perlite media with no NO(3)(-) achieved C(2)H(4) removal efficiencies 10-50% higher than the others. A NO(3)(-) concentration as high as 2 g L(-1) in the original nutrient solution may act as an inhibitor that suppresses the growth or activity of C(2)H(4) degraders. In addition, the perlite media resulted in higher C(2)H(4) removal efficiencies than GAC media, because the hydrophilic surface of the perlite leads to a higher moisture content and thus to favorable microbial growth. Copyright © 2012 Elsevier B.V. All rights reserved.

Copper removal and microbial community analysis in single-chamber microbial fuel cell.

PubMed

Wu, Yining; Zhao, Xin; Jin, Min; Li, Yan; Li, Shuai; Kong, Fanying; Nan, Jun; Wang, Aijie

2018-04-01

In this study, copper removal and electricity generation were investigated in a single-chamber microbial fuel cell (MFC). Result showed that copper was efficiently removed in the membrane-less MFC with removal efficiency of 98.3% at the tolerable Cu 2+ concentration of 12.5 mg L -1 , the corresponding open circuit voltage and maximum power density were 0.78 V and 10.2 W m -3 , respectively. The mechanism analysis demonstrated that microbial electrochemical reduction contributed to the copper removal with the products of Cu and Cu 2 O deposited at biocathode. Moreover, the microbial community analysis indicated that microbial communities changed with different copper concentrations. The dominant phyla were Proteobacteria and Bacteroidetes which could play key roles in electricity generation, while Actinobacteria and Acidobacteria were also observed which were responsible for Cu-resistant and copper removal. It will be of important guiding significance for the recovery of copper from low concentration wastewater through single-chamber MFC with simultaneous energy recovery. Copyright © 2018 Elsevier Ltd. All rights reserved.

Microbial Contamination on Touch Surfaces in Sick- and Well-Child Waiting Rooms in Pediatric Outpatient Facilities.

PubMed

Gudakova, Irina; Kim, JinYoung; Meredith, Jennifer F; Webb, Ginny

2017-12-01

Healthcare-associated infections are a significant public health burden resulting in approximately 1.7 million infections each year. Much work is done to study the contributing factors in inpatient settings; however, little has been done to study outpatient facilities and their roles in healthcare-associated infections. While many pediatric outpatient offices utilize separated waiting areas for sick and well children to decrease the spread of disease, research has not been done to determine whether this practice is of benefit. In this study, we aimed to determine whether there is a difference in microbial burden between sick- and well-child waiting areas and to identify surfaces with the highest levels of contamination. Touch surfaces in waiting rooms were swabbed and surveyed for total microbial growth, staphylococcal growth and Gram-negative enteric bacterial growth. Selected bacteria were identified to screen for pathogenic organisms. Surfaces sampled included seats, tables, children's tables, children's seats, magazines and books. We found seats, children's seats and children's books to have the highest microbial burden. No conclusions can be made on the differences in microbial contamination in sick- and well-child waiting areas because of high variation. Streptococcus pyogenes was isolated as were several opportunistic pathogens. This study suggests the need for better cleaning practices by pediatric outpatient facilities, to include the disinfection of additional surfaces as well as more frequent and thorough cleaning.

Metagenomic analysis of the rhizosphere soil microbiome with respect to phytic acid utilization.

PubMed

Unno, Yusuke; Shinano, Takuro

2013-01-01

While phytic acid is a major form of organic phosphate in many soils, plant utilization of phytic acid is normally limited; however, culture trials of Lotus japonicus using experimental field soil that had been managed without phosphate fertilizer for over 90 years showed significant usage of phytic acid applied to soil for growth and flowering and differences in the degree of growth, even in the same culture pot. To understand the key metabolic processes involved in soil phytic acid utilization, we analyzed rhizosphere soil microbial communities using molecular ecological approaches. Although molecular fingerprint analysis revealed changes in the rhizosphere soil microbial communities from bulk soil microbial community, no clear relationship between the microbiome composition and flowering status that might be related to phytic acid utilization of L. japonicus could be determined. However, metagenomic analysis revealed changes in the relative abundance of the classes Bacteroidetes, Betaproteobacteria, Chlorobi, Dehalococcoidetes and Methanobacteria, which include strains that potentially promote plant growth and phytic acid utilization, and some gene clusters relating to phytic acid utilization, such as alkaline phosphatase and citrate synthase, with the phytic acid utilization status of the plant. This study highlights phylogenetic and metabolic features of the microbial community of the L. japonicus rhizosphere and provides a basic understanding of how rhizosphere microbial communities affect the phytic acid status in soil.

Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance

PubMed Central

Roehe, Rainer; Dewhurst, Richard J.; Duthie, Carol-Anne; Rooke, John A.; McKain, Nest; Ross, Dave W.; Hyslop, Jimmy J.; Waterhouse, Anthony; Freeman, Tom C.

2016-01-01

Methane produced by methanogenic archaea in ruminants contributes significantly to anthropogenic greenhouse gas emissions. The host genetic link controlling microbial methane production is unknown and appropriate genetic selection strategies are not developed. We used sire progeny group differences to estimate the host genetic influence on rumen microbial methane production in a factorial experiment consisting of crossbred breed types and diets. Rumen metagenomic profiling was undertaken to investigate links between microbial genes and methane emissions or feed conversion efficiency. Sire progeny groups differed significantly in their methane emissions measured in respiration chambers. Ranking of the sire progeny groups based on methane emissions or relative archaeal abundance was consistent overall and within diet, suggesting that archaeal abundance in ruminal digesta is under host genetic control and can be used to genetically select animals without measuring methane directly. In the metagenomic analysis of rumen contents, we identified 3970 microbial genes of which 20 and 49 genes were significantly associated with methane emissions and feed conversion efficiency respectively. These explained 81% and 86% of the respective variation and were clustered in distinct functional gene networks. Methanogenesis genes (e.g. mcrA and fmdB) were associated with methane emissions, whilst host-microbiome cross talk genes (e.g. TSTA3 and FucI) were associated with feed conversion efficiency. These results strengthen the idea that the host animal controls its own microbiota to a significant extent and open up the implementation of effective breeding strategies using rumen microbial gene abundance as a predictor for difficult-to-measure traits on a large number of hosts. Generally, the results provide a proof of principle to use the relative abundance of microbial genes in the gastrointestinal tract of different species to predict their influence on traits e.g. human metabolism, health and behaviour, as well as to understand the genetic link between host and microbiome. PMID:26891056

Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance.

PubMed

Roehe, Rainer; Dewhurst, Richard J; Duthie, Carol-Anne; Rooke, John A; McKain, Nest; Ross, Dave W; Hyslop, Jimmy J; Waterhouse, Anthony; Freeman, Tom C; Watson, Mick; Wallace, R John

2016-02-01

Methane produced by methanogenic archaea in ruminants contributes significantly to anthropogenic greenhouse gas emissions. The host genetic link controlling microbial methane production is unknown and appropriate genetic selection strategies are not developed. We used sire progeny group differences to estimate the host genetic influence on rumen microbial methane production in a factorial experiment consisting of crossbred breed types and diets. Rumen metagenomic profiling was undertaken to investigate links between microbial genes and methane emissions or feed conversion efficiency. Sire progeny groups differed significantly in their methane emissions measured in respiration chambers. Ranking of the sire progeny groups based on methane emissions or relative archaeal abundance was consistent overall and within diet, suggesting that archaeal abundance in ruminal digesta is under host genetic control and can be used to genetically select animals without measuring methane directly. In the metagenomic analysis of rumen contents, we identified 3970 microbial genes of which 20 and 49 genes were significantly associated with methane emissions and feed conversion efficiency respectively. These explained 81% and 86% of the respective variation and were clustered in distinct functional gene networks. Methanogenesis genes (e.g. mcrA and fmdB) were associated with methane emissions, whilst host-microbiome cross talk genes (e.g. TSTA3 and FucI) were associated with feed conversion efficiency. These results strengthen the idea that the host animal controls its own microbiota to a significant extent and open up the implementation of effective breeding strategies using rumen microbial gene abundance as a predictor for difficult-to-measure traits on a large number of hosts. Generally, the results provide a proof of principle to use the relative abundance of microbial genes in the gastrointestinal tract of different species to predict their influence on traits e.g. human metabolism, health and behaviour, as well as to understand the genetic link between host and microbiome.

A microbial perspective of human developmental biology.

PubMed

Charbonneau, Mark R; Blanton, Laura V; DiGiulio, Daniel B; Relman, David A; Lebrilla, Carlito B; Mills, David A; Gordon, Jeffrey I

2016-07-07

When most people think of human development, they tend to consider only human cells and organs. Yet there is another facet that involves human-associated microbial communities. A microbial perspective of human development provides opportunities to refine our definitions of healthy prenatal and postnatal growth and to develop innovative strategies for disease prevention and treatment. Given the dramatic changes in lifestyles and disease patterns that are occurring with globalization, we issue a call for the establishment of 'human microbial observatories' designed to examine microbial community development in birth cohorts representing populations with diverse anthropological characteristics, including those undergoing rapid change.

Human developmental biology viewed from a microbial perspective

PubMed Central

Charbonneau, Mark R.; Blanton, Laura V.; DiGiulio, Daniel B.; Relman, David A.; Lebrilla, Carlito B.; Mills, David A.; Gordon, Jeffrey I.

2017-01-01

Preface Most people think of human development only in terms of ‘human’ cells and organs. Here, we discuss another facet involving human-associated microbial communities. A microbial perspective of human development provides opportunities to refine our definitions of healthy pre- and postnatal growth and to develop new strategies for disease prevention and treatment. Considering the dramatic changes in lifestyles and disease patterns that are occurring with globalization, we issue a call for human microbial observatory programs designed to examine microbial community development in birth cohorts representing populations with diverse anthropologic characteristics, including those undergoing rapid change. PMID:27383979

Microbial Electrochemistry and its Application to Energy and Environmental Issues

NASA Astrophysics Data System (ADS)

Hastings, Jason Thomas

Microbial electrochemistry forms the basis of a wide range of topics from microbial fuel cells to fermentation of carbon food sources. The ability to harness microbial electron transfer processes can lead to a greener and cleaner future. This study focuses on microbial electron transfer for liquid fuel production, novel electrode materials, subsurface environments and removal of unwanted byproducts. In the first chapter, exocellular electron transfer through direct contact utilizing passive electrodes for the enhancement of bio-fuel production was tested. Through the application of microbial growth in a 2-cell apparatus on an electrode surface ethanol production was enhanced by 22.7% over traditional fermentation. Ethanol production efficiencies of close to 95% were achieved in a fraction of the time required by traditional fermentation. Also, in this chapter, the effect of exogenous electron shuttles, electrode material selection and resistance was investigated. Power generation was observed using the 2-cell passive electrode system. An encapsulation method, which would also utilize exocellular transfer of electrons through direct contact, was hypothesized for the suspension of viable cells in a conductive polymer substrate. This conductive polymer substrate could have applications in bio-fuel production. Carbon black was added to a polymer solution to test electrospun polymer conductivity and cell viability. Polymer morphology and cell viability were imaged using electron and optical microscopy. Through proper encapsulation, higher fuel production efficiencies would be achievable. Electron transfer through endogenous exocellular protein shuttles was observed in this study. Secretion of a soluble redox active exocellular protein by Clostridium sp. have been shown utilizing a 2-cell apparatus. Cyclic voltammetry and gel electrophoresis were used to show the presence of the protein. The exocellular protein is capable of reducing ferrous iron in a membrane separated chamber. In experiments where the redox active protein was allowed to pass through the permeable membrane, iron dissolution was 14-fold greater than experiments where the protein was held to one chamber by a non-permeable membrane. Confirmation of a redox active protein could reshape or understanding of subsurface redox processes. The final topic in this study discusses electron transfer within the cell for production of fermentation products. Glycerol, which is an unwanted side-product of biodiesel transesterfication, is utilized as a carbon source for fermentation. Bacterial samples harvested from Galena Creek soil (NGC) are shown in this study to be efficient consumers of glycerol. NGC microbe was characterized through 16s rDNA genetic sequencing and determined to belong to genus Clostridium. Clostridium NGC was able to consume glycerol at 29.7gpl within 72hrs grown in a media containing 50gpl glycerol. All observed fermentation metabolites were characterized and quantified through an HPLC. Glycerol consumption rates and metabolite production rates were observed using varying media recipes. This study has found that NGC has higher selectivity for low weight acids at lower yeast extract concentration and higher selectivity for larger acids and alcohols at higher yeast extract concentrations.

Aging of biomixtures: Effects on carbofuran removal and microbial community structure.

PubMed

Castro-Gutiérrez, Víctor; Masís-Mora, Mario; Diez, María Cristina; Tortella, Gonzalo R; Rodríguez-Rodríguez, Carlos E

2017-02-01

The aim of this work was to determine the efficiency of a straw/compost/soil biomixture for pesticide depuration during its aging and continuous use, for a period of over a year, based on its capacity to remove carbofuran (CFN), while simultaneously monitoring the variations in microbial community structure. Successive CFN spikings were applied in the biomixture at 6-week intervals, and the removal efficiency was determined 48 h post-application. Initially, only a discrete degradation performance was observed (9.9%), but one CFN application was sufficient to induce efficient elimination (>88.5%) of the pesticide at subsequent influxes for a period of over 6 months. A statistically significant reduction on CFN removal efficiency after this time was detected, reaching levels similar to the fresh-prepared biomixture (14.8%) at the end of the experiment. Simultaneous DGGE analyses showed only modest changes on microbial community patterns through time for both, bacteria and fungi. The clustering of genetic fingerprints in chronological groups corresponding to significantly different CFN degradation efficiencies indicates that biomixture aging changes not only the composition of microbial communities, but also their suitability to engage in pesticide degradation. Periodic substitution of straw/compost/soil biomixture in biopurification systems or regular provision of easily-degradable organic substrates should be considered to maintain an adequate depuration capacity on this system. Copyright © 2016 Elsevier Ltd. All rights reserved.

Growing Rocks: Implications of Lithification for Microbial Communities and Nutrient Cycling

NASA Astrophysics Data System (ADS)

Corman, J. R.; Poret-Peterson, A. T.; Elser, J. J.

2014-12-01

Lithifying microbial communities ("microbialites") have left their signature on Earth's rock record for over 3.4 billion years and are regarded as important players in paleo-biogeochemical cycles. In this project, we study extant microbialites to understand the interactions between lithification and resource availability. All microbes need nutrients and energy for growth; indeed, nutrients are often a factor limiting microbial growth. We hypothesize that calcium carbonate deposition can sequester bioavailable phosphorus (P) and expect the growth of microbialites to be P-limited. To test our hypothesis, we first compared nutrient limitation in lithifying and non-lithifying microbial communities in Río Mesquites, Cuatro Ciénegas. Then, we experimentally manipulated calcification rates in the Río Mesquites microbialites. Our results suggest that lithifying microbialites are indeed P-limited, while non-lithifying, benthic microbial communities tend towards co-limitation by nitrogen (N) and P. Indeed, in microbialites, photosynthesis and aerobic respiration responded positively to P additions (P<0.05). Organic carbon (OC) additions caused shifts in bacterial community composition based on analysis of 16S rRNA genes. Unexpectedly, calcification rates increased with OC additions (P<0.05), but not with P additions, suggesting that sulfate reduction may be an important pathway for calcification. Experimental reductions in calcification rates caused changes to microbial biomass OC and P concentrations (P<0.01 and P<0.001, respectively), although shifts depended on whether calcification was decreased abiotically or biotically. These results show that resource availability does influence microbialite formation and that lithification may promote phosphorus limitation; however, further investigation is required to understand the mechanism by which the later occurs.

Role of microbial inoculation and industrial by-product phosphogypsum in growth and nutrient uptake of maize (Zea mays L.) grown in calcareous soil.

PubMed

Al-Enazy, Abdul-Aziz R; Al-Oud, Saud S; Al-Barakah, Fahad N; Usman, Adel Ra

2017-08-01

Alkaline soils with high calcium carbonate and low organic matter are deficient in plant nutrient availability. Use of organic and bio-fertilizers has been suggested to improve their properties. Therefore, a greenhouse experiment was conducted to evaluate the integrative role of phosphogypsum (PG; added at 0.0, 10, 30, and 50 g PG kg -1 ), cow manure (CM; added at 50 g kg -1 ) and mixed microbial inoculation (Incl.; Azotobacter chroococcum, and phosphate-solubilizing bacteria Bacillus megaterium var. phosphaticum and Pseudomonas fluorescens) on growth and nutrients (N, P, K, Fe, Mn, Zn and Cu) uptake of maize (Zea mays L.) in calcareous soil. Treatment effects on soil chemical and biological properties and the Cd and Pb availability to maize plants were also investigated. Applying PG decreased soil pH. The soil available P increased when soil was inoculated and/or treated with CM, especially with PG. The total microbial count and dehydrogenase activity were enhanced with PG+CM+Incl. Inoculated soils treated with PG showed significant increases in NPK uptake and maize plant growth. However, the most investigated treatments showed significant decreases in shoot micronutrients. Cd and Pb were not detected in maize shoots. Applying PG with microbial inoculation improved macronutrient uptake and plant growth. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Microbial Growth under Supercritical CO2

PubMed Central

Peet, Kyle C.; Freedman, Adam J. E.; Hernandez, Hector H.; Britto, Vanya; Boreham, Chris; Ajo-Franklin, Jonathan B.

2015-01-01

Growth of microorganisms in environments containing CO2 above its critical point is unexpected due to a combination of deleterious effects, including cytoplasmic acidification and membrane destabilization. Thus, supercritical CO2 (scCO2) is generally regarded as a sterilizing agent. We report isolation of bacteria from three sites targeted for geologic carbon dioxide sequestration (GCS) that are capable of growth in pressurized bioreactors containing scCO2. Analysis of 16S rRNA genes from scCO2 enrichment cultures revealed microbial assemblages of varied complexity, including representatives of the genus Bacillus. Propagation of enrichment cultures under scCO2 headspace led to isolation of six strains corresponding to Bacillus cereus, Bacillus subterraneus, Bacillus amyloliquefaciens, Bacillus safensis, and Bacillus megaterium. Isolates are spore-forming, facultative anaerobes and capable of germination and growth under an scCO2 headspace. In addition to these isolates, several Bacillus type strains grew under scCO2, suggesting that this may be a shared feature of spore-forming Bacillus spp. Our results provide direct evidence of microbial activity at the interface between scCO2 and an aqueous phase. Since microbial activity can influence the key mechanisms for permanent storage of sequestered CO2 (i.e., structural, residual, solubility, and mineral trapping), our work suggests that during GCS microorganisms may grow and catalyze biological reactions that influence the fate and transport of CO2 in the deep subsurface. PMID:25681188

Spatial and temporal features of the growth of a bacterial species colonizing the zebrafish gut.

PubMed

Jemielita, Matthew; Taormina, Michael J; Burns, Adam R; Hampton, Jennifer S; Rolig, Annah S; Guillemin, Karen; Parthasarathy, Raghuveer

2014-12-16

The vertebrate intestine is home to microbial ecosystems that play key roles in host development and health. Little is known about the spatial and temporal dynamics of these microbial communities, limiting our understanding of fundamental properties, such as their mechanisms of growth, propagation, and persistence. To address this, we inoculated initially germ-free zebrafish larvae with fluorescently labeled strains of an Aeromonas species, representing an abundant genus in the zebrafish gut. Using light sheet fluorescence microscopy to obtain three-dimensional images spanning the gut, we quantified the entire bacterial load, as founding populations grew from tens to tens of thousands of cells over several hours. The data yield the first ever measurements of the growth kinetics of a microbial species inside a live vertebrate intestine and show dynamics that robustly fit a logistic growth model. Intriguingly, bacteria were nonuniformly distributed throughout the gut, and bacterial aggregates showed considerably higher growth rates than did discrete individuals. The form of aggregate growth indicates intrinsically higher division rates for clustered bacteria, rather than surface-mediated agglomeration onto clusters. Thus, the spatial organization of gut bacteria both relative to the host and to each other impacts overall growth kinetics, suggesting that spatial characterizations will be an important input to predictive models of host-associated microbial community assembly. Our intestines are home to vast numbers of microbes that influence many aspects of health and disease. Though we now know a great deal about the constituents of the gut microbiota, we understand very little about their spatial structure and temporal dynamics in humans or in any animal: how microbial populations establish themselves, grow, fluctuate, and persist. To address this, we made use of a model organism, the zebrafish, and a new optical imaging technique, light sheet fluorescence microscopy, to visualize for the first time the colonization of a live, vertebrate gut by specific bacteria with sufficient resolution to quantify the population over a range from a few individuals to tens of thousands of bacterial cells. Our results provide unprecedented measures of bacterial growth kinetics and also show the influence of spatial structure on bacterial populations, which can be revealed only by direct imaging. Copyright © 2014 Jemielita et al.

Dynamics of Marine Microbial Metabolism and Physiology at Station ALOHA

NASA Astrophysics Data System (ADS)

Casey, John R.

Marine microbial communities influence global biogeochemical cycles by coupling the transduction of free energy to the transformation of Earth's essential bio-elements: H, C, N, O, P, and S. The web of interactions between these processes is extraordinarily complex, though fundamental physical and thermodynamic principles should describe its dynamics. In this collection of 5 studies, aspects of the complexity of marine microbial metabolism and physiology were investigated as they interact with biogeochemical cycles and direct the flow of energy within the Station ALOHA surface layer microbial community. In Chapter 1, and at the broadest level of complexity discussed, a method to relate cell size to metabolic activity was developed to evaluate allometric power laws at fine scales within picoplankton populations. Although size was predictive of metabolic rates, within-population power laws deviated from the broader size spectrum, suggesting metabolic diversity as a key determinant of microbial activity. In Chapter 2, a set of guidelines was proposed by which organic substrates are selected and utilized by the heterotrophic community based on their nitrogen content, carbon content, and energy content. A hierarchical experimental design suggested that the heterotrophic microbial community prefers high nitrogen content but low energy density substrates, while carbon content was not important. In Chapter 3, a closer look at the light-dependent dynamics of growth on a single organic substrate, glycolate, suggested that growth yields were improved by photoheterotrophy. The remaining chapters were based on the development of a genome-scale metabolic network reconstruction of the cyanobacterium Prochlorococcus to probe its metabolic capabilities and quantify metabolic fluxes. Findings described in Chapter 4 pointed to evolution of the Prochlorococcus metabolic network to optimize growth at low phosphate concentrations. Finally, in Chapter 5 and at the finest scale of complexity, a method was developed to predict hourly changes in both physiology and metabolic fluxes in Prochlorococcus by incorporating gene expression time-series data within the metabolic network model. Growth rates predicted by this method more closely matched experimental data, and diel changes in elemental composition and the energy content of biomass were predicted. Collectively, these studies identify and quantify the potential impact of variations in metabolic and physiological traits on the melee of microbial community interactions.

In situ detection of microbial respiration in soils and salt flats. [Nevada desert

NASA Technical Reports Server (NTRS)

Tew, R. W.

1973-01-01

Increase in CO2 partial pressures over a desert soil treated with casamino-acids glucose solution correlated with bacterial growth. Few or no increases in numbers of bacteria or CO2 concentrations were noted in similar plots treated with water only or receiving no treatment. Growth in the soil appeared to be severely nutrient limited during the 10 day experiment. Especially rapid growth took place between the third and fifth day, when temperatures ranged from 0 deg. (night) to a maximum of 17.4 deg. (day). Under the conditions of the experiment, intermittent CO2 assay was an insensitive indicator of growth, possibly because of restiction of gas escape by the desert pavement or solution, exchange, or precipitation of carbonate, but more likely because of inefficient sealing of hoods to and below the soil surface. CO2 assay was unable to detect microbial successions. The unpredictable course of these successions, plus unpredictable relative retentions mitigates against assay of organic gases as reliable in situ detection of microbial activity, except perhaps in very alkaline environments such as Owens Lake salts.

DEVELOPMENT OF AN ENVIRONMENTALLY BENIGN MICROBIAL INHIBITOR TO CONTROL INTERNAL PIPELINE CORROSION

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

Kristine L. Lowe; Bill W. Bogan; Wendy R. Sullivan

2004-07-30

The overall program objective is to develop and evaluate environmentally benign agents or products that are effective in the prevention, inhibition, and mitigation of microbially influenced corrosion (MIC) in the internal surfaces of metallic natural gas pipelines. The goal is to develop one or more environmentally benign (a.k.a. ''green'') products that can be applied to maintain the structure and dependability of the natural gas infrastructure. Previous testing indicated that the growth, and the metal corrosion caused by pure cultures of sulfate reducing bacteria were inhibited by hexane extracts of some pepper plants. This quarter tests were performed with mixed bacterialmore » cultures obtained from natural gas pipelines. Treatment with the pepper extracts affected the growth and metabolic activity of the microbial consortia. Specifically, the growth and metabolism of sulfate reducing bacteria was inhibited. The demonstration that pepper extracts can inhibit the growth and metabolism of sulfate reducing bacteria in mixed cultures is a significant observation validating a key hypothesis of the project. Future tests to determine the effects of pepper extracts on mature/established biofilms will be performed next.« less