Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy.

PubMed

Campanaro, Stefano; Treu, Laura; Kougias, Panagiotis G; De Francisci, Davide; Valle, Giorgio; Angelidaki, Irini

2016-01-01

Biogas production is an economically attractive technology that has gained momentum worldwide over the past years. Biogas is produced by a biologically mediated process, widely known as "anaerobic digestion." This process is performed by a specialized and complex microbial community, in which different members have distinct roles in the establishment of a collective organization. Deciphering the complex microbial community engaged in this process is interesting both for unraveling the network of bacterial interactions and for applicability potential to the derived knowledge. In this study, we dissect the bioma involved in anaerobic digestion by means of high throughput Illumina sequencing (~51 gigabases of sequence data), disclosing nearly one million genes and extracting 106 microbial genomes by a novel strategy combining two binning processes. Microbial phylogeny and putative taxonomy performed using >400 proteins revealed that the biogas community is a trove of new species. A new approach based on functional properties as per network representation was developed to assign roles to the microbial species. The organization of the anaerobic digestion microbiome is resembled by a funnel concept, in which the microbial consortium presents a progressive functional specialization while reaching the final step of the process (i.e., methanogenesis). Key microbial genomes encoding enzymes involved in specific metabolic pathways, such as carbohydrates utilization, fatty acids degradation, amino acids fermentation, and syntrophic acetate oxidation, were identified. Additionally, the analysis identified a new uncultured archaeon that was putatively related to Methanomassiliicoccales but surprisingly having a methylotrophic methanogenic pathway. This study is a pioneer research on the phylogenetic and functional characterization of the microbial community populating biogas reactors. By applying for the first time high-throughput sequencing and a novel binning strategy, the identified genes were anchored to single genomes providing a clear understanding of their metabolic pathways and highlighting their involvement in anaerobic digestion. The overall research established a reference catalog of biogas microbial genomes that will greatly simplify future genomic studies.

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.

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

NASA Astrophysics Data System (ADS)

Virdis, Bernardino; Dennis, Paul G.

2017-07-01

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

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

PubMed

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

2016-11-01

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

Analysis of Soil Vapor Extraction Expenses to Estimate Bioventing Expenses

DTIC Science & Technology

1995-11-01

Performance and Cost Summary. Brooks Air Force Base, Texas, July 1994. 2. Atlas , Ronald M, and Richard Bartha . Microbial Ecology : Fundamentals and...and straight-chain alkanes is highly dependent on molecular weight (carbon chain length) and the degree of branching. The book " Microbial Ecology ...must first be the presence of lower- molecular-weight aromatics (Heitkamp and Cerniglia 1988). The " Microbial Ecology " book also points out, on page

Semiquantitative analysis of gaps in microbiological performance of fish processing sector implementing current food safety management systems: a case study.

PubMed

Onjong, Hillary Adawo; Wangoh, John; Njage, Patrick Murigu Kamau

2014-08-01

Fish processing plants still face microbial food safety-related product rejections and the associated economic losses, although they implement legislation, with well-established quality assurance guidelines and standards. We assessed the microbial performance of core control and assurance activities of fish exporting processors to offer suggestions for improvement using a case study. A microbiological assessment scheme was used to systematically analyze microbial counts in six selected critical sampling locations (CSLs). Nine small-, medium- and large-sized companies implementing current food safety management systems (FSMS) were studied. Samples were collected three times on each occasion (n = 324). Microbial indicators representing food safety, plant and personnel hygiene, and overall microbiological performance were analyzed. Microbiological distribution and safety profile levels for the CSLs were calculated. Performance of core control and assurance activities of the FSMS was also diagnosed using an FSMS diagnostic instrument. Final fish products from 67% of the companies were within the legally accepted microbiological limits. Salmonella was absent in all CSLs. Hands or gloves of workers from the majority of companies were highly contaminated with Staphylococcus aureus at levels above the recommended limits. Large-sized companies performed better in Enterobacteriaceae, Escherichia coli, and S. aureus than medium- and small-sized ones in a majority of the CSLs, including receipt of raw fish material, heading and gutting, and the condition of the fish processing tables and facilities before cleaning and sanitation. Fish products of 33% (3 of 9) of the companies and handling surfaces of 22% (2 of 9) of the companies showed high variability in Enterobacteriaceae counts. High variability in total viable counts and Enterobacteriaceae was noted on fish products and handling surfaces. Specific recommendations were made in core control and assurance activities associated with sampling locations showing poor performance.

A paper-based microbial fuel cell array for rapid and high-throughput screening of electricity-producing bacteria.

PubMed

Choi, Gihoon; Hassett, Daniel J; Choi, Seokheun

2015-06-21

There is a large global effort to improve microbial fuel cell (MFC) techniques and advance their translational potential toward practical, real-world applications. Significant boosts in MFC performance can be achieved with the development of new techniques in synthetic biology that can regulate microbial metabolic pathways or control their gene expression. For these new directions, a high-throughput and rapid screening tool for microbial biopower production is needed. In this work, a 48-well, paper-based sensing platform was developed for the high-throughput and rapid characterization of the electricity-producing capability of microbes. 48 spatially distinct wells of a sensor array were prepared by patterning 48 hydrophilic reservoirs on paper with hydrophobic wax boundaries. This paper-based platform exploited the ability of paper to quickly wick fluid and promoted bacterial attachment to the anode pads, resulting in instant current generation upon loading of the bacterial inoculum. We validated the utility of our MFC array by studying how strategic genetic modifications impacted the electrochemical activity of various Pseudomonas aeruginosa mutant strains. Within just 20 minutes, we successfully determined the electricity generation capacity of eight isogenic mutants of P. aeruginosa. These efforts demonstrate that our MFC array displays highly comparable performance characteristics and identifies genes in P. aeruginosa that can trigger a higher power density.

[Application of microbial fuel cell (MFC) in solid waste composting].

PubMed

Cui, Jinxin; Wang, Xin; Tang, Jingchun

2012-03-01

Microbial fuel cell (MFC) is a new technology that can recover energy from biomass with simultaneous waste treatment. This technique has been developed fast in recent years in combining with environmental techniques such as wastewater treatment, degradation of toxic pollutants and desalination. With the increase of solid waste, applying MFC in composting is promising due to its property of waste disposal with simultaneous energy generation. In this paper, the microbial community of MFCs during composting was summarized. Four major influencing factors including electrodes, separators, oxygen supplement and configurations on the performance of composting MFCs were discussed. The characteristics of composting MFC as a new technique for reducing solid waste were as follows: high microbial biomass resulted in the high current density; adaptable to different environmental conditions; self-adjustable temperature with high energy efficiency; the transportation of proton from anode to cathode were limited by different solid substrates.

Enhancement of the microbial community biomass and diversity during air sparging bioremediation of a soil highly contaminated with kerosene and BTEX.

PubMed

Kabelitz, Nadja; Machackova, Jirina; Imfeld, Gwenaël; Brennerova, Maria; Pieper, Dietmar H; Heipieper, Hermann J; Junca, Howard

2009-03-01

In order to obtain insights in complexity shifts taking place in natural microbial communities under strong selective pressure, soils from a former air force base in the Czech Republic, highly contaminated with jet fuel and at different stages of a bioremediation air sparging treatment, were analyzed. By tracking phospholipid fatty acids and 16S rRNA genes, a detailed monitoring of the changes in quantities and composition of the microbial communities developed at different stages of the bioventing treatment progress was performed. Depending on the length of the air sparging treatment that led to a significant reduction in the contamination level, we observed a clear shift in the soil microbial community being dominated by Pseudomonads under the harsh conditions of high aromatic contamination to a status of low aromatic concentrations, increased biomass content, and a complex composition with diverse bacterial taxonomical branches.

Performance of food safety management systems in poultry meat preparation processing plants in relation to Campylobacter spp. contamination.

PubMed

Sampers, Imca; Jacxsens, Liesbeth; Luning, Pieternel A; Marcelis, Willem J; Dumoulin, Ann; Uyttendaele, Mieke

2010-08-01

A diagnostic instrument comprising a combined assessment of core control and assurance activities and a microbial assessment instrument were used to measure the performance of current food safety management systems (FSMSs) of two poultry meat preparation companies. The high risk status of the company's contextual factors, i.e., starting from raw materials (poultry carcasses) with possible high numbers and prevalence of pathogens such as Campylobacter spp., requires advanced core control and assurance activities in the FSMS to guarantee food safety. The level of the core FSMS activities differed between the companies, and this difference was reflected in overall microbial quality (mesophilic aerobic count), presence of hygiene indicators (Enterobacteriaceae, Staphylococcus aureus, and Escherichia coli), and contamination with pathogens such as Salmonella, Listeria monocytogenes, and Campylobacter spp. The food safety output expressed as a microbial safety profile was related to the variability in the prevalence and contamination levels of Campylobacter spp. in poultry meat preparations found in a Belgian nationwide study. Although a poultry meat processing company could have an advanced FSMS in place and a good microbial profile (i.e., lower prevalence of pathogens, lower microbial numbers, and less variability in microbial contamination), these positive factors might not guarantee pathogen-free products. Contamination could be attributed to the inability to apply effective interventions to reduce or eliminate pathogens in the production chain of (raw) poultry meat preparations.

Microbial barrier assessment of Tyvek stopper packaging for rubber closures.

PubMed

Moldenhauer, J E; Bass, S A; Kupinski, M J; Walters, M L; Rubio, S L

1996-01-01

Two types of Tyvek and high density polyethylene or polypropylene packaging used for sterilization of rubber closures were evaluated for Microbial Barrier properties. The packaging evaluated was "Ready to Sterilize" (1) stoppers and a second test package (Test 2) which was designated as appropriate for a clean room, filled with washed and siliconized stoppers and then heat sealed. Each type of packaging was subjected to three different sterilization temperatures (125 degrees C, 128 degrees C and 131 degrees C) in a production sterilizer (15-18 psi). Following sterilization, a microbial barrier assessment was performed, using Bacillus subtilis niger (ATCC 9372), to determine whether the packaging could maintain a sterile barrier following sterilization. Results of the testing indicated that a microbial barrier was maintained for products in "Ready to Sterilize" packages at 125 degrees C and 128 degrees C. For products sterilized in the Test 2 container a microbial barrier could not be maintained at 128 degrees C, and no further testing was performed. Following sterilization at 131 degrees C physical defects were noted for the "Ready to Sterilize" bag and a microbial barrier could not be maintained.

Validation of high throughput sequencing and microbial forensics applications

PubMed Central

2014-01-01

High throughput sequencing (HTS) generates large amounts of high quality sequence data for microbial genomics. The value of HTS for microbial forensics is the speed at which evidence can be collected and the power to characterize microbial-related evidence to solve biocrimes and bioterrorist events. As HTS technologies continue to improve, they provide increasingly powerful sets of tools to support the entire field of microbial forensics. Accurate, credible results allow analysis and interpretation, significantly influencing the course and/or focus of an investigation, and can impact the response of the government to an attack having individual, political, economic or military consequences. Interpretation of the results of microbial forensic analyses relies on understanding the performance and limitations of HTS methods, including analytical processes, assays and data interpretation. The utility of HTS must be defined carefully within established operating conditions and tolerances. Validation is essential in the development and implementation of microbial forensics methods used for formulating investigative leads attribution. HTS strategies vary, requiring guiding principles for HTS system validation. Three initial aspects of HTS, irrespective of chemistry, instrumentation or software are: 1) sample preparation, 2) sequencing, and 3) data analysis. Criteria that should be considered for HTS validation for microbial forensics are presented here. Validation should be defined in terms of specific application and the criteria described here comprise a foundation for investigators to establish, validate and implement HTS as a tool in microbial forensics, enhancing public safety and national security. PMID:25101166

Validation of high throughput sequencing and microbial forensics applications.

PubMed

Budowle, Bruce; Connell, Nancy D; Bielecka-Oder, Anna; Colwell, Rita R; Corbett, Cindi R; Fletcher, Jacqueline; Forsman, Mats; Kadavy, Dana R; Markotic, Alemka; Morse, Stephen A; Murch, Randall S; Sajantila, Antti; Schmedes, Sarah E; Ternus, Krista L; Turner, Stephen D; Minot, Samuel

2014-01-01

High throughput sequencing (HTS) generates large amounts of high quality sequence data for microbial genomics. The value of HTS for microbial forensics is the speed at which evidence can be collected and the power to characterize microbial-related evidence to solve biocrimes and bioterrorist events. As HTS technologies continue to improve, they provide increasingly powerful sets of tools to support the entire field of microbial forensics. Accurate, credible results allow analysis and interpretation, significantly influencing the course and/or focus of an investigation, and can impact the response of the government to an attack having individual, political, economic or military consequences. Interpretation of the results of microbial forensic analyses relies on understanding the performance and limitations of HTS methods, including analytical processes, assays and data interpretation. The utility of HTS must be defined carefully within established operating conditions and tolerances. Validation is essential in the development and implementation of microbial forensics methods used for formulating investigative leads attribution. HTS strategies vary, requiring guiding principles for HTS system validation. Three initial aspects of HTS, irrespective of chemistry, instrumentation or software are: 1) sample preparation, 2) sequencing, and 3) data analysis. Criteria that should be considered for HTS validation for microbial forensics are presented here. Validation should be defined in terms of specific application and the criteria described here comprise a foundation for investigators to establish, validate and implement HTS as a tool in microbial forensics, enhancing public safety and national security.

Effect of florfenicol on performance and microbial community of a sequencing batch biofilm reactor treating mariculture wastewater.

PubMed

Gao, Feng; Li, Zhiwei; Chang, Qingbo; Gao, Mengchun; She, Zonglian; Wu, Juan; Jin, Chunji; Zheng, Dong; Guo, Liang; Zhao, Yangguo; Wang, Sen

2018-02-01

The effects of florfenicol (FF) on the performance, microbial activity and microbial community of a sequencing batch biofilm reactor (SBBR) were evaluated in treating mariculture wastewater. The chemical oxygen demand (COD) and nitrogen removal were inhibited at high FF concentrations. The specific oxygen utilization rate (SOUR), specific ammonium oxidation rate (SAOR), specific nitrite oxidation rate (SNOR) and specific nitrate reduction rate (SNRR) were decreased with an increase in the FF concentration from 0 to 35 mg/L. The chemical compositions of loosely bound extracellular polymeric substances (LB-EPS) and tightly bound EPS (TB-EPS) could be affected with an increase in the FF concentration. The high-throughput sequencing indicated some obvious variations in the microbial community at different FF concentrations. The relative abundance of Nitrosomonas and Nitrospira showed a decreasing tendency with an increase in the FF concentration, suggesting that FF could affect the nitrification process of SBBR. Some genera capable of reducing nitrate to nitrogen gas could be inhibited by the addition of FF in the influent, such as Azospirillum and Hyphomicrobium.

Analysis of lipophilic pigments from a phototrophic microbial mat community by high performance liquid chromatography

NASA Technical Reports Server (NTRS)

Palmisano, A. C.; Cronin, S. E.; Des Marais, D. J.

1988-01-01

As assay for lipophilic pigments in phototrophic microbial mat communities using reverse phase-high performance liquid chromatography was developed which allows the separation of 15 carotenoids and chloropigments in a single 30 min program. Lipophilic pigments in a laminated mat from a commercial salina near Laguna Guerrero Negro, Baja California Sur, Mexico reflected their source organisms. Myxoxanthophyll, echinenone, canthaxanthin, and zeaxanthin were derived from cyanobacteria; chlorophyll c, and fucoxanthin from diatoms; chlorophyll a from cyanobacteria and diatoms; bacteriochlorophylls a and c, bacteriophaeophytin a, and gamma-carotene from Chloroflexus spp.; and beta-carotene from a variety of phototrophs. Sensitivity of detection was 0.6-6.1 ng for carotenoids and 1.7-12 ng for most chloropigments. This assay represents a significant improvement over previous analyses of lipophilic pigments in microbial mats and promises to have a wider application to other types of phototrophic communities.

Microbial bioelectrosynthesis of hydrogen: Current challenges and scale-up.

PubMed

Kitching, Michael; Butler, Robin; Marsili, Enrico

2017-01-01

Sustainable energy supplies are needed to supplement and eventually replace fossil fuels. Molecular hydrogen H 2 is a clean burning, high-energy fuel that is also used as reducing gas in industrial processes. H 2 is mainly synthesized by steam reforming of natural gas, a non-renewable fuel. There are biosynthetic strategies for H 2 production; however, they are associated with poor yield and have high cost. The application of an electrochemical driving force in a microbial electrolysis cell (MEC) improves the yield of biological reactions. The performance of the MEC is influenced by experimental parameters such as the electrode material, reactor design, microbial consortia and the substrate. In this review, factors that affect the performance of MECs are discussed and critically analysed. The potential for scale-up of H 2 bioelectrosynthesis is also discussed. Copyright © 2016 Elsevier Inc. All rights reserved.

Evaluation on the Nanoscale Zero Valent Iron Based Microbial Denitrification for Nitrate Removal from Groundwater

NASA Astrophysics Data System (ADS)

Peng, Lai; Liu, Yiwen; Gao, Shu-Hong; Chen, Xueming; Xin, Pei; Dai, Xiaohu; Ni, Bing-Jie

2015-07-01

Nanoscale zero valent iron (NZVI) based microbial denitrification has been demonstrated to be a promising technology for nitrate removal from groundwater. In this work, a mathematical model is developed to evaluate the performance of this new technology and to provide insights into the chemical and microbial interactions in the system in terms of nitrate reduction, ammonium accumulation and hydrogen turnover. The developed model integrates NZVI-based abiotic reduction of nitrate, NZVI corrosion for hydrogen production and hydrogen-based microbial denitrification and satisfactorily describes all of the nitrate and ammonium dynamics from two systems with highly different conditions. The high NZVI corrosion rate revealed by the model indicates the high reaction rate of NZVI with water due to their large specific surface area and high surface reactivity, leading to an effective microbial nitrate reduction by utilizing the produced hydrogen. The simulation results further suggest a NZVI dosing strategy (3-6 mmol/L in temperature range of 30-40 °C, 6-10 mmol/L in temperature range of 15-30 °C and 10-14 mmol/L in temperature range of 5-15 °C) during groundwater remediation to make sure a low ammonium yield and a high nitrogen removal efficiency.

Evaluation on the Nanoscale Zero Valent Iron Based Microbial Denitrification for Nitrate Removal from Groundwater

PubMed Central

Peng, Lai; Liu, Yiwen; Gao, Shu-Hong; Chen, Xueming; Xin, Pei; Dai, Xiaohu; Ni, Bing-Jie

2015-01-01

Nanoscale zero valent iron (NZVI) based microbial denitrification has been demonstrated to be a promising technology for nitrate removal from groundwater. In this work, a mathematical model is developed to evaluate the performance of this new technology and to provide insights into the chemical and microbial interactions in the system in terms of nitrate reduction, ammonium accumulation and hydrogen turnover. The developed model integrates NZVI-based abiotic reduction of nitrate, NZVI corrosion for hydrogen production and hydrogen-based microbial denitrification and satisfactorily describes all of the nitrate and ammonium dynamics from two systems with highly different conditions. The high NZVI corrosion rate revealed by the model indicates the high reaction rate of NZVI with water due to their large specific surface area and high surface reactivity, leading to an effective microbial nitrate reduction by utilizing the produced hydrogen. The simulation results further suggest a NZVI dosing strategy (3–6 mmol/L in temperature range of 30–40 °C, 6–10 mmol/L in temperature range of 15–30 °C and 10–14 mmol/L in temperature range of 5–15 °C) during groundwater remediation to make sure a low ammonium yield and a high nitrogen removal efficiency. PMID:26199053

Gut microbial communities of American pikas (Ochotona princeps): Evidence for phylosymbiosis and adaptations to novel diets.

PubMed

Kohl, Kevin D; Varner, Johanna; Wilkening, Jennifer L; Dearing, M Denise

2018-03-01

Gut microbial communities provide many physiological functions to their hosts, especially in herbivorous animals. We still lack an understanding of how these microbial communities are structured across hosts in nature, especially within a given host species. Studies on laboratory mice have demonstrated that host genetics can influence microbial community structure, but that diet can overwhelm these genetic effects. We aimed to test these ideas in a natural system, the American pika (Ochotona princeps). First, pikas are high-elevation specialists with significant population structure across various mountain ranges in the USA, allowing us to investigate whether similarities in microbial communities match host genetic differences. Additionally, pikas are herbivorous, with some populations exhibiting remarkable dietary plasticity and consuming high levels of moss, which is exceptionally high in fibre and low in protein. This allows us to investigate adaptations to an herbivorous diet, as well as to the especially challenging diet of moss. Here, we inventoried the microbial communities of pika caecal pellets from various populations using 16S rRNA sequencing to investigate structuring of microbial communities across various populations with different natural diets. Microbial communities varied significantly across populations, and differences in microbial community structure were congruent with genetic differences in host population structure, a pattern known as "phylosymbiosis." Several microbial members (Ruminococcus, Prevotella, Oxalobacter and Coprococcus) were detected across all samples, and thus likely represent a "core microbiome." These genera are known to perform a number of services for herbivorous hosts such as fibre fermentation and the degradation of plant defensive compounds, and thus are likely important for herbivory in pikas. Moreover, pikas that feed on moss harboured microbial communities highly enriched in Melainabacteria. This uncultivable candidate phylum has been proposed to ferment fibre for herbivores, and thus may contribute to the ability of some pika populations to consume high amounts of moss. These findings demonstrate that both host genetics and diet can influence the microbial communities of the American pika. These animals may be novel sources of fibre-degrading microbes. Last, we discuss the implications of population-specific microbial communities for conservation efforts in this species. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

Aerobic microbial taxa dominate deep subsurface cores from the Alberta oil sands.

PubMed

Ridley, Christina M; Voordouw, Gerrit

2018-06-01

Little is known about the microbial ecology of the subsurface oil sands in Northern Alberta, Canada. Biodegradation of low molecular weight hydrocarbons by indigenous microbes has enriched high molecular weight hydrocarbons, resulting in highly viscous bitumen. This extreme subsurface environment is further characterized by low nutrient availability and limited access to water, thus resulting in low microbial biomass. Improved DNA isolation protocols and increasingly sensitive sequencing methods have allowed an in-depth investigation of the microbial ecology of this unique subsurface environmental niche. Community analysis was performed on core samples (n = 62) that were retrieved from two adjacent sites located in the Athabasca Oil Sands at depths from 220 to 320 m below the surface. Microbial communities were dominated by aerobic taxa, including Pseudomonas and Acinetobacter. Only one core sample microbial community was dominated by anaerobic taxa, including the methanogen Methanoculleus, as well as Desulfomicrobium and Thauera. Although the temperature of the bitumen-containing subsurface is low (8°C), two core samples had high fractions of the potentially thermophilic taxon, Thermus. Predominance of aerobic taxa in the subsurface suggests the potential for in situ aerobic hydrocarbon degradation; however, more studies are required to determine the functional role of these taxa within this unique environment.

Activated microporous-mesoporous carbon derived from chestnut shell as a sustainable anode material for high performance microbial fuel cells.

PubMed

Chen, Qin; Pu, Wenhong; Hou, Huijie; Hu, Jingping; Liu, Bingchuan; Li, Jianfeng; Cheng, Kai; Huang, Long; Yuan, Xiqing; Yang, Changzhu; Yang, Jiakuan

2018-02-01

Microbial fuel cells (MFCs) are promising biotechnologies tool to harvest electricity by decomposing organic matter in waste water, and the anode material is a critical factor in determining the performance of MFCs. In this study, chestnut shell is proposed as a novel anode material with mesoporous and microporous structure prepared via a simple carbonization procedure followed by an activation process. The chemical activation process successfully modified the macroporous structure, created more mesoporous and microporous structure and decreased the O-content and pyridinic/pyrrolic N groups on the biomass anode, which were beneficial for improving charge transfer efficiency between the anode surface and microbial biofilm. The MFC with activated biomass anode achieved a maximum power density (23.6 W m -3 ) 2.3 times higher than carbon cloth anode (10.4 W m -3 ). This study introduces a promising and feasible strategy for the fabrication of high performance anodes for MFCs derived from cost-effective, sustainable natural materials. Copyright © 2017 Elsevier Ltd. All rights reserved.

History of adaptation determines short-term shifts in performance and community structure of hydrogen-producing microbial communities degrading wheat straw.

PubMed

Valdez-Vazquez, Idania; Morales, Ana L; Escalante, Ana E

2017-11-01

This study addresses the question of ecological interest for the determination of structure and diversity of microbial communities that degrade lignocellulosic biomasses to produce biofuels. Two microbial consortia with different history, native of wheat straw (NWS) and from a methanogenic digester (MD) fed with cow manure, were contrasted in terms of hydrogen performance, substrate disintegration and microbial diversity. NWS outperformed the hydrogen production rate of MD. Microscopic images revealed that NWS acted on the cuticle and epidermis, generating cellulose strands with high crystallinity, while MD degraded deeper layers, equally affecting all polysaccharides. The bacterial composition markedly differed according to the inocula origin. NWS almost solely comprised hydrogen producers of the phyla Firmicutes and Proteobacteria, with 38% members of Enterococcus. After hydrogen fermentation, NWS comprised 8% Syntrophococcus, an acetogen that cleaves aryl ethers of constituent groups on the aromatic components of lignin. Conversely, MD comprised thirteen phyla, primarily including Firmicutes with H 2 -producing members, and Bacteroidetes with non-H 2 -producing members, which reduced the hydrogen performance. Overall, the results of this study provide clear evidence that the history of adaptation of NWS enhanced the hydrogen performance from untreated wheat straw. Further, native wheat straw communities have the potential to refine cellulose fibers and produce biofuels simultaneously. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

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

PubMed

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

2017-10-01

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

Soil fertility and plant diversity enhance microbial performance in metal-polluted soils.

PubMed

Stefanowicz, Anna M; Kapusta, Paweł; Szarek-Łukaszewska, Grażyna; Grodzińska, Krystyna; Niklińska, Maria; Vogt, Rolf D

2012-11-15

This study examined the effects of soil physicochemical properties (including heavy metal pollution) and vegetation parameters on soil basal respiration, microbial biomass, and the activity and functional richness of culturable soil bacteria and fungi. In a zinc and lead mining area (S Poland), 49 sites were selected to represent all common plant communities and comprise the area's diverse soil types. Numerous variables describing habitat properties were reduced by PCA to 7 independent factors, mainly representing subsoil type (metal-rich mining waste vs. sand), soil fertility (exchangeable Ca, Mg and K, total C and N, organic C), plant species richness, phosphorus content, water-soluble heavy metals (Zn, Cd and Pb), clay content and plant functional diversity (based on graminoids, legumes and non-leguminous forbs). Multiple regression analysis including these factors explained much of the variation in most microbial parameters; in the case of microbial respiration and biomass, it was 86% and 71%, respectively. The activity of soil microbes was positively affected mainly by soil fertility and, apparently, by the presence of mining waste in the subsoil. The mining waste contained vast amounts of trace metals (total Zn, Cd and Pb), but it promoted microbial performance due to its inherently high content of macronutrients (total Ca, Mg, K and C). Plant species richness had a relatively strong positive effect on all microbial parameters, except for the fungal component. In contrast, plant functional diversity was practically negligible in its effect on microbes. Other explanatory variables had only a minor positive effect (clay content) or no significant influence (phosphorus content) on microbial communities. The main conclusion from this study is that high nutrient availability and plant species richness positively affected the soil microbes and that this apparently counteracted the toxic effects of metal contamination. Copyright © 2012 Elsevier B.V. All rights reserved.

Combination of microbial oxidation and biogenic schwertmannite immobilization: A potential remediation for highly arsenic-contaminated soil.

PubMed

Yang, Zhihui; Wu, Zijian; Liao, Yingping; Liao, Qi; Yang, Weichun; Chai, Liyuan

2017-08-01

Here, a novel strategy that combines microbial oxidation by As(III)-oxidizing bacterium and biogenic schwertmannite (Bio-SCH) immobilization was first proposed and applied for treating the highly arsenic-contaminated soil. Brevibacterium sp. YZ-1 isolated from a highly As-contaminated soil was used to oxidize As(III) in contaminated soils. Under optimum culture condition for microbial oxidation, 92.3% of water-soluble As(III) and 84.4% of NaHCO 3 -extractable As(III) in soils were removed. Bio-SCH synthesized through the oxidation of ferrous sulfate by Acidithiobacillus ferrooxidans immobilize As(V) in the contaminated soil effectively. Consequently, the combination of microbial oxidation and Bio-SCH immobilization performed better in treating the highly As-contaminated soil with immobilization efficiencies of 99.3% and 82.6% for water-soluble and NaHCO 3 -extractable total As, respectively. Thus, the combination can be considered as a green remediation strategy for developing a novel and valuable solution for As-contaminated soils. Copyright © 2017 Elsevier Ltd. All rights reserved.

Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation.

PubMed

Kantor, Rose S; Huddy, Robert J; Iyer, Ramsunder; Thomas, Brian C; Brown, Christopher T; Anantharaman, Karthik; Tringe, Susannah; Hettich, Robert L; Harrison, Susan T L; Banfield, Jillian F

2017-03-07

Remediation of industrial wastewater is important for preventing environmental contamination and enabling water reuse. Biological treatment for one industrial contaminant, thiocyanate (SCN - ), relies upon microbial hydrolysis, but this process is sensitive to high loadings. To examine the activity and stability of a microbial community over increasing SCN - loadings, we established and operated a continuous-flow bioreactor fed increasing loadings of SCN - . A second reactor was fed ammonium sulfate to mimic breakdown products of SCN - . Biomass was sampled from both reactors for metagenomics and metaproteomics, yielding a set of genomes for 144 bacteria and one rotifer that constituted the abundant community in both reactors. We analyzed the metabolic potential and temporal dynamics of these organisms across the increasing loadings. In the SCN - reactor, Thiobacillus strains capable of SCN - degradation were highly abundant, whereas the ammonium sulfate reactor contained nitrifiers and heterotrophs capable of nitrate reduction. Key organisms in the SCN - reactor expressed proteins involved in SCN - degradation, sulfur oxidation, carbon fixation, and nitrogen removal. Lower performance at higher loadings was linked to changes in microbial community composition. This work provides an example of how meta-omics can increase our understanding of industrial wastewater treatment and inform iterative process design and development.

MetaSort untangles metagenome assembly by reducing microbial community complexity

PubMed Central

Ji, Peifeng; Zhang, Yanming; Wang, Jinfeng; Zhao, Fangqing

2017-01-01

Most current approaches to analyse metagenomic data rely on reference genomes. Novel microbial communities extend far beyond the coverage of reference databases and de novo metagenome assembly from complex microbial communities remains a great challenge. Here we present a novel experimental and bioinformatic framework, metaSort, for effective construction of bacterial genomes from metagenomic samples. MetaSort provides a sorted mini-metagenome approach based on flow cytometry and single-cell sequencing methodologies, and employs new computational algorithms to efficiently recover high-quality genomes from the sorted mini-metagenome by the complementary of the original metagenome. Through extensive evaluations, we demonstrated that metaSort has an excellent and unbiased performance on genome recovery and assembly. Furthermore, we applied metaSort to an unexplored microflora colonized on the surface of marine kelp and successfully recovered 75 high-quality genomes at one time. This approach will greatly improve access to microbial genomes from complex or novel communities. PMID:28112173

Potential impact of Andrassy bentonite microbial diversity in the long-term performance of a deep nuclear waste repository

NASA Astrophysics Data System (ADS)

Tadza, M. Y. Mohd; Tadza, M. A. Mohd; Bag, R.; Harith, N. S. H.

2018-01-01

Copper and steel canning and bentonite buffer are normally forseen as the primary containment component of a deep nuclear waste repository. Distribution of microbes in subsurface environments have been found to be extensive and directly or indirectly may exert influence on waste canister corrosion and the mobility of radionuclides. The understanding of clays and microbial interaction with radionuclides will be useful in predicting the microbial impacts on the performance of the waste repositories. The present work characterizes the culture-dependent microbial diversity of Andrassy bentonite recovered from Tawau clay deposits. The evaluation of microbial populations shows the presence of a number of cultivable microbes (e.g. Staphylococcus, Micrococcus, Achromobacter, Bacillus, Paecilomyces, Trichoderma, and Fusarium). Additionally, a pigmented yeast strain Rhodotorula mucilaginosa was also recovered from the formation. Both Bacillus and Rhodotorula mucilaginosa have high tolerance towards U radiation and toxicity. The presence of Rhodotorula mucilaginosa in Andrassy bentonite might be able to change the speciation of radionuclides (e.g. uranium) in a future deep repository. However, concern over the presence of Fe (III) reduction microbes such as Bacillus also found in the formation could lead to corrosion of copper steel canister and affect the overall performance of the containment system.

Development of an Enhanced Metaproteomic Approach for Deepening the Microbiome Characterization of the Human Infant Gut

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

Xiong, Weili; Richard J. Giannone; Morowitz, Michael J.

The early-life microbiota establishment in the human infant gut is highly variable and plays a crucial role in host nutrients and immunity maturation. While high-performance mass spectrometry (MS)-based metaproteomics is a powerful method for the functional characterization of complex microbial communities, the construction of comprehensive metaproteomic information in human fecal samples is inhibited by the presence of abundant human proteins. To alleviate this restriction, we have designed a novel metaproteomic strategy based on Double Filtering (DF) to enhance microbial protein characterization in complex fecal samples from healthy premature infants. We improved the overall depth of infant gut proteome measurement, withmore » an increase in the number of identified low abundance proteins, and observed greater than twofold improvement in metrics for microbial protein identifications and quantifications with a relatively high rank correlation to control. We further showed the substantial enhancement of this approach for extensively interpreting microbial functional categories between infants by affording more detailed and confident identified categories. This approach provided an avenue for in-depth measurement in the microbial component of infant fecal samples and thus comprehensive characterization of infant gut microbiome functionality.« less

Development of an Enhanced Metaproteomic Approach for Deepening the Microbiome Characterization of the Human Infant Gut

DOE PAGES

Xiong, Weili; Richard J. Giannone; Morowitz, Michael J.; ...

2014-10-28

The early-life microbiota establishment in the human infant gut is highly variable and plays a crucial role in host nutrients and immunity maturation. While high-performance mass spectrometry (MS)-based metaproteomics is a powerful method for the functional characterization of complex microbial communities, the construction of comprehensive metaproteomic information in human fecal samples is inhibited by the presence of abundant human proteins. To alleviate this restriction, we have designed a novel metaproteomic strategy based on Double Filtering (DF) to enhance microbial protein characterization in complex fecal samples from healthy premature infants. We improved the overall depth of infant gut proteome measurement, withmore » an increase in the number of identified low abundance proteins, and observed greater than twofold improvement in metrics for microbial protein identifications and quantifications with a relatively high rank correlation to control. We further showed the substantial enhancement of this approach for extensively interpreting microbial functional categories between infants by affording more detailed and confident identified categories. This approach provided an avenue for in-depth measurement in the microbial component of infant fecal samples and thus comprehensive characterization of infant gut microbiome functionality.« less

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

PubMed

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

2015-05-19

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

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

PubMed

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

2017-02-01

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

Microbial Impact on Success of Human Exploration Missions

NASA Technical Reports Server (NTRS)

Pierson, Duane L.; Ott, C. Mark; Groves, T. O.; Paloski, W. H. (Technical Monitor)

2000-01-01

The purpose of this study is to identify microbiological risks associated with space exploration and identify potential countermeasures available. Identification of microbial risks associated with space habitation requires knowledge of the sources and expected types of microbial agents. Crew data along with environmental data from water, surfaces, air, and free condensate are utilized in risk examination. Data from terrestrial models are also used. Microbial risks to crew health include bacteria, fungi, protozoa, and viruses. Adverse effects of microbes include: infections, allergic reactions, toxin production, release of volatiles, food spoilage, plant disease, material degradation, and environmental contamination. Risk is difficult to assess because of unknown potential changes in microbes (e.g., mutation) and the human host (e.g., immune changes). Prevention of adverse microbial impacts is preferred over remediation. Preventative measures include engineering measures (e.g., air filtration), crew microbial screening, acceptability standards, and active verification by onboard monitoring. Microbiological agents are important risks to human health and performance during space flight and risks increase with mission duration. Acceptable risk level must be defined. Prevention must be given high priority. Careful screening of crewmembers and payloads is an important element of any risk mitigation plan. Improved quantitation of microbiological risks is a high priority.

Architecture engineering of hierarchically porous chitosan/vacuum-stripped graphene scaffold as bioanode for high performance microbial fuel cell.

PubMed

He, Ziming; Liu, Jing; Qiao, Yan; Li, Chang Ming; Tan, Timothy Thatt Yang

2012-09-12

The bioanode is the defining feature of microbial fuel cell (MFC) technology and often limits its performance. In the current work, we report the engineering of a novel hierarchically porous architecture as an efficient bioanode, consisting of biocompatible chitosan and vacuum-stripped graphene (CHI/VSG). With the hierarchical pores and unique VSG, an optimized bioanode delivered a remarkable maximum power density of 1530 mW m(-2) in a mediator-less MFC, 78 times higher than a carbon cloth anode.

Microbial Community in a Biofilter for Removal of Low Load Nitrobenzene Waste Gas

PubMed Central

Zhai, Jian; Wang, Zhu; Shi, Peng; Long, Chao

2017-01-01

To improve biofilter performance, the microbial community of a biofilter must be clearly defined. In this study, the performance of a lab-scale polyurethane biofilter for treating waste gas with low loads of nitrobenzene (NB) (< 20 g m-3 h-1) was investigated when using different empty bed residence times (EBRT) (64, 55.4 and 34 s, respectively). In addition, the variations of the bacterial community in the biofilm on the longitudinal distribution of the biofilters were analysed by using Illumina MiSeq high-throughput sequencing. The results showed that NB waste gas was successfully degraded in the biofilter. High-throughput sequencing data suggested that the phylum Actinobacteria and genus Rhodococcus played important roles in the degradation of NB. The variations of the microbial community were attributed to the different intermediate degradation products of NB in each layer. The strains identified in this study were potential candidates for purifying waste gas effluents containing NB. PMID:28114416

Population dynamics of electrogenic microbial communities in microbial fuel cells started with three different inoculum sources.

PubMed

Ishii, Shun'ichi; Suzuki, Shino; Yamanaka, Yuko; Wu, Angela; Nealson, Kenneth H; Bretschger, Orianna

2017-10-01

Microbial fuel cells (MFCs) are one of the bioelectrochemical systems that exploit microorganisms as biocatalysts to degrade organic matters and recover energy as electric power. Here, we explored how the established electrogenic microbial communities were influenced by three different inoculum sources; anaerobic sludge of the wastewater plant, rice paddy field soil, and coastal lagoon sediment. We periodically characterized both electricity generation with sucrose consumption and 16S rRNA-basis microbial community composition. The electrochemical features of MFCs were slightly different among three inocula, and the lagoon sediment-inoculated MFC showed the highest performance in terms of the treatment time. Meanwhile, although the inoculated microbial communities were highly diverse and quite different, only twelve genera affiliated with δ-Proteobacteria, γ-Proteobacteria, Bacilli, Clostridia/Negativicutes or Bacteroidetes were abundantly enriched in all MFC anode communities. Within them, several fermentative genera were clearly different due to the inocula, while the inocula-specific phylotypes were identified in an electrogenic genus Geobacter. The relative abundances of phylotypes closely-related to Geobacter metallireducens were increased in later stages of all the sucrose-fed MFCs. These results indicate that key microbial members for the functional electrogenic community widely exist in natural ecosystems, but the community members presenting in inoculum sources affected the MFC performances. Copyright © 2017 Elsevier B.V. All rights reserved.

New on-line separation workflow of microbial metabolites via hyphenation of analytical and preparative comprehensive two-dimensional liquid chromatography.

PubMed

Yan, Xia; Wang, Li-Juan; Wu, Zhen; Wu, Yun-Long; Liu, Xiu-Xiu; Chang, Fang-Rong; Fang, Mei-Juan; Qiu, Ying-Kun

2016-10-15

Microbial metabolites represent an important source of bioactive natural products, but always exhibit diverse of chemical structures or complicated chemical composition with low active ingredients content. Traditional separation methods rely mainly on off-line combination of open-column chromatography and preparative high performance liquid chromatography (HPLC). However, the multi-step and prolonged separation procedure might lead to exposure to oxygen and structural transformation of metabolites. In the present work, a new two-dimensional separation workflow for fast isolation and analysis of microbial metabolites from Chaetomium globosum SNSHI-5, a cytotoxic fungus derived from extreme environment. The advantage of this analytical comprehensive two-dimensional liquid chromatography (2D-LC) lies on its ability to analyze the composition of the metabolites, and to optimize the separation conditions for the preparative 2D-LC. Furthermore, gram scale preparative 2D-LC separation of the crude fungus extract could be performed on a medium-pressure liquid chromatograph×preparative high-performance liquid chromatography system, under the optimized condition. Interestingly, 12 cytochalasan derivatives, including two new compounds named cytoglobosin Ab (3) and isochaetoglobosin Db (8), were successfully obtained with high purity in a short period of time. The structures of the isolated metabolites were comprehensively characterized by HR ESI-MS and NMR. To be highlighted, this is the first report on the combination of analytical and preparative 2D-LC for the separation of microbial metabolites. The new workflow exhibited apparent advantages in separation efficiency and sample treatment capacity compared with conventional methods. Copyright © 2016 Elsevier B.V. All rights reserved.

Characterising microbial reduction of arsenate sorbed to ferrihydrite and its concurrence with iron reduction and the consequent impact on arsenic mobilisation

NASA Astrophysics Data System (ADS)

Huang, Jen-How

2014-05-01

Mobilisation of solid phase arsenic under reducing conditions involves a combination of microbial arsenate and iron reduction and is affected by secondary reactions of released products. A series of model anoxic incubations were performed to understand the concurrence between arsenate and ferrihydrite reduction by Shewanella putrefaciens strain CN-32 at different concentrations of arsenate, ferrihydrite and lactate, and with given ΔGrxn for arsenate and ferrihydrite reduction in non-growth conditions at pH 7. The reduction kinetics of arsenate sorbed to ferrihydrite is predominately controlled by the availability of dissolved arsenate, which is measured by the integral of dissolved arsenate concentrations against incubation time and shown to correlate with the first order rate constants. Thus, the mobilisation of adsorbed As(V) can be regarded as the rate determining step of microbial reduction of As(V) sorbed to ferrihydrite. High lactate concentrations slightly slowed down the rate of arsenate reduction due to the competition with arsenate for microbial contact. Under all experimental conditions, simultaneous arsenate and ferrihydrite reduction occurred following addition of S. putrefaciens inoculums and suggested no apparent competition between these two enzymatic reductions. Ferrous ions released from iron reduction might retard microbial arsenate reduction at high arsenate and ferrihydrite concentrations due to formation of ferrous arsenate. At high arsenate to ferrihydrite ratios, reductive dissolution of ferrihydrite shifted arsenate from sorption to dissolution and hence accelerated arsenate reduction. Reductive dissolution of ferrihydrite may cause additional releases of adsorbed As(V) into solution, which is especially effective at high As(V) to ferrihydrite ratios. In comparison, formation of Fe(II) secondary minerals during microbial Fe(III) reduction were responsible for trapping solution As(V) in the systems with high ferrihydrite but low As(V) concentrations. In summary, the interaction between microbial arsenate and ferrihydrite reduction did not correlate with ΔGrxn, but instead was governed by geochemical and microbial parameters, which may substantially influence the mobility of arsenic.

Functionally Stable and Phylogenetically Diverse Microbial Enrichments from Microbial Fuel Cells during Wastewater Treatment

PubMed Central

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

2012-01-01

Microbial fuel cells (MFCs) are devices that exploit microorganisms as biocatalysts to recover energy from organic matter in the form of electricity. One of the goals of MFC research is to develop the technology for cost-effective wastewater treatment. However, before practical MFC applications are implemented it is important to gain fundamental knowledge about long-term system performance, reproducibility, and the formation and maintenance of functionally-stable microbial communities. Here we report findings from a MFC operated for over 300 days using only primary clarifier effluent collected from a municipal wastewater treatment plant as the microbial resource and substrate. The system was operated in a repeat-batch mode, where the reactor solution was replaced once every two weeks with new primary effluent that consisted of different microbial and chemical compositions with every batch exchange. The turbidity of the primary clarifier effluent solution notably decreased, and 97% of biological oxygen demand (BOD) was removed after an 8–13 day residence time for each batch cycle. On average, the limiting current density was 1000 mA/m2, the maximum power density was 13 mW/m2, and coulombic efficiency was 25%. Interestingly, the electrochemical performance and BOD removal rates were very reproducible throughout MFC operation regardless of the sample variability associated with each wastewater exchange. While MFC performance was very reproducible, the phylogenetic analyses of anode-associated electricity-generating biofilms showed that the microbial populations temporally fluctuated and maintained a high biodiversity throughout the year-long experiment. These results suggest that MFC communities are both self-selecting and self-optimizing, thereby able to develop and maintain functional stability regardless of fluctuations in carbon source(s) and regular introduction of microbial competitors. These results contribute significantly toward the practical application of MFC systems for long-term wastewater treatment as well as demonstrating MFC technology as a useful device to enrich for functionally stable microbial populations. PMID:22347379

In situ formation of graphene layers on graphite surfaces for efficient anodes of microbial fuel cells.

PubMed

Tang, Jiahuan; Chen, Shanshan; Yuan, Yong; Cai, Xixi; Zhou, Shungui

2015-09-15

Graphene can be used to improve the performance of the anode in a microbial fuel cell (MFC) due to its good biocompatibility, high electrical conductivity and large surface area. However, the chemical production and modification of the graphene on the anode are environmentally hazardous because of the use of various harmful chemicals. This study reports a novel method based on the electrochemical exfoliation of a graphite plate (GP) for the in situ formation of graphene layers on the surface of a graphite electrode. When the resultant graphene-layer-based graphite plate electrode (GL/GP) was used as an anode in an MFC, a maximum power density of 0.67 ± 0.034 W/m(2) was achieved. This value corresponds to 1.72-, 1.56- and 1.26-times the maximum power densities of the original GP, exfoliated-graphene-modified GP (EG/GP) and chemically-reduced-graphene-modified GP (rGO/GP) anodes, respectively. Electrochemical measurements revealed that the high performance of the GL/GP anode was attributable to its macroporous structure, improved electron transfer and high electrochemical capacitance. The results demonstrated that the proposed method is a facile and environmentally friendly synthesis technique for the fabrication of high-performance graphene-based electrodes for use in microbial energy harvesting. Copyright © 2015 Elsevier B.V. All rights reserved.

Linking microbial community structure to membrane biofouling associated with varying dissolved oxygen concentrations.

PubMed

Gao, Da-wen; Fu, Yuan; Tao, Yu; Li, Xin-xin; Xing, Min; Gao, Xiu-hong; Ren, Nan-qi

2011-05-01

In order to elucidate how dissolved oxygen (DO) concentration influenced the generation of extracellular polymeric substance (EPS) and soluble microbial products (SMP) in mixed liquor and biocake, 16S rDNA fingerprinting analyses were performed to investigate the variation of the microbial community in an aerobic membrane bioreactor (MBR). The function of microbial community structure was proved to be ultimately responsible for biofouling. Obvious microbial community succession from the subphylum of Betaproteobacteria to Deltaproteobacteria was observed in biocake. High concentration of EPS in biocake under the low DO concentration (0.5 mg L(-1)) caused severe biofouling. The correlation coefficient of membrane fouling rate with EPS content in biocake (0.9941-0.9964) was much higher than that in mixed liquor (0.6689-0.8004). Copyright © 2011 Elsevier Ltd. All rights reserved.

Effect of zinc oxide nanoparticles on nitrogen removal, microbial activity and microbial community of CANON process in a membrane bioreactor.

PubMed

Zhang, Xiaojing; Zhang, Nan; Fu, Haoqiang; Chen, Tao; Liu, Sa; Zheng, Shuhua; Zhang, Jie

2017-11-01

In this study, a membrane bioreactor (MBR) was adopted for completely autotrophic nitrogen removal over nitrite (CANON) process. Zinc oxide nanoparticles (ZnO NPs) was step-wise increased to analyze the influence on nitrogen removal, microbial activity and microbial communities. Finally ZnO NPs was removed to study its recovery capability. The bioactivities of ammonia-oxidizing bacteria (AOB), anaerobic ammonia-oxidizing bacteria (AAOB) and nitrite-oxidizing bacteria (NOB) were detected by batch experiments. Results showed that the ZnO NPs with low concentration (≤5mgL -1 ) was profitable for nitrogen removal while the high concentration performed inhibition, and it lowered the abundance of both AOB and NOB while enhanced that of AAOB. ZnO NPs with high concentration (≥10mgL -1 ) suppressed both AOB and AAOB, and long-term exposure within ZnO NPs led to microbial diversity decrease. The inhibition threshold of ZnO NPs on CANON process was 10mgL -1 , and the profitable concentration was 1mgL -1 . Copyright © 2017 Elsevier Ltd. All rights reserved.

Development of an Enhanced Metaproteomic Approach for Deepening the Microbiome Characterization of the Human Infant Gut

PubMed Central

2015-01-01

The establishment of early life microbiota in the human infant gut is highly variable and plays a crucial role in host nutrient availability/uptake and maturation of immunity. Although high-performance mass spectrometry (MS)-based metaproteomics is a powerful method for the functional characterization of complex microbial communities, the acquisition of comprehensive metaproteomic information in human fecal samples is inhibited by the presence of abundant human proteins. To alleviate this restriction, we have designed a novel metaproteomic strategy based on double filtering (DF) the raw samples, a method that fractionates microbial from human cells to enhance microbial protein identification and characterization in complex fecal samples from healthy premature infants. This method dramatically improved the overall depth of infant gut proteome measurement, with an increase in the number of identified low-abundance proteins and a greater than 2-fold improvement in microbial protein identification and quantification. This enhancement of proteome measurement depth enabled a more extensive microbiome comparison between infants by not only increasing the confidence of identified microbial functional categories but also revealing previously undetected categories. PMID:25350865

Bioelectrochemical analysis of a hyperthermophilic microbial fuel cell generating electricity at temperatures above 80 °C.

PubMed

Fu, Qian; Fukushima, Naoya; Maeda, Haruo; Sato, Kozo; Kobayashi, Hajime

2015-01-01

We examined whether a hyperthermophilic microbial fuel cell (MFC) would be technically feasible. Two-chamber MFC reactors were inoculated with subsurface microorganisms indigenous to formation water from a petroleum reservoir and were started up at operating temperature 80 °C. The MFC generated a maximum current of 1.3 mA 45 h after the inoculation. Performance of the MFC improved with an increase in the operating temperature; the best performance was achieved at 95 °C with the maximum power density of 165 mWm(-2), which was approximately fourfold higher than that at 75 °C. Thus, to our knowledge, our study is the first to demonstrate generation of electricity in a hyperthermophilic MFC (operating temperature as high as 95 °C). Scanning electron microscopy showed that filamentous microbial cells were attached on the anode surface. The anodic microbial consortium showed limited phylogenetic diversity and primarily consisted of hyperthermophilic bacteria closely related to Caldanaerobacter subterraneus and Thermodesulfobacterium commune.

Impact of oxytetracycline and bacterial bioaugmentation on the efficiency and microbial community structure of a pesticide-degrading biomixture.

PubMed

Castro-Gutiérrez, Víctor; Masís-Mora, Mario; Carazo-Rojas, Elizabeth; Mora-López, Marielos; Rodríguez-Rodríguez, Carlos E

2018-04-01

An experimental study evaluating the effect of bioaugmentation and antibiotic (oxytetracycline) application on pesticide degradation and microbial community structure of a biomixture used in a biopurification system (BPR) was conducted. The bioaugmentation employed a carbofuran-degrading bacterial consortium. The non-bioaugmented biomixture showed excellent performance for removal of atrazine (t 1/2 : 9.9 days), carbendazim (t 1/2 : 3.0 days), carbofuran (t 1/2 : 2.8 days), and metalaxyl (t 1/2 : 2.7 days). Neither the addition of oxytetracycline nor bioaugmentation affected the efficiency of pesticide removal or microbial community (bacterial and fungal) structure, as determined by DGGE analysis. Instead, biomixture aging was mainly responsible for microbial population shifts. Even though the bioaugmentation did not enhance the biomixtures' performance, this matrix showed a high capability to sustain initial stresses related to antibiotic addition; therefore, simultaneous elimination of this particular mixture of pesticides together with oxytetracycline residues is not discouraged.

A comparison of microbial characteristics between the thermophilic and mesophilic anaerobic digesters exposed to elevated food waste loadings.

PubMed

Guo, Xiaohui; Wang, Cheng; Sun, Faqian; Zhu, Weijing; Wu, Weixiang

2014-01-01

Thermophilic and mesophilic anaerobic digestion reactors (TR and MR) using food waste as substrate were compared with emphasis on microbial responses to increasing organic loading rate (OLR). At OLR ranging from 1.0 to 2.5 g VS L(-1) d(-1), MR exhibited more stable performance compared to TR in terms of methane yield. Amplicons pyrosequencing results revealed the distinct microbial dynamics in the two reactors. Primarily, MR had greater richness and evenness of bacteria species. With OLR elevated, larger shifts of bacterial phylogeny were observed in MR; Methanosaeta dominated in archaeal community in MR while Methanothermobacter and Methanoculleus were favored in TR. The high functional redundancy in bacterial community integrated with acetoclastic methanogenesis in MR resulted in its better performance; whereas delicate interactions between hydrogen-producer and hydrogenotrophic methanogens in TR were much more prone to disruption. These results are conductive to understanding the microbial mechanisms of low methane yield during food waste anaerobic digestion. Copyright © 2013 Elsevier Ltd. All rights reserved.

Comparative Analysis of Performance and Microbial Characteristics Between High-Solid and Low-Solid Anaerobic Digestion of Sewage Sludge Under Mesophilic Conditions.

PubMed

Lu, Qin; Yi, Jing; Yang, Dianhai

2016-01-01

High-solid anaerobic digestion of sewage sludge achieves highly efficient volatile solid reduction, and production of volatile fatty acid (VFA) and methane compared with conventional low-solid anaerobic digestion. In this study, the potential mechanisms of the better performance in high-solid anaerobic digestion of sewage sludge were investigated by using 454 high-throughput pyrosequencing and real-time PCR to analyze the microbial characteristics in sewage sludge fermentation reactors. The results obtained by 454 high-throughput pyrosequencing revealed that the phyla Chloroflexi, Bacteroidetes, and Firmicutes were the dominant functional microorganisms in high-solid and low-solid anaerobic systems. Meanwhile, the real-time PCR assays showed that high-solid anaerobic digestion significantly increased the number of total bacteria, which enhanced the hydrolysis and acidification of sewage sludge. Further study indicated that the number of total archaea (dominated by Methanosarcina) in a high-solid anaerobic fermentation reactor was also higher than that in a low-solid reactor, resulting in higher VFA consumption and methane production. Hence, the increased key bacteria and methanogenic archaea involved in sewage sludge hydrolysis, acidification, and methanogenesis resulted in the better performance of high-solid anaerobic sewage sludge fermentation.

Microbial Activity and Silica Degradation in Rice Straw

NASA Astrophysics Data System (ADS)

Kim, Esther Jin-kyung

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

Microbial production of metabolites and associated enzymatic reactions under high pressure.

PubMed

Dong, Yongsheng; Jiang, Hua

2016-11-01

High environmental pressure exerts an external stress on the survival of microorganisms that are commonly found under normal pressure. In response, many growth traits alter, including cell morphology and physiology, cellular structure, metabolism, physical and chemical properties, the reproductive process, and defense mechanisms. The high-pressure technology (HP) has been industrially utilized in pressurized sterilization, synthesis of stress-induced products, and microbial/enzymatic transformation of chemicals. This article reviews current research on pressure-induced production of metabolites in normal-pressure microbes and their enzymatic reactions. Factors that affect the production of such metabolites are summarized, as well as the effect of pressure on the performance of microbial fermentation and the yield of flavoring compounds, different categories of induced enzymatic reactions and their characteristics in the supercritical carbon dioxide fluid, effects on enzyme activity, and the selection of desirable bacterial strains. Technological challenges are discussed, and future research directions are proposed. Information presented here will benefit the research, development, and application of the HP technology to improve microbial fermentation and enzymatic production of biologically active substances, thereby help to meet their increasing demand from the ever-expanding market.

Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation

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

Kantor, Rose S.; Huddy, Robert J.; Iyer, Ramsunder

Remediation of industrial wastewater is important for preventing environmental contamination and allowing water reuse. Biological treatment for one industrial contaminant, thiocyanate (SCN - ), relies upon microbial hydrolysis, but this process is sensitive to high loadings. To examine the activity and stability of a microbial community over increasing SCN - loadings, we established and operated a continuous-flow bioreactor fed increasing loadings of SCN - . A second reactor was fed ammonium sulfate to mimic breakdown products of SCN - . Biomass was sampled from both reactors for metagenomics and metaproteomics, yielding a set of genomes for 144 bacteria and onemore » rotifer that constituted the abundant community in both reactors. We analyzed the metabolic potential and temporal dynamics of these organisms across the increasing loadings. In the SCN - reactor, Thiobacillus strains capable of SCN - degradation were highly abundant, whereas the ammonium sulfate reactor contained nitrifiers and heterotrophs capable of nitrate reduction. Key organisms in the SCN - reactor expressed proteins involved in SCN - degradation, sulfur oxidation, carbon fixation, and nitrogen removal. Lower performance at higher loadings was linked to changes in microbial community composition. This work provides an example of how meta-omics can increase our understanding of industrial wastewater treatment and inform iterative process design and development.« less

Genome-Resolved Meta-Omics Ties Microbial Dynamics to Process Performance in Biotechnology for Thiocyanate Degradation

DOE PAGES

Kantor, Rose S.; Huddy, Robert J.; Iyer, Ramsunder; ...

2017-01-31

Remediation of industrial wastewater is important for preventing environmental contamination and allowing water reuse. Biological treatment for one industrial contaminant, thiocyanate (SCN - ), relies upon microbial hydrolysis, but this process is sensitive to high loadings. To examine the activity and stability of a microbial community over increasing SCN - loadings, we established and operated a continuous-flow bioreactor fed increasing loadings of SCN - . A second reactor was fed ammonium sulfate to mimic breakdown products of SCN - . Biomass was sampled from both reactors for metagenomics and metaproteomics, yielding a set of genomes for 144 bacteria and onemore » rotifer that constituted the abundant community in both reactors. We analyzed the metabolic potential and temporal dynamics of these organisms across the increasing loadings. In the SCN - reactor, Thiobacillus strains capable of SCN - degradation were highly abundant, whereas the ammonium sulfate reactor contained nitrifiers and heterotrophs capable of nitrate reduction. Key organisms in the SCN - reactor expressed proteins involved in SCN - degradation, sulfur oxidation, carbon fixation, and nitrogen removal. Lower performance at higher loadings was linked to changes in microbial community composition. This work provides an example of how meta-omics can increase our understanding of industrial wastewater treatment and inform iterative process design and development.« less

Bacterial communities in full-scale wastewater treatment systems.

PubMed

Cydzik-Kwiatkowska, Agnieszka; Zielińska, Magdalena

2016-04-01

Bacterial metabolism determines the effectiveness of biological treatment of wastewater. Therefore, it is important to define the relations between the species structure and the performance of full-scale installations. Although there is much laboratory data on microbial consortia, our understanding of dependencies between the microbial structure and operational parameters of full-scale wastewater treatment plants (WWTP) is limited. This mini-review presents the types of microbial consortia in WWTP. Information is given on extracellular polymeric substances production as factor that is key for formation of spatial structures of microorganisms. Additionally, we discuss data on microbial groups including nitrifiers, denitrifiers, Anammox bacteria, and phosphate- and glycogen-accumulating bacteria in full-scale aerobic systems that was obtained with the use of molecular techniques, including high-throughput sequencing, to shed light on dependencies between the microbial ecology of biomass and the overall efficiency and functional stability of wastewater treatment systems. Sludge bulking in WWTPs is addressed, as well as the microbial composition of consortia involved in antibiotic and micropollutant removal.

The Impact of Climate Change on Microbial Communities and Carbon Cycling in High Arctic Permafrost Soil from Spitsbergen, Northern Norway

NASA Astrophysics Data System (ADS)

de Leon, K. C.; Schwery, D.; Yoshikawa, K.; Christiansen, H. H.; Pearce, D.

2014-12-01

Permafrost-affected soils are among the most fragile ecosystems in which current microbial controls on organic matter decomposition are changing as a result of climate change. Warmer conditions in the high Arctic will lead to a deepening of the seasonal active layer of permafrost, provoking changes in microbial processes and possibly resulting in exacerbated carbon degradation under increasing anoxic conditions. The viable and non-viable fractions of the microbial community in a permafrost soil from Adventdalen, Spitsbergen, Norway were subjected to a comprehensive investigation using culture-dependent and culture-independent methods. Molecular analyses using FISH (with CTC-DAPI) and amplified rDNA restriction analysis (ARDRA) on a 257cm deep core, revealed the presence of all major microbial soil groups, with the active layer having more viable cells, and a higher microbial community diversity. Carbon dioxide (CO2) and methane (CH4) flux measurements were performed to show the amount of C stored in the sample. We demonstrated that the microbial community composition from the soil in the center of the core was most likely influenced by small scale variations in environmental conditions. Community structure showed distinct shift of presence of bacterial groups along the vertical temperature gradient profile and microbial counts and diversity was found to be highest in the surface layers, decreasing with depth. It was observed that soil properties driving microbial diversity and functional potential varied across the permafrost table. Data on the variability of CO2 and CH4 distribution described in peat structure heterogeneity are important for modeling emissions on a larger scale. Furthermore, linking microbial biomass to gas distribution may elucidate the cause of peak CO2 and CH4 and their changes in relation to environmental change and peat composition.

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.

Systems Biology of Microbial Exopolysaccharides Production

PubMed Central

Ates, Ozlem

2015-01-01

Exopolysaccharides (EPSs) produced by diverse group of microbial systems are rapidly emerging as new and industrially important biomaterials. Due to their unique and complex chemical structures and many interesting physicochemical and rheological properties with novel functionality, the microbial EPSs find wide range of commercial applications in various fields of the economy such as food, feed, packaging, chemical, textile, cosmetics and pharmaceutical industry, agriculture, and medicine. EPSs are mainly associated with high-value applications, and they have received considerable research attention over recent decades with their biocompatibility, biodegradability, and both environmental and human compatibility. However, only a few microbial EPSs have achieved to be used commercially due to their high production costs. The emerging need to overcome economic hurdles and the increasing significance of microbial EPSs in industrial and medical biotechnology call for the elucidation of the interrelations between metabolic pathways and EPS biosynthesis mechanism in order to control and hence enhance its microbial productivity. Moreover, a better understanding of biosynthesis mechanism is a significant issue for improvement of product quality and properties and also for the design of novel strains. Therefore, a systems-based approach constitutes an important step toward understanding the interplay between metabolism and EPS biosynthesis and further enhances its metabolic performance for industrial application. In this review, primarily the microbial EPSs, their biosynthesis mechanism, and important factors for their production will be discussed. After this brief introduction, recent literature on the application of omics technologies and systems biology tools for the improvement of production yields will be critically evaluated. Special focus will be given to EPSs with high market value such as xanthan, levan, pullulan, and dextran. PMID:26734603

Systems Biology of Microbial Exopolysaccharides Production.

PubMed

Ates, Ozlem

2015-01-01

Exopolysaccharides (EPSs) produced by diverse group of microbial systems are rapidly emerging as new and industrially important biomaterials. Due to their unique and complex chemical structures and many interesting physicochemical and rheological properties with novel functionality, the microbial EPSs find wide range of commercial applications in various fields of the economy such as food, feed, packaging, chemical, textile, cosmetics and pharmaceutical industry, agriculture, and medicine. EPSs are mainly associated with high-value applications, and they have received considerable research attention over recent decades with their biocompatibility, biodegradability, and both environmental and human compatibility. However, only a few microbial EPSs have achieved to be used commercially due to their high production costs. The emerging need to overcome economic hurdles and the increasing significance of microbial EPSs in industrial and medical biotechnology call for the elucidation of the interrelations between metabolic pathways and EPS biosynthesis mechanism in order to control and hence enhance its microbial productivity. Moreover, a better understanding of biosynthesis mechanism is a significant issue for improvement of product quality and properties and also for the design of novel strains. Therefore, a systems-based approach constitutes an important step toward understanding the interplay between metabolism and EPS biosynthesis and further enhances its metabolic performance for industrial application. In this review, primarily the microbial EPSs, their biosynthesis mechanism, and important factors for their production will be discussed. After this brief introduction, recent literature on the application of omics technologies and systems biology tools for the improvement of production yields will be critically evaluated. Special focus will be given to EPSs with high market value such as xanthan, levan, pullulan, and dextran.

Characterising microbial reduction of arsenate sorbed to ferrihydrite and its concurrence with iron reduction.

PubMed

Huang, Jen-How

2018-03-01

A series of model anoxic incubations were performed to understand the concurrence between arsenate and ferrihydrite reduction by Shewanella putrefaciens strain CN-32 at different concentrations of arsenate, ferrihydrite and lactate, and with given ΔG rxn for arsenate and ferrihydrite reduction in non-growth conditions. The reduction kinetics of arsenate sorbed to ferrihydrite is predominately controlled by the availability of dissolved arsenate, which is measured by the integral of dissolved arsenate concentrations against incubation time and shown to correlate with the first order rate constants. High lactate concentrations slightly slowed down the rate of arsenate reduction due to the competition with arsenate for microbial contact. Under all experimental conditions, simultaneous arsenate and ferrihydrite reduction occurred following addition of S. putrefaciens inoculums and suggested no apparent competition between these two enzymatic reductions. Ferrous ions released from iron reduction might retard microbial arsenate reduction at high arsenate and ferrihydrite concentrations due to formation of ferrous arsenate. At high arsenate to ferrihydrite ratios, reductive dissolution of ferrihydrite shifted arsenate from sorption to dissolution and hence accelerated arsenate reduction. The interaction between microbial arsenate and ferrihydrite reduction did not correlate with ΔG rxn , but instead was governed by other factors such as geochemical and microbial parameters. Copyright © 2017 Elsevier Ltd. All rights reserved.

Separation and determination of peptide metabolite of Bacillus licheniformis in a microbial fuel cell by high-speed capillary micellar electrokinetic chromatography.

PubMed

Wang, Wei; Bai, Ruiguang; Cai, Xiaoyu; Lin, Ping; Ma, Lihong

2017-11-01

A method using high-speed capillary micellar electrokinetic chromatography and a microbial fuel cell was applied to determine the metabolite of the peptides released by Bacillus licheniformis. Two peptides, l-carnosine and l-alanyl-l-glutamine were used as the substrate to feed Bacillus licheniformis in a microbial fuel cell. The metabolism process of the bacterium was monitored by analyzing the voltage outputs of the microbial fuel cell. A home-made spontaneous injection device was applied to perform high-speed capillary micellar electrokinetic chromatography. Under the optimized conditions, tryptophan, glycine, valine, tyrosine and the two peptides could be rapidly separated within 2.5 min with micellar electrokinetic chromatography mode. Then the method was applied to analyze the solutions sampled from the microbial fuel cell. After 92 h running, valine, as the metabolite, was successfully detected with concentration 3.90 × 10 -5 M. The results demonstrated that Bacillus licheniformis could convert l-carnosine and l-alanyl-l-glutamine into valine. The method employed in this work was proved to have great potential in analysis of metabolites, such as amino acids, for microorganisms. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electron harvest and treatment of amendment free municipal wastewater using microbial anodes: A case study

NASA Astrophysics Data System (ADS)

Rosa, Luis F. M.; Koch, Christin; Korth, Benjamin; Harnisch, Falk

2017-07-01

Microbial electrochemical technologies (METs) and especially microbial fuel cells (MFCs) are considered to allow energy harvest from the fuel wastewater during its treatment. However, the majority of studies use either "artificial" wastewater, amended wastewater, (i.e. with addition of chemicals), or pre-enriched microbial anodes. As these strategies might not be transferable to large scale, this study uses exclusively amendment free municipal wastewater as inoculum and sole carbon and energy source. It is shown that electrons can be harvested, at maximum current densities of 0.01 mA cm-2. In weekly cycles using batch systems (with 90 cm2 L-1 anode surface) only a minor fraction (<10%) of the available charge from COD-removal was turned into electricity by a highly diverse anodic microbial community. This performance is below those achieved by pre-enriched anodes or in amended wastewater studies, illustrating the need for more fundamental, application relevant studies.

Hydration status and diurnal trophic interactions shape microbial community function in desert biocrusts

NASA Astrophysics Data System (ADS)

Kim, Minsu; Or, Dani

2017-12-01

Biological soil crusts (biocrusts) are self-organised thin assemblies of microbes, lichens, and mosses that are ubiquitous in arid regions and serve as important ecological and biogeochemical hotspots. Biocrust ecological function is intricately shaped by strong gradients of water, light, oxygen, and dynamics in the abundance and spatial organisation of the microbial community within a few millimetres of the soil surface. We report a mechanistic model that links the biophysical and chemical processes that shape the functioning of biocrust representative microbial communities that interact trophically and respond dynamically to cycles of hydration, light, and temperature. The model captures key features of carbon and nitrogen cycling within biocrusts, such as microbial activity and distribution (during early stages of biocrust establishment) under diurnal cycles and the associated dynamics of biogeochemical fluxes at different hydration conditions. The study offers new insights into the highly dynamic and localised processes performed by microbial communities within thin desert biocrusts.

HPLC studio: a novel software utility to perform HPLC chromatogram comparison for screening purposes.

PubMed

García, J B; Tormo, José R

2003-06-01

A new tool, HPLC Studio, was developed for the comparison of high-performance liquid chromatography (HPLC) chromatograms from microbial extracts. The new utility makes it possible to create a virtual chromatogram by mixing up to 20 individual chromatograms. The virtual chromatogram is the first step in establishing a ranking of the microbial fermentation conditions based on either the area or diversity of HPLC peaks. The utility was used to maximize the diversity of secondary metabolites tested from a microorganism and therefore increase the chances of finding new lead compounds in a drug discovery program.

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.

Microbial characteristics in anaerobic digestion process of food waste for methane production-A review.

PubMed

Wang, Pan; Wang, Hongtao; Qiu, Yinquan; Ren, Lianhai; Jiang, Bin

2018-01-01

Food waste (FW) is rich in starch, fat, protein and cellulose. It is easy to decay and brings environmental pollution and other social problems. FW shows a high potential to produce methane by anaerobic digestion (AD) due to its high organic content. However, many inhibitors, such as accumulation of ammonia and volatile fatty acids (VFAs), usually result in inefficient performances and even process failure. Microorganisms play an important role in the process of hydrolysis, acidogenesis, acetogenesis and methanogenesis. This review provided a critical summary of microbial characteristics to obtain connects of microbial community structure with operational conditions at various states of AD, such as mesophilic and thermophilic, wet and dry, success and failure, pretreated or not, lab-scale and full-scale. This article emphasizes that it is necessary to analyze changes and mechanisms of microbial communities in unbalanced system and seek efficiency dynamic succession rules of the dominant microorganisms. Copyright © 2017. Published by Elsevier Ltd.

Bacteria-Affinity 3D Macroporous Graphene/MWCNTs/Fe3O4 Foams for High-Performance Microbial Fuel Cells.

PubMed

Song, Rong-Bin; Zhao, Cui-E; Jiang, Li-Ping; Abdel-Halim, Essam Sayed; Zhang, Jian-Rong; Zhu, Jun-Jie

2016-06-29

Promoting the performance of microbial fuel cells (MFCs) relies heavily on the structure design and composition tailoring of electrode materials. In this work, three-dimensional (3D) macroporous graphene foams incorporated with intercalated spacer of multiwalled carbon nanotubes (MWCNTs) and bacterial anchor of Fe3O4 nanospheres (named as G/MWCNTs/Fe3O4 foams) were first synthesized and used as anodes for Shewanella-inoculated microbial fuel cells (MFCs). Thanks to the macroporous structure of 3D graphene foams, the expanded electrode surface by MWCNTs spacing, as well as the high affinity of Fe3O4 nanospheres toward Shewanella oneidensis MR-1, the anode exhibited high bacterial loading capability. In addition to spacing graphene nanosheets for accommodating bacterial cells, MWCNTs paved a smoother way for electron transport in the electrode substrate of MFCs. Meanwhile, the embedded bioaffinity Fe3O4 nanospheres capable of preserving the bacterial metabolic activity provided guarantee for the long-term durability of the MFCs. With these merits, the constructed MFC possessed significantly higher power output and stronger stability than that with conventional graphite rod anode.

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

PubMed

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

2016-06-03

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

Seasonal Changes in Bacterial and Archaeal Gene Expression Patterns across Salinity Gradients in the Columbia River Coastal Margin

PubMed Central

Smith, Maria W.; Herfort, Lydie; Tyrol, Kaitlin; Suciu, Dominic; Campbell, Victoria; Crump, Byron C.; Peterson, Tawnya D.; Zuber, Peter; Baptista, Antonio M.; Simon, Holly M.

2010-01-01

Through their metabolic activities, microbial populations mediate the impact of high gradient regions on ecological function and productivity of the highly dynamic Columbia River coastal margin (CRCM). A 2226-probe oligonucleotide DNA microarray was developed to investigate expression patterns for microbial genes involved in nitrogen and carbon metabolism in the CRCM. Initial experiments with the environmental microarrays were directed toward validation of the platform and yielded high reproducibility in multiple tests. Bioinformatic and experimental validation also indicated that >85% of the microarray probes were specific for their corresponding target genes and for a few homologs within the same microbial family. The validated probe set was used to query gene expression responses by microbial assemblages to environmental variability. Sixty-four samples from the river, estuary, plume, and adjacent ocean were collected in different seasons and analyzed to correlate the measured variability in chemical, physical and biological water parameters to differences in global gene expression profiles. The method produced robust seasonal profiles corresponding to pre-freshet spring (April) and late summer (August). Overall relative gene expression was high in both seasons and was consistent with high microbial abundance measured by total RNA, heterotrophic bacterial production, and chlorophyll a. Both seasonal patterns involved large numbers of genes that were highly expressed relative to background, yet each produced very different gene expression profiles. April patterns revealed high differential gene expression in the coastal margin samples (estuary, plume and adjacent ocean) relative to freshwater, while little differential gene expression was observed along the river-to-ocean transition in August. Microbial gene expression profiles appeared to relate, in part, to seasonal differences in nutrient availability and potential resource competition. Furthermore, our results suggest that highly-active particle-attached microbiota in the Columbia River water column may perform dissimilatory nitrate reduction (both dentrification and DNRA) within anoxic particle microniches. PMID:20967204

Micro-sized microbial fuel cell: a mini-review.

PubMed

Wang, Hsiang-Yu; Bernarda, Angela; Huang, Chih-Yung; Lee, Duu-Jong; Chang, Jo-Shu

2011-01-01

This review presents the development of micro-sized microbial fuel cells (including mL-scale and μL-scale setups), with summarization of their advantageous characteristics, fabrication methods, performances, potential applications and possible future directions. The performance of microbial fuel cells (MFCs) is affected by issues such as mass transport, reaction kinetics and ohmic resistance. These factors are manipulated in micro-sized MFCs using specially allocated electrodes constructed with specified materials having physically or chemically modified surfaces. Both two-chamber and air-breathing cathodes are promising configurations for mL-scale MFCs. However, most of the existing μL-scale MFCs generate significantly lower volumetric power density compared with their mL-counterparts because of the high internal resistance. Although μL-scale MFCs have not yet to provide sufficient power for operating conventional equipment, they show great potential in rapid screening of electrochemically microbes and electrode performance. Additional possible applications and future directions are also provided for the development of micro-sized MFCs. Copyright © 2010 Elsevier Ltd. All rights reserved.

Microbial source tracking in highly vulnerable karst drinking water resources.

PubMed

Diston, D; Robbi, R; Baumgartner, A; Felleisen, R

2018-02-01

Water resources situated in areas with underlying karst geology are particularly vulnerable to fecal pollution. In such vulnerable systems, microbial source tracking (MST) methods are useful tools to elucidate the pathways of both animal and human fecal pollution, leading to more accurate water use risk assessments. Here, we describe the application of a MST toolbox using both culture-dependent bacteriophage and molecular-dependent 16S rRNA assays at spring and well sites in the karstic St Imier Valley, Switzerland. Culture-dependent and molecular-dependent marker performance varied significantly, with the 16S rRNA assays displaying greater sensitivity than their phage counterpart; HF183 was the best performing human wastewater-associated marker while Rum2Bac was the best performing ruminant marker. Differences were observed in pollution regimes between the well and spring sampling sites, with the spring water being more degraded than the well site. Our results inform the choice of marker selection for MST studies and highlight differences in microbial water quality between well and spring karst sites.

High-Fat Diet Consumption Induces Microbiota Dysbiosis and Intestinal Inflammation in Zebrafish.

PubMed

Arias-Jayo, Nerea; Abecia, Leticia; Alonso-Sáez, Laura; Ramirez-Garcia, Andoni; Rodriguez, Alfonso; Pardo, Miguel A

2018-05-07

Energy-dense foods and overnutrition represent major starting points altering lipid metabolism, systemic inflammation and gut microbiota. The aim of this work was to investigate the effects of a high-fat diet (HFD) over a period of 25 days on intestinal microbiota and inflammation in zebrafish. Microbial composition of HFD-fed animals was analysed and compared to controls by 16S rRNA sequencing and quantitative PCR. The expression level on several genes related to inflammation was tested. Furthermore, microscopic assessment of the intestine was performed in both conditions. The consumption of the HFD resulted in microbial dysbiosis, characterised by an increase in the relative abundance of the phylum Bacteroidetes. Moreover, an emerging intestinal inflammation via NF-κβ activation was confirmed by the overexpression of several genes related to signalling receptors, antimicrobial metabolism and the inflammatory cascade. The intestinal barrier was also damaged, with an increase of goblet cell mucin production. This is the first study performed in zebrafish which suggests that the consumption of a diet enriched with 10% fat changes the intestinal microbial community composition, which was correlated with low-grade inflammation.

Improved performance of the microbial electrolysis desalination and chemical-production cell with enlarged anode and high applied voltages.

PubMed

Ye, Bo; Luo, Haiping; Lu, Yaobin; Liu, Guangli; Zhang, Renduo; Li, Xiao

2017-11-01

The aim of this study was to improve performance of the microbial electrolysis desalination and chemical-production cell (MEDCC) using enlarged anode and high applied voltages. MEDCCs with anode lengths of 9 and 48cm (i.e., the 9cm-anode MEDCC and 48cm-anode MEDCC, respectively) were tested under different voltages (1.2-3.0V). Our results demonstrated for the first time that the MEDCC could maintain high performance even under the applied voltage higher than that for water dissociation (i.e., 1.8V). Under the applied voltage of 2.5V, the maximum current density in the 48cm-anode MEDCC reached 32.8±2.6A/m 2 , which is one of the highest current densities reported so far in the bioelectrochemical system (BES). The relative abundance of Geobacter was changed along the anode length. Our results show the great potential of the BES with enlarged anode and high applied voltages. Copyright © 2017 Elsevier Ltd. All rights reserved.

Engineering microbial consortia for controllable outputs

PubMed Central

Lindemann, Stephen R; Bernstein, Hans C; Song, Hyun-Seob; Fredrickson, Jim K; Fields, Matthew W; Shou, Wenying; Johnson, David R; Beliaev, Alexander S

2016-01-01

Much research has been invested into engineering microorganisms to perform desired biotransformations; nonetheless, these efforts frequently fall short of expected results due to the unforeseen effects of biofeedback regulation and functional incompatibility. In nature, metabolic function is compartmentalized into diverse organisms assembled into robust consortia, in which the division of labor is thought to lead to increased community efficiency and productivity. Here we consider whether and how consortia can be designed to perform bioprocesses of interest beyond the metabolic flexibility limitations of a single organism. Advances in post-genomic analysis of microbial consortia and application of high-resolution global measurements now offer the promise of systems-level understanding of how microbial consortia adapt to changes in environmental variables and inputs of carbon and energy. We argue that, when combined with appropriate modeling frameworks, systems-level knowledge can markedly improve our ability to predict the fate and functioning of consortia. Here we articulate our collective perspective on the current and future state of microbial community engineering and control while placing specific emphasis on ecological principles that promote control over community function and emergent properties. PMID:26967105

Engineering microbial consortia for controllable outputs

DOE PAGES

Lindemann, Stephen R.; Bernstein, Hans C.; Song, Hyun -Seob; ...

2016-03-11

In this study, much research has been invested into engineering microorganisms to perform desired biotransformations; nonetheless, these efforts frequently fall short of expected results due to the unforeseen effects of biofeedback regulation and functional incompatibility. In nature, metabolic function is compartmentalized into diverse organisms assembled into robust consortia, in which the division of labor is thought to lead to increased community efficiency and productivity. Here we consider whether and how consortia can be designed to perform bioprocesses of interest beyond the metabolic flexibility limitations of a single organism. Advances in post-genomic analysis of microbial consortia and application of high-resolution globalmore » measurements now offer the promise of systems-level understanding of how microbial consortia adapt to changes in environmental variables and inputs of carbon and energy. We argue that, when combined with appropriate modeling frameworks, systems-level knowledge can markedly improve our ability to predict the fate and functioning of consortia. Here we articulate our collective perspective on the current and future state of microbial community engineering and control while placing specific emphasis on ecological principles that promote control over community function and emergent properties.« less

Bacterial community shift and incurred performance in response to in situ microbial self-assembly graphene and polarity reversion in microbial fuel cell.

PubMed

Chen, Junfeng; Zhang, Lihua; Hu, Yongyou; Huang, Wantang; Niu, Zhuyu; Sun, Jian

2017-10-01

In this work, bacterial community shift and incurred performance of graphene modified bioelectrode (GM-BE) in microbial fuel cell (MFC) were illustrated by high throughput sequencing technology and electrochemical analysis. The results showed that Firmicutes occupied 48.75% in graphene modified bioanode (GM-BA), while Proteobacteria occupied 62.99% in graphene modified biocathode (GM-BC), both were dominant bacteria in phylum level respectively. Typical exoelectrogens, including Geobacter, Clostridium, Pseudomonas, Geothrix and Hydrogenophaga, were counted 26.66% and 17.53% in GM-BA and GM-BC. GM-BE was tended to decrease the bacterial diversity and enrich the dominant species. Because of the enrichment of exoelectrogens and excellent electrical conductivity of graphene, the maximum power density of MFC with GM-BA and GM-BC increased 33.1% and 21.6% respectively, and the transfer resistance decreased 83.8% and 73.6% compared with blank bioelectrode. This study aimed to enrich the microbial study in MFC and broaden the development and application for bioelectrode. Copyright © 2017 Elsevier Ltd. All rights reserved.

Carbon materials derived from waste tires as high-performance anodes in microbial fuel cells.

PubMed

Chen, Wei; Feng, Huajun; Shen, Dongsheng; Jia, Yufeng; Li, Na; Ying, Xianbin; Chen, Ting; Zhou, Yuyang; Guo, Jiayun; Zhou, Mengjiao

2018-03-15

In this study, carbonized waste tires were directly used as a high-performance anode material in microbial fuel cells (MFCs). The effect of the pyrolysis temperature used for waste tire carbonization on the current output performance was investigated to determine the optimal pyrolysis temperature. Thermal gravimetric analysis/differential scanning calorimetry showed that tire carbonization started at 200°C and ended at about 500°C; the weight loss was about 64%. When used in an MFC, the electrode obtained from waste tires carbonized at 800°C gave a current density of 23.1±1.4Am -2 , which is much higher than that achieved with traditional graphite felt anodes (5.5±0.1Am -2 ). The results of this study will be useful in optimizing the design of carbonized waste tire anodes for enhancing MFC performances and will alleviate the environmental problems caused by waste tires. Copyright © 2017 Elsevier B.V. All rights reserved.

Microbial community redundancy in anaerobic digestion drives process recovery after salinity exposure.

PubMed

De Vrieze, Jo; Christiaens, Marlies E R; Walraedt, Diego; Devooght, Arno; Ijaz, Umer Zeeshan; Boon, Nico

2017-03-15

Anaerobic digestion of high-salinity wastewaters often results in process inhibition due to the susceptibility of the methanogenic archaea. The ability of the microbial community to deal with increased salinity levels is of high importance to ensure process perseverance or recovery after failure. The exact strategy of the microbial community to ensure process endurance is, however, often unknown. In this study, we investigated how the microbial community is able to recover process performance following a disturbance through the application of high-salinity molasses wastewater. After a stable start-up, methane production quickly decreased from 625 ± 17 to 232 ± 35 mL CH 4 L -1 d -1 with a simultaneous accumulation in volatile fatty acids up to 20.5 ± 1.4 g COD L -1 , indicating severe process disturbance. A shift in feedstock from molasses wastewater to waste activated sludge resulted in complete process recovery. However, the bacterial and archaeal communities did not return to their original composition as before the disturbance, despite similar process conditions. Microbial community diversity was recovered to similar levels as before disturbance, which indicates that the metabolic potential of the community was maintained. A mild increase in ammonia concentration after process recovery did not influence methane production, indicating a well-balanced microbial community. Hence, given the change in community composition following recovery after salinity disturbance, it can be assumed that microbial community redundancy was the major strategy to ensure the continuation of methane production, without loss of functionality or metabolic flexibility. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Bacterial cellulose-polyaniline nano-biocomposite: A porous media hydrogel bioanode enhancing the performance of microbial fuel cell

NASA Astrophysics Data System (ADS)

Mashkour, Mehrdad; Rahimnejad, Mostafa; Mashkour, Mahdi

2016-09-01

Microbial fuel cells (MFCs) are one of the possible renewable energy supplies which microorganisms play an active role in bio-oxidize reactions of a substrate such as glucose. Electrode materials and surface modifications are highly effective tools in enhancing MFCs' Performance. In this study, new composite anodes are fabricated. Bacterial cellulose (BC) is used as continuous phase and polyaniline (PANI) as dispersed one which is synthesized by in situ chemical oxidative polymerization on BC's fibers. With hydrogel nature of BC as a novel feature and polyaniline conductivity there meet the favorable conditions to obtain an active microbial biofilm on anode surface. Maximum power density of 117.76 mW/m2 in current density of 617 mA/m2 is achieved for BC/PANI anode. The amounts demonstrate a considerable enhancement compared with graphite plate (1 mW/m2 and 10 mA/m2).

Microbial communities associated with wet flue gas desulfurization systems

PubMed Central

Brown, Bryan P.; Brown, Shannon R.; Senko, John M.

2012-01-01

Flue gas desulfurization (FGD) systems are employed to remove SOx gasses that are produced by the combustion of coal for electric power generation, and consequently limit acid rain associated with these activities. Wet FGDs represent a physicochemically extreme environment due to the high operating temperatures and total dissolved solids (TDS) of fluids in the interior of the FGD units. Despite the potential importance of microbial activities in the performance and operation of FGD systems, the microbial communities associated with them have not been evaluated. Microbial communities associated with distinct process points of FGD systems at several coal-fired electricity generation facilities were evaluated using culture-dependent and -independent approaches. Due to the high solute concentrations and temperatures in the FGD absorber units, culturable halothermophilic/tolerant bacteria were more abundant in samples collected from within the absorber units than in samples collected from the makeup waters that are used to replenish fluids inside the absorber units. Evaluation of bacterial 16S rRNA genes recovered from scale deposits on the walls of absorber units revealed that the microbial communities associated with these deposits are primarily composed of thermophilic bacterial lineages. These findings suggest that unique microbial communities develop in FGD systems in response to physicochemical characteristics of the different process points within the systems. The activities of the thermophilic microbial communities that develop within scale deposits could play a role in the corrosion of steel structures in FGD systems. PMID:23226147

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.

Construction of PAH-degrading mixed microbial consortia by induced selection in soil.

PubMed

Zafra, German; Absalón, Ángel E; Anducho-Reyes, Miguel Ángel; Fernandez, Francisco J; Cortés-Espinosa, Diana V

2017-04-01

Bioremediation of polycyclic aromatic hydrocarbons (PAHs)-contaminated soils through the biostimulation and bioaugmentation processes can be a strategy for the clean-up of oil spills and environmental accidents. In this work, an induced microbial selection method using PAH-polluted soils was successfully used to construct two microbial consortia exhibiting high degradation levels of low and high molecular weight PAHs. Six fungal and seven bacterial native strains were used to construct mixed consortia with the ability to tolerate high amounts of phenanthrene (Phe), pyrene (Pyr) and benzo(a)pyrene (BaP) and utilize these compounds as a sole carbon source. In addition, we used two engineered PAH-degrading fungal strains producing heterologous ligninolytic enzymes. After a previous selection using microbial antagonism tests, the selection was performed in microcosm systems and monitored using PCR-DGGE, CO 2 evolution and PAH quantitation. The resulting consortia (i.e., C1 and C2) were able to degrade up to 92% of Phe, 64% of Pyr and 65% of BaP out of 1000 mg kg -1 of a mixture of Phe, Pyr and BaP (1:1:1) after a two-week incubation. The results indicate that constructed microbial consortia have high potential for soil bioremediation by bioaugmentation and biostimulation and may be effective for the treatment of sites polluted with PAHs due to their elevated tolerance to aromatic compounds, their capacity to utilize them as energy source. Copyright © 2016 Elsevier Ltd. All rights reserved.

Study of Electrochemical Reduction of CO2 for Future Use in Secondary Microbial Electrochemical Technologies.

PubMed

Gimkiewicz, Carla; Hegner, Richard; Gutensohn, Mareike F; Koch, Christin; Harnisch, Falk

2017-03-09

The fluctuation and decentralization of renewable energy have triggered the search for respective energy storage and utilization. At the same time, a sustainable bioeconomy calls for the exploitation of CO 2 as feedstock. Secondary microbial electrochemical technologies (METs) allow both challenges to be tackled because the electrochemical reduction of CO 2 can be coupled with microbial synthesis. Because this combination creates special challenges, the electrochemical reduction of CO 2 was investigated under conditions allowing microbial conversions, that is, for their future use in secondary METs. A reproducible electrodeposition procedure of In on a graphite backbone allowed a systematic study of formate production from CO 2 with a high number of replicates. Coulomb efficiencies and formate production rates of up to 64.6±6.8 % and 0.013±0.002 mmol formate  h -1  cm -2 , respectively, were achieved. Electrode redeposition, reusability, and long-term performance were investigated. Furthermore, the effect of components used in microbial media, that is, yeast extract, trace elements, and phosphate salts, on the electrode performance was addressed. The results demonstrate that the integration of electrochemical reduction of CO 2 in secondary METs can become technologically relevant. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

High-resolution phylogenetic microbial community profiling

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

Singer, Esther; Coleman-Derr, Devin; Bowman, Brett

2014-03-17

The representation of bacterial and archaeal genome sequences is strongly biased towards cultivated organisms, which belong to merely four phylogenetic groups. Functional information and inter-phylum level relationships are still largely underexplored for candidate phyla, which are often referred to as microbial dark matter. Furthermore, a large portion of the 16S rRNA gene records in the GenBank database are labeled as environmental samples and unclassified, which is in part due to low read accuracy, potential chimeric sequences produced during PCR amplifications and the low resolution of short amplicons. In order to improve the phylogenetic classification of novel species and advance ourmore » knowledge of the ecosystem function of uncultivated microorganisms, high-throughput full length 16S rRNA gene sequencing methodologies with reduced biases are needed. We evaluated the performance of PacBio single-molecule real-time (SMRT) sequencing in high-resolution phylogenetic microbial community profiling. For this purpose, we compared PacBio and Illumina metagenomic shotgun and 16S rRNA gene sequencing of a mock community as well as of an environmental sample from Sakinaw Lake, British Columbia. Sakinaw Lake is known to contain a large age of microbial species from candidate phyla. Sequencing results show that community structure based on PacBio shotgun and 16S rRNA gene sequences is highly similar in both the mock and the environmental communities. Resolution power and community representation accuracy from SMRT sequencing data appeared to be independent of GC content of microbial genomes and was higher when compared to Illumina-based metagenome shotgun and 16S rRNA gene (iTag) sequences, e.g. full-length sequencing resolved all 23 OTUs in the mock community, while iTags did not resolve closely related species. SMRT sequencing hence offers various potential benefits when characterizing uncharted microbial communities.« less

Metagenome-scale analysis yields insights into the structure and function of microbial communities in a copper bioleaching heap.

PubMed

Zhang, Xian; Niu, Jiaojiao; Liang, Yili; Liu, Xueduan; Yin, Huaqun

2016-01-19

Metagenomics allows us to acquire the potential resources from both cultivatable and uncultivable microorganisms in the environment. Here, shotgun metagenome sequencing was used to investigate microbial communities from the surface layer of low grade copper tailings that were industrially bioleached at the Dexing Copper Mine, China. A bioinformatics analysis was further performed to elucidate structural and functional properties of the microbial communities in a copper bioleaching heap. Taxonomic analysis revealed unexpectedly high microbial biodiversity of this extremely acidic environment, as most sequences were phylogenetically assigned to Proteobacteria, while Euryarchaeota-related sequences occupied little proportion in this system, assuming that Archaea probably played little role in the bioleaching systems. At the genus level, the microbial community in mineral surface-layer was dominated by the sulfur- and iron-oxidizing acidophiles such as Acidithiobacillus-like populations, most of which were A. ferrivorans-like and A. ferrooxidans-like groups. In addition, Caudovirales were the dominant viral type observed in this extremely environment. Functional analysis illustrated that the principal participants related to the key metabolic pathways (carbon fixation, nitrogen metabolism, Fe(II) oxidation and sulfur metabolism) were mainly identified to be Acidithiobacillus-like, Thiobacillus-like and Leptospirillum-like microorganisms, indicating their vital roles. Also, microbial community harbored certain adaptive mechanisms (heavy metal resistance, low pH adaption, organic solvents tolerance and detoxification of hydroxyl radicals) as they performed their functions in the bioleaching system. Our study provides several valuable datasets for understanding the microbial community composition and function in the surface-layer of copper bioleaching heap.

GPU-Meta-Storms: computing the structure similarities among massive amount of microbial community samples using GPU.

PubMed

Su, Xiaoquan; Wang, Xuetao; Jing, Gongchao; Ning, Kang

2014-04-01

The number of microbial community samples is increasing with exponential speed. Data-mining among microbial community samples could facilitate the discovery of valuable biological information that is still hidden in the massive data. However, current methods for the comparison among microbial communities are limited by their ability to process large amount of samples each with complex community structure. We have developed an optimized GPU-based software, GPU-Meta-Storms, to efficiently measure the quantitative phylogenetic similarity among massive amount of microbial community samples. Our results have shown that GPU-Meta-Storms would be able to compute the pair-wise similarity scores for 10 240 samples within 20 min, which gained a speed-up of >17 000 times compared with single-core CPU, and >2600 times compared with 16-core CPU. Therefore, the high-performance of GPU-Meta-Storms could facilitate in-depth data mining among massive microbial community samples, and make the real-time analysis and monitoring of temporal or conditional changes for microbial communities possible. GPU-Meta-Storms is implemented by CUDA (Compute Unified Device Architecture) and C++. Source code is available at http://www.computationalbioenergy.org/meta-storms.html.

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

PubMed

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

2018-01-01

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

Effect of Substrate Conversion on Performance of Microbial Fuel Cells and Anodic Microbial Communities.

PubMed

Zhao, Yang-Guo; Zhang, Yi; She, Zonglian; Shi, Yue; Wang, Min; Gao, Mengchun; Guo, Liang

2017-09-01

Performance of microbial fuel cells (MFCs) was monitored during the influent nutrient change from lactate to glucose/acetate/propionate and then to lactate. Meanwhile, anodic microbial communities were characterized by culture-independent molecular biotechnologies. Results showed MFC performance recovered rapidly when the lactate was replaced by one of its metabolic intermediates acetate, while it needed a longer time to recover if lactate substrate was converted to glucose/propionate or acetate to lactate. Secondary lactate feed enhanced the enrichment of bacterial populations dominating in first lactate feed. Electricity-producing bacteria, Geobacter spp., and beneficial helpers, Anaeromusa spp. and Pseudomonas spp., revived from a low abundance as lactate secondary supply, but microbial communities were hard to achieve former profiles in structure and composition. Hence, microbial community profiles tended to recover when outside environmental condition were restored. Different substrates selected unique functional microbial populations.

Effect of UV on De-NOx performance and microbial community of a hybrid catalytic membrane biofilm reactor

NASA Astrophysics Data System (ADS)

Chen, Zhouyang; Huang, Zhensha; He, Yiming; Xiao, Xiaoliang; Wei, Zaishan

2018-02-01

The hybrid membrane catalytic biofilm reactor provides a new way of flue gas denitration. However, the effects of UV on denitrification performance, microbial community and microbial nitrogen metabolism are still unknown. In this study, the effects of UV on deNO x performance, nitrification and denitrification, microbial community and microbial nitrogen metabolism of a bench scale N-TiO2/PSF hybrid catalytic membrane biofilm reactor (HCMBR) were evaluated. The change from nature light to UV in the HCMBR leads to the fall of NO removal efficiency of HCMBR from 92.8% to 81.8%. UV affected the microbial community structure, but did not change microbial nitrogen metabolism, as shown by metagenomics sequencing method. Some dominant phyla, such as Gammaproteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, and Alphaproteobacteria, increased in abundance, whereas others, such as Proteobacteria and Betaproteobacteria, decreased. There were nitrification, denitrification, nitrogen fixation, and organic nitrogen metabolism in the HCMBR.

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

NASA Astrophysics Data System (ADS)

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

2015-08-01

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

The Biogeography of Putative Microbial Antibiotic Production

PubMed Central

Bryant, Jessica A.; Charkoudian, Louise K.; Docherty, Kathryn M.; Jones, Evan; Kembel, Steven W.; Green, Jessica L.; Bohannan, Brendan J. M.

2015-01-01

Understanding patterns in the distribution and abundance of functional traits across a landscape is of fundamental importance to ecology. Mapping these distributions is particularly challenging for species-rich groups with sparse trait measurement coverage, such as flowering plants, insects, and microorganisms. Here, we use likelihood-based character reconstruction to infer and analyze the spatial distribution of unmeasured traits. We apply this framework to a microbial dataset comprised of 11,732 ketosynthase alpha gene sequences extracted from 144 soil samples from three continents to document the spatial distribution of putative microbial polyketide antibiotic production. Antibiotic production is a key competitive strategy for soil microbial survival and performance. Additionally, novel antibiotic discovery is highly relevant to human health, making natural antibiotic production by soil microorganisms a major target for bioprospecting. Our comparison of trait-based biogeographical patterns to patterns based on taxonomy and phylogeny is relevant to our basic understanding of microbial biogeography as well as the pressing need for new antibiotics. PMID:26102275

Effects of organic loading rates on reactor performance and microbial community changes during thermophilic aerobic digestion process of high-strength food wastewater.

PubMed

Jang, Hyun Min; Lee, Jae Won; Ha, Jeong Hyub; Park, Jong Moon

2013-11-01

To evaluate the applicability of single-stage thermophilic aerobic digestion (TAD) process treating high-strength food wastewater (FWW), TAD process was operated at four organic loading rates (OLRs) from 9.2 to 37.2 kg COD/m(3)d. The effects of OLRs on microbial community changes were also examined. The highest volumetric removal rate (13.3 kg COD/m(3)d) and the highest thermo-stable protease activity (0.95 unit/mL) were detected at OLR=18.6 kg COD/m(3)d. Denaturing gradient gel electrophoresis (DGGE) profiles and quantitative PCR (qPCR) results showed significant microbial community shifts in response to changes in OLR. In particular, DGGE and phylogenetic analysis demonstrate that the presence of Bacillus sp. (phylum of Firmicutes) was strongly correlated with efficient removal of organic particulates from high-strength food wastewater. Copyright © 2013 Elsevier Ltd. All rights reserved.

Changes in microbial community structures due to varying operational conditions in the anaerobic digestion of oxytetracycline-medicated cow manure.

PubMed

Turker, Gokhan; Aydin, Sevcan; Akyol, Çağrı; Yenigun, Orhan; Ince, Orhan; Ince, Bahar

2016-07-01

Management of manure containing veterinary antibiotics is a major concern in anaerobic treatment systems because of their possible adverse effects on microbial communities. Therefore, the aim of study was to investigate how oxytetracycline (OTC) influences bacteria and acetoclastic and hydrogenotrophic methanogens under varying operational conditions in OTC-medicated and non-medicated anaerobic cow manure digesters. Concentrations of OTC and its metabolites throughout the anaerobic digestion were determined using ultraviolet-high-performance liquid chromatography (UV-HPLC) and tandem liquid chromatography-mass spectrometry (LC/MS/MS), respectively. Fluorescent in situ hybridization, denaturing gradient gel electrophoresis, cloning, and sequencing analyses were used to monitor changes in microbial community structures. According to the results of analytical and molecular approaches, operating conditions highly influence active microbial community dynamics and associate with biogas production and elimination of OTC and its metabolites during anaerobic digestion of cow manure in the presence of an average initial concentration of 2.2 mg OTC/L. The impact of operating conditions has a drastic effect on acetoclastic methanogens than hydrogenotrophic methanogens and bacteria.

Development and validation of a citrate synthase directed quantitative PCR marker for soil bacterial communities

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

Castro Gonzalez, Hector F; Classen, Aimee T; Austin, Emily E

2012-01-01

Molecular innovations in microbial ecology are allowing scientists to correlate microbial community characteristics to a variety of ecosystem functions. However, to date the majority of soil microbial ecology studies target phylogenetic rRNA markers, while a smaller number target functional markers linked to soil processes. We validated a new primer set targeting citrate synthase (gtlA), a central enzyme in the citric acid cycle linked to aerobic respiration. Primers for a 225 bp fragment suitable for qPCR were tested for specificity and assay performance verified on multiple soils. Clone libraries of the PCR-amplified gtlA gene exhibited high diversity and recovered most majormore » groups identified in a previous 16S rRNA gene study. Comparisons among bacterial communities based on gtlA sequencing using UniFrac revealed differences among the experimental soils studied. Conditions for gtlA qPCR were optimized and calibration curves were highly linear (R2 > 0.99) over six orders of magnitude (4.56 10^5 to 4.56 10^11 copies), with high amplification efficiencies (>1.7). We examined the performance of the gtlA qPCR across a variety of soils and ecosystems, spanning forests, old fields and agricultural areas. We were able to amplify gtlA genes in all tested soils, and detected differences in gtlA abundance within and among environments. These results indicate that a fully developed gtlA-targeted qPCR approach may have potential to link microbial community characteristics with changes in soil respiration.« less

High Acetic Acid Production Rate Obtained by Microbial Electrosynthesis from Carbon Dioxide.

PubMed

Jourdin, Ludovic; Grieger, Timothy; Monetti, Juliette; Flexer, Victoria; Freguia, Stefano; Lu, Yang; Chen, Jun; Romano, Mark; Wallace, Gordon G; Keller, Jurg

2015-11-17

High product specificity and production rate are regarded as key success parameters for large-scale applicability of a (bio)chemical reaction technology. Here, we report a significant performance enhancement in acetate formation from CO2, reaching comparable productivity levels as in industrial fermentation processes (volumetric production rate and product yield). A biocathode current density of -102 ± 1 A m(-2) and an acetic acid production rate of 685 ± 30 (g m(-2) day(-1)) have been achieved in this study. High recoveries of 94 ± 2% of the CO2 supplied as the sole carbon source and 100 ± 4% of electrons into the final product (acetic acid) were achieved after development of a mature biofilm, reaching an elevated product titer of up to 11 g L(-1). This high product specificity is remarkable for mixed microbial cultures, which would make the product downstream processing easier and the technology more attractive. This performance enhancement was enabled through the combination of a well-acclimatized and enriched microbial culture (very fast start-up after culture transfer), coupled with the use of a newly synthesized electrode material, EPD-3D. The throwing power of the electrophoretic deposition technique, a method suitable for large-scale production, was harnessed to form multiwalled carbon nanotube coatings onto reticulated vitreous carbon to generate a hierarchical porous structure.

Anaerobic Methane Oxidation Driven by Microbial Reduction of Natural Organic Matter in a Tropical Wetland

PubMed Central

Valenzuela, Edgardo I.; Prieto-Davó, Alejandra; López-Lozano, Nguyen E.; Hernández-Eligio, Alberto; Vega-Alvarado, Leticia; Juárez, Katy; García-González, Ana Sarahí; López, Mercedes G.

2017-01-01

ABSTRACT Wetlands constitute the main natural source of methane on Earth due to their high content of natural organic matter (NOM), but key drivers, such as electron acceptors, supporting methanotrophic activities in these habitats are poorly understood. We performed anoxic incubations using freshly collected sediment, along with water samples harvested from a tropical wetland, amended with 13C-methane (0.67 atm) to test the capacity of its microbial community to perform anaerobic oxidation of methane (AOM) linked to the reduction of the humic fraction of its NOM. Collected evidence demonstrates that electron-accepting functional groups (e.g., quinones) present in NOM fueled AOM by serving as a terminal electron acceptor. Indeed, while sulfate reduction was the predominant process, accounting for up to 42.5% of the AOM activities, the microbial reduction of NOM concomitantly occurred. Furthermore, enrichment of wetland sediment with external NOM provided a complementary electron-accepting capacity, of which reduction accounted for ∼100 nmol 13CH4 oxidized · cm−3 · day−1. Spectroscopic evidence showed that quinone moieties were heterogeneously distributed in the wetland sediment, and their reduction occurred during the course of AOM. Moreover, an enrichment derived from wetland sediments performing AOM linked to NOM reduction stoichiometrically oxidized methane coupled to the reduction of the humic analogue anthraquinone-2,6-disulfonate. Microbial populations potentially involved in AOM coupled to microbial reduction of NOM were dominated by divergent biota from putative AOM-associated archaea. We estimate that this microbial process potentially contributes to the suppression of up to 114 teragrams (Tg) of CH4 · year−1 in coastal wetlands and more than 1,300 Tg · year−1, considering the global wetland area. IMPORTANCE The identification of key processes governing methane emissions from natural systems is of major importance considering the global warming effects triggered by this greenhouse gas. Anaerobic oxidation of methane (AOM) coupled to the microbial reduction of distinct electron acceptors plays a pivotal role in mitigating methane emissions from ecosystems. Given their high organic content, wetlands constitute the largest natural source of atmospheric methane. Nevertheless, processes controlling methane emissions in these environments are poorly understood. Here, we provide tracer analysis with 13CH4 and spectroscopic evidence revealing that AOM linked to the microbial reduction of redox functional groups in natural organic matter (NOM) prevails in a tropical wetland. We suggest that microbial reduction of NOM may largely contribute to the suppression of methane emissions from tropical wetlands. This is a novel avenue within the carbon cycle in which slowly decaying NOM (e.g., humic fraction) in organotrophic environments fuels AOM by serving as a terminal electron acceptor. PMID:28341676

Anaerobic Methane Oxidation Driven by Microbial Reduction of Natural Organic Matter in a Tropical Wetland.

PubMed

Valenzuela, Edgardo I; Prieto-Davó, Alejandra; López-Lozano, Nguyen E; Hernández-Eligio, Alberto; Vega-Alvarado, Leticia; Juárez, Katy; García-González, Ana Sarahí; López, Mercedes G; Cervantes, Francisco J

2017-06-01

Wetlands constitute the main natural source of methane on Earth due to their high content of natural organic matter (NOM), but key drivers, such as electron acceptors, supporting methanotrophic activities in these habitats are poorly understood. We performed anoxic incubations using freshly collected sediment, along with water samples harvested from a tropical wetland, amended with 13 C-methane (0.67 atm) to test the capacity of its microbial community to perform anaerobic oxidation of methane (AOM) linked to the reduction of the humic fraction of its NOM. Collected evidence demonstrates that electron-accepting functional groups (e.g., quinones) present in NOM fueled AOM by serving as a terminal electron acceptor. Indeed, while sulfate reduction was the predominant process, accounting for up to 42.5% of the AOM activities, the microbial reduction of NOM concomitantly occurred. Furthermore, enrichment of wetland sediment with external NOM provided a complementary electron-accepting capacity, of which reduction accounted for ∼100 nmol 13 CH 4 oxidized · cm -3 · day -1 Spectroscopic evidence showed that quinone moieties were heterogeneously distributed in the wetland sediment, and their reduction occurred during the course of AOM. Moreover, an enrichment derived from wetland sediments performing AOM linked to NOM reduction stoichiometrically oxidized methane coupled to the reduction of the humic analogue anthraquinone-2,6-disulfonate. Microbial populations potentially involved in AOM coupled to microbial reduction of NOM were dominated by divergent biota from putative AOM-associated archaea. We estimate that this microbial process potentially contributes to the suppression of up to 114 teragrams (Tg) of CH 4 · year -1 in coastal wetlands and more than 1,300 Tg · year -1 , considering the global wetland area. IMPORTANCE The identification of key processes governing methane emissions from natural systems is of major importance considering the global warming effects triggered by this greenhouse gas. Anaerobic oxidation of methane (AOM) coupled to the microbial reduction of distinct electron acceptors plays a pivotal role in mitigating methane emissions from ecosystems. Given their high organic content, wetlands constitute the largest natural source of atmospheric methane. Nevertheless, processes controlling methane emissions in these environments are poorly understood. Here, we provide tracer analysis with 13 CH 4 and spectroscopic evidence revealing that AOM linked to the microbial reduction of redox functional groups in natural organic matter (NOM) prevails in a tropical wetland. We suggest that microbial reduction of NOM may largely contribute to the suppression of methane emissions from tropical wetlands. This is a novel avenue within the carbon cycle in which slowly decaying NOM (e.g., humic fraction) in organotrophic environments fuels AOM by serving as a terminal electron acceptor. Copyright © 2017 American Society for Microbiology.

Development of biosensors and their application in metabolic engineering.

PubMed

Zhang, Jie; Jensen, Michael K; Keasling, Jay D

2015-10-01

In a sustainable bioeconomy, many commodities and high value chemicals, including pharmaceuticals, will be manufactured using microbial cell factories from renewable feedstocks. These cell factories can be efficiently generated by constructing libraries of diversified genomes followed by screening for the desired phenotypes. However, methods available for microbial genome diversification far exceed our ability to screen and select for those variants with optimal performance. Genetically encoded biosensors have shown the potential to address this gap, given their ability to respond to small molecule binding and ease of implementation with high-throughput analysis. Here we describe recent progress in biosensor development and their applications in a metabolic engineering context. We also highlight examples of how biosensors can be integrated with synthetic circuits to exert feedback regulation on the metabolism for improved performance of cell factories. Copyright © 2015 Elsevier Ltd. All rights reserved.

Metal-Organic-Framework-Derived Dual Metal- and Nitrogen-Doped Carbon as Efficient and Robust Oxygen Reduction Reaction Catalysts for Microbial Fuel Cells.

PubMed

Tang, Haolin; Cai, Shichang; Xie, Shilei; Wang, Zhengbang; Tong, Yexiang; Pan, Mu; Lu, Xihong

2016-02-01

A new class of dual metal and N doped carbon catalysts with well-defined porous structure derived from metal-organic frameworks (MOFs) has been developed as a high-performance electrocatalyst for oxygen reduction reaction (ORR). Furthermore, the microbial fuel cell (MFC) device based on the as-prepared Ni/Co and N codoped carbon as air cathode catalyst achieves a maximum power density of 4335.6 mW m -2 and excellent durability.

Developing a modified preservative efficacy testing approach as a predictive tool for the evaluation of preservative systems in liquid home care products under variable test conditions.

PubMed

Hoyt, Anne L; Bushman, Don; Lewis, Nathan; Faber, Robert

2012-01-01

How can a formulator have confidence that a preservative system will perform as expected under adverse conditions? Extreme conditions that can lead to the development of "off odors" in the product can be a serious challenge for companies providing home care products in the global market. Formulation and stability testing occur under controlled parameters that simulate limited environmental conditions and microbial challenges are typically performed with a standard inoculum level. While this is an acceptable and dependable process, it does not necessarily assess how well a preservative system can perform under extreme environmental conditions or against unusually high levels of bacterial challenges. This is especially true when formulations are diluted and stored by the end-user. By modifying microbial challenge testing of a liquid dishwashing product to include unexpected dilution schemes, increased microbial assaults, and elevated temperatures, a pattern of preservative efficacy was established. The resulting approach proved to be a useful tool when developing use directions, recommended dilution levels, the overall surfactant system, preservative type, and storage restrictions.

The function of advanced treatment process in a drinking water treatment plant with organic matter-polluted source water.

PubMed

Lin, Huirong; Zhang, Shuting; Zhang, Shenghua; Lin, Wenfang; Yu, Xin

2017-04-01

To understand the relationship between chemical and microbial treatment at each treatment step, as well as the relationship between microbial community structure in biofilms in biofilters and their ecological functions, a drinking water plant with severe organic matter-polluted source water was investigated. The bacterial community dynamics of two drinking water supply systems (traditional and advanced treatment processes) in this plant were studied from the source to the product water. Analysis by 454 pyrosequencing was conducted to characterize the bacterial diversity in each step of the treatment processes. The bacterial communities in these two treatment processes were highly diverse. Proteobacteria, which mainly consisted of beta-proteobacteria, was the dominant phylum. The two treatment processes used in the plant could effectively remove organic pollutants and microbial polution, especially the advanced treatment process. Significant differences in the detection of the major groups were observed in the product water samples in the treatment processes. The treatment processes, particularly the biological pretreatment and O 3 -biological activated carbon in the advanced treatment process, highly influenced the microbial community composition and the water quality. Some opportunistic pathogens were found in the water. Nitrogen-relative microorganisms found in the biofilm of filters may perform an important function on the microbial community composition and water quality improvement.

Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage.

PubMed

Chen, Lin-xing; Hu, Min; Huang, Li-nan; Hua, Zheng-shuang; Kuang, Jia-liang; Li, Sheng-jin; Shu, Wen-sheng

2015-07-01

The microbial communities in acid mine drainage have been extensively studied to reveal their roles in acid generation and adaption to this environment. Lacking, however, are integrated community- and organism-wide comparative gene transcriptional analyses that could reveal the response and adaptation mechanisms of these extraordinary microorganisms to different environmental conditions. In this study, comparative metagenomics and metatranscriptomics were performed on microbial assemblages collected from four geochemically distinct acid mine drainage (AMD) sites. Taxonomic analysis uncovered unexpectedly high microbial biodiversity of these extremely acidophilic communities, and the abundant taxa of Acidithiobacillus, Leptospirillum and Acidiphilium exhibited high transcriptional activities. Community-wide comparative analyses clearly showed that the AMD microorganisms adapted to the different environmental conditions via regulating the expression of genes involved in multiple in situ functional activities, including low-pH adaptation, carbon, nitrogen and phosphate assimilation, energy generation, environmental stress resistance, and other functions. Organism-wide comparative analyses of the active taxa revealed environment-dependent gene transcriptional profiles, especially the distinct strategies used by Acidithiobacillus ferrivorans and Leptospirillum ferrodiazotrophum in nutrients assimilation and energy generation for survival under different conditions. Overall, these findings demonstrate that the gene transcriptional profiles of AMD microorganisms are closely related to the site physiochemical characteristics, providing clues into the microbial response and adaptation mechanisms in the oligotrophic, extremely acidic environments.

Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation

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

Xu, M.; Wu, W.-M.; Wu, L.

2010-02-15

A pilot-scale field test system with an inner loop nested within an outer loop was constructed for in situ U(VI) bioremediation at a US Department of Energy site, Oak Ridge, TN. The outer loop was used for hydrological protection of the inner loop where ethanol was injected for biostimulation of microorganisms for U(VI) reduction/immobilization. After 2 years of biostimulation with ethanol, U(VI) levels were reduced to below drinking water standard (<30 {micro}gl{sup -1}) in the inner loop monitoring wells. To elucidate the microbial community structure and functions under in situ uranium bioremediation conditions, we used a comprehensive functional gene arraymore » (GeoChip) to examine the microbial functional gene composition of the sediment samples collected from both inner and outer loop wells. Our study results showed that distinct microbial communities were established in the inner loop wells. Also, higher microbial functional gene number, diversity and abundance were observed in the inner loop wells than the outer loop wells. In addition, metal-reducing bacteria, such as Desulfovibrio, Geobacter, Anaeromyxobacter and Shewanella, and other bacteria, for example, Rhodopseudomonas and Pseudomonas, are highly abundant in the inner loop wells. Finally, the richness and abundance of microbial functional genes were highly correlated with the mean travel time of groundwater from the inner loop injection well, pH and sulfate concentration in groundwater. These results suggest that the indigenous microbial communities can be successfully stimulated for U bioremediation in the groundwater ecosystem, and their structure and performance can be manipulated or optimized by adjusting geochemical and hydrological conditions.« less

The Effect of a Reduction in Microbial Diversity on Greenhouse Gas Production in Alaskan Tundra Soils.

NASA Astrophysics Data System (ADS)

Wagner, R.; Oechel, W. C.; Lipson, D.

2017-12-01

Atmospheric methane accounts for 20% of the warming potential of all greenhouse gases, has increased by 150% since pre-industrial times, and has the potential to double again over the next century. Microbially mediated CH4 emissions from natural wetlands represent the highest uncertainty in relative contributions to atmospheric CH4 levels of all CH4 sources, with Arctic wetlands currently experiencing twice the rate of warming as the rest of the planet. Notwithstanding the central role that the soil microbial community plays, and the high uncertainty in CH4 emissions from this ecosystem, surprisingly little research has been done to directly connect the microbial community structure to methane production rates. This is especially disconcerting given that most current CH4 emission models completely neglect microbial characteristics, despite the fact that the soil microbial community is predicted to be heavily impacted by a changing climate. Here, the effect of an artificial reduction in soil microbial α-diversity was investigated with regard to methane production and respiration rates. The microbial community was serially diluted followed by re-inoculation of sterilized Arctic soils in a mesocosm experiment. Methane production and respiration rates were measured, metagenomic sequencing was performed to determine microbial community diversity measures, and the effect of the oxidation state of iron was investigated. Preliminary results indicate that microbial communities with reduced α-diversity have lowered respiration rates in these soils. Analyses are ongoing and are expected to provide critical observations linking the role of soil microbial community diversity and greenhouse gas production in Arctic tundra ecosystems.

GI-POP: a combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects.

PubMed

Lee, Chi-Ching; Chen, Yi-Ping Phoebe; Yao, Tzu-Jung; Ma, Cheng-Yu; Lo, Wei-Cheng; Lyu, Ping-Chiang; Tang, Chuan Yi

2013-04-10

Sequencing of microbial genomes is important because of microbial-carrying antibiotic and pathogenetic activities. However, even with the help of new assembling software, finishing a whole genome is a time-consuming task. In most bacteria, pathogenetic or antibiotic genes are carried in genomic islands. Therefore, a quick genomic island (GI) prediction method is useful for ongoing sequencing genomes. In this work, we built a Web server called GI-POP (http://gipop.life.nthu.edu.tw) which integrates a sequence assembling tool, a functional annotation pipeline, and a high-performance GI predicting module, in a support vector machine (SVM)-based method called genomic island genomic profile scanning (GI-GPS). The draft genomes of the ongoing genome projects in contigs or scaffolds can be submitted to our Web server, and it provides the functional annotation and highly probable GI-predicting results. GI-POP is a comprehensive annotation Web server designed for ongoing genome project analysis. Researchers can perform annotation and obtain pre-analytic information include possible GIs, coding/non-coding sequences and functional analysis from their draft genomes. This pre-analytic system can provide useful information for finishing a genome sequencing project. Copyright © 2012 Elsevier B.V. All rights reserved.

Engineering Escherichia coli for Conversion of Glucose to Medium-Chain ω-Hydroxy Fatty Acids and α,ω-Dicarboxylic Acids.

PubMed

Bowen, Christopher H; Bonin, Jeff; Kogler, Anna; Barba-Ostria, Carlos; Zhang, Fuzhong

2016-03-18

In search of sustainable approaches to plastics production, many efforts have been made to engineer microbial conversions of renewable feedstock to short-chain (C2-C8) bifunctional polymer precursors (e.g., succinic acid, cadaverine, 1,4-butanediol). Less attention has been given to medium-chain (C12-C14) monomers such as ω-hydroxy fatty acids (ω-OHFAs) and α,ω-dicarboxylic acids (α,ω-DCAs), which are precursors to high performance polyesters and polyamides. Here we engineer a complete microbial conversion of glucose to C12 and C14 ω-OHFAs and α,ω-DCAs, with precise control of product chain length. Using an expanded bioinformatics approach, we screen a wide range of enzymes across phyla to identify combinations that yield complete conversion of intermediates to product α,ω-DCAs. Finally, through optimization of culture conditions, we enhance production titer of C12 α,ω-DCA to nearly 600 mg/L. Our results indicate potential for this microbial factory to enable commercially relevant, renewable production of C12 α,ω-DCA-a valuable precursor to the high-performance plastic, nylon-6,12.

Fibrous polyaniline@manganese oxide nanocomposites as supercapacitor electrode materials and cathode catalysts for improved power production in microbial fuel cells.

PubMed

Ansari, Sajid Ali; Parveen, Nazish; Han, Thi Hiep; Ansari, Mohammad Omaish; Cho, Moo Hwan

2016-04-07

Fibrous Pani-MnO2 nanocomposite were prepared using a one-step and scalable in situ chemical oxidative polymerization method. The formation, structural and morphological properties were investigated using a range of characterization techniques. The electrochemical capacitive behavior of the fibrous Pani-MnO2 nanocomposite was examined by cyclic voltammetry and galvanostatic charge-discharge measurements using a three-electrode experimental setup in an aqueous electrolyte. The fibrous Pani-MnO2 nanocomposite achieved high capacitance (525 F g(-1) at a current density of 2 A g(-1)) and excellent cycling stability of 76.9% after 1000 cycles at 10 A g(-1). Furthermore, the microbial fuel cell constructed with the fibrous Pani-MnO2 cathode catalyst showed an improved power density of 0.0588 W m(-2), which was higher than that of pure Pani and carbon paper, respectively. The improved electrochemical supercapacitive performance and cathode catalyst performance in microbial fuel cells were attributed mainly to the synergistic effect of Pani and MnO2 in fibrous Pani-MnO2, which provides high surface area for the electrode/electrolyte contact as well as electronic conductive channels and exhibits pseudocapacitance behavior.

Power management systems for sediment microbial fuel cells in high power and continuous power applications

NASA Astrophysics Data System (ADS)

Donovan, Conrad Koble

The objective of this dissertation was to develop power management systems (PMS) for sediment microbial fuel cells (SFMCs) for high power and continuous applications. The first part of this dissertation covers a new method for testing the performance of SMFCs. This device called the microbial fuel cell tester was developed to automatically test power generation of PMS. The second part focuses on a PMS capable of delivering high power in burst mode. This means that for a small amount of time a large amount of power up to 2.5 Watts can be delivered from a SMFC only generating mW level power. The third part is aimed at developing a multi-potentiostat laboratory tool that measures the performance at fixed cell potentials of microbial fuel cells so that I can optimize them for use with the PMS. This tool is capable of controlling the anode potential or cathode potential and measuring current of six separate SMFCs simultaneously. By operating multiple potentiostats, I was able to run experiments that find ideal operating conditions for the sediment microbial fuel cells, and also I can optimize the power management system for these conditions. The fourth part of the dissertation is targeting a PMS that was able to operate a sensor continuously which was powered by an SMFC. In pervious applications involving SMFCs, the PMS operated in batch mode. In this PMS, the firmware on the submersible ultrasonic receiver (SUR) was modified for use with my PMS. This integration of PMS and SUR allowed for the continuous operation of the SUR without using a battery. Finally, the last part of the dissertation recommends a scale-up power management system to overcome the linearity scale up issue of SMFCs as future work. Concluding remarks are also added to summarize the goal and focus of this dissertation.

Microbial Routes to (2R,3R)-2,3-Butanediol: Recent Advances and Future Prospects.

PubMed

Xie, Neng-Zhong; Chen, Xian-Rui; Wang, Qing-Yan; Chen, Dong; Du, Qi-Shi; Zhou, Guo-Ping; Huang, Ri-Bo

2017-01-01

(2R,3R)-2,3-Butanediol has many industrial applications, such as it is used as an antifreeze agent and low freezing point fuel. In addition, it is particularly important to provide chiral groups in drugs. In recent years, this valuable bio-based chemical has attracted increasing attention, and significant progress has been made in the development of microbial cell factories for (2R,3R)-2,3-butanediol production. This article reviews recent advances and challenges in microbial routes to (2R,3R)-2,3- butanediol production, and highlights the metabolic engineering and synthetic biological approaches used to improve titers, yields, productivities, and optical purities. Finally, a systematic and integrative strategy for developing high-performance microbial cell factories is proposed. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Intestinal Microbial Community Differs between Acute Pancreatitis Patients and Healthy Volunteers.

PubMed

Zhang, Xi Mei; Zhang, Zheng Yu; Zhang, Chen Huan; Wu, Jing; Wang, You Xin; Zhang, Guo Xin

2018-01-01

A case control study including 45 acute pancreatitis and 44 healthy volunteers was performed to investigate the association between intestinal microbial community and acute pancreatitis. High-throughput 16S rRNA gene amplicon sequencing was used to profile the microbiological composition of the samples. In total, 27 microbial phyla were detected and the samples of pancreatitis patients contained fewer phyla. Samples from acute pancreatitis patients contained more Bacteroidetes and Proteobacteria and fewer Firmicutes and Actinobacteria than those from healthy volunteers. PCoA analyses distinguished the fecal microbial communities of acute pancreatitis patients from those of healthy volunteers. The intestinal microbes of acute pancreatitis patients are different from those of healthy volunteers. Modulation of the intestinal microbiome may serve as an alternative strategy for treating acute pancreatitis. Copyright © 2018 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

Electricity generation from food wastes and microbial community structure in microbial fuel cells.

PubMed

Jia, Jianna; Tang, Yu; Liu, Bingfeng; Wu, Di; Ren, Nanqi; Xing, Defeng

2013-09-01

Microbial fuel cell (MFC) was studied as an alternate and a novel way to dispose food wastes (FWs) in a waste-to-energy form. Different organic loading rate obviously affected the performance of MFCs fed with FWs. The maximum power density of ~18 W/m(3) (~556 mW/m(2)) was obtained at COD of 3200±400 mg/L and the maximum coulombic efficiency (CE) was ~27.0% at COD of 4900±350 mg/L. The maximum removals of COD, total carbohydrate (TC) and total nitrogen (TN) were ~86.4%, ~95.9% and ~16.1%, respectively. Microbial community analysis using 454 pyrosequencing of 16S rRNA gene demonstrated the combination of the dominant genera of the exoelectrogenic Geobacter and fermentative Bacteroides effectively drove highly efficient and reliable MFC systems with functions of organic matters degradation and electricity generation. Copyright © 2013 Elsevier Ltd. All rights reserved.

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.

Understanding microbial ecology can help improve biogas production in AD.

PubMed

Ferguson, Robert M W; Coulon, Frédéric; Villa, Raffaella

2018-06-16

454-Pyrosequencing and lipid fingerprinting were used to link anaerobic digestion (AD) process parameters (pH, alkalinity, volatile fatty acids (VFAs), biogas production and methane content) with the reactor microbial community structure and composition. AD microbial communities underwent stress conditions after changes in organic loading rate and digestion substrates. 454-Pyrosequencing analysis showed that, irrespectively of the substrate digested, methane content and pH were always significantly, and positively, correlated with community evenness. In AD, microbial communities with more even distributions of diversity are able to use parallel metabolic pathways and have greater functional stability; hence, they are capable of adapting and responding to disturbances. In all reactors, a decrease in methane content to <30% was always correlated with a 50% increase of Firmicutes sequences (particularly in operational taxonomic units (OTUs) related to Ruminococcaceae and Veillonellaceae). Whereas digesters producing higher methane content (above 60%), contained a high number of sequences related to Synergistetes and unidentified bacterial OTUs. Finally, lipid fingerprinting demonstrated that, under stress, the decrease in archaeal biomass was higher than the bacterial one, and that archaeal Phospholipid etherlipids (PLEL) levels were correlated to reactor performances. These results demonstrate that, across a number of parameters such as lipids, alpha and beta diversity, and OTUs, knowledge of the microbial community structure can be used to predict, monitor, or optimise AD performance. Copyright © 2018 Elsevier B.V. All rights reserved.

Bioreactor Scalability: Laboratory-Scale Bioreactor Design Influences Performance, Ecology, and Community Physiology in Expanded Granular Sludge Bed Bioreactors

PubMed Central

Connelly, Stephanie; Shin, Seung G.; Dillon, Robert J.; Ijaz, Umer Z.; Quince, Christopher; Sloan, William T.; Collins, Gavin

2017-01-01

Studies investigating the feasibility of new, or improved, biotechnologies, such as wastewater treatment digesters, inevitably start with laboratory-scale trials. However, it is rarely determined whether laboratory-scale results reflect full-scale performance or microbial ecology. The Expanded Granular Sludge Bed (EGSB) bioreactor, which is a high-rate anaerobic digester configuration, was used as a model to address that knowledge gap in this study. Two laboratory-scale idealizations of the EGSB—a one-dimensional and a three- dimensional scale-down of a full-scale design—were built and operated in triplicate under near-identical conditions to a full-scale EGSB. The laboratory-scale bioreactors were seeded using biomass obtained from the full-scale bioreactor, and, spent water from the distillation of whisky from maize was applied as substrate at both scales. Over 70 days, bioreactor performance, microbial ecology, and microbial community physiology were monitored at various depths in the sludge-beds using 16S rRNA gene sequencing (V4 region), specific methanogenic activity (SMA) assays, and a range of physical and chemical monitoring methods. SMA assays indicated dominance of the hydrogenotrophic pathway at full-scale whilst a more balanced activity profile developed during the laboratory-scale trials. At each scale, Methanobacterium was the dominant methanogenic genus present. Bioreactor performance overall was better at laboratory-scale than full-scale. We observed that bioreactor design at laboratory-scale significantly influenced spatial distribution of microbial community physiology and taxonomy in the bioreactor sludge-bed, with 1-D bioreactor types promoting stratification of each. In the 1-D laboratory bioreactors, increased abundance of Firmicutes was associated with both granule position in the sludge bed and increased activity against acetate and ethanol as substrates. We further observed that stratification in the sludge-bed in 1-D laboratory-scale bioreactors was associated with increased richness in the underlying microbial community at species (OTU) level and improved overall performance. PMID:28507535

Electricity Production and Characterization of High-Strength Industrial Wastewaters in Microbial Fuel Cell.

PubMed

Cetinkaya, Afsin Y; Ozdemir, Oguz Kaan; Demir, Ahmet; Ozkaya, Bestami

2017-06-01

Microbial fuel cells (MFCs) convert electrochemical energy into electrical energy immediately and have a big potential usage for the same time wastewater treatment and energy recovery via electro-active microorganisms. However, MFCs must be efficiently optimized due to its limitations such as high cost and low power production. Finding new materials to increase the cell performance and reduce cost for MFC anodes is mandatory. In the first step of this study, different inoculation sludges such as anaerobic gum industry wastewater, anaerobic brewery wastewater and anaerobic phosphate were tested, and MFC that was set up with anaerobic gum industry wastewater inoculation sludge exhibited the highest performance. In the second step of this study, various wastewaters such as chocolate industry, gum industry and slaughterhouse industry were investigated for anode bacteria sources. Several electrochemical techniques have been employed to elucidate how wastewaters affect the MFCs' performance. Among all the mentioned wastewaters, the best performance was achieved by the MFCs fed with slaughterhouse wastewater; this device produced a maximum power density of 267 mW·m -2 .

Characterisation of microbial biocoenosis in vertical subsurface flow constructed wetlands.

PubMed

Tietz, Alexandra; Kirschner, Alexander; Langergraber, Günter; Sleytr, Kirsten; Haberl, Raimund

2007-07-15

In this study a quantitative description of the microbial biocoenosis in subsurface vertical flow constructed wetlands fed with municipal wastewater was carried out. Three different methods (substrate induced respiration, ATP measurement and fumigation-extraction) were applied to measure the microbial biomass at different depths of planted and unplanted systems. Additionally, bacterial biomass was determined by epifluorescence microscopy and productivity was measured via (14)C leucine incorporation into bacterial biomass. All methods showed that >50% of microbial biomass and bacterial activity could be found in the first cm and about 95% in the first 10 cm of the filter layer. Bacterial biomass in the first 10 cm of the filter body accounted only for 16-19% of the total microbial biomass. Whether fungi or methodical uncertainties are mainly responsible for the difference between microbial and bacterial biomass remains to be examined. A comparison between the purification performance of planted and unplanted pilot-scale subsurface vertical flow constructed wetlands (PSCWs) showed no significant difference with the exception of the reduction of enterococci. The microbial biomass in all depths of the filter body was also not different in planted and unplanted systems. Compared with data from soils the microbial biomass in the PSCWs was high, although the specific surface area of the used sandy filter material available for biofilm growth was lower, especially in the beginning of the set-up of the PSCWs, due to missing clay and silt fraction.

Use of Bacillus thuringiensis supernatant from a fermentation process to improve bioremediation of chlorpyrifos in contaminated soils.

PubMed

Aceves-Diez, Angel E; Estrada-Castañeda, Kelly J; Castañeda-Sandoval, Laura M

2015-07-01

The aim of this research was to investigate the potential of a nutrient-rich organic waste, namely the cell-free supernatant of Bacillus thuringiensis (BtS) gathered from fermentation, as a biostimulating agent to improve and sustain microbial populations and their enzymatic activities, thereby assisting in the bioremediation of chlorpyrifos-contaminated soil at a high dose (70 mg kg(-1)). Experiments were performed for up to 80 d. Chlorpyrifos degradation and its major metabolic product, 3,5,6-trichloro-2-pyridinol (TCP), were quantified by high-performance liquid chromatography (HPLC); total microbial populations were enumerated by direct counts in specific medium; and fluorescein diacetate (FDA) hydrolysis was measured as an index of soil microbial activity. Throughout the experiment, there was higher chlorpyrifos degradation in soil supplemented with BtS (83.1%) as compared to non-supplemented soil. TCP formation and degradation occurred in all soils, but the greatest degradation (30.34%) was observed in soil supplemented with BtS. The total microbial populations were significantly improved by supplementation with BtS. The application of chlorpyrifos to soil inhibited the enzymatic activity; however, this negative effect was counteracted by BtS, inducing an increase of approximately 16% in FDA hydrolysis. These results demonstrate the potential of B. thuringiensis supernatant as a suitable biostimulation agent for enhancing chlorpyrifos and TCP biodegradation in chlorpyrifos-contaminated soils. Copyright © 2015 Elsevier Ltd. All rights reserved.

Performance assessment and microbial diversity of two pilot scale multi-stage sub-surface flow constructed wetland systems.

PubMed

Babatunde, A O; Miranda-CasoLuengo, Raul; Imtiaz, Mehreen; Zhao, Y Q; Meijer, Wim G

2016-08-01

This study assessed the performance and diversity of microbial communities in multi-stage sub-surface flow constructed wetland systems (CWs). Our aim was to assess the impact of configuration on treatment performance and microbial diversity in the systems. Results indicate that at loading rates up to 100gBOD5/(m(2)·day), similar treatment performances can be achieved using either a 3 or 4 stage configuration. In the case of phosphorus (P), the impact of configuration was less obvious and a minimum of 80% P removal can be expected for loadings up to 10gP/(m(2)·day) based on the performance results obtained within the first 16months of operation. Microbial analysis showed an increased bacterial diversity in stage four compared to the first stage. These results indicate that the design and configuration of multi-stage constructed wetland systems may have an impact on the treatment performance and the composition of the microbial community in the systems, and such knowledge can be used to improve their design and performance. Copyright © 2016. Published by Elsevier B.V.

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

NASA Astrophysics Data System (ADS)

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

2017-08-01

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

Microbial drivers of spatial heterogeneity of nitrous oxide pulse dynamics following drought in an experimental tropical rainforest

NASA Astrophysics Data System (ADS)

Young, J. C.; Sengupta, A.; U'Ren, J.; Van Haren, J. L. M.; Meredith, L. K.

2017-12-01

Nitrous oxide (N2O) is a long-lived, potent greenhouse gas with increasing atmospheric concentrations. Soil microbes in agricultural and natural ecosystems are the dominant source of N2O, which involves complex interactions between N-cycling microbes, metabolisms, soil properties, and plants. Tropical rainforests are the largest natural source of N2O, however the microbial and environmental drivers are poorly understood as few studies have been performed in these environments. Thus, there is an urgent need for further research to fill in knowledge gaps regarding tropical N-cycling, and the response of soil microbial communities to changes in precipitation patterns, temperature, nitrogen deposition, and land use. To address this data gap, we performed a whole-forest drought in the tropical rainforest biome in Biosphere 2 (B2) and analyzed connections between soil microbes, forest heterogeneity, and N2O emissions. The B2 rainforest is the hottest tropical rainforest on Earth, and is an important model system for studying the response of tropical forests to warming with controlled experimentation. In this study, we measured microbial community abundance and diversity profiles (16S rRNA and ITS2 amplicon sequencing) along with their association with soil properties (e.g. pH, C, N) during the drought and rewetting at five locations (3 depths), including regions that have been previously characterized with high and low N2O drought pulse dynamics (van Haren et al., 2005). In this study, we present the spatial distribution of soil microbial communities within the rainforest at Biosphere 2 and their correlations with edaphic factors. In particular, we focus on microbial, soil, and plant factors that drive high and low N2O pulse zones. As in the past, we found that N2O emissions were highest in response to rewetting in a zone hypothesized to be rich in nutrients from a nearby sugar palm. We will characterize microbial indicator species and nitrogen cycling genes to better resolve N cycling across the forest. Understanding how N2O formation is mediated by soil microbes in response to drought in tropical rainforests is challenging given the great diversity of microbial communities and metabolisms involved, but is critical for understanding the source of global increases in atmospheric N2O.

Microbial community composition of a multi-stage moving bed biofilm reactor and its interaction with kinetic model parameters estimation.

PubMed

Wang, Xiaodong; Bi, Xuejun; Hem, Lars John; Ratnaweera, Harsha

2018-07-15

Microbial community diversity determines the function of each chamber of multi-stage moving bed biofilm reactor (MBBR) systems. How the microbial community data can be further used to serve wastewater treatment process modelling and optimization has been rarely studied. In this study, a MBBR system was set up to investigate the microbial community diversity of biofilm in each functional chamber. The compositions of microbial community of biofilm from different chambers of MBBR were quantified by high-throughput sequencing. Significantly higher proportion of autotrophs were found in the second aerobic chamber (15.4%), while 4.3% autotrophs were found in the first aerobic chamber. Autotrophs in anoxic chamber were negligible. Moreover, ratios of active heterotrophic biomass and autotrophic biomass (X H /X A ) were obtained by performing respiration tests. By setting heterotroph/autotroph ratios obtained from sequencing analysis equal to X H /X A , a novel approach for kinetic model parameters estimation was developed. This work not only investigated microbial community of MBBR system, but also it provided an approach to make further use of molecular microbiology analysis results. Copyright © 2018 Elsevier Ltd. All rights reserved.

A comparative evaluation of different types of microbial electrolysis desalination cells for malic acid production.

PubMed

Liu, Guangli; Zhou, Ying; Luo, Haiping; Cheng, Xing; Zhang, Renduo; Teng, Wenkai

2015-12-01

The aim of this study was to investigate different microbial electrolysis desalination cells for malic acid production. The systems included microbial electrolysis desalination and chemical-production cell (MEDCC), microbial electrolysis desalination cell (MEDC) with bipolar membrane and anion exchange membrane (BP-A MEDC), MEDC with bipolar membrane and cation exchange membrane (BP-C MEDC), and modified microbial desalination cell (M-MDC). The microbial electrolysis desalination cells performed differently in terms of malic acid production and energy consumption. The MEDCC performed best with the highest malic acid production rate (18.4 ± 0.6 mmol/Lh) and the lowest energy consumption (0.35 ± 0.14 kWh/kg). The best performance of MEDCC was attributable to the neutral pH condition in the anode chamber, the lowest internal resistance, and the highest Geobacter percentage of the anode biofilm population among all the reactors. Copyright © 2015 Elsevier Ltd. All rights reserved.

Evaluation of Laminaria-based microbial fuel cells (LbMs) for electricity production.

PubMed

Gadhamshetty, Venkataramana; Belanger, Derek; Gardiner, Carly-Jeanne; Cummings, Anasha; Hynes, Anne

2013-01-01

Marine algae represents a sustainable feedstock in microbial fuel cells (MFCs) due to its low water and energy requirements for cultivation, higher capacity to sequester carbondioxide, and high carbohydrate content. Two-compartment MFCs were evaluated under batch-fed mode using Laminaria saccharina as the model for algae-based electron donor, and mixed microbial consortia as the biocatalyst, in the anode compartment. The Laminaria-based MFCs (LBMs) were studied with three different pretreatment conditions for the L. saccharina: (i) autoclaving (Auto), (ii) microwave irradiation (Micro), and (iii) as received treatment (No-Treat). A control was setup to establish base line performance for two-compartment MFCs using glucose as the electron donor in the anode. The performance of LBMs (250 mW/m(2) and 900 mA/m(2)) was on par with glucose-based MFCs. AC impedance analysis revealed that the charge transfer resistance was at least 50-fold higher than the corresponding ohmic losses in both LBMs and glucose-based MFCs. Copyright © 2012 Elsevier Ltd. All rights reserved.

The effect of octylglucoside and sodium cholate in Staphylococcus epidermidis and Pseudomonas aeruginosa adhesion to soft contact lenses.

PubMed

Santos, Lívia; Rodrigues, Diana; Lira, Madalena; Oliveira, Rosario; Real Oliveira, M Elisabete C D; Vilar, Eva Yebra-Pimentel; Azeredo, Joana

2007-05-01

In this study, the effect of the natural surfactants octylglucoside and sodium cholate in inhibiting Staphylococcus epidermidis and Pseudomonas aeruginosa adhesion to conventional and silicone-hydrogel contact lenses (CL) was assessed. Hydrophobicity was also evaluated to conditioned and nonconditioned CL. The inhibiting effect of the tested surfactants was determined through "in vitro" adhesion studies to conditioned and nonconditioned CL followed by image acquisition and cell enumeration. Hydrophobicity was evaluated through contact angle measurements using the advancing type technique on air. Sodium cholate exhibits a very low capability to inhibit microbial adhesion. Conversely, octylglucoside effectively inhibited microbial adhesion in both types of lenses. This surfactant exhibited an even greater performance than a multipurpose lens care solution used as control. Octylglucoside was the only tested surfactant able to lower the hydrophobicity of all CL, which can explain its high performance. The results obtained in this study point out the potential of octylglucoside as a conditioning agent to prevent microbial colonization.

New Tools For Understanding Microbial Diversity Using High-throughput Sequence Data

NASA Astrophysics Data System (ADS)

Knight, R.; Hamady, M.; Liu, Z.; Lozupone, C.

2007-12-01

High-throughput sequencing techniques such as 454 are straining the limits of tools traditionally used to build trees, choose OTUs, and perform other essential sequencing tasks. We have developed a workflow for phylogenetic analysis of large-scale sequence data sets that combines existing tools, such as the Arb phylogeny package and the NAST multiple sequence alignment tool, with new methods for choosing and clustering OTUs and for performing phylogenetic community analysis with UniFrac. This talk discusses the cyberinfrastructure we are developing to support the human microbiome project, and the application of these workflows to analyze very large data sets that contrast the gut microbiota with a range of physical environments. These tools will ultimately help to define core and peripheral microbiomes in a range of environments, and will allow us to understand the physical and biotic factors that contribute most to differences in microbial diversity.

The close relation between Lactococcus and Methanosaeta is a keystone for stable methane production from molasses wastewater in a UASB reactor.

PubMed

Kim, Tae Gwan; Yun, Jeonghee; Cho, Kyung-Suk

2015-10-01

The up-flow anaerobic sludge blanket (UASB) reactor is a promising method for the treatment of high-strength industrial wastewaters due to advantage of its high treatment capacity and settleable suspended biomass retention. Molasses wastewater as a sugar-rich waste is one of the most valuable raw material for bioenergy production due to its high organic strength and bioavailability. Interpretation for complex interactions of microbial community structures and operational parameters can help to establish stable biogas production. RNA-based approach for biogas production systems is recommended for analysis of functionally active community members which are significantly underestimated. In this study, methane production and active microbial community were characterized in an UASB reactor using molasses wastewater as feedstock. The UASB reactor achieved a stable process performance at an organic loading rate of 1.7~13.8-g chemical oxygen demand (COD,·L(-1) day(-1); 87-95 % COD removal efficiencies), and the maximum methane production rate was 4.01 L-CH4·at 13.8 g-COD L(-1) day(-1). Lactococcus and Methanosaeta were comprised up to 84 and 80 % of the active bacterial and archaeal communities, respectively. Network analysis of reactor performance and microbial community revealed that Lactococcus and Methanosaeta were network hub nodes and positively correlated each other. In addition, they were positively correlated with methane production and organic loading rate, and they shared the other microbial hub nodes as neighbors. The results indicate that the close association between Lactococcus and Methanosaeta is responsible for the stable production of methane in the UASB reactor using molasses wastewater.

Relationships between waste physicochemical properties, microbial activity and vegetation at coal ash and sludge disposal sites.

PubMed

Woch, Marcin W; Radwańska, Magdalena; Stanek, Małgorzata; Łopata, Barbara; Stefanowicz, Anna M

2018-06-11

The aim of the study was to assess the relationships between vegetation, physicochemical and microbial properties of substrate at coal ash and sludge disposal sites. The study was performed on 32 plots classified into 7 categories: dried ash sedimentation ponds, dominated by a grass Calamagrostis epigejos (AH-Ce), with the admixture of Pinus sylvestris (AH-CePs) or Robinia pseudoacacia (AH-CeRp), dry ash landfill dominated by Betula pendula and Pinus sylvestris (AD-BpPs) or Salix viminalis (AD-Sv) and coal sludge pond with drier parts dominated by Tussilago farfara (CS-Tf) and the wetter ones by Cyperus flavescens (CS-Cf). Ash sites were covered with soil layer imported as a part of technical reclamation. Ash had relatively high concentrations of some alkali and alkaline earth metals, Mn and pH, while coal sludge had high water and C, S, P and K contents. Concentrations of heavy metals were lower than allowable limits in all substrate types. Microbial biomass and, particularly, enzymatic activity in ash and sludge were generally low. The only exception were CS-Tf plots characterized by the highest microbial biomass, presumably due to large deposits of organic matter that became available for aerobic microbial biomass when water level fell. The properties of ash and sludge adversely affected microbial biomass and enzymatic activity as indicated by significant negative correlations between the content of alkali/alkaline earth metals, heavy metals, and macronutrients with enzymatic activity and/or microbial biomass, as well as positive correlations of these parameters with metabolic quotient (qCO 2 ). Plant species richness and cover were relatively high, which may be partly associated with alleviating influence of soil covering the ash. The effect of the admixture of R. pseudoacacia or P. sylvestris to stands dominated by C. epigejos was smaller than expected. The former species increased NNH 4 , NNO 3 and arylsulfatase activity, while the latter reduced activity of the enzyme. Copyright © 2018 Elsevier B.V. All rights reserved.

Ecosystem function in waste stabilisation ponds: Improving water quality through a better understanding of biophysical coupling

NASA Astrophysics Data System (ADS)

Ghadouani, Anas; Reichwaldt, Elke S.; Coggins, Liah X.; Ivey, Gregory N.; Ghisalberti, Marco; Zhou, Wenxu; Laurion, Isabelle; Chua, Andrew

2014-05-01

Wastewater stabilisation ponds (WSPs) are highly productive systems designed to treat wastewater using only natural biological and chemical processes. Phytoplankton, microbial communities and hydraulics play important roles for ecosystem functionality of these pond systems. Although WSPs have been used for many decades, they are still considered as 'black box' systems as very little is known about the fundamental ecological processes which occur within them. However, a better understanding of how these highly productive ecosystems function is particularly important for hydrological processes, as treated wastewater is commonly discharged into streams, rivers, and oceans, and subject to strict water quality guidelines. WSPs are known to operate at different levels of efficiency, and treatment efficiency of WSPs is dependent on physical (flow characteristics and sludge accumulation and distribution) and biological (microbial and phytoplankton communities) characteristics. Thus, it is important to gain a better understanding of the role and influence of pond hydraulics and vital microbial communities on pond performance and WSP functional stability. The main aim of this study is to investigate the processes leading to differences in treatment performance of WSPs. This study uses a novel and innovative approach to understand these factors by combining flow cytometry and metabolomics to investigate various biochemical characteristics, including the metabolite composition and microbial community within WSPs. The results of these analyses will then be combined with results from the characterisation of pond hydrodynamics and hydraulic performance, which will be performed using advanced hydrodynamic modelling and advanced sludge profiling technology. By understanding how hydrodynamic and biological processes influence each other and ecosystem function and stability in WSPs, we will be able to propose ways to improve the quality of the treatment using natural processes, with less reliance on chemical treatment. This will in turn contribute to the reduction in the cost of operation, but more importantly reduce the impact on the environment (i.e., discharge, GHGs), and increase water quality and the potential for water reuse worldwide.

Plant community influence on soil microbial response after a wildfire in Sierra Nevada National Park (Spain).

PubMed

Bárcenas-Moreno, Gema; García-Orenes, Fuensanta; Mataix-Solera, Jorge; Mataix-Beneyto, Jorge

2016-12-15

Plant community influence on microbial response after fire has been studied in a Sierra Nevada National Park area affected by a wildfire in 2005. Two different plant communities adapted to different altitudes were selected to analyse possible differences on soil microbial recolonisation process after fire, in oak forest and high mountain shrub communities. Microbial abundance, activity and community composition were monitored to evaluate medium-term changes. Microbial abundance was studied by mean of microbial biomass carbon and plate count methods; microbial activity was analysed by microbial respiration and bacterial growth while microbial community composition was determined by analysing phospholipid fatty acid pattern. Under unburnt conditions oak forest showed higher nutrient content, pH and microbial abundance and activity values than the high mountain shrubs community. Different parameters studied showed different trends with time, highlighting important changes in microbial community composition in high mountain shrubs from first sampling to the second one. Post-fire recolonisation process was different depending on plant community studied. Highlighting fungal response and microbial activity were stimulated in burnt high mountain shrubs community whilst it was negatively affected in oak forest. Fire induced changes in oak forest were almost neutralized 20months after the fire, while high mountain shrubs community still showed fire-induced changes at the end of the study. Copyright © 2016 Elsevier B.V. All rights reserved.

Effects of dietary resistant starch content on metabolic status, milk composition, and microbial profiling in lactating sows and on offspring performance.

PubMed

Yan, H; Lu, H; Almeida, V V; Ward, M G; Adeola, O; Nakatsu, C H; Ajuwon, K M

2017-02-01

In the present study, the effects of dietary resistant starch (RS) content on serum metabolite and hormone concentrations, milk composition, and faecal microbial profiling in lactating sows, as well as on offspring performance was investigated. Sixteen sows were randomly allotted at breeding to two treatments containing low- and high-RS contents from normal and high-amylose corn varieties, respectively, and each treatment had eight replicates (sows). Individual piglet body weight (BW) and litter size were recorded at birth and weaning. Milk samples were obtained on day 10 after farrowing for composition analysis. On day 2 before weaning, blood and faecal samples were collected to determine serum metabolite and hormone concentrations and faecal microbial populations, respectively. Litter size at birth and weaning were not influenced (p > 0.05) by the sow dietary treatments. Although feeding the RS-rich diet to sows reduced (p = 0.004) offspring birth BW, there was no difference in piglet BW at weaning (p > 0.05). High-RS diet increased (p < 0.05) serum triacylglycerol and nonesterified fatty acid concentrations and milk total solid content, and tended (p = 0.09) to increase milk fat content in lactating sows. Feeding the RS-rich diet to sows increased (p < 0.01) faecal bacterial population diversity. These results indicate that high-RS diets induce fatty acid mobilization and a greater intestinal bacterial richness in lactating sows, as well as a greater nutrient density in maternal milk, without affecting offspring performance at weaning. Journal of Animal Physiology and Animal Nutrition © 2016 Blackwell Verlag GmbH.

Can the black box be cracked? The augmentation of microbial ecology by high-resolution, automated sensing technologies.

PubMed

Shade, Ashley; Carey, Cayelan C; Kara, Emily; Bertilsson, Stefan; McMahon, Katherine D; Smith, Matthew C

2009-08-01

Automated sensing technologies, 'ASTs,' are tools that can monitor environmental or microbial-related variables at increasingly high temporal resolution. Microbial ecologists are poised to use AST data to couple microbial structure, function and associated environmental observations on temporal scales pertinent to microbial processes. In the context of aquatic microbiology, we discuss three applications of ASTs: windows on the microbial world, adaptive sampling and adaptive management. We challenge microbial ecologists to push AST potential in helping to reveal relationships between microbial structure and function.

A multivariate distance-based analytic framework for microbial interdependence association test in longitudinal study.

PubMed

Zhang, Yilong; Han, Sung Won; Cox, Laura M; Li, Huilin

2017-12-01

Human microbiome is the collection of microbes living in and on the various parts of our body. The microbes living on our body in nature do not live alone. They act as integrated microbial community with massive competing and cooperating and contribute to our human health in a very important way. Most current analyses focus on examining microbial differences at a single time point, which do not adequately capture the dynamic nature of the microbiome data. With the advent of high-throughput sequencing and analytical tools, we are able to probe the interdependent relationship among microbial species through longitudinal study. Here, we propose a multivariate distance-based test to evaluate the association between key phenotypic variables and microbial interdependence utilizing the repeatedly measured microbiome data. Extensive simulations were performed to evaluate the validity and efficiency of the proposed method. We also demonstrate the utility of the proposed test using a well-designed longitudinal murine experiment and a longitudinal human study. The proposed methodology has been implemented in the freely distributed open-source R package and Python code. © 2017 WILEY PERIODICALS, INC.

Succession of microbial communities and changes of incremental oil in a post-polymer flooded reservoir with nutrient stimulation.

PubMed

Gao, Peike; Li, Guoqiang; Le, Jianjun; Liu, Xiaobo; Liu, Fang; Ma, Ting

2018-02-01

Further exploitation of the residual oil underground in post-polymer flooded reservoirs is attractive and challengeable. In this study, indigenous microbial enhanced oil recovery (IMEOR) in a post-polymer flooded reservoir was performed. The succession of microbial communities was revealed by high-throughput sequencing of 16S rRNA genes and changes of incremental oil were analyzed. The results indicated that the abundances of reservoir microorganisms significantly increased, with alpha diversities decreased in the IMEOR process. With the intermittent nutrient injection, microbial communities showed a regular change and were alternately dominated by minority populations: Pseudomonas and Acinetobacter significantly increased when nutrients were injected; Thauera, Azovibrio, Arcobacter, Helicobacter, Desulfitobacterium, and Clostridium increased in the following water-flooding process. Accompanied by the stimulated populations, higher oil production was obtained. However, these populations did not contribute a persistent level of incremental oil in the reservoir. In summary, this study revealed the alternative succession of microbial communities and the changes of incremental oil in a post-polymer flooded reservoir with intermittent nutrient stimulation process.

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

USGS Publications Warehouse

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

2009-01-01

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

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

USGS Publications Warehouse

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

2009-01-01

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

Cellular content of biomolecules in sub-seafloor microbial communities

NASA Astrophysics Data System (ADS)

Braun, Stefan; Morono, Yuki; Becker, Kevin W.; Hinrichs, Kai-Uwe; Kjeldsen, Kasper U.; Jørgensen, Bo B.; Lomstein, Bente Aa.

2016-09-01

Microbial biomolecules, typically from the cell envelope, can provide crucial information about distribution, activity, and adaptations of sub-seafloor microbial communities. However, when cells die these molecules can be preserved in the sediment on timescales that are likely longer than the lifetime of their microbial sources. Here we provide for the first time measurements of the cellular content of biomolecules in sedimentary microbial cells. We separated intact cells from sediment matrices in samples from surficial, deeply buried, organic-rich, and organic-lean marine sediments by density centrifugation. Amino acids, amino sugars, muramic acid, and intact polar lipids were analyzed in both whole sediment and cell extract, and cell separation was optimized and evaluated in terms of purity, separation efficiency, taxonomic resemblance, and compatibility to high-performance liquid chromatography and mass spectrometry for biomolecule analyses. Because cell extracts from density centrifugation still contained considerable amounts of detrital particles and non-cellular biomolecules, we further purified cells from two samples by fluorescence-activated cell sorting (FACS). Cells from these highly purified cell extracts had an average content of amino acids and lipids of 23-28 fg cell-1 and 2.3 fg cell-1, respectively, with an estimated carbon content of 19-24 fg cell-1. In the sediment, the amount of biomolecules associated with vegetative cells was up to 70-fold lower than the total biomolecule content. We find that the cellular content of biomolecules in the marine subsurface is up to four times lower than previous estimates. Our approach will facilitate and improve the use of biomolecules as proxies for microbial abundance in environmental samples and ultimately provide better global estimates of microbial biomass.

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 pretreatment method for HPLC analysis of cypermethrin in microbial degradation systems.

PubMed

Liu, Shuliang; Yao, Kai; Jia, Dongying; Zhao, Nan; Lai, Wen; Yuan, Huaiyu

2012-07-01

In this paper, a pretreatment method for high-performance liquid chromatography (HPLC) determination of cypermethrin (CY) in microbial degradation systems was systemically studied, primarily to solve the problem of inaccurate determination of CY concentration caused by its uneven distribution in the systems. A suitable pretreatment method was established, including sampling, extraction and dehydration of CY. Partial sampling could be taken for bacterial and yeast systems in which CY was uniformly dispersed by an emulsifying agent, while total sampling was only suitable for mold systems with or without an emulsifying agent. CY could be fully extracted from the samples in which microbial cells were disrupted by ultrasonic treatment with acetonitrile under ultrasonic condition. The extract could be effectively dehydrated and purified by passing it through an anhydrous Na(2)SO(4) column followed by an elution with acetonitrile. The determination of CY in the pretreated sample by HPLC showed a high precision [relative standard deviation (RSD) = 1.14%, n = 5] and a good stability over a period of five days (RSD = 1.57%, n = 5). The recoveries of CY in microbial degradation systems at three different spiked levels ranged from 95.68 to 108.09% (RSD = 0.50-5.87%, n = 5).

Environmental proteomics reveals early microbial community responses to biostimulation at a uranium- and nitrate-contaminated site

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

Chourey, Karuna; Nissen, Silke; Vishnivetskaya, T.

2013-01-01

High performance mass spectrometry instrumentation coupled with improved protein extraction techniques enable metaproteomics to identify active members of soil and groundwater microbial communities. Metaproteomics workflows were applied to study the initial responses (i.e., 4 days post treatment) of the indigenous aquifer microbiota to biostimulation with emulsified vegetable oil (EVO) at a uranium-contaminated site. Members of the Betaproteobacteria (i.e., Dechloromonas, Ralstonia, Rhodoferax, Polaromonas, Delftia, Chromobacterium) and Firmicutes dominated the biostimulated aquifer community. Proteome characterization revealed distinct differences in protein expression between the microbial biomass collected from groundwater influenced by biostimulation and groundwater collected up-gradient of the EVO injection points. In particular,more » proteins involved in ammonium assimilation, EVO degradation, and polyhydroxybutyrate (PHB) granule formation were prominent following biostimulation. Interestingly, the atypical NosZ of a Dechloromonas sp. was highly expressed suggesting active nitrous oxide (N2O) respiration. c-type cytochromes were barely detected, as was citrate synthase, a biomarker for hexavalent uranium reduction activity, suggesting that metal reduction has not commenced 4 days post EVO delivery. Environmental metaproteomics identified microbial community responses to biostimulation and elucidated active pathways demonstrating the value of this technique for complementing nucleic acid-based approaches.« less

Prokaryotic diversity and biogeochemical characteristics of benthic microbial ecosystems at La Brava, a hypersaline lake at Salar de Atacama, Chile.

PubMed

Farias, Maria Eugenia; Rasuk, Maria Cecilia; Gallagher, Kimberley L; Contreras, Manuel; Kurth, Daniel; Fernandez, Ana Beatriz; Poiré, Daniel; Novoa, Fernando; Visscher, Pieter T

2017-01-01

Benthic microbial ecosystems of Laguna La Brava, Salar de Atacama, a high altitude hypersaline lake, were characterized in terms of bacterial and archaeal diversity, biogeochemistry, (including O2 and sulfide depth profiles and mineralogy), and physicochemical characteristics. La Brava is one of several lakes in the Salar de Atacama where microbial communities are growing in extreme conditions, including high salinity, high solar insolation, and high levels of metals such as lithium, arsenic, magnesium, and calcium. Evaporation creates hypersaline conditions in these lakes and mineral precipitation is a characteristic geomicrobiological feature of these benthic ecosystems. In this study, the La Brava non-lithifying microbial mats, microbialites, and rhizome-associated concretions were compared to each other and their diversity was related to their environmental conditions. All the ecosystems revealed an unusual community where Euryarchaeota, Crenarchaeota, Acetothermia, Firmicutes and Planctomycetes were the most abundant groups, and cyanobacteria, typically an important primary producer in microbial mats, were relatively insignificant or absent. This suggests that other microorganisms, and possibly novel pathways unique to this system, are responsible for carbon fixation. Depth profiles of O2 and sulfide showed active production and respiration. The mineralogy composition was calcium carbonate (as aragonite) and increased from mats to microbialites and rhizome-associated concretions. Halite was also present. Further analyses were performed on representative microbial mats and microbialites by layer. Different taxonomic compositions were observed in the upper layers, with Archaea dominating the non-lithifying mat, and Planctomycetes the microbialite. The bottom layers were similar, with Euryarchaeota, Crenarchaeota and Planctomycetes as dominant phyla. Sequences related to Cyanobacteria were very scarce. These systems may contain previously uncharacterized community metabolisms, some of which may be contributing to net mineral precipitation. Further work on these sites might reveal novel organisms and metabolisms of biotechnological interest.

Prokaryotic diversity and biogeochemical characteristics of benthic microbial ecosystems at La Brava, a hypersaline lake at Salar de Atacama, Chile

PubMed Central

Rasuk, Maria Cecilia; Gallagher, Kimberley L.; Contreras, Manuel; Kurth, Daniel; Fernandez, Ana Beatriz; Poiré, Daniel; Novoa, Fernando; Visscher, Pieter T.

2017-01-01

Benthic microbial ecosystems of Laguna La Brava, Salar de Atacama, a high altitude hypersaline lake, were characterized in terms of bacterial and archaeal diversity, biogeochemistry, (including O2 and sulfide depth profiles and mineralogy), and physicochemical characteristics. La Brava is one of several lakes in the Salar de Atacama where microbial communities are growing in extreme conditions, including high salinity, high solar insolation, and high levels of metals such as lithium, arsenic, magnesium, and calcium. Evaporation creates hypersaline conditions in these lakes and mineral precipitation is a characteristic geomicrobiological feature of these benthic ecosystems. In this study, the La Brava non-lithifying microbial mats, microbialites, and rhizome-associated concretions were compared to each other and their diversity was related to their environmental conditions. All the ecosystems revealed an unusual community where Euryarchaeota, Crenarchaeota, Acetothermia, Firmicutes and Planctomycetes were the most abundant groups, and cyanobacteria, typically an important primary producer in microbial mats, were relatively insignificant or absent. This suggests that other microorganisms, and possibly novel pathways unique to this system, are responsible for carbon fixation. Depth profiles of O2 and sulfide showed active production and respiration. The mineralogy composition was calcium carbonate (as aragonite) and increased from mats to microbialites and rhizome-associated concretions. Halite was also present. Further analyses were performed on representative microbial mats and microbialites by layer. Different taxonomic compositions were observed in the upper layers, with Archaea dominating the non-lithifying mat, and Planctomycetes the microbialite. The bottom layers were similar, with Euryarchaeota, Crenarchaeota and Planctomycetes as dominant phyla. Sequences related to Cyanobacteria were very scarce. These systems may contain previously uncharacterized community metabolisms, some of which may be contributing to net mineral precipitation. Further work on these sites might reveal novel organisms and metabolisms of biotechnological interest. PMID:29140980

Development of a microbial high-throughput screening instrument based on elastic light scatter patterns

NASA Astrophysics Data System (ADS)

Bae, Euiwon; Patsekin, Valery; Rajwa, Bartek; Bhunia, Arun K.; Holdman, Cheryl; Davisson, V. Jo; Hirleman, E. Daniel; Robinson, J. Paul

2012-04-01

A microbial high-throughput screening (HTS) system was developed that enabled high-speed combinatorial studies directly on bacterial colonies. The system consists of a forward scatterometer for elastic light scatter (ELS) detection, a plate transporter for sample handling, and a robotic incubator for automatic incubation. To minimize the ELS pattern-capturing time, a new calibration plate and correction algorithms were both designed, which dramatically reduced correction steps during acquisition of the circularly symmetric ELS patterns. Integration of three different control software programs was implemented, and the performance of the system was demonstrated with single-species detection for library generation and with time-resolved measurement for understanding ELS colony growth correlation, using Escherichia coli and Listeria. An in-house colony-tracking module enabled researchers to easily understand the time-dependent variation of the ELS from identical colony, which enabled further analysis in other biochemical experiments. The microbial HTS system provided an average scan time of 4.9 s per colony and the capability of automatically collecting more than 4000 ELS patterns within a 7-h time span.

Development of a Long-Life-Cycle, Highly Water-Resistant Solar Reflective Retrofit Roof Coating

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

Polyzos, Georgios; Hunter, Scott; Sharma, Jaswinder

2016-03-04

Highly water-resistant and solar-reflective coatings for low-slope roofs are potentially among the most economical retrofit approaches to thermal management of the building envelope. Therefore, they represent a key building technology research program within the Department of Energy. Research efforts in industry and the Department of Energy are currently under way to increase long-term solar reflectance on a number of fronts. These include new polymer coatings technologies to provide longer-lasting solar reflectivity and improved test methodologies to predict long-term soiling and microbial performance. The focus on long-term improvements in soiling and microbial resistance for maximum reflectance does not address the singlemore » most important factor impacting the long-term sustainability of low-slope roof coatings: excellent water resistance. The hydrophobic character of asphaltic roof products makes them uniquely suitable for water resistance, but their low albedo and poor exterior durability are disadvantages. A reflective coating that maintains very high water resistance with increased long-term resistance to soiling and microbial activity would provide additional energy savings and extend roof service life.« less

Controlling microbial contamination during hydrolysis of AFEX-pretreated corn stover and switchgrass: Effects on hydrolysate composition, microbial response and fermentation

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

Serate, Jose; Xie, Dan; Pohlmann, Edward

Microbial conversion of lignocellulosic feedstocks into biofuels remains an attractive means to produce sustainable energy. It is essential to produce lignocellulosic hydrolysates in a consistent manner in order to study microbial performance in different feedstock hydrolysates. Because of the potential to introduce microbial contamination from the untreated biomass or at various points during the process, it can be difficult to control sterility during hydrolysate production. In this study, we compared hydrolysates produced from AFEX-pretreated corn stover and switchgrass using two different methods to control contamination: either by autoclaving the pretreated feedstocks prior to enzymatic hydrolysis, or by introducing antibiotics duringmore » the hydrolysis of non-autoclaved feedstocks. We then performed extensive chemical analysis, chemical genomics, and comparative fermentations to evaluate any differences between these two different methods used for producing corn stover and switchgrass hydrolysates. Autoclaving the pretreated feedstocks could eliminate the contamination for a variety of feedstocks, whereas the antibiotic gentamicin was unable to control contamination consistently during hydrolysis. Compared to the addition of gentamicin, autoclaving of biomass before hydrolysis had a minimal effect on mineral concentrations, and showed no significant effect on the two major sugars (glucose and xylose) found in these hydrolysates. However, autoclaving elevated the concentration of some furanic and phenolic compounds. Chemical genomics analyses using Saccharomyces cerevisiae strains indicated a high correlation between the AFEX-pretreated hydrolysates produced using these two methods within the same feedstock, indicating minimal differences between the autoclaving and antibiotic methods. Comparative fermentations with S. cerevisiae and Zymomonas mobilis also showed that autoclaving the AFEX-pretreated feedstocks had no significant effects on microbial performance in these hydrolysates. In conclusion, our results showed that autoclaving the pretreated feedstocks offered advantages over the addition of antibiotics for hydrolysate production. The autoclaving method produced a more consistent quality of hydrolysate.« less

Controlling microbial contamination during hydrolysis of AFEX-pretreated corn stover and switchgrass: Effects on hydrolysate composition, microbial response and fermentation

DOE PAGES

Serate, Jose; Xie, Dan; Pohlmann, Edward; ...

2015-11-14

Microbial conversion of lignocellulosic feedstocks into biofuels remains an attractive means to produce sustainable energy. It is essential to produce lignocellulosic hydrolysates in a consistent manner in order to study microbial performance in different feedstock hydrolysates. Because of the potential to introduce microbial contamination from the untreated biomass or at various points during the process, it can be difficult to control sterility during hydrolysate production. In this study, we compared hydrolysates produced from AFEX-pretreated corn stover and switchgrass using two different methods to control contamination: either by autoclaving the pretreated feedstocks prior to enzymatic hydrolysis, or by introducing antibiotics duringmore » the hydrolysis of non-autoclaved feedstocks. We then performed extensive chemical analysis, chemical genomics, and comparative fermentations to evaluate any differences between these two different methods used for producing corn stover and switchgrass hydrolysates. Autoclaving the pretreated feedstocks could eliminate the contamination for a variety of feedstocks, whereas the antibiotic gentamicin was unable to control contamination consistently during hydrolysis. Compared to the addition of gentamicin, autoclaving of biomass before hydrolysis had a minimal effect on mineral concentrations, and showed no significant effect on the two major sugars (glucose and xylose) found in these hydrolysates. However, autoclaving elevated the concentration of some furanic and phenolic compounds. Chemical genomics analyses using Saccharomyces cerevisiae strains indicated a high correlation between the AFEX-pretreated hydrolysates produced using these two methods within the same feedstock, indicating minimal differences between the autoclaving and antibiotic methods. Comparative fermentations with S. cerevisiae and Zymomonas mobilis also showed that autoclaving the AFEX-pretreated feedstocks had no significant effects on microbial performance in these hydrolysates. In conclusion, our results showed that autoclaving the pretreated feedstocks offered advantages over the addition of antibiotics for hydrolysate production. The autoclaving method produced a more consistent quality of hydrolysate.« less

Phenolic root exudate and tissue compounds vary widely among temperate forest tree species and have contrasting effects on soil microbial respiration.

PubMed

Zwetsloot, Marie J; Kessler, André; Bauerle, Taryn L

2018-04-01

Root-soil interactions fundamentally affect the terrestrial carbon (C) cycle and thereby ecosystem feedbacks to climate change. This study addressed the question of whether the secondary metabolism of different temperate forest tree species can affect soil microbial respiration. We hypothesized that phenolics can both increase and decrease respiration depending on their function as food source, mobilizer of other soil resources, signaling compound, or toxin. We analyzed the phenolic compounds from root exudates and root tissue extracts of six tree species grown in a glasshouse using high-performance liquid chromatography. We then tested the effect of individual phenolic compounds, representing the major identified phenylpropanoid compound classes, on microbial respiration through a 5-d soil incubation. Phenolic root profiles were highly species-specific. Of the eight classes identified, flavonoids were the most abundant, with flavanols being the predominating sub-class. Phenolic effects on microbial respiration ranged from a 26% decrease to a 46% increase, with reduced respiration occurring in the presence of compounds possessing a catechol ring. Tree species variation in root phenolic composition influences the magnitude and direction of root effects on microbial respiration. Our data support the hypothesis that functional group rather than biosynthetic class determines the root phenolic effect on soil C cycling. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

High-throughput identification of the microbial biodiversity of cocoa bean fermentation by MALDI-TOF MS.

PubMed

Miescher Schwenninger, S; Freimüller Leischtfeld, S; Gantenbein-Demarchi, C

2016-11-01

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a powerful biotyping tool increasingly used for high-throughput identification of clinical microbial isolates, however, in food fermentation research this approach is still not well established. This study examines the microbial biodiversity of cocoa bean fermentation based on the isolation of micro-organisms in cocoa-producing regions, followed by MALDI-TOF MS in Switzerland. A preceding 6-week storage test to mimic lengthy transport of microbial samples from cocoa-producing regions to Switzerland was performed with strains of Lactobacillus plantarum, Acetobacter pasteurianus and Saccharomyces cerevisiae. Weekly MALDI-TOF MS analysis was able to successfully identify microbiota to the species level after storing live cultures on slant agar at mild temperatures (7°C) and/or in 75% aqueous ethanol at differing temperatures (-20, 7 and 30°C). The efficacy of this method was confirmed by on-site recording of the microbial biodiversity in cocoa bean fermentation in Bolivia and Brazil, with a total of 1126 randomly selected isolates. MALDI-TOF MS analyses revealed known dominant cocoa bean fermentation species with Lact. plantarum and Lactobacillus fermentum in the lactic acid bacteria taxon, Hanseniaspora opuntiae and S. cerevisiae in the yeast taxon, and Acet. pasteurianus, Acetobacter fabarum, Acetobacter ghanensis and Acetobacter senegalensis in the acetic acid bacteria taxon. Microbial identification with MALDI-TOF MS has increased the number of samples that can be analysed in a given time, a prerequisite for high-throughput methods. This method is already widely used for the identification of clinical microbial isolates, whereas in food fermentation research, including cocoa bean fermentation, microbiota is mostly identified by time-consuming, biochemical-based phenotyping and molecular approaches. This study presents the use of MALDI-TOF MS for characterizing the microbial biodiversity of cocoa bean fermentation. The feasibility of MALDI-TOF MS identification of cocoa-specific microbiota has been shown with samples collected during on-site studies in two countries of origin, Bolivia and Brazil. © 2016 The Society for Applied Microbiology.

Effect of shear on performance and microbial ecology of continuously stirred anaerobic digesters treating animal manure.

PubMed

Hoffmann, Rebecca A; Garcia, Marcelo L; Veskivar, Mehul; Karim, Khursheed; Al-Dahhan, Muthanna H; Angenent, Largus T

2008-05-01

We determined the effect of different mixing intensities on the performance, methanogenic population dynamics, and juxtaposition of syntrophic microbes in anaerobic digesters treating cow manure from a dairy farm. Computer automated radioactive particle tracking in conjunction with computational fluid dynamics was performed to quantify the shear levels locally. Four continuously stirred anaerobic digesters were operated at different mixing intensities of 1,500, 500, 250, and 50 revolutions per min (RPM) over a 260-day period at a temperature of 34 +/- 1 degrees C. Animal manure at a volatile solids (VS) concentration of 50 g/L was fed into the digesters daily at five different organic loading rates between 0.6 and 3.5 g VS/L day. The different mixing intensities had no effect on the biogas production rates and yields at steady-state conditions. A methane yield of 0.241 +/- 0.007 L CH(4)/g VS fed was obtained by pooling the data of all four digesters during steady-state periods. However, digester performance was affected negatively by mixing intensity during startup of the digesters, with lower biogas production rates and higher volatile fatty acids concentrations observed for the 1,500-RPM digester. Despite similar methane production yields and rates, the acetoclastic methanogenic populations were different for the high- and low-intensity mixed digesters with Methanosarcina spp. and Methanosaeta concilii as the predominant methanogens, respectively. For all four digesters, epifluorescence microscopy revealed decreasing microbial floc sizes beginning at week 4 and continuing through week 26 after which no microbial flocs remained. This decrease in size, and subsequent loss of microbial flocs did not, however, produce any long-term upsets in digester performance. Copyright 2007 Wiley Periodicals, Inc.

Microfluidics and microbial engineering.

PubMed

Kou, Songzi; Cheng, Danhui; Sun, Fei; Hsing, I-Ming

2016-02-07

The combination of microbial engineering and microfluidics is synergistic in nature. For example, microfluidics is benefiting from the outcome of microbial engineering and many reported point-of-care microfluidic devices employ engineered microbes as functional parts for the microsystems. In addition, microbial engineering is facilitated by various microfluidic techniques, due to their inherent strength in high-throughput screening and miniaturization. In this review article, we firstly examine the applications of engineered microbes for toxicity detection, biosensing, and motion generation in microfluidic platforms. Secondly, we look into how microfluidic technologies facilitate the upstream and downstream processes of microbial engineering, including DNA recombination, transformation, target microbe selection, mutant characterization, and microbial function analysis. Thirdly, we highlight an emerging concept in microbial engineering, namely, microbial consortium engineering, where the behavior of a multicultural microbial community rather than that of a single cell/species is delineated. Integrating the disciplines of microfluidics and microbial engineering opens up many new opportunities, for example in diagnostics, engineering of microbial motors, development of portable devices for genetics, high throughput characterization of genetic mutants, isolation and identification of rare/unculturable microbial species, single-cell analysis with high spatio-temporal resolution, and exploration of natural microbial communities.

High Performance Microbial Fuel Cells and Supercapacitors Using Micro-Electro-Mechanical System (MEMS) Technology

NASA Astrophysics Data System (ADS)

Ren, Hao

A Microbial fuel cell (MFC) is a bio-inspired carbon-neutral, renewable electrochemical converter to extract electricity from catabolic reaction of micro-organisms. It is a promising technology capable of directly converting the abundant biomass on the planet into electricity and potentially alleviate the emerging global warming and energy crisis. The current and power density of MFCs are low compared with conventional energy conversion techniques. Since its debut in 2002, many studies have been performed by adopting a variety of new configurations and structures to improve the power density. The reported maximum areal and volumetric power densities range from 19 mW/m2 to 1.57 W/m2 and from 6.3 W/m3 to 392 W/m 3, respectively, which are still low compared with conventional energy conversion techniques. In this dissertation, the impact of scaling effect on the performance of MFCs are investigated, and it is found that by scaling down the characteristic length of MFCs, the surface area to volume ratio increases and the current and power density improves. As a result, a miniaturized MFC fabricated by Micro-Electro-Mechanical System (MEMS) technology with gold anode is presented in this dissertation, which demonstrate a high power density of 3300 W/m3. The performance of the MEMS MFC is further improved by adopting anodes with higher surface area to volume ratio, such as carbon nanotube (CNT) and graphene based anodes, and the maximum power density is further improved to a record high power density of 11220 W/m3. A novel supercapacitor by regulating the respiration of the bacteria is also presented, and a high power density of 531.2 A/m2 (1,060,000 A/m3) and 197.5 W/m2 (395,000 W/m3), respectively, are marked, which are one to two orders of magnitude higher than any previously reported microbial electrochemical techniques.

A Terrestrial Microbial Fuel Cell for Powering a Single-Hop Wireless Sensor Network.

PubMed

Zhang, Daxing; Zhu, Yingmin; Pedrycz, Witold; Guo, Yongxian

2016-05-18

Microbial fuel cells (MFCs) are envisioned as one of the most promising alternative renewable energy sources because they can generate electric current continuously while treating waste. Terrestrial Microbial Fuel Cells (TMFCs) can be inoculated and work on the use of soil, which further extends the application areas of MFCs. Energy supply, as a primary influential factor determining the lifetime of Wireless Sensor Network (WSN) nodes, remains an open challenge in sensor networks. In theory, sensor nodes powered by MFCs have an eternal life. However, low power density and high internal resistance of MFCs are two pronounced problems in their operation. A single-hop WSN powered by a TMFC experimental setup was designed and experimented with. Power generation performance of the proposed TMFC, the relationships between the performance of the power generation and the environment temperature, the water content of the soil by weight were measured by experiments. Results show that the TMFC can achieve good power generation performance under special environmental conditions. Furthermore, the experiments with sensor data acquisition and wireless transmission of the TMFC powering WSN were carried out. We demonstrate that the obtained experimental results validate the feasibility of TMFCs powering WSNs.

A Terrestrial Microbial Fuel Cell for Powering a Single-Hop Wireless Sensor Network

PubMed Central

Zhang, Daxing; Zhu, Yingmin; Pedrycz, Witold; Guo, Yongxian

2016-01-01

Microbial fuel cells (MFCs) are envisioned as one of the most promising alternative renewable energy sources because they can generate electric current continuously while treating waste. Terrestrial Microbial Fuel Cells (TMFCs) can be inoculated and work on the use of soil, which further extends the application areas of MFCs. Energy supply, as a primary influential factor determining the lifetime of Wireless Sensor Network (WSN) nodes, remains an open challenge in sensor networks. In theory, sensor nodes powered by MFCs have an eternal life. However, low power density and high internal resistance of MFCs are two pronounced problems in their operation. A single-hop WSN powered by a TMFC experimental setup was designed and experimented with. Power generation performance of the proposed TMFC, the relationships between the performance of the power generation and the environment temperature, the water content of the soil by weight were measured by experiments. Results show that the TMFC can achieve good power generation performance under special environmental conditions. Furthermore, the experiments with sensor data acquisition and wireless transmission of the TMFC powering WSN were carried out. We demonstrate that the obtained experimental results validate the feasibility of TMFCs powering WSNs. PMID:27213346

Performance and microbial community dynamics of electricity-assisted sequencing batch reactor (SBR) for treatment of saline petrochemical wastewater.

PubMed

Liu, Jiaxin; Shi, Shengnan; Ji, Xiangyu; Jiang, Bei; Xue, Lanlan; Li, Meidi; Tan, Liang

2017-07-01

High-salinity wastewater is often difficult to treat by common biological technologies due to salinity stress on the bacterial community. Electricity-assisted anaerobic technologies have significantly enhanced the treatment performance by alleviating the impact of salinity stress on the bacterial community, but electricity-assisted aerobic technologies have less been reported. Herein, a novel bio-electrochemistry system has been designed and operated in which a pair of stainless iron mesh-graphite plate electrodes were installed into a sequencing batch reactor (SBR, designated as S1) to strengthen the performance of saline petrochemical wastewater under aerobic conditions. The removal efficiency of phenol and chemical oxygen demand (COD) in S1 were 94.1 and 91.2%, respectively, on day 45, which was clearly higher than the removal efficiency of a single SBR (S2) and an electrochemical reactor (S3), indicating that a coupling effect existed between the electrochemical process and biodegradation. A certain amount of salinity (≤8000 mg/L) could enhance the treatment performance in S1 but weaken that in S2. Illumina sequencing revealed that microbial communities in S1 on days 45 and 91 were richer and more diverse than in S2, which suggests that electrical stimulation could enhance the diversity and richness of the microbial community, and reduce the negative effect of salinity on the microorganisms and enrich some salt-adapted microorganisms, thus improve the ability of S1 to respond to salinity stress. This novel bio-electrochemistry system was shown to be an alternative technology for the high saline petrochemical wastewater.

Research on florfenicol residue in coastal area of dalian (northern china) and analysis of functional diversity of the microbial community in marine sediment.

PubMed

Zong, Humin; Ma, Deyi; Wang, Juying; Hu, Jiangtao

2010-02-01

An analytical method based on high performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS) has been developed to investigate florfenicol residues. Among 11 stations, florfenicol was detected in six water samples. The concentrations of florfenicol in the six samples were 64.2 microg L(-1), 390.6 microg L(-1), 1.1 x 10(4) microg L(-1), 29.8 microg L(-1), 61.6 microg L(-1), 34.9 microg L(-1), respectively. These results showed that high levels of florfenicol were observed in water samples collected from stations influenced by aquaculture discharges. However, no florfenicol residue was detected in the sediment samples. Furthermore, the functional diversities of microbial community in four marine sediment samples were analyzed by Biolog microplate. For the sediment samples from the stations where antibacterials had been used, the functional diversity of microbial community was much lower than those from the stations where antibacterials were not used.

Phenol-degrading anode biofilm with high coulombic efficiency in graphite electrodes microbial fuel cell.

PubMed

Zhang, Dongdong; Li, Zhiling; Zhang, Chunfang; Zhou, Xue; Xiao, Zhixing; Awata, Takanori; Katayama, Arata

2017-03-01

A microbial fuel cell (MFC), with graphite electrodes as both the anode and cathode, was operated with a soil-free anaerobic consortium for phenol degradation. This phenol-degrading MFC showed high efficiency with a current density of 120 mA/m 2 and a coulombic efficiency of 22.7%, despite the lack of a platinum catalyst cathode and inoculation of sediment/soil. Removal of planktonic bacteria by renewing the anaerobic medium did not decrease the performance, suggesting that the phenol-degrading MFC was not maintained by the planktonic bacteria but by the microorganisms in the anode biofilm. Cyclic voltammetry analysis of the anode biofilm showed distinct oxidation and reduction peaks. Analysis of the microbial community structure of the anode biofilm and the planktonic bacteria based on 16S rRNA gene sequences suggested that Geobacter sp. was the phenol degrader in the anode biofilm and was responsible for current generation. Copyright © 2016 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Carrot Juice Fermentations as Man-Made Microbial Ecosystems Dominated by Lactic Acid Bacteria.

PubMed

Wuyts, Sander; Van Beeck, Wannes; Oerlemans, Eline F M; Wittouck, Stijn; Claes, Ingmar J J; De Boeck, Ilke; Weckx, Stefan; Lievens, Bart; De Vuyst, Luc; Lebeer, Sarah

2018-06-15

Spontaneous vegetable fermentations, with their rich flavors and postulated health benefits, are regaining popularity. However, their microbiology is still poorly understood, therefore raising concerns about food safety. In addition, such spontaneous fermentations form interesting cases of man-made microbial ecosystems. Here, samples from 38 carrot juice fermentations were collected through a citizen science initiative, in addition to three laboratory fermentations. Culturing showed that Enterobacteriaceae were outcompeted by lactic acid bacteria (LAB) between 3 and 13 days of fermentation. Metabolite-target analysis showed that lactic acid and mannitol were highly produced, as well as the biogenic amine cadaverine. High-throughput 16S rRNA gene sequencing revealed that mainly species of Leuconostoc and Lactobacillus (as identified by 8 and 20 amplicon sequence variants [ASVs], respectively) mediated the fermentations in subsequent order. The analyses at the DNA level still detected a high number of Enterobacteriaceae , but their relative abundance was low when RNA-based sequencing was performed to detect presumptive metabolically active bacterial cells. In addition, this method greatly reduced host read contamination. Phylogenetic placement indicated a high LAB diversity, with ASVs from nine different phylogenetic groups of the Lactobacillus genus complex. However, fermentation experiments with isolates showed that only strains belonging to the most prevalent phylogenetic groups preserved the fermentation dynamics. The carrot juice fermentation thus forms a robust man-made microbial ecosystem suitable for studies on LAB diversity and niche specificity. IMPORTANCE The usage of fermented food products by professional chefs is steadily growing worldwide. Meanwhile, this interest has also increased at the household level. However, many of these artisanal food products remain understudied. Here, an extensive microbial analysis was performed of spontaneous fermented carrot juices which are used as nonalcoholic alternatives for wine in a Belgian Michelin star restaurant. Samples were collected through an active citizen science approach with 38 participants, in addition to three laboratory fermentations. Identification of the main microbial players revealed that mainly species of Leuconostoc and Lactobacillus mediated the fermentations in subsequent order. In addition, a high diversity of lactic acid bacteria was found; however, fermentation experiments with isolates showed that only strains belonging to the most prevalent lactic acid bacteria preserved the fermentation dynamics. Finally, this study showed that the usage of RNA-based 16S rRNA amplicon sequencing greatly reduces host read contamination. Copyright © 2018 American Society for Microbiology.

Graphite anode surface modification with controlled reduction of specific aryl diazonium salts for improved microbial fuel cells power output.

PubMed

Picot, Matthieu; Lapinsonnière, Laure; Rothballer, Michael; Barrière, Frédéric

2011-10-15

Graphite electrodes were modified with reduction of aryl diazonium salts and implemented as anodes in microbial fuel cells. First, reduction of 4-aminophenyl diazonium is considered using increased coulombic charge density from 16.5 to 200 mC/cm(2). This procedure introduced aryl amine functionalities at the surface which are neutral at neutral pH. These electrodes were implemented as anodes in "H" type microbial fuel cells inoculated with waste water, acetate as the substrate and using ferricyanide reduction at the cathode and a 1000 Ω external resistance. When the microbial anode had developed, the performances of the microbial fuel cells were measured under acetate saturation conditions and compared with those of control microbial fuel cells having an unmodified graphite anode. We found that the maximum power density of microbial fuel cell first increased as a function of the extent of modification, reaching an optimum after which it decreased for higher degree of surface modification, becoming even less performing than the control microbial fuel cell. Then, the effect of the introduction of charged groups at the surface was investigated at a low degree of surface modification. It was found that negatively charged groups at the surface (carboxylate) decreased microbial fuel cell power output while the introduction of positively charged groups doubled the power output. Scanning electron microscopy revealed that the microbial anode modified with positively charged groups was covered by a dense and homogeneous biofilm. Fluorescence in situ hybridization analyses showed that this biofilm consisted to a large extent of bacteria from the known electroactive Geobacter genus. In summary, the extent of modification of the anode was found to be critical for the microbial fuel cell performance. The nature of the chemical group introduced at the electrode surface was also found to significantly affect the performance of the microbial fuel cells. The method used for modification is easy to control and can be optimized and implemented for many carbon materials currently used in microbial fuel cells and other bioelectrochemical systems. Copyright © 2011 Elsevier B.V. All rights reserved.

Relationships between soil organic matter, nutrients, bacterial community structure, and the performance of microbial fuel cells.

PubMed

Dunaj, Sara J; Vallino, Joseph J; Hines, Mark E; Gay, Marcus; Kobyljanec, Christine; Rooney-Varga, Juliette N

2012-02-07

Microbial fuel cells (MFCs) offer the potential for generating electricity, mitigating greenhouse gas emissions, and bioremediating pollutants through utilization of a plentiful renewable resource: soil organic carbon. We analyzed bacterial community structure, MFC performance, and soil characteristics in different microhabitats within MFCs constructed from agricultural or forest soils in order to determine how soil type and bacterial dynamics influence MFC performance. Our results indicated that MFCs constructed from agricultural soil had power output about 17 times that of forest soil-based MFCs and respiration rates about 10 times higher than forest soil MFCs. Agricultural soil MFCs had lower C:N ratios, polyphenol content, and acetate concentrations than forest soil MFCs. Bacterial community profile data indicate that the bacterial communities at the anode of the high power MFCs were less diverse than in low power MFCs and were dominated by Deltaproteobacteria, Geobacter, and to a lesser extent, Clostridia, while low-power MFC anode communities were dominated by Clostridia. These results suggest that the presence of organic carbon substrate (acetate) was not the major limiting factor in selecting for highly electrogenic bacterial communities, while the quality of available organic matter may have played a significant role in supporting high performing bacterial communities.

Changes in the ginsenoside content during the fermentation process using microbial strains.

PubMed

Lee, So Jin; Kim, Yunjeong; Kim, Min-Gul

2015-10-01

Red ginseng (RG) is processed from Panax ginseng via several methods including heat treatment, mild acid hydrolysis, and microbial conversion to transform the major ginsenosides into minor ginsenosides, which have greater pharmaceutical activities. During the fermentation process using microbial strains in a machine for making red ginseng, a change of composition occurs after heating. Therefore, we confirmed that fermentation had occurred using only microbial strains and evaluated the changes in the ginsenosides and their chemical composition. To confirm the fermentation by microbial strains, the fermented red ginseng was made with microbial strains (w-FRG) or without microbial strains (n-FRG), and the fermentation process was performed to tertiary fermentation. The changes in the ginsenoside composition of the self-manufactured FRG using the machine were evaluated using HPLC, and the 20 ginsenosides were analyzed. Additionally, we investigated changes of the reducing sugar and polyphenol contents during fermentation process. In the fermentation process, ginsenosides Re, Rg1, and Rb1 decreased but ginsenosides Rh1, F2, Rg3, and Compound Y (C.Y) increased in primary FRG more than in the raw ginseng and RG. The content of phenolic compounds was high in FRG and the highest in the tertiary w-FRG. Moreover, the reducing sugar content was approximately three times higher in the tertiary w-FRG than in the other n-FRG. As the results indicate, we confirmed the changes in the ginsenoside content and the role of microbial strains in the fermentation process.

Development of transparent microwell arrays for optical monitoring and dissection of microbial communities

DOE PAGES

Halsted, Michelle; Wilmoth, Jared L.; Briggs, Paige A.; ...

2016-09-29

Microbial communities are incredibly complex systems that dramatically and ubiquitously influence our lives. They help to shape our climate and environment, impact agriculture, drive business, and have a tremendous bearing on healthcare and physical security. Spatial confinement, as well as local variations in physical and chemical properties, affects development and interactions within microbial communities that occupy critical niches in the environment. Recent work has demonstrated the use of silicon based microwell arrays, combined with parylene lift-off techniques, to perform both deterministic and stochastic assembly of microbial communities en masse, enabling the high-throughput screening of microbial communities for their response tomore » growth in confined environments under different conditions. The implementation of a transparent microwell array platform can expand and improve the imaging modalities that can be used to characterize these assembled communities. In this paper, the fabrication and characterization of a next generation transparent microwell array is described. The transparent arrays, comprised of SU-8 patterned on a glass coverslip, retain the ability to use parylene lift-off by integrating a low temperature atomic layer deposition of silicon dioxide into the fabrication process. This silicon dioxide layer prevents adhesion of the parylene material to the patterned SU-8, facilitating dry lift-off, and maintaining the ability to easily assemble microbial communities within the microwells. These transparent microwell arrays can screen numerous community compositions using continuous, high resolution, imaging. Finally, the utility of the design was successfully demonstrated through the stochastic seeding and imaging of green fluorescent protein expressing Escherichia coli using both fluorescence and brightfield microscopies.« less

Influences of dissolved oxygen concentration on biocathodic microbial communities in microbial fuel cells.

PubMed

Rago, Laura; Cristiani, Pierangela; Villa, Federica; Zecchin, Sarah; Colombo, Alessandra; Cavalca, Lucia; Schievano, Andrea

2017-08-01

Dissolved oxygen (DO) at cathodic interface is a critical factor influencing microbial fuel cells (MFC) performance. In this work, three MFCs were operated with cathode under different DO conditions: i) air-breathing (A-MFC); ii) water-submerged (W-MFC) and iii) assisted by photosynthetic microorganisms (P-MFC). A plateau of maximum current was reached at 1.06±0.03mA, 1.48±0.06mA and 1.66±0.04mA, increasing respectively for W-MFC, P-MFC and A-MFC. Electrochemical and microbiological tools (Illumina sequencing, confocal microscopy and biofilm cryosectioning) were used to explore anodic and cathodic biofilm in each MFC type. In all cases, biocathodes improved oxygen reduction reaction (ORR) as compared to abiotic condition and A-MFC was the best performing system. Photosynthetic cultures in the cathodic chamber supplied high DO level, up to 16mg O2 L -1 , which sustained aerobic microbial community in P-MFC biocathode. Halomonas, Pseudomonas and other microaerophilic genera reached >50% of the total OTUs. The presence of sulfur reducing bacteria (Desulfuromonas) and purple non-sulfur bacteria in A-MFC biocathode suggested that the recirculation of sulfur compounds could shuttle electrons to sustain the reduction of oxygen as final electron acceptor. The low DO concentration limited the cathode in W-MFC. A model of two different possible microbial mechanisms is proposed which can drive predominantly cathodic ORR. Copyright © 2017 Elsevier B.V. All rights reserved.

Assessment of microbiome changes after rumen transfaunation: implications on improving feed efficiency in beef cattle.

PubMed

Zhou, Mi; Peng, Yong-Jia; Chen, Yanhong; Klinger, Christen M; Oba, Masahito; Liu, Jian-Xin; Guan, Le Luo

2018-03-27

Understanding the host impact on its symbiotic microbiota is important in redirecting the rumen microbiota and thus improving animal performance. The current study aimed to understand how rumen microbiota were altered and re-established after being emptied and receiving content from donor, thus to understand the impact of such process on rumen microbial fermentation and to explore the microbial phylotypes with higher manipulation potentials. Individual animal had strong effect on the re-establishment of the bacterial community according to the observed profiles detected by both fingerprinting and pyrosequencing. Most of the bacterial profile recovery patterns and extents at genus level varied among steers; and each identified bacterial genus responded to transfaunation differently within each host. Coriobacteriaceae, Coprococcus, and Lactobacillus were found to be the most responsive and tunable genera by exchanging rumen content. Besides, the association of 18 bacterial phylotypes with host fermentation parameters suggest that these phylotypes should also be considered as the regulating targets in improving host feed efficiency. In addition, the archaeal community had different re-establishment patterns for each host as determined by fingerprint profiling: it was altered after receiving non-native microbiome in some animals, while it resumed its original status after the adaptation period in the other ones. The highly individualized microbial re-establishment process suggested the importance of considering host genetics, microbial functional genomics, and host fermentation/performance assessment when developing effective and selective microbial manipulation methods for improving animal feed efficiency.

Temperature and solids retention time control microbial population dynamics and volatile fatty acid production in replicated anaerobic digesters

PubMed Central

Vanwonterghem, Inka; Jensen, Paul D.; Rabaey, Korneel; Tyson, Gene W.

2015-01-01

Anaerobic digestion is a widely used technology for waste stabilization and generation of biogas, and has recently emerged as a potentially important process for the production of high value volatile fatty acids (VFAs) and alcohols. Here, three reactors were seeded with inoculum from a stably performing methanogenic digester, and selective operating conditions (37°C and 55°C; 12 day and 4 day solids retention time) were applied to restrict methanogenesis while maintaining hydrolysis and fermentation. Replicated experiments performed at each set of operating conditions led to reproducible VFA production profiles which could be correlated with specific changes in microbial community composition. The mesophilic reactor at short solids retention time showed accumulation of propionate and acetate (42 ± 2% and 15 ± 6% of CODhydrolyzed, respectively), and dominance of Fibrobacter and Bacteroidales. Acetate accumulation (>50% of CODhydrolyzed) was also observed in the thermophilic reactors, which were dominated by Clostridium. Under all tested conditions, there was a shift from acetoclastic to hydrogenotrophic methanogenesis, and a reduction in methane production by >50% of CODhydrolyzed. Our results demonstrate that shortening the SRT and increasing the temperature are effective strategies for driving microbial communities towards controlled production of high levels of specific volatile fatty acids. PMID:25683239

CO2 Fixation, Lipid Production, and Power Generation by a Novel Air-Lift-Type Microbial Carbon Capture Cell System.

PubMed

Hu, Xia; Liu, Baojun; Zhou, Jiti; Jin, Ruofei; Qiao, Sen; Liu, Guangfei

2015-09-01

An air-lift-type microbial carbon capture cell (ALMCC) was constructed for the first time by using an air-lift-type photobioreactor as the cathode chamber. The performance of ALMCC in fixing high concentration of CO2, producing energy (power and biodiesel), and removing COD together with nutrients was investigated and compared with the traditional microbial carbon capture cell (MCC) and air-lift-type photobioreactor (ALP). The ALMCC system produced a maximum power density of 972.5 mW·m(-3) and removed 86.69% of COD, 70.52% of ammonium nitrogen, and 69.24% of phosphorus, which indicate that ALMCC performed better than MCC in terms of power generation and wastewater treatment efficiency. Besides, ALMCC demonstrated 9.98- and 1.88-fold increases over ALP and MCC in the CO2 fixation rate, respectively. Similarly, the ALMCC significantly presented a higher lipid productivity compared to those control reactors. More importantly, the preliminary analysis of energy balance suggested that the net energy of the ALMCC system was significantly superior to other systems and could theoretically produce enough energy to cover its consumption. In this work, the established ALMCC system simultaneously achieved the high level of CO2 fixation, energy recycle, and municipal wastewater treatment effectively and efficiently.

Metagenomic and metaproteomic analyses of Accumulibacter phosphatis-enriched floccular and granular biofilm.

PubMed

Barr, Jeremy J; Dutilh, Bas E; Skennerton, Connor T; Fukushima, Toshikazu; Hastie, Marcus L; Gorman, Jeffrey J; Tyson, Gene W; Bond, Philip L

2016-01-01

Biofilms are ubiquitous in nature, forming diverse adherent microbial communities that perform a plethora of functions. Here we operated two laboratory-scale sequencing batch reactors enriched with Candidatus Accumulibacter phosphatis (Accumulibacter) performing enhanced biological phosphorus removal. Reactors formed two distinct biofilms, one floccular biofilm, consisting of small, loose, microbial aggregates, and one granular biofilm, forming larger, dense, spherical aggregates. Using metagenomic and metaproteomic methods, we investigated the proteomic differences between these two biofilm communities, identifying a total of 2022 unique proteins. To understand biofilm differences, we compared protein abundances that were statistically enriched in both biofilm states. Floccular biofilms were enriched with pathogenic secretion systems suggesting a highly competitive microbial community. Comparatively, granular biofilms revealed a high-stress environment with evidence of nutrient starvation, phage predation pressure, and increased extracellular polymeric substance and cell lysis. Granular biofilms were enriched in outer membrane transport proteins to scavenge the extracellular milieu for amino acids and other metabolites, likely released through cell lysis, to supplement metabolic pathways. This study provides the first detailed proteomic comparison between Accumulibacter-enriched floccular and granular biofilm communities, proposes a conceptual model for the granule biofilm, and offers novel insights into granule biofilm formation and stability. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Digestion performance and microbial community in full-scale methane fermentation of stillage from sweet potato-shochu production.

PubMed

Kobayashi, Tsutomu; Tang, Yueqin; Urakami, Toyoshi; Morimura, Shigeru; Kida, Kenji

2014-02-01

Sweet potato shochu is a traditional Japanese spirit produced mainly in the South Kyushu area in Japan. The amount of stillage reaches approximately 8 x 10(5) tons per year. Wastewater mainly containing stillage from the production of sweet potato-shochu was treated thermophilically in a full-scale treatment plant using fixed-bed reactors (8 reactors x 283 m3). Following the addition of Ni2+ and Co2+, the reactors have been stably operated for six years at a high chemical oxygen demand (COD) loading rate of 14 kg/(m3 x day). Analysis of coenzyme content and microbial communities indicated that similar microbial communities were present in the liquid phase and on the fiber carriers installed in reactors. Bacteria in the phyla Firmicutes as well as Bacteroidetes were dominant bacteria, and Methanosarcina thermophila as well as Methanothermobacter crinale were dominant methanogens in the reactors. This study reveals that stillage from sweet potato-shochu production can be treated effectively in a full-scale fixed-bed reactor under thermophilic conditions with the help of Ni2+ and Co2+. The high diversity of bacterial community and the coexistence of both aceticlastic and hydrogenotrophic methanogens contributed to the excellent fermentation performance.

Temperature and solids retention time control microbial population dynamics and volatile fatty acid production in replicated anaerobic digesters

NASA Astrophysics Data System (ADS)

Vanwonterghem, Inka; Jensen, Paul D.; Rabaey, Korneel; Tyson, Gene W.

2015-02-01

Anaerobic digestion is a widely used technology for waste stabilization and generation of biogas, and has recently emerged as a potentially important process for the production of high value volatile fatty acids (VFAs) and alcohols. Here, three reactors were seeded with inoculum from a stably performing methanogenic digester, and selective operating conditions (37°C and 55°C 12 day and 4 day solids retention time) were applied to restrict methanogenesis while maintaining hydrolysis and fermentation. Replicated experiments performed at each set of operating conditions led to reproducible VFA production profiles which could be correlated with specific changes in microbial community composition. The mesophilic reactor at short solids retention time showed accumulation of propionate and acetate (42 +/- 2% and 15 +/- 6% of CODhydrolyzed, respectively), and dominance of Fibrobacter and Bacteroidales. Acetate accumulation (>50% of CODhydrolyzed) was also observed in the thermophilic reactors, which were dominated by Clostridium. Under all tested conditions, there was a shift from acetoclastic to hydrogenotrophic methanogenesis, and a reduction in methane production by >50% of CODhydrolyzed. Our results demonstrate that shortening the SRT and increasing the temperature are effective strategies for driving microbial communities towards controlled production of high levels of specific volatile fatty acids.

A Spike Cocktail Approach to Improve Microbial Performance Monitoring for Water Reuse

EPA Science Inventory

Water reuse, via either centralized treatment of traditional wastewater or decentralized treatment and on-site reuse, is becoming an increasingly important element of sustainable water management. Despite advances in waterborne pathogen detection methods, low and highly variable ...

PERFORMANCE OF STORMWATER RETENTION PONDS AND CONSTRUCTED WETLANDS IN REDUCING MICROBIAL CONCENTRATIONS

EPA Science Inventory

Stormwater runoff can transport high concentrations of pathogens to receiving waters. Bacteria indicator organisms, as surrogates for pathogens, are the most often reported cause of receiving water impairments. Stormwater best management practices (BMPs) are often considered ef...

Soil microbial respiration and PICT responses to an industrial and historic lead pollution: a field study.

PubMed

Bérard, Annette; Capowiez, Line; Mombo, Stéphane; Schreck, Eva; Dumat, Camille; Deola, Frédéric; Capowiez, Yvan

2016-03-01

We performed a field investigation to study the long-term impacts of Pb soil contamination on soil microbial communities and their catabolic structure in the context of an industrial site consisting of a plot of land surrounding a secondary lead smelter. Microbial biomass, catabolic profiles, and ecotoxicological responses (PICT) were monitored on soils sampled at selected locations along 110-m transects established on the site. We confirmed the high toxicity of Pb on respirations and microbial and fungal biomasses by measuring positive correlations with distance from the wall factory and negative correlation with total Pb concentrations. Pb contamination also induced changes in microbial and fungal catabolic structure (from carbohydrates to amino acids through carboxylic malic acid). Moreover, PICT measurement allowed to establish causal linkages between lead and its effect on biological communities taking into account the contamination history of the ecosystem at community level. The positive correlation between qCO2 (based on respiration and substrate use) and PICT suggested that the Pb stress-induced acquisition of tolerance came at a greater energy cost for microbial communities in order to cope with the toxicity of the metal. In this industrial context of long-term polymetallic contamination dominated by Pb in a field experiment, we confirmed impacts of this metal on soil functioning through microbial communities, as previously observed for earthworm communities.

Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion.

PubMed

Vanwonterghem, Inka; Jensen, Paul D; Rabaey, Korneel; Tyson, Gene W

2016-09-01

Our understanding of the complex interconnected processes performed by microbial communities is hindered by our inability to culture the vast majority of microorganisms. Metagenomics provides a way to bypass this cultivation bottleneck and recent advances in this field now allow us to recover a growing number of genomes representing previously uncultured populations from increasingly complex environments. In this study, a temporal genome-centric metagenomic analysis was performed of lab-scale anaerobic digesters that host complex microbial communities fulfilling a series of interlinked metabolic processes to enable the conversion of cellulose to methane. In total, 101 population genomes that were moderate to near-complete were recovered based primarily on differential coverage binning. These populations span 19 phyla, represent mostly novel species and expand the genomic coverage of several rare phyla. Classification into functional guilds based on their metabolic potential revealed metabolic networks with a high level of functional redundancy as well as niche specialization, and allowed us to identify potential roles such as hydrolytic specialists for several rare, uncultured populations. Genome-centric analyses of complex microbial communities across diverse environments provide the key to understanding the phylogenetic and metabolic diversity of these interactive communities. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Principal Factors for High Performance of Odor and Methane degrading Biocover using Network Analysis

NASA Astrophysics Data System (ADS)

Jung, H.; Yun, J.; O, G. C.; Ryu, H. W.; Jeon, J. M.; Cho, K. S.

2016-12-01

Methane is 25 times more powerful greenhouse gas than carbon dioxide and plays an important role in global warming. Landfills are one of the biggest methane sources and have emitted 37% of anthropogenic methane in Korea. Applying biocovers in landfills is known to be efficient for the simultaneous mitigation of methane as well as odor which occurs severe civil claims. In this study, three pilot-scale biocovers (2.5mx5mx1m) were constructed in a sanitary landfill at Gwangyang, Korea to establish the optimal operational conditions of biocover. All biocovers are filled with soil, EG microbial agent, food waste compost, and perlite with different combination. Pilot-scale biocovers have been operated since January in this year for simultaneous removal of odor and methane. The concentrations of methane and odors such as ammonia, H2S, methyl mercaptane, methylsulfide, dimetyl disulfide, i-valeraldehyde, and styrene were measured at the inlet and outlet of biocovers each month using GC and HPLC for removal performance evaluation. The biocover with highest removal efficiency eliminated 98.4% of odor and 100.0% of methane. All removal efficiencies of odor measured during experiment are in 81.1 98.4% range, and those of methane are in 3.6 100.0%. Three months later after biocover construction, all biocovers with mixed packing material showed better methane degradation performance than the biocovers packed only with soil. The packing materials of biocovers were sampled during winter (January), spring (April) and summer (July), and their microbial communities were examined based on 16S rDNA using 454 pyrosequencing to detect microbial factors that affects the removal efficiency. Methanotrophs which are known as methane-degradable bacteria take 10 25% of microbial community in biocovers, and most of those found in biocovers are type methanothrophs. Network analysis is performed and principal factors for performance improvement of biocovers are derived. Based on this study, well-designed biocovers will be newly set up in the operational landfill with the consideration of derived principal factors for high efficiency. This research was supported by the Korea Ministry of Environment as a "Converging Technology Project (2015001640003)".

Performance and microbial ecology of air-cathode microbial fuel cells with layered electrode assemblies.

PubMed

Butler, Caitlyn S; Nerenberg, Robert

2010-05-01

Microbial fuel cells (MFCs) can be built with layered electrode assemblies, where the anode, proton exchange membrane (PEM), and cathode are pressed into a single unit. We studied the performance and microbial community structure of MFCs with layered assemblies, addressing the effect of materials and oxygen crossover on the community structure. Four MFCs with layered assemblies were constructed using Nafion or Ultrex PEMs and a plain carbon cloth electrode or a cathode with an oxygen-resistant polytetrafluoroethylene diffusion layer. The MFC with Nafion PEM and cathode diffusion layer achieved the highest power density, 381 mW/m(2) (20 W/m(3)). The rates of oxygen diffusion from cathode to anode were three times higher in the MFCs with plain cathodes compared to those with diffusion-layer cathodes. Microsensor studies revealed little accumulation of oxygen within the anode cloth. However, the abundance of bacteria known to use oxygen as an electron acceptor, but not known to have exoelectrogenic activity, was greater in MFCs with plain cathodes. The MFCs with diffusion-layer cathodes had high abundance of exoelectrogenic bacteria within the genus Geobacter. This work suggests that cathode materials can significantly influence oxygen crossover and the relative abundance of exoelectrogenic bacteria on the anode, while PEM materials have little influence on anode community structure. Our results show that oxygen crossover can significantly decrease the performance of air-cathode MFCs with layered assemblies, and therefore limiting crossover may be of particular importance for these types of MFCs.

Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities.

PubMed

Parks, Donovan H; Beiko, Robert G

2013-01-01

High-throughput sequencing techniques have made large-scale spatial and temporal surveys of microbial communities routine. Gaining insight into microbial diversity requires methods for effectively analyzing and visualizing these extensive data sets. Phylogenetic β-diversity measures address this challenge by allowing the relationship between large numbers of environmental samples to be explored using standard multivariate analysis techniques. Despite the success and widespread use of phylogenetic β-diversity measures, an extensive comparative analysis of these measures has not been performed. Here, we compare 39 measures of phylogenetic β diversity in order to establish the relative similarity of these measures along with key properties and performance characteristics. While many measures are highly correlated, those commonly used within microbial ecology were found to be distinct from those popular within classical ecology, and from the recently recommended Gower and Canberra measures. Many of the measures are surprisingly robust to different rootings of the gene tree, the choice of similarity threshold used to define operational taxonomic units, and the presence of outlying basal lineages. Measures differ considerably in their sensitivity to rare organisms, and the effectiveness of measures can vary substantially under alternative models of differentiation. Consequently, the depth of sequencing required to reveal underlying patterns of relationships between environmental samples depends on the selected measure. Our results demonstrate that using complementary measures of phylogenetic β diversity can further our understanding of how communities are phylogenetically differentiated. Open-source software implementing the phylogenetic β-diversity measures evaluated in this manuscript is available at http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity.

Metal-Free Carbon-Based Materials: Promising Electrocatalysts for Oxygen Reduction Reaction in Microbial Fuel Cells

PubMed Central

Sawant, Sandesh Y.; Han, Thi Hiep; Cho, Moo Hwan

2016-01-01

Microbial fuel cells (MFCs) are a promising green approach for wastewater treatment with the simultaneous advantage of energy production. Among the various limiting factors, the cathodic limitation, with respect to performance and cost, is one of the main obstacles to the practical applications of MFCs. Despite the high performance of platinum and other metal-based cathodes, their practical use is limited by their high cost, low stability, and environmental toxicity. Oxygen is the most favorable electron acceptor in the case of MFCs, which reduces to water through a complicated oxygen reduction reaction (ORR). Carbon-based ORR catalysts possessing high surface area and good electrical conductivity improve the ORR kinetics by lowering the cathodic overpotential. Recently, a range of carbon-based materials have attracted attention for their exceptional ORR catalytic activity and high stability. Doping the carbon texture with a heteroatom improved their ORR activity remarkably through the favorable adsorption of oxygen and weaker molecular bonding. This review provides better insight into ORR catalysis for MFCs and the properties, performance, and applicability of various metal-free carbon-based electrocatalysts in MFCs to find the most appropriate cathodic catalyst for the practical applications. The approaches for improvement, key challenges, and future opportunities in this field are also explored. PMID:28029116

Microbial characterization of microbial ecosystems associated to evaporites domes of gypsum in Salar de Llamara in Atacama desert.

PubMed

Rasuk, Maria Cecilia; Kurth, Daniel; Flores, Maria Regina; Contreras, Manuel; Novoa, Fernando; Poire, Daniel; Farias, Maria Eugenia

2014-10-01

The Central Andes in northern Chile contains a large number of closed basins whose central depression is occupied by saline lakes and salt crusts (salars). One of these basins is Salar de Llamara (850 m a.s.l.), where large domed structures of seemingly evaporitic origin forming domes can be found. In this work, we performed a detailed microbial characterization of these domes. Mineralogical studies revealed gypsum (CaSO(4)) as a major component. Microbial communities associated to these structures were analysed by 454 16S rDNA amplicon sequencing and compared between winter and summer seasons. Bacteroidetes Proteobacteria and Planctomycetes remained as the main phylogenetic groups, an increased diversity was found in winter. Comparison of the upper air-exposed part and the lower water-submerged part of the domes in both seasons showed little variation in the upper zone, showing a predominance of Chromatiales (Gammaproteobacteria), Rhodospirillales (Alphaproteobacteria), and Sphingobacteriales (Bacteroidetes). However, the submerged part showed marked differences between seasons, being dominated by Proteobacteria (Alpha and Gamma) and Verrucomicrobia in summer, but with more diverse phyla found in winter. Even though not abundant by sequence, Cyanobacteria were visually identified by scanning electron microscopy (SEM), which also revealed the presence of diatoms. Photosynthetic pigments were detected by high-performance liquid chromatography, being more diverse on the upper photosynthetic layer. Finally, the system was compared with other endoevaporite, mats microbialite and Stromatolites microbial ecosystems, showing higher similitude with evaporitic ecosystems from Atacama and Guerrero Negro. This environment is of special interest for extremophile studies because microbial life develops associated to minerals in the driest desert all over the world. Nevertheless, it is endangered by mining activity associated to copper and lithium extraction; thus, its environmental protection preservation is strongly encouraged.

Microbial sensor for drug susceptibility testing of Mycobacterium tuberculosis.

PubMed

Zhang, Z-T; Wang, D-B; Li, C-Y; Deng, J-Y; Zhang, J-B; Bi, L-J; Zhang, X-E

2018-01-01

Drug susceptibility testing (DST) of clinical isolates of Mycobacterium tuberculosis is critical in treating tuberculosis. We demonstrate the possibility of using a microbial sensor to perform DST of M. tuberculosis and shorten the time required for DST. The sensor is made of an oxygen electrode with M. tuberculosis cells attached to its surface. This sensor monitors the residual oxygen consumption of M. tuberculosis cells after treatment with anti-TB drugs with glycerine as a carbon source. In principle, after drug pretreatment for 4-5 days, the response differences between the sensors made of drug-sensitive isolates are distinguishable from the sensors made of drug-resistant isolates. The susceptibility of the M. tuberculosis H37Ra strain, its mutants and 35 clinical isolates to six common anti-TB drugs: rifampicin, isoniazid, streptomycin, ethambutol, levofloxacin and para-aminosalicylic acid were tested using the proposed method. The results agreed well with the gold standard method (LJ) and were determined in significantly less time. The whole procedure takes approximately 11 days and therefore has the potential to inform clinical decisions. To our knowledge, this is the first study that demonstrates the possible application of a dissolved oxygen electrode-based microbial sensor in M. tuberculosis drug resistance testing. This study used the microbial sensor to perform DST of M. tuberculosis and shorten the time required for DST. The overall detection result of the microbial sensor agreed well with that of the conventional LJ proportion method and takes less time than the existing phenotypic methods. In future studies, we will build an O 2 electrode array microbial sensor reactor to enable a high-throughput drug resistance analysis. © 2017 The Authors. Journal of Applied Microbiology published by John Wiley & Sons Ltd on behalf of The Society for Applied Microbiology.

MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota.

PubMed

Zhang, Xu; Ning, Zhibin; Mayne, Janice; Moore, Jasmine I; Li, Jennifer; Butcher, James; Deeke, Shelley Ann; Chen, Rui; Chiang, Cheng-Kang; Wen, Ming; Mack, David; Stintzi, Alain; Figeys, Daniel

2016-06-24

The gut microbiota has been shown to be closely associated with human health and disease. While next-generation sequencing can be readily used to profile the microbiota taxonomy and metabolic potential, metaproteomics is better suited for deciphering microbial biological activities. However, the application of gut metaproteomics has largely been limited due to the low efficiency of protein identification. Thus, a high-performance and easy-to-implement gut metaproteomic approach is required. In this study, we developed a high-performance and universal workflow for gut metaproteome identification and quantification (named MetaPro-IQ) by using the close-to-complete human or mouse gut microbial gene catalog as database and an iterative database search strategy. An average of 38 and 33 % of the acquired tandem mass spectrometry (MS) spectra was confidently identified for the studied mouse stool and human mucosal-luminal interface samples, respectively. In total, we accurately quantified 30,749 protein groups for the mouse metaproteome and 19,011 protein groups for the human metaproteome. Moreover, the MetaPro-IQ approach enabled comparable identifications with the matched metagenome database search strategy that is widely used but needs prior metagenomic sequencing. The response of gut microbiota to high-fat diet in mice was then assessed, which showed distinct metaproteome patterns for high-fat-fed mice and identified 849 proteins as significant responders to high-fat feeding in comparison to low-fat feeding. We present MetaPro-IQ, a metaproteomic approach for highly efficient intestinal microbial protein identification and quantification, which functions as a universal workflow for metaproteomic studies, and will thus facilitate the application of metaproteomics for better understanding the functions of gut microbiota in health and disease.

Evaluation of an integrated continuous stirred microbial electrochemical reactor: Wastewater treatment, energy recovery and microbial community.

PubMed

Wang, Haiman; Qu, Youpeng; Li, Da; Zhou, Xiangtong; Feng, Yujie

2015-11-01

A continuous stirred microbial electrochemical reactor (CSMER) was developed by integrating anaerobic digestion (AD) and microbial electrochemical system (MES). The system was capable of treating high strength artificial wastewater and simultaneously recovering electric and methane energy. Maximum power density of 583±9, 562±7, 533±10 and 572±6 mW m(-2) were obtained by each cell in a four-independent circuit mode operation at an OLR of 12 kg COD m(-3) d(-1). COD removal and energy recovery efficiency were 87.1% and 32.1%, which were 1.6 and 2.5 times higher than that of a continuous stirred tank reactor (CSTR). Larger amount of Deltaproteobacteria (5.3%) and hydrogenotrophic methanogens (47%) can account for the better performance of CSMER, since syntrophic associations among them provided more degradation pathways compared to the CSTR. Results demonstrate the CSMER holds great promise for efficient wastewater treatment and energy recovery. Copyright © 2015 Elsevier Ltd. All rights reserved.

Dynamic bacterial and fungal microbiomes during sweet sorghum ensiling impact bioethanol production.

PubMed

Gallagher, Daniella; Parker, David; Allen, Damian J; Tsesmetzis, Nicolas

2018-05-23

Significant low-cost biofuel production volumes could be achieved from commercial-scale silage by redirecting lactic acid fermentation to ethanol production. A temporal metagenomic analysis on ensiled sweet sorghum inoculated with an ethanologenic yeast has been conducted to understand the underlying microbial processes during bioethanol production. Individual silage buckets approximating silage piles were prepared with freshly harvested material and supplemented with ethanologenic yeast, sulfuric acid or both. The ensiling progress was assessed using high performance liquid chromatography, microbial taxonomic identification and abundance. The combined treatment with Saccharomyces and acid led to a steady reduction of bacterial abundance and microbial diversity with Lactobacillus becoming the dominant genus during the late timepoints. Furthermore, the addition of acid to inhibit bacterial growth hindered Saccharomyces ability to compete with native yeasts like Candida. Knowledge of the response of the in-situ microbial community to the various treatments during ensiling will help improve current methodologies for bioethanol production. Copyright © 2018 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Methane-producing microbial community in a coal bed of the Illinois basin.

PubMed

Strapoc, Dariusz; Picardal, Flynn W; Turich, Courtney; Schaperdoth, Irene; Macalady, Jennifer L; Lipp, Julius S; Lin, Yu-Shih; Ertefai, Tobias F; Schubotz, Florence; Hinrichs, Kai-Uwe; Mastalerz, Maria; Schimmelmann, Arndt

2008-04-01

A series of molecular and geochemical studies were performed to study microbial, coal bed methane formation in the eastern Illinois Basin. Results suggest that organic matter is biodegraded to simple molecules, such as H(2) and CO(2), which fuel methanogenesis and the generation of large coal bed methane reserves. Small-subunit rRNA analysis of both the in situ microbial community and highly purified, methanogenic enrichments indicated that Methanocorpusculum is the dominant genus. Additionally, we characterized this methanogenic microorganism using scanning electron microscopy and distribution of intact polar cell membrane lipids. Phylogenetic studies of coal water samples helped us develop a model of methanogenic biodegradation of macromolecular coal and coal-derived oil by a complex microbial community. Based on enrichments, phylogenetic analyses, and calculated free energies at in situ subsurface conditions for relevant metabolisms (H(2)-utilizing methanogenesis, acetoclastic methanogenesis, and homoacetogenesis), H(2)-utilizing methanogenesis appears to be the dominant terminal process of biodegradation of coal organic matter at this location.

Electricity generation from acetate and glucose by sedimentary bacterium attached to electrode in microbial-anode fuel cells

NASA Astrophysics Data System (ADS)

Zhang, Enren; Xu, Wei; Diao, Guowang; Shuang, Chendong

Microbial-anode fuel cells (MAFCs) with high electron recovery (>50%) from acetate and glucose have been constructed in this study. By inoculating fresh sedimentary microorganisms into anaerobic anode compartments, a stable current (∼0.42 mA for acetate-fed MAFCs; ∼0.35 mA for glucose-fed MAFCs) is generated from the oxidation of the added organic matter until its concentration decreases to a low level. SEM micrographs indicate that thick biofilms of microbial communities (coccoid cells with a diameter of ∼0.5 μm in acetate-fed MAFCs; rod-shaped cells with a length of 2.0-4.0 μm and a width of 0.5-0.7 μm in glucose-fed MAFCs) completely cover the anode electrodes. These anodophillic biofilms are thought to be responsible for the current generation, and make these microbial-anode fuel cells exhibit good performance even when the growth medium is replaced by a salt buffer without any growth factor. In comparison with those microbial fuel cells that require the addition of artificial electron transfer-mediating compounds, the findings in this study imply a potential way to develop excellent mediator-less MAFCs for electricity generation from organic matter by using substrate-induced anodophillic microbial species.

Effects of salinity build-up on the performance and microbial community of partial-denitrification granular sludge with high nitrite accumulation.

PubMed

Ji, Jiantao; Peng, Yongzhen; Wang, Bo; Mai, Wenke; Li, Xiyao; Zhang, Qiong; Wang, Shuying

2018-05-31

High inorganic salts inevitably impose a toxic impact on biological treatment processes. In this study, the effect of salinity on the performance and microbial community structures of partial-denitrification (PD) was firstly investigated. Results showed the denitrifying activities of non-domesticated PD sludge were completely inhibited under a temporary high salinity (≥1.5 wt%). However, after domestication, denitrifying activities maintained above 50% of the maximum with salinity build-up step-by-step from 0.0 wt% to 3.0 wt%. High nitrite production was stably achieved during 120 days with nitrate-to-nitrite transformation ratio around 90%. Further investigation showed extracellular polymeric substances content of PD sludge increased from 184.59 mg gVSS -1 to 560.64 mg gVSS -1 , accompanied by the elevation of average particle size. This occurred against high salinity as a protective response of PD bacteria. Moreover, Thauera, the functional bacteria of PD system, was still dominant with the relative abundance increasing to 83.36% (3.0 wt%) from 51.33% (0.0 wt%). Copyright © 2018 Elsevier Ltd. All rights reserved.

Identification of Inhibitors in Lignocellulosic Slurries and Determination of Their Effect on Hydrocarbon-Producing Microorganisms

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

Yang, Shihui; Franden, Mary A; Yang, Qing

The aim of this work was to identify inhibitors in pretreated lignocellulosic slurries, evaluate high-throughput screening strategies, and investigate the impact of inhibitors on potential hydrocarbon-producing microorganisms. Compounds present in slurries that could inhibit microbial growth were identified through a detailed analysis of saccharified slurries by applying a combination of approaches of high-performance liquid chromatography, GC-MS, LC-DAD-MS, and ICP-MS. Several high-throughput assays were then evaluated to generate toxicity profiles. Our results demonstrated that Bioscreen C was useful for analyzing bacterial toxicity but not for yeast. AlamarBlue reduction assay can be a useful high-throughput assay for both bacterial and yeast strainsmore » as long as medium components do not interfere with fluorescence measurements. In addition, this work identified two major inhibitors (furfural and ammonium acetate) for three potential hydrocarbon-producing bacterial species that include Escherichia coli, Cupriavidus necator, and Rhodococcus opacus PD630, which are also the primary inhibitors for ethanologens. Here, this study was strived to establish a pipeline to quantify inhibitory compounds in biomass slurries and high-throughput approaches to investigate the effect of inhibitors on microbial biocatalysts, which can be applied for various biomass slurries or hydrolyzates generated through different pretreatment and enzymatic hydrolysis processes or different microbial candidates.« less

Identification of Inhibitors in Lignocellulosic Slurries and Determination of Their Effect on Hydrocarbon-Producing Microorganisms

DOE PAGES

Yang, Shihui; Franden, Mary A; Yang, Qing; ...

2018-04-04

The aim of this work was to identify inhibitors in pretreated lignocellulosic slurries, evaluate high-throughput screening strategies, and investigate the impact of inhibitors on potential hydrocarbon-producing microorganisms. Compounds present in slurries that could inhibit microbial growth were identified through a detailed analysis of saccharified slurries by applying a combination of approaches of high-performance liquid chromatography, GC-MS, LC-DAD-MS, and ICP-MS. Several high-throughput assays were then evaluated to generate toxicity profiles. Our results demonstrated that Bioscreen C was useful for analyzing bacterial toxicity but not for yeast. AlamarBlue reduction assay can be a useful high-throughput assay for both bacterial and yeast strainsmore » as long as medium components do not interfere with fluorescence measurements. In addition, this work identified two major inhibitors (furfural and ammonium acetate) for three potential hydrocarbon-producing bacterial species that include Escherichia coli, Cupriavidus necator, and Rhodococcus opacus PD630, which are also the primary inhibitors for ethanologens. Here, this study was strived to establish a pipeline to quantify inhibitory compounds in biomass slurries and high-throughput approaches to investigate the effect of inhibitors on microbial biocatalysts, which can be applied for various biomass slurries or hydrolyzates generated through different pretreatment and enzymatic hydrolysis processes or different microbial candidates.« less

Molecular assessment of the sensitivity of sulfate-reducing microbial communities remediating mine drainage to aerobic stress.

PubMed

Lefèvre, Emilie; Pereyra, Luciana P; Hiibel, Sage R; Perrault, Elizabeth M; De Long, Susan K; Reardon, Kenneth F; Pruden, Amy

2013-09-15

Sulfate-reducing permeable reactive zones (SR-PRZs) are microbially-driven anaerobic systems designed for the removal of heavy metals and sulfate in mine drainage. Environmental perturbations, such as oxygen exposure, may adversely affect system stability and long-term performance. The objective of this study was to examine the effect of two successive aerobic stress events on the performance and microbial community composition of duplicate laboratory-scale lignocellulosic SR-PRZs operated using the following microbial community management strategies: biostimulation with ethanol or carboxymethylcellulose; bioaugmentation with sulfate-reducing or cellulose-degrading enrichments; inoculation with dairy manure only; and no inoculation. A functional gene-based approach employing terminal restriction fragment length polymorphism and quantitative polymerase chain reaction targeting genes of sulfate-reducing (dsrA), cellulose-degrading (cel5, cel48), fermentative (hydA), and methanogenic (mcrA) microbes was applied. In terms of performance (i.e., sulfate removal), biostimulation with ethanol was the only strategy that clearly had an effect (positive) following exposure to oxygen. In terms of microbial community composition, significant shifts were observed over the course of the experiment. Results suggest that exposure to oxygen more strongly influenced microbial community shifts than the different microbial community management strategies. Sensitivity to oxygen exposure varied among different populations and was particularly pronounced for fermentative bacteria. Although the community structure remained altered after exposure, system performance recovered, indicating that SR-PRZ microbial communities were functionally redundant. Results suggest that pre-exposure to oxygen might be a more effective strategy to improve the resilience of SR-PRZ microbial communities relative to bioaugmentation or biostimulation. Copyright © 2013 Elsevier Ltd. All rights reserved.

A Spike Cocktail Approach to Improve Microbial Performance Monitoring for Water Reuse.

PubMed

Zimmerman, Brian D; Korajkic, Asja; Brinkman, Nichole E; Grimm, Ann C; Ashbolt, Nicholas J; Garland, Jay L

  Water reuse, via either centralized treatment of traditional wastewater or decentralized treatment and on-site reuse, is becoming an increasingly important element of sustainable water management. Despite advances in waterborne pathogen detection methods, low and highly variable pathogen levels limit their utility for routine evaluation of health risks in water reuse systems. Therefore, there is a need to improve our understanding of the linkage between pathogens and more readily measured process indicators during treatment. This paper describes an approach for constructing spiking experiments to relate the behavior of viral, bacterial, and protozoan pathogens with relevant process indicators. General issues are reviewed, and the spiking protocol is applied as a case study example to improve microbial performance monitoring and health risk evaluation in a water reuse system. This approach provides a foundation for the development of novel approaches to improve real or near-real time performance monitoring of water recycling systems.

Construction and performance evaluation of mediator-less microbial fuel cell using carbon nanotubes as an anode material.

PubMed

Roh, Sung-Hee; Kim, Sun-Il

2012-05-01

A microbial fuel cell (MFC) is a device that converts chemical energy to electrical energy using the catalytic reaction of microorganisms. We investigated the performance of mediator-less MFC with carbon nanotubes (CNTs)/graphite felt composite electrodes. The addition of CNTs to a graphite felt electrode increases the specific surface area of the electrode and enhances the charge transfer capability so as to cause considerable improvement of the electrochemical activity for the anode reaction in a MFC. The performance of the MFC using CNTs/graphite felt electrode has been compared against a plain graphite felt electrode based MFC. A CNTs/graphite felt electrode showed as high as 15% increase in the power density (252 mW/m2) compared to graphite felt electrode (214 mW/m2). The CNTs/graphite felt anode therefore offers good prospects for application in MFCs.

Maintenance of soil functioning following erosion of microbial diversity.

PubMed

Wertz, Sophie; Degrange, Valérie; Prosser, James I; Poly, Franck; Commeaux, Claire; Freitag, Thomas; Guillaumaud, Nadine; Roux, Xavier Le

2006-12-01

The paradigm that soil microbial communities, being very diverse, have high functional redundancy levels, so that erosion of microbial diversity is less important for ecosystem functioning than erosion of plant or animal diversity, is often taken for granted. However, this has only been demonstrated for decomposition/respiration functions, performed by a large proportion of the total microbial community, but not for specialized microbial groups. Here, we determined the impact of a decrease in soil microbial diversity on soil ecosystem processes using a removal approach, in which less abundant species were removed preferentially. This was achieved by inoculation of sterile soil microcosms with serial dilutions of a suspension obtained from the same non-sterile soil and subsequent incubation, to enable recovery of community size. The sensitivity to diversity erosion was evaluated for three microbial functional groups with known contrasting taxonomic diversities (ammonia oxidizers < denitrifiers < heterotrophs). Diversity erosion within each functional group was characterized using molecular fingerprinting techniques: ribosomal intergenic spacer analysis (RISA) for the eubacterial community, denaturing gradient gel electrophoresis (DGGE) analysis of nirK genes for denitrifiers, and DGGE analysis of 16S rRNA genes for betaproteobacterial ammonia oxidizers. In addition, we simulated the impact of the removal approach by dilution on the number of soil bacterial species remaining in the inoculum using values of abundance distribution of bacterial species reported in the literature. The reduction of the diversity of the functional groups observed from genetic fingerprints did not impair the associated functioning of these groups, i.e. carbon mineralization, denitrification and nitrification. This was remarkable, because the amplitude of diversity erosion generated by the dilution approach was huge (level of bacterial species loss was estimated to be around 99.99% for the highest dilution). Our results demonstrate that the vast diversity of the soil microbiota makes soil ecosystem functioning largely insensitive to biodiversity erosion even for functions performed by specialized groups.

Effect of copper on the performance and bacterial communities of activated sludge using Illumina MiSeq platforms.

PubMed

Sun, Fu-Lin; Fan, Lei-Lei; Xie, Guang-Jian

2016-08-01

The anaerobic-anoxic-aerobic (A2O) process is a highly efficient sewage treatment method, which uses complex bacterial communities. However, the effect of copper on this process and the bacterial communities involved remains unknown. In this study, a systematic investigation of the effect of persistent exposure of copper in the A2O wastewater treatment system was performed. An A2O device was designed to examine the effect of copper on the removal efficiency and microbial community compositions of activated sludge that was continuously treated with 10, 20, and 40 mg L(-1) copper, respectively. Surprisingly, a decrease in chemical oxygen demand (COD) and ammonia nitrogen (NH4N) removal efficiency was observed, and the toxicity of high copper concentration was significantly greater at 7d than at 1d. Proteobacteria, Bacteroidetes, Acidobacteria, Chlorobi, and Nitrospirae were the dominant bacterial taxa in the A2O system, and significant changes in microbial community were observed during the exposure period. Most of the dominant bacterial groups were easily susceptible to copper toxicity and diversely changed at different copper concentrations. However, not all the bacterial taxa were inhibited by copper treatment. At high copper concentration, many bacterial species were stimulated and their abundance increased. Cluster analysis and principal coordinate analysis (PCoA) based on operational taxonomic units (OTUs) revealed clear differences in the bacterial communities among the samples. These findings indicated that copper severely affected the performance and key microbial populations in the A2O system as well as disturbed the stability of the bacterial communities in the system, thus decreasing the removal efficiency. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

PubMed

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

2018-05-17

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

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

PubMed

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

2018-01-01

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

Genome-centric metatranscriptomes and ecological roles of the active microbial populations during cellulosic biomass anaerobic digestion.

PubMed

Jia, Yangyang; Ng, Siu-Kin; Lu, Hongyuan; Cai, Mingwei; Lee, Patrick K H

2018-01-01

Although anaerobic digestion for biogas production is used worldwide in treatment processes to recover energy from carbon-rich waste such as cellulosic biomass, the activities and interactions among the microbial populations that perform anaerobic digestion deserve further investigations, especially at the population genome level. To understand the cellulosic biomass-degrading potentials in two full-scale digesters, this study examined five methanogenic enrichment cultures derived from the digesters that anaerobically digested cellulose or xylan for more than 2 years under 35 or 55 °C conditions. Metagenomics and metatranscriptomics were used to capture the active microbial populations in each enrichment culture and reconstruct their meta-metabolic network and ecological roles. 107 population genomes were reconstructed from the five enrichment cultures using a differential coverage binning approach, of which only a subset was highly transcribed in the metatranscriptomes. Phylogenetic and functional convergence of communities by enrichment condition and phase of fermentation was observed for the highly transcribed populations in the metatranscriptomes. In the 35 °C cultures grown on cellulose, Clostridium cellulolyticum -related and Ruminococcus -related bacteria were identified as major hydrolyzers and primary fermenters in the early growth phase, while Clostridium leptum -related bacteria were major secondary fermenters and potential fatty acid scavengers in the late growth phase. While the meta-metabolism and trophic roles of the cultures were similar, the bacterial populations performing each function were distinct between the enrichment conditions. Overall, a population genome-centric view of the meta-metabolism and functional roles of key active players in anaerobic digestion of cellulosic biomass was obtained. This study represents a major step forward towards understanding the microbial functions and interactions at population genome level during the microbial conversion of lignocellulosic biomass to methane. The knowledge of this study can facilitate development of potential biomarkers and rational design of the microbiome in anaerobic digesters.

Response of anaerobic membrane bioreactor to the presence of nano-Bi2WO6: reactor performance, supernatant characteristics, and microbial community.

PubMed

Chen, Lin; Wang, Yue; Cao, Chuqing; Liu, Chang; Zhu, Liang

2017-11-01

Considering the increasing incorporation of manufactured nano-material into consumer products, there is a concern about its potential impacts in biological wastewater treatment. In this study, the response of anaerobic sludge to the presence of Bi 2 WO 6 nano-particles (NPs) was investigated in the anaerobic membrane bioreactor (AnMBR). As the concentration of Bi 2 WO 6 in the reactor was controlled around 1 mg/L, there was no significant difference in effluent water quality or bacterial activities before and after NP exposure, partially due to the microbial-induced NP aggregation and stable complex formation. However, with the increasing dosage of Bi 2 WO 6 from 5 to 40 mg/L, great influences on the AnMBR performance were observed, including the reduction of COD removal efficiency, inhibition of the mechanization step, increased production of soluble microbial products, and enhanced secretion of extracellular polymer substrates. Additional investigation with high-throughput sequencing was conducted, clearly demonstrating that Bi 2 WO 6 NPs induced changes in the bacterial community.

An Overview of Electron Acceptors in Microbial Fuel Cells

PubMed Central

Ucar, Deniz; Zhang, Yifeng; Angelidaki, Irini

2017-01-01

Microbial fuel cells (MFC) have recently received increasing attention due to their promising potential in sustainable wastewater treatment and contaminant removal. In general, contaminants can be removed either as an electron donor via microbial catalyzed oxidization at the anode or removed at the cathode as electron acceptors through reduction. Some contaminants can also function as electron mediators at the anode or cathode. While previous studies have done a thorough assessment of electron donors, cathodic electron acceptors and mediators have not been as well described. Oxygen is widely used as an electron acceptor due to its high oxidation potential and ready availability. Recent studies, however, have begun to assess the use of different electron acceptors because of the (1) diversity of redox potential, (2) needs of alternative and more efficient cathode reaction, and (3) expanding of MFC based technologies in different areas. The aim of this review was to evaluate the performance and applicability of various electron acceptors and mediators used in MFCs. This review also evaluated the corresponding performance, advantages and disadvantages, and future potential applications of select electron acceptors (e.g., nitrate, iron, copper, perchlorate) and mediators. PMID:28469607

Responses of microbial capacity and community on the performance of mesophilic co-digestion of food waste and waste activated sludge in a high-frequency feeding CSTR.

PubMed

Li, Qian; Yuwen, Chaosui; Cheng, Xinru; Yang, Xiaohuan; Chen, Rong; Wang, Xiaochang C

2018-07-01

To understand the relationship between microbes and digester performance of high-frequency feeding CSTR, which could achieve stable CH 4 production at high OLR by easing instantaneous feeding shock, attentions were paid on the variations of methanogenic capacity (MC) and microbial community with OLR increasing. Results showed that the MC for feedstock degradation could satisfy the need of effective conversion from feedstock to CH 4 when the OLR remained below 16.4 g-TS/L/d. Furthermore, the MC for acetate, propionate and butyrate degradation increased by 73.8%, 303%, and 164%, respectively, with OLR increasing from 3.03 g-TS/L/d 12.6 g-TS/L/d. The evolution of both bacterial and archaeal communities provided additional information on the adaptation of functional microbes to environmental factors. The significant increase of abundance of Methanoculleus and Methanomassiliicoccus likely promoted the utilization of H 2 , thus facilitating syntrophic methanogenesis, and consequently ensuring efficient CH 4 production in stable stage. Copyright © 2018 Elsevier Ltd. All rights reserved.

Successive DNA extractions improve characterization of soil microbial communities

PubMed Central

de Hollander, Mattias; Smidt, Hauke; van Veen, Johannes A.

2017-01-01

Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied. To determine whether successive DNA extractions of the same soil sample would lead to different observations in terms of microbial abundance and community composition, we performed three successive extractions, with two widely used commercial kits, on a range of clay and sandy soils. Successive extractions increased DNA yield considerably (1–374%), as well as total bacterial and fungal abundances in most of the soil samples. Analysis of the 16S and 18S ribosomal RNA genes using 454-pyrosequencing, revealed that microbial community composition (taxonomic groups) observed in the successive DNA extractions were similar. However, successive DNA extractions did reveal several additional microbial groups. For some soil samples, shifts in microbial community composition were observed, mainly due to shifts in relative abundance of a number of microbial groups. Our results highlight that performing successive DNA extractions optimize DNA yield, and can lead to a better picture of overall community composition. PMID:28168105

Study on Microbial Deposition and Contamination onto Six Surfaces Commonly Used in Chemical and Microbiological Laboratories

PubMed Central

Tamburini, Elena; Donegà, Valentina; Marchetti, Maria Gabriella; Pedrini, Paola; Monticelli, Cecilia; Balbo, Andrea

2015-01-01

The worktops in both chemical and microbiological laboratories are the surfaces most vulnerable to damage and exposure to contamination by indoor pollutants. The rate at which particles are deposited on indoor surfaces is an important parameter to determine human exposure to airborne biological particles. In contrast to what has been established for inorganic pollutants, no limit has been set by law for microbial contamination in indoor air. To our knowledge, a comparative study on the effect of surfaces on the deposition of microbes has not been carried out. An evaluation of the microbial contamination of worktop materials could be of crucial importance, both for safety reasons and for the reliability of tests and experiments that need to be carried out in non-contaminated environments. The aim of this study was to evaluate the overall microbial contamination (fungi, mesophilic and psychrophilic bacteria, staphylococci) on six widely used worktop materials in laboratories (glass, stainless steel, fine porcelain stoneware, post-forming laminate, high-performing laminate and enamel steel) and to correlate it with the characteristics of the surfaces. After cleaning, the kinetics of microbial re-contamination were also evaluated for all surfaces. PMID:26193296

Microbial community differentiation between active and inactive sulfide chimneys of the Kolumbo submarine volcano, Hellenic Volcanic Arc.

PubMed

Christakis, Christos A; Polymenakou, Paraskevi N; Mandalakis, Manolis; Nomikou, Paraskevi; Kristoffersen, Jon Bent; Lampridou, Danai; Kotoulas, Georgios; Magoulas, Antonios

2018-01-01

Over the last decades, there has been growing interest about the ecological role of hydrothermal sulfide chimneys, their microbial diversity and associated biotechnological potential. Here, we performed dual-index Illumina sequencing of bacterial and archaeal communities on active and inactive sulfide chimneys collected from the Kolumbo hydrothermal field, situated on a geodynamic convergent setting. A total of 15,701 OTUs (operational taxonomic units) were assigned to 56 bacterial and 3 archaeal phyla, 133 bacterial and 16 archaeal classes. Active chimney communities were dominated by OTUs related to thermophilic members of Epsilonproteobacteria, Aquificae and Deltaproteobacteria. Inactive chimney communities were dominated by an OTU closely related to the archaeon Nitrosopumilus sp., and by members of Gammaproteobacteria, Deltaproteobacteria, Planctomycetes and Bacteroidetes. These lineages are closely related to phylotypes typically involved in iron, sulfur, nitrogen, hydrogen and methane cycling. Overall, the inactive sulfide chimneys presented highly diverse and uniform microbial communities, in contrast to the active chimney communities, which were dominated by chemolithoautotrophic and thermophilic lineages. This study represents one of the most comprehensive investigations of microbial diversity in submarine chimneys and elucidates how the dissipation of hydrothermal activity affects the structure of microbial consortia in these extreme ecological niches.

Noise-free accurate count of microbial colonies by time-lapse shadow image analysis.

PubMed

Ogawa, Hiroyuki; Nasu, Senshi; Takeshige, Motomu; Funabashi, Hisakage; Saito, Mikako; Matsuoka, Hideaki

2012-12-01

Microbial colonies in food matrices could be counted accurately by a novel noise-free method based on time-lapse shadow image analysis. An agar plate containing many clusters of microbial colonies and/or meat fragments was trans-illuminated to project their 2-dimensional (2D) shadow images on a color CCD camera. The 2D shadow images of every cluster distributed within a 3-mm thick agar layer were captured in focus simultaneously by means of a multiple focusing system, and were then converted to 3-dimensional (3D) shadow images. By time-lapse analysis of the 3D shadow images, it was determined whether each cluster comprised single or multiple colonies or a meat fragment. The analytical precision was high enough to be able to distinguish a microbial colony from a meat fragment, to recognize an oval image as two colonies contacting each other, and to detect microbial colonies hidden under a food fragment. The detection of hidden colonies is its outstanding performance in comparison with other systems. The present system attained accuracy for counting fewer than 5 colonies and is therefore of practical importance. Copyright © 2012 Elsevier B.V. All rights reserved.

Terminal Restriction Fragment Length Polymorphism Analysis Program, a Web-Based Research Tool for Microbial Community Analysis

PubMed Central

Marsh, Terence L.; Saxman, Paul; Cole, James; Tiedje, James

2000-01-01

Rapid analysis of microbial communities has proven to be a difficult task. This is due, in part, to both the tremendous diversity of the microbial world and the high complexity of many microbial communities. Several techniques for community analysis have emerged over the past decade, and most take advantage of the molecular phylogeny derived from 16S rRNA comparative sequence analysis. We describe a web-based research tool located at the Ribosomal Database Project web site (http://www.cme.msu.edu/RDP/html/analyses.html) that facilitates microbial community analysis using terminal restriction fragment length polymorphism of 16S ribosomal DNA. The analysis function (designated TAP T-RFLP) permits the user to perform in silico restriction digestions of the entire 16S sequence database and derive terminal restriction fragment sizes, measured in base pairs, from the 5′ terminus of the user-specified primer to the 3′ terminus of the restriction endonuclease target site. The output can be sorted and viewed either phylogenetically or by size. It is anticipated that the site will guide experimental design as well as provide insight into interpreting results of community analysis with terminal restriction fragment length polymorphisms. PMID:10919828

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

Halsted, Michelle; Wilmoth, Jared L.; Briggs, Paige A.

Microbial communities are incredibly complex systems that dramatically and ubiquitously influence our lives. They help to shape our climate and environment, impact agriculture, drive business, and have a tremendous bearing on healthcare and physical security. Spatial confinement, as well as local variations in physical and chemical properties, affects development and interactions within microbial communities that occupy critical niches in the environment. Recent work has demonstrated the use of silicon based microwell arrays, combined with parylene lift-off techniques, to perform both deterministic and stochastic assembly of microbial communities en masse, enabling the high-throughput screening of microbial communities for their response tomore » growth in confined environments under different conditions. The implementation of a transparent microwell array platform can expand and improve the imaging modalities that can be used to characterize these assembled communities. In this paper, the fabrication and characterization of a next generation transparent microwell array is described. The transparent arrays, comprised of SU-8 patterned on a glass coverslip, retain the ability to use parylene lift-off by integrating a low temperature atomic layer deposition of silicon dioxide into the fabrication process. This silicon dioxide layer prevents adhesion of the parylene material to the patterned SU-8, facilitating dry lift-off, and maintaining the ability to easily assemble microbial communities within the microwells. These transparent microwell arrays can screen numerous community compositions using continuous, high resolution, imaging. Finally, the utility of the design was successfully demonstrated through the stochastic seeding and imaging of green fluorescent protein expressing Escherichia coli using both fluorescence and brightfield microscopies.« less

Environmental proteomics reveals early microbial community responses to biostimulation at a uranium- and nitrate-contaminated site.

PubMed

Chourey, Karuna; Nissen, Silke; Vishnivetskaya, Tatiana; Shah, Manesh; Pfiffner, Susan; Hettich, Robert L; Löffler, Frank E

2013-10-01

High-performance MS instrumentation coupled with improved protein extraction techniques enables metaproteomics to identify active members of soil and groundwater microbial communities. Metaproteomics workflows were applied to study the initial responses (i.e. 4 days post treatment) of the indigenous aquifer microbiota to biostimulation with emulsified vegetable oil (EVO) at a uranium-contaminated site. Members of the Betaproteobacteria (i.e. Dechloromonas, Ralstonia, Rhodoferax, Polaromonas, Delftia, Chromobacterium) and the Firmicutes dominated the biostimulated aquifer community. Proteome characterization revealed distinct differences between the microbial biomass collected from groundwater influenced by biostimulation and groundwater collected upgradient of the EVO injection points. In particular, proteins involved in ammonium assimilation, EVO degradation, and polyhydroxybutyrate granule formation were prominent following biostimulation. Interestingly, the atypical NosZ of Dechloromonas spp. was highly abundant, suggesting active nitrous oxide (N2 O) respiration. c-Type cytochromes were barely detected, as was citrate synthase, a biomarker for hexavalent uranium reduction activity, suggesting that uranium reduction has not commenced 4 days post EVO amendment. Environmental metaproteomics identified microbial community responses to biostimulation and elucidated active pathways demonstrating the value of this technique as a monitoring tool and for complementing nucleic acid-based approaches. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Online flow cytometry reveals microbial dynamics influenced by concurrent natural and operational events in groundwater used for drinking water treatment.

PubMed

Besmer, Michael D; Epting, Jannis; Page, Rebecca M; Sigrist, Jürg A; Huggenberger, Peter; Hammes, Frederik

2016-12-07

Detailed measurements of physical, chemical and biological dynamics in groundwater are key to understanding the important processes in place and their influence on water quality - particularly when used for drinking water. Measuring temporal bacterial dynamics at high frequency is challenging due to the limitations in automation of sampling and detection of the conventional, cultivation-based microbial methods. In this study, fully automated online flow cytometry was applied in a groundwater system for the first time in order to monitor microbial dynamics in a groundwater extraction well. Measurements of bacterial concentrations every 15 minutes during 14 days revealed both aperiodic and periodic dynamics that could not be detected previously, resulting in total cell concentration (TCC) fluctuations between 120 and 280 cells μL -1 . The aperiodic dynamic was linked to river water contamination following precipitation events, while the (diurnal) periodic dynamic was attributed to changes in hydrological conditions as a consequence of intermittent groundwater extraction. Based on the high number of measurements, the two patterns could be disentangled and quantified separately. This study i) increases the understanding of system performance, ii) helps to optimize monitoring strategies, and iii) opens the possibility for more sophisticated (quantitative) microbial risk assessment of drinking water treatment systems.

Online flow cytometry reveals microbial dynamics influenced by concurrent natural and operational events in groundwater used for drinking water treatment

PubMed Central

Besmer, Michael D.; Epting, Jannis; Page, Rebecca M.; Sigrist, Jürg A.; Huggenberger, Peter; Hammes, Frederik

2016-01-01

Detailed measurements of physical, chemical and biological dynamics in groundwater are key to understanding the important processes in place and their influence on water quality – particularly when used for drinking water. Measuring temporal bacterial dynamics at high frequency is challenging due to the limitations in automation of sampling and detection of the conventional, cultivation-based microbial methods. In this study, fully automated online flow cytometry was applied in a groundwater system for the first time in order to monitor microbial dynamics in a groundwater extraction well. Measurements of bacterial concentrations every 15 minutes during 14 days revealed both aperiodic and periodic dynamics that could not be detected previously, resulting in total cell concentration (TCC) fluctuations between 120 and 280 cells μL−1. The aperiodic dynamic was linked to river water contamination following precipitation events, while the (diurnal) periodic dynamic was attributed to changes in hydrological conditions as a consequence of intermittent groundwater extraction. Based on the high number of measurements, the two patterns could be disentangled and quantified separately. This study i) increases the understanding of system performance, ii) helps to optimize monitoring strategies, and iii) opens the possibility for more sophisticated (quantitative) microbial risk assessment of drinking water treatment systems. PMID:27924920

Natural Microbial Assemblages Reflect Distinct Organismal and Functional Partitioning

NASA Astrophysics Data System (ADS)

Wilmes, P.; Andersson, A.; Kalnejais, L. H.; Verberkmoes, N. C.; Lefsrud, M. G.; Wexler, M.; Singer, S. W.; Shah, M.; Bond, P. L.; Thelen, M. P.; Hettich, R. L.; Banfield, J. F.

2007-12-01

The ability to link microbial community structure to function has long been a primary focus of environmental microbiology. With the advent of community genomic and proteomic techniques, along with advances in microscopic imaging techniques, it is now possible to gain insights into the organismal and functional makeup of microbial communities. Biofilms growing within highly acidic solutions inside the Richmond Mine (Iron Mountain, Redding, California) exhibit distinct macro- and microscopic morphologies. They are composed of microorganisms belonging to the three domains of life, including archaea, bacteria and eukarya. The proportion of each organismal type depends on sampling location and developmental stage. For example, mature biofilms floating on top of acid mine drainage (AMD) pools exhibit layers consisting of a densely packed bottom layer of the chemoautolithotroph Leptospirillum group II, a less dense top layer composed mainly of archaea, and fungal filaments spanning across the entire biofilm. The expression of cytochrome 579 (the most highly abundant protein in the biofilm, believed to be central to iron oxidation and encoded by Leptospirillum group II) is localized at the interface of the biofilm with the AMD solution, highlighting that biofilm architecture is reflected at the functional gene expression level. Distinct functional partitioning is also apparent in a biological wastewater treatment system that selects for distinct polyphosphate accumulating organisms. Community genomic data from " Candidatus Accumulibacter phosphatis" dominated activated sludge has enabled high mass-accuracy shotgun proteomics for identification of key metabolic pathways. Comprehensive genome-wide alignment of orthologous proteins suggests distinct partitioning of protein variants involved in both core-metabolism and specific metabolic pathways among the dominant population and closely related species. In addition, strain- resolved proteogenomic analysis of the AMD biofilms also highlights the importance of strain heterogeneity for the maintenance of community structure and function. These findings explain the importance of genetic diversity in facilitating the stable performance of complex microbial processes. Furthermore, although very different in terms of habitat, both microbial communities exhibit distinct functional compartmentalization and demonstrate its role in sustaining microbial community structure.

Role of biochar as an additive in organic waste composting.

PubMed

Sanchez-Monedero, M A; Cayuela, M L; Roig, A; Jindo, K; Mondini, C; Bolan, N

2018-01-01

The use of biochar in organic waste composting has attracted interest in the last decade due to the environmental and agronomical benefits obtained during the process. Biochar presents favourable physicochemical properties, such as large porosity, surface area and high cation exchange capacity, enabling interaction with major nutrient cycles and favouring microbial growth in the composting pile. The enhanced environmental conditions can promote a change in the microbial communities that can affect important microbially mediated biogeochemical cycles: organic matter degradation and humification, nitrification, denitrification and methanogenesis. The main benefits of the use of biochar in composting are reviewed in this article, with special attention to those related to the process performance, compost microbiology, organic matter degradation and humification, reduction of N losses and greenhouse gas emissions and fate of heavy metals. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

Microbial fuel cells in saline and hypersaline environments: Advancements, challenges and future perspectives.

PubMed

Grattieri, Matteo; Minteer, Shelley D

2018-04-01

This review is aimed to report the possibility to utilize microbial fuel cells for the treatment of saline and hypersaline solutions. An introduction to the issues related with the biological treatment of saline and hypersaline wastewater is reported, discussing the limitation that characterizes classical aerobic and anaerobic digestions. The microbial fuel cell (MFC) technology, and the possibility to be applied in the presence of high salinity, is discussed before reviewing the most recent advancements in the development of MFCs operating in saline and hypersaline conditions, with their different and interesting applications. Specifically, the research performed in the last 5years will be the main focus of this review. Finally, the future perspectives for this technology, together with the most urgent research needs, are presented. Copyright © 2017 Elsevier B.V. All rights reserved.

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

PubMed

Xu, Jianping

2006-06-01

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

Single chamber microbial fuel cell with spiral anode for dairy wastewater treatment.

PubMed

Mardanpour, Mohammad Mahdi; Nasr Esfahany, Mohsen; Behzad, Tayebeh; Sedaqatvand, Ramin

2012-01-01

This study reports on the fabrication of a novel annular single chamber microbial fuel cell (ASCMFC) with spiral anode. The stainless steel mesh anode with graphite coating was used as anode. Dairy wastewater, containing complex organic matter, was used as substrate. ASCMFC had been operated for 450 h and results indicated a high open circuit voltage (about 810 mV) compared with previously published results. The maximum power density of 20.2 W/m(3) obtained in this study is significantly greater than the power densities reported in previous studies. Besides, a maximum coulombic efficiency of 26.87% with 91% COD removal was achieved. Good bacterial adhesion on the spiral anode is clearly shown in SEM micrographs. High power density and a successful performance in wastewater treatment in ASCMFC suggest it as a promising alternative to conventional MFCs for power generation and wastewater treatment. ASCMFC performance as a power generator was characterized based on polarization behavior and cell potentials. Copyright © 2012 Elsevier B.V. All rights reserved.

Methanogenic and Sulfate-Reducing Activities in a Hypersaline Microbial Mat and Associated Microbial Diversity.

PubMed

Cadena, Santiago; García-Maldonado, José Q; López-Lozano, Nguyen E; Cervantes, Francisco J

2018-05-01

Methanogenesis and sulfate reduction are important microbial processes in hypersaline environments. However, key aspects determining substrate competition between these microbial processes have not been well documented. We evaluated competitive and non-competitive substrates for stimulation of both processes through microcosm experiments of hypersaline microbial mat samples from Guerrero Negro, Baja California Sur, Mexico, and we assessed the effect of these substrates on the microbial community composition. Methylotrophic methanogenesis evidenced by sequences belonging to methanogens of the family Methanosarcinaceae was found as the dominant methanogenic pathway in the studied hypersaline microbial mat. Nevertheless, our results showed that incubations supplemented with acetate and lactate, performed in absence of sulfate, also produced methane after 40 days of incubation, apparently driven by hydrogenotrophic methanogens affiliated to the family Methanomicrobiaceae. Sulfate reduction was mainly stimulated by addition of acetate and lactate; however, after 40 days of incubation, an increase of the H 2 S concentrations in microcosms amended with trimethylamine and methanol was also observed, suggesting that these substrates are putatively used for sulfate reduction. Moreover, 16S rRNA gene sequencing analysis showed remarkable differences in the microbial community composition among experimental treatments. In the analyzed sample amended with acetate, sulfate-reducing bacteria (SRB) belonging to the family Desulfobacteraceae were dominant, while members of Desulfohalobiaceae, Desulfomicrobiaceae, and Desulfovibrionaceae were found in the incubation with lactate. Additionally, we detected an unexpected high abundance of unclassified Hydrogenedentes (near 25%) in almost all the experimental treatments. This study contributes to better understand methanogenic and sulfate-reducing activities, which play an important role in the functioning of hypersaline environments.

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.

Detection of antibiotics in goat's milk: effect of detergents on the response of microbial inhibitor tests.

PubMed

Romero, Tamara; Beltrán, María Carmen; Althaus, Rafael Lisandro; Molina, María Pilar

2014-08-01

The aim of the study was to evaluate the interference of acid and alkaline detergents employed in the cleaning of milking equipment of caprine dairy farms on the performance of microbial tests used in antibiotic control (BRT MRL, Delvotest MCS, and Eclipse 100). Eight concentrations of commercial detergents, five acid (0-0.25%) and five alkaline (0-1%) were add to antimicrobial-free goat's milk to evaluate the detergent effect on the response of microbial inhibitor tests. To evaluate the effect of detergents on the detection capability of microbial tests two detergents at 0.5 ml/l (one acid and one basic) and eight concentrations of four β-lactam antibiotics (ampicillin, amoxicillin, cloxacillin and benzylpenicillin) were used. Milk without detergents was used as control. The spiked samples were analysed twelve times by three microbial tests. The results showed that the presence of acid detergents did not affect the response of microbial tests for any of the concentrations tested. However, at concentrations equal to or greater than 2 ml/l alkaline detergents positive results were found in microbial tests (16.7-100%). The detection limits of the screening tests for penicillins were not modified substantially by the presence of detergents. In general, the presence of acid and alkaline detergents in goat's milk did not produce a great interference in the microbial tests, only high concentrations of detergents could cause non-compliant results, but these concentrations are difficult to find in practice if proper cleaning procedures are applied in goat dairy farms.

Effect of probiotics (Saccharomyces boulardii) on microbial translocation and inflammation in HIV-treated patients: a double-blind, randomized, placebo-controlled trial.

PubMed

Villar-García, Judit; Hernández, Juan J; Güerri-Fernández, Robert; González, Alicia; Lerma, Elisabet; Guelar, Ana; Saenz, David; Sorlí, Lluisa; Montero, Milagro; Horcajada, Juan P; Knobel Freud, Hernando

2015-03-01

Microbial translocation has been associated with an increase in immune activation and inflammation in HIV infection despite effective highly active antiretroviral therapy. It has been shown that some probiotics have a beneficial effect by reducing intestinal permeability and, consequently, microbial translocation. To assess changes in microbial translocation and inflammation after treatment with probiotics (Saccharomyces boulardii) in HIV-1-infected patients with virologic suppression. A double-blind, randomized, placebo-controlled trial was conducted in 44 nonconsecutive HIV-1-infected patients with viral load of <20 copies per milliliter for at least 2 years. Patients were randomized to oral supplementation with probiotics or placebo during 12 weeks. Markers of microbial translocation (lipopolysaccharide-binding protein [LBP] and soluble CD14), inflammation (interleukin 6 [IL-6], tumor necrosis factor alpha, interferon gamma, high-sensitivity C-reactive protein), and immunological and clinical data were determined before and after the intervention and 3 months after treatment discontinuation. Quantitative variables were compared using the Mann-Whitney U test, and categorical variables were compared using the Fisher exact test. After 12 weeks of treatment, differences between the probiotic arm and the placebo arm were observed in LBP values (-0.30 vs +0.70 pg/mL) and IL-6 (-0.60 vs +0.78 pg/mL). These differences were also noted at 3 months after treatment withdrawal. Qualitative analysis was performed, defining a variable as "decreased" or "increased" from baseline LBP. A significant decrease of LBP at 12 weeks of treatment was observed (57.9% patients in the probiotic group vs 6.2% in the placebo group, P = 0.002). Treatment with S. boulardii decreases microbial translocation (LBP) and inflammation parameters (IL-6) in HIV-1-infected patients with long-term virologic suppression.

Microbial community functional structure in response to micro-aerobic conditions in sulfate-reducing sulfur-producing bioreactor.

PubMed

Yu, Hao; Chen, Chuan; Ma, Jincai; Xu, Xijun; Fan, Ronggui; Wang, Aijie

2014-05-01

Limited oxygen supply to anaerobic wastewater treatment systems had been demonstrated as an effective strategy to improve elemental sulfur (S(0)) recovery, coupling sulfate reduction and sulfide oxidation. However, little is known about the impact of dissolved oxygen (DO) on the microbial functional structures in these systems. We used a high throughput tool (GeoChip) to evaluate the microbial community structures in a biological desulfurization reactor under micro-aerobic conditions (DO: 0.02-0.33 mg/L). The results indicated that the microbial community functional compositions and structures were dramatically altered with elevated DO levels. The abundances of dsrA/B genes involved in sulfate reduction processes significantly decreased (p < 0.05, LSD test) at relatively high DO concentration (DO: 0.33 mg/L). The abundances of sox and fccA/B genes involved in sulfur/sulfide oxidation processes significantly increased (p < 0.05, LSD test) in low DO concentration conditions (DO: 0.09 mg/L) and then gradually decreased with continuously elevated DO levels. Their abundances coincided with the change of sulfate removal efficiencies and elemental sulfur (S(0)) conversion efficiencies in the bioreactor. In addition, the abundance of carbon degradation genes increased with the raising of DO levels, showing that the heterotrophic microorganisms (e.g., fermentative microorganisms) were thriving under micro-aerobic condition. This study provides new insights into the impacts of micro-aerobic conditions on the microbial functional structure of sulfate-reducing sulfur-producing bioreactors, and revealed the potential linkage between functional microbial communities and reactor performance. Copyright © 2014 The Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.

Biotransformation of nitrogen- and sulfur-containing pollutants during coking wastewater treatment: Correspondence of performance to microbial community functional structure.

PubMed

Joshi, Dev Raj; Zhang, Yu; Gao, Yinxin; Liu, Yuan; Yang, Min

2017-09-15

Although coking wastewater is generally considered to contain high concentration of nitrogen- and sulfur-containing pollutants, the biotransformation processes of these compounds have not been well understood. Herein, a high throughput functional gene array (GeoChip 5.0) in combination with Illumina MiSeq sequencing of the 16S rRNA gene were used to identify microbial functional traits and their role in biotransformation of nitrogen- and sulfur-containing compounds in a bench-scale aerobic coking wastewater treatment system operated for 488 days. Biotransformation of nitrogen and sulfur-containing pollutants deteriorated when pH of the bioreactor was increased to >8.0, and the microbial community functional structure was significantly associated with pH (Mantels test, P < 0.05). The release of ammonia nitrogen and sulfate was correlated with both the taxonomic and functional microbial community structure (P < 0.05). Considering the abundance and correlation with the release of ammonia nitrogen and sulfate, aromatic dioxygenases (e.g. xylXY, nagG), nitrilases (e.g. nhh, nitrilase), dibenzothiophene oxidase (DbtAc), and thiocyanate hydrolase (scnABC) were important functional genes for biotransformation of nitrogen- and sulfur-containing pollutants. Functional characterization of taxa and network analysis suggested that Burkholderiales, Actinomycetales, Rhizobiales, Pseudomonadales, and Hydrogenophiliales (Thiobacillus) were key functional taxa. Variance partitioning analysis showed that pH and influent ammonia nitrogen jointly explained 25.9% and 35.5% of variation in organic pollutant degrading genes and microbial community structure, respectively. This study revealed a linkage between microbial community functional structure and the likely biotransformation of nitrogen- and sulfur-containing pollutants, along with a suitable range of pH (7.0-7.5) for stability of the biological system treating coking wastewater. Copyright © 2017 Elsevier Ltd. All rights reserved.

Life Support Systems Microbial Challenges

NASA Technical Reports Server (NTRS)

Roman, Monsi C.

2010-01-01

Many microbiological studies were performed during the development of the Space Station Water Recovery and Management System from1990-2009. Studies include assessments of: (1) bulk phase (planktonic) microbial population (2) biofilms, (3) microbially influenced corrosion (4) biofouling treatments. This slide presentation summarizes the studies performed to assess the bulk phase microbial community during the Space Station Water Recovery Tests (WRT) from 1990 to 1998. This report provides an overview of some of the microbiological analyses performed during the Space Station WRT program. These tests not only integrated several technologies with the goal of producing water that met NASA s potable water specifications, but also integrated humans, and therefore human flora into the protocols. At the time these tests were performed, not much was known (or published) about the microbial composition of these types of wastewater. It is important to note that design changes to the WRS have been implemented over the years and results discussed in this report might be directly related to test configurations that were not chosen for the final flight configuration. Results microbiological analyses performed Conclusion from the during the WRT showed that it was possible to recycle water from different sources, including urine, and produce water that can exceed the quality of municipally produced water.

MetaMap: An atlas of metatranscriptomic reads in human disease-related RNA-seq data.

PubMed

Simon, L M; Karg, S; Westermann, A J; Engel, M; Elbehery, A H A; Hense, B; Heinig, M; Deng, L; Theis, F J

2018-06-12

With the advent of the age of big data in bioinformatics, large volumes of data and high performance computing power enable researchers to perform re-analyses of publicly available datasets at an unprecedented scale. Ever more studies imply the microbiome in both normal human physiology and a wide range of diseases. RNA sequencing technology (RNA-seq) is commonly used to infer global eukaryotic gene expression patterns under defined conditions, including human disease-related contexts, but its generic nature also enables the detection of microbial and viral transcripts. We developed a bioinformatic pipeline to screen existing human RNA-seq datasets for the presence of microbial and viral reads by re-inspecting the non-human-mapping read fraction. We validated this approach by recapitulating outcomes from 6 independent controlled infection experiments of cell line models and comparison with an alternative metatranscriptomic mapping strategy. We then applied the pipeline to close to 150 terabytes of publicly available raw RNA-seq data from >17,000 samples from >400 studies relevant to human disease using state-of-the-art high performance computing systems. The resulting data of this large-scale re-analysis are made available in the presented MetaMap resource. Our results demonstrate that common human RNA-seq data, including those archived in public repositories, might contain valuable information to correlate microbial and viral detection patterns with diverse diseases. The presented MetaMap database thus provides a rich resource for hypothesis generation towards the role of the microbiome in human disease. Additionally, codes to process new datasets and perform statistical analyses are made available at https://github.com/theislab/MetaMap.

New Performance Metrics for Quantitative Polymerase Chain Reaction-Based Microbial Source Tracking Methods

EPA Science Inventory

Binary sensitivity and specificity metrics are not adequate to describe the performance of quantitative microbial source tracking methods because the estimates depend on the amount of material tested and limit of detection. We introduce a new framework to compare the performance ...

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

PubMed

Cerrillo, Míriam; Viñas, Marc; Bonmatí, August

2017-03-01

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

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

PubMed

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

2015-01-01

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

The long-term effects of UV exclusion on the microbial composition and photosynthetic competence of bacteria in hot-spring microbial mats.

PubMed

Norris, Tracy B; McDermott, Timothy R; Castenholz, Richard W

2002-03-01

The primary objective of this study was to determine whether the long-term exclusion of ultraviolet (UV) radiation (UVR) from hot-spring microbial mats resulted in an alteration of microbial composition, such as a shift to more UV-sensitive species. Over a 1-3-month period, microbial mats in two alkaline geothermal streams in Yellowstone National Park were covered with filters that excluded or transmitted UVR. Over some, 25% transmission neutral density screens were also used. In the 40-47 degrees C range, there were no apparent changes in community composition during the summer with or without high or low UVR, as assessed by denaturing gradient gel electrophoresis (DGGE) profiles after polymerase chain reaction amplification of 16S-rRNA genes with general Bacteria and Cyanobacteria primers. Major bands were purified from the DGGE gels and sequenced. Only one of the cyanobacterial sequences matched known strains in the database; the others appear to be unique. Although the bacterial composition of these communities was apparently stable, surface layers of cyanobacteria protected from UVR were not as competent photosynthetically as those that had been maintained under UVR. This decrease in competence was expressed as a loss of the ability to perform at a maximum rate under full UVR plus visible irradiance. However, even +UV-maintained cyanobacteria performed better when UVR was excluded during the photosynthesis tests. It is probable that the large differences in photosynthetic competence observed reflect changes at the level of gene expression in the dominant species rather than changes in species composition.

Evaluating the performance of microbial fuel cells powering electronic devices

NASA Astrophysics Data System (ADS)

Dewan, Alim; Donovan, Conrad; Heo, Deukhyoun; Beyenal, Haluk

A microbial fuel cell (MFC) is capable of powering an electronic device if we store the energy in an external storage device, such as a capacitor, and dispense that energy intermittently in bursts of high-power when needed. Therefore its performance needs to be evaluated using an energy-storing device such as a capacitor which can be charged and discharged rather than other evaluation techniques, such as continuous energy dissipation through a resistor. In this study, we develop a method of testing microbial fuel cell performance based on storing energy in a capacitor. When a capacitor is connected to a MFC it acts like a variable resistor and stores energy from the MFC at a variable rate. In practice the application of this method to testing microbial fuel cells is very challenging and time consuming; therefore we have custom-designed a microbial fuel cell tester (MFCT). The MFCT evaluates the performance of a MFC as a power source. It uses a capacitor as an energy storing device and waits until a desired amount of energy is stored then discharges the capacitor. The entire process is controlled using an analog-to-digital converter (ADC) board controlled by a custom-written computer program. The utility of our method and the MFCT is demonstrated using a laboratory microbial fuel cell (LMFC) and a sediment microbial fuel cell (SMFC). We determine (1) how frequently a MFC can charge a capacitor, (2) which electrode is current-limiting, (3) what capacitor value will allow the maximum harvested energy from a MFC, which is called the "optimum charging capacitor value," and (4) what capacitor charging potential will harvest the maximum energy from a MFC, which is called the "optimum charging potential." Using a LMFC we find that (1) the time needed to charge a 3-F capacitor from 0 to 500 mV is 108 min, (2) the optimum charging capacitor value is 3 F, and (3) the optimum charging potential is 300 mV. Using a SMFC we find that (1) the time needed to charge a 3-F capacitor from 0 to 500 mV is 5 min, (2) the optimum charging capacitor value is 3 F, and (3) the optimum charging potential is 500 mV. Our results demonstrate that the developed method and the MFCT can be used to evaluate and optimize energy harvesting when a MFC is used with a capacitor to power wireless sensors monitoring the environment.

Nitrogen amendments have predictable effects on soil microbial communities and processes

NASA Astrophysics Data System (ADS)

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

2011-12-01

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

Effects of dissolved oxygen on performance and microbial community structure in a micro-aerobic hydrolysis sludge in situ reduction process.

PubMed

Niu, Tianhao; Zhou, Zhen; Shen, Xuelian; Qiao, Weimin; Jiang, Lu-Man; Pan, Wei; Zhou, Jijun

2016-03-01

A sludge process reduction activated sludge (SPRAS), with a sludge process reduction module composed of a micro-aerobic tank and a settler positioned before conventional activated sludge process, showed good performance of pollutant removal and sludge reduction. Two SPRAS systems were operated to investigate effects of micro-aeration on sludge reduction performance and microbial community structure. When dissolved oxygen (DO) concentration in the micro-aerobic tank decreased from 2.5 (SPH) to 0.5 (SPL) mg/L, the sludge reduction efficiency increased from 42.9% to 68.3%. Compared to SPH, activated sludge in SPL showed higher contents of extracellular polymeric substances and dissolved organic matter. Destabilization of floc structure in the settler, and cell lysis in the sludge process reduction module were two major reasons for sludge reduction. Illumina-MiSeq sequencing showed that microbial diversity decreased under high DO concentration. Proteobacteria, Bacteroidetes and Chloroflexi were the most abundant phyla in the SPRAS. Specific comparisons down to the class and genus level showed that fermentative, predatory and slow-growing bacteria in SPL community were more abundant than in SPH. The results revealed that micro-aeration in the SPRAS improved hydrolysis efficiency and enriched fermentative and predatory bacteria responsible for sludge reduction. Copyright © 2016 Elsevier Ltd. All rights reserved.

In-Drift Microbial Communities

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

D. Jolley

2000-11-09

As directed by written work direction (CRWMS M and O 1999f), Performance Assessment (PA) developed a model for microbial communities in the engineered barrier system (EBS) as documented here. The purpose of this model is to assist Performance Assessment and its Engineered Barrier Performance Section in modeling the geochemical environment within a potential repository drift for TSPA-SR/LA, thus allowing PA to provide a more detailed and complete near-field geochemical model and to answer the key technical issues (KTI) raised in the NRC Issue Resolution Status Report (IRSR) for the Evolution of the Near Field Environment (NFE) Revision 2 (NRC 1999).more » This model and its predecessor (the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document, CRWMS M and O 1998a) was developed to respond to the applicable KTIs. Additionally, because of the previous development of the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a), the M and O was effectively able to resolve a previous KTI concern regarding the effects of microbial processes on seepage and flow (NRC 1998). This document supercedes the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a). This document provides the conceptual framework of the revised in-drift microbial communities model to be used in subsequent performance assessment (PA) analyses.« less

A Microbial Assessment Scheme to measure microbial performance of Food Safety Management Systems.

PubMed

Jacxsens, L; Kussaga, J; Luning, P A; Van der Spiegel, M; Devlieghere, F; Uyttendaele, M

2009-08-31

A Food Safety Management System (FSMS) implemented in a food processing industry is based on Good Hygienic Practices (GHP), Hazard Analysis Critical Control Point (HACCP) principles and should address both food safety control and assurance activities in order to guarantee food safety. One of the most emerging challenges is to assess the performance of a present FSMS. The objective of this work is to explain the development of a Microbial Assessment Scheme (MAS) as a tool for a systematic analysis of microbial counts in order to assess the current microbial performance of an implemented FSMS. It is assumed that low numbers of microorganisms and small variations in microbial counts indicate an effective FSMS. The MAS is a procedure that defines the identification of critical sampling locations, the selection of microbiological parameters, the assessment of sampling frequency, the selection of sampling method and method of analysis, and finally data processing and interpretation. Based on the MAS assessment, microbial safety level profiles can be derived, indicating which microorganisms and to what extent they contribute to food safety for a specific food processing company. The MAS concept is illustrated with a case study in the pork processing industry, where ready-to-eat meat products are produced (cured, cooked ham and cured, dried bacon).

Microbial Community in High Arsenic Shallow Groundwater Aquifers in Hetao Basin of Inner Mongolia, China

PubMed Central

Li, Ping; Wang, Yanhong; Dai, Xinyue; Zhang, Rui; Jiang, Zhou; Jiang, Dawei; Wang, Shang; Jiang, Hongchen; Wang, Yanxin; Dong, Hailiang

2015-01-01

A survey was carried out on the microbial community of 20 groundwater samples (4 low and 16 high arsenic groundwater) and 19 sediments from three boreholes (two high arsenic and one low arsenic boreholes) in a high arsenic groundwater system located in Hetao Basin, Inner Mongolia, using the 454 pyrosequencing approach. A total of 233,704 sequence reads were obtained and classified into 12–267 operational taxonomic units (OTUs). Groundwater and sediment samples were divided into low and high arsenic groups based on measured geochemical parameters and microbial communities, by hierarchical clustering and principal coordinates analysis. Richness and diversity of the microbial communities in high arsenic sediments are higher than those in high arsenic groundwater. Microbial community structure was significantly different either between low and high arsenic samples or between groundwater and sediments. Acinetobacter, Pseudomonas, Psychrobacter and Alishewanella were the top four genera in high arsenic groundwater, while Thiobacillus, Pseudomonas, Hydrogenophaga, Enterobacteriaceae, Sulfuricurvum and Arthrobacter dominated high arsenic sediments. Archaeal sequences in high arsenic groundwater were mostly related to methanogens. Biota-environment matching and co-inertia analyses showed that arsenic, total organic carbon, SO4 2-, SO4 2-/total sulfur ratio, and Fe2+ were important environmental factors shaping the observed microbial communities. The results of this study expand our current understanding of microbial ecology in high arsenic groundwater aquifers and emphasize the potential importance of microbes in arsenic transformation in the Hetao Basin, Inner Mongolia. PMID:25970606

Microbial community in high arsenic shallow groundwater aquifers in Hetao Basin of Inner Mongolia, China.

PubMed

Li, Ping; Wang, Yanhong; Dai, Xinyue; Zhang, Rui; Jiang, Zhou; Jiang, Dawei; Wang, Shang; Jiang, Hongchen; Wang, Yanxin; Dong, Hailiang

2015-01-01

A survey was carried out on the microbial community of 20 groundwater samples (4 low and 16 high arsenic groundwater) and 19 sediments from three boreholes (two high arsenic and one low arsenic boreholes) in a high arsenic groundwater system located in Hetao Basin, Inner Mongolia, using the 454 pyrosequencing approach. A total of 233,704 sequence reads were obtained and classified into 12-267 operational taxonomic units (OTUs). Groundwater and sediment samples were divided into low and high arsenic groups based on measured geochemical parameters and microbial communities, by hierarchical clustering and principal coordinates analysis. Richness and diversity of the microbial communities in high arsenic sediments are higher than those in high arsenic groundwater. Microbial community structure was significantly different either between low and high arsenic samples or between groundwater and sediments. Acinetobacter, Pseudomonas, Psychrobacter and Alishewanella were the top four genera in high arsenic groundwater, while Thiobacillus, Pseudomonas, Hydrogenophaga, Enterobacteriaceae, Sulfuricurvum and Arthrobacter dominated high arsenic sediments. Archaeal sequences in high arsenic groundwater were mostly related to methanogens. Biota-environment matching and co-inertia analyses showed that arsenic, total organic carbon, SO4(2-), SO4(2-)/total sulfur ratio, and Fe(2+) were important environmental factors shaping the observed microbial communities. The results of this study expand our current understanding of microbial ecology in high arsenic groundwater aquifers and emphasize the potential importance of microbes in arsenic transformation in the Hetao Basin, Inner Mongolia.

Impact of biotic and a-biotic parameters on structure and function of microbial communities living on sclerotia of the soil-borne pathogenic fungus Rhizoctonia solani

PubMed Central

Zachow, Christin; Grosch, Rita; Berg, Gabriele

2011-01-01

The plant pathogen Rhizoctonia solani is very difficult to control due to its persistent, long-living sclerotial structures in soil. Sclerotia are the main source of infection for Rhizoctonia diseases, which cause high yield losses on a broad host range world-wide. Little is known about micro-organisms associated with sclerotia in soil. Therefore, microbial communities of greenhouse and field incubated Rhizoctonia sclerotia were analysed by a multiphasic approach. Using microbial fingerprints performed by PCR-SSCP, sclerotia-associated bacterial communities showed a high diversity, whereas only a few fungi could be detected. Statistical analysis of fingerprints revealed the influence of soil types, incubation conditions (greenhouse, field), and incubation time (5 and 12 weeks) on the bacterial as well as fungal community. No significant differences were found for the microbial community associated with different Rhizoctonia anastomosis sub-groups (AG 1-IB and AG 1-IC). Rhizoctonia sclerotia are an interesting bio-resource: high proportions of fungal cell-wall degrading isolates as well as those with antagonistic activity towards R. solani were found. While a fraction of 28.4% of sclerotia-associated bacteria (=40 isolates) with antagonistic properties was determined, only 4.4% (=6 isolates) of the fungal isolates were antagonistic. We identified strong antagonists of the genera Bacillus, Enterobacter, Pseudomonas, and Stenotrophomonas, which can be used as biological control agents incorporated in soil or applied to Rhizoctonia host plants. PMID:26109749

Deciphering chicken gut microbial dynamics based on high-throughput 16S rRNA metagenomics analyses.

PubMed

Mohd Shaufi, Mohd Asrore; Sieo, Chin Chin; Chong, Chun Wie; Gan, Han Ming; Ho, Yin Wan

2015-01-01

Chicken gut microbiota has paramount roles in host performance, health and immunity. Understanding the topological difference in gut microbial community composition is crucial to provide knowledge on the functions of each members of microbiota to the physiological maintenance of the host. The gut microbiota profiling of the chicken was commonly performed previously using culture-dependent and early culture-independent methods which had limited coverage and accuracy. Advances in technology based on next-generation sequencing (NGS), offers unparalleled coverage and depth in determining microbial gut dynamics. Thus, the aim of this study was to investigate the ileal and caecal microbiota development as chicken aged, which is important for future effective gut modulation. Ileal and caecal contents of broiler chicken were extracted from 7, 14, 21 and 42-day old chicken. Genomic DNA was then extracted and amplified based on V3 hyper-variable region of 16S rRNA. Bioinformatics, ecological and statistical analyses such as Principal Coordinate Analysis (PCoA) was performed in mothur software and plotted using PRIMER 6. Additional analyses for predicted metagenomes were performed through PICRUSt and STAMP software package based on Greengenes databases. A distinctive difference in bacterial communities was observed between ilea and caeca as the chicken aged (P < 0.001). The microbial communities in the caeca were more diverse in comparison to the ilea communities. The potentially pathogenic bacteria such as Clostridium were elevated as the chicken aged and the population of beneficial microbe such as Lactobacillus was low at all intervals. On the other hand, based on predicted metagenomes analysed, clear distinction in functions and roles of gut microbiota such as gene pathways related to nutrient absorption (e.g. sugar and amino acid metabolism), and bacterial proliferation and colonization (e.g. bacterial motility proteins, two-component system and bacterial secretion system) were observed between ilea and caeca, respectively (P < 0.05). The caeca microbial communities were more diverse in comparison to ilea. The main functional differences between the two sites were found to be related to nutrient absorption and bacterial colonization. Based on the composition of the microbial community, future gut modulation with beneficial bacteria such as probiotics may benefit the host.

Microbial community structure and function in sediments from e-waste contaminated rivers at Guiyu area of China.

PubMed

Liu, Jun; Chen, Xi; Shu, Hao-Yue; Lin, Xue-Rui; Zhou, Qi-Xing; Bramryd, Torleif; Shu, Wen-Sheng; Huang, Li-Nan

2018-04-01

The release of toxic organic pollutants and heavy metals by primitive electronic waste (e-waste) processing to waterways has raised significant concerns, but little is known about their potential ecological effects on aquatic biota especially microorganisms. We characterized the microbial community composition and diversity in sediments sampled along two rivers consistently polluted by e-waste, and explored how community functions may respond to the complex combined pollution. High-throughput 16S rRNA gene sequencing showed that Proteobacteria (particularly Deltaproteobacteria) dominated the sediment microbial assemblages followed by Bacteroidetes, Acidobacteria, Chloroflexi and Firmicutes. PICRUSt metagenome inference provided an initial insight into the metabolic potentials of these e-waste affected communities, speculating that organic pollutants degradation in the sediment might be mainly performed by some of the dominant genera (such as Sulfuricurvum, Thiobacillus and Burkholderia) detected in situ. Statistical analyses revealed that toxic organic compounds contributed more to the observed variations in sediment microbial community structure and predicted functions (24.68% and 8.89%, respectively) than heavy metals (12.18% and 4.68%), and Benzo(a)pyrene, bioavailable lead and electrical conductivity were the key contributors. These results have shed light on the microbial assemblages in e-waste contaminated river sediments, indicating a potential influence of e-waste pollution on the microbial community structure and function in aquatic ecosystems. Copyright © 2017 Elsevier Ltd. All rights reserved.

A thiotrophic microbial community in an acidic brine lake in Northern Chile.

PubMed

Escudero, Lorena; Oetiker, Nia; Gallardo, Karem; Tebes-Cayo, Cinthya; Guajardo, Mariela; Nuñez, Claudia; Davis-Belmar, Carol; Pueyo, J J; Chong Díaz, Guillermo; Demergasso, Cecilia

2018-05-10

The endorheic basins of the Northern Chilean Altiplano contain saline lakes and salt flats. Two of the salt flats, Gorbea and Ignorado, have high acidic brines. The causes of the local acidity have been attributed to the occurrence of volcanic native sulfur, the release of sulfuric acid by oxidation, and the low buffering capacity of the rocks in the area. Understanding the microbial community composition and available energy in this pristine ecosystem is relevant in determining the origin of the acidity and in supporting the rationale of conservation policies. Besides, a comparison between similar systems in Australia highlights key microbial components and specific ones associated with geological settings and environmental conditions. Sediment and water samples from the Salar de Gorbea were collected, physicochemical parameters measured and geochemical and molecular biological analyses performed. A low diversity microbial community was observed in brines and sediments dominated by Actinobacteria, Algae, Firmicutes and Proteobacteria. Most of the constituent genera have been reported to be either sulfur oxidizing microorganisms or ones having the potential for sulfur oxidation given available genomic data and information drawn from the literature on cultured relatives. In addition, a link between sulfur oxidation and carbon fixation was observed. In contrast, to acid mine drainage communities, Gorbea microbial diversity is mainly supported by chemolithoheterotrophic, facultative chemolithoautotrophic and oligotrophic sulfur oxidizing populations indicating that microbial activity should also be considered as a causative agent of local acidity.

Microbial electrolysis cells turning to be versatile technology: recent advances and future challenges.

PubMed

Zhang, Yifeng; Angelidaki, Irini

2014-06-01

Microbial electrolysis cells (MECs) are an electricity-mediated microbial bioelectrochemical technology, which is originally developed for high-efficiency biological hydrogen production from waste streams. Compared to traditional biological technologies, MECs can overcome thermodynamic limitations and achieve high-yield hydrogen production from wide range of organic matters at relatively mild conditions. This approach greatly reduces the electric energy cost for hydrogen production in contrast to direct water electrolysis. In addition to hydrogen production, MECs may also support several energetically unfavorable biological/chemical reactions. This unique advantage of MECs has led to several alternative applications such as chemicals synthesis, recalcitrant pollutants removal, resources recovery, bioelectrochemical research platform and biosensors, which have greatly broaden the application scopes of MECs. MECs are becoming a versatile platform technology and offer a new solution for emerging environmental issues related to waste streams treatment and energy and resource recovery. Different from previous reviews that mainly focus on hydrogen production, this paper provides an up-to-date review of all the new applications of MECs and their resulting performance, current challenges and prospects of future. Copyright © 2014 Elsevier Ltd. All rights reserved.

Microbial community structure associated with the high loading anaerobic codigestion of olive mill and abattoir wastewaters.

PubMed

Gannoun, Hana; Omri, Ilhem; Chouari, Rakia; Khelifi, Eltaief; Keskes, Sajiaa; Godon, Jean-Jacques; Hamdi, Moktar; Sghir, Abdelghani; Bouallagui, Hassib

2016-02-01

The effect of increasing the organic loading rates (OLRs) on the performance of the anaerobic codigestion of olive mill (OMW) and abattoir wastewaters (AW) was investigated under mesophilic and thermophilic conditions. The structure of the microbial community was also monitored. Increasing OLR to 9g of chemical oxygen demand (COD) L(-1)d(-1) affected significantly the biogas yield and microbial diversity at 35°C. However, at 55°C digester remained stable until OLR of 12g of CODL(-1)d(-1) with higher COD removal (80%) and biogas yield (0.52Lg(-1) COD removed). Significant differences in the bacterial communities were detected between mesophilic and thermophilic conditions. The dominant phyla detected in the digester at both phases were the Firmicutes, Actinobacteria, Bacteroidetes, Synergistetes and Spirochaete. However, Verrucomicrobia, Proteobacteria and the candidate division BRC1 were only detected at thermophilic conditions. The Methanobacteriales and the Thermoplasmales were found as a high predominant archaeal member in the anaerobic sludge. Copyright © 2015 Elsevier Ltd. All rights reserved.

Effect of power shape on energy extraction from microbial fuel cell

NASA Astrophysics Data System (ADS)

Alaraj, Muhannad; Feng, Shuo; Roane, Timberley M.; Park, Jae-Do

2017-10-01

Microbial fuel cells (MFCs) generate renewable energy in the form of direct current (DC) power. Harvesting energy from MFCs started with passive components such as resistors and capacitors, then charge pumps were introduced with some more advantages. Power electronics converters were later preferred due to their higher efficiency and controllability; however, they introduce high frequency current ripple due to their high frequency switching. In this paper, the effect of shape of power extraction on MFC performance was investigated using three types of current shapes: continuous, square-wave, and triangular-wave. Simultaneously, chemical parameters, such as pH, dissolved oxygen, electrical conductivity, and redox potential, in the anode chamber were monitored to see how these parameters change with the shape of the electrical power extraction. Results showed that the shape of the extracted current did not have a substantial effect on the MFC life span, output power, and energy extraction, nor on the chemical parameters. The outcome of this study provided insight for the electrical impact by power electronics converters on some microbial and chemical aspects of an MFC system.

Cometabolic degradation of chloramphenicol via a meta-cleavage pathway in a microbial fuel cell and its microbial community.

PubMed

Zhang, Qinghua; Zhang, Yanyan; Li, Daping

2017-04-01

The performance of a microbial fuel cell (MFC) in terms of degradation of chloramphenicol (CAP) was investigated. Approximately 84% of 50mg/L CAP was degraded within 12h in the MFC. A significant interaction of pH, temperature, and initial CAP concentration was found on removal of CAP, and a maximum degradation rate of 96.53% could theoretically be achieved at 31.48°C, a pH of 7.12, and an initial CAP concentration of 106.37mg/L. Moreover, CAP was further degraded through a ring-cleavage pathway. The antibacterial activity of CAP towards Escherichia coli ATCC 25922 and Shewanella oneidensis MR-1 was largely eliminated by MFC treatment. High-throughput sequencing analysis indicated that Azonexus, Comamonas, Nitrososphaera, Chryseobacterium, Azoarcus, Rhodococcus, and Dysgonomonas were the predominant genera in the MFC anode biofilm. In conclusion, the MFC shows potential for the treatment of antibiotic residue-containing wastewater due to its high rates of CAP removal and energy recovery. Copyright © 2017 Elsevier Ltd. All rights reserved.

Effect of high loading on substrate utilization kinetics and microbial community structure in super fast submerged membrane bioreactor.

PubMed

Sözen, S; Çokgör, E U; Başaran, S Teksoy; Aysel, M; Akarsubaşı, A; Ergal, I; Kurt, H; Pala-Ozkok, I; Orhon, D

2014-05-01

The study investigated the effect of high substrate loading on substrate utilization kinetics, and changes inflicted on the composition of the microbial community in a superfast submerged membrane bioreactor. Submerged MBR was sequentially fed with a substrate mixture and acetate; its performance was monitored at steady-state, at extremely low sludge age values of 2.0, 1.0 and 0.5d, all adjusted to a single hydraulic retention time of 8.0 h. Each MBR run was repeated when substrate feeding was increased from 200 mg COD/L to 1000 mg COD/L. Substrate utilization kinetics was altered to significantly lower levels when the MBR was adjusted to higher substrate loadings. Molecular analysis of the biomass revealed that variable process kinetics could be correlated with parallel changes in the composition of the microbial community, mainly by a replacement mechanism, where newer species, better adapted to the new growth conditions, substituted others that are washed out from the system. Copyright © 2014 Elsevier Ltd. All rights reserved.

Development of an analytical microbial consortia method for enhancing performance monitoring at aerobic wastewater treatment plants.

PubMed

Razban, Behrooz; Nelson, Kristina Y; McMartin, Dena W; Cullimore, D Roy; Wall, Michelle; Wang, Dunling

2012-01-01

An analytical method to produce profiles of bacterial biomass fatty acid methyl esters (FAME) was developed employing rapid agitation followed by static incubation (RASI) using selective media of wastewater microbial communities. The results were compiled to produce a unique library for comparison and performance analysis at a Wastewater Treatment Plant (WWTP). A total of 146 samples from the aerated WWTP, comprising 73 samples of each secondary and tertiary effluent, were included analyzed. For comparison purposes, all samples were evaluated via a similarity index (SI) with secondary effluents producing an SI of 0.88 with 2.7% variation and tertiary samples producing an SI 0.86 with 5.0% variation. The results also highlighted significant differences between the fatty acid profiles of the tertiary and secondary effluents indicating considerable shifts in the bacterial community profile between these treatment phases. The WWTP performance results using this method were highly replicable and reproducible indicating that the protocol has potential as a performance-monitoring tool for aerated WWTPs. The results quickly and accurately reflect shifts in dominant bacterial communities that result when processes operations and performance change.

Microbial community activities during establishment, performance, and decline of bench-scale passive treatment systems for mine drainage.

PubMed

Logan, Miranda V; Reardon, Kenneth F; Figueroa, Linda A; McLain, Jean E T; Ahmann, Dianne M

2005-11-01

Permeable reactive barrier (PRB) technology, in which sulfate-reducing bacteria (SRB) facilitate precipitation of metal sulfides, is a promising approach for remediation of sulfate- and metal-laden mine drainage. While PRBs are easily established, they often decline for reasons not well understood. SRB depend on or compete with multiple dynamic microbial populations within a PRB; as a result, performance depends on the changing PRB chemical composition and on succession and competition within the microbial community. To investigate these interactions, we constructed and monitored eight bench-scale PRBs to define periods of establishment, performance, and decline. We then conducted short-term batch studies, using substrate-supplemented column materials, on Days 0 (pre-establishment), 27 (establishment), 41 (performance), and 99 (decline) to reveal potential activities of cellulolytic bacteria, fermenters + anaerobic respirers, SRB, and methanogens. PRBs showed active sulfate reduction, with sulfate removal rates (SRR) of approximately 1-3 mol/m3/d, as well as effective removal of Zn2+. Potential activities of fermentative + anaerobic respiratory bacteria were initially high but diminished greatly during establishment and dropped further during performance and decline. In contrast, potential SRB activity rose during establishment, peaked during performance, and diminished as performance declined. Potential methanogen activity was low; in addition, SRB-methanogen substrate competition was shown not to limit SRB activity. Cellulolytic bacteria showed no substrate limitation at any time. However, fermenters experienced substrate limitation by Day 0, SRB by Day 27, and methanogens by Day 41, showing the dependence of each group on upstream populations to provide substrates. All potential activities, except methanogenesis, were ultimately limited by cellulose hydrolysis; in addition, all potential activities except methanogenesis declined substantially by Day 99, showing that long-term substrate deprivation strongly diminished the intrinsic capacity of the PRB community to perform.

Development of a high temperature microbial fermentation process for butanol

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

Jeor, Jeffery D. St.; Reed, David W.; Daubaras, Dayna L.

2015-08-01

Transforming renewable biomass into cost-competitive high-performance biofuels and bioproducts is key to the U.S. future energy and chemical needs. Butanol production by microbial fermentation for chemical conversion to polyolefins, elastomers, drop-in jet or diesel fuel, and other chemicals is a promising solution. A high temperature fermentation process could decrease energy costs, capital cost, give higher butanol production, and allow for continuous fermentation. In this paper, we describe our approach to genetically transform Geobacillus caldoxylosiliticus, using a pUCG18 plasmid, for potential insertion of a butanol production pathway. Transformation methods tested were electroporation of electrocompetent cells, ternary conjugation with E. coli donormore » and helper strains, and protoplast fusion. These methods have not been successful using the current plasmid. Growth controls show cells survive the various methods tested, suggesting the possibility of transformation inhibition from a DNA restriction modification system in G. caldoxylosiliticus, as reported in the literature.« less

Methane-producing microbial community in a coal bed of the Illinois Basin

USGS Publications Warehouse

Strapoc, D.; Picardal, F.W.; Turich, C.; Schaperdoth, I.; Macalady, J.L.; Lipp, J.S.; Lin, Y.-S.; Ertefai, T.F.; Schubotz, F.; Hinrichs, K.-U.; Mastalerz, Maria; Schimmelmann, A.

2008-01-01

A series of molecular and geochemical studies were performed to study microbial, coal bed methane formation in the eastern Illinois Basin. Results suggest that organic matter is biodegraded to simple molecules, such as H 2 and CO2, which fuel methanogenesis and the generation of large coal bed methane reserves. Small-subunit rRNA analysis of both the in situ microbial community and highly purified, methanogenic enrichments indicated that Methanocorpusculum is the dominant genus. Additionally, we characterized this methanogenic microorganism using scanning electron microscopy and distribution of intact polar cell membrane lipids. Phylogenetic studies of coal water samples helped us develop a model of methanogenic biodegradation of macromolecular coal and coal-derived oil by a complex microbial community. Based on enrichments, phylogenetic analyses, and calculated free energies at in situ subsurface conditions for relevant metabolisms (H2-utilizing methanogenesis, acetoclastic methanogenesis, and homoacetogenesis), H 2-utilizing methanogenesis appears to be the dominant terminal process of biodegradation of coal organic matter at this location. Copyright ?? 2008, American Society for Microbiology. All Rights Reserved.

Numerical modelling of biophysicochemical effects on multispecies reactive transport in porous media involving Pseudomonas putida for potential microbial enhanced oil recovery application.

PubMed

Sivasankar, P; Rajesh Kanna, A; Suresh Kumar, G; Gummadi, Sathyanarayana N

2016-07-01

pH and resident time of injected slug plays a critical role in characterizing the reservoir for potential microbial enhanced oil recovery (MEOR) application. To investigate MEOR processes, a multispecies (microbes-nutrients) reactive transport model in porous media was developed by coupling kinetic and transport model. The present work differs from earlier works by explicitly determining parametric values required for kinetic model by experimental investigations using Pseudomonas putida at different pH conditions and subsequently performing sensitivity analysis of pH, resident time and water saturation on concentrations of microbes, nutrients and biosurfactant within reservoir. The results suggest that nutrient utilization and biosurfactant production are found to be maximum at pH 8 and 7.5 respectively. It is also found that the sucrose and biosurfactant concentrations are highly sensitive to pH rather than reservoir microbial concentration, while at larger resident time and water saturation, the microbial and nutrient concentrations were lesser due to enhanced dispersion. Copyright © 2016 Elsevier Ltd. All rights reserved.

The mechanisms of granulation of activated sludge in wastewater treatment, its optimization, and impact on effluent quality.

PubMed

Wilén, Britt-Marie; Liébana, Raquel; Persson, Frank; Modin, Oskar; Hermansson, Malte

2018-06-01

Granular activated sludge has gained increasing interest due to its potential in treating wastewater in a compact and efficient way. It is well-established that activated sludge can form granules under certain environmental conditions such as batch-wise operation with feast-famine feeding, high hydrodynamic shear forces, and short settling time which select for dense microbial aggregates. Aerobic granules with stable structure and functionality have been obtained with a range of different wastewaters seeded with different sources of sludge at different operational conditions, but the microbial communities developed differed substantially. In spite of this, granule instability occurs. In this review, the available literature on the mechanisms involved in granulation and how it affects the effluent quality is assessed with special attention given to the microbial interactions involved. To be able to optimize the process further, more knowledge is needed regarding the influence of microbial communities and their metabolism on granule stability and functionality. Studies performed at conditions similar to full-scale such as fluctuation in organic loading rate, hydrodynamic conditions, temperature, incoming particles, and feed water microorganisms need further investigations.

Influence of reflux ratio on two-stage anoxic/oxic with MBR for leachate treatment: Performance and microbial community structure.

PubMed

Liu, Jianbo; Tian, Zhiyong; Zhang, Panyue; Qiu, Guanglei; Wu, Yan; Zhang, Haibo; Xu, Rui; Fang, Wei; Ye, Jie; Song, Yonghui; Zeng, Guangming

2018-05-01

A lab-scale two-stage Anoxic/Oxic with MBR (AO/AO-MBR) system was operated for 81 days for leachate treatment with different reflux ratio (R). The best system performances were observed with a R value of 150%, and the average removal efficiencies of chemical oxygen demand, ammonia and total nitrogen were 85.6%, 99.1%, and 77.6%, respectively. The microbial community were monitored and evaluated using high-throughput sequencing. Proteobacteria were dominant in all process. Phylogenetic trees were described at species level, genus Thiopseudomonas, Amaricoccus, Nitrosomonas and Nitrobacter played significant roles in nitrogen removal. Co-occurrence analyzing top 20 genera showed that Nitrosomonas-Nitrobacter presented perfect positive relationship, as well as Paracoccus-Brevundimonas and Pusillimonas-Halobacteriovorax. Copyright © 2018 Elsevier Ltd. All rights reserved.

Spatial And Temporal Distribution Of Microbial Communities In A TCE DNAPL Site: SABRE Field Studies

EPA Science Inventory

The SABRE (Source Area BioREmediation) project was conducted to evaluate accelerated anaerobic bioremediation of chlorinated solvents in areas of high concentration, such as DNAPL source areas. To study performance of this technology, a test cell was constructed with a longitudi...

Development, registration and commercialization of microbial pesticides for plant protection.

PubMed

Montesinos, Emilio

2003-12-01

Plant protection against pathogens, pests and weeds has been progressively reoriented from a therapeutic approach to a rational use of pesticide chemicals in which consumer health and environmental preservation prevail over any other productive or economic considerations. Microbial pesticides are being introduced in this new scenario of crop protection and currently several beneficial microorganisms are the active ingredients of a new generation of microbial pesticides or the basis for many natural products of microbial origin. The development of a microbial pesticide requires several steps addressed to its isolation in pure culture and screening by means of efficacy bioassays performed in vitro, ex vivo, in vivo, or in pilot trials under real conditions of application (field, greenhouse, post-harvest). For the commercial delivery of a microbial pesticide, the biocontrol agent must be produced at an industrial scale (fermentation), preserved for storage and formulated by means of biocompatible additives to increase survival and to improve the application and stability of the final product. Despite the relative high number of patents for biopesticides, only a few of them have materialized in a register for agricultural use. The excessive specificity in most cases and biosafety or environmental concerns in others are major limiting factors. Non-target effects may be possible in particular cases, such as displacement of beneficial microorganisms, allergenicity, toxinogencity (production of secondary metabolites toxic to plants, animals, or humans), pathogenicity (to plants or animals) by the agent itself or due to contaminants, or horizontal gene transfer of these characteristics to non-target microorganisms. However, these non-target effects should not be evaluated in an absolute manner, but relative to chemical control or the absence of any control of the target disease (for example, toxins derived from the pathogen). Consumer concerns about live microbes due to emerging food-borne diseases and bioterrorism do not help to create a socially receptive environment to microbial pesticides. The future of microbial pesticides is not only in developing new active ingredients based on microorganisms beneficial to plants, but in producing self-protected plants (so-called plant-incorporated pesticides) by transforming agronomically high-value crop plants with genes from biological control agents.

Constraining Biomarkers of Dissolved Organic Matter Sourcing Using Microbial Incubations of Vascular Plant Leachates of the California landscape

NASA Astrophysics Data System (ADS)

Harfmann, J.; Hernes, P.; Chuang, C. Y.; Kaiser, K.; Spencer, R. G.; Guillemette, F.

2017-12-01

Source origin of dissolved organic matter (DOM) is crucial in determining reactivity, driving chemical and biological processing of carbon. DOM source biomarkers such as lignin (a vascular plant marker) and D-amino acids (bacterial markers) are well-established tools in tracing DOM origin and fate. The development of high-resolution mass spectrometry and optical studies has expanded our toolkit; yet despite these advances, our understanding of DOM sources and fate remains largely qualitative. Quantitative data on DOM pools and fluxes become increasingly necessary as we refine our comprehension of its composition. In this study, we aim to calibrate and quantify DOM source endmembers by performing microbial incubations of multiple vascular plant leachates, where total DOM is constrained by initial vascular plant input and microbial production. Derived endmembers may be applied to endmember mixing models to quantify DOM source contributions in aquatic systems.

Enhanced vanadium (V) reduction and bioelectricity generation in microbial fuel cells with biocathode

NASA Astrophysics Data System (ADS)

Qiu, Rui; Zhang, Baogang; Li, Jiaxin; Lv, Qing; Wang, Song; Gu, Qian

2017-08-01

Microbial fuel cells (MFCs) represent a promising approach for remediation of toxic vanadium (V) contaminated environment. Herein, enhanced V(V) reduction and bioelectricity generation are realized in MFCs with biocathode. Synergistically electrochemical and microbial reductions result in the nearly complete removals of V(V) within 7 d operation with initial concentration of 200 mg L-1. Maximum power density of 529 ± 12 mW m-2 is obtained. Electrochemical tests reveal that biocathode promotes electron transfers and reduces charge transfer resistance. XPS analysis confirms that V(IV) is the main reduction product, which precipitates naturally under neutral conditions. High-throughput 16S rRNA gene sequencing analysis indicates that the newly appeared Dysgonomonas is responsible for V(V) reduction and Klebsiella contributes mainly to bioelectricity generation in MFCs with biocathode. This study further improves the performance of remediating V(V) contaminated environment based on MFC technology.

A Survey of Environmental Microbial Flora During Closed Chamber Studies

NASA Technical Reports Server (NTRS)

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

1999-01-01

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

A survey of microbial community diversity in marine sediments impacted by petroleum hydrocarbons from the Gulf of Mexico and Atlantic shorelines, Texas to Florida

USGS Publications Warehouse

Lisle, John T.; Stellick, Sarah H.

2011-01-01

Microbial community genomic DNA was extracted from sediment samples collected along the Gulf of Mexico and Atlantic coasts from Texas to Florida. Sample sites were identified as being ecologically sensitive and (or) as having high potential of being impacted by Macondo-1 (M-1) well oil from the Deepwater Horizon blowout. The diversity within the microbial communities associated with the collected sediments provides a baseline dataset to which microbial community-diversity data from impacted sites could be compared. To determine the microbial community diversity in the samples, genetic fingerprints were generated and compared. Specific sequences within the community genomic DNA were first amplified using the polymerase chain reaction (PCR) with a primer set that provides possible resolution to the species level. A second nested PCR was performed on the primary PCR products using a primer set on which a GC-clamp was attached to one of the primers. The nested PCR products were separated using denaturing-gradient gel electrophoresis (DGGE) that resolves the nested PCR products based on sequence dissimilarities (or similarities), forming a genomic fingerprint of the microbial diversity within the respective samples. Samples with similar fingerprints were grouped and compared to oil-fingerprint data from the same sites (Rosenbauer and others, 2011). The microbial community fingerprints were generally grouped into sites that had been shown to contain background concentrations of non-Deepwater Horizon oil. However, these groupings also included sites where no oil signature was detected. This report represents some of the first information on naturally occurring microbial communities in sediment from shorelines along the Gulf of Mexico and Atlantic coasts from Texas to Florida.

ACCUMULATION RATE OF MICROBIAL BIOMASS AT TWO PERMEABLE REACTIVE BARRIER SITES

EPA Science Inventory

Accumulation of mineral precipitates and microbial biomass are key factors that impact the long-term performance of in-situ Permeable Reactive Barriers for treating contaminated groundwater. Both processes can impact remedial performance by decreasing zero-valent iron reactivity...

Too big or too narrow? Disturbance characteristics determine the functional resilience in virtual microbial ecosystems

NASA Astrophysics Data System (ADS)

König, Sara; Firle, Anouk-Letizia; Koehnke, Merlin; Banitz, Thomas; Frank, Karin

2017-04-01

In general ecology, there is an ongoing debate about the influence of fragmentation on extinction thresholds. Whether this influence is positive or negative depends on the considered type of fragmentation: whereas habitat fragmentation often has a negative influence on population extinction thresholds, spatially fragmented disturbances are observed to have mostly positive effects on the extinction probability. Besides preventing population extinction, in soil systems ecology we are interested in analyzing how ecosystem functions are maintained despite disturbance events. Here, we analyzed the influence of disturbance size and fragmentation on the functional resilience of a microbial soil ecosystem. As soil is a highly heterogeneous environment exposed to disturbances of different spatial configurations, the identification of critical disturbance characteristics for maintaining its functions is crucial. We used the numerical simulation model eColony considering bacterial growth, degradation and dispersal for analyzing the dynamic response of biodegradation examplary for an important microbial ecosystem service to disturbance events of different spatial configurations. We systematically varied the size and the degree of fragmentation of the affected area (disturbance pattern). We found that the influence of the disturbance size on functional recovery and biodegradation performance highly depends on the spatial fragmentation of the disturbance. Generally, biodegradation performance decreases with increasing clumpedness and increasing size of the affected area. After spatially correlated disturbance events, biodegradation performance decreases linear with increasing disturbance size. After spatially fragmented disturbance events, on the other hand, an increase in disturbance size has no influence on the biodegradation performance until a critical disturbance size is reached. Is the affected area bigger than this critical size, the functional performance decreases dramatically. Under recurrent disturbance events, this threshold is shifted to lower disturbance sizes. The more frequent disturbances are recurring, the lower is the critical disturbance size. Our simulation results indicate the importance of spatial characteristics of disturbance events for the functional resilience of microbial ecosystems. Critical values for disturbance size and fragmentation emerge from an interplay between both characteristics. In consequence, a precise definition of the specific disturbance regime is necessary for analysing functional resilience. With this study, we show that we need to consider the influence of fragmentation in terrestrial environments not only on population extincions but also on the resilience of ecosystem functions. Moreover, spatial disturbance characteristics - which are widely discussed on landscape scale - are an important factor on smaller scales, too.

The Arsenite Oxidation Potential of Native Microbial Communities from Arsenic-Rich Freshwaters.

PubMed

Fazi, Stefano; Crognale, Simona; Casentini, Barbara; Amalfitano, Stefano; Lotti, Francesca; Rossetti, Simona

2016-07-01

Microorganisms play an important role in speciation and mobility of arsenic in the environment, by mediating redox transformations of both inorganic and organic species. Since arsenite [As(III)] is more toxic than arsenate [As(V)] to the biota, the microbial driven processes of As(V) reduction and As(III) oxidation may play a prominent role in mediating the environmental impact of arsenic contamination. However, little is known about the ecology and dynamics of As(III)-oxidizing populations within native microbial communities exposed to natural high levels of As. In this study, two techniques for single cell quantification (i.e., flow cytometry, CARD-FISH) were used to analyze the structure of aquatic microbial communities across a gradient of arsenic (As) contamination in different freshwater environments (i.e., groundwaters, surface and thermal waters). Moreover, we followed the structural evolution of these communities and their capacity to oxidize arsenite, when experimentally exposed to high As(III) concentrations in experimental microcosms. Betaproteobacteria and Deltaproteobacteria were the main groups retrieved in groundwaters and surface waters, while Beta and Gammaproteobacteria dominated the bacteria community in thermal waters. At the end of microcosm incubations, the communities were able to oxidize up to 95 % of arsenite, with an increase of Alphaproteobacteria in most of the experimental conditions. Finally, heterotrophic As(III)-oxidizing strains (one Alphaproteobacteria and two Gammaproteobacteria) were isolated from As rich waters. Our findings underlined that native microbial communities from different arsenic-contaminated freshwaters can efficiently perform arsenite oxidation, thus contributing to reduce the overall As toxicity to the aquatic biota.

Benefits to decomposition rates when using digestate as compost co-feedstock: Part II - Focus on microbial community dynamics.

PubMed

Arab, Golnaz; Razaviarani, Vahid; Sheng, Zhiya; Liu, Yang; McCartney, Daryl

2017-10-01

Linkage between composting reactor performance and microbial community dynamics was investigated during co-composting of digestate and fresh feedstock (organic fraction of municipal solid waste) using 25L reactors. Previously, the relationship between composting performance and various physicochemical parameters were reported in Part I of the study (Arab and McCartney, 2017). Three digestate to fresh feedstock ratios (0, 40, and 100%; wet weight basis) were selected for analysis of microbial community dynamics. The 40% ratio was selected because it was found to perform the best (Arab and McCartney, 2017). Illumina sequencing results revealed that the reactor with a greater composting performance (higher organic matter degradation and higher heat generation; 40% ratio) was associated with higher microbial diversity. Two specific bacterial orders that might result in higher performance were Thermoactinomycetaceae and Actinomycetales with a higher sequence abundance during thermophilic composting phase and during the maturing composting phase, respectively. Galactomyces, Pichia, Chaetomium, and Acremonium were the four fungal genera that are probably also involved in higher organic matter degradation in the reactor with better performance. The redundancy analysis (RDA) biplot indicated that among the studied environmental variables, temperature, total ammonia nitrogen and nitrate concentration accounted for much of the major shifts in microbial sequence abundance during the co-composting process. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

Qualitative analysis of the vaginal microbiota of healthy cattle and cattle with genital-tract disease.

PubMed

Rodrigues, N F; Kästle, J; Coutinho, T J D; Amorim, A T; Campos, G B; Santos, V M; Marques, L M; Timenetsky, J; de Farias, S T

2015-06-12

The microbial community of the reproductive appara-tus, when known, can provide information about the health of the host. Metagenomics has been used to characterize and obtain genetic infor-mation about microbial communities in various environments and can relate certain diseases with changes in this community composition. In this study, samples of vaginal surface mucosal secretions were col-lected from five healthy cows and five cows that showed symptoms of reproductive disorders. Following high-throughput sequencing of the isolated microbial DNA, data were processed using the Mothur soft-ware to remove low-quality sequences and chimeras, and released to the Ribosomal Database Project for classification of operational taxo-nomic units (OTUs). Local BLASTn was performed and results were loaded into the MEGAN program for viewing profiles and taxonomic microbial attributes. The control profile comprised a total of 15 taxa, with Bacteroides, Enterobacteriaceae, and Victivallis comprising the highest representation of OTUs; the reproductive disorder-positive profile comprised 68 taxa, with Bacteroides, Enterobacteriaceae, His-tophilus, Victivallis, Alistipes, and Coriobacteriaceae being the taxa with the most OTU representation. A change was observed in both the community composition as well as in the microbial attributes of the profiles, suggesting that a relationship might exist between the patho-gen and representative taxa, reflecting the production of metabolites to disease progression.

A bridging study for oxytetracycline in the edible fillet of rainbow trout: Analysis by a liquid chromatographic method and the official microbial inhibition assay

USGS Publications Warehouse

Stehly, G.R.; Gingerich, W.H.; Kiessling, C.R.; Cutting, J.H.

1999-01-01

Oxytetracycline (OTC) is a drug approved by the U.S. Food and Drug Administration (FDA) to control certain diseases in salmonids and catfish. OTC is also a likely control agent for diseases of other fish species and for other diseases of salmonids and catfish not currently on the label. One requirement for FDA to extend and expand the approval of this antibacterial agent to other fish species is residue depletion studies. The current regulatory method for OTC in fish tissue, based on microbial inhibition, lacks sensitivity and specificity. To conduct residue depletion studies for OTC in fish with a liquid chromatographic method, a bridging study was required to determine its relationship with the official microbial inhibition assay. Triplicate samples of rainbow trout fillet tissue fortified with OTC at 0.3, 0.6, 1.2, 2.4, 4.8, and 9.6 ppm and fillet tissue with incurred OTC at approximately 0.75, 1.5, and 3.75 ppm were analyzed by high-performance liquid chromatography (HPLC) and the microbial inhibition assay. The results indicated that the 2 methods are essentially identical in the tested range, with mean coefficients of variation of 1.05% for the HPLC method and 3.94% for the microbial inhibition assay.

Microbial community dynamics and biogas production from manure fractions in sludge bed anaerobic digestion.

PubMed

Nordgård, A S R; Bergland, W H; Bakke, R; Vadstein, O; Østgaard, K; Bakke, I

2015-12-01

To elucidate how granular sludge inoculum and particle-rich organic loading affect the structure of the microbial communities and process performance in upflow anaerobic sludge bed (UASB) reactors. We investigated four reactors run on dairy manure filtrate and four on pig manure supernatant for three months achieving similar methane yields. The reactors fed with less particle rich pig manure stabilized faster and had highest capacity. Microbial community dynamics analysed by a PCR/denaturing gradient gel electrophoresis approach showed that influent was a major determinant for the composition of the reactor communities. Comparisons of pre- and non-adapted inoculum in the reactors run on pig manure supernatant showed that the community structure of the nonadapted inoculum adapted in approximately two months. Microbiota variance partitioning analysis revealed that running time, organic loading rate and inoculum together explained 26 and 31% of the variance in bacterial and archaeal communities respectively. The microbial communities of UASBs adapted to the reactor conditions in treatment of particle rich manure fractions, obtaining high capacity, especially on pig manure supernatant. These findings provide relevant insight into the microbial community dynamics in startup and operation of sludge bed reactors for methane production from slurry fractions, a major potential source of biogas. © 2015 The Society for Applied Microbiology.

The impact of cotton growing practices on soil microbiology and its relation to plant and soil health

NASA Astrophysics Data System (ADS)

Pereg, Lily

2013-04-01

Crop production and agricultural practices heavily impact the soil microbial communities, which differ among varying types of soils and environmental conditions. Soil-borne microbial communities in cotton production systems, as in every other cropping system, consist of microbial populations that may either be pathogenic, beneficial or neutral with respect to the cotton crop. Crop production practices have major roles in determining the composition of microbial communities and function of microbial populations in soils. The structure and function of any given microbial community is determined by various factors, including those that are influenced by farming and those not controlled by farming activities. Examples of the latter are environmental conditions such as soil type, temperature, daylight length and UV radiation, air humidity, atmospheric pressure and some abiotic features of the soil. On the other hand, crop production practices may determine other abiotic soil properties, such as water content, density, oxygen levels, mineral and elemental nutrient levels and the load of other crop-related soil amendments. Moreover, crop production highly influences the biotic properties of the soil and has a major role in determining the fate of soil-borne microbial communities associated with the crop plant. Various microbial strains react differently to the presence of certain plants and plant exudates. Therefore, the type of plant and crop rotations are important factors determining microbial communities. In addition, practice management, e.g. soil cultivation versus crop stubble retention, have a major effect on the soil conditions and, thus, on microbial community structure and function. All of the above-mentioned factors can lead to preferential selection of certain microbial population over others. It may affect not only the composition of microbial communities (diversity and abundance of microbial members) but also the function of the community (the ability of different microbes to perform certain activities). Therefore, agricultural practices may determine the ability of beneficial microbes to realise their plant growth promoting potential or the pathogenic expression of others. This presentation will review the current knowledge about the impact of cotton growing practices on microbial communities and soil health in different environments as well as endeavour to identify gaps worthwhile exploring in future research for promoting plant growth in healthy soils.

Lignocellulose-derived thin stillage composition and efficient biological treatment with a high-rate hybrid anaerobic bioreactor system.

PubMed

Oosterkamp, Margreet J; Méndez-García, Celia; Kim, Chang-H; Bauer, Stefan; Ibáñez, Ana B; Zimmerman, Sabrina; Hong, Pei-Ying; Cann, Isaac K; Mackie, Roderick I

2016-01-01

This study aims to chemically characterize thin stillage derived from lignocellulosic biomass distillation residues in terms of organic strength, nutrient, and mineral content. The feasibility of performing anaerobic digestion on these stillages at mesophilic (40 °C) and thermophilic (55 °C) temperatures to produce methane was demonstrated. The microbial communities involved were further characterized. Energy and sugar cane stillage have a high chemical oxygen demand (COD of 43 and 30 g/L, respectively) and low pH (pH 4.3). Furthermore, the acetate concentration in sugar cane stillage was high (45 mM) but was not detected in energy cane stillage. There was also a high amount of lactate in both types of stillage (35-37 mM). The amount of sugars was 200 times higher in energy cane stillage compared to sugar cane stillage. Although there was a high concentration of sulfate (18 and 23 mM in sugar and energy cane stillage, respectively), both thin stillages were efficiently digested anaerobically with high COD removal under mesophilic and thermophilic temperature conditions and with an organic loading rate of 15-21 g COD/L/d. The methane production rate was 0.2 L/g COD, with a methane percentage of 60 and 64, and 92 and 94 % soluble COD removed, respectively, by the mesophilic and thermophilic reactors. Although both treatment processes were equally efficient, there were different microbial communities involved possibly arising from the differences in the composition of energy cane and sugar cane stillage. There was more acetic acid in sugar cane stillage which may have promoted the occurrence of aceticlastic methanogens to perform a direct conversion of acetate to methane in reactors treating sugar cane stillage. Results showed that thin stillage contains easily degradable compounds suitable for anaerobic digestion and that hybrid reactors can efficiently convert thin stillage to methane under mesophilic and thermophilic conditions. Furthermore, we found that optimal conditions for biological treatment of thin stillage were similar for both mesophilic and thermophilic reactors. Bar-coded pyrosequencing of the 16S rRNA gene identified different microbial communities in mesophilic and thermophilic reactors and these differences in the microbial communities could be linked to the composition of the thin stillage.

Microbial Community Structure in Lake and Wetland Sediments from a High Arctic Polar Desert Revealed by Targeted Transcriptomics

PubMed Central

Stoeva, Magdalena K.; Aris-Brosou, Stéphane; Chételat, John; Hintelmann, Holger; Pelletier, Philip; Poulain, Alexandre J.

2014-01-01

While microbial communities play a key role in the geochemical cycling of nutrients and contaminants in anaerobic freshwater sediments, their structure and activity in polar desert ecosystems are still poorly understood, both across heterogeneous freshwater environments such as lakes and wetlands, and across sediment depths. To address this question, we performed targeted environmental transcriptomics analyses and characterized microbial diversity across three depths from sediment cores collected in a lake and a wetland, located on Cornwallis Island, NU, Canada. Microbial communities were characterized based on 16S rRNA and two functional gene transcripts: mcrA, involved in archaeal methane cycling and glnA, a bacterial housekeeping gene implicated in nitrogen metabolism. We show that methane cycling and overall bacterial metabolic activity are the highest at the surface of lake sediments but deeper within wetland sediments. Bacterial communities are highly diverse and structured as a function of both environment and depth, being more diverse in the wetland and near the surface. Archaea are mostly methanogens, structured by environment and more diverse in the wetland. McrA transcript analyses show that active methane cycling in the lake and wetland corresponds to distinct communities with a higher potential for methane cycling in the wetland. Methanosarcina spp., Methanosaeta spp. and a group of uncultured Archaea are the dominant methanogens in the wetland while Methanoregula spp. predominate in the lake. PMID:24594936

Microbial and Functional Diversity within the Phyllosphere of Espeletia Species in an Andean High-Mountain Ecosystem.

PubMed

Ruiz-Pérez, Carlos A; Restrepo, Silvia; Zambrano, María Mercedes

2016-01-08

Microbial populations residing in close contact with plants can be found in the rhizosphere, in the phyllosphere as epiphytes on the surface, or inside plants as endophytes. Here, we analyzed the microbiota associated with Espeletia plants, endemic to the Páramo environment of the Andes Mountains and a unique model for studying microbial populations and their adaptations to the adverse conditions of high-mountain neotropical ecosystems. Communities were analyzed using samples from the rhizosphere, necromass, and young and mature leaves, the last two analyzed separately as endophytes and epiphytes. The taxonomic composition determined by performing sequencing of the V5-V6 region of the 16S rRNA gene indicated differences among populations of the leaf phyllosphere, the necromass, and the rhizosphere, with predominance of some phyla but only few shared operational taxonomic units (OTUs). Functional profiles predicted on the basis of taxonomic affiliations differed from those obtained by GeoChip microarray analysis, which separated community functional capacities based on plant microenvironment. The identified metabolic pathways provided insight regarding microbial strategies for colonization and survival in these ecosystems. This study of novel plant phyllosphere microbiomes and their putative functional ecology is also the first step for future bioprospecting studies in search of enzymes, compounds, or microorganisms relevant to industry or for remediation efforts. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Microbial and Functional Diversity within the Phyllosphere of Espeletia Species in an Andean High-Mountain Ecosystem

PubMed Central

Restrepo, Silvia

2016-01-01

Microbial populations residing in close contact with plants can be found in the rhizosphere, in the phyllosphere as epiphytes on the surface, or inside plants as endophytes. Here, we analyzed the microbiota associated with Espeletia plants, endemic to the Páramo environment of the Andes Mountains and a unique model for studying microbial populations and their adaptations to the adverse conditions of high-mountain neotropical ecosystems. Communities were analyzed using samples from the rhizosphere, necromass, and young and mature leaves, the last two analyzed separately as endophytes and epiphytes. The taxonomic composition determined by performing sequencing of the V5-V6 region of the 16S rRNA gene indicated differences among populations of the leaf phyllosphere, the necromass, and the rhizosphere, with predominance of some phyla but only few shared operational taxonomic units (OTUs). Functional profiles predicted on the basis of taxonomic affiliations differed from those obtained by GeoChip microarray analysis, which separated community functional capacities based on plant microenvironment. The identified metabolic pathways provided insight regarding microbial strategies for colonization and survival in these ecosystems. This study of novel plant phyllosphere microbiomes and their putative functional ecology is also the first step for future bioprospecting studies in search of enzymes, compounds, or microorganisms relevant to industry or for remediation efforts. PMID:26746719

Microbial and chemical properties of log ponds along the Oregon Coast.

Treesearch

Iwan Ho; Ching Yan Li

1987-01-01

The microbial and chemical properties of log ponds along the Oregon coast were investigated. The log ponds were highly eutrophic, containing high concentrations of ammonium and nitrate nitrogen, phosphate, and organic compounds. Because of large microbial populations, the biochemical oxygen demand was high and dissolved oxygen was low. Bacterial species in log ponds...

Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment

PubMed Central

Hsu, Tiffany; Joice, Regina; Vallarino, Jose; Abu-Ali, Galeb; Hartmann, Erica M.; Shafquat, Afrah; DuLong, Casey; Baranowski, Catherine; Gevers, Dirk; Green, Jessica L.; Spengler, John D.

2016-01-01

ABSTRACT Public transit systems are ideal for studying the urban microbiome and interindividual community transfer. In this study, we used 16S amplicon and shotgun metagenomic sequencing to profile microbial communities on multiple transit surfaces across train lines and stations in the Boston metropolitan transit system. The greatest determinant of microbial community structure was the transit surface type. In contrast, little variation was observed between geographically distinct train lines and stations serving different demographics. All surfaces were dominated by human skin and oral commensals such as Propionibacterium, Corynebacterium, Staphylococcus, and Streptococcus. The detected taxa not associated with humans included generalists from alphaproteobacteria, which were especially abundant on outdoor touchscreens. Shotgun metagenomics further identified viral and eukaryotic microbes, including Propionibacterium phage and Malassezia globosa. Functional profiling showed that Propionibacterium acnes pathways such as propionate production and porphyrin synthesis were enriched on train holding surfaces (holds), while electron transport chain components for aerobic respiration were enriched on touchscreens and seats. Lastly, the transit environment was not found to be a reservoir of antimicrobial resistance and virulence genes. Our results suggest that microbial communities on transit surfaces are maintained from a metapopulation of human skin commensals and environmental generalists, with enrichments corresponding to local interactions with the human body and environmental exposures. IMPORTANCE Mass transit environments, specifically, urban subways, are distinct microbial environments with high occupant densities, diversities, and turnovers, and they are thus especially relevant to public health. Despite this, only three culture-independent subway studies have been performed, all since 2013 and all with widely differing designs and conclusions. In this study, we profiled the Boston subway system, which provides 238 million trips per year overseen by the Massachusetts Bay Transportation Authority (MBTA). This yielded the first high-precision microbial survey of a variety of surfaces, ridership environments, and microbiological functions (including tests for potential pathogenicity) in a mass transit environment. Characterizing microbial profiles for multiple transit systems will become increasingly important for biosurveillance of antibiotic resistance genes or pathogens, which can be early indicators for outbreak or sanitation events. Understanding how human contact, materials, and the environment affect microbial profiles may eventually allow us to rationally design public spaces to sustain our health in the presence of microbial reservoirs. Author Video: An author video summary of this article is available. PMID:27822528

Electrochemical and impedance characterization of Microbial Fuel Cells based on 2D and 3D anodic electrodes working with seawater microorganisms under continuous operation.

PubMed

Hidalgo, D; Sacco, A; Hernández, S; Tommasi, T

2015-11-01

A mixed microbial population naturally presents in seawater was used as active anodic biofilm of two Microbial Fuel Cells (MFCs), employing either a 2D commercial carbon felt or 3D carbon-coated Berl saddles as anode electrodes, with the aim to compare their electrochemical behavior under continuous operation. After an initial increase of the maximum power density, the felt-based cell reduced its performance at 5 months (from 7 to 4 μW cm(-2)), while the saddle-based MFC exceeds 9 μW cm(-2) (after 2 months) and maintained such performance for all the tests. Electrochemical impedance spectroscopy was used to identify the MFCs controlling losses and indicates that the mass-transport limitations at the biofilm-electrolyte interface have the main contribution (>95%) to their internal resistance. The activation resistance was one order of magnitude lower with the Berl saddles than with carbon felt, suggesting an enhanced charge-transfer in the high surface-area 3D electrode, due to an increase in bacteria population growth. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

PubMed

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

2017-10-15

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

Invited review: Essential oils as modifiers of rumen microbial fermentation.

PubMed

Calsamiglia, S; Busquet, M; Cardozo, P W; Castillejos, L; Ferret, A

2007-06-01

Microorganisms in the rumen degrade nutrients to produce volatile fatty acids and synthesize microbial protein as an energy and protein supply for the ruminant, respectively. However, this fermentation process has energy (losses of methane) and protein (losses of ammonia N) inefficiencies that may limit production performance and contribute to the release of pollutants to the environment. Antibiotic ionophores have been very successful in reducing these energy and protein losses in the rumen, but the use of antibiotics in animal feeds is facing reduced social acceptance, and their use has been banned in the European Union since January 2006. For this reason, scientists have become interested in evaluating other alternatives to control specific microbial populations to modulate rumen fermentation. Essential oils can interact with microbial cell membranes and inhibit the growth of some gram-positive and gram-negative bacteria. As a result of such inhibition, the addition of some plant extracts to the rumen results in an inhibition of deamination and methanogenesis, resulting in lower ammonia N, methane, and acetate, and in higher propionate and butyrate concentrations. Results have indicated that garlic oil, cinnamaldehyde (the main active component of cinnamon oil), eugenol (the main active component of the clove bud), capsaicin (the active component of hot peppers), and anise oil, among others, may increase propionate production, reduce acetate or methane production, and modify proteolysis, peptidolysis, or deamination in the rumen. However, the effects of some of these essential oils are pH and diet dependent, and their use may be beneficial only under specific conditions and production systems. For example, capsaicin appears to have small effects in high-forage diets, whereas the changes observed in high-concentrate diets (increases in dry matter intake and total VFA, and reduction in the acetateto-propionate ratio and ammonia N concentration) may be beneficial. Because plant extracts may act at different levels in the carbohydrate and protein degradation pathways, their careful selection and combination may provide a useful tool to manipulate rumen microbial fermentation effectively. However, additional research is required to establish the optimal dose in vivo in units of the active component, to consider the potential adaptation of microbial populations to their activities, to examine the presence of residues in the products (milk or meat), and to demonstrate improvements in animal performance.

Water Microbiology Kit/Microbial Capture Devices (WMK MCD)

NASA Image and Video Library

2009-08-04

ISS020-E-027318 (4 Aug. 2009) --- Canadian Space Agency astronaut Robert Thirsk, Expedition 20 flight engineer, performs a subsequent in-flight analysis with a Water Microbiology Kit/Microbial Capture Devices (WMK MCD) for microbial traces in the Destiny laboratory of the International Space Station.

A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city.

PubMed

Dorado-Morales, Pedro; Vilanova, Cristina; Peretó, Juli; Codoñer, Francisco M; Ramón, Daniel; Porcar, Manuel

2016-07-05

Microorganisms colonize a wide range of natural and artificial environments although there are hardly any data on the microbial ecology of one the most widespread man-made extreme structures: solar panels. Here we show that solar panels in a Mediterranean city (Valencia, Spain) harbor a highly diverse microbial community with more than 500 different species per panel, most of which belong to drought-, heat- and radiation-adapted bacterial genera, and sun-irradiation adapted epiphytic fungi. The taxonomic and functional profiles of this microbial community and the characterization of selected culturable bacteria reveal the existence of a diverse mesophilic microbial community on the panels' surface. This biocenosis proved to be more similar to the ones inhabiting deserts than to any human or urban microbial ecosystem. This unique microbial community shows different day/night proteomic profiles; it is dominated by reddish pigment- and sphingolipid-producers, and is adapted to withstand circadian cycles of high temperatures, desiccation and solar radiation.

A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city

PubMed Central

Dorado-Morales, Pedro; Vilanova, Cristina; Peretó, Juli; Codoñer, Francisco M.; Ramón, Daniel; Porcar, Manuel

2016-01-01

Microorganisms colonize a wide range of natural and artificial environments although there are hardly any data on the microbial ecology of one the most widespread man-made extreme structures: solar panels. Here we show that solar panels in a Mediterranean city (Valencia, Spain) harbor a highly diverse microbial community with more than 500 different species per panel, most of which belong to drought-, heat- and radiation-adapted bacterial genera, and sun-irradiation adapted epiphytic fungi. The taxonomic and functional profiles of this microbial community and the characterization of selected culturable bacteria reveal the existence of a diverse mesophilic microbial community on the panels’ surface. This biocenosis proved to be more similar to the ones inhabiting deserts than to any human or urban microbial ecosystem. This unique microbial community shows different day/night proteomic profiles; it is dominated by reddish pigment- and sphingolipid-producers, and is adapted to withstand circadian cycles of high temperatures, desiccation and solar radiation. PMID:27378552

To improve the performance of sediment microbial fuel cell through amending colloidal iron oxyhydroxide into freshwater sediments.

PubMed

Zhou, Yan-Li; Yang, Ying; Chen, Mo; Zhao, Zhi-Wei; Jiang, He-Long

2014-05-01

Effects of iron oxide amendment into freshwater sediments on performance of sediment microbial fuel cell (SMFC) were investigated. It was found that amending amorphous bulk ferric oxyhydroxide, and crystalline goethite and magnetite did not affect SMFC operation. However, amendment of the mixed solution including soluble ferric citrate and colloidal iron oxyhydroxide, stably improved SMFC performance with voltage outputs up to threefolds higher than those without amendment. The enhanced voltage production corresponded to lower anode potential, but was not related to organic matter removal in sediments. Further experiments demonstrated that colloidal iron oxyhydroxide instead of soluble ferric iron played an important role in voltage production through maintaining high-concentration ferrous iron in pore water of sediments as electron shuttle and for chemical oxidation on the anode. Thus, colloidal iron oxyhydroxide amendment was a promising strategy to improve power production from SMFC employed in sediments especially with low content of organic matters. Copyright © 2014 Elsevier Ltd. All rights reserved.

Improving startup performance with carbon mesh anodes in separator electrode assembly microbial fuel cells.

PubMed

Zhang, Fang; Xia, Xue; Luo, Yong; Sun, Dan; Call, Douglas F; Logan, Bruce E

2013-04-01

In a separator electrode assembly microbial fuel cell, oxygen crossover from the cathode inhibits current generation by exoelectrogenic bacteria, resulting in poor reactor startup and performance. To determine the best approach for improving startup performance, the effect of acclimation to a low set potential (-0.2V, versus standard hydrogen electrode) was compared to startup at a higher potential (+0.2 V) or no set potential, and inoculation with wastewater or pre-acclimated cultures. Anodes acclimated to -0.2 V produced the highest power of 1330±60 mW m(-2) for these different anode conditions, but unacclimated wastewater inocula produced inconsistent results despite the use of this set potential. By inoculating reactors with transferred cell suspensions, however, startup time was reduced and high power was consistently produced. These results show that pre-acclimation at -0.2 V consistently improves power production compared to use of a more positive potential or the lack of a set potential. Copyright © 2013 Elsevier Ltd. All rights reserved.

Linking TFT-LCD wastewater treatment performance to microbial population abundance of Hyphomicrobium and Thiobacillus spp.

PubMed

Fukushima, Toshikazu; Whang, Liang-Ming; Chen, Po-Chun; Putri, Dyah Wulandari; Chang, Ming-Yu; Wu, Yi-Ju; Lee, Ya-Ching

2013-08-01

This study investigated the linkage between performance of two full-scale membrane bioreactor (MBR) systems treating thin-film transistor liquid crystal display (TFT-LCD) wastewater and the population dynamics of dimethylsulfoxide (DMSO)/dimethylsulfide (DMS) degrading bacteria. High DMSO degradation efficiencies were achieved in both MBRs, while the levels of nitrification inhibition due to DMS production from DMSO degradation were different in the two MBRs. The results of real-time PCR targeting on DMSO/DMS degrading populations, including Hyphomicrobium and Thiobacillus spp., indicated that a higher DMSO oxidation efficiency occurred at a higher Hyphomicrobium spp. abundance in the systems, suggesting that Hyphomicrobium spp. may be more important for complete DMSO oxidation to sulfate compared with Thiobacillus spp. Furthermore, Thiobacillus spp. was more abundant during poor nitrification, while Hyphomicrobium spp. was more abundant during good nitrification. It is suggested that microbial population of DMSO/DMS degrading bacteria is closely linking to both DMSO/DMS degradation efficiency and nitrification performance. Copyright © 2013 Elsevier Ltd. All rights reserved.

Acidic and alkaline pretreatments of activated carbon and their effects on the performance of air-cathodes in microbial fuel cells.

PubMed

Wang, Xin; Gao, Ningshengjie; Zhou, Qixing; Dong, Heng; Yu, Hongbing; Feng, Yujie

2013-09-01

Activated carbon (AC) is a high performing and cost effective catalyst for oxygen reduction reactions (ORRs) of air-cathodes in microbial fuel cells (MFCs). Acidic (HNO3) and alkaline (KOH) pretreatments on AC at low temperature (85°C) are conducted to enhance the performance of MFCs. The alkaline pretreatment increased the power density by 16% from 804±70 to 957±31 mW m(-2), possibly due to the decrease of ohmic resistance (from 20.58 to 19.20 Ω) and the increase of ORR activities provided by the adsorbed hydroxide ion and extra micropore area/volume after alkaline pretreatment. However, acidic pretreatment decreased the power output to 537±36 mW m(-2), which can be mainly attributed to the corrosion by adsorbed proton at the interface of AC powder and stainless steel mesh and the decreased pore area. Copyright © 2013 Elsevier Ltd. All rights reserved.

Soil microbial succession along a chronosequence on a High Arctic glacier foreland, Ny-Ålesund, Svalbard: 10 years' change

NASA Astrophysics Data System (ADS)

Yoshitake, Shinpei; Uchida, Masaki; Iimura, Yasuo; Ohtsuka, Toshiyuki; Nakatsubo, Takayuki

2018-06-01

Rapid glacial retreat in the High Arctic causes the expansion of new habitats, but the successional trajectories of soil microbial communities are not fully understood. We examined microbial succession along a chronosequence twice with a 10-year interval in a High Arctic glacier foreland. Soil samples were collected from five study sites with different ages and phospholipid fatty acids analysis was conducted to investigate the microbial biomass and community structure. Microbial biomass did not differ significantly between the two sampling times but tended to increase with the chronosequence and showed a significant correlation with soil carbon (C) and nitrogen (N) content. Microbial community structure clearly differed along the chronosequence and was correlated with C and N content. The largest shift in community structure over 10 years was observed in the newly exposed sites after deglaciation. The accumulation of soil organic matter was regarded as an important determinant both of microbial biomass and community structure over the successional period. In contrast, the initial microbial community on the newly exposed soil changed rapidly even in the High Arctic, suggesting that some key soil processes such as C and N cycling can also shift within the relatively short period after rapid glacial retreat.

Electrochemical Performance and Microbial Characterization of Thermophilic Microbial Fuel Cells

NASA Astrophysics Data System (ADS)

Wrighton, K. C.; Agbo, P.; Brodie, E. L.; Weber, K. A.; Desantis, T. Z.; Anderson, G. L.; Coates, J. D.

2007-12-01

Significant research effort is currently focused on microbial fuel cells (MFC) as a source of renewable energy. To date, most of these efforts have concentrated on MFCs operating at mesophilic temperatures. However, many previous studies have reported on the superiority of thermophilic conditions in anaerobic digestion and demonstrated a net gain in energy yield, in terms of methane, relative to the increased energy requirements of operation. Because of this, our recent studies on MFCs focused on investigating the operation and microbiology associated with thermophilic MFCs operating at 55°C. Over 100-day operation, these MFCs were highly stable and achieved a maximum power density of 24mW/m2 and a columbic efficiency of 89 percent with acetate as the sole electron donor. In order to characterize the microbial community involved in thermophilic electricity generation, DNA and RNA were isolated from the electrode and PhyloChip analyses performed. Exploring the changes in the microbial community over time in electricity producing MFC revealed an increase in relative abundance of populations belonging to the Firmicutes, Chloroflexi, and alpha Proteobacteria by at least one order of magnitude. In contrast, these populations decreased in the open circuit and no electron donor amended controls. In order to better characterize the active microbial populations, we enriched and isolated a novel organism, strain JR, from samples collected from an operating MFC. Based on 16S rRNA sequence analysis strain JR was a member of the family Peptococcaceae, within the Phylum Firmicutes, clustering with Thermincola ferriacetica (98 percent similarity). Phenotypic characterization revealed that strain JR was capable of thermophilic dissimilatory reduction of insoluble electron acceptors such as amorphous Fe(III); as well as reduction of the model quinone 2,6-anthraquinone disulfonate. Thermincola strain JR was also capable of producing current by coupling acetate oxidation to anodic electron transfer. This represents the first organism isolated from a thermophilic microbial fuel cell and also the first representative of this genus capable of anodic electron transfer. The results of this study indicate the potential advantages for thermophilic MFCs and the novel microbiology associated with their operation.

Development of a High Temperature Microbial Fermentation Processfor Butanol Production

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

Jeor, Jeffery D.; Reed, David W.; Daubaras, Dayna L.

2016-06-01

Transforming renewable biomass into cost competitive high-performance biofuels and bioproducts is key to US energy security. Butanol production by microbial fermentation and chemical conversion to polyolefins, elastomers, drop-in jet or diesel fuel, and other chemicals is a promising solution. A high temperature fermentation process can facilitate butanol recovery up to 40%, by using gas stripping. Other benefits of fermentation at high temperatures are optimal hydrolysis rates in the saccharification of biomass which leads to maximized butanol production, decrease in energy costs associated with reactor cooling and capital cost associated with reactor design, and a decrease in contamination and cost formore » maintaining a sterile environment. Butanol stripping at elevated temperatures gives higher butanol production through constant removal and continuous fermentation. We describe methods used in an attempt to genetically prepare Geobacillus caldoxylosiliticus for insertion of a butanol pathway. Methods used were electroporation of electrocompetent cells, ternary conjugation with E. coli, and protoplast fusion.« less

Stratified Bacterial Diversity along Physico-chemical Gradients in High-Altitude Modern Stromatolites

PubMed Central

Toneatti, Diego M.; Albarracín, Virginia H.; Flores, Maria R.; Polerecky, Lubos; Farías, María E.

2017-01-01

At an altitude of 3,570 m, the volcanic lake Socompa in the Argentinean Andes is presently the highest site where actively forming stromatolite-like structures have been reported. Interestingly, pigment and microsensor analyses performed through the different layers of the stromatolites (50 mm-deep) showed steep vertical gradients of light and oxygen, hydrogen sulfide and pH in the porewater. Given the relatively good characterization of these physico-chemical gradients, the aim of this follow-up work was to specifically address how the bacterial diversity stratified along the top six layers of the stromatolites which seems the most metabolically important and diversified zone of the whole microbial community. We herein discussed how, in only 7 mm, a drastic succession of metabolic adaptations occurred: i.e., microbial communities shift from a UV-high/oxic world to an IR-low/anoxic/high H2S environment which force stratification and metabolic specialization of the bacterial community, thus, modulating the chemical faces of the Socompa stromatolites. The oxic zone was dominated by Deinococcus sp. at top surface (0.3 mm), followed by a second layer of Coleofasciculus sp. (0.3 to ∼2 mm). Sequences from anoxygenic phototrophic Alphaproteobacteria, along with an increasing diversity of phyla including Bacteroidetes, Spirochaetes were found at middle layers 3 and 4. Deeper layers (5–7 mm) were mostly occupied by sulfate reducers of Deltaproteobacteria, Bacteroidetes and Firmicutes, next to a high diversity and equitable community of rare, unclassified and candidate phyla. This analysis showed how microbial communities stratified in a physicochemical vertical profile and according to the light source. It also gives an insight of which bacterial metabolic capabilities might operate and produce a microbial cooperative strategy to thrive in one of the most extreme environments on Earth. PMID:28446906

Stratified Bacterial Diversity along Physico-chemical Gradients in High-Altitude Modern Stromatolites.

PubMed

Toneatti, Diego M; Albarracín, Virginia H; Flores, Maria R; Polerecky, Lubos; Farías, María E

2017-01-01

At an altitude of 3,570 m, the volcanic lake Socompa in the Argentinean Andes is presently the highest site where actively forming stromatolite-like structures have been reported. Interestingly, pigment and microsensor analyses performed through the different layers of the stromatolites (50 mm-deep) showed steep vertical gradients of light and oxygen, hydrogen sulfide and pH in the porewater. Given the relatively good characterization of these physico-chemical gradients, the aim of this follow-up work was to specifically address how the bacterial diversity stratified along the top six layers of the stromatolites which seems the most metabolically important and diversified zone of the whole microbial community. We herein discussed how, in only 7 mm, a drastic succession of metabolic adaptations occurred: i.e., microbial communities shift from a UV-high/oxic world to an IR-low/anoxic/high H 2 S environment which force stratification and metabolic specialization of the bacterial community, thus, modulating the chemical faces of the Socompa stromatolites. The oxic zone was dominated by Deinococcus sp. at top surface (0.3 mm), followed by a second layer of Coleofasciculus sp. (0.3 to ∼2 mm). Sequences from anoxygenic phototrophic Alphaproteobacteria, along with an increasing diversity of phyla including Bacteroidetes, Spirochaetes were found at middle layers 3 and 4. Deeper layers (5-7 mm) were mostly occupied by sulfate reducers of Deltaproteobacteria, Bacteroidetes and Firmicutes, next to a high diversity and equitable community of rare, unclassified and candidate phyla. This analysis showed how microbial communities stratified in a physicochemical vertical profile and according to the light source. It also gives an insight of which bacterial metabolic capabilities might operate and produce a microbial cooperative strategy to thrive in one of the most extreme environments on Earth.

40 CFR 158.2160 - Microbial pesticides product performance data requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

... unless the pesticide product bears a claim to control public health pests, such as pest microorganisms... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Microbial pesticides product... AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Microbial Pesticides § 158.2160...

40 CFR 158.2160 - Microbial pesticides product performance data requirements.

Code of Federal Regulations, 2013 CFR

2013-07-01

... unless the pesticide product bears a claim to control public health pests, such as pest microorganisms... 40 Protection of Environment 25 2013-07-01 2013-07-01 false Microbial pesticides product... AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Microbial Pesticides § 158.2160...

40 CFR 158.2160 - Microbial pesticides product performance data requirements.

Code of Federal Regulations, 2014 CFR

2014-07-01

... unless the pesticide product bears a claim to control public health pests, such as pest microorganisms... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Microbial pesticides product... AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Microbial Pesticides § 158.2160...

40 CFR 158.2160 - Microbial pesticides product performance data requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

... unless the pesticide product bears a claim to control public health pests, such as pest microorganisms... 40 Protection of Environment 24 2011-07-01 2011-07-01 false Microbial pesticides product... AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Microbial Pesticides § 158.2160...

40 CFR 158.2160 - Microbial pesticides product performance data requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

... unless the pesticide product bears a claim to control public health pests, such as pest microorganisms... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Microbial pesticides product... AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Microbial Pesticides § 158.2160...

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

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.

A Spike Cocktail Approach to Improve Microbial Performance ...

EPA Pesticide Factsheets

Water reuse, via either centralized treatment of traditional wastewater or decentralized treatment and on-site reuse, is becoming an increasingly important element of sustainable water management. Despite advances in waterborne pathogen detection methods, low and highly variable pathogen levels limit their utility for routine evaluation of health risks in water reuse systems. Therefore, there is a need to improve our understanding of the linkage between pathogens and more readily measured process indicators during treatment. This paper describes an approach for constructing spiking experiments to relate the behavior of viral, bacterial, and protozoan pathogens with relevant process indicators. General issues are reviewed, and the spiking protocol is applied as a case study example to improve microbial performance monitoring and health risk evaluation in a water reuse system. This approach provides a foundation for the development of novel approaches to improve real or near-real time performance monitoring of water recycling systems. This manuscrupt details an approach for developing "spike cocktail", a mixture of microorganisms that can be used to evaluate the performance of engineered and natural systems.

Allee effect: the story behind the stabilization or extinction of microbial ecosystem.

PubMed

Goswami, Madhurankhi; Bhattacharyya, Purnita; Tribedi, Prosun

2017-03-01

A population exhibiting Allee effect shows a positive correlation between population fitness and population size or density. Allee effect decides the extinction or conservation of a microbial population and thus appears to be an important criterion in population ecology. The underlying factor of Allee effect that decides the stabilization and extinction of a particular population density is the threshold or the critical density of their abundance. According to Allee, microbial populations exhibit a definite, critical or threshold density, beyond which the population fitness of a particular population increases with the rise in population density and below it, the population fitness goes down with the decrease in population density. In particular, microbial population displays advantageous traits such as biofilm formation, expression of virulence genes, spore formation and many more only at a high population density. It has also been observed that microorganisms exhibiting a lower population density undergo complete extinction from the residual microbial ecosystem. In reference to Allee effect, decrease in population density or size introduces deleterious mutations among the population density through genetic drift. Mutations are carried forward to successive generations resulting in its accumulation among the population density thus reducing its microbial fitness and thereby increasing the risk of extinction of a particular microbial population. However, when the microbial load is high, the chance of genetic drift is less, and through the process of biofilm formation, the cooperation existing among the microbial population increases that increases the microbial fitness. Thus, the high microbial population through the formation of microbial biofilm stabilizes the ecosystem by increasing fitness. Taken together, microbial fitness shows positive correlation with the ecosystem conservation and negative correlation with ecosystem extinction.

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

PubMed Central

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

2014-01-01

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

Clinical impact of pre-transplant gut microbial diversity on outcomes of allogeneic hematopoietic stem cell transplantation.

PubMed

Doki, Noriko; Suyama, Masahiro; Sasajima, Satoshi; Ota, Junko; Igarashi, Aiko; Mimura, Iyo; Morita, Hidetoshi; Fujioka, Yuki; Sugiyama, Daisuke; Nishikawa, Hiroyoshi; Shimazu, Yutaka; Suda, Wataru; Takeshita, Kozue; Atarashi, Koji; Hattori, Masahira; Sato, Eiichi; Watakabe-Inamoto, Kyoko; Yoshioka, Kosuke; Najima, Yuho; Kobayashi, Takeshi; Kakihana, Kazuhiko; Takahashi, Naoto; Sakamaki, Hisashi; Honda, Kenya; Ohashi, Kazuteru

2017-09-01

Post-transplant microbial diversity in the gastrointestinal tract is closely associated with clinical outcomes following allogeneic hematopoietic stem cell transplantation (allo-HSCT). However, little is known about the impact of the fecal microbiota before allo-HSCT. We analyzed fecal samples approximately 2 weeks before conditioning among 107 allo-HSCT recipients between 2013 and 2015. Microbial analysis was performed using 16S rRNA gene sequencing. Operational taxonomic unit-based microbial diversity was estimated by calculating the Shannon index. Patients were classified into three groups based on the diversity index: low (<2), intermediate (2, 3), and high (>3) diversity (18 (16.8%), 48 (44.9%), and 41 (38.3%) patients, respectively). There were no significant differences in the 20-month overall survival, cumulative incidence of relapse, and non-relapse mortality among three groups. The cumulative incidence of grade II to IV acute graft-versus-host disease (aGVHD) was similar among the three groups (low 55.6%; intermediate 35.4%; high 48.8%, p = 0.339, at day 100). Furthermore, we found no differences in the cumulative incidence of grade II to IV acute gastrointestinal GVHD among the three groups (low 38.9%; intermediate 21.3%; high 24.4%, p = 0.778, at day 100). Regarding the composition of microbiota before allo-HSCT, aGVHD patients showed a significantly higher abundance of phylum Firmicutes (p < 0.01) and a lower tendency for Bacteroidetes (p = 0.106) than non-aGVHD patients. Maintenance of Bacteroidetes throughout allo-HSCT may be a strategy to prevent aGVHD.

Effect of Phenotypic Residual Feed Intake and Dietary Forage Content on the Rumen Microbial Community of Beef Cattle

PubMed Central

Carberry, Ciara A.; Kenny, David A.; Han, Sukkyan; McCabe, Matthew S.

2012-01-01

Feed-efficient animals have lower production costs and reduced environmental impact. Given that rumen microbial fermentation plays a pivotal role in host nutrition, the premise that rumen microbiota may contribute to host feed efficiency is gaining momentum. Since diet is a major factor in determining rumen community structure and fermentation patterns, we investigated the effect of divergence in phenotypic residual feed intake (RFI) on ruminal community structure of beef cattle across two contrasting diets. PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR) were performed to profile the rumen bacterial population and to quantify the ruminal populations of Entodinium spp., protozoa, Fibrobacter succinogenes, Ruminococcus flavefaciens, Ruminococcus albus, Prevotella brevis, the genus Prevotella, and fungi in 14 low (efficient)- and 14 high (inefficient)-RFI animals offered a low-energy, high-forage diet, followed by a high-energy, low-forage diet. Canonical correspondence and Spearman correlation analyses were used to investigate associations between physiological variables and rumen microbial structure and specific microbial populations, respectively. The effect of RFI on bacterial profiles was influenced by diet, with the association between RFI group and PCR-DGGE profiles stronger for the higher forage diet. qPCR showed that Prevotella abundance was higher (P < 0.0001) in inefficient animals. A higher (P < 0.0001) abundance of Entodinium and Prevotella spp. and a lower (P < 0.0001) abundance of Fibrobacter succinogenes were observed when animals were offered the low-forage diet. Thus, differences in the ruminal microflora may contribute to host feed efficiency, although this effect may also be modulated by the diet offered. PMID:22562991

Effect of phenotypic residual feed intake and dietary forage content on the rumen microbial community of beef cattle.

PubMed

Carberry, Ciara A; Kenny, David A; Han, Sukkyan; McCabe, Matthew S; Waters, Sinead M

2012-07-01

Feed-efficient animals have lower production costs and reduced environmental impact. Given that rumen microbial fermentation plays a pivotal role in host nutrition, the premise that rumen microbiota may contribute to host feed efficiency is gaining momentum. Since diet is a major factor in determining rumen community structure and fermentation patterns, we investigated the effect of divergence in phenotypic residual feed intake (RFI) on ruminal community structure of beef cattle across two contrasting diets. PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR) were performed to profile the rumen bacterial population and to quantify the ruminal populations of Entodinium spp., protozoa, Fibrobacter succinogenes, Ruminococcus flavefaciens, Ruminococcus albus, Prevotella brevis, the genus Prevotella, and fungi in 14 low (efficient)- and 14 high (inefficient)-RFI animals offered a low-energy, high-forage diet, followed by a high-energy, low-forage diet. Canonical correspondence and Spearman correlation analyses were used to investigate associations between physiological variables and rumen microbial structure and specific microbial populations, respectively. The effect of RFI on bacterial profiles was influenced by diet, with the association between RFI group and PCR-DGGE profiles stronger for the higher forage diet. qPCR showed that Prevotella abundance was higher (P < 0.0001) in inefficient animals. A higher (P < 0.0001) abundance of Entodinium and Prevotella spp. and a lower (P < 0.0001) abundance of Fibrobacter succinogenes were observed when animals were offered the low-forage diet. Thus, differences in the ruminal microflora may contribute to host feed efficiency, although this effect may also be modulated by the diet offered.

Geobacter Dominates the Inner Layers of a Stratified Biofilm on a Fluidized Anode During Brewery Wastewater Treatment

PubMed Central

Tejedor-Sanz, Sara; Fernández-Labrador, Patricia; Hart, Steven; Torres, Cesar I.; Esteve-Núñez, Abraham

2018-01-01

In this study, we designed a microbial electrochemical fluidized bed reactor (ME-FBR), with an electroconductive anodic bed made of activated carbon particles for treating a brewery wastewater. Under a batch operating mode, acetate and propionate consumption rates were 13-fold and 2.4-fold higher, respectively, when the fluidized anode was polarized (0.2 V) with respect to open circuit conditions. Operating in a continuous mode, this system could effectively treat the brewery effluent at organic loading rates (OLR) over 1.7 kg m-3NRV d-1 and with removal efficiencies of 95 ± 1.4% (hydraulic retention time of 1 day and an influent of 1.7 g-COD L-1). The coulombic efficiency values highly depended upon the OLR applied, and varied from a 56 ± 15% to 10 ± 1%. Fluorescence in situ hybridization (FISH) analysis revealed a relative high abundance of Geobacter species (ca. 20%), and clearly showed a natural microbial stratification. Interestingly, the Geobacter cluster was highly enriched in the innermost layers of the biofilm (thickness of 10 μm), which were in contact with the electroconductive particles of bed, whereas the rest of bacteria were located in the outermost layers. To our knowledge, this is the first time that such a clear microbial stratification has been observed on an anode-respiring biofilm. Our results revealed the relevant role of Geobacter in switching between the electrode and other microbial communities performing metabolic reactions in the outermost environment of the biofilm. PMID:29568284

Porous Ni0.1Mn0.9O1.45 microellipsoids as high-performance anode electrocatalyst for microbial fuel cells.

PubMed

Zeng, Lizhen; Zhang, Wenguang; Xia, Pan; Tu, Wenqiang; Ye, Changchun; He, Miao

2018-04-15

A novel bi-component composite of porous self-assembled micro-/nanostructured Ni 0.1 Mn 0.9 O 1.45 microellipsoids as high-performance anode electrocatalyst for microbial fuel cells (MFCs) is successfully synthesized via a simple coprecipitation reaction in microemulsion and calcination method in air atmosphere. The morphology and structural characterization indicate that the as-fabricated Ni 0.1 Mn 0.9 O 1.45 product is consist of Mn 2 O 3 and NiMn 2 O 4 (n(Mn 2 O 3) : n(NiMn 2 O 4 ) = 0.35: 0.1) and has a porous microellipsoidal morphology. The microellipsoids are compose of numerous layered micro-/nanostructured blocks and the special porous microellipsoids structure of Ni 0.1 Mn 0.9 O 1.45 offers a large specific surface area for bacteria adhesion. The porous Ni 0.1 Mn 0.9 O 1.45 microellipsoids as anode electrocatalyst for MFCs exhibits excellent electrocatalytic activity to promote the extracellular electron transfer (EET) between the anode and bacteria, hence improves the performance of MFC. The MFC equipped with Ni 0.1 Mn 0.9 O 1.45 /CF anode achieves a maximum power density of 1.39 ± 0.02Wm -2 , is significantly higher than that of commercial carbon felt anode. This work proposes a new method for the synthesis of high-performance and environmentally friendly anode electrocatalyst for MFCs. Copyright © 2017 Elsevier B.V. All rights reserved.

Supplementation with Ca salts of soybean oil interacts with concentrate level in grazing dairy cows: intake, ingestive behavior, and ruminal parameters.

PubMed

Macedo, Fernanda Lopes; Batistel, Fernanda; de Souza, Jonas; Chagas, Lucas Jado; Santos, Flávio Augusto Portela

2016-12-01

In this study, we investigated the associative effects of concentrate levels and Ca salts of soybean oil (CSSO) supplementation on performance and ruminal parameters of mid-lactation dairy cows grazing on tropical pasture. Twenty-four Jersey × Holstein cows were used in a randomized block design and assigned to four treatments arranged in a 2 × 2 factorial design. Factors evaluated were concentrate levels (low, 3 kg/day vs. high, 7 kg/day of concentrate) and CSSO supplementation (without CSSO vs. with 250 g CSSO cow/day). All cows grazed on elephant grass (Pennisetum purpureum cv. Cameroon) and received the supplemental treatments for a 90-day period. The high concentrate level decreased forage intake and grazing time. In addition, the high concentrate level increased rumen propionate concentration and microbial synthesis and tended to decrease ammonia-N compared with low concentrate level. The addition of CSSO tended to decrease valerate, isobutyrate, isovalerate, and microbial synthesis. In conclusion, feeding CSSO for mid lactating cows grazing on tropical pasture had negative effects on rumen function. In contrast, CSSO supplementation tended to interact with concentrate level and increased energy intake when fed at low concentrate level. Feeding the high level of concentrate was an effective strategy to increase energy intake and microbial synthesis and improve N utilization.

Rumen microbial protein synthesis and nitrogen efficiency as affected by tanniferous and non-tanniferous forage legumes incubated individually or together in Rumen Simulation Technique.

PubMed

Grosse Brinkhaus, Anja; Bee, Giuseppe; Schwarm, Angela; Kreuzer, Michael; Dohme-Meier, Frigga; Zeitz, Johanna O

2018-03-01

A limited availability of microbial protein can impair productivity in ruminants. Ruminal nitrogen efficiency might be optimised by combining high-quality forage legumes such as red clover (RC), which has unfavourably high ruminal protein degradability, with tanniferous legumes like sainfoin (SF) and birdsfoot trefoil (BT). Silages from SF and from BT cultivars [Bull (BB) and Polom (BP)] were incubated singly or in combination with RC using the Rumen Simulation Technique (n = 6). The tanniferous legumes, when compared to RC, changed the total short-chain fatty acid profile by increasing propionate proportions at the expense of butyrate. Silage from SF contained the most condensed tannins (CTs) (136 g CT kg -1 dry matter) and clearly differed in various traits from the BT and RC silages. The apparent nutrient degradability (small with SF), microbial protein synthesis, and calculated content of potentially utilisable crude protein (large with SF) indicated that SF had the greatest efficiency in ruminal protein synthesis. The effects of combining SF with RC were mostly linear. The potential of sainfoin to improve protein supply, demonstrated either individually or in combination with a high-performance forage legume, indicates its potential usefulness in complementing protein-deficient ruminant diets and high-quality forages rich in rumen-degradable protein. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Separator electrode assembly (SEA) with 3-dimensional bioanode and removable air-cathode boosts microbial fuel cell performance

NASA Astrophysics Data System (ADS)

Oliot, M.; Etcheverry, L.; Mosdale, A.; Basseguy, R.; Délia, M.-L.; Bergel, A.

2017-07-01

Separator electrode assemblies (SEAs) were designed by associating a microbial anode with an air-cathode on each side of three different kinds of separator: plastic grid, J-cloth and baking paper. The SEA was designed to allow the air-cathode be removed and replaced without disturbing the bioanode. Power densities up to 6.4 W m-2 were produced by the Grid-SEAs (on average 5.9 ± 0.5 W m-2) while JCloth-SEAs and Paper-SEAs produced 4.8 ± 0.3 and 1.8 ± 0.1 W m-2, respectively. Power densities decreased with time mainly because of fast deterioration of the cathode kinetics. They always increased again when the air-cathodes were replaced by new ones; the Grid-SEAs were thus boosted above 4 W m-2 after 7 weeks of operation. The theoretical analysis of SEA functioning suggested that the high performance of the Grid-SEAs was due to the combination of several virtuous phenomena: the efficient pH balance thanks to free diffusion through the large-mesh grid, the likely mitigation of oxygen crossover thanks to the 3-dimensional structure of the bioanode and the possibility of overcoming cathode fouling by replacing it during MFC operation. Finally, the microbial community of all bioanodes showed stringent selection of Proteiniphilum acetatigenes in proportion with the performance.

Single-stage versus two-stage anaerobic fluidized bed bioreactors in treating municipal wastewater: Performance, foulant characteristics, and microbial community.

PubMed

Wu, Bing; Li, Yifei; Lim, Weikang; Lee, Shi Lin; Guo, Qiming; Fane, Anthony G; Liu, Yu

2017-03-01

This study examined the receptive performance, membrane foulant characteristics, and microbial community in the single-stage and two-stage anaerobic fluidized membrane bioreactor (AFMBR) treating settled raw municipal wastewater with the aims to explore fouling mechanisms and microbial community structure in both systems. Both AFMBRs exhibited comparable organic removal efficiency and membrane performances. In the single-stage AFMBR, less soluble organic substances were removed through biosorption by GAC and biodegradation than those in the two-stage AFMBR. Compared to the two-stage AFMBR, the formation of cake layer was the main cause of the observed membrane fouling in the single-stage AFMBR at the same employed flux. The accumulation rate of the biopolymers was linearly correlated with the membrane fouling rate. In the chemical-cleaned foulants, humic acid-like substances and silicon were identified as the predominant organic and inorganic fouants respectively. As such, the fluidized GAC particles might not be effective in removing these substances from the membrane surfaces. High-throughout pyrosequencing analysis further revealed that beta-Proteobacteria were predominant members in both AFMBRs, which contributed to the development of biofilms on the fluidized GAC and membrane surfaces. However, it was also noted that the abundance of the identified dominant in the membrane surface-associated biofilm seemed to be related to the permeate flux and reactor configuration. Copyright © 2016 Elsevier Ltd. All rights reserved.

Electricity generation and brewery wastewater treatment from sequential anode-cathode microbial fuel cell.

PubMed

Wen, Qing; Wu, Ying; Zhao, Li-xin; Sun, Qian; Kong, Fan-ying

2010-02-01

A sequential anode-cathode double-chamber microbial fuel cell (MFC), in which the effluent of anode chamber was used as a continuous feed for an aerated cathode chamber, was constructed in this experiment to investigate the performance of brewery wastewater treatment in conjugation with electricity generation. Carbon fiber was used as anode and plain carbon felt with biofilm as cathode. When hydraulic retention time (HRT) was 14.7 h, a relatively high chemical oxygen demand (COD) removal efficiency of 91.7%-95.7% was achieved under long-term stable operation. The MFC displayed an open circuit voltage of 0.434 V and a maximum power density of 830 mW/m(3) at an external resistance of 300 Omega. To estimate the electrochemical performance of the MFC, electrochemical measurements were carried out and showed that polarization resistance of anode was the major limiting factor in the MFC. Since a high COD removal efficiency was achieved, we conclude that the sequential anode-cathode MFC constructed with bio-cathode in this experiment could provide a new approach for brewery wastewater treatment.

Macroporous graphitic carbon foam decorated with polydopamine as a high-performance anode for microbial fuel cell

NASA Astrophysics Data System (ADS)

Jiang, Hongmei; Yang, Lu; Deng, Wenfang; Tan, Yueming; Xie, Qingji

2017-09-01

Herein, a macroporous graphitic carbon foam (MGCF) electrode decorated with polydopamine (PDA) is used as a high-performance anode for microbial fuel cell (MFC) applications. The MGCF is facilely prepared by pyrolysis of a powder mixture comprising maltose, nickel nitrate, and ammonia chloride, without using solid porous template. The MGCF is coated with PDA by self-polymerization of dopamine in a basic solution. The MGCF can provide a large surface area for bacterial attachment, and PDA coated on the MGCF electrode can further promote bacterial adhesion resulting from the improved hydrophility, so the MGCF-PDA electrode as an anode in a MFC can show ultrahigh bacterial loading capacity. Moreover, the electrochemical oxidation of flavins at the MGCF-PDA electrode is greatly accelerated, so the extracellular electron transfer mediated by flavins is improved. As a result, the MFC equipped with a MGCF-PDA anode can show a maximum power density of 1735 mW cm-2, which is 6.7 times that of a MFC equipped with a commercial carbon felt anode, indicating a promising anode for MFC applications.

Different Lactobacillus populations dominate in "Chorizo de León" manufacturing performed in different production plants.

PubMed

Quijada, Narciso M; De Filippis, Francesca; Sanz, José Javier; García-Fernández, María Del Camino; Rodríguez-Lázaro, David; Ercolini, Danilo; Hernández, Marta

2018-04-01

"Chorizo de Léon" is a high-value Spanish dry fermented sausage traditionally manufactured without the use of starter cultures, owing to the activity of a house-specific autochthonous microbiota that naturally contaminates the meat from the environment, the equipment and the raw materials. Lactic acid bacteria (particularly Lactobacillus) and coagulase-negative cocci (mainly Staphylococcus) have been reported as the most important bacterial groups regarding the organoleptic and safety properties of the dry fermented sausages. In this study, samples from raw minced meat to final products were taken from five different producers and the microbial diversity was investigated by high-throughput sequencing of 16S rRNA gene amplicons. The diverse microbial composition observed during the first stages of "Chorizo de Léon" evolved during ripening to a microbiota mainly composed by Lactobacillus in the final product. Oligotyping performed on 16S rRNA gene sequences of Lactobacillus and Staphylococcus populations revealed sub-genus level diversity within the different manufacturers, likely responsible of the characteristic organoleptic properties of the products from different companies. Copyright © 2017 Elsevier Ltd. All rights reserved.

Electricity generation and brewery wastewater treatment from sequential anode-cathode microbial fuel cell*

PubMed Central

Wen, Qing; Wu, Ying; Zhao, Li-xin; Sun, Qian; Kong, Fan-ying

2010-01-01

A sequential anode-cathode double-chamber microbial fuel cell (MFC), in which the effluent of anode chamber was used as a continuous feed for an aerated cathode chamber, was constructed in this experiment to investigate the performance of brewery wastewater treatment in conjugation with electricity generation. Carbon fiber was used as anode and plain carbon felt with biofilm as cathode. When hydraulic retention time (HRT) was 14.7 h, a relatively high chemical oxygen demand (COD) removal efficiency of 91.7%–95.7% was achieved under long-term stable operation. The MFC displayed an open circuit voltage of 0.434 V and a maximum power density of 830 mW/m3 at an external resistance of 300 Ω. To estimate the electrochemical performance of the MFC, electrochemical measurements were carried out and showed that polarization resistance of anode was the major limiting factor in the MFC. Since a high COD removal efficiency was achieved, we conclude that the sequential anode-cathode MFC constructed with bio-cathode in this experiment could provide a new approach for brewery wastewater treatment. PMID:20104642

Oxygen - Enemy or Friend for Microbial Fuel Cell Anode Performance?

USDA-ARS?s Scientific Manuscript database

Until recently, scientists and engineers have held a strong belief that oxygen intrusion into the anode chamber of a bioelectrochemical system (BES) is detrimental to microbial fuel cell (MFC) performance because oxygen acts as an alternate electron acceptor. This would, according to recent beliefs...

Long-term performance of anaerobic digestion for crop residues containing heavy metals and response of microbial communities.

PubMed

Lee, Jongkeun; Kim, Joonrae Roger; Jeong, Seulki; Cho, Jinwoo; Kim, Jae Young

2017-01-01

In order to investigate the long-term stability on the performance of the anaerobic digestion process, a laboratory-scale continuous stirred-tank reactor (CSTR) was operated for 1100 days with sunflower harvested in a heavy metal contaminated site. Changes of microbial communities during digestion were identified using pyrosequencing. According to the results, soluble heavy metal concentrations were lower than the reported inhibitory level and the reactor performance remained stable up to OLR of 2.0g-VS/L/day at HRT of 20days. Microbial communities commonly found in anaerobic digestion for cellulosic biomass were observed and stably established with respect to the substrate. Thus, the balance of microbial metabolism was maintained appropriately and anaerobic digestion seems to be feasible for disposal of heavy metal-containing crop residues from phytoremediation sites. Copyright © 2016 Elsevier Ltd. All rights reserved.

Performance improvement of microbial fuel cell (MFC) using suitable electrode and Bioengineered organisms: A review

PubMed Central

Choudhury, Payel; Prasad Uday, Uma Shankar; Bandyopadhyay, Tarun Kanti; Ray, Rup Narayan

2017-01-01

ABSTRACT There is an urgent need to find an environment friendly and sustainable technology for alternative energy due to rapid depletion of fossil fuel and industrialization. Microbial Fuel Cells (MFCs) have operational and functional advantages over the current technologies for energy generation from organic matter as it directly converts electricity from substrate at ambient temperature. However, MFCs are still unsuitable for high energy demands due to practical limitations. The overall performance of an MFC depends on microorganism, appropriate electrode materials, suitable MFC designs, and optimizing process parameters which would accelerate commercialization of this technology in near future. In this review, we put forth the recent developments on microorganism and electrode material that are critical for the generation of bioelectricity generation. This would give a comprehensive insight into the characteristics, options, modifications, and evaluations of these parameters and their effects on process development of MFCs. PMID:28453385

Performance improvement of microbial fuel cell (MFC) using suitable electrode and Bioengineered organisms: A review.

PubMed

Choudhury, Payel; Prasad Uday, Uma Shankar; Bandyopadhyay, Tarun Kanti; Ray, Rup Narayan; Bhunia, Biswanath

2017-09-03

There is an urgent need to find an environment friendly and sustainable technology for alternative energy due to rapid depletion of fossil fuel and industrialization. Microbial Fuel Cells (MFCs) have operational and functional advantages over the current technologies for energy generation from organic matter as it directly converts electricity from substrate at ambient temperature. However, MFCs are still unsuitable for high energy demands due to practical limitations. The overall performance of an MFC depends on microorganism, appropriate electrode materials, suitable MFC designs, and optimizing process parameters which would accelerate commercialization of this technology in near future. In this review, we put forth the recent developments on microorganism and electrode material that are critical for the generation of bioelectricity generation. This would give a comprehensive insight into the characteristics, options, modifications, and evaluations of these parameters and their effects on process development of MFCs.

Microbial fuel cells: recent developments in design and materials

NASA Astrophysics Data System (ADS)

Bhargavi, G.; Venu, V.; Renganathan, S.

2018-03-01

Microbial Fuel Cells (MFCs) are the promising devices which can produce electricity by anaerobic fermentation of organic / inorganic matter from easily metabolized biomass to complex wastewater using microbes as biocatalysts. MFC technology has been found as a potential technology for electricity generation and concomitant wastewater treatment. However, the high cost of the components and low efficiency are barricading the commercialization of MFC when compared with other energy generating systems. The performance of an MFC is largely relying on the reactor design and electrode materials. On the way to improve the efficiency of an MFC, tremendous exercises have been carried out to explore new electrode materials and reactor designs in recent decades. The current review is excogitated to amass the progress in design and electrode materials, which could bolster further investigations on MFCs to improve their performance, mitigate the cost and successful implementation of technology in field applications as well.

Effect of Increasing Total Solids Contents on Anaerobic Digestion of Food Waste under Mesophilic Conditions: Performance and Microbial Characteristics Analysis

PubMed Central

Jin, Jingwei; Dai, Xiaohu

2014-01-01

The total solids content of feedstocks affects the performances of anaerobic digestion and the change of total solids content will lead the change of microbial morphology in systems. In order to increase the efficiency of anaerobic digestion, it is necessary to understand the role of the total solids content on the behavior of the microbial communities involved in anaerobic digestion of organic matter from wet to dry technology. The performances of mesophilic anaerobic digestion of food waste with different total solids contents from 5% to 20% were compared and the microbial communities in reactors were investigated using 454 pyrosequencing technology. Three stable anaerobic digestion processes were achieved for food waste biodegradation and methane generation. Better performances mainly including volatile solids reduction and methane yield were obtained in the reactors with higher total solids content. Pyrosequencing results revealed significant shifts in bacterial community with increasing total solids contents. The proportion of phylum Chloroflexi decreased obviously with increasing total solids contents while other functional bacteria showed increasing trend. Methanosarcina absolutely dominated in archaeal communities in three reactors and the relative abundance of this group showed increasing trend with increasing total solids contents. These results revealed the effects of the total solids content on the performance parameters and the behavior of the microbial communities involved in the anaerobic digestion of food waste from wet to dry technologies. PMID:25051352

Effect of increasing total solids contents on anaerobic digestion of food waste under mesophilic conditions: performance and microbial characteristics analysis.

PubMed

Yi, Jing; Dong, Bin; Jin, Jingwei; Dai, Xiaohu

2014-01-01

The total solids content of feedstocks affects the performances of anaerobic digestion and the change of total solids content will lead the change of microbial morphology in systems. In order to increase the efficiency of anaerobic digestion, it is necessary to understand the role of the total solids content on the behavior of the microbial communities involved in anaerobic digestion of organic matter from wet to dry technology. The performances of mesophilic anaerobic digestion of food waste with different total solids contents from 5% to 20% were compared and the microbial communities in reactors were investigated using 454 pyrosequencing technology. Three stable anaerobic digestion processes were achieved for food waste biodegradation and methane generation. Better performances mainly including volatile solids reduction and methane yield were obtained in the reactors with higher total solids content. Pyrosequencing results revealed significant shifts in bacterial community with increasing total solids contents. The proportion of phylum Chloroflexi decreased obviously with increasing total solids contents while other functional bacteria showed increasing trend. Methanosarcina absolutely dominated in archaeal communities in three reactors and the relative abundance of this group showed increasing trend with increasing total solids contents. These results revealed the effects of the total solids content on the performance parameters and the behavior of the microbial communities involved in the anaerobic digestion of food waste from wet to dry technologies.

Electrochemical performance and microbial community profiles in microbial fuel cells in relation to electron transfer mechanisms.

PubMed

Uria, Naroa; Ferrera, Isabel; Mas, Jordi

2017-10-18

Microbial fuel cells (MFCs) operating with complex microbial communities have been extensively reported in the past, and are commonly used in applications such as wastewater treatment, bioremediation or in-situ powering of environmental sensors. However, our knowledge on how the composition of the microbial community and the different types of electron transfer to the anode affect the performance of these bioelectrochemical systems is far from complete. To fill this gap of knowledge, we designed a set of three MFCs with different constrains limiting direct and mediated electron transfer to the anode. The results obtained indicate that MFCs with a naked anode on which a biofilm was allowed unrestricted development (MFC-A) had the most diverse archaeal and bacterial community, and offered the best performance. In this MFC both, direct and mediated electron transfer, occurred simultaneously, but direct electron transfer was the predominant mechanism. Microbial fuel cells in which the anode was enclosed in a dialysis membrane and biofilm was not allowed to develop (MFC-D), had a much lower power output (about 60% lower), and a prevalence of dissolved redox species that acted as putative electron shuttles. In the anolyte of this MFC, Arcobacter and Methanosaeta were the prevalent bacteria and archaea respectively. In the third MFC, in which the anode had been covered by a cation selective nafion membrane (MFC-N), power output decreased a further 5% (95% less than MFC-A). In this MFC, conventional organic electron shuttles could not operate and the low power output obtained was presumably attributed to fermentation end-products produced by some of the organisms present in the anolyte, probably Pseudomonas or Methanosaeta. Electron transfer mechanisms have an impact on the development of different microbial communities and in turn on MFC performance. Although a stable current was achieved in all cases, direct electron transfer MFC showed the best performance concluding that biofilms are the major contributors to current production in MFCs. Characterization of the complex microbial assemblages in these systems may help us to unveil new electrogenic microorganisms and improve our understanding on their role to the functioning of MFCs.

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

PubMed

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

2015-12-01

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

Human Immune Function and Microbial Pathogenesis in Human Spaceflight

NASA Technical Reports Server (NTRS)

Pierson, Duane J.; Ott, M.

2006-01-01

This oral presentation was requested by Conference conveners. The requested subject is microbial risk assessment considering changes in the human immune system during flight and microbial diversity of environmental samples aboard the International Space Station (ISS). The presentation will begin with an introduction discussing the goals and limitations of microbial risk assessment during flight. The main portion of the presentation will include changes in the immune system that have been published, historical data from microbial analyses, and initial modeling of the environmental flora aboard ISS. The presentation will conclude with future goals and techniques to enhance our ability to perform microbial risk assessment on long duration missions.

Polypyrrole/sargassum activated carbon modified stainless-steel sponge as high-performance and low-cost bioanode for microbial fuel cells

NASA Astrophysics Data System (ADS)

Wu, Gaoming; Bao, Han; Xia, Zheng; Yang, Bin; Lei, Lecheng; Li, Zhongjian; Liu, Chunxian

2018-04-01

Anode materials, as the core component of microbial fuel cells (MFCs), have huge impacts on power generation performance and overall cost. Stainless-steel sponge (SS) can be a promising material for MFC anodes, due to its open continuous three-dimensional structure, high conductivity and low cost. However, poor biocompatibility limits its application. In this paper, a polypyrrole/sargassum activated carbon modified SS anode (Ppy/SAC/SS) is developed by electrochemical polymerization of pyrrole on the SS with the SAC as a dopant. The maximum power density achieved with the Ppy/SAC/SS anode is 45.2 W/m3, which is increased by 2 orders of magnitude and 2.9 times compared with an unmodified SS anode and a solely Ppy modified SS anode (Ppy/SS), respectively. In addition, the Ppy/SAC layer effectively eliminates electrochemical corrosion of the SS substrate. Electrochemical impedance spectroscopy reveals that Ppy/SAC modification decreases electron transfer resistance between the bacteria and the electrode. Furthermore, in vivo fluorescence imaging indicates that a more uniform biofilm is formed on the Ppy/SAC/SS compared to the unmodified SS and Ppy/SS. Due to the low cost of the materials, easy fabrication process and relatively high performance, our developed Ppy/SAC/SS can be a cost efficient anode material for MFCs in practical applications.

Sources of Variation in the Gut Microbial Community of Lycaeides melissa Caterpillars.

PubMed

Chaturvedi, Samridhi; Rego, Alexandre; Lucas, Lauren K; Gompert, Zachariah

2017-09-12

Microbes can mediate insect-plant interactions and have been implicated in major evolutionary transitions to herbivory. Whether microbes also play a role in more modest host shifts or expansions in herbivorous insects is less clear. Here we evaluate the potential for gut microbial communities to constrain or facilitate host plant use in the Melissa blue butterfly (Lycaeides melissa). We conducted a larval rearing experiment where caterpillars from two populations were fed plant tissue from two hosts. We used 16S rRNA sequencing to quantify the relative effects of sample type (frass versus whole caterpillar), diet (plant species), butterfly population and development (caterpillar age) on the composition and diversity of the caterpillar gut microbial communities, and secondly, to test for a relationship between microbial community and larval performance. Gut microbial communities varied over time (that is, with caterpillar age) and differed between frass and whole caterpillar samples. Diet (host plant) and butterfly population had much more limited effects on microbial communities. We found no evidence that gut microbe community composition was associated with caterpillar weight, and thus, our results provide no support for the hypothesis that variation in microbial community affects performance in L. melissa.

Impact of long-term salinity exposure in anaerobic membrane bioreactors treating phenolic wastewater: Performance robustness and endured microbial community.

PubMed

Muñoz Sierra, Julian D; Oosterkamp, Margreet J; Wang, Wei; Spanjers, Henri; van Lier, Jules B

2018-05-07

Industrial wastewaters are becoming increasingly associated with extreme conditions such as the presence of refractory compounds and high salinity that adversely affect biomass retention or reduce biological activity. Hence, this study evaluated the impact of long-term salinity increase to 20 gNa + .L -1 on the bioconversion performance and microbial community composition in anaerobic membrane bioreactors treating phenolic wastewater. Phenol removal efficiency of up to 99.9% was achieved at 14 gNa + .L -1 . Phenol conversion rates of 5.1 mgPh.gVSS -1 .d -1 , 4.7 mgPh.gVSS -1 .d -1 , and 11.7 mgPh.gVSS -1 .d -1 were obtained at 16 gNa + .L -1 ,18 gNa + .L -1 and 20 gNa + .L -1 , respectively. The AnMBR's performance was not affected by short-term step-wise salinity fluctuations of 2 gNa + .L -1 in the last phase of the experiment. It was also demonstrated in batch tests that the COD removal and methane production rate were higher at a K + :Na + ratio of 0.05, indicating the importance of potassium to maintain the methanogenic activity. The salinity increase adversely affected the transmembrane pressure likely due to a particle size decrease from 185 μm at 14 gNa + .L -1 to 16 μm at 20 gNa + .L -1 . Microbial community was dominated by bacteria belonging to the Clostridium genus and archaea by Methanobacterium and Methanosaeta genus. Syntrophic phenol degraders, such as Pelotomaculum genus were found to be increased when the maximum phenol conversion rate was attained at 20 gNa + .L -1 . Overall, the observed robustness of the AnMBR performance indicated an endured microbial community to salinity changes in the range of the sodium concentrations applied. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Environmental monitoring: data trending using a frequency model.

PubMed

Caputo, Ross A; Huffman, Anne

2004-01-01

Environmental monitoring programs for the oversight of classified environments have used traditional statistical control charts to monitor trends in microbial recovery for classified environments. These methodologies work well for environments that yield measurable microbial recoveries. However, today successful increased control of microbial content yields numerous instances where microbial recovery in a sample is generally zero. As a result, traditional control chart methods cannot be used appropriately. Two methods to monitor the performance of a classified environment where microbial recovery is zero are presented. Both methods use the frequency between non-zero microbial recovery as an event. Therefore, the frequency of events is monitored rather than the microbial recovery count. Both methods are shown to be appropriate for use in the described instances.

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

PubMed

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

2017-01-01

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

Comparison of Microbial Communities Isolated from Feces of Asymptomatic Salmonella-Shedding and Non-Salmonella Shedding Dairy Cows

PubMed Central

Haley, Bradd J.; Pettengill, James; Gorham, Sasha; Ottesen, Andrea; Karns, Jeffrey S.; Van Kessel, Jo Ann S.

2016-01-01

In the United States Salmonella enterica subsp. enterica serotypes Kentucky and Cerro are frequently isolated from asymptomatic dairy cows. However, factors that contribute to colonization of the bovine gut by these two serotypes have not been identified. To investigate associations between Salmonella status and bacterial diversity, as well as the diversity of the microbial community in the dairy cow hindgut, the bacterial and archaeal communities of fecal samples from cows on a single dairy farm were determined by high-throughput sequencing of 16S rRNA gene amplicons. Fecal grab samples were collected from two Salmonella-positive cows and two Salmonella-negative cows on five sampling dates (n = 20 cows), and 16S rRNA gene amplicons from these samples were sequenced on the Illumina MiSeq platform. A high level of alpha (within) and beta diversity (between) samples demonstrated that microbial profiles of dairy cow hindguts are quite diverse. To determine whether Salmonella presence, sampling year, or sampling date explained a significant amount of the variation in microbial diversity, we performed constrained ordination analyses (distance based RDA) on the unifrac distance matrix produced with QIIME. Results indicated that there was not a significant difference in the microbial diversity associated with Salmonella presence (P > 0.05), but there were significant differences between sampling dates and years (Pseudo-F = 2.157 to 4.385, P < 0.05). Based on these data, it appears that commensal Salmonella infections with serotypes Cerro and Kentucky in dairy cows have little or no association with changes in the abundance of major bacterial groups in the hindgut. Rather, our results indicated that temporal dynamics and other undescribed parameters associated with them were the most influential drivers of the differences in microbial diversity and community structure in the dairy cow hindgut. PMID:27313565

Microbial flora analysis for the degradation of beta-cypermethrin.

PubMed

Qi, Zhang; Wei, Zhang

2017-03-01

In the Xinjiang region of Eurasia, sustained long-term and continuous cropping of cotton over a wide expanse of land is practiced, which requires application of high levels of pyrethroid and other classes of pesticides-resulting in high levels of pesticide residues in the soil. In this study, soil samples were collected from areas of long-term continuous cotton crops with the aim of obtaining microbial resources applicable for remediation of pyrethroid pesticide contamination suitable for the soil type and climate of that area. Soil samples were first used to culture microbial flora capable of degrading beta-cypermethrin using an enrichment culture method. Structural changes and ultimate microbial floral composition during enrichment were analyzed by high-throughput sequencing. Four strains capable of degrading beta-cypermethrin were isolated and preliminarily classified. Finally, comparative rates and speeds of degradation of beta-cypermethrin between relevant microbial flora and single strains were determined. After continuous subculture for 3 weeks, soil sample microbial flora formed a new type of microbial flora by rapid succession, which showed stable growth by utilizing beta-cypermethrin as the sole carbon source (GXzq). This microbial flora mainly consisted of Pseudomonas, Hyphomicrobium, Dokdonella, and Methyloversatilis. Analysis of the microbial flora also permitted separation of four additional strains; i.e., GXZQ4, GXZQ6, GXZQ7, and GXZQ13 that, respectively, belonged to Streptomyces, Enterobacter, Streptomyces, and Pseudomonas. Under culture conditions of 37 °C and 180 rpm, the degradation rate of beta-cypermethrin by GXzq was as high as 89.84% within 96 h, which exceeded that achieved by the single strains GXZQ4, GXZQ6, GXZQ7, and GXZQ13 and their derived microbial flora GXh.

Assessing the effectiveness of pollutant removal by macrophytes in a floating wetland for wastewater treatment

NASA Astrophysics Data System (ADS)

Prajapati, Meera; van Bruggen, Johan J. A.; Dalu, Tatenda; Malla, Rabin

2017-12-01

The study aimed to evaluate the removal of pollutants by floating treatment wetlands (FTWs) using an edible floating plant, and emergent macrophytes. All experiments were performed under ambient conditions. Physico-chemical parameters were measured, along with microbiological analysis of biofilm within the roots, water column, and sludge and gravel zone. Nitrification and denitrification rates were high in the water zone of Azolla filiculoides, Lemna minor, Lactuca sativa, P. stratiotes, and Phragmites australis. Phosphate removal efficiencies were 23, 10, and 15% for the free-floating hydrophytes, emergent macrophytes, and control and edible plants, respectively. The microbial community was relatively more active in the root zone compared to other zones. Pistia stratiotes was found to be the efficient in ammonium (70%) and total nitrogen (59%) removal. Pistia stratiotes also showed the highest microbial activity of 1306 mg day-1, which was 62% of the total volume. Microbial activity was found in the water zone of all FTWs expect for P. australis. The use of P. stratiotes and the edible plant L. sativa could be a potential option to treat domestic wastewater due to relatively high nutrient and organic matter removal efficiency.

Biosynthesis and engineering of kaempferol in Saccharomyces cerevisiae.

PubMed

Duan, Lijin; Ding, Wentao; Liu, Xiaonan; Cheng, Xiaozhi; Cai, Jing; Hua, Erbing; Jiang, Huifeng

2017-09-26

Kaempferol is a flavonol with broad bioactivity of anti-oxidant, anti-cancer, anti-diabetic, anti-microbial, cardio-protective and anti-asthma. Microbial synthesis of kaempferol is a promising strategy because of the low content in primary plant source. In this study, the biosynthesis pathway of kaempferol was constructed in the budding yeast Saccharomyces cerevisiae to produce kaempferol de novo, and several biological measures were taken for high production. Firstly, a high efficient flavonol synthases (FLS) from Populus deltoides was introduced into the biosynthetic pathway of kaempferol. Secondly, a S. cerevisiae recombinant was constructed for de novo synthesis of kaempferol, which generated about 6.97 mg/L kaempferol from glucose. To further promote kaempferol production, the acetyl-CoA biosynthetic pathway was overexpressed and p-coumarate was supplied as substrate, which improved kaempferol titer by about 23 and 120%, respectively. Finally, a fed-batch process was developed for better kaempferol fermentation performance, and the production reached 66.29 mg/L in 40 h. The titer of kaempferol in our engineered yeast is 2.5 times of the highest reported titer. Our study provides a possible strategy to produce kaempferol using microbial cell factory.

Exposure to microbial components and allergens in population studies: a comparison of two house dust collection methods applied by participants and fieldworkers.

PubMed

Schram-Bijkerk, D; Doekes, G; Boeve, M; Douwes, J; Riedler, J; Ublagger, E; von Mutius, E; Benz, M; Pershagen, G; Wickman, M; Alfvén, T; Braun-Fahrländer, C; Waser, M; Brunekreef, B

2006-12-01

Dust collection by study participants instead of fieldworkers would be a practical and cost-effective alternative in large-scale population studies estimating exposure to indoor allergens and microbial agents. We aimed to compare dust weights and biological agent levels in house dust samples taken by study participants with nylon socks, with those in samples taken by fieldworkers using the sampling nozzle of the Allergology Laboratory Copenhagen (ALK). In homes of 216 children, parents and fieldworkers collected house dust within the same year. Dust samples were analyzed for levels of allergens, endotoxin, (1-->3)-beta-D-glucans and fungal extracellular polysaccharides (EPS). Socks appeared to yield less dust from mattresses at relatively low dust amounts and more dust at high dust amounts than ALK samples. Correlations between the methods ranged from 0.47-0.64 for microbial agents and 0.64-0.87 for mite and pet allergens. Cat allergen levels were two-fold lower and endotoxin levels three-fold higher in socks than in ALK samples. Levels of allergens and microbial agents in sock samples taken by study participants are moderately to highly correlated to levels in ALK samples taken by fieldworkers. Absolute levels may differ, probably because of differences in the method rather than in the person who performed the sampling. Practical Implications Dust collection by participants is a reliable and practical option for allergen and microbial agent exposure assessment. Absolute levels of biological agents are not (always) comparable between studies using different dust collection methods, even when expressed per gram dust, because of potential differences in particle-size constitution of the collected dust.

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.

2015-08-01

SHIMMER (Soil biogeocHemIcal Model for Microbial Ecosystem Response) is a new numerical modelling framework which is developed as part of an interdisciplinary, iterative, model-data based approach fully integrating fieldwork and laboratory experiments with model development, testing, and application. SHIMMER is designed to simulate the establishment of microbial biomass and associated biogeochemical cycling during the initial stages of 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 model mechanistically describes and predicts transformations in carbon, nitrogen and phosphorus through aggregated components of the microbial community as a set of coupled ordinary differential equations. The rationale for development of the model arises from decades of empirical observation on the initial stages of soil development in glacier forefields. SHIMMER enables a quantitative and process focussed approach to synthesising the existing empirical data and advancing understanding of microbial and biogeochemical dynamics. Here, we provide a detailed description of SHIMMER. The performance of SHIMMER is then tested in two case studies using published data from the Damma Glacier forefield in Switzerland and the Athabasca Glacier in Canada. In addition, a sensitivity analysis helps 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. Simulation results indicate that primary production is responsible for the initial build-up of substrate that subsequently supports heterotrophic growth. However, allochthonous contributions of organic matter are identified as important in sustaining this productivity. Microbial production in young soils is supported by labile organic matter, whereas carbon stocks in older soils are more refractory. Nitrogen fixing bacteria are responsible for the initial accumulation of available nitrates in the soil. Biogeochemical rates are highly seasonal, as observed in experimental data. The development and application of SHIMMER not only provides important new insights into forefield dynamics, but also highlights aspects of these systems that require further field and laboratory research. The most pressing advances need to come in quantifying nutrient budgets and biogeochemical rates, in exploring seasonality, the fate of allochthonous deposition in relation to autochthonous production, and empirical studies of microbial growth and cell death, to increase understanding of how glacier forefield development contributes to the global biogeochemical cycling and climate in the future.

Taxonomic and Functional Differences between Microbial Communities in Qinghai Lake and Its Input Streams

PubMed Central

Ren, Ze; Wang, Fang; Qu, Xiaodong; Elser, James J.; Liu, Yang; Chu, Limin

2017-01-01

Understanding microbial communities in terms of taxon and function is essential to decipher the biogeochemical cycling in aquatic ecosystems. Lakes and their input streams are highly linked. However, the differences between microbial assemblages in streams and lakes are still unclear. In this study, we conducted an intensive field sampling of microbial communities from lake water and stream biofilms in the Qinghai Lake watershed, the largest lake in China. We determined bacterial communities using high-throughput 16S rRNA gene sequencing and predicted functional profiles using PICRUSt to determine the taxonomic and functional differences between microbial communities in stream biofilms and lake water. The results showed that stream biofilms and lake water harbored distinct microbial communities. The microbial communities were different taxonomically and functionally between stream and lake. Moreover, streams biofilms had a microbial network with higher connectivity and modularity than lake water. Functional beta diversity was strongly correlated with taxonomic beta diversity in both the stream and lake microbial communities. Lake microbial assemblages displayed greater predicted metabolic potentials of many metabolism pathways while the microbial assemblages in stream biofilms were more abundant in xenobiotic biodegradation and metabolism and lipid metabolism. Furthermore, lake microbial assemblages had stronger predicted metabolic potentials in amino acid metabolism, carbon fixation, and photosynthesis while stream microbial assemblages were higher in carbohydrate metabolism, oxidative phosphorylation, and nitrogen metabolism. This study adds to our knowledge of stream-lake linkages from the functional and taxonomic composition of microbial assemblages. PMID:29213266

Effects of phosphorus and nitrogen additions on tropical soil microbial activity in the context of experimental warming

NASA Astrophysics Data System (ADS)

Foley, M.; Nottingham, A.; Turner, B. L.

2017-12-01

Soil warming is generally predicted to increase microbial mineralization rates and accelerate soil C losses which could establish a positive feedback to climatic warming. Tropical rain forests account for a third of global soil C, yet the responseto of tropical soil C a warming climate remains poorly understood. Despite predictions of soil C losses, decomposition of soil organic matter (SOM) in tropical soils may be constrained by several factors including microbial nutrient deficiencies. We performed an incubation experiment in conjunction with an in-situ soil warming experiment in a lowland tropical forest on Barro Colorado Island, Panama, to measure microbial response to two key nutrient additions in shallow (0-10cm) and deep (50-100 cm) soils. We compared the response of lowland tropical soils to montane tropical soils, predicting that lowland soils would display the strongest response to phosphorus additions. Soils were treated with either carbon alone (C), nitrogen (CN), phosphorus (CP) or nitrogen and phosphorus combined (CNP). Carbon dioxide (CO2) production was measured by NaOH capture and titrimetric analysis for 10 days. Cumulative CO2 production in montane soils increased significantly with all additions, suggesting these soils are characterized by a general microbial nutrient deficiency. The cumulative amount of C respired in deep soils from the lowland site increased significantly with CP and CNP additions, suggesting that microbial processes in deep lowland tropical soils are phosphorus-limited. These results support the current understanding that lowland tropical forests are growing on highly weathered, phosphorus-deplete soils, and provide novel insight that deep tropical SOM may be stabilized by a lack of biologically-available phosphorus. Further, this data suggests tropical soil C losses under elevated temperature may be limited by a strong microbial phosphorus deficiency.

Italian multicentre study on microbial environmental contamination in dental clinics: a pilot study.

PubMed

Pasquarella, Cesira; Veronesi, Licia; Castiglia, Paolo; Liguori, Giorgio; Montagna, Maria Teresa; Napoli, Christian; Rizzetto, Rolando; Torre, Ida; Masia, Maria Dolores; Di Onofrio, Valeria; Colucci, Maria Eugenia; Tinteri, Carola; Tanzi, Marialuisa

2010-09-01

The dental practice is associated with a high risk of infections, both for patients and healthcare operators, and the environment may play an important role in the transmission of infectious diseases. A microbiological environmental investigation was carried out in six dental clinics as a pilot study for a larger multicentre study that will be performed by the Italian SItI (Society of Hygiene, Preventive Medicine and Public Health) working group "Hygiene in Dentistry". Microbial contamination of water, air and surfaces was assessed in each clinic during the five working days of the week, before and during treatments. Air and surfaces were also examined at the end of the daily activity. A wide variation was found in microbial environmental contamination, both within the participating clinics and relative to the different sampling times. Microbial water contamination in Dental Unit Water Systems (DUWS) reached values of up to 26x10(4)cfu/mL (colony forming units per millilitre). P. aeruginosa was found in 33% of the sampled DUWS and Legionella spp. in 50%. A significant decrease in the Total Viable Count (TVC) was recorded during the activity. Microbial air contamination showed the highest levels during dental treatments and tended to decrease at the end of the working activity (p<0.05). Microbial buildup on surfaces increased significantly during the working hours. As these findings point out, research on microbial environmental contamination and the related risk factors in dental clinics should be expanded and should also be based on larger collections of data, in order to provide the essential knowledge aimed at targeted preventive interventions. Copyright 2010 Elsevier B.V. All rights reserved.

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

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

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

2005-05-26

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

Single gene-based distinction of individual microbial genomes from a mixed population of microbial cells.

PubMed

Tamminen, Manu V; Virta, Marko P J

2015-01-01

Recent progress in environmental microbiology has revealed vast populations of microbes in any given habitat that cannot be detected by conventional culturing strategies. The use of sensitive genetic detection methods such as CARD-FISH and in situ PCR have been limited by the cell wall permeabilization requirement that cannot be performed similarly on all cell types without lysing some and leaving some nonpermeabilized. Furthermore, the detection of low copy targets such as genes present in single copies in the microbial genomes, has remained problematic. We describe an emulsion-based procedure to trap individual microbial cells into picoliter-volume polyacrylamide droplets that provide a rigid support for genetic material and therefore allow complete degradation of cellular material to expose the individual genomes. The polyacrylamide droplets are subsequently converted into picoliter-scale reactors for genome amplification. The amplified genomes are labeled based on the presence of a target gene and differentiated from those that do not contain the gene by flow cytometry. Using the Escherichia coli strains XL1 and MC1061, which differ with respect to the presence (XL1), or absence (MC1061) of a single copy of a tetracycline resistance gene per genome, we demonstrate that XL1 genomes present at 0.1% of MC1061 genomes can be differentiated using this method. Using a spiked sediment microbial sample, we demonstrate that the method is applicable to highly complex environmental microbial communities as a target gene-based screen for individual microbes. The method provides a novel tool for enumerating functional cell populations in complex microbial communities. We envision that the method could be optimized for fluorescence-activated cell sorting to enrich genetic material of interest from complex environmental samples.

Microbial community functional structure in response to antibiotics in pharmaceutical wastewater treatment systems.

PubMed

Zhang, Yu; Xie, Jianping; Liu, Miaomiao; Tian, Zhe; He, Zhili; van Nostrand, Joy D; Ren, Liren; Zhou, Jizhong; Yang, Min

2013-10-15

It is widely demonstrated that antibiotics in the environment affect microbial community structure. However, direct evidence regarding the impacts of antibiotics on microbial functional structures in wastewater treatment systems is limited. Herein, a high-throughput functional gene array (GeoChip 3.0) in combination with quantitative PCR and clone libraries were used to evaluate the microbial functional structures in two biological wastewater treatment systems, which treat antibiotic production wastewater mainly containing oxytetracycline. Despite the bacteriostatic effects of antibiotics, the GeoChip detected almost all key functional gene categories, including carbon cycling, nitrogen cycling, etc., suggesting that these microbial communities were functionally diverse. Totally 749 carbon-degrading genes belonging to 40 groups (24 from bacteria and 16 from fungi) were detected. The abundance of several fungal carbon-degrading genes (e.g., glyoxal oxidase (glx), lignin peroxidase or ligninase (lip), manganese peroxidase (mnp), endochitinase, exoglucanase_genes) was significantly correlated with antibiotic concentrations (Mantel test; P < 0.05), showing that the fungal functional genes have been enhanced by the presence of antibiotics. However, from the fact that the majority of carbon-degrading genes were derived from bacteria and diverse antibiotic resistance genes were detected in bacteria, it was assumed that many bacteria could survive in the environment by acquiring antibiotic resistance and may have maintained the position as a main player in nutrient removal. Variance partitioning analysis showed that antibiotics could explain 24.4% of variations in microbial functional structure of the treatment systems. This study provides insights into the impacts of antibiotics on microbial functional structure of a unique system receiving antibiotic production wastewater, and reveals the potential importance of the cooperation between fungi and bacteria with antibiotic resistance in maintaining the stability and performance of the systems. Copyright © 2013 Elsevier Ltd. All rights reserved.

Linking N2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community

PubMed Central

Harter, Johannes; Krause, Hans-Martin; Schuettler, Stefanie; Ruser, Reiner; Fromme, Markus; Scholten, Thomas; Kappler, Andreas; Behrens, Sebastian

2014-01-01

Nitrous oxide (N2O) contributes 8% to global greenhouse gas emissions. Agricultural sources represent about 60% of anthropogenic N2O emissions. Most agricultural N2O emissions are due to increased fertilizer application. A considerable fraction of nitrogen fertilizers are converted to N2O by microbiological processes (that is, nitrification and denitrification). Soil amended with biochar (charcoal created by pyrolysis of biomass) has been demonstrated to increase crop yield, improve soil quality and affect greenhouse gas emissions, for example, reduce N2O emissions. Despite several studies on variations in the general microbial community structure due to soil biochar amendment, hitherto the specific role of the nitrogen cycling microbial community in mitigating soil N2O emissions has not been subject of systematic investigation. We performed a microcosm study with a water-saturated soil amended with different amounts (0%, 2% and 10% (w/w)) of high-temperature biochar. By quantifying the abundance and activity of functional marker genes of microbial nitrogen fixation (nifH), nitrification (amoA) and denitrification (nirK, nirS and nosZ) using quantitative PCR we found that biochar addition enhanced microbial nitrous oxide reduction and increased the abundance of microorganisms capable of N2-fixation. Soil biochar amendment increased the relative gene and transcript copy numbers of the nosZ-encoded bacterial N2O reductase, suggesting a mechanistic link to the observed reduction in N2O emissions. Our findings contribute to a better understanding of the impact of biochar on the nitrogen cycling microbial community and the consequences of soil biochar amendment for microbial nitrogen transformation processes and N2O emissions from soil. PMID:24067258

Reactor performances and microbial communities of biogas reactors: effects of inoculum sources.

PubMed

Han, Sheng; Liu, Yafeng; Zhang, Shicheng; Luo, Gang

2016-01-01

Anaerobic digestion is a very complex process that is mediated by various microorganisms, and the understanding of the microbial community assembly and its corresponding function is critical in order to better control the anaerobic process. The present study investigated the effect of different inocula on the microbial community assembly in biogas reactors treating cellulose with various inocula, and three parallel biogas reactors with the same inoculum were also operated in order to reveal the reproducibility of both microbial communities and functions of the biogas reactors. The results showed that the biogas production, volatile fatty acid (VFA) concentrations, and pH were different for the biogas reactors with different inocula, and different steady-state microbial community patterns were also obtained in different biogas reactors as reflected by Bray-Curtis similarity matrices and taxonomic classification. It indicated that inoculum played an important role in shaping the microbial communities of biogas reactor in the present study, and the microbial community assembly in biogas reactor did not follow the niche-based ecology theory. Furthermore, it was found that the microbial communities and reactor performances of parallel biogas reactors with the same inoculum were different, which could be explained by the neutral-based ecology theory and stochastic factors should played important roles in the microbial community assembly in the biogas reactors. The Bray-Curtis similarity matrices analysis suggested that inoculum affected more on the microbial community assembly compared to stochastic factors, since the samples with different inocula had lower similarity (10-20 %) compared to the samples from the parallel biogas reactors (30 %).

Microbial fuel cells with highly active aerobic biocathodes

NASA Astrophysics Data System (ADS)

Milner, Edward M.; Popescu, Dorin; Curtis, Tom; Head, Ian M.; Scott, Keith; Yu, Eileen H.

2016-08-01

Microbial fuel cells (MFCs), which convert organic waste to electricity, could be used to make the wastewater infrastructure more energy efficient and sustainable. However, platinum and other non-platinum chemical catalysts used for the oxygen reduction reaction (ORR) at the cathode of MFCs are unsustainable due to their high cost and long-term degradation. Aerobic biocathodes, which use microorganisms as the biocatalysts for cathode ORR, are a good alternative to chemical catalysts. In the current work, high-performing aerobic biocathodes with an onset potential for the ORR of +0.4 V vs. Ag/AgCl were enriched from activated sludge in electrochemical half-cells poised at -0.1 and + 0.2 V vs. Ag/AgCl. Gammaproteobacteria, distantly related to any known cultivated gammaproteobacterial lineage, were identified as dominant in these working electrode biofilms (23.3-44.3% of reads in 16S rRNA gene Ion Torrent libraries), and were in very low abundance in non-polarised control working electrode biofilms (0.5-0.7%). These Gammaproteobacteria were therefore most likely responsible for the high activity of biologically catalysed ORR. In MFC tests, a high-performing aerobic biocathode increased peak power 9-fold from 7 to 62 μW cm-2 in comparison to an unmodified carbon cathode, which was similar to peak power with a platinum-doped cathode at 70 μW cm-2.

Sacrificing power for more cost-effective treatment: A techno-economic approach for engineering microbial fuel cells.

PubMed

Stoll, Zachary A; Ma, Zhaokun; Trivedi, Christopher B; Spear, John R; Xu, Pei

2016-10-01

Microbial fuel cells (MFCs) are a promising energy-positive wastewater treatment technology, however, the system's cost-effectiveness has been overlooked. In this study, two new anode materials - hard felt (HF) and carbon foam (CF) - were evaluated against the standard graphite brush (GB) to determine if using inexpensive materials with less than ideal properties can achieve more cost-effective treatment than high-cost, high-performing materials. Using domestic wastewater as the substrate, power densities for the GB, HF and CF-MFCs were 393, 339 and 291 mW m(-2) normalized by cathodic surface area, respectively. Higher power densities correlated with larger anodic surface areas and anodic current densities but not with electrical conductivity. Cyclic voltammetry revealed that redox systems used for extracellular electron transport in the GB, HF and CF-MFCs were similar (-0.143 ± 0.046, -0.158 ± 0.004 and -0.100 ± 0.014 V vs. Ag/AgCl) and that the electrochemical kinetics of the MFCs showed no correlation with their respective electrical conductivity. 16S rRNA sequencing showed the GB, HF and CF microbial community compositions were not statistically different while organic removal rates were nearly identical for all MFCs. The HF-MFC generated a power output to electrode cost (W $(-1)) 1.9 times greater than the GB-MFC, despite producing 14% less power and 15% less anodic current, while having 2.6 times less anodic surface area, 2.1 times larger charge transfer resistance and an electrical conductivity three orders of magnitude lower. The results demonstrate that inexpensive materials are capable of achieving more cost-effective treatment than high-performing materials despite generating lower power when treating real wastewater. Copyright © 2016 Elsevier Ltd. All rights reserved.

Quality challenges associated with microbial-based cleaning products from the Industry Perspective.

PubMed

Teasdale, Steve M; Kademi, Ali

2018-06-01

Microbial-based cleaning products (MBCPs) continue to gain popularity in the market as environmentally friendly cleaners. The majority of these products contain spores of various Bacillus species. Although the microorganisms used in MBCPs are subject to regulation in Canada under the Canadian Environmental Protection Act, the products themselves are not. Unlike other types of microbial products such as probiotics and biopesticides, the use, manufacture and quality parameters of MBCPs in Canada and other countries are poorly defined and not specifically subject to any required standards. Due to their complexity and nature, these products feature unique quality challenges. We noted the existing MBCPs we analyzed vary vastly in quality; external microbial contaminants, viability of the spores and the biocompatibility of the ingredients are issues that greatly affect product quality. A proper taxonomic identification of the bacterial species used also seems to be a major challenge for a number of manufacturers. A good understanding of the mechanisms governing these quality challenges and the adoption of good practices for the cultivation, harvesting, formulation, and manufacture of these types of products are essential for achieving high-quality performance standards. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

In situ relationships between microbiota and potential pathobiota in Arabidopsis thaliana.

PubMed

Bartoli, Claudia; Frachon, Léa; Barret, Matthieu; Rigal, Mylène; Huard-Chauveau, Carine; Mayjonade, Baptiste; Zanchetta, Catherine; Bouchez, Olivier; Roby, Dominique; Carrère, Sébastien; Roux, Fabrice

2018-05-30

A current challenge in microbial pathogenesis is to identify biological control agents that may prevent and/or limit host invasion by microbial pathogens. In natura, hosts are often infected by multiple pathogens. However, most of the current studies have been performed under laboratory controlled conditions and by taking into account the interaction between a single commensal species and a single pathogenic species. The next step is therefore to explore the relationships between host-microbial communities (microbiota) and microbial members with potential pathogenic behavior (pathobiota) in a realistic ecological context. In the present study, we investigated such relationships within root-associated and leaf-associated bacterial communities of 163 ecologically contrasted Arabidopsis thaliana populations sampled across two seasons in southwest of France. In agreement with the theory of the invasion paradox, we observed a significant humped-back relationship between microbiota and pathobiota α-diversity that was robust between both seasons and plant organs. In most populations, we also observed a strong dynamics of microbiota composition between seasons. Accordingly, the potential pathobiota composition was explained by combinations of season-specific microbiota operational taxonomic units. This result suggests that the potential biomarkers controlling pathogen's invasion are highly dynamic.

Analysis of the functional gene structure and metabolic potential of microbial community in high arsenic groundwater.

PubMed

Li, Ping; Jiang, Zhou; Wang, Yanhong; Deng, Ye; Van Nostrand, Joy D; Yuan, Tong; Liu, Han; Wei, Dazhun; Zhou, Jizhong

2017-10-15

Microbial functional potential in high arsenic (As) groundwater ecosystems remains largely unknown. In this study, the microbial community functional composition of nineteen groundwater samples was investigated using a functional gene array (GeoChip 5.0). Samples were divided into low and high As groups based on the clustering analysis of geochemical parameters and microbial functional structures. The results showed that As related genes (arsC, arrA), sulfate related genes (dsrA and dsrB), nitrogen cycling related genes (ureC, amoA, and hzo) and methanogen genes (mcrA, hdrB) in groundwater samples were correlated with As, SO 4 2- , NH 4 + or CH 4 concentrations, respectively. Canonical correspondence analysis (CCA) results indicated that some geochemical parameters including As, total organic content, SO 4 2- , NH 4 + , oxidation-reduction potential (ORP) and pH were important factors shaping the functional microbial community structures. Alkaline and reducing conditions with relatively low SO 4 2- , ORP, and high NH 4 + , as well as SO 4 2- and Fe reduction and ammonification involved in microbially-mediated geochemical processes could be associated with As enrichment in groundwater. This study provides an overall picture of functional microbial communities in high As groundwater aquifers, and also provides insights into the critical role of microorganisms in As biogeochemical cycling. Copyright © 2017 Elsevier Ltd. All rights reserved.

Strong linkage between active microbial communities and microbial carbon usage in a deglaciated terrain of the High Arctic

NASA Astrophysics Data System (ADS)

Kim, M.; Gyeong, H. R.; Lee, Y. K.

2017-12-01

Soil microorganisms play pivotal roles in ecosystem development and carbon cycling in newly exposed glacier forelands. However, little is known about carbon utilization pattern by metabolically active microbes over the course of ecosystem succession in these nutrient-poor environments. We investigated RNA-based microbial community dynamics and its relation to microbial carbon usage along the chronosequence of a High Arctic glacier foreland. Among microbial taxa surveyed (bacteria, archaea and fungi), bacteria are among the most metabolically active taxa with a dominance of Cyanobacteria and Actinobacteria. There was a strong association between microbial carbon usage and active Actinobacterial communities, suggesting that member of Actinobacteria are actively involved in organic carbon degradation in glacier forelands. Both bacterial community and microbial carbon usage are converged towards later stage of succession, indicating that the composition of soil organic carbon plays important roles in structuring bacterial decomposer communities during ecosystem development.

Effects of hydraulic pressure on the performance of single chamber air-cathode microbial fuel cells.

PubMed

Cheng, Shaoan; Liu, Weifeng; Guo, Jian; Sun, Dan; Pan, Bin; Ye, Yaoli; Ding, Weijun; Huang, Haobin; Li, Fujian

2014-06-15

Scaling up of microbial fuel cells (MFCs) without losing power density requires a thorough understanding of the effect of hydraulic pressure on MFC performance. In this work, the performance of an activated carbon air-cathode MFC was evaluated under different hydraulic pressures. The MFC under 100 mmH2O hydraulic pressure produced a maximum power density of 1260 ± 24 mW m(-2), while the power density decreased by 24.4% and 44.7% as the hydraulic pressure increased to 500 mmH2O and 2000 mmH2O, respectively. Notably, the performance of both the anode and the cathode had decreased under high hydraulic pressures. Electrochemical impedance spectroscopy tests of the cathode indicated that both charge transfer resistance and diffusion transfer resistance increased with the increase in hydraulic pressure. Denaturing gradient gel electrophoresis of PCR-amplified partial 16S rRNA genes demonstrated that the similarity among anodic biofilm communities under different hydraulic pressures was ≥ 90%, and the communities of all MFCs were dominated by Geobacter sp. These results suggested that the reduction in power output of the single chamber air-cathode MFC under high hydraulic pressures can be attributed to water flooding of the cathode and suppression the metabolism of anodic exoelectrogenic bacteria. Copyright © 2014 Elsevier B.V. All rights reserved.

Community Structure of Lithotrophically-Driven Hydrothermal Microbial Mats from the Mariana Arc and Back-Arc

PubMed Central

Hager, Kevin W.; Fullerton, Heather; Butterfield, David A.; Moyer, Craig L.

2017-01-01

The Mariana region exhibits a rich array of hydrothermal venting conditions in a complex geological setting, which provides a natural laboratory to study the influence of local environmental conditions on microbial community structure as well as large-scale patterns in microbial biogeography. We used high-throughput amplicon sequencing of the bacterial small subunit (SSU) rRNA gene from 22 microbial mats collected from four hydrothermally active locations along the Mariana Arc and back-arc to explore the structure of lithotrophically-based microbial mat communities. The vent effluent was classified as iron- or sulfur-rich corresponding with two distinct community types, dominated by either Zetaproteobacteria or Epsilonproteobacteria, respectively. The Zetaproteobacterial-based communities had the highest richness and diversity, which supports the hypothesis that Zetaproteobacteria function as ecosystem engineers creating a physical habitat within a chemical environment promoting enhanced microbial diversity. Gammaproteobacteria were also high in abundance within the iron-dominated mats and some likely contribute to primary production. In addition, we also compare sampling scale, showing that bulk sampling of microbial mats yields higher diversity than micro-scale sampling. We present a comprehensive analysis and offer new insights into the community structure and diversity of lithotrophically-driven microbial mats from a hydrothermal region associated with high microbial biodiversity. Our study indicates an important functional role of for the Zetaproteobacteria altering the mat habitat and enhancing community interactions and complexity. PMID:28970817

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass-Spectrometry (MALDI-TOF MS) Based Microbial Identifications: Challenges and Scopes for Microbial Ecologists

PubMed Central

Rahi, Praveen; Prakash, Om; Shouche, Yogesh S.

2016-01-01

Matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (MALDI-TOF MS) based biotyping is an emerging technique for high-throughput and rapid microbial identification. Due to its relatively higher accuracy, comprehensive database of clinically important microorganisms and low-cost compared to other microbial identification methods, MALDI-TOF MS has started replacing existing practices prevalent in clinical diagnosis. However, applicability of MALDI-TOF MS in the area of microbial ecology research is still limited mainly due to the lack of data on non-clinical microorganisms. Intense research activities on cultivation of microbial diversity by conventional as well as by innovative and high-throughput methods has substantially increased the number of microbial species known today. This important area of research is in urgent need of rapid and reliable method(s) for characterization and de-replication of microorganisms from various ecosystems. MALDI-TOF MS based characterization, in our opinion, appears to be the most suitable technique for such studies. Reliability of MALDI-TOF MS based identification method depends mainly on accuracy and width of reference databases, which need continuous expansion and improvement. In this review, we propose a common strategy to generate MALDI-TOF MS spectral database and advocated its sharing, and also discuss the role of MALDI-TOF MS based high-throughput microbial identification in microbial ecology studies. PMID:27625644

Scalable Biomarker Discovery for Diverse High-Dimensional Phenotypes

DTIC Science & Technology

2015-11-23

bytes: Computational analysis methods for microbial communities," University of Oregon BioBE center seminar. Eugene, OR, 2013 35- "From microbial...analysis methods for microbial communities," University of Oregon BioBE center seminar. Eugene, OR, 2013 • "From microbial surveys to mechanisms of

Design of Iron(II) Phthalocyanine-Derived Oxygen Reduction Electrocatalysts for High-Power-Density Microbial Fuel Cells.

PubMed

Santoro, Carlo; Gokhale, Rohan; Mecheri, Barbara; D'Epifanio, Alessandra; Licoccia, Silvia; Serov, Alexey; Artyushkova, Kateryna; Atanassov, Plamen

2017-08-24

Iron(II) phthalocyanine (FePc) deposited onto two different carbonaceous supports was synthesized through an unconventional pyrolysis-free method. The obtained materials were studied in the oxygen reduction reaction (ORR) in neutral media through incorporation in an air-breathing cathode structure and tested in an operating microbial fuel cell (MFC) configuration. Rotating ring disk electrode (RRDE) analysis revealed high performances of the Fe-based catalysts compared with that of activated carbon (AC). The FePc supported on Black-Pearl carbon black [Fe-BP(N)] exhibits the highest performance in terms of its more positive onset potential, positive shift of the half-wave potential, and higher limiting current as well as the highest power density in the operating MFC of (243±7) μW cm -2 , which was 33 % higher than that of FePc supported on nitrogen-doped carbon nanotubes (Fe-CNT(N); 182±5 μW cm -2 ). The power density generated by Fe-BP(N) was 92 % higher than that of the MFC utilizing AC; therefore, the utilization of platinum group metal-free catalysts can boost the performances of MFCs significantly. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nano-molybdenum carbide/carbon nanotubes composite as bifunctional anode catalyst for high-performance Escherichia coli-based microbial fuel cell.

PubMed

Wang, Yaqiong; Li, Bin; Cui, Dan; Xiang, Xingde; Li, Weishan

2014-01-15

A novel electrode, carbon felt-supported nano-molybdenum carbide (Mo2C)/carbon nanotubes (CNTs) composite, was developed as platinum-free anode of high performance microbial fuel cell (MFC). The Mo2C/CNTs composite was synthesized by using the microwave-assisted method with Mo(CO)6 as a single source precursor and characterized by using X-ray diffraction and transmission electron microscopy. The activity of the composite as anode electrocatalyst of MFC based on Escherichia coli (E. coli) was investigated with cyclic voltammetry, chronoamperometry, and cell discharge test. It is found that the carbon felt electrode with 16.7 wt% Mo Mo2C/CNTs composite exhibits a comparable electrocatalytic activity to that with 20 wt% platinum as anode electrocatalyst. The superior performance of the developed platinum-free electrode can be ascribed to the bifunctional electrocatalysis of Mo2C/CNTs for the conversion of organic substrates into electricity through bacteria. The composite facilitates the formation of biofilm, which is necessary for the electron transfer via c-type cytochrome and nanowires. On the other hand, the composite exhibits the electrocatalytic activity towards the oxidation of hydrogen, which is the common metabolite of E. coli. © 2013 Elsevier B.V. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

Influence of Bicarbonate, Sulfate, and Electron Donors on Biological reduction of Uranium and Microbial Community Composition

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

Luo, Wensui; Zhou, Jizhong; Wu, Weimin

2007-01-01

A microcosm study was performed to investigate the effect of ethanol and acetate on uranium(VI) biological reduction and microbial community changes under various geochemical conditions. Each microcosm contained an uranium-contaminated sediment (up to 2.8 g U/kg) suspended in buffer with bicarbonate at concentrations of either 1 mM or 40 mM and sulfate at either 1.1 or 3.2 mM. Ethanol or acetate was used as an electron donor. Results indicate that ethanol yielded in significantly higher U(VI) reduction rates than acetate. A low bicarbonate concentration (1 mM) was favored for U(VI) bioreduction to occur in sediments, but high concentrations of bicarbonatemore » (40 mM) and sulfate (3.2 mM) decreased the reduction rates of U(VI). Microbial communities were dominated by species from the Geothrix genus and Proteobacteria phylum in all microcosms. However, species in the Geobacteraceae family capable of reducing U(VI) were significantly enriched by ethanol and acetate in low bicarbonate buffer. Ethanol increased the population of unclassified Desulfuromonales, while acetate increased the population of Desulfovibrio. Additionally, species in the Geobacteraceae family were not enriched in high bicarbonate buffer, but the Geothrix and the unclassified Betaproteobacteria species were enriched. This study concludes that ethanol could be a better electron donor than acetate for reducing U(VI) under given experimental conditions, and electron donor and geoundwater geochemistry alter microbial communities responsible for U(VI) reduction.« less

Phylosymbiosis: Relationships and Functional Effects of Microbial Communities across Host Evolutionary History

PubMed Central

Brooks, Andrew W.; Kohl, Kevin D.; Brucker, Robert M.; van Opstal, Edward J.; Bordenstein, Seth R.

2016-01-01

Phylosymbiosis was recently proposed to describe the eco-evolutionary pattern, whereby the ecological relatedness of host-associated microbial communities parallels the phylogeny of related host species. Here, we test the prevalence of phylosymbiosis and its functional significance under highly controlled conditions by characterizing the microbiota of 24 animal species from four different groups (Peromyscus deer mice, Drosophila flies, mosquitoes, and Nasonia wasps), and we reevaluate the phylosymbiotic relationships of seven species of wild hominids. We demonstrate three key findings. First, intraspecific microbiota variation is consistently less than interspecific microbiota variation, and microbiota-based models predict host species origin with high accuracy across the dataset. Interestingly, the age of host clade divergence positively associates with the degree of microbial community distinguishability between species within the host clades, spanning recent host speciation events (~1 million y ago) to more distantly related host genera (~108 million y ago). Second, topological congruence analyses of each group's complete phylogeny and microbiota dendrogram reveal significant degrees of phylosymbiosis, irrespective of host clade age or taxonomy. Third, consistent with selection on host–microbiota interactions driving phylosymbiosis, there are survival and performance reductions when interspecific microbiota transplants are conducted between closely related and divergent host species pairs. Overall, these findings indicate that the composition and functional effects of an animal's microbial community can be closely allied with host evolution, even across wide-ranging timescales and diverse animal systems reared under controlled conditions. PMID:27861590

Enteral High Fat-Polyunsaturated Fatty Acid Blend Alters the Pathogen Composition of the Intestinal Microbiome in Premature Infants with an Enterostomy

PubMed Central

Younge, Noelle; Yang, Qing; Seed, Patrick C.

2016-01-01

Objective To determine the effect of enteral fish oil and safflower oil supplementation on the intestinal microbiome in premature infants with an enterostomy. Study design Premature infants with an enterostomy were randomized to receive early enteral supplementation with a high fat-polyunsaturated fatty acid (HF-PUFA) blend of fish oil and safflower oil versus standard nutritional therapy. We used 16S rRNA gene sequencing for longitudinal profiling of the microbiome from the time of study entry until bowel reanastomosis. We used weighted gene co-expression network analysis to identify microbial community modules that differed between study groups over time. We performed imputed metagenomic analysis to determine metabolic pathways associated with the microbial genes. Results Sixteen infants were randomized to receive enteral HF-PUFA supplementation and 16 infants received standard care. The intestinal microbiota of infants in the treatment group differed from those in the control group, with greater bacterial diversity and lower abundance of Streptococcus, Clostridium, and many pathogenic genera within the Enterobacteriaceae family. We identified four microbial community modules with significant differences between groups over time. Imputed metagenomic analysis of the microbial genes revealed metabolic pathways that differed between groups, including metabolism of amino acids, carbohydrates, fatty acids, and secondary bile acid synthesis. Conclusion Enteral HF-PUFA supplementation was associated with decreased abundance of pathogenic bacteria, greater bacterial diversity, and shifts in the potential metabolic functions of intestinal microbiota. Trial registration ClinicalTrials.gov: NCT01306838 PMID:27856001

Enteral High Fat-Polyunsaturated Fatty Acid Blend Alters the Pathogen Composition of the Intestinal Microbiome in Premature Infants with an Enterostomy.

PubMed

Younge, Noelle; Yang, Qing; Seed, Patrick C

2017-02-01

To determine the effect of enteral fish oil and safflower oil supplementation on the intestinal microbiome in infants with an enterostomy born premature. Infants with an enterostomy born premature were randomized to receive early enteral supplementation with a high-fat polyunsaturated fatty acid (HF-PUFA) blend of fish oil and safflower oil vs standard nutritional therapy. We used 16S rRNA gene sequencing for longitudinal profiling of the microbiome from the time of study entry until bowel reanastomosis. We used weighted gene coexpression network analysis to identify microbial community modules that differed between study groups over time. We performed imputed metagenomic analysis to determine metabolic pathways associated with the microbial genes. Sixteen infants were randomized to receive enteral HF-PUFA supplementation, and 16 infants received standard care. The intestinal microbiota of infants in the treatment group differed from those in the control group, with greater bacterial diversity and lower abundance of Streptococcus, Clostridium, and many pathogenic genera within the Enterobacteriaceae family. We identified 4 microbial community modules with significant differences between groups over time. Imputed metagenomic analysis of the microbial genes revealed metabolic pathways that differed between groups, including metabolism of amino acids, carbohydrates, fatty acids, and secondary bile acid synthesis. Enteral HF-PUFA supplementation was associated with decreased abundance of pathogenic bacteria, greater bacterial diversity, and shifts in the potential metabolic functions of intestinal microbiota. ClinicalTrials.gov:NCT01306838. Copyright © 2016 Elsevier Inc. All rights reserved.

Optimizing the performance of microbial fuel cells fed a combination of different synthetic organic fractions in municipal solid waste.

PubMed

Pendyala, Brahmaiah; Chaganti, Subba Rao; Lalman, Jerald A; Heath, Daniel D

2016-03-01

The objective of this study was to establish the impact of different steam exploded organic fractions in municipal solid waste (MSW) on electricity production using microbial fuel cells (MFCs). In particular, the influence of individual steam exploded liquefied waste components (food waste (FW), paper-cardboard waste (PCW) and garden waste (GW)) and their blends on chemical oxygen demand (COD) removal, columbic efficiency (CE) and microbial diversity was examined using a mixture design. Maximum power densities from 0.56 to 0.83 W m(-2) were observed for MFCs fed with different feedstocks. The maximum COD removed and minimum CE were observed for a GW feed. However, a reverse trend (minimum COD removed and maximum CE) was observed for the FW feed. A maximum COD removal (78%) accompanied with a maximum CE (24%) was observed for a combined feed of FW, PCW plus GW in a 1:1:1 ratio. Lactate, the major byproduct detected, was unutilized by the anodic biofilm community. The organic fraction of municipal solid waste (OFMSW) could serve as a potential feedstock for electricity generation in MFCs; however, elevated protein levels will lead to reduced COD removal. The microbial communities in cultures fed FW and PCW was highly diversified; however, the communities in cultures fed FW or a feed mixture containing high FW levels were similar and dominated by Bacteroidetes and β-proteobacteria. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Validation of Vapor Phase Hydrogen Peroxide Microbial Reduction for Planetary Protection and a Proposed Vacuum Process Specification

NASA Technical Reports Server (NTRS)

Chung, Shirley; Barengoltz, Jack; Kern, Roger; Koukol, Robert; Cash, Howard

2006-01-01

The Jet Propulsion Laboratory, in conjunction with the NASA Planetary Protection Officer, has selected the vapor phase hydrogen peroxide sterilization process for continued development as a NASA approved sterilization technique for spacecraft subsystems and systems. The goal is to include this technique, with an appropriate specification, in NPR 8020.12C as a low temperature complementary technique to the dry heat sterilization process.To meet microbial reduction requirements for all Mars in-situ life detection and sample return missions, various planetary spacecraft subsystems will have to be exposed to a qualified sterilization process. This process could be the elevated temperature dry heat sterilization process (115 C for 40 hours) which was used to sterilize the Viking lander spacecraft. However, with utilization of such elements as highly sophisticated electronics and sensors in modern spacecraft, this process presents significant materials challenges and is thus an undesirable bioburden reduction method to design engineers. The objective of this work is to introduce vapor hydrogen peroxide (VHP) as an alternative to dry heat microbial reduction to meet planetary protection requirements.The VHP process is widely used by the medical industry to sterilize surgical instruments and biomedical devices, but high doses of VHP may degrade the performance of flight hardware, or compromise material properties. Our goal for this study was to determine the minimum VHP process conditions to achieve microbial reduction levels acceptable for planetary protection.

SOLID PHASE EXTRACTION AND HIGH PERFORMANCE LIQUID CHROMATOGRAPHY WITH PHOTODIODE ARRAY DETECTION OF CHEMICAL INDICATORS OF HUMAN FECAL CONTAMINATION IN WATER

EPA Science Inventory

Faster and more sensitive analysis of water that is contaminated by human fecal matter is very important for health. The current microbiological methods to assess water quality do not meet this need. Alternate non-microbial human fecal indicators have been proposed by various r...

Effects of dietary tannin source on performance, feed efficiency, ruminal fermentation, and carcass and non-carcass traits in steers fed a high-grain diet

USDA-ARS?s Scientific Manuscript database

Tannins are polyphenolic secondary plant compounds that have been shown to affect microbial activity to impact fermentation, protein degradation, methane production, and potential to mitigate foodborne pathogens. This study was conducted to examine the effects of source of tannin (condensed, CT, vs....

An open source platform for multi-scale spatially distributed simulations of microbial ecosystems

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

Segre, Daniel

2014-08-14

The goal of this project was to develop a tool for facilitating simulation, validation and discovery of multiscale dynamical processes in microbial ecosystems. This led to the development of an open-source software platform for Computation Of Microbial Ecosystems in Time and Space (COMETS). COMETS performs spatially distributed time-dependent flux balance based simulations of microbial metabolism. Our plan involved building the software platform itself, calibrating and testing it through comparison with experimental data, and integrating simulations and experiments to address important open questions on the evolution and dynamics of cross-feeding interactions between microbial species.

Multitrophic microbial interactions for eco- and agro-biotechnological processes: theory and practice.

PubMed

Saleem, Muhammad; Moe, Luke A

2014-10-01

Multitrophic level microbial loop interactions mediated by protist predators, bacteria, and viruses drive eco- and agro-biotechnological processes such as bioremediation, wastewater treatment, plant growth promotion, and ecosystem functioning. To what extent these microbial interactions are context-dependent in performing biotechnological and ecosystem processes remains largely unstudied. Theory-driven research may advance the understanding of eco-evolutionary processes underlying the patterns and functioning of microbial interactions for successful development of microbe-based biotechnologies for real world applications. This could also be a great avenue to test the validity or limitations of ecology theory for managing diverse microbial resources in an era of altering microbial niches, multitrophic interactions, and microbial diversity loss caused by climate and land use changes. Copyright © 2014 Elsevier Ltd. All rights reserved.

Comparison of electrochemical performances and microbial community structures of two photosynthetic microbial fuel cells.

PubMed

Zheng, Wei; Cai, Teng; Huang, Manhong; Chen, Donghui

2017-11-01

Microbial fuel cells (MFCs) have attracted intensive interest for their power generation and pollutants removal characteristics. Electrochemical performances and community structures of two algae cathode photosynthetic MFCs were investigated and compared. Microbial consortia of these two MFCs were taken from wetland sediment (named SMFC) and an up-flow anaerobic wastewater treatment reactor (named UMFC). Maximum power density of the SMFC and UMFC achieved 202.9 ± 18.1 mW/m 2 and 158.2±15.1 mW/m 2 , respectively. The SMFC displayed higher columbic efficiency but lower chemical oxygen demand (COD) removal efficiency than that of UMFC. The results also revealed the addition of riboflavin (RF) and neutral red (NR) decreased the redox current of the SMFC but promoted that of UMFC. Community structure analysis showed the SMFC was dominated by photosynthetic genus Rhodopseudomonas (61.25%), while bacterial genera in the UMFC were more evenly distributed. The difference of electrochemical activities of the two MFCs was caused by the different roles of exoelectrogens such as Rhodopseudomonas spp. and Citrobacter spp. in the electron transfer process. Newly developed photosynthetic microbial fuel cells (PMFCs) provide a suitable process to generate power and remove pollutants. The consortia have a significant role in the performance and microbial community of the system. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

High performance spiral wound microbial fuel cell with hydraulic characterization.

PubMed

Haeger, Alexander; Forrestal, Casey; Xu, Pei; Ren, Zhiyong Jason

2014-12-01

The understanding and development of functioning systems are crucial steps for microbial fuel cell (MFC) technology advancement. In this study, a compact spiral wound MFC (swMFC) was developed and hydraulic residence time distribution (RTD) tests were conducted to investigate the flow characteristics in the systems. Results show that two-chamber swMFCs have high surface area to volume ratios of 350-700m(2)/m(3), and by using oxygen cathode without metal-catalysts, the maximum power densities were 42W/m(3) based on total volume and 170W/m(3) based on effective volume. The hydraulic step-input tracer study identified 20-67% of anodic flow dead space, which presents new opportunities for system improvement. Electrochemical tools revealed very low ohmic resistance but high charge transfer and diffusion resistance due to catalyst-free oxygen reduction. The spiral wound configuration combined with RTD tool offers a holistic approach for MFC development and optimization. Copyright © 2014 Elsevier Ltd. All rights reserved.

Archaea-based microbial fuel cell operating at high ionic strength conditions.

PubMed

Abrevaya, Ximena C; Sacco, Natalia; Mauas, Pablo J D; Cortón, Eduardo

2011-11-01

In this work, two archaea microorganisms (Haloferax volcanii and Natrialba magadii) used as biocatalyst at a microbial fuel cell (MFC) anode were evaluated. Both archaea are able to grow at high salt concentrations. By increasing the media conductivity, the internal resistance was diminished, improving the MFC's performance. Without any added redox mediator, maximum power (P (max)) and current at P (max) were 11.87/4.57/0.12 μW cm(-2) and 49.67/22.03/0.59 μA cm(-2) for H. volcanii, N. magadii and E. coli, respectively. When neutral red was used as the redox mediator, P (max) was 50.98 and 5.39 μW cm(-2) for H. volcanii and N. magadii, respectively. In this paper, an archaea MFC is described and compared with other MFC systems; the high salt concentration assayed here, comparable with that used in Pt-catalyzed alkaline hydrogen fuel cells, will open new options when MFC scaling up is the objective necessary for practical applications.

Biofiltration of xylene using wood charcoal as the biofilter media under transient and high loading conditions.

PubMed

Singh, Kiran; Giri, B S; Sahi, Amrita; Geed, S R; Kureel, M K; Singh, Sanjay; Dubey, S K; Rai, B N; Kumar, Surendra; Upadhyay, S N; Singh, R S

2017-10-01

The main objective of this study was to evaluate the performance of wood charcoal as biofilter media under transient and high loading condition. Biofiltration of xylene was investigated for 150days in a laboratory scale unit packed with wood charcoal and inoculated with mixed microbial culture at the xylene loading rates ranged from 12 to 553gm -3 h -1 . The kinetic analysis of the xylene revealed absence of substrate inhibition and possibility of achieving higher elimination under optimum condition. The pH, temperature, pressure drop and CO 2 production rate were regularly monitored during the experiments. Throughout experimental period, the removal efficiency (RE) was found to be in the range of 65-98.7% and the maximum elimination capacity (EC) was 405.7gm -3 h -1 . Molecular characterization results show Bacillus sp. as dominating microbial group in the biofilm. Copyright © 2017 Elsevier Ltd. All rights reserved.

Compositional Changes and Baking Performance of Rye Dough As Affected by Microbial Transglutaminase and Xylanase.

PubMed

Grossmann, Isabel; Döring, Clemens; Jekle, Mario; Becker, Thomas; Koehler, Peter

2016-07-20

Doughs supplemented with endoxylanase (XYL) and varying amounts of microbial transglutaminase (TG) were analyzed by sequential protein extraction, quantitation of protein fractions and protein types, and determination of water-extractable arabinoxylans. With increasing TG activity, the concentration of prolamins and glutelins decreased and increased, respectively, and the prolamin-to-glutelin ratio strongly declined. The overall amount of extractable protein decreased with increasing TG level showing that cross-linking by TG provided high-molecular-weight protein aggregates. The decrease of the high-molecular-weight arabinoxylan fraction and the concurrent increase of the medium-molecular-weight fraction confirmed the degradation of arabinoxylans by XYL. However, XYL addition did not lead to significant improved cross-linking of rye proteins by TG. Volume and crumb hardness measurements of bread showed increased protein connectivity induced by XYL and TG. Significant positive effects on the final bread quality were especially obtained by XYL addition.

Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries

PubMed Central

Xie, Wei; Wang, Fengping; Guo, Lei; Chen, Zeling; Sievert, Stefan M; Meng, Jun; Huang, Guangrui; Li, Yuxin; Yan, Qingyu; Wu, Shan; Wang, Xin; Chen, Shangwu; He, Guangyuan; Xiao, Xiang; Xu, Anlong

2011-01-01

Deep-sea hydrothermal vent chimneys harbor a high diversity of largely unknown microorganisms. Although the phylogenetic diversity of these microorganisms has been described previously, the adaptation and metabolic potential of the microbial communities is only beginning to be revealed. A pyrosequencing approach was used to directly obtain sequences from a fosmid library constructed from a black smoker chimney 4143-1 in the Mothra hydrothermal vent field at the Juan de Fuca Ridge. A total of 308 034 reads with an average sequence length of 227 bp were generated. Comparative genomic analyses of metagenomes from a variety of environments by two-way clustering of samples and functional gene categories demonstrated that the 4143-1 metagenome clustered most closely with that from a carbonate chimney from Lost City. Both are highly enriched in genes for mismatch repair and homologous recombination, suggesting that the microbial communities have evolved extensive DNA repair systems to cope with the extreme conditions that have potential deleterious effects on the genomes. As previously reported for the Lost City microbiome, the metagenome of chimney 4143-1 exhibited a high proportion of transposases, implying that horizontal gene transfer may be a common occurrence in the deep-sea vent chimney biosphere. In addition, genes for chemotaxis and flagellar assembly were highly enriched in the chimney metagenomes, reflecting the adaptation of the organisms to the highly dynamic conditions present within the chimney walls. Reconstruction of the metabolic pathways revealed that the microbial community in the wall of chimney 4143-1 was mainly fueled by sulfur oxidation, putatively coupled to nitrate reduction to perform inorganic carbon fixation through the Calvin–Benson–Bassham cycle. On the basis of the genomic organization of the key genes of the carbon fixation and sulfur oxidation pathways contained in the large genomic fragments, both obligate and facultative autotrophs appear to be present and contribute to biomass production. PMID:20927138

Sustainable Hypersaline Microbial Fuel Cells: Inexpensive Recyclable Polymer Supports for Carbon Nanotube Conductive Paint Anodes.

PubMed

Grattieri, Matteo; Shivel, Nelson D; Sifat, Iram; Bestetti, Massimiliano; Minteer, Shelley D

2017-05-09

Microbial fuel cells are an emerging technology for wastewater treatment, but to be commercially viable and sustainable, the electrode materials must be inexpensive, recyclable, and reliable. In this study, recyclable polymeric supports were explored for the development of anode electrodes to be applied in single-chamber microbial fuel cells operated in field under hypersaline conditions. The support was covered with a carbon nanotube (CNT) based conductive paint, and biofilms were able to colonize the electrodes. The single-chamber microbial fuel cells with Pt-free cathodes delivered a reproducible power output after 15 days of operation to achieve 12±1 mW m -2 at a current density of 69±7 mA m -2 . The decrease of the performance in long-term experiments was mostly related to inorganic precipitates on the cathode electrode and did not affect the performance of the anode, as shown by experiments in which the cathode was replaced and the fuel cell performance was regenerated. The results of these studies show the feasibility of polymeric supports coated with CNT-based paint for microbial fuel cell applications. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Pilot scale biodiesel production from microbial oil of Rhodosporidium toruloides DEBB 5533 using sugarcane juice: Performance in diesel engine and preliminary economic study.

PubMed

Soccol, Carlos Ricardo; Dalmas Neto, Carlos José; Soccol, Vanete Thomaz; Sydney, Eduardo Bittencourt; da Costa, Eduardo Scopel Ferreira; Medeiros, Adriane Bianchi Pedroni; Vandenberghe, Luciana Porto de Souza

2017-01-01

A successful pilot-scale process for biodiesel production from microbial oil (Biooil) produced by Rhodosporidium toruloides DEBB 5533 is presented. Using fed-batch strategy (1000L working volume), a lipid productivity of 0.44g/L.h was obtained using a low-cost medium composed by sugarcane juice and urea. The microbial oil was used for biodiesel production and its performance was evaluated in diesel engine tests, showing very good performance, especially for the blend B20 SCO, when operating at 2500rpm with lower pollutant emissions (CO 2 - 220% less; CO - 7-fold less; NO X 50% less and no detectable HC emissions (<0.11ppm)) when compared with the blends of standard biofuel from soybean oil. A preliminary analysis showed that microbial biodiesel is economically competitive (US$ 0.76/L) when compared to the vegetable biodiesel (US$ 0.81/L). Besides, the yield of biodiesel from microbial oil is higher (4172L/ha of cultivated sugarcane) that represents 6.3-fold the yield of standard biodiesel (661L/ha of cultivated soybean). Copyright © 2016 Elsevier Ltd. All rights reserved.

Phytoremediation using microbially mediated metal accumulation in Sorghum bicolor.

PubMed

Phieler, René; Merten, Dirk; Roth, Martin; Büchel, Georg; Kothe, Erika

2015-12-01

Reclaiming land that has been anthropogenically contaminated with multiple heavy metal elements, e.g., during mining operations, is a growing challenge worldwide. The use of phytoremediation has been discussed with varying success. Here, we show that a careful examination of options of microbial determination of plant performance is a key element in providing a multielement remediation option for such landscapes. We used both (a) mycorrhiza with Rhizophagus irregularis and (b) bacterial amendments with Streptomyces acidiscabies E13 and Streptomyces tendae F4 to mediate plant-promoting and metal-accumulating properties to Sorghum bicolor. In pot experiments, the effects on plant growth and metal uptake were scored, and in a field trial at a former uranium leaching heap site near Ronneburg, Germany, we could show the efficacy under field conditions. Different metals could be extracted at the same time, with varying microbial inoculation and soil amendment scenarios possible when a certain metal is the focus of interest. Especially, manganese was extracted at very high levels which might be useful even for phytomining approaches.

[Development of a low-cost single chamber microbial fuel cell type BOD sensor].

PubMed

Wu, Feng; Liu, Zhi; Zhou, Ben; Zhou, Shun-gui; Rao, Li-qun; Wang, Yue-qiang

2010-07-01

The principle of the detector is based on the effect of microbial toxicity of water sample on the electricity generation in microbial fuel cell (MFC). The performance of the MFC-type biotoxicity detector was evaluated with the synthetic water containing heavy metals of Cd2+ and Cu2+. The experimental results demonstrated that: (1) relative to the conventional methods, the MFC-type detector is easy to operate, and suitable for on-line measurements with high sensitivity; (2) it only requires 4 h to complete measurements, and can get ready for next measurement within 4 h; (3) there is a significant linear correlation between the concentration of toxic metal(s) and inhibition ratios in Coulombic yields of MFC. As the IC20 (concentration causing 20% inhibition) of Cd2+, Cu2+ and mixed metals (Cd2+ and Cu2+) were 0.6, 0.8 and 0.25 mg/L, the regression coefficients were shown to be 0.9960, 0.9744 and 0.9907.

Microbial aetiology and sensitivity of asymptomatic bacteriuria among ante-natal mothers in Mulago hospital, Uganda.

PubMed

Andabati, G; Byamugisha, J

2010-12-01

Asymptomatic bacteriuria in pregnancy is associated with potential urinary and obstetric complications. However the prevalence aetiology and antimicrobial sensitivity patterns of asymptomatic bacteriurea among women attending ante-natal care in our Hospital is not known. To determine the prevalence and identify the aetiological agents associated with asymptomatic bacteriurea in antenatal mothers in Mulago Hospital. We also intended to determine the anti-microbial sensitivity patterns of the common uropathogen in this population We performed culture and anti-microbial sensitivity tests on urine samples from 218 consecutive ante-natal mothers in Mulago Hospital. All participants did not have any clinical symptoms attributable to urinary tract infection. Twenty nine (13.3%) of the samples had significant bacterial growth and E.coli was the commonest isolate (51.2%). There was a high level (20-62%) of anti-bacterial resistance to the commonly used antibiotics. Asymptomatic bacteriuria is common among ante-natal mothers in Mulago. E. Coli that is resistant to the most commonly used antibiotics is the commonest isolate."

Challenges in microbial ecology: building predictive understanding of community function and dynamics

PubMed Central

Widder, Stefanie; Allen, Rosalind J; Pfeiffer, Thomas; Curtis, Thomas P; Wiuf, Carsten; Sloan, William T; Cordero, Otto X; Brown, Sam P; Momeni, Babak; Shou, Wenying; Kettle, Helen; Flint, Harry J; Haas, Andreas F; Laroche, Béatrice; Kreft, Jan-Ulrich; Rainey, Paul B; Freilich, Shiri; Schuster, Stefan; Milferstedt, Kim; van der Meer, Jan R; Groβkopf, Tobias; Huisman, Jef; Free, Andrew; Picioreanu, Cristian; Quince, Christopher; Klapper, Isaac; Labarthe, Simon; Smets, Barth F; Wang, Harris; Soyer, Orkun S

2016-01-01

The importance of microbial communities (MCs) cannot be overstated. MCs underpin the biogeochemical cycles of the earth's soil, oceans and the atmosphere, and perform ecosystem functions that impact plants, animals and humans. Yet our ability to predict and manage the function of these highly complex, dynamically changing communities is limited. Building predictive models that link MC composition to function is a key emerging challenge in microbial ecology. Here, we argue that addressing this challenge requires close coordination of experimental data collection and method development with mathematical model building. We discuss specific examples where model–experiment integration has already resulted in important insights into MC function and structure. We also highlight key research questions that still demand better integration of experiments and models. We argue that such integration is needed to achieve significant progress in our understanding of MC dynamics and function, and we make specific practical suggestions as to how this could be achieved. PMID:27022995

Indigenous Bacteria and Fungi Drive Traditional Kimoto Sake Fermentations

PubMed Central

Bokulich, Nicholas A.; Ohta, Moe; Lee, Morgan

2014-01-01

Sake (Japanese rice wine) production is a complex, multistage process in which fermentation is performed by a succession of mixed fungi and bacteria. This study employed high-throughput rRNA marker gene sequencing, quantitative PCR, and terminal restriction fragment length polymorphism to characterize the bacterial and fungal communities of spontaneous sake production from koji to product as well as brewery equipment surfaces. Results demonstrate a dynamic microbial succession, with koji and early moto fermentations dominated by Bacillus, Staphylococcus, and Aspergillus flavus var. oryzae, succeeded by Lactobacillus spp. and Saccharomyces cerevisiae later in the fermentations. The microbiota driving these fermentations were also prevalent in the production environment, illustrating the reservoirs and routes for microbial contact in this traditional food fermentation. Interrogating the microbial consortia of production environments in parallel with food products is a valuable approach for understanding the complete ecology of food production systems and can be applied to any food system, leading to enlightened perspectives for process control and food safety. PMID:24973064

Gut microbiota dictates the metabolic response of Drosophila to diet

PubMed Central

Wong, Adam C.-N.; Dobson, Adam J.; Douglas, Angela E.

2014-01-01

Animal nutrition is profoundly influenced by the gut microbiota, but knowledge of the scope and core mechanisms of the underlying animal–microbiota interactions is fragmentary. To investigate the nutritional traits shaped by the gut microbiota of Drosophila, we determined the microbiota-dependent response of multiple metabolic and performance indices to systematically varied diet composition. Diet-dependent differences between Drosophila bearing its unmanipulated microbiota (conventional flies) and experimentally deprived of its microbiota (axenic flies) revealed evidence for: microbial sparing of dietary B vitamins, especially riboflavin, on low-yeast diets; microbial promotion of protein nutrition, particularly in females; and microbiota-mediated suppression of lipid/carbohydrate storage, especially on high sugar diets. The microbiota also sets the relationship between energy storage and body mass, indicative of microbial modulation of the host signaling networks that coordinate metabolism with body size. This analysis identifies the multiple impacts of the microbiota on the metabolism of Drosophila, and demonstrates that the significance of these different interactions varies with diet composition and host sex. PMID:24577449

Indigenous bacteria and fungi drive traditional kimoto sake fermentations.

PubMed

Bokulich, Nicholas A; Ohta, Moe; Lee, Morgan; Mills, David A

2014-09-01

Sake (Japanese rice wine) production is a complex, multistage process in which fermentation is performed by a succession of mixed fungi and bacteria. This study employed high-throughput rRNA marker gene sequencing, quantitative PCR, and terminal restriction fragment length polymorphism to characterize the bacterial and fungal communities of spontaneous sake production from koji to product as well as brewery equipment surfaces. Results demonstrate a dynamic microbial succession, with koji and early moto fermentations dominated by Bacillus, Staphylococcus, and Aspergillus flavus var. oryzae, succeeded by Lactobacillus spp. and Saccharomyces cerevisiae later in the fermentations. The microbiota driving these fermentations were also prevalent in the production environment, illustrating the reservoirs and routes for microbial contact in this traditional food fermentation. Interrogating the microbial consortia of production environments in parallel with food products is a valuable approach for understanding the complete ecology of food production systems and can be applied to any food system, leading to enlightened perspectives for process control and food safety. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Analysis of Nitrification Efficiency and Microbial Community in a Membrane Bioreactor Fed with Low COD/N-Ratio Wastewater

PubMed Central

Ma, Jinxing; Wang, Zhiwei; Zhu, Chaowei; Liu, Shumeng; Wang, Qiaoying; Wu, Zhichao

2013-01-01

In this study, an approach using influent COD/N ratio reduction was employed to improve process performance and nitrification efficiency in a membrane bioreactor (MBR). Besides sludge reduction, membrane fouling alleviation was observed during 330 d operation, which was attributed to the decreased production of soluble microbial products (SMP) and efficient carbon metabolism in the autotrophic nitrifying community. 454 high-throughput 16S rRNA gene pyrosequencing revealed that the diversity of microbial sequences was mainly determined by the feed characteristics, and that microbes could derive energy by switching to a more autotrophic metabolism to resist the environmental stress. The enrichment of nitrifiers in an MBR with a low COD/N-ratio demonstrated that this condition stimulated nitrification, and that the community distribution of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) resulted in faster nitrite uptake rates. Further, ammonia oxidation was the rate-limiting step during the full nitrification. PMID:23667573

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

PubMed

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

2017-04-01

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

Distinct signatures of host–microbial meta-metabolome and gut microbiome in two C57BL/6 strains under high-fat diet

PubMed Central

Walker, Alesia; Pfitzner, Barbara; Neschen, Susanne; Kahle, Melanie; Harir, Mourad; Lucio, Marianna; Moritz, Franco; Tziotis, Dimitrios; Witting, Michael; Rothballer, Michael; Engel, Marion; Schmid, Michael; Endesfelder, David; Klingenspor, Martin; Rattei, Thomas; Castell, Wolfgang zu; de Angelis, Martin Hrabé; Hartmann, Anton; Schmitt-Kopplin, Philippe

2014-01-01

A combinatory approach using metabolomics and gut microbiome analysis techniques was performed to unravel the nature and specificity of metabolic profiles related to gut ecology in obesity. This study focused on gut and liver metabolomics of two different mouse strains, the C57BL/6J (C57J) and the C57BL/6N (C57N) fed with high-fat diet (HFD) for 3 weeks, causing diet-induced obesity in C57N, but not in C57J mice. Furthermore, a 16S-ribosomal RNA comparative sequence analysis using 454 pyrosequencing detected significant differences between the microbiome of the two strains on phylum level for Firmicutes, Deferribacteres and Proteobacteria that propose an essential role of the microbiome in obesity susceptibility. Gut microbial and liver metabolomics were followed by a combinatory approach using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and ultra performance liquid chromatography time of tlight MS/MS with subsequent multivariate statistical analysis, revealing distinctive host and microbial metabolome patterns between the C57J and the C57N strain. Many taurine-conjugated bile acids (TBAs) were significantly elevated in the cecum and decreased in liver samples from the C57J phenotype likely displaying different energy utilization behavior by the bacterial community and the host. Furthermore, several metabolite groups could specifically be associated with the C57N phenotype involving fatty acids, eicosanoids and urobilinoids. The mass differences based metabolite network approach enabled to extend the range of known metabolites to important bile acids (BAs) and novel taurine conjugates specific for both strains. In summary, our study showed clear alterations of the metabolome in the gastrointestinal tract and liver within a HFD-induced obesity mouse model in relation to the host–microbial nutritional adaptation. PMID:24906017

Bioaugmentation of anaerobic sludge digestion with iron-reducing bacteria: process and microbial responses to variations in hydraulic retention time.

PubMed

Baek, Gahyun; Kim, Jaai; Shin, Seung Gu; Lee, Changsoo

2016-01-01

Although anaerobic digestion (AD) is a widely used option to manage waste activated sludge (WAS), there are some drawbacks related to its slow reaction rate and low energy productivity. This study examined an anaerobic WAS digester, augmented with an iron-reducing microbial consortium, relative to changes in microbial community structure and process performance at decreasing hydraulic retention times (HRTs) of 20 to 10 days. The enhanced methanation performance (approximately 40 % increase in methane yield) by the bioaugmentation was sustained until the HRT was decreased to 12.5 days, under Fe(3+)-rich conditions (ferric oxyhydroxide, 20 mM Fe). Enhanced iron-reducing activity was evidenced by the increased Fe(2+) to total Fe ratio maintained above 50 % during the stable operational phases. A further decrease in HRT to 10 days resulted in a significant performance deterioration, along with a drop in the Fe(2+) to total Fe ratio to <35 %, after four turnovers of operation. Prevailing existence of putative iron-reducing bacteria (IRBs) was identified by denaturing gradient gel electrophoresis (DGGE), with Spirochaetaceae- and Thauera-related organisms being dominant members, and clear dominance shifts among them with respect to decrease in HRT were observed. Lowering HRT led to evident shifts in bacterial community structure likely associated with washout of IRBs, leading to decreases in iron respiration activity and AD performance at a lower HRT. The bacterial community structure shifted dynamically over phases, and the community transitions correlated well with the changes in process performance. Overall, the combined biostimulation and bioaugmentation investigated in this study proved effective for enhanced methane recovery from anaerobic WAS digestion, which suggests an interesting potential for high-rate AD.

Response of furniture factory workers to work-related airborne allergens.

PubMed

Skórska, Czesława; Krysińska-Traczyk, Ewa; Milanowski, Janusz; Cholewa, Grazyna; Sitkowska, Jolanta; Góra, Anna; Dutkiewicz, Jacek

2002-01-01

The aim of this work was to determine the reactivity of furniture factory workers to microbial allergens associated with wood dust. Allergological examinations by skin and precipitin tests were performed in 48 workers employed in a factory producing furniture from fibreboards and chipboards, and in 32 healthy urban dwellers not exposed to organic dusts (referents). The skin test was performed by the intradermal method with the saline extracts of the cultures of 3 microbial species (Rahnella sp., Arthrobacter globiformis, Aspergillus fumigatus) associated with wood dust. Skin reactions were recorded after 20 minutes, 8 hours and 24 hours and graded 1-4, depending on the diameter of the reaction. The agar-gel test for the presence of precipitins in serum was performed with the extracts of 15 microbial isolates. The furniture factory workers showed a high skin response to the extracts of environmental microbes. The frequency of early grade 2 reactions (diameter 10 mm) to the extract of Rahnella sp. was 64.6% among furniture workers, being significantly higher (p < 0.001) compared to reference group (18.7%). High frequencies of grade 2 reactions in furniture workers were also found with the extracts of A. globiformis and A. fumigatus (52.1% and 62.5%, respectively). The frequencies of grade 2 delayed (after 8 h) and late (after 24 h) reactions to Rahnella sp. in furniture workers were non-specifically high (97.9%/93.7%) while the response rates to A. globiformis and A. fumigatus were much lower (10.4%/25.0%, and 4.2%/37.5%, respectively). In agar-gel test for detection of precipitins, in most cases very low percentages of positive reactions (0-2.1%) were noted in furniture factory workers. The only exception was a high percentage of positive reactions (27.1%) to the antigen of Pseudomonas maltophilia, which was significantly greater in furniture workers compared to the reference group (p < 0.01). The obtained results suggest that early allergic reactions to microorganisms associated with wood dust are common among workers of furniture industry, which may increase a potential risk of work-related disease in this occupational group.

Predicting Microbial Fuel Cell Biofilm Communities and Bioreactor Performance using Artificial Neural Networks.

PubMed

Lesnik, Keaton Larson; Liu, Hong

2017-09-19

The complex interactions that occur in mixed-species bioelectrochemical reactors, like microbial fuel cells (MFCs), make accurate predictions of performance outcomes under untested conditions difficult. While direct correlations between any individual waste stream characteristic or microbial community structure and reactor performance have not been able to be directly established, the increase in sequencing data and readily available computational power enables the development of alternate approaches. In the current study, 33 MFCs were evaluated under a range of conditions including eight separate substrates and three different wastewaters. Artificial Neural Networks (ANNs) were used to establish mathematical relationships between wastewater/solution characteristics, biofilm communities, and reactor performance. ANN models that incorporated biotic interactions predicted reactor performance outcomes more accurately than those that did not. The average percent error of power density predictions was 16.01 ± 4.35%, while the average percent error of Coulombic efficiency and COD removal rate predictions were 1.77 ± 0.57% and 4.07 ± 1.06%, respectively. Predictions of power density improved to within 5.76 ± 3.16% percent error through classifying taxonomic data at the family versus class level. Results suggest that the microbial communities and performance of bioelectrochemical systems can be accurately predicted using data-mining, machine-learning techniques.

The Changing Microbial Community Along the Orca Basin Pycnocline

NASA Astrophysics Data System (ADS)

Hyde, A.; Nigro, L. M.; Montoya, J. P.; Joye, S. B.; Teske, A.

2016-02-01

Orca Basin in the Gulf of Mexico is the largest seafloor brine basin in the world, with a brine depth up to 220 m and an areal extent of 123 km2. Within the chemocline and pycnocline of Orca Basin, salinity, temperature, oxygen concentration, porewater chemistry, and microbial community composition change within approx. 100 meters, from fully oxic and marine saline deepwater conditions at 2150 m to anoxic hypersaline brine at 2250 m depth. Previous surveys of Orca Basin have detected distinct peaks of metal-cycling bacteria, and of archaeal lipids in the Orca Basin chemocline. The steep pycnocline slows down the sinking speed and therefore concentrates organic matter and microbial populations from the water column; it also allows in-situ growth of microbial populations that can take advantage of coexisting electron donors and acceptors. To survey the microbial community structure and stratification in Orca Basin, we performed a high-throughput bacterial 16S rRNA gene sequencing of filter samples from the Orca Basin deep water, chemocline and brine, collected in April 2014 on RV Atlantis. Widely spaced 50 m sample intervals from 1800 to 2350 m depth were complemented with fine-scale sampling every ten meters between 2150 and 2250 m depth, centered on the pycno- and chemocline as evident from CTD data, and with additional samples taken at 2125, 2275, and 2375 m depth. While we expect abundant and diverse chemosynthetic interface bacteria and halophiles, we are also exploring the possibility that the Orca Basin pycnocline preserves and amplifies microbial hydrocarbon signatures in the Gulf of Mexico, as in a long-term particle trap.

Automated DNA extraction platforms offer solutions to challenges of assessing microbial biofouling in oil production facilities.

PubMed

Oldham, Athenia L; Drilling, Heather S; Stamps, Blake W; Stevenson, Bradley S; Duncan, Kathleen E

2012-11-20

The analysis of microbial assemblages in industrial, marine, and medical systems can inform decisions regarding quality control or mitigation. Modern molecular approaches to detect, characterize, and quantify microorganisms provide rapid and thorough measures unbiased by the need for cultivation. The requirement of timely extraction of high quality nucleic acids for molecular analysis is faced with specific challenges when used to study the influence of microorganisms on oil production. Production facilities are often ill equipped for nucleic acid extraction techniques, making the preservation and transportation of samples off-site a priority. As a potential solution, the possibility of extracting nucleic acids on-site using automated platforms was tested. The performance of two such platforms, the Fujifilm QuickGene-Mini80™ and Promega Maxwell®16 was compared to a widely used manual extraction kit, MOBIO PowerBiofilm™ DNA Isolation Kit, in terms of ease of operation, DNA quality, and microbial community composition. Three pipeline biofilm samples were chosen for these comparisons; two contained crude oil and corrosion products and the third transported seawater. Overall, the two more automated extraction platforms produced higher DNA yields than the manual approach. DNA quality was evaluated for amplification by quantitative PCR (qPCR) and end-point PCR to generate 454 pyrosequencing libraries for 16S rRNA microbial community analysis. Microbial community structure, as assessed by DGGE analysis and pyrosequencing, was comparable among the three extraction methods. Therefore, the use of automated extraction platforms should enhance the feasibility of rapidly evaluating microbial biofouling at remote locations or those with limited resources.

Automated DNA extraction platforms offer solutions to challenges of assessing microbial biofouling in oil production facilities

PubMed Central

2012-01-01

The analysis of microbial assemblages in industrial, marine, and medical systems can inform decisions regarding quality control or mitigation. Modern molecular approaches to detect, characterize, and quantify microorganisms provide rapid and thorough measures unbiased by the need for cultivation. The requirement of timely extraction of high quality nucleic acids for molecular analysis is faced with specific challenges when used to study the influence of microorganisms on oil production. Production facilities are often ill equipped for nucleic acid extraction techniques, making the preservation and transportation of samples off-site a priority. As a potential solution, the possibility of extracting nucleic acids on-site using automated platforms was tested. The performance of two such platforms, the Fujifilm QuickGene-Mini80™ and Promega Maxwell®16 was compared to a widely used manual extraction kit, MOBIO PowerBiofilm™ DNA Isolation Kit, in terms of ease of operation, DNA quality, and microbial community composition. Three pipeline biofilm samples were chosen for these comparisons; two contained crude oil and corrosion products and the third transported seawater. Overall, the two more automated extraction platforms produced higher DNA yields than the manual approach. DNA quality was evaluated for amplification by quantitative PCR (qPCR) and end-point PCR to generate 454 pyrosequencing libraries for 16S rRNA microbial community analysis. Microbial community structure, as assessed by DGGE analysis and pyrosequencing, was comparable among the three extraction methods. Therefore, the use of automated extraction platforms should enhance the feasibility of rapidly evaluating microbial biofouling at remote locations or those with limited resources. PMID:23168231

Identification of microbial species present in a pesticide dissipation process in biobed systems using typical substrates from southeastern Mexico as a biomixture at a laboratory scale.

PubMed

Góngora-Echeverría, Virgilio R; Quintal-Franco, Carlos; Arena-Ortiz, María Leticia; Giácoman-Vallejos, Germán; Ponce-Caballero, Carmen

2018-07-01

Biobed systems are an important option to control point pollution in agricultural areas. Substrates used and microbial diversity present in a biomixture perform an essential function in pesticide dissipation. In this study, the effects of soil (50% of volume/volume [V/V] proportion for all biomixtures) and four soil-based biomixtures (miniaturized biobeds; addition of novel substrates from southeastern Mexico) on dissipation of high concentrations of 2,4-dichlorophenoxyacetic acid (2,4-D), atrazine, carbofuran, diazinon, and glyphosate and on microbial diversity in biomixtures were evaluated. Small residual amounts of all pesticides at 20 (<2%) and 41 (<1%) days were observed; however, the lowest efficiency rates were observed in soil. Glyphosate was the only pesticide that completely dissipated in soil and biomixtures. Archaea, bacteria, and fungi were identified in biobeds, with bacteria being the most diverse microorganisms according to the identified species. The presence of white-rot fungi (normally related to pesticide degradation in biomixtures) was observed. Effects of the pesticide type and of biomixtures on pesticide dissipation were significant (P<0.05); however, only the effect of biomixtures on microbial diversity was significant (P<0.05); microbial diversity and richness had a significant effect on the residual amount of pesticides (P<0.05). Microbial diversity in terms of phyla was directly related to physicochemical parameters such as organic matter, lignin, water-holding capacity, and pH of soil and biomixtures. Copyright © 2018 Elsevier B.V. All rights reserved.

Review article: the gut microbiome in inflammatory bowel disease-avenues for microbial management.

PubMed

McIlroy, J; Ianiro, G; Mukhopadhya, I; Hansen, R; Hold, G L

2018-01-01

The concept of an altered collective gut microbiota rather than identification of a single culprit is possibly the most significant development in inflammatory bowel disease research. We have entered the "omics" era, which now allows us to undertake large-scale/high-throughput microbiota analysis which may well define how we approach diagnosis and treatment of inflammatory bowel disease (IBD) in the future, with a strong steer towards personalised therapeutics. To assess current epidemiological, experimental and clinical evidence of the current status of knowledge relating to the gut microbiome, and its role in IBD, with emphasis on reviewing the evidence relating to microbial therapeutics and future microbiome modulating therapeutics. A Medline search including items 'intestinal microbiota/microbiome', 'inflammatory bowel disease', 'ulcerative colitis', 'Crohn's disease', 'faecal microbial transplantation', 'dietary manipulation' was performed. Disease remission and relapse are associated with microbial changes in both mucosal and luminal samples. In particular, a loss of species richness in Crohn's disease has been widely observed. Existing therapeutic approaches broadly fall into 3 categories, namely: accession, reduction or indirect modulation of the microbiome. In terms of microbial therapeutics, faecal microbial transplantation appears to hold the most promise; however, differences in study design/methodology mean it is currently challenging to elegantly translate results into clinical practice. Existing approaches to modulate the gut microbiome are relatively unrefined. Looking forward, the future of microbiome-modulating therapeutics looks bright with several novel strategies/technologies on the horizon. Taken collectively, it is clear that ignoring the microbiome in IBD is not an option. © 2017 John Wiley & Sons Ltd.

The microbial community of a passive biochemical reactor treating arsenic, zinc, and sulfate-rich seepage.

PubMed

Baldwin, Susan Anne; Khoshnoodi, Maryam; Rezadehbashi, Maryam; Taupp, Marcus; Hallam, Steven; Mattes, Al; Sanei, Hamed

2015-01-01

Sulfidogenic biochemical reactors (BCRs) for metal removal that use complex organic carbon have been shown to be effective in laboratory studies, but their performance in the field is highly variable. Successful operation depends on the types of microorganisms supported by the organic matrix, and factors affecting the community composition are unknown. A molecular survey of a field-based BCR that had been removing zinc and arsenic for over 6 years revealed that the microbial community was dominated by methanogens related to Methanocorpusculum sp. and Methanosarcina sp., which co-occurred with Bacteroidetes environmental groups, such as Vadin HA17, in places where the organic matter was more degraded. The metabolic potential for organic matter decomposition by Ruminococcaceae was prevalent in samples with more pyrolyzable carbon. Rhodobium- and Hyphomicrobium-related genera within the Rhizobiales order that have the metabolic potential for dark hydrogen fermentation and methylotrophy, and unclassified Comamonadaceae were the dominant Proteobacteria. The unclassified environmental group Sh765B-TzT-29 was an important Delta-Proteobacteria group in this BCR that co-occurred with the dominant Rhizobiales operational taxonomic units. Organic matter degradation is one driver for shifting the microbial community composition and therefore possibly the performance of these bioreactors over time.

Performance of two quantitative PCR methods for microbial source tracking of human sewage and implications for microbial risk assessment in recreational waters

EPA Science Inventory

Before new, rapid quantitative PCR (qPCR) methods for recreational water quality assessment and microbial source tracking (MST) can be useful in a regulatory context, an understanding of the ability of the method to detect a DNA target (marker) when the contaminant soure has been...

Size and Carbon Content of Sub-seafloor Microbial Cells at Landsort Deep, Baltic Sea

PubMed Central

Braun, Stefan; Morono, Yuki; Littmann, Sten; Kuypers, Marcel; Aslan, Hüsnü; Dong, Mingdong; Jørgensen, Bo B.; Lomstein, Bente Aa.

2016-01-01

The discovery of a microbial ecosystem in ocean sediments has evoked interest in life under extreme energy limitation and its role in global element cycling. However, fundamental parameters such as the size and the amount of biomass of sub-seafloor microbial cells are poorly constrained. Here we determined the volume and the carbon content of microbial cells from a marine sediment drill core retrieved by the Integrated Ocean Drilling Program (IODP), Expedition 347, at Landsort Deep, Baltic Sea. To determine their shape and volume, cells were separated from the sediment matrix by multi-layer density centrifugation and visualized via epifluorescence microscopy (FM) and scanning electron microscopy (SEM). Total cell-carbon was calculated from amino acid-carbon, which was analyzed by high-performance liquid chromatography (HPLC) after cells had been purified by fluorescence-activated cell sorting (FACS). The majority of microbial cells in the sediment have coccoid or slightly elongated morphology. From the sediment surface to the deepest investigated sample (~60 m below the seafloor), the cell volume of both coccoid and elongated cells decreased by an order of magnitude from ~0.05 to 0.005 μm3. The cell-specific carbon content was 19–31 fg C cell−1, which is at the lower end of previous estimates that were used for global estimates of microbial biomass. The cell-specific carbon density increased with sediment depth from about 200 to 1000 fg C μm−3, suggesting that cells decrease their water content and grow small cell sizes as adaptation to the long-term subsistence at very low energy availability in the deep biosphere. We present for the first time depth-related data on the cell volume and carbon content of sedimentary microbial cells buried down to 60 m below the seafloor. Our data enable estimates of volume- and biomass-specific cellular rates of energy metabolism in the deep biosphere and will improve global estimates of microbial biomass. PMID:27630628

Winter ecology of a subalpine grassland: Effects of snow removal on soil respiration, microbial structure and function.

PubMed

Gavazov, Konstantin; Ingrisch, Johannes; Hasibeder, Roland; Mills, Robert T E; Buttler, Alexandre; Gleixner, Gerd; Pumpanen, Jukka; Bahn, Michael

2017-07-15

Seasonal snow cover provides essential insulation for mountain ecosystems, but expected changes in precipitation patterns and snow cover duration due to global warming can influence the activity of soil microbial communities. In turn, these changes have the potential to create new dynamics of soil organic matter cycling. To assess the effects of experimental snow removal and advanced spring conditions on soil carbon (C) and nitrogen (N) dynamics, and on the biomass and structure of soil microbial communities, we performed an in situ study in a subalpine grassland in the Austrian Alps, in conjunction with soil incubations under controlled conditions. We found substantial winter C-mineralisation and high accumulation of inorganic and organic N in the topsoil, peaking at snowmelt. Soil microbial biomass doubled under the snow, paralleled by a fivefold increase in its C:N ratio, but no apparent change in its bacteria-dominated community structure. Snow removal led to a series of mild freeze-thaw cycles, which had minor effects on in situ soil CO 2 production and N mineralisation. Incubated soil under advanced spring conditions, however, revealed an impaired microbial metabolism shortly after snow removal, characterised by a limited capacity for C-mineralisation of both fresh plant-derived substrates and existing soil organic matter (SOM), leading to reduced priming effects. This effect was transient and the observed recovery in microbial respiration and SOM priming towards the end of the winter season indicated microbial resilience to short-lived freeze-thaw disturbance under field conditions. Bacteria showed a higher potential for uptake of plant-derived C substrates during this recovery phase. The observed temporary loss in microbial C-mineralisation capacity and the promotion of bacteria over fungi can likely impede winter SOM cycling in mountain grasslands under recurrent winter climate change events, with plausible implications for soil nutrient availability and plant-soil interactions. Copyright © 2017 Elsevier B.V. All rights reserved.

Gut microbial and short-chain fatty acid profiles in adults with chronic constipation before and after treatment with lubiprostone.

PubMed

Kang, Dae-Wook; DiBaise, John K; Ilhan, Zehra Esra; Crowell, Michael D; Rideout, Jai Ram; Caporaso, J Gregory; Rittmann, Bruce E; Krajmalnik-Brown, Rosa

2015-06-01

Identifying specific gut microorganisms associated with chronic constipation may be useful for diagnostic and therapeutic purposes. The objective of this study was to evaluate whether or not the gut microbial community of constipated subjects had specific microbial signatures and to assess the effects of lubiprostone treatment on the gut microbial community. Stool diaries, breath H2 and CH4 levels, and stool samples were collected from ten healthy subjects and nine patients meeting the Rome III criteria for chronic functional constipation. Constipated subjects received lubiprostone for four weeks, during which stool diaries were maintained. Stool samples were evaluated for gut microbial communities using pyrosequencing and quantitative real-time PCR (qPCR) targeting 16S-rRNA gene, along with concentrations of short-chain fatty acids (SCFAs) using high-performance liquid chromatography. Prior to treatment, gut microbial profiles were similar between constipated subjects and healthy subjects, while iso-butyrate levels were significantly higher in constipated subjects compared with healthy subjects. Despite increases in stool frequency and improvements in consistency after lubiprostone treatment, gut microbial profiles and community diversity after treatment showed no significant change compared to before treatment. While we did not observe a significant difference in either breath methane or archaeal abundance between the stool samples of healthy and constipated subjects, we confirmed a strong correlation between archaeal abundance measured by qPCR and the amount of methane gas exhaled in the fasting breath. Butyrate levels, however, were significantly higher in the stool samples of constipated subjects after lubiprostone treatment, suggesting that lubiprostone treatment had an effect on the net accumulation of SCFAs in the gut. In conclusion, lubiprostone treatment improved constipation symptoms and increased levels of butyrate without substantial modification of the gut microbial structure. Copyright © 2015 Elsevier Ltd. All rights reserved.

The structural and functional contributions of β-glucosidase-producing microbial communities to cellulose degradation in composting.

PubMed

Zang, Xiangyun; Liu, Meiting; Fan, Yihong; Xu, Jie; Xu, Xiuhong; Li, Hongtao

2018-01-01

Compost habitats sustain a vast ensemble of microbes that engender the degradation of cellulose, which is an important part of global carbon cycle. β-Glucosidase is the rate-limiting enzyme of degradation of cellulose. Thus, analysis of regulation of β-glucosidase gene expression in composting is beneficial to a better understanding of cellulose degradation mechanism. Genetic diversity and expression of β-glucosidase-producing microbial communities, and relationships of cellulose degradation, metabolic products and the relative enzyme activity during natural composting and inoculated composting were evaluated. Compared with natural composting, adding inoculation agent effectively improved the degradation of cellulose, and maintained high level of the carboxymethyl cellulose (CMCase) and β-glucosidase activities in thermophilic phase. Gene expression analysis showed that glycoside hydrolase family 1 (GH1) family of β-glucosidase genes contributed more to β-glucosidase activity in the later thermophilic phase in inoculated compost. In the cooling phase of natural compost, glycoside hydrolase family 3 (GH3) family of β-glucosidase genes contributed more to β-glucosidase activity. Intracellular β-glucosidase activity played a crucial role in the regulation of β-glucosidase gene expression, and upregulation or downregulation was also determined by extracellular concentration of glucose. At sufficiently high glucose concentrations, the functional microbial community in compost was altered, which may contribute to maintaining β-glucosidase activity despite the high glucose content. This research provides an ecological functional map of microorganisms involved in carbon metabolism in cattle manure-rice straw composting. The performance of the functional microbial groups in the two composting treatments is different, which is related to the cellulase activity and cellulose degradation, respectively.

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

NASA Astrophysics Data System (ADS)

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

2009-04-01

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

Microbial Community of High Arsenic Groundwater in Agricultural Irrigation Area of Hetao Plain, Inner Mongolia

PubMed Central

Wang, Yanhong; Li, Ping; Jiang, Zhou; Sinkkonen, Aki; Wang, Shi; Tu, Jin; Wei, Dazhun; Dong, Hailiang; Wang, Yanxin

2016-01-01

Microbial communities can play important role in arsenic release in groundwater aquifers. To investigate the microbial communities in high arsenic groundwater aquifers in agricultural irrigation area, 17 groundwater samples with different arsenic concentrations were collected along the agricultural drainage channels of Hangjinhouqi County, Inner Mongolia and examined by illumina MiSeq sequencing approach targeting the V4 region of the 16S rRNA genes. Both principal component analysis and hierarchical clustering results indicated that these samples were divided into two groups (high and low arsenic groups) according to the variation of geochemical characteristics. Arsenic concentrations showed strongly positive correlations with NH4+ and total organic carbon (TOC). Sequencing results revealed that a total of 329–2823 operational taxonomic units (OTUs) were observed at the 97% OTU level. Microbial richness and diversity of high arsenic groundwater samples along the drainage channels were lower than those of low arsenic groundwater samples but higher than those of high arsenic groundwaters from strongly reducing areas. The microbial community structure in groundwater along the drainage channels was different from those in strongly reducing arsenic-rich aquifers of Hetao Plain and other high arsenic groundwater aquifers including Bangladesh, West Bengal, and Vietnam. Acinetobacter and Pseudomonas dominated with high percentages in both high and low arsenic groundwaters. Alishewanella, Psychrobacter, Methylotenera, and Crenothrix showed relatively high abundances in high arsenic groundwater, while Rheinheimera and the unidentified OP3 were predominant populations in low arsenic groundwater. Archaeal populations displayed a low occurrence and mainly dominated by methanogens such as Methanocorpusculum and Methanospirillum. Microbial community compositions were different between high and low arsenic groundwater samples based on the results of principal coordinate analysis and co-inertia analysis. Other geochemical variables including TOC, NH4+, oxidation-reduction potential, and Fe might also affect the microbial composition. PMID:27999565

Indigenous microbial capability in solid manure residues to start-up solid-phase anaerobic digesters.

PubMed

Yap, S D; Astals, S; Jensen, P D; Batstone, D J; Tait, S

2017-06-01

Batch solid-phase anaerobic digestion is a technology for sustainable on-farm treatment of solid residues, but is an emerging technology that is yet to be optimised with respect to start-up and inoculation. In the present study, spent bedding from two piggeries (site A and B) were batch digested at total solids (TS) concentration of 5, 10 and 20% at mesophilic (37°C) and thermophilic (55°C) temperatures, without adding an external inoculum. The results showed that the indigenous microbial community present in spent bedding was able to recover the full methane potential of the bedding (140±5 and 227±6L CH 4 kgVS fed -1 for site A and B, respectively), but longer treatment times were required than for digestion with an added external inoculum. Nonetheless, at high solid loadings (i.e. TS level>10%), the digestion performance was affected by chemical inhibition due to ammonia and/or humic acid. Thermophilic temperatures did not influence digestion performance but did increase start-up failure risk. Further, inoculation of residues from the batch digestion to subsequent batch enhanced start-up and achieved full methane potential recovery of the bedding. Inoculation with liquid residue (leachate) was preferred over a solid residue, to preserve treatment capacity for fresh substrate. Overall, the study highlighted that indigenous microbial community in the solid manure residue was capable of recovering full methane potential and that solid-phase digestion was ultimately limited by chemical inhibition rather than lack of suitable microbial community. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evaluating the performance of water purification in a vegetated groundwater recharge basin maintained by short-term pulsed infiltration events.

PubMed

Mindl, Birgit; Hofer, Julia; Kellermann, Claudia; Stichler, Willibald; Teichmann, Günter; Psenner, Roland; Danielopol, Dan L; Neudorfer, Wolfgang; Griebler, Christian

2015-01-01

Infiltration of surface water constitutes an important pillar in artificial groundwater recharge. However, insufficient transformation of organic carbon and nutrients, as well as clogging of sediments often cause major problems. The attenuation efficiency of dissolved organic carbon (DOC), nutrients and pathogens versus the risk of bioclogging for intermittent recharge were studied in an infiltration basin covered with different kinds of macrovegetation. The quality and concentration of organic carbon, major nutrients, as well as bacterial biomass, activity and diversity in the surface water, the porewater, and the sediment matrix were monitored over one recharge period. Additionally, the numbers of viral particles and Escherichia coli were assessed. Our study showed a fast establishment of high microbial activity. DOC and nutrients have sustainably been reduced within 1.2 m of sediment passage. Numbers of E. coli, which were high in the topmost centimetres of sediment porewater, dropped below the detection limit. Reed cover was found to be advantageous over bushes and trees, since it supported higher microbial activities along with a good infiltration and purification performance. Short-term infiltration periods of several days followed by a break of similar time were found suitable for providing high recharge rates, and good water purification without the risk of bioclogging.

Effects of wastewater constituents and operational conditions on the composition and dynamics of anodic microbial communities in bioelectrochemical systems.

PubMed

Kokko, Marika; Epple, Stefanie; Gescher, Johannes; Kerzenmacher, Sven

2018-06-01

Over the last decade, there has been an ever-growing interest in bioelectrochemical systems (BES) as a sustainable technology enabling simultaneous wastewater treatment and biological production of, e.g. electricity, hydrogen, and further commodities. A key component of any BES degrading organic matter is the anode where electric current is biologically generated from the oxidation of organic compounds. The performance of BES depends on the interactions of the anodic microbial communities. To optimize the operational parameters and process design of BES a better comprehension of the microbial community dynamics and interactions at the anode is required. This paper reviews the abundance of different microorganisms in anodic biofilms and discusses their roles and possible side reactions with respect to their implications on the performance of BES utilizing wastewaters. The most important operational parameters affecting anodic microbial communities grown with wastewaters are highlighted and guidelines for controlling the composition of microbial communities are given. Copyright © 2018 Elsevier Ltd. All rights reserved.

Effects of feeding wheat or corn-wheat dried distillers grains with solubles in low- or high-crude protein diets on ruminal function, omasal nutrient flows, urea-N recycling, and performance in cows.

PubMed

Chibisa, G E; Mutsvangwa, T

2013-10-01

A study was conducted to determine the effects of including either wheat-based (W-DDGS) or corn-wheat blend (B-DDGS) dried distillers grains with solubles as the major protein source in low- or high-crude protein (CP) diets fed to dairy cows on ruminal function, microbial protein synthesis, omasal nutrient flows, urea-N recycling, and milk production. Eight lactating Holstein cows (768.5 ± 57.7 kg of body weight; 109.5 ± 40.0 d in milk) were used in a replicated 4 × 4 Latin square design with 28-d periods (18d of dietary adaptation and 10d of measurements) and a 2 × 2 factorial arrangement of dietary treatments. Four cows in one Latin square were ruminally cannulated for the measurement of ruminal fermentation characteristics, microbial protein synthesis, urea-N recycling kinetics, and omasal nutrient flow. The treatment factors were type of distillers co-product (W-DDGS vs. B-DDGS) and dietary CP content [15.2 vs. 17.3%; dry matter (DM) basis]. The B-DDGS was produced from a mixture of 15% wheat and 85% corn grain. All diets were formulated to contain 10% W-DDGS or B-DDGS on a DM basis. No diet effect was observed on DM intake. Yields of milk, fat, protein, and lactose, and plasma urea-N and milk urea-N concentrations were lower in cows fed the low-CP compared with those fed the high-CP diet. Although feeding B-DDGS tended to reduce ruminal ammonia-N (NH3-N) concentration compared with feeding W-DDGS (9.3 vs. 10.5mg/dL), no differences were observed in plasma urea-N and milk urea-N concentrations. Additionally, dietary inclusion of B-DDGS compared with W-DDGS did not affect rumen-degradable protein supply, omasal flows of total N, microbial nonammonia N (NAN), rumen-undegradable protein, and total NAN, or urea-N recycling kinetics and milk production. However, cows fed the low-CP diet had lower N intake, rumen-degradable protein supply, ruminal NH3-N concentration, and omasal flows of N, microbial NAN, and total NAN compared with those fed the high-CP diet. Feeding the low-CP compared with the high-CP diet also resulted in lower endogenous urea-N production, urea-N recycled to the gastrointestinal tract, and urea-N excretion in urine. In summary, our results indicate that both W-DDGS and B-DDGS can be included as the major protein sources in dairy cow diets without compromising nutrient supply and production performance. However, feeding the low-CP diet lowered omasal flows of microbial protein and metabolizable protein, which, in turn, resulted in lower milk production compared with feeding the high-CP diet. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

The Grapevine and Wine Microbiome: Insights from High-Throughput Amplicon Sequencing

PubMed Central

Morgan, Horatio H.; du Toit, Maret; Setati, Mathabatha E.

2017-01-01

From the time when microbial activity in wine fermentation was first demonstrated, the microbial ecology of the vineyard, grape, and wine has been extensively investigated using culture-based methods. However, the last 2 decades have been characterized by an important change in the approaches used for microbial examination, due to the introduction of DNA-based community fingerprinting methods such as DGGE, SSCP, T-RFLP, and ARISA. These approaches allowed for the exploration of microbial community structures without the need to cultivate, and have been extensively applied to decipher the microbial populations associated with the grapevine as well as the microbial dynamics throughout grape berry ripening and wine fermentation. These techniques are well-established for the rapid more sensitive profiling of microbial communities; however, they often do not provide direct taxonomic information and possess limited ability to detect the presence of rare taxa and taxa with low abundance. Consequently, the past 5 years have seen an upsurge in the application of high-throughput sequencing methods for the in-depth assessment of the grapevine and wine microbiome. Although a relatively new approach in wine sciences, these methods reveal a considerably greater diversity than previously reported, and identified several species that had not yet been reported. The aim of the current review is to highlight the contribution of high-throughput next generation sequencing and metagenomics approaches to vineyard microbial ecology especially unraveling the influence of vineyard management practices on microbial diversity. PMID:28553266

The Grapevine and Wine Microbiome: Insights from High-Throughput Amplicon Sequencing.

PubMed

Morgan, Horatio H; du Toit, Maret; Setati, Mathabatha E

2017-01-01

From the time when microbial activity in wine fermentation was first demonstrated, the microbial ecology of the vineyard, grape, and wine has been extensively investigated using culture-based methods. However, the last 2 decades have been characterized by an important change in the approaches used for microbial examination, due to the introduction of DNA-based community fingerprinting methods such as DGGE, SSCP, T-RFLP, and ARISA. These approaches allowed for the exploration of microbial community structures without the need to cultivate, and have been extensively applied to decipher the microbial populations associated with the grapevine as well as the microbial dynamics throughout grape berry ripening and wine fermentation. These techniques are well-established for the rapid more sensitive profiling of microbial communities; however, they often do not provide direct taxonomic information and possess limited ability to detect the presence of rare taxa and taxa with low abundance. Consequently, the past 5 years have seen an upsurge in the application of high-throughput sequencing methods for the in-depth assessment of the grapevine and wine microbiome. Although a relatively new approach in wine sciences, these methods reveal a considerably greater diversity than previously reported, and identified several species that had not yet been reported. The aim of the current review is to highlight the contribution of high-throughput next generation sequencing and metagenomics approaches to vineyard microbial ecology especially unraveling the influence of vineyard management practices on microbial diversity.

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.

Influence of aeolian activities on the distribution of microbial abundance in glacier ice

NASA Astrophysics Data System (ADS)

Chen, Y.; Li, X.-K.; Si, J.; Wu, G.-J.; Tian, L.-D.; Xiang, S.-R.

2014-10-01

Microorganisms are continuously blown onto the glacier snow, and thus the glacial depth profiles provide excellent archives of microbial communities and climatic and environmental changes. However, it is uncertain about how aeolian processes that cause climatic changes control the distribution of microorganisms in the glacier ice. In the present study, microbial density, stable isotopic ratios, 18O / 16O in the precipitation, and mineral particle concentrations along the glacial depth profiles were collected from ice cores from the Muztag Ata glacier and the Dunde ice cap. The ice core data showed that microbial abundance was often, but not always associated with high concentrations of particles. Results also revealed clear seasonal patterning with high microbial abundance occurring in both the cooling autumn and warming spring-summer seasons. Microbial comparisons among the neighbouring glaciers display a heterogeneous spatial pattern, with the highest microbial cell density in the glaciers lying adjacent to the central Asian deserts and lowest microbial density in the southwestern margin of the Tibetan Plateau. In conclusion, microbial data of the glaciers indicates the aeolian deposits of microorganisms in the glacier ice and that the spatial patterns of microorgansisms are related to differences in sources of microbial flux and intensity of aeolian activities in the current regions. The results strongly support our hypothesis of aeolian activities being the main agents controlling microbial load in the glacier ice.

Halotolerant extremophile bacteria from the Great Salt Lake for recycling pollutants in microbial fuel cells

NASA Astrophysics Data System (ADS)

Grattieri, Matteo; Suvira, Milomir; Hasan, Kamrul; Minteer, Shelley D.

2017-07-01

The treatment of hypersaline wastewater (approximately 5% of the wastewater worldwide) cannot be performed by classical biological techniques. Herein the halotolerant extremophile bacteria obtained from the Great Salt Lake (Utah) were explored in single chamber microbial fuel cells with Pt-free cathodes for more than 18 days. The bacteria samples collected in two different locations of the lake (Stansbury Bay and Antelope Island) showed different electrochemical performances. The maximum achieved power output of 36 mW m-2 was from the microbial fuel cell based on the sample originated from Stansbury Bay, at a current density of 820 mA m-2. The performances throughout the long-term operation are discussed and a bioelectrochemical mechanism is proposed.

Analysis of Microbial Functions in the Rhizosphere Using a Metabolic-Network Based Framework for Metagenomics Interpretation

PubMed Central

Ofaim, Shany; Ofek-Lalzar, Maya; Sela, Noa; Jinag, Jiandong; Kashi, Yechezkel; Minz, Dror; Freilich, Shiri

2017-01-01

Advances in metagenomics enable high resolution description of complex bacterial communities in their natural environments. Consequently, conceptual approaches for community level functional analysis are in high need. Here, we introduce a framework for a metagenomics-based analysis of community functions. Environment-specific gene catalogs, derived from metagenomes, are processed into metabolic-network representation. By applying established ecological conventions, network-edges (metabolic functions) are assigned with taxonomic annotations according to the dominance level of specific groups. Once a function-taxonomy link is established, prediction of the impact of dominant taxa on the overall community performances is assessed by simulating removal or addition of edges (taxa associated functions). This approach is demonstrated on metagenomic data describing the microbial communities from the root environment of two crop plants – wheat and cucumber. Predictions for environment-dependent effects revealed differences between treatments (root vs. soil), corresponding to documented observations. Metabolism of specific plant exudates (e.g., organic acids, flavonoids) was linked with distinct taxonomic groups in simulated root, but not soil, environments. These dependencies point to the impact of these metabolite families as determinants of community structure. Simulations of the activity of pairwise combinations of taxonomic groups (order level) predicted the possible production of complementary metabolites. Complementation profiles allow formulating a possible metabolic role for observed co-occurrence patterns. For example, production of tryptophan-associated metabolites through complementary interactions is unique to the tryptophan-deficient cucumber root environment. Our approach enables formulation of testable predictions for species contribution to community activity and exploration of the functional outcome of structural shifts in complex bacterial communities. Understanding community-level metabolism is an essential step toward the manipulation and optimization of microbial function. Here, we introduce an analysis framework addressing three key challenges of such data: producing quantified links between taxonomy and function; contextualizing discrete functions into communal networks; and simulating environmental impact on community performances. New technologies will soon provide a high-coverage description of biotic and a-biotic aspects of complex microbial communities such as these found in gut and soil. This framework was designed to allow the integration of high-throughput metabolomic and metagenomic data toward tackling the intricate associations between community structure, community function, and metabolic inputs. PMID:28878756

Genome-scale biological models for industrial microbial systems.

PubMed

Xu, Nan; Ye, Chao; Liu, Liming

2018-04-01

The primary aims and challenges associated with microbial fermentation include achieving faster cell growth, higher productivity, and more robust production processes. Genome-scale biological models, predicting the formation of an interaction among genetic materials, enzymes, and metabolites, constitute a systematic and comprehensive platform to analyze and optimize the microbial growth and production of biological products. Genome-scale biological models can help optimize microbial growth-associated traits by simulating biomass formation, predicting growth rates, and identifying the requirements for cell growth. With regard to microbial product biosynthesis, genome-scale biological models can be used to design product biosynthetic pathways, accelerate production efficiency, and reduce metabolic side effects, leading to improved production performance. The present review discusses the development of microbial genome-scale biological models since their emergence and emphasizes their pertinent application in improving industrial microbial fermentation of biological products.

Impact of the start-up process on the microbial communities in biocathodes for electrosynthesis.

PubMed

Mateos, Raúl; Sotres, Ana; Alonso, Raúl M; Escapa, Adrián; Morán, Antonio

2018-06-01

This study seeks to understand how the bacterial communities that develop on biocathodes are influenced by inocula diversity and electrode potential during start-up. Two different inocula are used: one from a highly diverse environment (river mud) and the other from a low diverse milieu (anaerobic digestion). In addition, both inocula were subjected to two different polarising voltages: oxidative (+0.2 V vs. Ag/AgCl) and reductive (-0.8 V vs. Ag/AgCl). Bacterial communities were analysed by means of high throughput sequencing. Possible syntrophic interactions and competitions between archaea and eubacteria were described together with a discussion of their potential role in product formation and current production. The results confirmed that reductive potentials lead to an inconsistent start-up procedure regardless of the inoculum used. However, imposing oxidative potentials help to quickly develop an electroactive biofilm ready to withstand reductive potentials (i.e. biocathodic operation). The microbial structure that finally developed on them was highly dependent on the raw community present in the inoculum. Using a non-specialised inoculum resulted in a highly specialised biofilm, which was accompanied by an improved performance in terms of consumed current and product generation. Interestingly, a much more specialised inoculum promoted a rediversification in the biofilm, with a lower general cell performance. Copyright © 2018 Elsevier B.V. All rights reserved.

Enhancement of methane production in anaerobic digestion of sewage sludge by thermal hydrolysis pretreatment.

PubMed

Choi, Jae-Min; Han, Sun-Kee; Lee, Chae-Young

2018-07-01

This study was performed to optimize thermal hydrolysis pretreatment (THP) of sewage sludge for enhanced anaerobic digestion (AD). Using the response surface methodology (RSM), the optimal conditions were found 180 °C of reaction temperature and 76 min of reaction time. Through THP under optimal conditions, high molecular substances in sewage sludge such as soluble microbial by-products (SMPs) and extracellular polymeric substances (EPSs) were hydrolyzed into low molecular ones without the generation of refractory compounds. The microbial community analysis revealed that relative abundances of Methanomicrobia such as Methanosarcina, Methanosaeta (acetoclastic methanogens), and Methanoculleus (hydrogenotrophic methanogens) in AD with THP were higher than those in conventional AD. Copyright © 2018. Published by Elsevier Ltd.

Performance of polyacrylonitrile-carbon nanotubes composite on carbon cloth as electrode material for microbial fuel cells.

PubMed

Kim, Sun-Il; Lee, Jae-Wook; Roh, Sung-Hee

2011-02-01

The performance of carbon nanotubes composite-modified carbon cloth electrodes in two-chambered microbial fuel cell (MFC) was investigated. The electrode modified with polyacrylonitrile-carbon nanotubes (PAN-CNTs) composite showed better electrochemical performance than that of plain carbon cloth. The MFC with the composite-modified anode containing 5 mg/cm2 PAN-CNTs exhibited a maximum power density of 480 mW/m2.

Sustainable design of high-performance microsized microbial fuel cell with carbon nanotube anode and air cathode.

PubMed

Mink, Justine E; Hussain, Muhammad Mustafa

2013-08-27

Microbial fuel cells (MFCs) are a promising alternative energy source that both generates electricity and cleans water. Fueled by liquid wastes such as wastewater or industrial wastes, the microbial fuel cell converts waste into energy. Microsized MFCs are essentially miniature energy harvesters that can be used to power on-chip electronics, lab-on-a-chip devices, and/or sensors. As MFCs are a relatively new technology, microsized MFCs are also an important rapid testing platform for the comparison and introduction of new conditions or materials into macroscale MFCs, especially nanoscale materials that have high potential for enhanced power production. Here we report a 75 μL microsized MFC on silicon using CMOS-compatible processes and employ a novel nanomaterial with exceptional electrochemical properties, multiwalled carbon nanotubes (MWCNTs), as the on-chip anode. We used this device to compare the usage of the more commonly used but highly expensive anode material gold, as well as a more inexpensive substitute, nickel. This is the first anode material study done using the most sustainably designed microsized MFC to date, which utilizes ambient oxygen as the electron acceptor with an air cathode instead of the chemical ferricyanide and without a membrane. Ferricyanide is unsustainable, as the chemical must be continuously refilled, while using oxygen, naturally found in air, makes the device mobile and is a key step in commercializing this for portable technology such as lab-on-a-chip for point-of-care diagnostics. At 880 mA/m(2) and 19 mW/m(2) the MWCNT anode outperformed the others in both current and power densities with between 6 and 20 times better performance. All devices were run for over 15 days, indicating a stable and high-endurance energy harvester already capable of producing enough power for ultra-low-power electronics and able to consistently power them over time.

Next-Generation High-Throughput Functional Annotation of Microbial Genomes.

PubMed

Baric, Ralph S; Crosson, Sean; Damania, Blossom; Miller, Samuel I; Rubin, Eric J

2016-10-04

Host infection by microbial pathogens cues global changes in microbial and host cell biology that facilitate microbial replication and disease. The complete maps of thousands of bacterial and viral genomes have recently been defined; however, the rate at which physiological or biochemical functions have been assigned to genes has greatly lagged. The National Institute of Allergy and Infectious Diseases (NIAID) addressed this gap by creating functional genomics centers dedicated to developing high-throughput approaches to assign gene function. These centers require broad-based and collaborative research programs to generate and integrate diverse data to achieve a comprehensive understanding of microbial pathogenesis. High-throughput functional genomics can lead to new therapeutics and better understanding of the next generation of emerging pathogens by rapidly defining new general mechanisms by which organisms cause disease and replicate in host tissues and by facilitating the rate at which functional data reach the scientific community. Copyright © 2016 Baric et al.

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.

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.

Field and Lab-Based Microbiological Investigations of the Marcellus Shale

NASA Astrophysics Data System (ADS)

Wishart, J. R.; Neumann, K.; Edenborn, H. M.; Hakala, A.; Yang, J.; Torres, M. E.; Colwell, F. S.

2013-12-01

The recent exploration of shales for natural gas resources has provided the opportunity to study their subsurface geochemistry and microbiology. Evidence indicates that shale environments are marked by extreme conditions such as high temperature and pressure, low porosity, permeability and connectivity, and the presence of heavy metals and radionuclides. It has been postulated that many of these shales are naturally sterile due to the high pressure and temperature conditions under which they were formed. However, it has been shown in the Antrim and New Albany shales that microbial communities do exist in these environments. Here we review geochemical and microbiological evidence for the possible habitation of the Marcellus shale by microorganisms and compare these conditions to other shales in the U.S. Furthermore, we describe the development of sampling and analysis techniques used to evaluate microbial communities present in the Marcellus shale and associated hydraulic fracturing fluid. Sampling techniques thus far have consisted of collecting flowback fluids from wells and water impoundments and collecting core material from previous drilling expeditions. Furthermore, DNA extraction was performed on Marcellus shale sub-core with a MoBio PowerSoil kit to determine its efficiency. Assessment of the Marcellus shale indicates that it has low porosity and permeability that are not conducive to dense microbial populations; however, moderate temperatures and a natural fracture network may support a microbial community especially in zones where the Marcellus intersects more porous geologic formations. Also, hydraulic fracturing extends this fracture network providing more environments where microbial communities can exist. Previous research which collected flowback fluids has revealed a diverse microbial community that may be derived from hydrofrac fluid production or from the subsurface. DNA extraction from 10 g samples of Marcellus shale sub-core were unsuccessful even when samples were spiked with 8x108 cells/g of shale. This indicated that constituents of shale such as high levels of carbonates, humic acids and metals likely inhibited components of the PowerSoil kit. Future research is focused on refining sample collection and analyses to gain a full understanding of the microbiology of the Marcellus shale and associated flowback fluids. This includes the development of an in situ osmosampler, which will collect temporally relevant fluid and colonized substrate samples. The design of the osmosampler for hydraulic fracturing wells is being adapted from those used to sample marine environments. Furthermore, incubation experiments are underway to study interactions between microbial communities associated with hydraulic fracturing fluid and Marcellus shale samples. In conclusion, evidence suggests that the Marcellus shale is a possible component of the subsurface biosphere. Future studies will be valuable in determining the microbial community structure and function in relation to the geochemistry of the Marcellus shale and its future development as a natural gas resource.

Functional gene diversity of soil microbial communities from five oil-contaminated fields in China.

PubMed

Liang, Yuting; Van Nostrand, Joy D; Deng, Ye; He, Zhili; Wu, Liyou; Zhang, Xu; Li, Guanghe; Zhou, Jizhong

2011-03-01

To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites.

Functional gene diversity of soil microbial communities from five oil-contaminated fields in China

PubMed Central

Liang, Yuting; Van Nostrand, Joy D; Deng, Ye; He, Zhili; Wu, Liyou; Zhang, Xu; Li, Guanghe; Zhou, Jizhong

2011-01-01

To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites. PMID:20861922

Biofilm formation and granule properties in anaerobic digestion at high salinity.

PubMed

Gagliano, M C; Ismail, S B; Stams, A J M; Plugge, C M; Temmink, H; Van Lier, J B

2017-09-15

For the anaerobic biological treatment of saline wastewater, Anaerobic Digestion (AD) is currently a possibility, even though elevated salt concentrations can be a major obstacle. Anaerobic consortia and especially methanogenic archaea are very sensitive to fluctuations in salinity. When working with Upflow Sludge Blanket Reactor (UASB) technology, in which the microorganisms are aggregated and retained in the system as a granular biofilm, high sodium concentration negatively affects aggregation and consequently process performances. In this research, we analysed the structure of the biofilm and granules formed during the anaerobic treatment of high salinity (at 10 and 20 g/L of sodium) synthetic wastewater at lab scale. The acclimated inoculum was able to accomplish high rates of organics removal at all the salinity levels tested. 16S rRNA gene clonal analysis and Fluorescence In Situ Hybridization (FISH) analyses identified the acetoclastic Methanosaeta harundinacea as the key player involved acetate degradation and microbial attachment/granulation. When additional calcium (1 g/L) was added to overcome the negative effect of sodium on microbial aggregation, during the biofilm formation process microbial attachment and acetate degradation decreased. The same result was observed on granules formation: while calcium had a positive effect on granules strength when added to UASB reactors, Methanosaeta filaments were not present and the degradation of the partially acidified substrate was negatively influenced. This research demonstrated the possibility to get granulation at high salinity, bringing to the forefront the importance of a selection towards Methanosaeta cells growing in filamentous form to obtain strong and healthy granules. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Chlorine stress mediates microbial surface attachment in drinking water systems.

PubMed

Liu, Li; Le, Yang; Jin, Juliang; Zhou, Yuliang; Chen, Guowei

2015-03-01

Microbial attachment to drinking water pipe surfaces facilitates pathogen survival and deteriorates disinfection performance, directly threatening the safety of drinking water. Notwithstanding that the formation of biofilm has been studied for decades, the underlying mechanisms for the origins of microbial surface attachment in biofilm development in drinking water pipelines remain largely elusive. We combined experimental and mathematical methods to investigate the role of environmental stress-mediated cell motility on microbial surface attachment in chlorination-stressed drinking water distribution systems. Results show that at low levels of disinfectant (0.0-1.0 mg/L), the presence of chlorine promotes initiation of microbial surface attachment, while higher amounts of disinfectant (>1.0 mg/L) inhibit microbial attachment. The proposed mathematical model further demonstrates that chlorination stress (0.0-5.0 mg/L)-mediated microbial cell motility regulates the frequency of cell-wall collision and thereby controls initial microbial surface attachment. The results reveal that transport processes and decay patterns of chlorine in drinking water pipelines regulate microbial cell motility and, thus, control initial surface cell attachment. It provides a mechanistic understanding of microbial attachment shaped by environmental disinfection stress and leads to new insights into microbial safety protocols in water distribution systems.

Microbiology of sugar-rich environments: diversity, ecology and system constraints.

PubMed

Lievens, Bart; Hallsworth, John E; Pozo, Maria I; Belgacem, Zouhaier Ben; Stevenson, Andrew; Willems, Kris A; Jacquemyn, Hans

2015-02-01

Microbial habitats that contain an excess of carbohydrate in the form of sugar are widespread in the microbial biosphere. Depending on the type of sugar, prevailing water activity and other substances present, sugar-rich environments can be highly dynamic or relatively stable, osmotically stressful, and/or destabilizing for macromolecular systems, and can thereby strongly impact the microbial ecology. Here, we review the microbiology of different high-sugar habitats, including their microbial diversity and physicochemical parameters, which act to impact microbial community assembly and constrain the ecosystem. Saturated sugar beet juice and floral nectar are used as case studies to explore the differences between the microbial ecologies of low and higher water-activity habitats respectively. Nectar is a paradigm of an open, dynamic and biodiverse habitat populated by many microbial taxa, often yeasts and bacteria such as, amongst many others, Metschnikowia spp. and Acinetobacter spp., respectively. By contrast, thick juice is a relatively stable, species-poor habitat and is typically dominated by a single, xerotolerant bacterium (Tetragenococcus halophilus). A number of high-sugar habitats contain chaotropic solutes (e.g. ethyl acetate, phenols, ethanol, fructose and glycerol) and hydrophobic stressors (e.g. ethyl octanoate, hexane, octanol and isoamyl acetate), all of which can induce chaotropicity-mediated stresses that inhibit or prevent multiplication of microbes. Additionally, temperature, pH, nutrition, microbial dispersion and habitat history can determine or constrain the microbiology of high-sugar milieux. Findings are discussed in relation to a number of unanswered scientific questions. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Experimental evidence of two mechanisms coupling leaf-level C assimilation to rhizosphere CO2 release

Treesearch

Zachary Kayler; Claudia Keitel; Kirstin Jansen; Arthur Gessler

2017-01-01

The time span needed for carbon fixed by plants to induce belowground responses of root and rhizosphere microbial metabolic processing is of high importance for quantifying the coupling between plant canopy physiology and soil biogeochemistry, but recent observations of a rapid link cannot be explained by new assimilate transport by phloem mass flow alone. We performed...

Performance and molecular evaluation of an anaerobic system with suspended biomass for treating wastewater with high fat content after enzymatic hydrolysis.

PubMed

Rosa, Daniela R; Duarte, Iolanda C S; Saavedra, N Katia; Varesche, Maria B; Zaiat, Marcelo; Cammarota, Magali C; Freire, Denise M G

2009-12-01

The effect of a lipase-rich fungal enzymatic preparation, produced by a Penicillium sp. during solid-state fermentation, was evaluated in an anaerobic digester treating dairy wastewater with 1200 mg of oil and grease/L. The oil and grease hydrolysis step was carried out with 0.1% (w/v) of solid enzymatic preparation at 30 degrees C for 24 h, and resulted in a final free acid concentration eight times higher than the initial value. The digester operated in sequential batches of 48 h at 30 degrees C for 245 days, and had high chemical oxygen demand (COD) removal efficiencies (around 90%) when fed with pre-hydrolyzed wastewater. However, when the pre-hydrolysis step was removed, the anaerobic digester performed poorly (with an average COD removal of 32%), as the oil and grease accumulated in the biomass and effluent oil and grease concentration increased throughout the operational period. PCR-DGGE analysis of the Bacteria and Archaea domains revealed remarkable differences in the microbial profiles in trials conducted with and without the pre-hydrolysis step, indicating that differences observed in overall parameters were intrinsically related to the microbial diversity of the anaerobic sludge.

Effects of cow diet on the microbial community and organic matter and nitrogen content of feces.

PubMed

van Vliet, P C J; Reijs, J W; Bloem, J; Dijkstra, J; de Goede, R G M

2007-11-01

Knowledge of the effects of cow diet on manure composition is required to improve nutrient use efficiency and to decrease emissions of N to the environment. Therefore, we performed an experiment with nonlactating cows to determine the consequences of changes in cow rations for the chemical characteristics and the traits of the microbial community in the feces. In this experiment, 16 cows were fed 8 diets, differing in crude protein, neutral detergent fiber, starch, and net energy content. These differences were achieved by changing dietary ingredients or roughage to concentrate ratio. After an adaptation period of 3 wk, fecal material was collected and analyzed. Observed results were compared with simulated values using a mechanistic model that provides insight into the mechanisms involved in the effect of dietary variation on fecal composition. Feces produced on a high-fiber, low-protein diet had a high C:N ratio (>16) and had lower concentrations of both organic and inorganic N than feces on a low-fiber, high-protein diet. Fecal bacterial biomass concentration was highest in high-protein, high-energy diets. The fraction of inorganic N in the feces was not significantly different between the different feces. Microbial biomass in the feces ranged from 1,200 to 8,000 microg of C/g of dry matter (average: 3,700 microg of C/g of dry matter). Bacterial diversity was similar for all fecal materials, but the different protein levels in the feeding regimens induced changes in the community structure present in the different feces. The simulated total N content (N(total)) in the feces ranged from 1.0 to 1.5 times the observed concentrations, whereas the simulated C:N(total) of the feces ranged from 0.7 to 0.9 times the observed C:N(total). However, bacterial biomass C was not predicted satisfactorily (simulated values being on average 3 times higher than observed), giving rise to further discussion on the definition of microbial C in feces. Based on these observations, it was concluded that diet composition affected fecal chemical composition and microbial biomass. These changes may affect the nutrient use and efficiency of the manure. Because the present experiment used a limited number of dry cows and extreme diet regimens, extrapolation of results to other dairy cow situations should be done with care.

Can volatile organic metabolites be used to simultaneously assess microbial and mite contamination level in cereal grains and coffee beans?

PubMed

Salvador, Angelo C; Baptista, Inês; Barros, António S; Gomes, Newton C M; Cunha, Angela; Almeida, Adelaide; Rocha, Silvia M

2013-01-01

A novel approach based on headspace solid-phase microextraction (HS-SPME) combined with comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC×GC-ToFMS) was developed for the simultaneous screening of microbial and mite contamination level in cereals and coffee beans. The proposed approach emerges as a powerful tool for the rapid assessment of the microbial contamination level (ca. 70 min versus ca. 72 to 120 h for bacteria and fungi, respectively, using conventional plate counts), and mite contamination (ca. 70 min versus ca. 24 h). A full-factorial design was performed for optimization of the SPME experimental parameters. The methodology was applied to three types of rice (rough, brown, and white rice), oat, wheat, and green and roasted coffee beans. Simultaneously, microbiological analysis of the samples (total aerobic microorganisms, moulds, and yeasts) was performed by conventional plate counts. A set of 54 volatile markers was selected among all the compounds detected by GC×GC-ToFMS. Principal Component Analysis (PCA) was applied in order to establish a relationship between potential volatile markers and the level of microbial contamination. Methylbenzene, 3-octanone, 2-nonanone, 2-methyl-3-pentanol, 1-octen-3-ol, and 2-hexanone were associated to samples with higher microbial contamination level, especially in rough rice. Moreover, oat exhibited a high GC peak area of 2-hydroxy-6-methylbenzaldehyde, a sexual and alarm pheromone for adult mites, which in the other matrices appeared as a trace component. The number of mites detected in oat grains was correlated to the GC peak area of the pheromone. The HS-SPME/GC×GC-ToFMS methodology can be regarded as the basis for the development of a rapid and versatile method that can be applied in industry to the simultaneous assessment the level of microbiological contamination and for detection of mites in cereals grains and coffee beans.

Can Volatile Organic Metabolites Be Used to Simultaneously Assess Microbial and Mite Contamination Level in Cereal Grains and Coffee Beans?

PubMed Central

Salvador, Ângelo C.; Baptista, Inês; Barros, António S.; Gomes, Newton C. M.; Cunha, Ângela; Almeida, Adelaide; Rocha, Silvia M.

2013-01-01

A novel approach based on headspace solid-phase microextraction (HS-SPME) combined with comprehensive two-dimensional gas chromatography–time-of-flight mass spectrometry (GC×GC–ToFMS) was developed for the simultaneous screening of microbial and mite contamination level in cereals and coffee beans. The proposed approach emerges as a powerful tool for the rapid assessment of the microbial contamination level (ca. 70 min versus ca. 72 to 120 h for bacteria and fungi, respectively, using conventional plate counts), and mite contamination (ca. 70 min versus ca. 24 h). A full-factorial design was performed for optimization of the SPME experimental parameters. The methodology was applied to three types of rice (rough, brown, and white rice), oat, wheat, and green and roasted coffee beans. Simultaneously, microbiological analysis of the samples (total aerobic microorganisms, moulds, and yeasts) was performed by conventional plate counts. A set of 54 volatile markers was selected among all the compounds detected by GC×GC–ToFMS. Principal Component Analysis (PCA) was applied in order to establish a relationship between potential volatile markers and the level of microbial contamination. Methylbenzene, 3-octanone, 2-nonanone, 2-methyl-3-pentanol, 1-octen-3-ol, and 2-hexanone were associated to samples with higher microbial contamination level, especially in rough rice. Moreover, oat exhibited a high GC peak area of 2-hydroxy-6-methylbenzaldehyde, a sexual and alarm pheromone for adult mites, which in the other matrices appeared as a trace component. The number of mites detected in oat grains was correlated to the GC peak area of the pheromone. The HS-SPME/GC×GC–ToFMS methodology can be regarded as the basis for the development of a rapid and versatile method that can be applied in industry to the simultaneous assessment the level of microbiological contamination and for detection of mites in cereals grains and coffee beans. PMID:23613710

Changes in the Structure and Function of Microbial Communities in Drinking Water Treatment Bioreactors upon Addition of Phosphorus▿ †

PubMed Central

Li, Xu; Upadhyaya, Giridhar; Yuen, Wangki; Brown, Jess; Morgenroth, Eberhard; Raskin, Lutgarde

2010-01-01

Phosphorus was added as a nutrient to bench-scale and pilot-scale biologically active carbon (BAC) reactors operated for perchlorate and nitrate removal from contaminated groundwater. The two bioreactors responded similarly to phosphorus addition in terms of microbial community function (i.e., reactor performance), while drastically different responses in microbial community structure were detected. Improvement in reactor performance with respect to perchlorate and nitrate removal started within a few days after phosphorus addition for both reactors. Microbial community structures were evaluated using molecular techniques targeting 16S rRNA genes. Clone library results showed that the relative abundance of perchlorate-reducing bacteria (PRB) Dechloromonas and Azospira in the bench-scale reactor increased from 15.2% and 0.6% to 54.2% and 11.7% after phosphorus addition, respectively. Real-time quantitative PCR (qPCR) experiments revealed that these increases started within a few days after phosphorus addition. In contrast, after phosphorus addition, the relative abundance of Dechloromonas in the pilot-scale reactor decreased from 7.1 to 0.6%, while Zoogloea increased from 17.9 to 52.0%. The results of this study demonstrated that similar operating conditions for bench-scale and pilot-scale reactors resulted in similar contaminant removal performances, despite dramatically different responses from microbial communities. These findings suggest that it is important to evaluate the microbial community compositions inside bioreactors used for drinking water treatment, as they determine the microbial composition in the effluent and impact downstream treatment requirements for drinking water production. This information could be particularly relevant to drinking water safety, if pathogens or disinfectant-resistant bacteria are detected in the bioreactors. PMID:20889793

Microbial community structure in a shallow hydrocarbon-contaminated aquifer associated with high electrical conductivity

NASA Astrophysics Data System (ADS)

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

2003-04-01

Little is known about the complex interactions between microbial communities and electrical properties in contaminated aquifers. In order to investigate possible connections between these parameters a study was undertaken to investigate the hypothesis that the degradation of hydrocarbons by resident microbial communities causes a local increase in organic acid concentrations, which in turn cause an increase in native mineral weathering and a concurrent increase in the bulk electrical conductivity of soil. Microbial community structure was analyzed using a 96-well most probable number (MPN) method and rDNA intergenic spacer region analysis (RISA). Microbial community structure was found to change in the presence of hydrocarbon contaminants and these changes were consistently observed in regions of high electrical conductivity. We infer from this relationship that geophysical methods for monitoring the subsurface are a promising new technology for monitoring changes in microbial community structure and simultaneous changes in geochemistry that are associated with hydrocarbon degradation.

Lytic to temperate switching of viral communities

NASA Astrophysics Data System (ADS)

Knowles, B.; Silveira, C. B.; Bailey, B. A.; Barott, K.; Cantu, V. A.; Cobián-Güemes, A. G.; Coutinho, F. H.; Dinsdale, E. A.; Felts, B.; Furby, K. A.; George, E. E.; Green, K. T.; Gregoracci, G. B.; Haas, A. F.; Haggerty, J. M.; Hester, E. R.; Hisakawa, N.; Kelly, L. W.; Lim, Y. W.; Little, M.; Luque, A.; McDole-Somera, T.; McNair, K.; de Oliveira, L. S.; Quistad, S. D.; Robinett, N. L.; Sala, E.; Salamon, P.; Sanchez, S. E.; Sandin, S.; Silva, G. G. Z.; Smith, J.; Sullivan, C.; Thompson, C.; Vermeij, M. J. A.; Youle, M.; Young, C.; Zgliczynski, B.; Brainard, R.; Edwards, R. A.; Nulton, J.; Thompson, F.; Rohwer, F.

2016-03-01

Microbial viruses can control host abundances via density-dependent lytic predator-prey dynamics. Less clear is how temperate viruses, which coexist and replicate with their host, influence microbial communities. Here we show that virus-like particles are relatively less abundant at high host densities. This suggests suppressed lysis where established models predict lytic dynamics are favoured. Meta-analysis of published viral and microbial densities showed that this trend was widespread in diverse ecosystems ranging from soil to freshwater to human lungs. Experimental manipulations showed viral densities more consistent with temperate than lytic life cycles at increasing microbial abundance. An analysis of 24 coral reef viromes showed a relative increase in the abundance of hallmark genes encoded by temperate viruses with increased microbial abundance. Based on these four lines of evidence, we propose the Piggyback-the-Winner model wherein temperate dynamics become increasingly important in ecosystems with high microbial densities; thus ‘more microbes, fewer viruses’.

Microbial inocula alter the ruminal environment and animal performance of post-weaned dairy calves

USDA-ARS?s Scientific Manuscript database

The purpose of the experiment was to determine if the composition of microbial inoculum affects the ruminal environment and performance of post-weaned dairy calves. Holstein bull calves (n=20) were housed individually with sand bedding and provided texturized calf starter (19.1±0.8% CP, 19.5±3.9% aN...

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

Analysis of microbial community composition in a lab-scale membrane distillation bioreactor.

PubMed

Zhang, Q; Shuwen, G; Zhang, J; Fane, A G; Kjelleberg, S; Rice, S A; McDougald, D

2015-04-01

Membrane distillation bioreactors (MDBR) have potential for industrial applications where wastewater is hot or waste heat is available, but the role of micro-organisms in MDBRs has never been determined, and thus was the purpose of this study. Microbial communities were characterized by bacterial and archaeal 16S and eukaryotic 18S rRNA gene tag-encoded pyrosequencing of DNA obtained from sludge. Taxonomy-independent analysis revealed that bacterial communities had a relatively low richness and diversity, and community composition strongly correlated with conductivity, total nitrogen and bound extracellular polymeric substances (EPS). Taxonomy-dependent analysis revealed that Rubrobacter and Caldalkalibacillus were abundant members of the bacterial community, but no archaea were detected. Eukaryotic communities had a relatively high richness and diversity, and both changes in community composition and abundance of the dominant genus, Candida, correlated with bound EPS. Thermophilic MDBR communities were comprised of a low diversity bacterial community and a highly diverse eukaryotic community with no archea detected. Communities exhibited low resilience to changes in operational parameters. Specifically, retenatate nutrient composition and concentration was strongly correlated with the dominant species. This study provides an understanding of microbial community diversity in an MDBR, which is fundamental to the optimization of reactor performance. © 2015 The Authors published by John Wiley & Sons Ltd on behalf of Society for Applied Microbiology.

Analysis of microbial community composition in a lab-scale membrane distillation bioreactor

PubMed Central

Zhang, Q; Shuwen, G; Zhang, J; Fane, AG; Kjelleberg, S; Rice, SA; McDougald, D

2015-01-01

Aims Membrane distillation bioreactors (MDBR) have potential for industrial applications where wastewater is hot or waste heat is available, but the role of micro-organisms in MDBRs has never been determined, and thus was the purpose of this study. Methods and Results Microbial communities were characterized by bacterial and archaeal 16S and eukaryotic 18S rRNA gene tag-encoded pyrosequencing of DNA obtained from sludge. Taxonomy-independent analysis revealed that bacterial communities had a relatively low richness and diversity, and community composition strongly correlated with conductivity, total nitrogen and bound extracellular polymeric substances (EPS). Taxonomy-dependent analysis revealed that Rubrobacter and Caldalkalibacillus were abundant members of the bacterial community, but no archaea were detected. Eukaryotic communities had a relatively high richness and diversity, and both changes in community composition and abundance of the dominant genus, Candida, correlated with bound EPS. Conclusions Thermophilic MDBR communities were comprised of a low diversity bacterial community and a highly diverse eukaryotic community with no archea detected. Communities exhibited low resilience to changes in operational parameters. Specifically, retenatate nutrient composition and concentration was strongly correlated with the dominant species. Significance and Impact of the Study This study provides an understanding of microbial community diversity in an MDBR, which is fundamental to the optimization of reactor performance. PMID:25604265

New concepts of microbial treatment processes for the nitrogen removal: effect of protein and amino acids degradation.

PubMed

González-Martínez, Alejandro; Calderón, Kadiya; González-López, Jesús

2016-05-01

High concentrations of proteins and amino acids can be found in wastewater and wastewater stream produced in anaerobic digesters, having shown that amino acids could persist over different managements for nitrogen removal affecting the nitrogen removal processes. Nitrogen removal is completely necessary because of their implications and the significant adverse environmental impact of ammonium such as eutrophication and toxicity to aquatic life on the receiving bodies. In the last decade, the treatment of effluents with high ammonium concentration through anammox-based bioprocesses has been enhanced because these biotechnologies are cheaper and more environmentally friendly than conventional technologies. However, it has been shown that the presence of important amounts of proteins and amino acids in the effluents seriously affects the microbial autotrophic consortia leading to important losses in terms of ammonium oxidation efficiency. Particularly the presence of sulfur amino acids such as methionine and cysteine has been reported to drastically decrease the autotrophic denitrification processes as well as affect the microbial community structure promoting the decline of ammonium oxidizing bacteria in favor of other phylotypes. In this context we discuss that new biotechnological processes that improve the degradation of protein and amino acids must be considered as a priority to increase the performance of the autotrophic denitrification biotechnologies.

Remediation of soil co-contaminated with petroleum and heavy metals by the integration of electrokinetics and biostimulation.

PubMed

Dong, Zhi-Yong; Huang, Wen-Hui; Xing, Ding-Feng; Zhang, Hong-Feng

2013-09-15

Successful remediation of soil co-contaminated with high levels of organics and heavy metals is a challenging task, because that metal pollutants in soil can partially or completely suppress normal heterotrophic microbial activity and thus hamper biodegradation of organics. In this study, the benefits of integrating electrokinetic (EK) remediation with biodegradation for decontaminating soil co-contaminated with crude oil and Pb were evaluated in laboratory-scale experiments lasting for 30 days. The treated soil contained 12,500 mg/kg of total petroleum hydrocarbons (TPH) and 450 mg/kg Pb. The amendments of EDTA and Tween 80, together with a regular refreshing of electrolyte showed the best performance to remediate this contaminated soil. An important function of EDTA-enhanced EK treatment was to eliminate heavy metal toxicity from the soil, thus activating microbial degradation of oil. Although Tween 80 reduced current, it could serve as a second substrate for enhancing microbial growth and biodegradation. It was found that oil biodegradation degree and microbial numbers increased toward the anode and cathode. Microbial metabolism was found to be beneficial to metal release from the soil matrix. Under the optimum conditions, the soil Pb and TPH removal percentages after 30 days of running reached 81.7% and 88.3%, respectively. After treatment, both the residual soil Pb and TPH concentrations met the requirement of the Chinese soil environmental quality standards. Copyright © 2013 Elsevier B.V. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2015-01-01

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

Key factors controlling microbial community response after a fire: importance of severity and recurrence

NASA Astrophysics Data System (ADS)

Lombao, Alba; Barreiro, Ana; Martín, Ángela; Díaz-Raviña, Montserrat

2015-04-01

Microorganisms play an important role in forest ecosystems, especially after fire when vegetation is destroyed and soil is bared. Fire severity and recurrence might be one of main factors controlling the microbial response after a wildfire but information about this topic is scarce. The aim of this study is to evaluate the influence of fire regimen (recurrence and severity) on soil microbial community structure by means of the analysis of phospholipid fatty acid (PLFA). The study was performed with unburned and burned samples collected from the top layer of a soil affected by a high severity fire (Laza, NW Spain) heated under laboratory conditions at different temperatures (50°C, 75°C, 100°C, 125°C, 150°C, 175°C, 200°C, 300°C) to simulate different fire intensities; the process was repeated after further soil recovery (1 month incubation) to simulate fire recurrence. The soil temperature was measured with thermocouples and used to calculate the degree-hours as estimation of the amount of heat supplied to the samples (fire severity). The PLFA analysis was used to estimate total biomass and the biomass of specific groups (bacteria, fungi, gram-positive bacteria and gram-negative bacteria) as well as microbial community structure (PLFA pattern) and PLFA data were analyzed by means of principal component analysis (PCA) in order to identify main factors determining microbial community structure. The results of PCA, performed with the whole PLFA data set, showed that first component explained 35% of variation and clearly allow us to differentiate unburned samples from the corresponding burned samples, while the second component, explaining 16% of variation, separated samples according the heating temperature. A marked impact of fire regimen on soil microorganisms was detected; the microbial community response varied depending on previous history of soil heating and the magnitude of changes in the PLFA pattern was related to the amount of heat supplied to the samples. Thus, wildfire was the main factor determining the microbial community structure followed, in less extent, by fire severity. The total biomass and the biomass of specifics microbial groups decreased notably as consequence of wildfire and minor changes were detected due to soil heating under laboratory conditions. The results clearly showed the usefulness of PLFA pattern combined with PCA to study the relationships between fire regimen (recurrence and severity) and associated direct and indirect changes in soil microorganisms. The data also indicated that degree-hours methodology rather than temperature is adequate for evaluating the impact of soil heating on microbial communities. Keywords: wildfire, heating temperature, degree-hours, PLFA pattern, microbial biomass Acknowledgements. This study was supported by the Ministerio Español de Economía y Competitividad (AGL2012-39688-C02-01). A Lombao is recipient of FPU grant from Ministerio Español de Educación.

Compartmentalized metabolic network reconstruction of microbial communities to determine the effect of agricultural intervention on soils

PubMed Central

Álvarez-Yela, Astrid Catalina; Gómez-Cano, Fabio; Zambrano, María Mercedes; Husserl, Johana; Danies, Giovanna; Restrepo, Silvia; González-Barrios, Andrés Fernando

2017-01-01

Soil microbial communities are responsible for a wide range of ecological processes and have an important economic impact in agriculture. Determining the metabolic processes performed by microbial communities is crucial for understanding and managing ecosystem properties. Metagenomic approaches allow the elucidation of the main metabolic processes that determine the performance of microbial communities under different environmental conditions and perturbations. Here we present the first compartmentalized metabolic reconstruction at a metagenomics scale of a microbial ecosystem. This systematic approach conceives a meta-organism without boundaries between individual organisms and allows the in silico evaluation of the effect of agricultural intervention on soils at a metagenomics level. To characterize the microbial ecosystems, topological properties, taxonomic and metabolic profiles, as well as a Flux Balance Analysis (FBA) were considered. Furthermore, topological and optimization algorithms were implemented to carry out the curation of the models, to ensure the continuity of the fluxes between the metabolic pathways, and to confirm the metabolite exchange between subcellular compartments. The proposed models provide specific information about ecosystems that are generally overlooked in non-compartmentalized or non-curated networks, like the influence of transport reactions in the metabolic processes, especially the important effect on mitochondrial processes, as well as provide more accurate results of the fluxes used to optimize the metabolic processes within the microbial community. PMID:28767679

Removal of volatile fatty acids and ammonia recovery from unstable anaerobic digesters with a microbial electrolysis cell.

PubMed

Cerrillo, Míriam; Viñas, Marc; Bonmatí, August

2016-11-01

Continuous assays with a microbial electrolysis cell (MEC) fed with digested pig slurry were performed to evaluate its stability and robustness to malfunction periods of an anaerobic digestion (AD) reactor and its feasibility as a strategy to recover ammonia. When performing punctual pulses of volatile fatty acids (VFA) in the anode compartment of the MEC, simulating a malfunction of the AD process, an increase in the current density was produced (up to 14 times, reaching values of 3500mAm(-2)) as a result of the added chemical oxygen demand (COD), especially when acetate was used. Furthermore, ammonium diffusion from the anode to the cathode compartment was enhanced and the removal efficiency achieved up to 60% during daily basis VFA pulses. An AD-MEC combined system has proven to be a robust and stable configuration to obtain a high quality effluent, with a lower organic and ammonium content. Copyright © 2016 Elsevier Ltd. All rights reserved.

Impact of volatile fatty acids on microbial electrolysis cell performance.

PubMed

Yang, Nan; Hafez, Hisham; Nakhla, George

2015-10-01

This study investigated the performance of microbial electrolysis cells (MECs) fed with three common fermentation products: acetate, butyrate, and propionate. Each substrate was fed to the reactor for three consecutive-batch cycles. The results showed high current densities for acetate, but low current densities for butyrate and propionate (maximum values were 6.0 ± 0.28, 2.5 ± 0.06, 1.6 ± 0.14 A/m(2), respectively). Acetate also showed a higher coulombic efficiency of 87 ± 5.7% compared to 72 ± 2.0 and 51 ± 6.4% for butyrate and propionate, respectively. This paper also revealed that acetate could be easily oxidized by anode respiring bacteria in MEC, while butyrate and propionate could not be oxidized to the same degree. The utilization rate of the substrates in MEC followed the order: acetate > butyrate > propionate. The ratio of suspended biomass to attached biomass was approximately 1:4 for all the three substrates. Copyright © 2015 Elsevier Ltd. All rights reserved.

Need for optimizing catalyst loading for achieving affordable microbial fuel cells.

PubMed

Singh, Inderjeet; Chandra, Amreesh

2013-08-01

Microbial fuel cell (MFC) technology is a promising technology for electricity production together with simultaneous water treatment. Catalysts play an important role in deciding the MFC performance. In most reports, effect of catalyst - both type and quantity is not optimized. In this paper, synthesis of nanorods of MnO2-catalyst particles for application in Pt-free MFCs is reported. The effect of catalyst loading i.e., weight ratio, with respect to conducting element and binder has been optimized by employing large number of combinations. Using simple theoretical model, it is shown that too high (or low) concentration of catalysts result in loss of MFC performance. The operation of MFC has been investigated using domestic wastewater as source of bio-waste for obtaining real world situation. Maximum power density of ∼61 mW/m(2) was obtained when weight ratio of catalyst and conducting species was 1:1. Suitable reasons are given to explain the outcomes. Copyright © 2013 Elsevier Ltd. All rights reserved.

A novel membrane bioreactor inoculated with symbiotic sludge bacteria and algae: Performance and microbial community analysis.

PubMed

Sun, Li; Tian, Yu; Zhang, Jun; Li, Lipin; Zhang, Jian; Li, Jianzheng

2018-03-01

This study combined sludge MBR technology with algae to establish an effective wastewater treatment and low membrane fouling system (ASB-MBR). Compared with control-MBR (C-MBR), the amelioration of microbial activity and the improvement of sludge properties and system environment were achieved after introducing algae resulting in high nutrients removal in the combined system. Further statistical analysis revealed that the symbiosis of algae and sludge displayed more remarkable impacts on nutrients removal than either of them. Additionally, membrane permeability was improved in ASB-MBR with respect to the decreased concentration, the changed of characteristics and the broken particular functional groups of extracellular polymeric substances (EPSs). Moreover, the algae inoculation reduced sludge diversity and shifted sludge community structure. Meantime, the stimulated bacteria selectively excite algal members that would benefit for the formation of algal-bacterial consortia. Consequently, the stimulated or inhibited of some species might be responsible for the performance of ASB-MBR. Copyright © 2017 Elsevier Ltd. All rights reserved.

The performance and microbial diversity of temperature-phased hyperthermophilic and thermophilic anaerobic digestion system fed with organic waste.

PubMed

Lee, M Y; Cheon, J H; Hidaka, T; Tsuno, H

2008-01-01

The objective of this study was to evaluate the performances and microbial diversities for development of the effective hyperthermophilic digester system that consists of a hyperthermophilic reactor and hyperthermophilic or thermophilic reactor in series. Lab-scale reactors were operated continuously fed with artificial kitchen garbage. The effect of temperature on the acidification step was firstly investigated. Results indicated that 20.8% of COD solubilization was achieved at 70 degrees C, with 12.6% at 80 degrees C. The average protein solubilization reached 31% at 80 degrees C. Methane conversion efficiency following the acidification was around 85% on average at 55 degrees C, but decreased with increasing temperature and methane gas was not produced over 73 degrees C. As well, bacteria affiliated with the methanogens dominated the population below 65 degrees C, while those affiliated with acidogens were predominant over 73 degrees C. These results indicated that the hyperthermophilic process has considerable benefits to treat wastewater or waste containing high concentration of protein.

Performance of anaerobic fluidized membrane bioreactors using effluents of microbial fuel cells treating domestic wastewater.

PubMed

Kim, Kyoung-Yeol; Yang, Wulin; Ye, Yaoli; LaBarge, Nicole; Logan, Bruce E

2016-05-01

Anaerobic fluidized membrane bioreactors (AFMBRs) have been mainly developed as a post-treatment process to produce high quality effluent with very low energy consumption. The performance of an AFMBR was examined using the effluent from a microbial fuel cell (MFC) treating domestic wastewater, as a function of AFMBR hydraulic retention times (HRTs) and organic matter loading rates. The MFC-AFMBR achieved 89 ± 3% removal of the chemical oxygen demand (COD), with an effluent of 36 ± 6 mg-COD/L over 112 days operation. The AFMBR had very stable operation, with no significant changes in COD removal efficiencies, for HRTs ranging from 1.2 to 3.8h, although the effluent COD concentration increased with organic loading. Transmembrane pressure (TMP) was low, and could be maintained below 0.12 bar through solids removal. This study proved that the AFMBR could be operated with a short HRT but a low COD loading rate was required to achieve low effluent COD. Copyright © 2016 Elsevier Ltd. All rights reserved.

Separators used in microbial electrochemical technologies: Current status and future prospects.

PubMed

Daud, Siti Mariam; Kim, Byung Hong; Ghasemi, Mostafa; Daud, Wan Ramli Wan

2015-11-01

Microbial electrochemical technologies (METs) are emerging green processes producing useful products from renewable sources without causing environmental pollution and treating wastes. The separator, an important part of METs that greatly affects the latter's performance, is commonly made of Nafion proton exchange membrane (PEM). However, many problems have been identified associated with the Nafion PEM such as high cost of membrane, significant oxygen and substrate crossovers, and transport of cations other than protons protons and biofouling. A variety of materials have been offered as alternative separators such as ion-exchange membranes, salt bridges, glass fibers, composite membranes and porous materials. It has been claimed that low cost porous materials perform better than PEM. These include J-cloth, nylon filter, glass fiber mat, non-woven cloth, earthen pot and ceramics that enable non-ion selective charge transfer. This paper provides an up-to-date review on porous separators and plots directions for future studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

PhyloChip microarray analysis reveals altered gastrointestinal microbial communities in a rat model of colonic hypersensitivity

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

Nelson, T.A.; Holmes, S.; Alekseyenko, A.V.

Irritable bowel syndrome (IBS) is a chronic, episodic gastrointestinal disorder that is prevalent in a significant fraction of western human populations; and changes in the microbiota of the large bowel have been implicated in the pathology of the disease. Using a novel comprehensive, high-density DNA microarray (PhyloChip) we performed a phylogenetic analysis of the microbial community of the large bowel in a rat model in which intracolonic acetic acid in neonates was used to induce long lasting colonic hypersensitivity and decreased stool water content and frequency, representing the equivalent of human constipation-predominant IBS. Our results revealed a significantly increased compositionalmore » difference in the microbial communities in rats with neonatal irritation as compared with controls. Even more striking was the dramatic change in the ratio of Firmicutes relative to Bacteroidetes, where neonatally irritated rats were enriched more with Bacteroidetes and also contained a different composition of species within this phylum. Our study also revealed differences at the level of bacterial families and species. The PhyloChip is a useful and convenient method to study enteric microflora. Further, this rat model system may be a useful experimental platform to study the causes and consequences of changes in microbial community composition associated with IBS.« less

Temporal variation of nitrogen balance within constructed wetlands treating slightly polluted water using a stable nitrogen isotope experiment.

PubMed

Zhang, Wanguang; Lei, Qiongye; Li, Zhengkui; Han, Huayang

2016-02-01

Slightly polluted water has become one of the main sources of nitrogen contaminants in recent years, for which constructed wetlands (CW) is a typical and efficient treatment. However, the knowledge about contribution of individual nitrogen removal pathways and nitrogen balance in constructed wetlands is still limited. In this study, a stable-isotope-addition experiment was performed in laboratory-scale constructed wetlands treating slightly polluted water to determine quantitative contribution of different pathways and temporal variation of nitrogen balance using Na(15)NO3 as tracer. Microbial conversion and substrate retention were found to be the dominant pathways in nitrogen removal contributing 24.4-79.9 and 8.9-70.7 %, respectively, while plant contributed only 4.6-11.1 % through direct assimilation but promoted the efficiency of other pathways. In addition, microbial conversion became the major way to remove N whereas nitrogen retained in substrate at first was gradually released to be utilized by microbes and plants over time. The findings indicated that N2 emission representing microbial conversion was not only the major but also permanent nitrogen removal process, thus keeping a high efficiency of microbial conversion is important for stable and efficient nitrogen removal in constructed wetlands.

Rumen Bacterial Diversity of 80 to 110-Day-Old Goats Using 16S rRNA Sequencing

PubMed Central

Han, Xufeng; Yang, Yuxin; Yan, Hailong; Wang, Xiaolong; Qu, Lei; Chen, Yulin

2015-01-01

The ability of rumen microorganisms to use fibrous plant matter plays an important role in ruminant animals; however, little information about rumen colonization by microbial populations after weaning has been reported. In this study, high-throughput sequencing was used to investigate the establishment of this microbial population in 80 to 110-day-old goats. Illumina sequencing of goat rumen samples yielded 101,356,610 nucleotides that were assembled into 256,868 reads with an average read length of 394 nucleotides. Taxonomic analysis of metagenomic reads indicated that the predominant phyla were distinct at different growth stages. The phyla Firmicutes and Synergistetes were predominant in samples taken from 80 to 100-day-old goats, but Bacteroidetes and Firmicutes became the most abundant phyla in samples from 110-day-old animals. There was a remarkable variation in the microbial populations with age; Firmicutes and Synergistetes decreased after weaning, but Bacteroidetes and Proteobacteria increased from 80 to 110 day of age. These findings suggested that colonization of the rumen by microorganisms is related to their function in the rumen digestive system. These results give a better understanding of the role of rumen microbes and the establishment of the microbial population, which help to maintain the host’s health and improve animal performance. PMID:25700157

Virophage control of antarctic algal host–virus dynamics

PubMed Central

Yau, Sheree; Lauro, Federico M.; DeMaere, Matthew Z.; Brown, Mark V.; Thomas, Torsten; Raftery, Mark J.; Andrews-Pfannkoch, Cynthia; Lewis, Matthew; Hoffman, Jeffrey M.; Gibson, John A.; Cavicchioli, Ricardo

2011-01-01

Viruses are abundant ubiquitous members of microbial communities and in the marine environment affect population structure and nutrient cycling by infecting and lysing primary producers. Antarctic lakes are microbially dominated ecosystems supporting truncated food webs in which viruses exert a major influence on the microbial loop. Here we report the discovery of a virophage (relative of the recently described Sputnik virophage) that preys on phycodnaviruses that infect prasinophytes (phototrophic algae). By performing metaproteogenomic analysis on samples from Organic Lake, a hypersaline meromictic lake in Antarctica, complete virophage and near-complete phycodnavirus genomes were obtained. By introducing the virophage as an additional predator of a predator–prey dynamic model we determined that the virophage stimulates secondary production through the microbial loop by reducing overall mortality of the host and increasing the frequency of blooms during polar summer light periods. Virophages remained abundant in the lake 2 y later and were represented by populations with a high level of major capsid protein sequence variation (25–100% identity). Virophage signatures were also found in neighboring Ace Lake (in abundance) and in two tropical lakes (hypersaline and fresh), an estuary, and an ocean upwelling site. These findings indicate that virophages regulate host–virus interactions, influence overall carbon flux in Organic Lake, and play previously unrecognized roles in diverse aquatic ecosystems. PMID:21444812

Virophage control of antarctic algal host-virus dynamics.

PubMed

Yau, Sheree; Lauro, Federico M; DeMaere, Matthew Z; Brown, Mark V; Thomas, Torsten; Raftery, Mark J; Andrews-Pfannkoch, Cynthia; Lewis, Matthew; Hoffman, Jeffrey M; Gibson, John A; Cavicchioli, Ricardo

2011-04-12

Viruses are abundant ubiquitous members of microbial communities and in the marine environment affect population structure and nutrient cycling by infecting and lysing primary producers. Antarctic lakes are microbially dominated ecosystems supporting truncated food webs in which viruses exert a major influence on the microbial loop. Here we report the discovery of a virophage (relative of the recently described Sputnik virophage) that preys on phycodnaviruses that infect prasinophytes (phototrophic algae). By performing metaproteogenomic analysis on samples from Organic Lake, a hypersaline meromictic lake in Antarctica, complete virophage and near-complete phycodnavirus genomes were obtained. By introducing the virophage as an additional predator of a predator-prey dynamic model we determined that the virophage stimulates secondary production through the microbial loop by reducing overall mortality of the host and increasing the frequency of blooms during polar summer light periods. Virophages remained abundant in the lake 2 y later and were represented by populations with a high level of major capsid protein sequence variation (25-100% identity). Virophage signatures were also found in neighboring Ace Lake (in abundance) and in two tropical lakes (hypersaline and fresh), an estuary, and an ocean upwelling site. These findings indicate that virophages regulate host-virus interactions, influence overall carbon flux in Organic Lake, and play previously unrecognized roles in diverse aquatic ecosystems.

Degradation of seed mucilage by soil microflora promotes early seedling growth of a desert sand dune plant.

PubMed

Yang, Xuejun; Baskin, Carol C; Baskin, Jerry M; Zhang, Wenhao; Huang, Zhenying

2012-05-01

In contrast to the extensive understanding of seed mucilage biosynthesis, much less is known about how mucilage is biodegraded and what role it plays in the soil where seeds germinate. We studied seed mucilage biodegradation by a natural microbial community. High-performance anion-exchange chromatography (HPAEC) was used to determine monosaccharide composition in achene mucilage of Artemisia sphaerocephala. Mucilage degradation by the soil microbial community from natural habitats was examined by monosaccharide utilization tests using Biolog plates, chemical assays and phospholipid fatty acid (PLFA) analysis. Glucose (29.4%), mannose (20.3%) and arabinose (19.5%) were found to be the main components of achene mucilage. The mucilage was biodegraded to CO(2) and soluble sugars, and an increase in soil microbial biomass was observed during biodegradation. Fluorescence microscopy showed the presence of mucilage (or its derivatives) in seedling tissues after growth with fluorescein isothiocyanate (FITC)-labelled mucilage. The biodegradation also promoted early seedling growth in barren sand dunes, which was associated with a large soil microbial community that supplies substances promoting seedling establishment. We conclude that biodegradation of seed mucilage can play an ecologically important role in the life cycles of plants especially in harsh desert environments to which A. sphaerocephala is well-adapted. © 2011 Blackwell Publishing Ltd.

Microbial community analysis in a combined anaerobic and aerobic digestion system for treatment of cellulosic ethanol production wastewater.

PubMed

Shan, Lili; Yu, Yanling; Zhu, Zebing; Zhao, Wei; Wang, Haiman; Ambuchi, John J; Feng, Yujie

2015-11-01

This study investigated the microbial diversity established in a combined system composed of a continuous stirred tank reactor (CSTR), expanded granular sludge bed (EGSB) reactor, and sequencing batch reactor (SBR) for treatment of cellulosic ethanol production wastewater. Excellent wastewater treatment performance was obtained in the combined system, which showed a high chemical oxygen demand removal efficiency of 95.8% and completely eliminated most complex organics revealed by gas chromatography-mass spectrometry (GC-MS). Denaturing gradient gel electrophoresis (DGGE) analysis revealed differences in the microbial community structures of the three reactors. Further identification of the microbial populations suggested that the presence of Lactobacillus and Prevotella in CSTR played an active role in the production of volatile fatty acids (VFAs). The most diverse microorganisms with analogous distribution patterns of different layers were observed in the EGSB reactor, and bacteria affiliated with Firmicutes, Synergistetes, and Thermotogae were associated with production of acetate and carbon dioxide/hydrogen, while all acetoclastic methanogens identified belonged to Methanosaetaceae. Overall, microorganisms associated with the ability to degrade cellulose, hemicellulose, and other biomass-derived organic carbons were observed in the combined system. The results presented herein will facilitate the development of an improved cellulosic ethanol production wastewater treatment system.

Optimization of microbial detoxification for an aquatic mercury-contaminated environment.

PubMed

Figueiredo, Neusa L; Canário, João; Serralheiro, Maria Luísa; Carvalho, Cristina

2017-01-01

Mercury (Hg) reduction performed by microorganisms is well recognized as a biological means for remediation of contaminated environment. Recently, studies demonstrated that Hg-resistant microorganisms of Tagus Estuary are involved in metal reduction processes. In the present study, aerobic microbial community isolated from a highly Hg-contaminated area of Tagus Estuary was used to determine the optimization of the reduction process in conditions such as the contaminated ecosystem. Factorial design methodology was employed to examine the influence of glucose, sulfate, iron, and chloride on Hg reduction. In the presence of several concentrations of these elements, microbial community reduced Hg in a range of 37-61% of the initial 0.1 mg/ml Hg 2+ levels. The response prediction through central composite design showed that the increase of sulfate concentration led to an optimal response in Hg reduction by microbial community, while the rise in chloride levels markedly decreased metal reduction. Iron may exert antagonistic effects depending upon the media composition. These results are useful in understanding the persistence of Hg contamination in Tagus Estuary after inactivation of critical industrial units, as well as data might also be beneficial for development of new bioremediation strategies either in Tagus Estuary and/or in other Hg-contaminated aquatic environments.

Microbial community assessment of mealworm larvae (Tenebrio molitor) and grasshoppers (Locusta migratoria migratorioides) sold for human consumption.

PubMed

Stoops, J; Crauwels, S; Waud, M; Claes, J; Lievens, B; Van Campenhout, L

2016-02-01

In Western countries, the popularity of edible insects as an alternative animal protein source is increasing. Nevertheless, there is a lack of profound insight into the microbial safety and shelf life of living insects sold for human consumption. The purpose of this study was to characterise the microflora of fresh edible mealworm larvae and grasshoppers in a quantitative and qualitative way. Therefore, culture-dependent analyses (the total viable aerobic count, Enterobacteriaceae, lactic acid bacteria, yeasts and moulds, and bacterial endospores) and next-generation sequencing (454amplicon pyrosequencing) were performed. High microbial counts were obtained for both insect species. Different insect batches resulted in quite similar microbial numbers, except for bacterial endospores. However, the bacterial community composition differed between both insect species. The most abundant operational taxonomic unit in mealworm larvae was Propionibacterium. Also members of the genera Haemophilus, Staphylococcus and Clostridium were found. Grasshoppers were mainly dominated by Weissella, Lactococcus and Yersinia/Rahnella. Overall, a variety of potential spoilage bacteria and food pathogens were characterised. The results of this study suggest that a processing step with a microbiocidal effect is required to avoid or minimize risks involved with the consumption of edible insects. Copyright © 2015 Elsevier Ltd. All rights reserved.

Gene finding in metatranscriptomic sequences.

PubMed

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

2014-01-01

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

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

Evaluation of anti-microbial activities of ZnO, citric acid and a mixture of both against Propionibacterium acnes.

PubMed

Bae, J Y; Park, S N

2016-12-01

In this study, anti-microbial activities of ZnO of three different particle sizes of citric acid (CA) and of mixtures of ZnO and CA were confirmed against Propionibacterium acnes. ZnO with the smallest particle size showed relatively high anti-microbial activity by disc diffusion assay and broth macrodilution assay. The mixtures of ZnO and CA also showed relatively high anti-microbial activity when the particle size of ZnO was the smallest. Furthermore, anti-microbial activities of ZnO, CA and the mixtures of ZnO and CA were compared through the checkerboard assay. The results indicated that a 1 : 1 ratio of ZnO and CA resulted in the highest anti-microbial activity. The substances were confirmed to have synergic anti-microbial effects. With the time-kill curve assay, the mixture of ZnO-containing CA reduced the surviving microbial content the most after 24 h. The results of our study suggest that ZnO may not only be an anti-microbial ingredient for the prevention of and treatment of acne. The results of our study suggest that ZnO may be an anti-microbial ingredient for the prevention of and treatment of acne when mixed with CA. © 2016 Society of Cosmetic Scientists and the Société Française de Cosmétologie.

Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics

PubMed Central

Ruvindy, Rendy; White III, Richard Allen; Neilan, Brett Anthony; Burns, Brendan Paul

2016-01-01

Modern microbial mats are potential analogues of some of Earth's earliest ecosystems. Excellent examples can be found in Shark Bay, Australia, with mats of various morphologies. To further our understanding of the functional genetic potential of these complex microbial ecosystems, we conducted for the first time shotgun metagenomic analyses. We assembled metagenomic next-generation sequencing data to classify the taxonomic and metabolic potential across diverse morphologies of marine mats in Shark Bay. The microbial community across taxonomic classifications using protein-coding and small subunit rRNA genes directly extracted from the metagenomes suggests that three phyla Proteobacteria, Cyanobacteria and Bacteriodetes dominate all marine mats. However, the microbial community structure between Shark Bay and Highbourne Cay (Bahamas) marine systems appears to be distinct from each other. The metabolic potential (based on SEED subsystem classifications) of the Shark Bay and Highbourne Cay microbial communities were also distinct. Shark Bay metagenomes have a metabolic pathway profile consisting of both heterotrophic and photosynthetic pathways, whereas Highbourne Cay appears to be dominated almost exclusively by photosynthetic pathways. Alternative non-rubisco-based carbon metabolism including reductive TCA cycle and 3-hydroxypropionate/4-hydroxybutyrate pathways is highly represented in Shark Bay metagenomes while not represented in Highbourne Cay microbial mats or any other mat forming ecosystems investigated to date. Potentially novel aspects of nitrogen cycling were also observed, as well as putative heavy metal cycling (arsenic, mercury, copper and cadmium). Finally, archaea are highly represented in Shark Bay and may have critical roles in overall ecosystem function in these modern microbial mats. PMID:26023869

Novel microbial fuel cell design to operate with different wastewaters simultaneously.

PubMed

Mathuriya, Abhilasha Singh

2016-04-01

A novel single cathode chamber and multiple anode chamber microbial fuel cell design (MAC-MFC) was developed by incorporating multiple anode chambers into a single unit and its performance was checked. During 60 days of operation, performance of MAC-MFC was assessed and compared with standard single anode/cathode chamber microbial fuel cell (SC-MFC). The tests showed that MAC-MFC generated stable and higher power outputs compared with SC-MFC and each anode chamber contributed efficiently. Further, MAC-MFCs were incorporated with different wastewaters in different anode chambers and their behavior in MFC performance was observed. MAC-MFC efficiently treated multiple wastewaters simultaneously at low cost and small space, which claims its candidature for future possible scale-up applications. Copyright © 2015. Published by Elsevier B.V.

Studying Microbial Mat Functioning Amidst "Unexpected Diversity": Methodological Approaches and Initial Results from Metatranscriptomes of Mats Over Diel cycles, iTags from Long Term Manipulations, and Biogeochemical Cycling in Simplified Microbial Mats Constructed from Cultures

NASA Astrophysics Data System (ADS)

Bebout, B.; Bebout, L. E.; Detweiler, A. M.; Everroad, R. C.; Lee, J.; Pett-Ridge, J.; Weber, P. K.

2014-12-01

Microbial mats are famously amongst the most diverse microbial ecosystems on Earth, inhabiting some of the most inclement environments known, including hypersaline, dry, hot, cold, nutrient poor, and high UV environments. The high microbial diversity of microbial mats makes studies of microbial ecology notably difficult. To address this challenge, we have been using a combination of metagenomics, metatranscriptomics, iTags and culture-based simplified microbial mats to study biogeochemical cycling (H2 production, N2 fixation, and fermentation) in microbial mats collected from Elkhorn Slough, Monterey Bay, California. Metatranscriptomes of microbial mats incubated over a diel cycle have revealed that a number of gene systems activate only during the day in Cyanobacteria, while the remaining appear to be constitutive. The dominant cyanobacterium in the mat (Microcoleus chthonoplastes) expresses several pathways for nitrogen scavenging undocumented in cultured strains, as well as the expression of two starch storage and utilization cycles. Community composition shifts in response to long term manipulations of mats were assessed using iTags. Changes in community diversity were observed as hydrogen fluxes increased in response to a lowering of sulfate concentrations. To produce simplified microbial mats, we have isolated members of 13 of the 15 top taxa from our iTag libraries into culture. Simplified microbial mats and simple co-cultures and consortia constructed from these isolates reproduce many of the natural patterns of biogeochemical cycling in the parent natural microbial mats, but against a background of far lower overall diversity, simplifying studies of changes in gene expression (over the short term), interactions between community members, and community composition changes (over the longer term), in response to environmental forcing.

Bioreactor performance and functional gene analysis of microbial community in a limited-oxygen fed bioreactor for co-reduction of sulfate and nitrate with high organic input.

PubMed

Xu, Xi-jun; Chen, Chuan; Wang, Ai-jie; Yu, Hao; Zhou, Xu; Guo, Hong-liang; Yuan, Ye; Lee, Duu-jong; Zhou, Jizhong; Ren, Nan-qi

2014-08-15

Limited-oxygen mediated synergistic relationships between sulfate-reducing bacteria (SRB), nitrate-reducing bacteria (NRB) and sulfide-oxidizing bacteria (SOB, including nitrate-reducing, sulfide-oxidizing bacteria NR-SOB) were predicted to simultaneously remove contaminants of nitrate, sulfate and high COD, and eliminate sulfide generation. A lab-scale experiment was conducted to examine the impact of limited oxygen on these oxy-anions degradation, sulfide oxidation and associated microbial functional responses. In all scenarios tested, the reduction of both nitrate and sulfate was almost complete. When limited-oxygen was fed into bioreactors, S(0) formation was significantly improved up to ∼ 70%. GeoChip 4.0, a functional gene microarray, was used to determine the microbial gene diversity and functional potential for nitrate and sulfate reduction, and sulfide oxidation. The diversity of the microbial community in bioreactors was increased with the feeding of limited oxygen. Whereas the intensities of the functional genes involved in sulfate reduction did not show a significant difference, the abundance of the detected denitrification genes decreased in limited oxygen samples. More importantly, sulfide-oxidizing bacteria may alter their populations/genes in response to limited oxygen potentially to function more effectively in sulfide oxidation, especially to elemental sulfur. The genes fccA/fccB from nitrate-reducing, sulfide-oxidizing bacteria (NR-SOB), such as Paracoccus denitrificans, Thiobacillus denitrificans, Beggiatoa sp., Thiomicrospira sp., and Thioalkalivibrio sp., were more abundant under limited-oxygen condition. Copyright © 2014 Elsevier B.V. All rights reserved.

Microbial models with data-driven parameters predict stronger soil carbon responses to climate change.

PubMed

Hararuk, Oleksandra; Smith, Matthew J; Luo, Yiqi

2015-06-01

Long-term carbon (C) cycle feedbacks to climate depend on the future dynamics of soil organic carbon (SOC). Current models show low predictive accuracy at simulating contemporary SOC pools, which can be improved through parameter estimation. However, major uncertainty remains in global soil responses to climate change, particularly uncertainty in how the activity of soil microbial communities will respond. To date, the role of microbes in SOC dynamics has been implicitly described by decay rate constants in most conventional global carbon cycle models. Explicitly including microbial biomass dynamics into C cycle model formulations has shown potential to improve model predictive performance when assessed against global SOC databases. This study aimed to data-constrained parameters of two soil microbial models, evaluate the improvements in performance of those calibrated models in predicting contemporary carbon stocks, and compare the SOC responses to climate change and their uncertainties between microbial and conventional models. Microbial models with calibrated parameters explained 51% of variability in the observed total SOC, whereas a calibrated conventional model explained 41%. The microbial models, when forced with climate and soil carbon input predictions from the 5th Coupled Model Intercomparison Project (CMIP5), produced stronger soil C responses to 95 years of climate change than any of the 11 CMIP5 models. The calibrated microbial models predicted between 8% (2-pool model) and 11% (4-pool model) soil C losses compared with CMIP5 model projections which ranged from a 7% loss to a 22.6% gain. Lastly, we observed unrealistic oscillatory SOC dynamics in the 2-pool microbial model. The 4-pool model also produced oscillations, but they were less prominent and could be avoided, depending on the parameter values. © 2014 John Wiley & Sons Ltd.

Three-dimensional graphene nanosheets as cathode catalysts in standard and supercapacitive microbial fuel cell

NASA Astrophysics Data System (ADS)

Santoro, Carlo; Kodali, Mounika; Kabir, Sadia; Soavi, Francesca; Serov, Alexey; Atanassov, Plamen

2017-07-01

Three-dimensional graphene nanosheets (3D-GNS) were used as cathode catalysts for microbial fuel cells (MFCs) operating in neutral conditions. 3D-GNS catalysts showed high performance towards oxygen electroreduction in neutral media with high current densities and low hydrogen peroxide generation compared to activated carbon (AC). 3D-GNS was incorporated into air-breathing cathodes based on AC with three different loadings (2, 6 and 10 mgcm-2). Performances in MFCs showed that 3D-GNS had the highest performances with power densities of 2.059 ± 0.003 Wm-2, 1.855 ± 0.007 Wm-2 and 1.503 ± 0.005 Wm-2 for loading of 10, 6 and 2 mgcm-2 respectively. Plain AC had the lowest performances (1.017 ± 0.009 Wm-2). The different cathodes were also investigated in supercapacitive MFCs (SC-MFCs). The addition of 3D-GNS decreased the ohmic losses by 14-25%. The decrease in ohmic losses allowed the SC-MFC with 3D-GNS (loading 10 mgcm-2) to have the maximum power (Pmax) of 5.746 ± 0.186 Wm-2. At 5 mA, the SC-MFC featured an "apparent" capacitive response that increased from 0.027 ± 0.007 F with AC to 0.213 ± 0.026 F with 3D-GNS (loading 2 mgcm-2) and further to 1.817 ± 0.040 F with 3D-GNS (loading 10 mgcm-2).

Reactor performance and microbial community of an EGSB reactor operated at 20 and 15 degrees C.

PubMed

Xing, W; Zuo, J-E; Dai, N; Cheng, J; Li, J

2009-09-01

To investigate the effects of low temperatures on the performance and microbial community of anaerobic wastewater treatment. An expanded granular sludge bed (EGSB) reactor was employed to treat synthetic brewery wastewater at 20 and 15 degrees C. Reactor performance was represented by chemical oxygen demand (COD) removal efficiency, while the microbial community was analysed using denaturing gradient gel electrophoresis (DGGE) and clone technology. When the hydraulic retention time (HRT) was maintained at 18 h, COD removal efficiencies above 85% were obtained at both 20 and 15 degrees C, with influent COD concentrations up to 7300 and 4100 mg l(-1), respectively. At 15 degrees C, the COD removal efficiency was more easily manipulated by increasing the influent COD concentration. DGGE and clone results for both temperatures revealed that Methanosaeta and Methanobacterium were two dominant methanogens, and that the majority of the eubacterial clones were represented by Firmicutes. When the temperature decreased from 20 to 15 degrees C, both archaeal and eubacterial communities had higher diversity, and the proportion of Methanosaeta (acetate-utilizing methanogens) decreased markedly from 60.0% to 49.3%, together with an increase in proportions of hydrogen-utilizing methanogens (especially Methanospirillum). The feasibility of psychrophilic anaerobic treatment of low and medium strength organic wastewaters was demonstrated, although lower temperature could significantly affect both reactor performance and the anaerobic microbial community. The findings enrich the theory involving the microbial community and the application of anaerobic treatment in a psychrophilic environment.

Illumina MiSeq sequencing reveals microbial community in HA process for dyeing wastewater treatment fed with different co-substrates.

PubMed

Xie, Xuehui; Liu, Na; Ping, Jing; Zhang, Qingyun; Zheng, Xiulin; Liu, Jianshe

2018-06-01

In present study, a hydrolysis acidification (HA) reactor was used for simulated dyeing wastewater treatment. Co-substrates included starch, glucose, sucrose, yeast extract (YE) and peptone were fed sequentially into the HA reactor to enhance the HA process effects. The performance of the HA reactor and the microbial community structure in HA process were investigated under different co-substrates conditions. Results showed that different co-substrates had different influences on the performance of HA reactor. The highest decolorization (50.64%) and COD removal rate (60.73%) of the HA reactor were obtained when sucrose was as the co-substrate. And it found that carbon co-substrates starch, glucose and sucrose exhibited better decolorization and higher COD removal efficiency of the HA reactor than the nitrogen co-substrates YE and peptone. Microbial community structure in the HA process was analyzed by Illumina MiSeq sequencing. Results revealed different co-substrates had different influences on the community structure and microbial diversity in HA process. It was considered that sucrose could enrich the species such as Raoultella, Desulfovibrio, Tolumonas, Clostridium, which might be capable of degrading the dyes. Sucrose was considered to be the best co-substrate of enhancing the HA reactor's performance in this study. This work would provide deep insight into the influence of many different co-substrates on HA reactor performance and microbial communities in HA process. Copyright © 2018 Elsevier Ltd. All rights reserved.

Recent advances in microbial production of mannitol: utilization of low-cost substrates, strain development and regulation strategies.

PubMed

Zhang, Min; Gu, Lei; Cheng, Chao; Ma, Jiangfeng; Xin, Fengxue; Liu, Junli; Wu, Hao; Jiang, Min

2018-02-26

Mannitol has been widely used in fine chemicals, pharmaceutical industries, as well as functional foods due to its excellent characteristics, such as antioxidant protecting, regulation of osmotic pressure and non-metabolizable feature. Mannitol can be naturally produced by microorganisms. Compared with chemical manufacturing, microbial production of mannitol provides high yield and convenience in products separation; however the fermentative process has not been widely adopted yet. A major obstacle to microbial production of mannitol under industrial-scale lies in the low economical efficiency, owing to the high cost of fermentation medium, leakage of fructose, low mannitol productivity. In this review, recent advances in improving the economical efficiency of microbial production of mannitol were reviewed, including utilization of low-cost substrates, strain development for high mannitol yield and process regulation strategies for high productivity.

Microbial utilization of litter carbon under the effect of extreme weather events

NASA Astrophysics Data System (ADS)

Heinrich, Steffen; Kuzyakov, Yakov; Glaser, Bruno

2015-04-01

Climate change is expected to not only lead to an increase of average annual temperature but also to increase the frequency of extreme meteorological events. For example, extreme summer-droughts followed by heavy rainfall events are likely to increase. This may change SOM quality, composition, microbial community functioning and thus C turnover in temperate forest ecosystems. Therefore, we performed a tracer experiment in the "Fichtelgebirge" (Northern Bavaria) to verify the influence of strong drying followed by intensive rewetting on the microbial community structure and decomposition of litter-derived 13C by individual microbial groups. In 2010, sheltered plots with artificially simulated drought, those with additional irrigation and control sites under natural conditions were established at a Norway spruce forest. At each plot, we added 13C enriched spruce litter to simulate annual litter fall. Thereafter, we assessed the effect of extreme weather events on microbial community structure by phospholipid fatty acid (PLFA) analysis. In addition, we analyzed the 13C incorporation into bulk soil, microbial biomass and PLFA of the organic horizon and the mineral soil up to 10 cm. Additionally respired CO2 was quantified by closed chambers. Drought reduced the microbial biomass only in the organic horizon, while in the mineral soil the microbial abundance did not decrease compared to the control and irrigated plots. The decrease in microbial biomass in the organic horizon of the drought plots resulted also in a strongly reduced incorporation of litter derived C: Incorporation of litter 13C was a magnitude of three lower in the drought plots compared to the control and irrigation plots. Furthermore, after the drought period of 90 days the proportion of 13C in CO2 from soil respiration was reduced by about 95% on the drought plots compared to the control and irrigated plots. This is in agreement with the reduced degradation of litter derived C and thus a reduced C turnover under dry conditions. PLFA analysis showed high amounts of gram positive and gram negative bacterial as well as fungal fatty acids, whereas actinomycets and protozoa represented minor groups. An increased ratio of the cy-PLFA to (16:1w7c+18:1w7c) on the drought plots of the organic layer suggest that bacteria suffered from water stress. In comparison to other microbial groups only the fungi were not depleted by drought showing the advantage of hyphae in resisting unfavourable environmental conditions compared to the single cells organisms. Both, in the organic horizon and the mineral soil, most 13C was incorporated into the gram negative bacteria and into fungi, whereas actinomycetes and protozoa showed the lowest incorporation. This tendency is even enhanced for the drought plots. Gram positive bacteria showed a low incorporation of litter derived C despite their high abundance, which reflects their general preference for old SOM-derived C sources. Combining 13C-labeling and 13C partitioning in microbial and SOM pools provides a powerful method combination to understand the mechanisms of SOM turnover especially those which are microbially controlled. This will fundamentally improve our understanding of C pool dynamics under changing environmental conditions like extreme whether events.

The Environment and the Microbial Ecology of Human Skin

PubMed Central

McBride, Mollie E.; Duncan, W. Christopher; Knox, J. M.

1977-01-01

Microbial flora of the skin of three human population groups representing different natural environments was examined quantitatively and qualitatively to determine whether environmental differences in temperature and humidity can influence the microbial flora of normal skin. Five anatomical skin sites - hands, back, axillae, groin, and feet - were sampled from 10 subjects working in a high-humidity, high-temperature environment, 10 subjects from a low-temperature, high-humidity environment, and 10 subjects working in a moderate-temperature and low-humidity environment. Bacterial populations were significantly larger from the back, axillae, and feet in individuals from the high-temperature and high-humidity environment as compared to the moderate-temperature, low-humidity environment. High humidity and low temperature had no significant effect on total populations, but this group showed a higher frequency of isolation of fungi, and gram-negative bacteria from the back and feet. Although there was an indication that increase in the environmental humidity could result in an increased frequency of isolation of gram-negative bacteria, there was no evidence that an increase in either temperature or humidity altered the relative proportions of gram-negative bacteria in the predominantly gram-positive microbial flora found on normal skin. It was concluded that, although climatic changes may cause fluctation in microbial populations from certain sites, they are not a major influence on the ecology of the microbial flora of normal skin in the natural environment. The variables introduced by studying individuals in their natural environment and the influence of these on the results are discussed. PMID:16345214

Microbial communities in natural rubber coagula during maturation: impacts on technological properties of dry natural rubber.

PubMed

Salomez, M; Subileau, M; Vallaeys, T; Santoni, S; Bonfils, F; Sainte-Beuve, J; Intapun, J; Granet, F; Vaysse, L; Dubreucq, É

2018-02-01

To characterize microbial communities present in natural rubber (NR) coagula from Hevea brasiliensis latex during maturation and identify microbial taxa (bacteria and fungi) having an impact on dry NR properties. Microbial community dynamics in NR coagula maturated under controlled conditions were compared and related with the evolution of dry NR properties. The pyrosequencing of 16S (119 837 effective reads) and 18S (131 879 effective reads) rRNA gene regions was performed on 21 samples covering different maturation times and two aeration conditions. Results showed a relatively high bacterial richness (Chao1 estimates of 200-1000) associated with significant bacterial dynamics. Lactic acid bacteria (LAB) were dominant in the first days of maturation. Then, in aerobic conditions, development of Actinobacteria represented by the family Microbacteriaceae was associated with alkalinization of the samples and a higher sensitivity of NR to thermo-oxidation as evaluated by its plasticity retention index (PRI). In anaerobiosis, the reduced development of bacteria, mostly LAB present, was associated with improved NR properties (higher initial plasticity P 0 and PRI). The involvement of micro-organisms in the evolution of dry NR properties during the maturation of NR coagula was confirmed. The importance of the structure and dynamics of microbial communities is specifically highlighted. Natural rubber is a key elastomer for the tyre industry and for a variety of other applications. The majority of raw NR is obtained by natural coagulation of H. brasiliensis latex under the activity of micro-organisms. An improved understanding of the microbial communities involved in the maturation of NR coagula may lead to an improvement in the production process of raw NR to provide a better consistency in NR quality. © 2017 The Society for Applied Microbiology.

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

PubMed

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

2012-10-01

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

Sequencing Insights into Microbial Communities in the Water and Sediments of Fenghe River, China.

PubMed

Lu, Sidan; Sun, Yujiao; Zhao, Xuan; Wang, Lei; Ding, Aizhong; Zhao, Xiaohui

2016-07-01

The connection between microbial community structure and spatial variation and pollution in river waters has been widely investigated. However, water and sediments together have rarely been explored. In this study, Illumina high-throughput sequencing was performed to analyze microbes in 24 water and sediment samples from natural to anthropogenic sources and from headstream to downstream areas. These data were used to assess variability in microbial community structure and diversity along in the Fenghe River, China. The relationship between bacterial diversity and environmental parameters was statistically analyzed. An average of 1682 operational taxonomic units was obtained. Microbial diversity increased from the headstream to downstream and tended to be greater in sediment compared with water. The water samples near the headstream endured relatively low Shannon and Chao1 indices. These diversity indices and the number of observed species in the water and sediment samples increase downstream. The parameters also differ in the two river tributaries. Community structures shift based on the extent of nitrogen pollution variation in the sediment and water samples. The four most dominant genera in the water community were Escherichia, Acinetobacter, Comamonadaceae, and Pseudomonas. In the sediments, the most dominant genera were Stramenopiles, Flavobacterium, Pseudomonas, and Comamonadaceae. The number of ammonia-oxidizing archaea in the headstream water slightly differed from that in the sediment but varied considerably in the downstream sediments. Statistical analysis showed that community variation is correlated with changes in ammonia nitrogen, total nitrogen, and nitrate nitrogen. This study identified different microbial community structures in river water and sediments. Overall this study emphasized the need to elucidate spatial variations in bacterial diversity in water and sediments associated with physicochemical gradients and to show the effects of such variation on waterborne microbial community structures.

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

USGS Publications Warehouse

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

2014-01-01

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

Deconvolving molecular signatures of interactions between microbial colonies

PubMed Central

Harn, Y.-C.; Powers, M. J.; Shank, E. A.; Jojic, V.

2015-01-01

Motivation: The interactions between microbial colonies through chemical signaling are not well understood. A microbial colony can use different molecules to inhibit or accelerate the growth of other colonies. A better understanding of the molecules involved in these interactions could lead to advancements in health and medicine. Imaging mass spectrometry (IMS) applied to co-cultured microbial communities aims to capture the spatial characteristics of the colonies’ molecular fingerprints. These data are high-dimensional and require computational analysis methods to interpret. Results: Here, we present a dictionary learning method that deconvolves spectra of different molecules from IMS data. We call this method MOLecular Dictionary Learning (MOLDL). Unlike standard dictionary learning methods which assume Gaussian-distributed data, our method uses the Poisson distribution to capture the count nature of the mass spectrometry data. Also, our method incorporates universally applicable information on common ion types of molecules in MALDI mass spectrometry. This greatly reduces model parameterization and increases deconvolution accuracy by eliminating spurious solutions. Moreover, our method leverages the spatial nature of IMS data by assuming that nearby locations share similar abundances, thus avoiding overfitting to noise. Tests on simulated datasets show that this method has good performance in recovering molecule dictionaries. We also tested our method on real data measured on a microbial community composed of two species. We confirmed through follow-up validation experiments that our method recovered true and complete signatures of molecules. These results indicate that our method can discover molecules in IMS data reliably, and hence can help advance the study of interaction of microbial colonies. Availability and implementation: The code used in this paper is available at: https://github.com/frizfealer/IMS_project. Contact: vjojic@cs.unc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26072476

Functional structure of laminated microbial sediments from a supratidal sandy beach of the German Wadden Sea (St. Peter-Ording)

NASA Astrophysics Data System (ADS)

Bühring, Solveig I.; Kamp, Anja; Wörmer, Lars; Ho, Stephanie; Hinrichs, Kai-Uwe

2014-01-01

Hidden for the untrained eye through a thin layer of sand, laminated microbial sediments occur in supratidal beaches along the North Sea coast. The inhabiting microbial communities organize themselves in response to vertical gradients of light, oxygen or sulfur compounds. We performed a fine-scale investigation on the vertical zonation of the microbial communities using a lipid biomarker approach, and assessed the biogeochemical processes using a combination of microsensor measurements and a 13C-labeling experiment. Lipid biomarker fingerprinting showed the overarching importance of cyanobacteria and diatoms in these systems, and heterocyst glycolipids revealed the presence of diazotrophic cyanobacteria even in 9 to 20 mm depth. High abundance of ornithine lipids (OL) throughout the system may derive from sulfate reducing bacteria, while a characteristic OL profile between 5 and 8 mm may indicate presence of purple non-sulfur bacteria. The fate of 13C-labeled bicarbonate was followed by experimentally investigating the uptake into microbial lipids, revealing an overarching importance of cyanobacteria for carbon fixation. However, in deeper layers, uptake into purple sulfur bacteria was evident, and a close microbial coupling could be shown by uptake of label into lipids of sulfate reducing bacteria in the deepest layer. Microsensor measurements in sediment cores collected at a later time point revealed the same general pattern as the biomarker analysis and the labeling experiments. Oxygen and pH-microsensor profiles showed active photosynthesis in the top layer. The sulfide that diffuses from deeper down and decreases just below the layer of active oxygenic photosynthesis indicates the presence of sulfur bacteria, like anoxygenic phototrophs that use sulfide instead of water for photosynthesis.

Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

PubMed Central

Lee, On On; Wang, Yong; Yang, Jiangke; Lafi, Feras F; Al-Suwailem, Abdulaziz; Qian, Pei-Yuan

2011-01-01

Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to investigate in depth the microbial communities associated with three Red Sea sponges, Hyrtios erectus, Stylissa carteri and Xestospongia testudinaria. We revealed highly diverse sponge-associated bacterial communities with up to 1000 microbial operational taxonomic units (OTUs) and richness estimates of up to 2000 species. Altogether, 26 bacterial phyla were detected from the Red Sea sponges, 11 of which were absent from the surrounding sea water and 4 were recorded in sponges for the first time. Up to 100 OTUs with richness estimates of up to 300 archaeal species were revealed from a single sponge species. This is by far the highest archaeal diversity ever recorded for sponges. A non-negligible proportion of unclassified reads was observed in sponges. Our results demonstrated that the sponge-associated microbial communities remained highly consistent in the same sponge species from different locations, although they varied at different degrees among different sponge species. A significant proportion of the tag sequences from the sponges could be assigned to one of the sponge-specific clusters previously defined. In addition, the sponge-associated microbial communities were consistently divergent from those present in the surrounding sea water. Our results suggest that the Red Sea sponges possess highly sponge-specific or even sponge-species-specific microbial communities that are resistant to environmental disturbance, and much of their microbial diversity remains to be explored. PMID:21085196

Shifts of system performance and microbial community structure in a constructed wetland after exposing silver nanoparticles.

PubMed

Cao, Chong; Huang, Juan; Yan, Chunni; Liu, Jialiang; Hu, Qian; Guan, Wenzhu

2018-05-01

The increasing utilization of silver nanoparticles (Ag NPs) in industry and commerce inevitably raises its release into wastewater. In this work, effects of Ag NPs on system performance and microbial community along the way of a vertical flow constructed wetland (VFCW) were investigated, along with the removal and fate of Ag NPs within the system. Results showed that the performance of control wetland kept stable during the experimental period, and the top substrate layer (soil layer) of wetland could remove most of pollutants in the influent. The study also suggested that addition of Ag NPs did not significantly affect organic matters removal. However, adverse effects were observed on the nitrogen and phosphorus removal. Removal efficiencies of TN, NH 4 + -N and TP approximately obviously reduced by approximately 10.10%, 8.42% and 28.35% respectively in contrast to before dosing after exposing 100 μg/L Ag NPs for 94 d, while the no dosing wetland with the stable performance. It was found that Ag NPs accumulated in the upper soil layer more than in the lower soil layer, and Ag NPs could enter into the plant tissues. After continuous input of Ag NPs, removal efficiency of Ag NPs was measured as 95.72%, which showed that the CW could effectively remove Ag NPs from the wastewater. The high-throughput sequencing results revealed that Ag NPs caused the shifts in microbial community structures and changed the relative abundances of key functional bacteria, which finally resulted in a lower efficiency of biological nitrogen and phosphorus removal. Copyright © 2018 Elsevier Ltd. All rights reserved.

Impact of an indigenous microbial enhanced oil recovery field trial on microbial community structure in a high pour-point oil reservoir.

PubMed

Zhang, Fan; She, Yue-Hui; Li, Hua-Min; Zhang, Xiao-Tao; Shu, Fu-Chang; Wang, Zheng-Liang; Yu, Long-Jiang; Hou, Du-Jie

2012-08-01

Based on preliminary investigation of microbial populations in a high pour-point oil reservoir, an indigenous microbial enhanced oil recovery (MEOR) field trial was carried out. The purpose of the study is to reveal the impact of the indigenous MEOR process on microbial community structure in the oil reservoir using 16Sr DNA clone library technique. The detailed monitoring results showed significant response of microbial communities during the field trial and large discrepancies of stimulated microorganisms in the laboratory and in the natural oil reservoir. More specifically, after nutrients injection, the original dominant populations of Petrobacter and Alishewanella in the production wells almost disappeared. The expected desirable population of Pseudomonas aeruginosa, determined by enrichment experiments in laboratory, was stimulated successfully in two wells of the five monitored wells. Unexpectedly, another potential population of Pseudomonas pseudoalcaligenes which were not detected in the enrichment culture in laboratory was stimulated in the other three monitored production wells. In this study, monitoring of microbial community displayed a comprehensive alteration of microbial populations during the field trial to remedy the deficiency of culture-dependent monitoring methods. The results would help to develop and apply more MEOR processes.

High Microbial Diversity Promotes Soil Ecosystem Functioning.

PubMed

Maron, Pierre-Alain; Sarr, Amadou; Kaisermann, Aurore; Lévêque, Jean; Mathieu, Olivier; Guigue, Julien; Karimi, Battle; Bernard, Laetitia; Dequiedt, Samuel; Terrat, Sébastien; Chabbi, Abad; Ranjard, Lionel

2018-05-01

In soil, the link between microbial diversity and carbon transformations is challenged by the concept of functional redundancy. Here, we hypothesized that functional redundancy may decrease with increasing carbon source recalcitrance and that coupling of diversity with C cycling may change accordingly. We manipulated microbial diversity to examine how diversity decrease affects the decomposition of easily degradable (i.e., allochthonous plant residues) versus recalcitrant (i.e., autochthonous organic matter) C sources. We found that a decrease in microbial diversity (i) affected the decomposition of both autochthonous and allochthonous carbon sources, thereby reducing global CO 2 emission by up to 40%, and (ii) shaped the source of CO 2 emission toward preferential decomposition of most degradable C sources. Our results also revealed that the significance of the diversity effect increases with nutrient availability. Altogether, these findings show that C cycling in soil may be more vulnerable to microbial diversity changes than expected from previous studies, particularly in ecosystems exposed to nutrient inputs. Thus, concern about the preservation of microbial diversity may be highly relevant in the current global-change context assumed to impact soil biodiversity and the pulse inputs of plant residues and rhizodeposits into the soil. IMPORTANCE With hundreds of thousands of taxa per gram of soil, microbial diversity dominates soil biodiversity. While numerous studies have established that microbial communities respond rapidly to environmental changes, the relationship between microbial diversity and soil functioning remains controversial. Using a well-controlled laboratory approach, we provide empirical evidence that microbial diversity may be of high significance for organic matter decomposition, a major process on which rely many of the ecosystem services provided by the soil ecosystem. These new findings should be taken into account in future studies aimed at understanding and predicting the functional consequences of changes in microbial diversity on soil ecosystem services and carbon storage in soil. Copyright © 2018 American Society for Microbiology.

Learning Microbial Community Structures with Supervised and Unsupervised Non-negative Matrix Factorization.

PubMed

Cai, Yun; Gu, Hong; Kenney, Toby

2017-08-31

Learning the structure of microbial communities is critical in understanding the different community structures and functions of microbes in distinct individuals. We view microbial communities as consisting of many subcommunities which are formed by certain groups of microbes functionally dependent on each other. The focus of this paper is on methods for extracting the subcommunities from the data, in particular Non-Negative Matrix Factorization (NMF). Our methods can be applied to both OTU data and functional metagenomic data. We apply the existing unsupervised NMF method and also develop a new supervised NMF method for extracting interpretable information from classification problems. The relevance of the subcommunities identified by NMF is demonstrated by their excellent performance for classification. Through three data examples, we demonstrate how to interpret the features identified by NMF to draw meaningful biological conclusions and discover hitherto unidentified patterns in the data. Comparing whole metagenomes of various mammals, (Muegge et al., Science 332:970-974, 2011), the biosynthesis of macrolides pathway is found in hindgut-fermenting herbivores, but not carnivores. This is consistent with results in veterinary science that macrolides should not be given to non-ruminant herbivores. For time series microbiome data from various body sites (Caporaso et al., Genome Biol 12:50, 2011), a shift in the microbial communities is identified for one individual. The shift occurs at around the same time in the tongue and gut microbiomes, indicating that the shift is a genuine biological trait, rather than an artefact of the method. For whole metagenome data from IBD patients and healthy controls (Qin et al., Nature 464:59-65, 2010), we identify differences in a number of pathways (some known, others new). NMF is a powerful tool for identifying the key features of microbial communities. These identified features can not only be used to perform difficult classification problems with a high degree of accuracy, they are also very interpretable and can lead to important biological insights into the structure of the communities. In addition, NMF is a dimension-reduction method (similar to PCA) in that it reduces the extremely complex microbial data into a low-dimensional representation, allowing a number of analyses to be performed more easily-for example, searching for temporal patterns in the microbiome. When we are interested in the differences between the structures of two groups of communities, supervised NMF provides a better way to do this, while retaining all the advantages of NMF-e.g. interpretability and a simple biological intuition.

Long-term performance and characterization of microbial desalination cells in treating domestic wastewater.

PubMed

Luo, Haiping; Xu, Pei; Ren, Zhiyong

2012-09-01

Microbial desalination cell represents a new technology for simultaneous wastewater treatment, water desalination, and energy production. This study characterized the long-term performance of MDC during wastewater treatment and identified the key factors that caused performance decline. The 8-month operation shows that MDC performance decreased over time, as indicated by a 47% decline in current density, a 46% drop in Columbic efficiency, and a 27% decrease in desalination efficiency. Advanced electrochemical, microscopy, and spectroscopy analyses all confirmed biofouling on the anion exchange membrane, which increased system resistance and reduced ionic transfer and energy conversion efficiency. Minor chemical scaling was found on the cation exchange membrane surface. Microbial communities became less diverse at the end of operation, and Proteobacteria spp. was dominant on both anode and AEM fouling layer surface. These results provide insights into the viability of long-term MDC operation on reactor performance and direct system development through membrane optimization. Copyright © 2012 Elsevier Ltd. All rights reserved.

Long-term cathode performance and the microbial communities that develop in microbial fuel cells fed different fermentation endproducts.

PubMed

Kiely, Patrick D; Rader, Geoffrey; Regan, John M; Logan, Bruce E

2011-01-01

To better understand how cathode performance and substrates affected communities that evolved in these reactors over long periods of time, microbial fuel cells were operated for more than 1 year with individual endproducts of lignocellulose fermentation (acetic acid, formic acid, lactic acid, succinic acid, or ethanol). Large variations in reactor performance were primarily due to the specific substrates, with power densities ranging from 835 ± 21 to 62 ± 1mW/m(3). Cathodes performance degraded over time, as shown by an increase in power of up to 26% when the cathode biofilm was removed, and 118% using new cathodes. Communities that developed on the anodes included exoelectrogenic families, such as Rhodobacteraceae, Geobacteraceae, and Peptococcaceae, with the Deltaproteobacteria dominating most reactors. Pelobacter propionicus was the predominant member in reactors fed acetic acid, and it was abundant in several other MFCs. These results provide valuable insights into the effects of long-term MFC operation on reactor performance. Copyright © 2010 Elsevier Ltd. All rights reserved.

High Carbon Use Efficiency is Not Explained by Production of Storage Compounds

NASA Astrophysics Data System (ADS)

Dijkstra, Paul; van Groenigen, Kees-Jan

2015-04-01

The efficiency with which microbes use substrate to make new microbial biomass (Carbon Use Efficiency or CUE; mol C / mol C) is an important variable in soil and ecosystem C cycling models. Estimates of CUE in soil microbial communities vary widely. It has been hypothesized that high values of CUE are associated with production of storage compounds following a sudden increases in substrate availability during CUE measurements. In that case, these high CUE values would not be representative for balanced microbial growth (i.e. the production of all compounds needed to make new microbial cells). To test this hypothesis, we added position-specific 13C-labeled glucose isotopomers in parallel incubations of a ponderosa pine and piñon-juniper soil. We compared the measured pattern of CO2 release for the six glucose C atoms with patterns of CO2 production expected for balanced growth with a low, medium, or high CUE, and with CO2 production patterns associated with production of storage compounds (glycogen, lipids, or polyhydroxybutyrate). The measured position-specific CO2 production did not match that for production of glycogen, lipids, or polyhydroxybutyrate, but agreed closely with that expected for balanced growth at high CUE and high pentose phosphate pathway activity. We conclude that soil microbial communities utilize glucose substrate for biomass growth with high CUE, and that addition of small amounts of 13C-labeled glucose tracers do not affect CUE or induce storage compounds production. We submit that the measurement of position-specific CO2 production offers a quick and easy way to test biochemically explicit hypotheses concerning microbial growth metabolism.

Final Report Systems Level Analysis of the Function and Adaptive Responses of Methanogenic Consortia

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

Lovley, Derek R.

The purpose of this research was to determine whether the syntrophic microbial associations that are central to the functioning of methane-producing terrestrial wetlands can be predictively modeled with coupled multi-species genome-scale metabolic models. Such models are important because methane is an important greenhouse gas and there is a need to predictively model how the methane-producing microbial communities will respond to environmental perturbations, such as global climate change. The research discovered that the most prodigious methane-producing microorganisms on earth participate in a previously unrecognized form of energy exchange. The methane-producers Methanosaeta and Methanosarcina forge biological electrical connections with other microbes inmore » order to obtain electrons to reduce carbon dioxide to methane. This direct interspecies electron transfer (DIET) was demonstrated in complex microbial communities as well as in defined co-cultures. For example, metatranscriptomic analysis of gene expression in both natural communities and defined co-cultures demonstrated that Methanosaeta species highly expressed genes for the enzymes for the reduction of carbon dioxide to methane. Furthermore, Methanosaeta’s electron-donating partners highly expressed genes for the biological electrical connections known as microbial nanowires. A series of studies involving transcriptomics, genome resequencing, and analysis of the metabolism of a series of strains with targeted gene deletions, further elucidated the mechanisms and energetics of DIET in methane-producing co-cultures, as well as in a co-culture of Geobacter metallireducens and Geobacter sulfurreducens, which provided a system for studying DIET with two genetically tractable partners. Genome-scale modeling of DIET in the G. metallireducens/G. sulfurreducens co-culture suggested that DIET provides more energy to the electron-donating partner that electron exchange via interspecies hydrogen transfer, but that the performance of DIET may be strongly influenced by environmental factors. These studies have significantly modified conceptual models for carbon and electron flow in methane-producing environments and have developed a computational framework for predictive modeling the influence of environmental perturbations on methane-producing microbial communities. The results have important implications for modeling the response of methane-producing microbial communities to climate change as well as for the bioenergy strategy of converting wastes and biomass to methane.« less

Monitoring and modeling of microbial and biological water quality

USDA-ARS?s Scientific Manuscript database

Microbial and biological water quality informs on the health of water systems and their suitability for uses in irrigation, recreation, aquaculture, and other activities. Indicators of microbial and biological water quality demonstrate high spatial and temporal variability. Therefore, monitoring str...

Vertical Geochemical Profiling Across a 3.33 Ga Microbial Mat from Barberton

NASA Astrophysics Data System (ADS)

Westall, F.; Lemelle, L.; Simionovici, A.; Southam, G.; Maclean, L.; Salomé, M.; Wirick, S.; Toporski, J.; Jauss, A.

2008-03-01

The Josefdal Chert (3.33 Ga), Barberton, contains a superbly preserved microbial mat. High resolution geochemical profiling across the mat documents textures and compositions indicative of a mixed microbial community of anoxygenic photosynthesisers and probably SRBs.

Microbial biosurfactants with their high-value functional properties

USDA-ARS?s Scientific Manuscript database

Microbial world is a rich source for finding valuable industrial chemicals and ingredients. Specifically, many microbial metabolites are surface-active compounds that can be developed into bio-based surfactants, detergents, and emulsifiers. Techno-economic analyses for the production of bio-based ...

Complementary Microorganisms in Highly Corrosive Biofilms from an Offshore Oil Production Facility.

PubMed

Vigneron, Adrien; Alsop, Eric B; Chambers, Brian; Lomans, Bartholomeus P; Head, Ian M; Tsesmetzis, Nicolas

2016-04-01

Offshore oil production facilities are frequently victims of internal piping corrosion, potentially leading to human and environmental risks and significant economic losses. Microbially influenced corrosion (MIC) is believed to be an important factor in this major problem for the petroleum industry. However, knowledge of the microbial communities and metabolic processes leading to corrosion is still limited. Therefore, the microbial communities from three anaerobic biofilms recovered from the inside of a steel pipe exhibiting high corrosion rates, iron oxide deposits, and substantial amounts of sulfur, which are characteristic of MIC, were analyzed in detail. Bacterial and archaeal community structures were investigated by automated ribosomal intergenic spacer analysis, multigenic (16S rRNA and functional genes) high-throughput Illumina MiSeq sequencing, and quantitative PCR analysis. The microbial community analysis indicated that bacteria, particularly Desulfovibrio species, dominated the biofilm microbial communities. However, other bacteria, such as Pelobacter, Pseudomonas, and Geotoga, as well as various methanogenic archaea, previously detected in oil facilities were also detected. The microbial taxa and functional genes identified suggested that the biofilm communities harbored the potential for a number of different but complementary metabolic processes and that MIC in oil facilities likely involves a range of microbial metabolisms such as sulfate, iron, and elemental sulfur reduction. Furthermore, extreme corrosion leading to leakage and exposure of the biofilms to the external environment modify the microbial community structure by promoting the growth of aerobic hydrocarbon-degrading organisms. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Complementary Microorganisms in Highly Corrosive Biofilms from an Offshore Oil Production Facility

PubMed Central

Alsop, Eric B.; Chambers, Brian; Lomans, Bartholomeus P.; Head, Ian M.; Tsesmetzis, Nicolas

2016-01-01

Offshore oil production facilities are frequently victims of internal piping corrosion, potentially leading to human and environmental risks and significant economic losses. Microbially influenced corrosion (MIC) is believed to be an important factor in this major problem for the petroleum industry. However, knowledge of the microbial communities and metabolic processes leading to corrosion is still limited. Therefore, the microbial communities from three anaerobic biofilms recovered from the inside of a steel pipe exhibiting high corrosion rates, iron oxide deposits, and substantial amounts of sulfur, which are characteristic of MIC, were analyzed in detail. Bacterial and archaeal community structures were investigated by automated ribosomal intergenic spacer analysis, multigenic (16S rRNA and functional genes) high-throughput Illumina MiSeq sequencing, and quantitative PCR analysis. The microbial community analysis indicated that bacteria, particularly Desulfovibrio species, dominated the biofilm microbial communities. However, other bacteria, such as Pelobacter, Pseudomonas, and Geotoga, as well as various methanogenic archaea, previously detected in oil facilities were also detected. The microbial taxa and functional genes identified suggested that the biofilm communities harbored the potential for a number of different but complementary metabolic processes and that MIC in oil facilities likely involves a range of microbial metabolisms such as sulfate, iron, and elemental sulfur reduction. Furthermore, extreme corrosion leading to leakage and exposure of the biofilms to the external environment modify the microbial community structure by promoting the growth of aerobic hydrocarbon-degrading organisms. PMID:26896143

Microbial fuel cell (MFC) power performance improvement through enhanced microbial electrogenicity.

PubMed

Li, Ming; Zhou, Minghua; Tian, Xiaoyu; Tan, Chaolin; McDaniel, Cameron T; Hassett, Daniel J; Gu, Tingyue

Within the past 5 years, tremendous advances have been made to maximize the performance of microbial fuel cells (MFCs) for both "clean" bioenergy production and bioremediation. Most research efforts have focused on parameters including (i) optimizing reactor configuration, (ii) electrode construction, (iii) addition of redox-active, electron donating mediators, (iv) biofilm acclimation and feed nutrient adjustment, as well as (v) other parameters that contribute to enhanced MFC performance. To date, tremendous advances have been made, but further improvements are needed for MFCs to be economically practical. In this review, the diversity of electrogenic microorganisms and microbial community changes in mixed cultures are discussed. More importantly, different approaches including chemical/genetic modifications and gene regulation of exoelectrogens, synthetic biology approaches and bacterial community cooperation are reviewed. Advances in recent years in metagenomics and microbiomes have allowed researchers to improve bacterial electrogenicity of robust biofilms in MFCs using novel, unconventional approaches. Taken together, this review provides some important and timely information to researchers who are examining additional means to enhance power production of MFCs. Copyright © 2018 Elsevier Inc. All rights reserved.

Performance of Microbial Concrete Developed Using Bacillus Subtilus JC3

NASA Astrophysics Data System (ADS)

Rao, M. V. Seshagiri; Reddy, V. Srinivasa; Sasikala, Ch.

2017-12-01

Concrete is vulnerable to deterioration, corrosion, and cracks, and the consequent damage and loss of strength requires immensely expensive remediation and repair. So need for special concrete that they would respond to crack formation with an autonomous self-healing action lead to research and development of microbial concrete. The microbial concrete works on the principle of calcite mineral precipitation by a specific group of alkali-resistant spore-forming bacteria related to the genus Bacillus called Bacillus subtilis JC3, this phenomenon is called biomineralization or Microbiologically Induced Calcite Crystal Precipitation. Bacillus subtilis JC3, a common soil bacterium, has inherent ability to precipitate calcite crystals continuously which enhances the strength and durability performance of concrete enormously. This microbial concrete can be called as a "Self healing Bacterial Concrete" because it can remediate its cracks by itself without any human intervention and would make the concrete more durable and sustainable. This paper discuss the incorporation of microorganism Bacillus subtilis JC3 (developed at JNTU, India) into concrete and presents the results of experimental investigations carried out to study the improved durability and sustainability characteristics of microbial concrete.