Developing methanogenic microbial consortia from diverse coal sources and environments

DOE PAGES

Fuertez, John; Boakye, Richard; McLennan, John; ...

2017-08-18

Biogenic gas production is a promising alternative or supplement to conventional methane extraction from coalbeds. Adsorbed and free gas, generated over geologic time, can be supplemented with biogenic gas during short-term engineering operations. There are two generic protocols for doing this. The first is to contact the coal with nutrients to support native bacterial development. The second approach is to inject appropriately cultured ex-situ consortia into subsurface coal accumulations. Research has mainly focused on the former: in-situ stimulation of native microbial communities with added nutrients. Relatively few studies have been conducted on the strategies for enriching ex-situ microbial populations undermore » initial atmospheric exposure for subsequent injection into coal seams to stimulate biodegradation, and methanogenesis. In order to evaluate the feasibility of ex-situ cultivation, natural microbial populations were collected from various hydrocarbon-rich environments and locations characterized by natural methanogenesis. Different rank coals (i.e., lignite, sub-bituminous, bituminous), complex hydrocarbon sources (i.e., oil shale, waxy crude), hydrocarbon seeps, and natural biogenic environments were incorporated in the sampling. Three levels of screening (down-selection to high grade the most productive consortia) allowed selection of microbial populations, favorable nutrient amendments, sources of the microbial community, and quantification of methane produced from various coal types. Incubation periods of up to twenty-four weeks were evaluated at 23 °C. Headspace concentrations of CH 4 and CO 2 were analyzed by gas chromatography. After a two-week incubation period of the most promising microbes, generated headspace gas concentrations reached 873,400 ppm (154 sft 3/ton or 4.8 scm 3/g) for methane and 176,370 ppm (31 sft 3/ton or 0.9 scm 3/g) for carbon dioxide. Rudimentary statistical assessments – variance analysis (ANOVA) of a single factor - were used to identify trends and levels of significance or impact of the consortia enrichment. We then demonstrated that microbial communities from coal and lake sediments can be enriched and adapted to effectively generate methane under initial atmospheric exposure. The development and enrichment of these methanogenic consortia is described.« less

Developing methanogenic microbial consortia from diverse coal sources and environments

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

Fuertez, John; Boakye, Richard; McLennan, John

Biogenic gas production is a promising alternative or supplement to conventional methane extraction from coalbeds. Adsorbed and free gas, generated over geologic time, can be supplemented with biogenic gas during short-term engineering operations. There are two generic protocols for doing this. The first is to contact the coal with nutrients to support native bacterial development. The second approach is to inject appropriately cultured ex-situ consortia into subsurface coal accumulations. Research has mainly focused on the former: in-situ stimulation of native microbial communities with added nutrients. Relatively few studies have been conducted on the strategies for enriching ex-situ microbial populations undermore » initial atmospheric exposure for subsequent injection into coal seams to stimulate biodegradation, and methanogenesis. In order to evaluate the feasibility of ex-situ cultivation, natural microbial populations were collected from various hydrocarbon-rich environments and locations characterized by natural methanogenesis. Different rank coals (i.e., lignite, sub-bituminous, bituminous), complex hydrocarbon sources (i.e., oil shale, waxy crude), hydrocarbon seeps, and natural biogenic environments were incorporated in the sampling. Three levels of screening (down-selection to high grade the most productive consortia) allowed selection of microbial populations, favorable nutrient amendments, sources of the microbial community, and quantification of methane produced from various coal types. Incubation periods of up to twenty-four weeks were evaluated at 23 °C. Headspace concentrations of CH 4 and CO 2 were analyzed by gas chromatography. After a two-week incubation period of the most promising microbes, generated headspace gas concentrations reached 873,400 ppm (154 sft 3/ton or 4.8 scm 3/g) for methane and 176,370 ppm (31 sft 3/ton or 0.9 scm 3/g) for carbon dioxide. Rudimentary statistical assessments – variance analysis (ANOVA) of a single factor - were used to identify trends and levels of significance or impact of the consortia enrichment. We then demonstrated that microbial communities from coal and lake sediments can be enriched and adapted to effectively generate methane under initial atmospheric exposure. The development and enrichment of these methanogenic consortia is described.« less

Competitive resource allocation to metabolic pathways contributes to overflow metabolisms and emergent properties in cross-feeding microbial consortia.

PubMed

Carlson, Ross P; Beck, Ashley E; Phalak, Poonam; Fields, Matthew W; Gedeon, Tomas; Hanley, Luke; Harcombe, William R; Henson, Michael A; Heys, Jeffrey J

2018-04-17

Resource scarcity is a common stress in nature and has a major impact on microbial physiology. This review highlights microbial acclimations to resource scarcity, focusing on resource investment strategies for chemoheterotrophs from the molecular level to the pathway level. Competitive resource allocation strategies often lead to a phenotype known as overflow metabolism; the resulting overflow byproducts can stabilize cooperative interactions in microbial communities and can lead to cross-feeding consortia. These consortia can exhibit emergent properties such as enhanced resource usage and biomass productivity. The literature distilled here draws parallels between in silico and laboratory studies and ties them together with ecological theories to better understand microbial stress responses and mutualistic consortia functioning. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Bioremediation of organophosphorus pesticide phorate in soil by microbial consortia.

PubMed

Jariyal, Monu; Jindal, Vikas; Mandal, Kousik; Gupta, Virash Kamal; Singh, Balwinder

2018-09-15

Microbial consortia isolated from aged phorate contaminated soil were used to degrade phorate. The consortia of three microorganisms (Brevibacterium frigoritolerans, Bacillus aerophilus and Pseudomonas fulva) could degrade phorate, and the highest phorate removal (between 97.65 and 98.31%) was found in soils inoculated with mixed cultures of all the three bacterial species. However, the mixed activity of any of two of these bacteria was lower than mixed consortia of all the three bacterial species. The highest degradation by individual mixed consortia of (B. frigoritolerans+B.aerophilus, B. aerophilus+P. fulva and B. frigoritolerans+P. fulva) appeared in soil between (92.28-94.09%, 95.45-97.15% and 94.08-97.42%, respectively). Therefore, inoculation of highly potential microbial consortia isolated from in situ contaminated soil could result in most effective bioremediation consortia for significantly relieving soils from phorate residues. This much high phorate remediation from phorate contaminated soils have never been reported earlier by mixed culture of native soil bacterial isolates. Copyright © 2018 Elsevier Inc. 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

Microbial Consortia Engineering for Cellular Factories: in vitro to in silico systems

PubMed Central

Bernstein, Hans C; Carlson, Ross P

2012-01-01

This mini-review discusses the current state of experimental and computational microbial consortia engineering with a focus on cellular factories. A discussion of promising ecological theories central to community resource usage is presented to facilitate interpretation of consortial designs. Recent case studies exemplifying different resource usage motifs and consortial assembly templates are presented. The review also highlights in silico approaches to design and to analyze consortia with an emphasis on stoichiometric modeling methods. The discipline of microbial consortia engineering possesses a widely accepted potential to generate highly novel and effective bio-catalysts for applications from biofuels to specialty chemicals to enhanced mineral recovery. PMID:24688677

Microbial succession in response to pollutants in batch-enrichment culture

PubMed Central

Jiao, Shuo; Chen, Weimin; Wang, Entao; Wang, Junman; Liu, Zhenshan; Li, Yining; Wei, Gehong

2016-01-01

As a global problem, environmental pollution is an important factor to shape the microbial communities. The elucidation of the succession of microbial communities in response to pollutants is essential for developing bioremediation procedures. In the present study, ten batches of soil-enrichment subcultures were subjected to four treatments: phenanthrene, n-octadecane, phenanthrene + n-octadecane, or phenanthrene + n-octadecane + CdCl2. Forty pollutant-degrading consortia, corresponding to each batch of the four treatments were obtained. High-throughput sequencing of the 16S rRNA gene revealed that the diversity, richness and evenness of the consortia decreased throughout the subculturing procedure. The well-known hydrocarbon degraders Acinetobacter, Gordonia, Sphingobium, Sphingopyxis, and Castellaniella and several other genera, including Niabella and Naxibacter, were detected in the enriched consortia. The predominant microbes varied and the microbial community in the consortia gradually changed during the successive subculturing depending on the treatment, indicating that the pollutants influenced the microbial successions. Comparison of the networks in the treatments indicated that organic pollutants and CdCl2 affected the co-occurrence patterns in enriched consortia. In conclusion, single environmental factors, such as the addition of nutrients or selection pressure, can shape microbial communities and partially explain the extensive differences in microbial community structures among diverse environments. PMID:26905741

Ecological perspectives on synthetic biology: insights from microbial population biology

PubMed Central

Escalante, Ana E.; Rebolleda-Gómez, María; Benítez, Mariana; Travisano, Michael

2015-01-01

The metabolic capabilities of microbes are the basis for many major biotechnological advances, exploiting microbial diversity by selection or engineering of single strains. However, there are limits to the advances that can be achieved with single strains, and attention has turned toward the metabolic potential of consortia and the field of synthetic ecology. The main challenge for the synthetic ecology is that consortia are frequently unstable, largely because evolution by constituent members affects their interactions, which are the basis of collective metabolic functionality. Current practices in modeling consortia largely consider interactions as fixed circuits of chemical reactions, which greatly increases their tractability. This simplification comes at the cost of essential biological realism, stripping out the ecological context in which the metabolic actions occur and the potential for evolutionary change. In other words, evolutionary stability is not engineered into the system. This realization highlights the necessity to better identify the key components that influence the stable coexistence of microorganisms. Inclusion of ecological and evolutionary principles, in addition to biophysical variables and stoichiometric modeling of metabolism, is critical for microbial consortia design. This review aims to bring ecological and evolutionary concepts to the discussion on the stability of microbial consortia. In particular, we focus on the combined effect of spatial structure (connectivity of molecules and cells within the system) and ecological interactions (reciprocal and non-reciprocal) on the persistence of microbial consortia. We discuss exemplary cases to illustrate these ideas from published studies in evolutionary biology and biotechnology. We conclude by making clear the relevance of incorporating evolutionary and ecological principles to the design of microbial consortia, as a way of achieving evolutionarily stable and sustainable systems. PMID:25767468

Fermentation Enhancement of Methanogenic Archaea Consortia from an Illinois Basin Coalbed via DOL Emulsion Nutrition

PubMed Central

Xiao, Dong; Peng, Su-Ping; Wang, En-Yuan

2015-01-01

Microbially enhanced coalbed methane technology must be used to increase the methane content in mining and generate secondary biogenic gas. In this technology, the metabolic processes of methanogenic consortia are the basis for the production of biomethane from some of the organic compounds in coal. Thus, culture nutrition plays an important role in remediating the nutritional deficiency of a coal seam. To enhance the methane production rates for microorganism consortia, different types of nutrition solutions were examined in this study. Emulsion nutrition solutions containing a novel nutritional supplement, called dystrophy optional modification latex, increased the methane yield for methanogenic consortia. This new nutritional supplement can help methanogenic consortia form an enhanced anaerobic environment, optimize the microbial balance in the consortia, and improve the methane biosynthesis rate. PMID:25884952

Functional Stability Of A Mixed Microbial Consortia Producing PHA From Waste Carbon Sources

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

David N. Thompson; Erik R. Coats; William A. Smith

2006-04-01

Polyhydroxyalkanoates (PHAs), naturally-occurring biological polyesters that are microbially synthesized from a myriad of carbon sources, can be utilized as biodegradable substitutes for petroleum-derived thermoplastics. However, current PHA commercialization schemes are limited by high feedstock costs, the requirement for aseptic reactors, and high separation and purification costs. Bacteria indigenous to municipal waste streams can accumulate large quantities of PHA under environmentally controlled conditions; hence, a potentially more environmentally-effective method of production would utilize these consortia to produce PHAs from inexpensive waste carbon sources. In this study, PHA production was accomplished in sequencing batch bioreactors utilizing mixed microbial consortia from municipal activatedmore » sludge as inoculum, in cultures grown on real wastewaters. PHA production averaged 85%, 53%, and 10% of the cell dry weight from methanol-enriched pulp-and-paper mill foul condensate, fermented municipal primary solids, and biodiesel wastewater, respectively. The PHA-producing microbial consortia were examined to explore the microbial community changes that occurred during reactor operations, employing denaturing gradient gel electrophoresis (DGGE) of 16S-rDNA from PCR-amplified DNA extracts. Distinctly different communities were observed both between and within wastewaters following enrichment. More importantly, stable functions were maintained despite the differing and contrasting microbial populations.« less

Polycyclic aromatic hydrocarbons (PAHs) biodegradation potential and diversity of microbial consortia enriched from tsunami sediments in Miyagi, Japan.

PubMed

Bacosa, Hernando Pactao; Inoue, Chihiro

2015-01-01

The Great East Japan Earthquake caused tsunamis and resulted in widespread damage to human life and infrastructure. The disaster also resulted in contamination of the environment by chemicals such as polycyclic aromatic hydrocarbons (PAHs). This study was conducted to investigate the degradation potential and describe the PAH-degrading microbial communities from tsunami sediments in Miyagi, Japan. PAH-degrading bacteria were cultured by enrichment using PAH mixture or pyrene alone as carbon and energy sources. Among the ten consortia tested for PAH mixture, seven completely degraded fluorene and more than 95% of phenanthrene in 10 days, while only four consortia partially degraded pyrene. Six consortia partially degraded pyrene as a single substrate. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) revealed that each sample was dominated by unique microbial populations, regardless of sampling location. The consortia were dominated by known PAHs degraders including Sphingomonas, Pseudomonas, and Sphingobium; and previously unknown degraders such as Dokdonella and Luteimonas. A potentially novel and PAH-degrading Dokdonella was detected for the first time. PAH-ring hydroxylating dioxygenase (PAH-RHDα) gene was shown to be more effective than nidA in estimating pyrene-degrading bacteria in the enriched consortia. The consortia obtained in this study are potential candidates for remediation of PAHs contaminated soils. Copyright © 2014 Elsevier B.V. All rights reserved.

Biodegradation of different petroleum hydrocarbons by free and immobilized microbial consortia.

PubMed

Shen, Tiantian; Pi, Yongrui; Bao, Mutai; Xu, Nana; Li, Yiming; Lu, Jinren

2015-12-01

The efficiencies of free and immobilized microbial consortia in the degradation of different types of petroleum hydrocarbons were investigated. In this study, the biodegradation rates of naphthalene, phenanthrene, pyrene and crude oil reached about 80%, 30%, 56% and 48% under the optimum environmental conditions of free microbial consortia after 7 d. We evaluated five unique co-metabolic substances with petroleum hydrocarbons, α-lactose was the best co-metabolic substance among glucose, α-lactose, soluble starch, yeast powder and urea. The orthogonal biodegradation analysis results showed that semi-coke was the best immobilized carrier followed by walnut shell and activated carbon. Meanwhile, the significance of various factors that contribute to the biodegradation of semi-coke immobilized microbial consortia followed the order of: α-lactose > semi-coke > sodium alginate > CaCl2. Moreover, the degradation rate of the immobilized microbial consortium (47%) was higher than that of a free microbial consortium (26%) under environmental conditions such as the crude oil concentration of 3 g L(-1), NaCl concentration of 20 g L(-1), pH at 7.2-7.4 and temperature of 25 °C after 5 d. SEM and FTIR analyses revealed that the structure of semi-coke became more porous and easily adhered to the microbial consortium; the functional groups (e.g., hydroxy and phosphate) were identified in the microbial consortium and were changed by immobilization. This study demonstrated that the ability of microbial adaptation to the environment can be improved by immobilization which expands the application fields of microbial remediation.

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.

Improvement of Biogas Production by Bioaugmentation

PubMed Central

Kovács, K. L.; Ács, N.; Kovács, E.; Wirth, R.; Rákhely, G.; Strang, Orsolya; Herbel, Zsófia; Bagi, Z.

2013-01-01

Biogas production technologies commonly involve the use of natural anaerobic consortia of microbes. The objective of this study was to elucidate the importance of hydrogen in this complex microbial food chain. Novel laboratory biogas reactor prototypes were designed and constructed. The fates of pure hydrogen-producing cultures of Caldicellulosiruptor saccharolyticus and Enterobacter cloacae were followed in time in thermophilic and mesophilic natural biogas-producing communities, respectively. Molecular biological techniques were applied to study the altered ecosystems. A systematic study in 5-litre CSTR digesters revealed that a key fermentation parameter in the maintenance of an altered population balance is the loading rate of total organic solids. Intensification of the biogas production was observed and the results corroborate that the enhanced biogas productivity is associated with the increased abundance of the hydrogen producers. Fermentation parameters did not indicate signs of failure in the biogas production process. Rational construction of more efficient and sustainable biogas-producing microbial consortia is proposed. PMID:23484123

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.

Method of dispersing a hydrocarbon using bacteria

DOEpatents

Tyndall, R.L.

1996-09-24

A new protozoan derived microbial consortia and method for their isolation are provided. The isolated consortia and bacteria are useful for treating wastes such as trichloroethylene and trinitrotoluene. The isolated consortia, bacteria, and dispersants are useful for dispersing hydrocarbons such as oil, creosote, wax, and grease.

Bacteria isolated from amoebae/bacteria consortium

DOEpatents

Tyndall, R.L.

1995-05-30

New protozoan derived microbial consortia and method for their isolation are provided. Consortia and bacteria isolated therefrom are useful for treating wastes such as trichloroethylene and trinitrotoluene. Consortia, bacteria isolated therefrom, and dispersants isolated therefrom are useful for dispersing hydrocarbons such as oil, creosote, wax, and grease.

Bacteria isolated from amoebae/bacteria consortium

DOEpatents

Tyndall, Richard L.

1995-01-01

New protozoan derived microbial consortia and method for their isolation are provided. Consortia and bacteria isolated therefrom are useful for treating wastes such as trichloroethylene and trinitrotoluene. Consortia, bacteria isolated therefrom, and dispersants isolated therefrom are useful for dispersing hydrocarbons such as oil, creosote, wax, and grease.

Integrating ecological and engineering concepts of resilience in microbial communities

DOE PAGES

Song, Hyun -Seob; Renslow, Ryan S.; Fredrickson, Jim K.; ...

2015-12-01

We note that many definitions of resilience have been proffered for natural and engineered ecosystems, but a conceptual consensus on resilience in microbial communities is still lacking. Here, we argue that the disconnect largely results from the wide variance in microbial community complexity, which range from simple synthetic consortia to complex natural communities, and divergence between the typical practical outcomes emphasized by ecologists and engineers. Viewing microbial communities as elasto-plastic systems, we argue that this gap between the engineering and ecological definitions of resilience stems from their respective emphases on elastic and plastic deformation, respectively. We propose that the twomore » concepts may be fundamentally united around the resilience of function rather than state in microbial communities and the regularity in the relationship between environmental variation and a community’s functional response. Furthermore, we posit that functional resilience is an intrinsic property of microbial communities, suggesting that state changes in response to environmental variation may be a key mechanism driving resilience in microbial communities.« less

Method of separating bacteria from free living amoebae

DOEpatents

Tyndall, Richard L.

1994-01-01

New protozoan derived microbial consortia and method for their isolation are provided. Consortia and bacteria isolated therefrom are useful for treating wastes such as trichloroethylene and trinitrotoluene. Consortia, bacteria isolated therefrom, and dispersants isolated therefrom are useful for dispersing hydrocarbons such as oil, creosote, wax, and grease.

Method of dispersing a hydrocarbon using bacteria

DOEpatents

Tyndall, Richard L.

1996-01-01

New protozoan derived microbial consortia and method for their isolation are provided. Consortia and bacteria isolated therefrom are useful for treating wastes such as trichloroethylene and trinitrotoluene. Consortia, bacteria isolated therefrom, and dispersants isolated therefrom are useful for dispersing hydrocarbons such as oil, creosote, wax, and grease.

Characterization of three plant biomass-degrading microbial consortia by metagenomics- and metasecretomics-based approaches.

PubMed

Jiménez, Diego Javier; de Lima Brossi, Maria Julia; Schückel, Julia; Kračun, Stjepan Krešimir; Willats, William George Tycho; van Elsas, Jan Dirk

2016-12-01

The selection of microbes by enrichment on plant biomass has been proposed as an efficient way to develop new strategies for lignocellulose saccharification. Here, we report an in-depth analysis of soil-derived microbial consortia that were trained to degrade once-used wheat straw (WS1-M), switchgrass (SG-M) and corn stover (CS-M) under aerobic and mesophilic conditions. Molecular fingerprintings, bacterial 16S ribosomal RNA (rRNA) gene amplicon sequencing and metagenomic analyses showed that the three microbial consortia were taxonomically distinct. Based on the taxonomic affiliation of protein-encoding sequences, members of the Bacteroidetes (e.g. Chryseobacterium, Weeksella, Flavobacterium and Sphingobacterium) were preferentially selected on WS1-M, whereas SG-M and CS-M favoured members of the Proteobacteria (e.g. Caulobacter, Brevundimonas, Stenotrophomonas and Xanthomonas). The highest degradation rates of lignin (~59 %) were observed with SG-M, whereas CS-M showed a high consumption of cellulose and hemicellulose. Analyses of the carbohydrate-active enzymes in the three microbial consortia showed the dominance of glycosyl hydrolases (e.g. of families GH3, GH43, GH13, GH10, GH29, GH28, GH16, GH4 and GH92). In addition, proteins of families AA6, AA10 and AA2 were detected. Analysis of secreted protein fractions (metasecretome) for each selected microbial consortium mainly showed the presence of enzymes able to degrade arabinan, arabinoxylan, xylan, β-glucan, galactomannan and rhamnogalacturonan. Notably, these metasecretomes contain enzymes that enable us to produce oligosaccharides directly from wheat straw, sugarcane bagasse and willow. Thus, the underlying microbial consortia constitute valuable resources for the production of enzyme cocktails for the efficient saccharification of plant biomass.

Computer-guided design of optimal microbial consortia for immune system modulation

PubMed Central

Szabady, Rose L; Bhattarai, Shakti K; Olle, Bernat; Norman, Jason M; Suda, Wataru; Oshima, Kenshiro; Hattori, Masahira; Gerber, Georg K; Sander, Chris; Honda, Kenya

2018-01-01

Manipulation of the gut microbiota holds great promise for the treatment of diseases. However, a major challenge is the identification of therapeutically potent microbial consortia that colonize the host effectively while maximizing immunologic outcome. Here, we propose a novel workflow to select optimal immune-inducing consortia from microbiome compositicon and immune effectors measurements. Using published and newly generated microbial and regulatory T-cell (Treg) data from germ-free mice, we estimate the contributions of twelve Clostridia strains with known immune-modulating effect to Treg induction. Combining this with a longitudinal data-constrained ecological model, we predict the ability of every attainable and ecologically stable subconsortium in promoting Treg activation and rank them by the Treg Induction Score (TrIS). Experimental validation of selected consortia indicates a strong and statistically significant correlation between predicted TrIS and measured Treg. We argue that computational indexes, such as the TrIS, are valuable tools for the systematic selection of immune-modulating bacteriotherapeutics. PMID:29664397

Computer-guided design of optimal microbial consortia for immune system modulation.

PubMed

Stein, Richard R; Tanoue, Takeshi; Szabady, Rose L; Bhattarai, Shakti K; Olle, Bernat; Norman, Jason M; Suda, Wataru; Oshima, Kenshiro; Hattori, Masahira; Gerber, Georg K; Sander, Chris; Honda, Kenya; Bucci, Vanni

2018-04-17

Manipulation of the gut microbiota holds great promise for the treatment of diseases. However, a major challenge is the identification of therapeutically potent microbial consortia that colonize the host effectively while maximizing immunologic outcome. Here, we propose a novel workflow to select optimal immune-inducing consortia from microbiome compositicon and immune effectors measurements. Using published and newly generated microbial and regulatory T-cell (T reg ) data from germ-free mice, we estimate the contributions of twelve Clostridia strains with known immune-modulating effect to T reg induction. Combining this with a longitudinal data-constrained ecological model, we predict the ability of every attainable and ecologically stable subconsortium in promoting T reg activation and rank them by the T reg Induction Score (TrIS). Experimental validation of selected consortia indicates a strong and statistically significant correlation between predicted TrIS and measured T reg . We argue that computational indexes, such as the TrIS, are valuable tools for the systematic selection of immune-modulating bacteriotherapeutics. © 2018, Stein et al.

Visualizing Microbial Biogeochemistry: NanoSIMS and Stable Isotope Probing (Invited)

NASA Astrophysics Data System (ADS)

Pett-Ridge, J.; Weber, P. K.

2009-12-01

Linking phylogenetic information to function in microbial communities is a key challenge for microbial ecology. Isotope-labeling experiments provide a useful means to investigate the ecophysiology of microbial populations and cells in the environment and allow measurement of nutrient transfers between cell types, symbionts and consortia. The combination of Nano-Secondary Ion Mass Spectrometry (NanoSIMS) analysis, in situ labeling and high resolution microscopy allows isotopic analysis to be linked to phylogeny and morphology and holds great promise for fine-scale studies of microbial systems. In NanoSIMS analysis, samples are sputtered with an energetic primary beam (Cs+, O-) liberating secondary ions that are separated by the mass spectrometer and detected in a suite of electron multipliers. Five isotopic species may be analyzed concurrently with spatial resolution as fine as 50nm. A high sensitivity isotope ratio ‘map’ can then be generated for the analyzed area. NanoSIMS images of 13C, 15N and Mo (a nitrogenase co-factor) localization in diazotrophic cyanobacteria show how cells differentially allocate resources within filaments and allow calculation of nutrient uptake rates on a cell by cell basis. Images of AM fungal hyphae-root and cyanobacteria-rhizobia associations indicate the mobilization and sharing (stealing?) of newly fixed C and N. In a related technique, “El-FISH”, stable isotope labeled biomass is probed with oligonucleotide-elemental labels and then imaged by NanoSIMS. In microbial consortia and cyanobacterial mats, this technique helps link microbial structure and function simultaneously even in systems with unknown and uncultivated microbes. Finally, the combination of re-engineered universal 16S oligonucleotide microarrays with NanoSIMS analyses may allow microbial identity to be linked to functional roles in complex systems such as mats and cellulose degrading hindgut communities. These newly developed methods provide correlated oligonucleotide, functional enzyme and metabolic image data and should help unravel the metabolic processes of complex microbial communities in soils, biofilms and aquatic systems.

Metagenomes from two microbial consortia associated with Santa Barbara seep oil.

PubMed

Hawley, Erik R; Malfatti, Stephanie A; Pagani, Ioanna; Huntemann, Marcel; Chen, Amy; Foster, Brian; Copeland, Alexander; del Rio, Tijana Glavina; Pati, Amrita; Jansson, Janet R; Gilbert, Jack A; Tringe, Susannah Green; Lorenson, Thomas D; Hess, Matthias

2014-12-01

The metagenomes from two microbial consortia associated with natural oils seeping into the Pacific Ocean offshore the coast of Santa Barbara (California, USA) were determined to complement already existing metagenomes generated from microbial communities associated with hydrocarbons that pollute the marine ecosystem. This genomics resource article is the first of two publications reporting a total of four new metagenomes from oils that seep into the Santa Barbara Channel. Copyright © 2014 Elsevier B.V. All rights reserved.

Halotolerant microbial consortia able to degrade highly recalcitrant plant biomass substrate.

PubMed

Cortes-Tolalpa, Larisa; Norder, Justin; van Elsas, Jan Dirk; Falcao Salles, Joana

2018-03-01

The microbial degradation of plant-derived compounds under salinity stress remains largely underexplored. The pretreatment of lignocellulose material, which is often needed to improve the production of lignocellulose monomers, leads to high salt levels, generating a saline environment that raises technical considerations that influence subsequent downstream processes. Here, we constructed halotolerant lignocellulose degrading microbial consortia by enriching a salt marsh soil microbiome on a recalcitrant carbon and energy source, i.e., wheat straw. The consortia were obtained after six cycles of growth on fresh substrate (adaptation phase), which was followed by four cycles on pre-digested (highly-recalcitrant) substrate (stabilization phase). The data indicated that typical salt-tolerant bacteria made up a large part of the selected consortia. These were "trained" to progressively perform better on fresh substrate, but a shift was observed when highly recalcitrant substrate was used. The most dominant bacteria in the consortia were Joostella marina, Flavobacterium beibuense, Algoriphagus ratkowskyi, Pseudomonas putida, and Halomonas meridiana. Interestingly, fungi were sparsely present and negatively affected by the change in the substrate composition. Sarocladium strictum was the single fungal strain recovered at the end of the adaptation phase, whereas it was deselected by the presence of recalcitrant substrate. Consortia selected in the latter substrate presented higher cellulose and lignin degradation than consortia selected on fresh substrate, indicating a specialization in transforming the recalcitrant regions of the substrate. Moreover, our results indicate that bacteria have a prime role in the degradation of recalcitrant lignocellulose under saline conditions, as compared to fungi. The final consortia constitute an interesting source of lignocellulolytic haloenzymes that can be used to increase the efficiency of the degradation process, while decreasing the associated costs.

Biodegradation Of Thiocyanate Using Microbial Consortia Cultured From Gold Mine Tailings

NASA Astrophysics Data System (ADS)

Moreau, J. W.; Watts, M. P.; Spurr, L. P.; Vu, H. P.

2015-12-01

Some bacteria possess the capability to degrade SCN-; therefore, harnessing this metabolic trait offers a biotechnological remediation strategy for SCN- produced in gold ore processing. A tailings storage facility (TSF) at a gold mine in Victoria, Australia holds large quantities of thiocyanate (SCN-) contaminated mine waste. The surface water in the TSF typically contains SCN- concentrations of >800 mg L-1, and seepage from the facility has contaminated the groundwater at the site. This study aimed to culture SCN-degrading microbes from the TSF, characterize the microbial consortia and test its operational parameters for use in a thiocyanate-degrading bioreactor. Surface samples were obtained from several locations around the TSF facility and used to inoculate medium reflective of the moderately saline and alkaline tailings water at the TSF, in the absence of organic carbon but subject to additions of phosphate and trace metals. Four microbial consortia capable of rapid SCN- degradation were successfully cultured. Sequencing of 16S rRNA genes found that the consortia were dominated by Thiobacillus species, a genus of known SCN- degraders. Lower abundances of other SCN- degraders; Sphingopyxis and Rhodobacter, were also identified. The impact of a number of geochemical conditions, including pH, temperature and SCN- concentration, upon the growth and SCN- degrading capacity of these consortia was determined. These results informed the optimization of a lab-scale thiocyanate degrading bioreactor. In summary, the cultured bacterial consortia proved effective towards SCN- degradation at the prevailing geochemical conditions of the TSF, requiring minimal nutrient additions. These consortia were dominated by genera of known autotrophic SCN- degraders. The comprehensive characterisation of these SCN- degrading consortia will provide the fundamental operational parameters required for deployment of this technique at the field scale.

The effect of the source of microorganisms on adaptation of hydrolytic consortia dedicated to anaerobic digestion of maize silage.

PubMed

Poszytek, Krzysztof; Pyzik, Adam; Sobczak, Adam; Lipinski, Leszek; Sklodowska, Aleksandra; Drewniak, Lukasz

2017-08-01

The main aim of this study was to evaluate the effect of the source of microorganisms on the selection of hydrolytic consortia dedicated to anaerobic digestion of maize silage. The selection process was investigated based on the analysis of changes in the hydrolytic activity and the diversity of microbial communities derived from (i) a hydrolyzer of a commercial agricultural biogas plant, (ii) cattle slurry and (iii) raw sewage sludge, during a series of 10 passages. Following the selection process, the adapted consortia were thoroughly analyzed for their ability to utilize maize silage and augmentation of anaerobic digestion communities. The results of selection of the consortia showed that every subsequent passage of each consortium leads to their adaptation to degradation of maize silage, which was manifested by the increased hydrolytic activity of the adapted consortia. Biodiversity analysis (based on the 16S rDNA amplicon sequencing) confirmed the changes microbial community of each consortium, and showed that after the last (10th) passage all microbial communities were dominated by the representatives of Lactobacillaceae, Prevotellaceae, Veillonellaceae. The results of the functional analyses showed that the adapted consortia improved the efficiency of maize silage degradation, as indicated by the increase in the concentration of glucose and volatile fatty acids (VFAs), as well as the soluble chemical oxygen demand (sCOD). Moreover, bioaugmentation of anaerobic digestion communities by the adapted hydrolytic consortia increased biogas yield by 10-29%, depending on the origin of the community. The obtained results also indicate that substrate input (not community origin) was the driving force responsible for the changes in the community structure of hydrolytic consortia dedicated to anaerobic digestion. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

Song, Hyun -Seob; Renslow, Ryan S.; Fredrickson, Jim K.

We note that many definitions of resilience have been proffered for natural and engineered ecosystems, but a conceptual consensus on resilience in microbial communities is still lacking. Here, we argue that the disconnect largely results from the wide variance in microbial community complexity, which range from simple synthetic consortia to complex natural communities, and divergence between the typical practical outcomes emphasized by ecologists and engineers. Viewing microbial communities as elasto-plastic systems, we argue that this gap between the engineering and ecological definitions of resilience stems from their respective emphases on elastic and plastic deformation, respectively. We propose that the twomore » concepts may be fundamentally united around the resilience of function rather than state in microbial communities and the regularity in the relationship between environmental variation and a community’s functional response. Furthermore, we posit that functional resilience is an intrinsic property of microbial communities, suggesting that state changes in response to environmental variation may be a key mechanism driving resilience in microbial communities.« less

Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass.

PubMed

Gladden, John M; Allgaier, Martin; Miller, Christopher S; Hazen, Terry C; VanderGheynst, Jean S; Hugenholtz, Philip; Simmons, Blake A; Singer, Steven W

2011-08-15

Industrial-scale biofuel production requires robust enzymatic cocktails to produce fermentable sugars from lignocellulosic biomass. Thermophilic bacterial consortia are a potential source of cellulases and hemicellulases adapted to harsher reaction conditions than commercial fungal enzymes. Compost-derived microbial consortia were adapted to switchgrass at 60°C to develop thermophilic biomass-degrading consortia for detailed studies. Microbial community analysis using small-subunit rRNA gene amplicon pyrosequencing and short-read metagenomic sequencing demonstrated that thermophilic adaptation to switchgrass resulted in low-diversity bacterial consortia with a high abundance of bacteria related to thermophilic paenibacilli, Rhodothermus marinus, and Thermus thermophilus. At lower abundance, thermophilic Chloroflexi and an uncultivated lineage of the Gemmatimonadetes phylum were observed. Supernatants isolated from these consortia had high levels of xylanase and endoglucanase activities. Compared to commercial enzyme preparations, the endoglucanase enzymes had a higher thermotolerance and were more stable in the presence of 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), an ionic liquid used for biomass pretreatment. The supernatants were used to saccharify [C2mim][OAc]-pretreated switchgrass at elevated temperatures (up to 80°C), demonstrating that these consortia are an excellent source of enzymes for the development of enzymatic cocktails tailored to more extreme reaction conditions.

Novel bacterial consortia isolated from plastic garbage processing areas demonstrated enhanced degradation for low density polyethylene.

PubMed

Skariyachan, Sinosh; Manjunatha, Vishal; Sultana, Subiya; Jois, Chandana; Bai, Vidya; Vasist, Kiran S

2016-09-01

This study aimed to formulate novel microbial consortia isolated from plastic garbage processing areas and thereby devise an eco-friendly approach for enhanced degradation of low-density polyethylene (LDPE). The LDPE degrading bacteria were screened and microbiologically characterized. The best isolates were formulated as bacterial consortia, and degradation efficiency was compared with the consortia formulated using known isolates obtained from the Microbial Culture Collection Centre (MTCC). The degradation products were analyzed by FTIR, GC-FID, tensile strength, and SEM. The bacterial consortia were characterized by 16S ribosomal DNA (rDNA) sequencing. The formulated bacterial consortia demonstrated 81 ± 4 and 38 ± 3 % of weight reduction for LDPE strips and LDPE pellets, respectively, over a period of 120 days. However, the consortia formulated by MTCC strains demonstrated 49 ± 4 and 20 ± 2 % of weight reduction for LDPE strips and pellets, respectively, for the same period. Furthermore, the three isolates in its individual application exhibited 70 ± 4, 68 ± 4, and 64 ± 4 % weight reduction for LDPE strips and 21 ± 2, 28 ± 2, 24 ± 2 % weight reduction for LDPE pellets over a period of 120 days (p < 0.05). The end product analysis showed structural changes and formation of bacterial film on degraded LDPE strips. The 16S rDNA characterization of bacterial consortia revealed that these organisms were novel strains and designated as Enterobacter sp. bengaluru-btdsce01, Enterobacter sp. bengaluru-btdsce02, and Pantoea sp. bengaluru-btdsce03. The current study thus suggests that industrial scale-up of these microbial consortia probably provides better insights for waste management of LDPE and similar types of plastic garbage.

Ex situ bioremediation of oil-contaminated soil.

PubMed

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

2010-04-15

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

Metataxonomic profiling and prediction of functional behaviour of wheat straw degrading microbial consortia

PubMed Central

2014-01-01

Background Mixed microbial cultures, in which bacteria and fungi interact, have been proposed as an efficient way to deconstruct plant waste. The characterization of specific microbial consortia could be the starting point for novel biotechnological applications related to the efficient conversion of lignocellulose to cello-oligosaccharides, plastics and/or biofuels. Here, the diversity, composition and predicted functional profiles of novel bacterial-fungal consortia are reported, on the basis of replicated aerobic wheat straw enrichment cultures. Results In order to set up biodegradative microcosms, microbial communities were retrieved from a forest soil and introduced into a mineral salt medium containing 1% of (un)treated wheat straw. Following each incubation step, sequential transfers were carried out using 1 to 1,000 dilutions. The microbial source next to three sequential batch cultures (transfers 1, 3 and 10) were analyzed by bacterial 16S rRNA gene and fungal ITS1 pyrosequencing. Faith’s phylogenetic diversity values became progressively smaller from the inoculum to the sequential batch cultures. Moreover, increases in the relative abundances of Enterobacteriales, Pseudomonadales, Flavobacteriales and Sphingobacteriales were noted along the enrichment process. Operational taxonomic units affiliated with Acinetobacter johnsonii, Pseudomonas putida and Sphingobacterium faecium were abundant and the underlying strains were successfully isolated. Interestingly, Klebsiella variicola (OTU1062) was found to dominate in both consortia, whereas K. variicola-affiliated strains retrieved from untreated wheat straw consortia showed endoglucanase/xylanase activities. Among the fungal players with high biotechnological relevance, we recovered members of the genera Penicillium, Acremonium, Coniochaeta and Trichosporon. Remarkably, the presence of peroxidases, alpha-L-fucosidases, beta-xylosidases, beta-mannases and beta-glucosidases, involved in lignocellulose degradation, was indicated by predictive bacterial metagenome reconstruction. Reassuringly, tests for specific (hemi)cellulolytic enzymatic activities, performed on the consortial secretomes, confirmed the presence of such gene functions. Conclusion In an in-depth characterization of two wheat straw degrading microbial consortia, we revealed the enrichment and selection of specific bacterial and fungal taxa that were presumably involved in (hemi) cellulose degradation. Interestingly, the microbial community composition was strongly influenced by the wheat straw pretreatment. Finally, the functional bacterial-metagenome prediction and the evaluation of enzymatic activities (at the consortial secretomes) revealed the presence and enrichment of proteins involved in the deconstruction of plant biomass. PMID:24955113

Population dynamics of two antilisterial cheese surface consortia revealed by temporal temperature gradient gel electrophoresis

PubMed Central

2010-01-01

Background Surface contamination of smear cheese by Listeria spp. is of major concern for the industry. Complex smear ecosystems have been shown to harbor antilisterial potential but the microorganisms and mechanisms involved in the inhibition mostly remain unclear, and are likely related to complex interactions than to production of single antimicrobial compounds. Bacterial biodiversity and population dynamics of complex smear ecosystems exhibiting antilisterial properties in situ were investigated by Temporal temperature gradient gel electrophoresis (TTGE), a culture independent technique, for two microbial consortia isolated from commercial Raclette type cheeses inoculated with defined commercial ripening cultures (F) or produced with an old-young smearing process (M). Results TTGE revealed nine bacterial species common to both F and M consortia, but consortium F exhibited a higher diversity than consortium M, with thirteen and ten species, respectively. Population dynamics were studied after application of the consortia on fresh-produced Raclette cheeses. TTGE analyses revealed a similar sequential development of the nine species common to both consortia. Beside common cheese surface bacteria (Staphylococcus equorum, Corynebacterium spp., Brevibacterium linens, Microbacterium gubbeenense, Agrococcus casei), the two consortia contained marine lactic acid bacteria (Alkalibacterium kapii, Marinilactibacillus psychrotolerans) that developed early in ripening (day 14 to 20), shortly after the growth of staphylococci (day 7). A decrease of Listeria counts was observed on cheese surface inoculated at day 7 with 0.1-1 × 102 CFU cm-2, when cheeses were smeared with consortium F or M. Listeria counts went below the detection limit of the method between day 14 and 28 and no subsequent regrowth was detected over 60 to 80 ripening days. In contrast, Listeria grew to high counts (105 CFU cm-2) on cheeses smeared with a defined surface culture. Conclusions This work reports the first population dynamics study of complex smear ecosystems exhibiting in situ antilisterial activity. TTGE revealed the presence of marine lactic acid bacteria that are likely related to the strong Listeria inhibition, as their early development in the smear occurred simultaneously with a decrease in Listeria cell count. PMID:20222967

Microbial degradation of Cold Lake Blend and Western Canadian select dilbits by freshwater enrichments.

PubMed

Deshpande, Ruta S; Sundaravadivelu, Devi; Techtmann, Stephen; Conmy, Robyn N; Santo Domingo, Jorge W; Campo, Pablo

2018-06-15

Treatability experiments were conducted to determine the biodegradation of diluted bitumen (dilbit) at 5 and 25 °C for 72 and 60 days, respectively. Microbial consortia obtained from the Kalamazoo River Enbridge Energy spill site were enriched on dilbit at both 5 (cryo) and 25 (meso) ºC. On every sampling day, triplicates were sacrificed and residual hydrocarbon concentrations (alkanes and polycyclic aromatic hydrocarbons) were determined by GCMS/MS. The composition and relative abundance of different bacterial groups were identified by 16S rRNA gene sequencing analysis. While some physicochemical differences were observed between the two dilbits, their biodegradation profiles were similar. The rates and extent of degradation were greater at 25 °C. Both consortia metabolized 99.9% of alkanes; however, the meso consortium was more effective at removing aromatics than the cryo consortium (97.5 vs 70%). Known hydrocarbon-degrading bacteria were present in both consortia (Pseudomonas, Rhodococcus, Hydrogenophaga, Parvibaculum, Arthrobacter, Acidovorax), although their relative abundances depended on the temperatures at which they were enriched. Regardless of the dilbit type, the microbial community structure significantly changed as a response to the diminishing hydrocarbon load. Our results demonstrate that dilbit can be effectively degraded by autochthonous microbial consortia from sites with recent exposure to dilbit contamination. Published by Elsevier B.V.

Unveiling the metabolic potential of two soil-derived microbial consortia selected on wheat straw

PubMed Central

Jiménez, Diego Javier; Chaves-Moreno, Diego; van Elsas, Jan Dirk

2015-01-01

Based on the premise that plant biomass can be efficiently degraded by mixed microbial cultures and/or enzymes, we here applied a targeted metagenomics-based approach to explore the metabolic potential of two forest soil-derived lignocellulolytic microbial consortia, denoted RWS and TWS (bred on wheat straw). Using the metagenomes of three selected batches of two experimental systems, about 1.2 Gb of sequence was generated. Comparative analyses revealed an overrepresentation of predicted carbohydrate transporters (ABC, TonB and phosphotransferases), two-component sensing systems and β-glucosidases/galactosidases in the two consortia as compared to the forest soil inoculum. Additionally, “profiling” of carbohydrate-active enzymes showed significant enrichments of several genes encoding glycosyl hydrolases of families GH2, GH43, GH92 and GH95. Sequence analyses revealed these to be most strongly affiliated to genes present on the genomes of Sphingobacterium, Bacteroides, Flavobacterium and Pedobacter spp. Assembly of the RWS and TWS metagenomes generated 16,536 and 15,902 contigs of ≥10 Kb, respectively. Thirteen contigs, containing 39 glycosyl hydrolase genes, constitute novel (hemi)cellulose utilization loci with affiliation to sequences primarily found in the Bacteroidetes. Overall, this study provides deep insight in the plant polysaccharide degrading capabilities of microbial consortia bred from forest soil, highlighting their biotechnological potential. PMID:26343383

Methyl tert-butyl ether biodegradation by microbial consortia obtained from soil samples of gasoline-polluted sites in Mexico.

PubMed

Morales, Marcia; Velázquez, Elia; Jan, Janet; Revah, Sergio; González, Uriel; Razo-Flores, Elías

2004-02-01

Microbial consortia obtained from soil samples of gasoline-polluted sites were individually enriched with pentane, hexane, isooctane and toluene. Cometabolism with methyl tert-butyl ether, (MTBE), gave maximum degradation rates of 49, 12, 32 and 0 mg g(-1)protein h(-1), respectively. MTBE was fully degraded even when pentane was completely depleted with a cometabolic coefficient of 1 mgMTBE mg(-1)pentane. The analysis of 16S rDNA from isolated microorganisms in the pentane-adapted consortia showed that microorganisms could be assigned to Pseudomonas. This is the first work reporting the cometabolic mineralization of MTBE by consortium of this genus.

The microbiology of biomining: development and optimization of mineral-oxidizing microbial consortia.

PubMed

Rawlings, Douglas E; Johnson, D Barrie

2007-02-01

Biomining, the use of micro-organisms to recover precious and base metals from mineral ores and concentrates, has developed into a successful and expanding area of biotechnology. While careful considerations are made in the design and engineering of biomining operations, microbiological aspects have been subjected to far less scrutiny and control. Biomining processes employ microbial consortia that are dominated by acidophilic, autotrophic iron- or sulfur-oxidizing prokaryotes. Mineral biooxidation takes place in highly aerated, continuous-flow, stirred-tank reactors or in irrigated dump or heap reactors, both of which provide an open, non-sterile environment. Continuous-flow, stirred tanks are characterized by homogeneous and constant growth conditions where the selection is for rapid growth, and consequently tank consortia tend to be dominated by two or three species of micro-organisms. In contrast, heap reactors provide highly heterogeneous growth environments that change with the age of the heap, and these tend to be colonized by a much greater variety of micro-organisms. Heap micro-organisms grow as biofilms that are not subject to washout and the major challenge is to provide sufficient biodiversity for optimum performance throughout the life of a heap. This review discusses theoretical and pragmatic aspects of assembling microbial consortia to process different mineral ores and concentrates, and the challenges for using constructed consortia in non-sterile industrial-scale operations.

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

PubMed

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

2007-05-01

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

Biodegradation and surfactant-mediated biodegradation of diesel fuel by 218 microbial consortia are not correlated to cell surface hydrophobicity.

PubMed

Owsianiak, Mikołaj; Szulc, Alicja; Chrzanowski, Łukasz; Cyplik, Paweł; Bogacki, Mariusz; Olejnik-Schmidt, Agnieszka K; Heipieper, Hermann J

2009-09-01

In this study, we elucidated the role of cell surface hydrophobicity (microbial adhesion to hydrocarbons method, MATH) and the effect of anionic rhamnolipids and nonionic Triton X-100 surfactants on biodegradation of diesel fuel employing 218 microbial consortia isolated from petroleum-contaminated soils. Applied enrichment procedure with floating diesel fuel as a sole carbon source in liquid cultures resulted in consortia of varying biodegradation potential and diametrically different cell surface properties, suggesting that cell surface hydrophobicity is a conserved parameter. Surprisingly, no correlations between cell surface hydrophobicity and biodegradation of diesel fuel were found. Nevertheless, both surfactants altered cell surface hydrophobicity of the consortia in similar manner: increased for the hydrophilic and decreased for the hydrophobic cultures. In addition to this, the surfactants exhibited similar influence on diesel fuel biodegradation: Increase was observed for initially slow-degrading cultures and the opposite for fast degraders. This indicates that in the surfactant-mediated biodegradation, effectiveness of surfactants depends on the specification of microorganisms and not on the type of surfactant. In contrary to what was previously reported for pure strains, cell surface hydrophobicity, as determined by MATH, is not a good descriptor of biodegrading potential for mixed cultures.

Egypt's Red Sea coast: phylogenetic analysis of cultured microbial consortia in industrialized sites.

PubMed

Mustafa, Ghada A; Abd-Elgawad, Amr; Abdel-Haleem, Alyaa M; Siam, Rania

2014-01-01

The Red Sea possesses a unique geography, and its shores are rich in mangrove, macro-algal and coral reef ecosystems. Various sources of pollution affect Red Sea biota, including microbial life. We assessed the effects of industrialization on microbes along the Egyptian Red Sea coast at eight coastal sites and two lakes. The bacterial communities of sediment samples were analyzed using bacterial 16S rDNA pyrosequencing of V6-V4 hypervariable regions. The taxonomic assignment of 131,402 significant reads to major bacterial taxa revealed five main bacterial phyla dominating the sampled sites: Proteobacteria (68%), Firmicutes (13%), Fusobacteria (12%), Bacteriodetes (6%), and Spirochetes (0.03%). Further analysis revealed distinct bacterial consortia that primarily included (1) marine Vibrio spp.-suggesting a "marine Vibrio phenomenon"; (2) potential human pathogens; and (3) oil-degrading bacteria. We discuss two divergent microbial consortia that were sampled from Solar Lake West near Taba/Eilat and Saline Lake in Ras Muhammad; these consortia contained the highest abundance of human pathogens and no pathogens, respectively. Our results draw attention to the effects of industrialization on the Red Sea and suggest the need for further analysis to overcome the hazardous effects observed at the impacted sites.

Anti-inflammatory effect of microbial consortia during the utilization of dietary polysaccharides.

PubMed

Thomson, Pamela; Medina, Daniel A; Ortúzar, Verónica; Gotteland, Martín; Garrido, Daniel

2018-07-01

The gut microbiome has a significant impact on host health, especially at the metabolic level. Dietary compounds arriving at the colon have a large influence on the composition of the gut microbiome. High fiber diets have been associated to health benefits that are mediated in great part by short chain fatty acids (SCFA). Gut microbial interactions are relevant for the utilization of complex carbohydrates in the gut microbiome. In this work we characterized the utilization of two dietary polysaccharides by combinations of representative adult gut microbes, and the impact of their activities on a cellular inflammation model. Paired combinations of Bifidobacterium adolescentis, Bacteroides dorei, Lactobacillus plantarum, Escherichia coli and Clostridium symbiosum were grown in inulin or xylan as carbon source. Their relative abundance, substrate consumption and major SCFAs produced were determined. Higher cell growth was observed during inulin consumption, and B. adolescentis and L. plantarum were dominant in co-cultures. The co-culture of B. dorei and C. symbiosum was dominant in xylan. In several cases the combined bacterial growth was lower in co-cultures than monocultures, with a few exceptions of synergistic growth between microorganisms. Inulin fermentation resulted in larger acetate and lactate concentrations, and several combinations grown in xylan containing C. symbiosum were characterized by high amounts of butyrate. These microbial consortia were scaled to batch bioreactor fermentations reaching high cell densities and similar profiles to co-culture experiments. Interestingly, a microbial combination producing high amounts of butyrate was able to reduce IL-8 expression in HT-29 cells co-incubated with TNFα. In summary, this work shows that microbial interactions during the utilization of dietary polysaccharides are complex and substrate dependent. Moreover, certain combinations deploy potent anti-inflammatory effects, which are independent of individual microbial growth, and could be mediated in part by higher butyrate production. Copyright © 2018 Elsevier Ltd. All rights reserved.

Genomic Reconstruction of Carbohydrate Utilization Capacities in Microbial-Mat Derived Consortia

PubMed Central

Leyn, Semen A.; Maezato, Yukari; Romine, Margaret F.; Rodionov, Dmitry A.

2017-01-01

Two nearly identical unicyanobacterial consortia (UCC) were previously isolated from benthic microbial mats that occur in a heliothermal saline lake in northern Washington State. Carbohydrates are a primary source of carbon and energy for most heterotrophic bacteria. Since CO2 is the only carbon source provided, the cyanobacterium must provide a source of carbon to the heterotrophs. Available genomic sequences for all members of the UCC provide opportunity to investigate the metabolic routes of carbon transfer between autotroph and heterotrophs. Here, we applied a subsystem-based comparative genomics approach to reconstruct carbohydrate utilization pathways and identify glycohydrolytic enzymes, carbohydrate transporters and pathway-specific transcriptional regulators in 17 heterotrophic members of the UCC. The reconstructed metabolic pathways include 800 genes, near a one-fourth of which encode enzymes, transporters and regulators with newly assigned metabolic functions resulting in discovery of novel functional variants of carbohydrate utilization pathways. The in silico analysis revealed the utilization capabilities for 40 carbohydrates and their derivatives. Two Halomonas species demonstrated the largest number of sugar catabolic pathways. Trehalose, sucrose, maltose, glucose, and beta-glucosides are the most commonly utilized saccharides in this community. Reconstructed regulons for global regulators HexR and CceR include central carbohydrate metabolism genes in the members of Gammaproteobacteria and Alphaproteobacteria, respectively. Genomics analyses were supplemented by experimental characterization of metabolic phenotypes in four isolates derived from the consortia. Measurements of isolate growth on the defined medium supplied with individual carbohydrates confirmed most of the predicted catabolic phenotypes. Not all consortia members use carbohydrates and only a few use complex polysaccharides suggesting a hierarchical carbon flow from cyanobacteria to each heterotroph. In summary, the genomics-based identification of carbohydrate utilization capabilities provides a basis for future experimental studies of carbon flow in UCC. PMID:28751880

Selection and screening of microbial consortia for efficient and ecofriendly degradation of plastic garbage collected from urban and rural areas of Bangalore, India.

PubMed

Skariyachan, Sinosh; Megha, M; Kini, Meghna Niranjan; Mukund, Kamath Manali; Rizvi, Alya; Vasist, Kiran

2015-01-01

Industrialization and urbanization have led to massive accumulation of plastic garbage all over India. The persistence of plastic in soil and aquatic environment has become ecological threat to the metropolitan city such as Bangalore, India. Present study investigates an ecofriendly, efficient and cost-effective approach for plastic waste management by the screening of novel microbial consortia which are capable of degrading plastic polymers. Plastic-contaminated soil and water samples were collected from six hot spots of urban and rural areas of Bangalore. The plastic-degrading bacteria were enriched, and degradation ability was determined by zone of clearance method. The percentage of polymer degradation was initially monitored by weight loss method, and the main isolates were characterized by standard microbiology protocols. These isolates were used to form microbial consortia, and the degradation efficiency of the consortia was compared with individual isolate and known strains obtained from the Microbial Type Culture Collection (MTCC) and Gene Bank, India. One of the main enzymes responsible for polymer degradation was identified, and the biodegradation mechanism was hypothesized by bioinformatics studies. From this study, it is evident that the bacteria utilized the plastic polymer as a sole source of carbon and showed 20-50% weight reduction over a period of 120 days. The two main bacteria responsible for the degradation were microbiologically characterized to be Pseudomonas spp. These bacteria could grow optimally at 37 °C in pH 9.0 and showed 35-40% of plastic weight reduction over 120 days. These isolates were showed better degradation ability than known strains from MTCC. The current study further revealed that the microbial consortia formulated by combining Psuedomonas spp. showed 40 plastic weight reduction over a period of 90 days. Further, extracellular lipase, one of the main enzymes responsible for polymer degradation, was identified. The computational docking studies suggested that polyethylene glycol and polystyrene present in the plastics might have good interaction towards the microbial lipase with stable binding and interacting forces which probably could be one of the reasons for the degradative mechanisms.

Evidence of the Generation of Isosaccharinic Acids and Their Subsequent Degradation by Local Microbial Consortia within Hyper-Alkaline Contaminated Soils, with Relevance to Intermediate Level Radioactive Waste Disposal

PubMed Central

Rout, Simon P.; Charles, Christopher J.; Garratt, Eva J.; Laws, Andrew P.; Gunn, John; Humphreys, Paul N.

2015-01-01

The contamination of surface environments with hydroxide rich wastes leads to the formation of high pH (>11.0) soil profiles. One such site is a legacy lime works at Harpur Hill, Derbyshire where soil profile indicated in-situ pH values up to pH 12. Soil and porewater profiles around the site indicated clear evidence of the presence of the α and β stereoisomers of isosaccharinic acid (ISA) resulting from the anoxic, alkaline degradation of cellulosic material. ISAs are of particular interest with regards to the disposal of cellulosic materials contained within the intermediate level waste (ILW) inventory of the United Kingdom, where they may influence radionuclide mobility via complexation events occurring within a geological disposal facility (GDF) concept. The mixing of uncontaminated soils with the alkaline leachate of the site resulted in ISA generation, where the rate of generation in-situ is likely to be dependent upon the prevailing temperature of the soil. Microbial consortia present in the uncontaminated soil were capable of surviving conditions imposed by the alkaline leachate and demonstrated the ability to utilise ISAs as a carbon source. Leachate-contaminated soil was sub-cultured in a cellulose degradation product driven microcosm operating at pH 11, the consortia present were capable of the degradation of ISAs and the generation of methane from the resultant H2/CO2 produced from fermentation processes. Following microbial community analysis, fermentation processes appear to be predominated by Clostridia from the genus Alkaliphilus sp, with methanogenesis being attributed to Methanobacterium and Methanomassiliicoccus sp. The study is the first to identify the generation of ISA within an anthropogenic environment and advocates the notion that microbial activity within an ILW-GDF is likely to influence the impact of ISAs upon radionuclide migration. PMID:25748643

Evidence of the generation of isosaccharinic acids and their subsequent degradation by local microbial consortia within hyper-alkaline contaminated soils, with relevance to intermediate level radioactive waste disposal.

PubMed

Rout, Simon P; Charles, Christopher J; Garratt, Eva J; Laws, Andrew P; Gunn, John; Humphreys, Paul N

2015-01-01

The contamination of surface environments with hydroxide rich wastes leads to the formation of high pH (>11.0) soil profiles. One such site is a legacy lime works at Harpur Hill, Derbyshire where soil profile indicated in-situ pH values up to pH 12. Soil and porewater profiles around the site indicated clear evidence of the presence of the α and β stereoisomers of isosaccharinic acid (ISA) resulting from the anoxic, alkaline degradation of cellulosic material. ISAs are of particular interest with regards to the disposal of cellulosic materials contained within the intermediate level waste (ILW) inventory of the United Kingdom, where they may influence radionuclide mobility via complexation events occurring within a geological disposal facility (GDF) concept. The mixing of uncontaminated soils with the alkaline leachate of the site resulted in ISA generation, where the rate of generation in-situ is likely to be dependent upon the prevailing temperature of the soil. Microbial consortia present in the uncontaminated soil were capable of surviving conditions imposed by the alkaline leachate and demonstrated the ability to utilise ISAs as a carbon source. Leachate-contaminated soil was sub-cultured in a cellulose degradation product driven microcosm operating at pH 11, the consortia present were capable of the degradation of ISAs and the generation of methane from the resultant H2/CO2 produced from fermentation processes. Following microbial community analysis, fermentation processes appear to be predominated by Clostridia from the genus Alkaliphilus sp, with methanogenesis being attributed to Methanobacterium and Methanomassiliicoccus sp. The study is the first to identify the generation of ISA within an anthropogenic environment and advocates the notion that microbial activity within an ILW-GDF is likely to influence the impact of ISAs upon radionuclide migration.

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

PubMed Central

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

2016-01-01

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

Enhanced methane production via repeated batch bioaugmentation pattern of enriched microbial consortia.

PubMed

Yang, Zhiman; Guo, Rongbo; Xu, Xiaohui; Wang, Lin; Dai, Meng

2016-09-01

Using batch and repeated batch cultivations, this study investigated the effects of bioaugmentation with enriched microbial consortia (named as EMC) on methane production from effluents of hydrogen-producing stage of potato slurry, as well as on the indigenous bacterial community. The results demonstrated that the improved methane production and shift of the indigenous bacterial community structure were dependent on the EMC/sludge ratio and bioaugmentation patterns. The methane yield and production rate in repeated batch bioaugmentation pattern of EMC were, respectively, average 15% and 10% higher than in one-time bioaugmentation pattern of EMC. DNA-sequencing approach showed that the enhanced methane production in the repeated batch bioaugmentation pattern of EMC mainly resulted from the enriched iron-reducing bacteria and the persistence of the introduced Syntrophomonas, which led to a rapid degradation of individual VFAs to methane. The findings contributed to understanding the correlation between the bioaugmentation of microbial consortia, community shift, and methane production. Copyright © 2016 Elsevier Ltd. All rights reserved.

Phylogenetic analysis of TCE-dechlorinating consortia enriched on a variety of electron donors.

PubMed

Freeborn, Ryan A; West, Kimberlee A; Bhupathiraju, Vishvesh K; Chauhan, Sadhana; Rahm, Brian G; Richardson, Ruth E; Alvarez-Cohen, Lisa

2005-11-01

Two rapidly fermented electron donors, lactate and methanol, and two slowly fermented electron donors, propionate and butyrate, were selected for enrichment studies to evaluate the characteristics of anaerobic microbial consortia that reductively dechlorinate TCE to ethene. Each electron donor enrichment subculture demonstrated the ability to dechlorinate TCE to ethene through several serial transfers. Microbial community analyses based upon 16S rDNA, including terminal restriction fragment length polymorphism (T-RFLP) and clone library/sequencing, were performed to assess major changes in microbial community structure associated with electron donors capable of stimulating reductive dechlorination. Results demonstrated that five phylogenic subgroups or genera of bacteria were present in all consortia, including Dehalococcoides sp., low G+C Gram-positives (mostly Clostridium and Eubacterium sp.), Bacteroides sp., Citrobacter sp., and delta Proteobacteria (mostly Desulfovibrio sp.). Phylogenetic association indicates that only minor shifts in the microbial community structure occurred between the four alternate electron donor enrichments and the parent consortium. Inconsistent detection of Dehalococcoides spp. in clone libraries and T-RFLP of enrichment subcultures was resolved using quantitative polymerase chain reaction (Q-PCR). Q-PCR with primers specific to Dehalococcoides 16S rDNA resulted in positive detection of this species in all enrichments. Our results suggest that TCE-dechlorinating consortia can be stably maintained on a variety of electron donors and that quantities of Dehalococcoides cells detected with Dehalococcoides specific 16S rDNA primer/probe sets do not necessarily correlate well with solvent degradation rates.

Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh

PubMed Central

Wilbanks, Elizabeth G; Jaekel, Ulrike; Salman, Verena; Humphrey, Parris T; Eisen, Jonathan A; Facciotti, Marc T; Buckley, Daniel H; Zinder, Stephen H; Druschel, Gregory K; Fike, David A; Orphan, Victoria J

2014-01-01

Microbial metabolism is the engine that drives global biogeochemical cycles, yet many key transformations are carried out by microbial consortia over short spatiotemporal scales that elude detection by traditional analytical approaches. We investigate syntrophic sulfur cycling in the ‘pink berry’ consortia of the Sippewissett Salt Marsh through an integrative study at the microbial scale. The pink berries are macroscopic, photosynthetic microbial aggregates composed primarily of two closely associated species: sulfide-oxidizing purple sulfur bacteria (PB-PSB1) and sulfate-reducing bacteria (PB-SRB1). Using metagenomic sequencing and 34S-enriched sulfate stable isotope probing coupled with nanoSIMS, we demonstrate interspecies transfer of reduced sulfur metabolites from PB-SRB1 to PB-PSB1. The pink berries catalyse net sulfide oxidation and maintain internal sulfide concentrations of 0–500 μm. Sulfide within the berries, captured on silver wires and analysed using secondary ion mass spectrometer, increased in abundance towards the berry interior, while δ34S-sulfide decreased from 6‰ to −31‰ from the exterior to interior of the berry. These values correspond to sulfate–sulfide isotopic fractionations (15–53‰) consistent with either sulfate reduction or a mixture of reductive and oxidative metabolisms. Together this combined metagenomic and high-resolution isotopic analysis demonstrates active sulfur cycling at the microscale within well-structured macroscopic consortia consisting of sulfide-oxidizing anoxygenic phototrophs and sulfate-reducing bacteria. PMID:24428801

Egypt's Red Sea coast: phylogenetic analysis of cultured microbial consortia in industrialized sites

PubMed Central

Mustafa, Ghada A.; Abd-Elgawad, Amr; Abdel-Haleem, Alyaa M.; Siam, Rania

2014-01-01

The Red Sea possesses a unique geography, and its shores are rich in mangrove, macro-algal and coral reef ecosystems. Various sources of pollution affect Red Sea biota, including microbial life. We assessed the effects of industrialization on microbes along the Egyptian Red Sea coast at eight coastal sites and two lakes. The bacterial communities of sediment samples were analyzed using bacterial 16S rDNA pyrosequencing of V6-V4 hypervariable regions. The taxonomic assignment of 131,402 significant reads to major bacterial taxa revealed five main bacterial phyla dominating the sampled sites: Proteobacteria (68%), Firmicutes (13%), Fusobacteria (12%), Bacteriodetes (6%), and Spirochetes (0.03%). Further analysis revealed distinct bacterial consortia that primarily included (1) marine Vibrio spp.—suggesting a “marine Vibrio phenomenon”; (2) potential human pathogens; and (3) oil-degrading bacteria. We discuss two divergent microbial consortia that were sampled from Solar Lake West near Taba/Eilat and Saline Lake in Ras Muhammad; these consortia contained the highest abundance of human pathogens and no pathogens, respectively. Our results draw attention to the effects of industrialization on the Red Sea and suggest the need for further analysis to overcome the hazardous effects observed at the impacted sites. PMID:25157243

A bacterial pioneer produces cellulase complexes that persist through community succession

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

Kolinko, Sebastian; Wu, Yu-Wei; Tachea, Firehiwot

Cultivation of microbial consortia provides low-complexity communities that can serve as tractable models to understand community dynamics. Time-resolved metagenomics demonstrated that an aerobic cellulolytic consortium cultivated from compost exhibited community dynamics consistent with the definition of an endogenous heterotrophic succession. The genome of the proposed pioneer population, 'Candidatus Reconcilibacillus cellulovorans', possessed a gene cluster containing multidomain glycoside hydrolases (GHs). Purification of the soluble cellulase activity from a 300litre cultivation of this consortium revealed that ~70% of the activity arose from the 'Ca. Reconcilibacillus cellulovorans' multidomain GHs assembled into cellulase complexes through glycosylation. These remarkably stable complexes have supramolecular structures formore » enzymatic cellulose hydrolysis that are distinct from cellulosomes. The persistence of these complexes during cultivation indicates that they may be active through multiple cultivations of this consortium and act as public goods that sustain the community. Thus, the provision of extracellular GHs as public goods may influence microbial community dynamics in native biomass-deconstructing communities relevant to agriculture, human health and biotechnology.« less

A bacterial pioneer produces cellulase complexes that persist through community succession

DOE PAGES

Kolinko, Sebastian; Wu, Yu-Wei; Tachea, Firehiwot; ...

2017-11-06

Cultivation of microbial consortia provides low-complexity communities that can serve as tractable models to understand community dynamics. Time-resolved metagenomics demonstrated that an aerobic cellulolytic consortium cultivated from compost exhibited community dynamics consistent with the definition of an endogenous heterotrophic succession. The genome of the proposed pioneer population, 'Candidatus Reconcilibacillus cellulovorans', possessed a gene cluster containing multidomain glycoside hydrolases (GHs). Purification of the soluble cellulase activity from a 300litre cultivation of this consortium revealed that ~70% of the activity arose from the 'Ca. Reconcilibacillus cellulovorans' multidomain GHs assembled into cellulase complexes through glycosylation. These remarkably stable complexes have supramolecular structures formore » enzymatic cellulose hydrolysis that are distinct from cellulosomes. The persistence of these complexes during cultivation indicates that they may be active through multiple cultivations of this consortium and act as public goods that sustain the community. Thus, the provision of extracellular GHs as public goods may influence microbial community dynamics in native biomass-deconstructing communities relevant to agriculture, human health and biotechnology.« less

A bacterial pioneer produces cellulase complexes that persist through community succession.

PubMed

Kolinko, Sebastian; Wu, Yu-Wei; Tachea, Firehiwot; Denzel, Evelyn; Hiras, Jennifer; Gabriel, Raphael; Bäcker, Nora; Chan, Leanne Jade G; Eichorst, Stephanie A; Frey, Dario; Chen, Qiushi; Azadi, Parastoo; Adams, Paul D; Pray, Todd R; Tanjore, Deepti; Petzold, Christopher J; Gladden, John M; Simmons, Blake A; Singer, Steven W

2018-01-01

Cultivation of microbial consortia provides low-complexity communities that can serve as tractable models to understand community dynamics. Time-resolved metagenomics demonstrated that an aerobic cellulolytic consortium cultivated from compost exhibited community dynamics consistent with the definition of an endogenous heterotrophic succession. The genome of the proposed pioneer population, 'Candidatus Reconcilibacillus cellulovorans', possessed a gene cluster containing multidomain glycoside hydrolases (GHs). Purification of the soluble cellulase activity from a 300litre cultivation of this consortium revealed that ~70% of the activity arose from the 'Ca. Reconcilibacillus cellulovorans' multidomain GHs assembled into cellulase complexes through glycosylation. These remarkably stable complexes have supramolecular structures for enzymatic cellulose hydrolysis that are distinct from cellulosomes. The persistence of these complexes during cultivation indicates that they may be active through multiple cultivations of this consortium and act as public goods that sustain the community. The provision of extracellular GHs as public goods may influence microbial community dynamics in native biomass-deconstructing communities relevant to agriculture, human health and biotechnology.

Ecological genomics of the newly discovered diazotrophic filamentous cyanobacterium ESFC-1

NASA Astrophysics Data System (ADS)

Everroad, C.; Bebout, B.; Bebout, L. E.; Detweiler, A. M.; Lee, J.; Mayali, X.; Singer, S. W.; Stuart, R.; Weber, P. K.; Woebken, D.; Pett-Ridge, J.

2014-12-01

Cyanobacteria-dominated microbial mats played a key role in the evolution of the early Earth and provide a model for exploring the relationships between ecology, evolution and biogeochemistry. A recently described nonheterocystous filamentous cyanobacterium, strain ESFC-1, has been shown to be a major diazotroph year round in the intertidal microbial mat system at Elkhorn Slough, CA, USA. Based on phylogenetic analyses of the 16s RNA gene, ESFC-1 appears to belong to a unique, genus-level divergence within the cyanobacteria. Consequently, the draft genome sequence of this strain has been determined. Here we report features of this genome, particularly as they relate to the ecological functions and capabilities of strain ESFC-1. One striking feature of this cyanobacterium is the apparent lack of a functional bi-directional hydrogenase typically expected to be found within a diazotroph; consortia- and culture-based experiments exploring the metabolic processes of ESFC-1 also indicate that this hydrogenase is absent. Co-culture studies with ESFC-1 and some of the dominant heterotrophic members within the microbial mat system, including the ubiquitous Flavobacterium Muricauda sp., which often is found associated with cyanobacteria in nature and in culture collections worldwide, have also been performed. We report on these species-species interactions, including materials exchange between the cyanobacterium and heterotrophic bacterium. The combination of genomics with culture- and consortia-based experimental research is a powerful tool for understanding microbial processes and interactions in complex ecosystems.

Substrate-Specific Development of Thermophilic Bacterial Consortia by Using Chemically Pretreated Switchgrass.

PubMed

Eichorst, Stephanie A; Joshua, Chijioke; Sathitsuksanoh, Noppadon; Singh, Seema; Simmons, Blake A; Singer, Steven W

2014-12-01

Microbial communities that deconstruct plant biomass have broad relevance in biofuel production and global carbon cycling. Biomass pretreatments reduce plant biomass recalcitrance for increased efficiency of enzymatic hydrolysis. We exploited these chemical pretreatments to study how thermophilic bacterial consortia adapt to deconstruct switchgrass (SG) biomass of various compositions. Microbial communities were adapted to untreated, ammonium fiber expansion (AFEX)-pretreated, and ionic-liquid (IL)-pretreated SG under aerobic, thermophilic conditions using green waste compost as the inoculum to study biomass deconstruction by microbial consortia. After microbial cultivation, gravimetric analysis of the residual biomass demonstrated that both AFEX and IL pretreatment enhanced the deconstruction of the SG biomass approximately 2-fold. Two-dimensional nuclear magnetic resonance (2D-NMR) experiments and acetyl bromide-reactive-lignin analysis indicated that polysaccharide hydrolysis was the dominant process occurring during microbial biomass deconstruction, and lignin remaining in the residual biomass was largely unmodified. Small-subunit (SSU) rRNA gene amplicon libraries revealed that although the dominant taxa across these chemical pretreatments were consistently represented by members of the Firmicutes, the Bacteroidetes, and Deinococcus-Thermus, the abundance of selected operational taxonomic units (OTUs) varied, suggesting adaptations to the different substrates. Combining the observations of differences in the community structure and the chemical and physical structure of the biomass, we hypothesize specific roles for individual community members in biomass deconstruction. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Proteomic profiling of an undefined microbial consortium cultured in fermented dairy manure: Methods development.

PubMed

Hanson, Andrea J; Paszczynski, Andrzej J; Coats, Erik R

2016-03-01

The production of polyhydroxyalkanoates (PHA; bioplastics) from waste or surplus feedstocks using mixed microbial consortia (MMC) and aerobic dynamic feeding (ADF) is a growing field within mixed culture biotechnology. This study aimed to optimize a 2DE workflow to investigate the proteome dynamics of an MMC synthesizing PHA from fermented dairy manure. To mitigate the challenges posed to effective 2DE by this complex sample matrix, the bacterial biomass was purified using Accudenz gradient centrifugation (AGC) before protein extraction. The optimized 2DE method yielded high-quality gels suitable for quantitative comparative analysis and subsequent protein identification by LC-MS/MS. The optimized 2DE method could be adapted to other proteomic investigations involving MMC in complex organic or environmental matrices. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Decoding molecular interactions in microbial communities

PubMed Central

Abreu, Nicole A.; Taga, Michiko E.

2016-01-01

Microbial communities govern numerous fundamental processes on earth. Discovering and tracking molecular interactions among microbes is critical for understanding how single species and complex communities impact their associated host or natural environment. While recent technological developments in DNA sequencing and functional imaging have led to new and deeper levels of understanding, we are limited now by our inability to predict and interpret the intricate relationships and interspecies dependencies within these communities. In this review, we highlight the multifaceted approaches investigators have taken within their areas of research to decode interspecies molecular interactions that occur between microbes. Understanding these principles can give us greater insight into ecological interactions in natural environments and within synthetic consortia. PMID:27417261

Combined use of microbial consortia isolated from different agricultural soils and cyclodextrin as a bioremediation technique for herbicide contaminated soils.

PubMed

Villaverde, J; Rubio-Bellido, M; Lara-Moreno, A; Merchan, F; Morillo, E

2018-02-01

The phenylurea herbicide diuron is persistent in soil, water and groundwater and is considered to be a highly toxic molecule. The principal product of its biodegradation, 3,4-dichloroaniline, exhibits greater toxicity than diuron and is persistent in the environment. Five diuron degrading microbial consortia (C1C5), isolated from different agricultural soils, were investigated for diuron mineralization activity. The C2 consortium was able to mineralize 81.6% of the diuron in solution, while consortium C3 was only able to mineralize 22.9%. Isolated consortia were also tested in soil slurries and in all cases, except consortium C4, DT 50 (the time required for the diuron concentration to decline to half of its initial value) was drastically reduced, from 700 days (non-inoculated control) to 546, 351, and 171 days for the consortia C5, C2, and C1, respectively. In order to test the effectiveness of the isolated consortium C1 in a more realistic scenario, soil diuron mineralization assays were performed under static conditions (40% of the soil water-holding capacity). A significant enhancement of diuron mineralization was observed after C1 inoculation, with 23.2% of the herbicide being mineralized in comparison to 13.1% for the control experiment. Hydroxypropyl-β-cyclodextrin, a biodegradable organic enhancer of pollutant bioavailability, used in combination with C1 bioaugmentation in static conditions, resulted in a significant decrease in the DT 50 (214 days; 881 days, control experiment). To the best of our knowledge, this is the first report of the use of soil-isolated microbial consortia in combination with cyclodextrins proposed as a bioremediation technique for pesticide contaminated soils. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

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

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

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

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

DOE PAGES

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

2016-02-25

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

Analysis of microbial community and nitrogen transition with enriched nitrifying soil microbes for organic hydroponics.

PubMed

Saijai, Sakuntala; Ando, Akinori; Inukai, Ryuya; Shinohara, Makoto; Ogawa, Jun

2016-06-27

Nitrifying microbial consortia were enriched from bark compost in a water system by regulating the amounts of organic nitrogen compounds and by controlling the aeration conditions with addition of CaCO 3 for maintaining suitable pH. Repeated enrichment showed reproducible mineralization of organic nitrogen via the conversion of ammonium ions ([Formula: see text]) and nitrite ions ([Formula: see text]) into nitrate ions ([Formula: see text]). The change in microbial composition during the enrichment was investigated by PCR-DGGE analysis with a focus on prokaryote, ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, and eukaryote cell types. The microbial transition had a simple profile and showed clear relation to nitrogen ions transition. Nitrosomonas and Nitrobacter were mainly detected during [Formula: see text] and [Formula: see text] oxidation, respectively. These results revealing representative microorganisms acting in each ammonification and nitrification stages will be valuable for the development of artificial simple microbial consortia for organic hydroponics that consisted of identified heterotrophs and autotrophic nitrifying bacteria.

Effect of copper and lead on two consortia of phototrophic microorganisms and their capacity to sequester metals.

PubMed

Burgos, A; Maldonado, J; De Los Rios, A; Solé, A; Esteve, I

2013-09-15

The roles of consortia of phototrophic microorganisms have been investigated in this paper to determine their potential role to tolerate or resist metals and to capture them from polluted cultures. With this purpose, two consortia of microorganisms: on one hand, Geitlerinema sp. DE2011 (Ge) and Scenedesmus sp. DE2009 (Sc) (both identified in this paper by molecular biology methods) isolated from Ebro Delta microbial mats, and on the other, Spirulina sp. PCC 6313 (Sp) and Chroococcus sp. PCC 9106 (Ch), from Pasteur culture collection were polluted with copper and lead. In order to analyze the ability of these consortia to tolerate and capture metals, copper and lead were selected, because both have been detected in Ebro Delta microbial mats. The tolerance-resistance to copper and lead for both consortia was determined in vivo and at cellular level by Confocal Laser Scanning Microscopy (CLSM-λscan function). The results obtained demonstrate that both consortia are highly tolerant-resistant to lead and that the limits between the copper concentration having cytotoxic effect and that having an essential effect are very close in these microorganisms. The capacity of both consortia to capture extra- and intracellular copper and lead was determined by Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM) respectively, coupled to an Energy Dispersive X-ray detector (EDX). The results showed that all the microorganisms assayed were able to capture copper extracellularly in the extrapolymeric substances, and lead extra- and intracellularly in polyphosphate inclusions. Moreover, the studied micro-organisms did not exert any inhibitory effect on each other's metal binding capacity. From the results obtained in this paper, it can be concluded that consortia of phototrophic microorganisms could play a very important role in biorepairing sediments polluted by metals, as a result of their ability to tolerate or resist high concentrations of metals and to bioaccumulate them, extra- and intracellulary. Copyright © 2013 Elsevier B.V. All rights reserved.

Modulation of microbial consortia enriched from different polluted environments during petroleum biodegradation.

PubMed

Omrani, Rahma; Spini, Giulia; Puglisi, Edoardo; Saidane, Dalila

2018-04-01

Environmental microbial communities are key players in the bioremediation of hydrocarbon pollutants. Here we assessed changes in bacterial abundance and diversity during the degradation of Tunisian Zarzatine oil by four indigenous bacterial consortia enriched from a petroleum station soil, a refinery reservoir soil, a harbor sediment and seawater. The four consortia were found to efficiently degrade up to 92.0% of total petroleum hydrocarbons after 2 months of incubation. Illumina 16S rRNA gene sequencing revealed that the consortia enriched from soil and sediments were dominated by species belonging to Pseudomonas and Acinetobacter genera, while in the seawater-derived consortia Dietzia, Fusobacterium and Mycoplana emerged as dominant genera. We identified a number of species whose relative abundances bloomed from small to high percentages: Dietzia daqingensis in the seawater microcosms, and three OTUs classified as Acinetobacter venetianus in all two soils and sediment derived microcosms. Functional analyses on degrading genes were conducted by comparing PCR results of the degrading genes alkB, ndoB, cat23, xylA and nidA1 with inferences obtained by PICRUSt analysis of 16S amplicon data: the two data sets were partly in agreement and suggest a relationship between the catabolic genes detected and the rate of biodegradation obtained. The work provides detailed insights about the modulation of bacterial communities involved in petroleum biodegradation and can provide useful information for in situ bioremediation of oil-related pollution.

Microbial mats: an ecological niche for fungi

PubMed Central

Cantrell, Sharon A.; Duval-Pérez, Lisabeth

2013-01-01

Fungi were documented in tropical hypersaline microbial mats and their role in the degradation of complex carbohydrates (exopolymeric substance – EPS) was explored. Fungal diversity is higher during the wet season with Acremonium, Aspergillus, Cladosporium, and Penicillium among the more common genera. Diversity is also higher in the oxic layer and in young and transient mats. Enrichments with xanthan (a model EPS) show that without antibiotics (full community) degradation is faster than enrichments with antibacterial (fungal community) and antifungal (bacterial community) agents, suggesting that degradation is performed by a consortium of organisms (bacteria and fungi). The combined evidence from all experiments indicates that bacteria carried out approximately two-third of the xanthan degradation. The pattern of degradation is similar between seasons and layers but degradation is faster in enrichments from the wet season. The research suggests that fungi thrive in these hypersaline consortia and may participate in the carbon cycle through the degradation of complex carbohydrates. PMID:23577004

The inside tract: The appendicular, cecal, and colonic microbiome of captive aye-ayes.

PubMed

Greene, Lydia K; McKenney, Erin A

2018-04-17

The aye-aye (Daubentonia madagascariensis) is famous for its feeding strategies that target structurally defended, but high-quality resources. Nonetheless, the influence of this digestible diet on gut microbial contributions to aye-aye metabolism and nutrition remains unexplored. When four captive aye-ayes were unexpectedly lost to persin toxicity, we opportunistically collected samples along the animals' gastrointestinal tracts. Here we describe the diversity and composition of appendicular, cecal, and colonic consortia relative to the aye-aye's unusual feeding ecology. During necropsies, we collected digestive content from the appendix, cecum, and distal colon. We determined microbiome structure at these sites via amplicon sequencing of the 16S rRNA gene and an established bioinformatics pipeline. The aye-ayes' microbiomes exhibited low richness and diversity compared to the consortia of other lemurs housed at the same facility, and were dominated by a single genus, Prevotella. Appendicular microbiomes were differentiated from more homogenized cecal and colonic consortia by lower richness and diversity, greater evenness, and a distinct taxonomic composition. The simplicity of the aye-aye's gut microbiome could be attributed to captivity-induced dysbiosis, or it may reflect this species' extreme foraging investment in a digestible diet that requires little microbial metabolism. Site-specific appendicular consortia, but more similar cecal and colonic consortia, support the theory that the appendix functions as a safe-house for beneficial bacteria, and confirm fecal communities as fairly reliable proxies for consortia along the lower gut. We encourage others to make similar use of natural or accidental losses for probing the primate gut microbiome. © 2018 Wiley Periodicals, Inc.

Classes of organic molecules targeted by a methanogenic microbial consortium grown on sedimentary rocks of various maturities

PubMed Central

Meslé, Margaux; Dromart, Gilles; Haeseler, Frank; Oger, Philippe M.

2015-01-01

Organic-rich shales are populated by methanogenic consortia that are able to degrade the fossilized organic matter into methane gas. To identify the organic fraction effectively degraded, we have sequentially depleted two types of organic-rich sedimentary rocks, shale, and coal, at two different maturities, by successive solvent extractions to remove the most soluble fractions (maltenes and asphaltenes) and isolate kerogen. We show the ability of the consortia to produce methane from all rock samples, including those containing the most refractory organic matter, i.e., the kerogen. Shales yielded higher methane production than lignite and coal. Mature rocks yielded more methane than immature rocks. Surprisingly, the efficiency of the consortia was not influenced by the removal of the easily biodegradable fractions contained in the maltenes and asphaltenes. This suggests that one of the limitations of organic matter degradation in situ may be the accessibility to the carbon and energy source. Indeed, bitumen has a colloidal structure that may prevent the microbial consortia from reaching the asphaltenes in the bulk rock. Solvent extractions might favor the access to asphaltenes and kerogen by modifying the spatial organization of the molecules in the rock matrix. PMID:26136731

Ecogenomics of microbial communities in bioremediation of chlorinated contaminated sites

PubMed Central

Maphosa, Farai; Lieten, Shakti H.; Dinkla, Inez; Stams, Alfons J.; Smidt, Hauke; Fennell, Donna E.

2012-01-01

Organohalide compounds such as chloroethenes, chloroethanes, and polychlorinated benzenes are among the most significant pollutants in the world. These compounds are often found in contamination plumes with other pollutants such as solvents, pesticides, and petroleum derivatives. Microbial bioremediation of contaminated sites, has become commonplace whereby key processes involved in bioremediation include anaerobic degradation and transformation of these organohalides by organohalide respiring bacteria and also via hydrolytic, oxygenic, and reductive mechanisms by aerobic bacteria. Microbial ecogenomics has enabled us to not only study the microbiology involved in these complex processes but also develop tools to better monitor and assess these sites during bioremediation. Microbial ecogenomics have capitalized on recent advances in high-throughput and -output genomics technologies in combination with microbial physiology studies to address these complex bioremediation problems at a system level. Advances in environmental metagenomics, transcriptomics, and proteomics have provided insights into key genes and their regulation in the environment. They have also given us clues into microbial community structures, dynamics, and functions at contaminated sites. These techniques have not only aided us in understanding the lifestyles of common organohalide respirers, for example Dehalococcoides, Dehalobacter, and Desulfitobacterium, but also provided insights into novel and yet uncultured microorganisms found in organohalide respiring consortia. In this paper, we look at how ecogenomic studies have aided us to understand the microbial structures and functions in response to environmental stimuli such as the presence of chlorinated pollutants. PMID:23060869

Ecological Inferences from a deep screening of the Complex Bacterial Consortia associated with the coral, Porites astreoides.

PubMed

Rodriguez-Lanetty, Mauricio; Granados-Cifuentes, Camila; Barberan, Albert; Bellantuono, Anthony J; Bastidas, Carolina

2013-08-01

The functional role of the bacterial organisms in the reef ecosystem and their contribution to the coral well-being remain largely unclear. The first step in addressing this gap of knowledge relies on in-depth characterization of the coral microbial community and its changes in diversity across coral species, space and time. In this study, we focused on the exploration of microbial community assemblages associated with an ecologically important Caribbean scleractinian coral, Porites astreoides, using Illumina high-throughput sequencing of the V5 fragment of 16S rRNA gene. We collected data from a large set of biological replicates, allowing us to detect patterns of geographical structure and resolve co-occurrence patterns using network analyses. The taxonomic analysis of the resolved diversity showed consistent and dominant presence of two OTUs affiliated with the order Oceanospirillales, which corroborates a specific pattern of bacterial association emerging for this coral species and for many other corals within the genus Porites. We argue that this specific association might indicate a symbiotic association with the adult coral partner. Furthermore, we identified a highly diverse rare bacterial 'biosphere' (725 OTUs) also living along with the dominant bacterial symbionts, but the assemblage of this biosphere is significantly structured along the geographical scale. We further discuss that some of these rare bacterial members show significant association with other members of the community reflecting the complexity of the networked consortia within the coral holobiont. © 2013 John Wiley & Sons Ltd.

Engineering Escherichia coli coculture systems for the production of biochemical products.

PubMed

Zhang, Haoran; Pereira, Brian; Li, Zhengjun; Stephanopoulos, Gregory

2015-07-07

Engineering microbial consortia to express complex biosynthetic pathways efficiently for the production of valuable compounds is a promising approach for metabolic engineering and synthetic biology. Here, we report the design, optimization, and scale-up of an Escherichia coli-E. coli coculture that successfully overcomes fundamental microbial production limitations, such as high-level intermediate secretion and low-efficiency sugar mixture utilization. For the production of the important chemical cis,cis-muconic acid, we show that the coculture approach achieves a production yield of 0.35 g/g from a glucose/xylose mixture, which is significantly higher than reported in previous reports. By efficiently producing another compound, 4-hydroxybenzoic acid, we also demonstrate that the approach is generally applicable for biosynthesis of other important industrial products.

Fed-batch anaerobic valorization of slaughterhouse by-products with mesophilic microbial consortia without methane production.

PubMed

Pessiot, J; Nouaille, R; Jobard, M; Singhania, R R; Bournilhas, A; Christophe, G; Fontanille, P; Peyret, P; Fonty, G; Larroche, C

2012-07-01

This work aimed at setting up a fully instrumented, laboratory-scale bioreactor enabling anaerobic valorization of solid substrates through hydrogen and/or volatile fatty acid (VFA) production using mixed microbial populations (consortia). The substrate used was made of meat-based wastes, especially from slaughterhouses, which are becoming available in large amounts as a consequence of the growing constraints for waste disposal from meat industry. A reconstituted microbial mesophilic consortium without Archaebacteria (methanogens), named PBr, was cultivated in a 5-L anaerobic bioreactor on slaughterhouse wastes. The experiments were carried out with sequential fed-batch operations, including liquid medium removal from the bioreactor and addition of fresh substrate. VFAs and nitrogen were the main metabolites observed, while hydrogen accumulation was very low and no methane production was evidenced. After 1,300 h of culture, yields obtained for VFAs reached 0.38 g/g dry matter. Strain composition of the microbial consortium was also characterized using molecular tools (temporal temperature gradient gel electrophoresis and gene sequencing).

Microbial consortia at steady supply

PubMed Central

Taillefumier, Thibaud; Posfai, Anna; Meir, Yigal; Wingreen, Ned S

2017-01-01

Metagenomics has revealed hundreds of species in almost all microbiota. In a few well-studied cases, microbial communities have been observed to coordinate their metabolic fluxes. In principle, microbes can divide tasks to reap the benefits of specialization, as in human economies. However, the benefits and stability of an economy of microbial specialists are far from obvious. Here, we physically model the population dynamics of microbes that compete for steadily supplied resources. Importantly, we explicitly model the metabolic fluxes yielding cellular biomass production under the constraint of a limited enzyme budget. We find that population dynamics generally leads to the coexistence of different metabolic types. We establish that these microbial consortia act as cartels, whereby population dynamics pins down resource concentrations at values for which no other strategy can invade. Finally, we propose that at steady supply, cartels of competing strategies automatically yield maximum biomass, thereby achieving a collective optimum. DOI: http://dx.doi.org/10.7554/eLife.22644.001 PMID:28473032

Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass

PubMed Central

Minty, Jeremy J.; Singer, Marc E.; Scholz, Scott A.; Bae, Chang-Hoon; Ahn, Jung-Ho; Foster, Clifton E.; Liao, James C.; Lin, Xiaoxia Nina

2013-01-01

Synergistic microbial communities are ubiquitous in nature and exhibit appealing features, such as sophisticated metabolic capabilities and robustness. This has inspired fast-growing interest in engineering synthetic microbial consortia for biotechnology development. However, there are relatively few reports of their use in real-world applications, and achieving population stability and regulation has proven to be challenging. In this work, we bridge ecology theory with engineering principles to develop robust synthetic fungal-bacterial consortia for efficient biosynthesis of valuable products from lignocellulosic feedstocks. The required biological functions are divided between two specialists: the fungus Trichoderma reesei, which secretes cellulase enzymes to hydrolyze lignocellulosic biomass into soluble saccharides, and the bacterium Escherichia coli, which metabolizes soluble saccharides into desired products. We developed and experimentally validated a comprehensive mathematical model for T. reesei/E. coli consortia, providing insights on key determinants of the system’s performance. To illustrate the bioprocessing potential of this consortium, we demonstrate direct conversion of microcrystalline cellulose and pretreated corn stover to isobutanol. Without costly nutrient supplementation, we achieved titers up to 1.88 g/L and yields up to 62% of theoretical maximum. In addition, we show that cooperator–cheater dynamics within T. reesei/E. coli consortia lead to stable population equilibria and provide a mechanism for tuning composition. Although we offer isobutanol production as a proof-of-concept application, our modular system could be readily adapted for production of many other valuable biochemicals. PMID:23959872

Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass.

PubMed

Minty, Jeremy J; Singer, Marc E; Scholz, Scott A; Bae, Chang-Hoon; Ahn, Jung-Ho; Foster, Clifton E; Liao, James C; Lin, Xiaoxia Nina

2013-09-03

Synergistic microbial communities are ubiquitous in nature and exhibit appealing features, such as sophisticated metabolic capabilities and robustness. This has inspired fast-growing interest in engineering synthetic microbial consortia for biotechnology development. However, there are relatively few reports of their use in real-world applications, and achieving population stability and regulation has proven to be challenging. In this work, we bridge ecology theory with engineering principles to develop robust synthetic fungal-bacterial consortia for efficient biosynthesis of valuable products from lignocellulosic feedstocks. The required biological functions are divided between two specialists: the fungus Trichoderma reesei, which secretes cellulase enzymes to hydrolyze lignocellulosic biomass into soluble saccharides, and the bacterium Escherichia coli, which metabolizes soluble saccharides into desired products. We developed and experimentally validated a comprehensive mathematical model for T. reesei/E. coli consortia, providing insights on key determinants of the system's performance. To illustrate the bioprocessing potential of this consortium, we demonstrate direct conversion of microcrystalline cellulose and pretreated corn stover to isobutanol. Without costly nutrient supplementation, we achieved titers up to 1.88 g/L and yields up to 62% of theoretical maximum. In addition, we show that cooperator-cheater dynamics within T. reesei/E. coli consortia lead to stable population equilibria and provide a mechanism for tuning composition. Although we offer isobutanol production as a proof-of-concept application, our modular system could be readily adapted for production of many other valuable biochemicals.

Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia

PubMed Central

Hatzenpichler, Roland; Connon, Stephanie A.; Goudeau, Danielle; Malmstrom, Rex R.; Woyke, Tanja; Orphan, Victoria J.

2016-01-01

To understand the biogeochemical roles of microorganisms in the environment, it is important to determine when and under which conditions they are metabolically active. Bioorthogonal noncanonical amino acid tagging (BONCAT) can reveal active cells by tracking the incorporation of synthetic amino acids into newly synthesized proteins. The phylogenetic identity of translationally active cells can be determined by combining BONCAT with rRNA-targeted fluorescence in situ hybridization (BONCAT-FISH). In theory, BONCAT-labeled cells could be isolated with fluorescence-activated cell sorting (BONCAT-FACS) for subsequent genetic analyses. Here, in the first application, to our knowledge, of BONCAT-FISH and BONCAT-FACS within an environmental context, we probe the translational activity of microbial consortia catalyzing the anaerobic oxidation of methane (AOM), a dominant sink of methane in the ocean. These consortia, which typically are composed of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria, have been difficult to study due to their slow in situ growth rates, and fundamental questions remain about their ecology and diversity of interactions occurring between ANME and associated partners. Our activity-correlated analyses of >16,400 microbial aggregates provide the first evidence, to our knowledge, that AOM consortia affiliated with all five major ANME clades are concurrently active under controlled conditions. Surprisingly, sorting of individual BONCAT-labeled consortia followed by whole-genome amplification and 16S rRNA gene sequencing revealed previously unrecognized interactions of ANME with members of the poorly understood phylum Verrucomicrobia. This finding, together with our observation that ANME-associated Verrucomicrobia are found in a variety of geographically distinct methane seep environments, suggests a broader range of symbiotic relationships within AOM consortia than previously thought. PMID:27357680

Visualizing in situ translational activity for identifying and sorting slow-growing archaeal-bacterial consortia

DOE PAGES

Hatzenpichler, Roland; Connon, Stephanie A.; Goudeau, Danielle; ...

2016-06-28

To understand the biogeochemical roles of microorganisms in the environment, it is important to determine when and under which conditions they are metabolically active. Bioorthogonal noncanonical amino acid tagging (BONCAT) can reveal active cells by tracking the incorporation of synthetic amino acids into newly synthesized proteins. The phylogenetic identity of translationally active cells can be determined by combining BONCAT with rRNA-targeted fluorescence in situ hybridization (BONCAT-FISH). In theory, BONCAT-labeled cells could be isolated with fluorescence-activated cell sorting (BONCAT-FACS) for subsequent genetic analyses. Here, in the first application, to our knowledge, of BONCAT-FISH and BONCAT-FACS within an environmental context, we probemore » the translational activity of microbial consortia catalyzing the anaerobic oxidation of methane (AOM), a dominant sink of methane in the ocean. These consortia, which typically are composed of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria, have been difficult to study due to their slow in situ growth rates, and fundamental questions remain about their ecology and diversity of interactions occurring between ANME and associated partners. Our activity-correlated analyses of > 16,400 microbial aggregates provide the first evidence, to our knowledge, that AOM consortia affiliated with all five major ANME clades are concurrently active under controlled conditions. Surprisingly, sorting of individual BONCAT-labeled consortia followed by whole-genome amplification and 16S rRNA gene sequencing revealed previously unrecognized interactions of ANME with members of the poorly understood phylum Verrucomicrobia. This finding, together with our observation that ANME-associated Verrucomicrobia are found in a variety of geographically distinct methane seep environments, suggests a broader range of symbiotic relationships within AOM consortia than previously thought.« less

Visualizing in situ translational activity for identifying and sorting slow-growing archaeal-bacterial consortia

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

Hatzenpichler, Roland; Connon, Stephanie A.; Goudeau, Danielle

To understand the biogeochemical roles of microorganisms in the environment, it is important to determine when and under which conditions they are metabolically active. Bioorthogonal noncanonical amino acid tagging (BONCAT) can reveal active cells by tracking the incorporation of synthetic amino acids into newly synthesized proteins. The phylogenetic identity of translationally active cells can be determined by combining BONCAT with rRNA-targeted fluorescence in situ hybridization (BONCAT-FISH). In theory, BONCAT-labeled cells could be isolated with fluorescence-activated cell sorting (BONCAT-FACS) for subsequent genetic analyses. Here, in the first application, to our knowledge, of BONCAT-FISH and BONCAT-FACS within an environmental context, we probemore » the translational activity of microbial consortia catalyzing the anaerobic oxidation of methane (AOM), a dominant sink of methane in the ocean. These consortia, which typically are composed of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria, have been difficult to study due to their slow in situ growth rates, and fundamental questions remain about their ecology and diversity of interactions occurring between ANME and associated partners. Our activity-correlated analyses of > 16,400 microbial aggregates provide the first evidence, to our knowledge, that AOM consortia affiliated with all five major ANME clades are concurrently active under controlled conditions. Surprisingly, sorting of individual BONCAT-labeled consortia followed by whole-genome amplification and 16S rRNA gene sequencing revealed previously unrecognized interactions of ANME with members of the poorly understood phylum Verrucomicrobia. This finding, together with our observation that ANME-associated Verrucomicrobia are found in a variety of geographically distinct methane seep environments, suggests a broader range of symbiotic relationships within AOM consortia than previously thought.« less

Complex pectin metabolism by gut bacteria reveals novel catalytic functions

PubMed Central

Baslé, Arnaud; Gray, Joseph; Venditto, Immacolata; Briggs, Jonathon; Zhang, Xiaoyang; Labourel, Aurore; Terrapon, Nicolas; Buffetto, Fanny; Nepogodiev, Sergey; Xiao, Yao; Field, Robert A.; Zhu, Yanping; O’Neil, Malcolm A.; Urbanowicz, Breeana R.; York, William S.; Davies, Gideon J.; Abbott, D. Wade; Ralet, Marie-Christine; Martens, Eric C.; Henrissat, Bernard; Gilbert, Harry J.

2017-01-01

Carbohydrate polymers drive microbial diversity in the human gut microbiota. It is unclear, however, whether bacterial consortia or single organisms are required to depolymerize highly complex glycans. Here we show that the gut bacterium Bacteroides thetaiotaomicron utilizes the most structurally complex glycan known; the plant pectic polysaccharide rhamnogalacturonan-II, cleaving all but one of its 21 distinct glycosidic linkages. We show that rhamnogalacturonan-II side-chain and backbone deconstruction are coordinated, to overcome steric constraints, and that degradation reveals previously undiscovered enzyme families and novel catalytic activities. The degradome informs revision of the current structural model of RG-II and highlights how individual gut bacteria orchestrate manifold enzymes to metabolize the most challenging glycans in the human diet. PMID:28329766

Direct cloning from enrichment cultures, a reliable strategy for isolation of complete operons and genes from microbial consortia.

PubMed

Entcheva, P; Liebl, W; Johann, A; Hartsch, T; Streit, W R

2001-01-01

Enrichment cultures of microbial consortia enable the diverse metabolic and catabolic activities of these populations to be studied on a molecular level and to be explored as potential sources for biotechnology processes. We have used a combined approach of enrichment culture and direct cloning to construct cosmid libraries with large (>30-kb) inserts from microbial consortia. Enrichment cultures were inoculated with samples from five environments, and high amounts of avidin were added to the cultures to favor growth of biotin-producing microbes. DNA was extracted from three of these enrichment cultures and used to construct cosmid libraries; each library consisted of between 6,000 and 35,000 clones, with an average insert size of 30 to 40 kb. The inserts contained a diverse population of genomic DNA fragments isolated from the consortia organisms. These three libraries were used to complement the Escherichia coli biotin auxotrophic strain ATCC 33767 Delta(bio-uvrB). Initial screens resulted in the isolation of seven different complementing cosmid clones, carrying biotin biosynthesis operons. Biotin biosynthesis capabilities and growth under defined conditions of four of these clones were studied. Biotin measured in the different culture supernatants ranged from 42 to 3,800 pg/ml/optical density unit. Sequencing the identified biotin synthesis genes revealed high similarities to bio operons from gram-negative bacteria. In addition, random sequencing identified other interesting open reading frames, as well as two operons, the histidine utilization operon (hut), and the cluster of genes involved in biosynthesis of molybdopterin cofactors in bacteria (moaABCDE).

Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition.

PubMed

Wang, Cheng; Dong, Da; Wang, Haoshu; Müller, Karin; Qin, Yong; Wang, Hailong; Wu, Weixiang

2016-01-01

Compost habitats sustain a vast ensemble of microbes specializing in the degradation of lignocellulosic plant materials and are thus important both for their roles in the global carbon cycle and as potential sources of biochemical catalysts for advanced biofuels production. Studies have revealed substantial diversity in compost microbiomes, yet how this diversity relates to functions and even to the genes encoding lignocellulolytic enzymes remains obscure. Here, we used a metagenomic analysis of the rice straw-adapted (RSA) microbial consortia enriched from compost ecosystems to decipher the systematic and functional contexts within such a distinctive microbiome. Analyses of the 16S pyrotag library and 5 Gbp of metagenomic sequence showed that the phylum Actinobacteria was the predominant group among the Bacteria in the RSA consortia, followed by Proteobacteria, Firmicutes, Chloroflexi, and Bacteroidetes. The CAZymes profile revealed that CAZyme genes in the RSA consortia were also widely distributed within these bacterial phyla. Strikingly, about 46.1 % of CAZyme genes were from actinomycetal communities, which harbored a substantially expanded catalog of the cellobiohydrolase, β-glucosidase, acetyl xylan esterase, arabinofuranosidase, pectin lyase, and ligninase genes. Among these communities, a variety of previously unrecognized species was found, which reveals a greater ecological functional diversity of thermophilic Actinobacteria than previously assumed. These data underline the pivotal role of thermophilic Actinobacteria in lignocellulose biodegradation processes in the compost habitat. Besides revealing a new benchmark for microbial enzymatic deconstruction of lignocelluloses, the results suggest that actinomycetes found in compost ecosystems are potential candidates for mining efficient lignocellulosic enzymes in the biofuel industry.

Characteristics and performance of aerobic algae-bacteria granular consortia in a photo-sequencing batch reactor.

PubMed

Liu, Lin; Zeng, Zhichao; Bee, Mingyang; Gibson, Valerie; Wei, Lili; Huang, Xu; Liu, Chaoxiang

2018-05-05

The characteristics and performance of algae-bacteria granular consortia which cultivated with aerobic granules and targeted algae (Chlorella and Scenedesmus), and the essential difference between granular consortia and aerobic granules were investigated in this experiment. The result indicated that algae-bacteria granular consortia could be successfully developed, and the algae present in the granular consortia were mainly Chlorella and Scenedesmus. Although the change of chlorophyll composition revealed the occurrence of light limitation for algal growth, the granular consortia could maintain stable granular structure, and even showed better settling property than aerobic granules. Total nitrogen and phosphate in the algal-bacterial granular system showed better removal efficiencies (50.2% and 35.7%) than those in the aerobic granular system (32.8% and 25.6%) within one cycle (6 h). The biodiesel yield of aerobic granules could be significantly improved by algal coupled process, yet methyl linolenate and methyl palmitoleate were the dominant composition of biodiesel obtained from granular consortia and aerobic granules, respectively. Meanwhile, the difference of dominant bacterial communities in the both granules was found at the order level and family level, and alpha diversity indexes revealed the granular consortia had a higher microbial diversity. Copyright © 2018. Published by Elsevier B.V.

Enhanced biodegradation of low and high-density polyethylene by novel bacterial consortia formulated from plastic-contaminated cow dung under thermophilic conditions.

PubMed

Skariyachan, Sinosh; Setlur, Anagha Shamsundar; Naik, Sujay Yashwant; Naik, Ashwini Amaresh; Usharani, Makam; Vasist, Kiran S

2017-03-01

The current study aimed to devise eco-friendly, safe, and cost-effective strategies for enhanced degradation of low- and high-density polyethylene (LDPE and HDPE) using newly formulated thermophilic microbial consortia from cow dung and to assess the biodegradation end products. The plastic-degrading bacteria from cow dung samples gathered from highly plastic-acclimated environments were enriched by standard protocols. The degradation ability was comprehended by zone of clearance method, and the percentage of degradation was monitored by weight reduction process. The best isolates were characterized by standard microbiological and molecular biology protocols. The best isolates were employed to form several combinations of microbial consortia, and the degradation end products were analyzed. The stability of 16S ribosomal DNA (rDNA) was predicted by bioinformatics approach. This study identified 75 ± 2, 55 ± 2, 60 ± 3, and 43 ± 3% degradation for LDPE strips, pellets, HDPE strips, and pellets, respectively, for a period of 120 days (p < 0.05) at 55 °C by the formulated consortia of IS1-IS4, and the degradation efficiency was found to be better in comparison with other formulations. The end product analysis by Fourier transform infrared, scanning electron microscopy, energy-dispersive spectroscopy, and nuclear magnetic resonance showed major structural changes and formation of bacterial biofilm on plastic surfaces. These novel isolates were designated as Bacillus vallismortis bt-dsce01, Psuedomonas protegens bt-dsce02, Stenotrophomonas sp. bt-dsce03, and Paenibacillus sp.bt-dsce04 by 16S rDNA sequencing and suggested good gene stability with minimum Gibb's free energy. Therefore, this study imparts substantial information regarding the utilization of these thermophilic microbial consortia from cow dung for rapid polyethylene removal.

Ionic liquid biodegradability depends on specific wastewater microbial consortia.

PubMed

Docherty, Kathryn M; Aiello, Steven W; Buehler, Barbara K; Jones, Stuart E; Szymczyna, Blair R; Walker, Katherine A

2015-10-01

Complete biodegradation of a newly-synthesized chemical in a wastewater treatment plant (WWTP) eliminates the potential for novel environmental pollutants. However, differences within- and between-WWTP microbial communities may alter expectations for biodegradation. WWTP communities can also serve as a source of unique consortia that, when enriched, can metabolize chemicals that tend to resist degradation, but are otherwise promising green alternatives. We tested the biodegradability of three ionic liquids (ILs): 1-octyl-3-methylpyridinium bromide (OMP), 1-butyl-3-methylpyridinium bromide (BMP) and 1-butyl-3-methylimidazolium chloride (BMIM). We performed tests using communities from two WWTPs at three time points. Site-specific and temporal variation both influenced community composition, which impacted the success of OMP biodegradability. Neither BMP nor BMIM degraded in any test, suggesting that these ILs are unlikely to be removed by traditional treatment. Following standard biodegradation assays, we enriched for three consortia that were capable of quickly degrading OMP, BMP and BMIM. Our results indicate WWTPs are not functionally redundant with regard to biodegradation of specific ionic liquids. However, consortia can be enriched to degrade chemicals that fail biodegradability assays. This information can be used to prepare pre-treatment procedures and prevent environmental release of novel pollutants. Copyright © 2015 Elsevier Ltd. All rights reserved.

Simultaneous Removal of Phenol and Dissolved Solids from Wastewater Using Multichambered Microbial Desalination Cell.

PubMed

Pradhan, Harapriya; Jain, Sumat Chand; Ghangrekar, Makarand M

2015-12-01

Microbial desalination cell (MDC) has great potential toward direct electricity generation from wastewater and concurrent desalination through potential difference developed due to microbial activity. Degradation of phenol by isolate Pseudomonas aeruginosa in anodic chamber and simultaneous desalination of water in middle desalination chamber of multichamber MDC is demonstrated in this study. Performance of the MDCs with different anodic inoculum conditions, namely pure culture of P. aeruginosa (MDC-1), 50 % v/v mixture of P. aeruginosa and anaerobic mixed consortia (MDC-2) and anaerobic mixed consortia (MDC-3), was evaluated to compare the phenol degradation in anodic chamber, bioelectricity generation, and simultaneous total dissolved solids (TDS) removal from saline water in desalination chamber. Synergistic effect between P. aeruginosa and mixed anaerobic consortia as inoculum was evident in MDC-2 demonstrating phenol degradation of 90 %, TDS removal of 75 % in 72 h of reaction time along with higher power generation of 27.5 mW/m(2) as compared to MDC-1 (95 %, 64 %, 12.8 mW/m(2), respectively) and MDC-3 (58 %, 52 %, 4.8 mW/m(2), respectively). The results illustrate that the multichamber MDC-2 is effective for simultaneous removal of phenol and dissolved solids contained in industrial wastewaters.

Identities of epilithic hydrocarbon-utilizing diazotrophic bacteria from the Arabian Gulf Coasts, and their potential for oil bioremediation without nitrogen supplementation.

PubMed

Radwan, Samir; Mahmoud, Huda; Khanafer, Majida; Al-Habib, Aamar; Al-Hasan, Redha

2010-08-01

Gravel particles from four sites along the Arabian Gulf coast in autumn, winter, and spring were naturally colonized with microbial consortia containing between 7 and 400 × 10(2) cm(-2) of cultivable oil-utilizing bacteria. The 16S rRNA gene sequences of 70 representatives of oil-utilizing bacteria revealed that they were predominantly affiliated with the Gammaproteobacteria and the Actinobacteria. The Gammaproteobacteria comprised among others, the genera Pseudomonas, Pseudoalteromonas, Shewanella, Marinobacter, Psychrobacter, Idiomarina, Alcanivorax, Cobetia, and others. Actinobacteria comprised the genera Dietzia, Kocuria, Isoptericola, Rhodococcus, Microbacterium, and others. In autumn, Firmicutes members were isolated from bay and nonbay stations while Alphaproteobacteria were detected only during winter from Anjefa bay station. Fingerprinting by denaturing gradient gel electrophoresis of amplified 16S rRNA genes of whole microbial consortia confirmed the culture-based bacterial diversities in the various epilithons in various sites and seasons. Most of the representative oil-utilizing bacteria isolated from the epilithons were diazotrophic and could attenuate oil also in nitrogen-rich (7.9-62%) and nitrogen-free (4-54%) cultures, which, makes the microbial consortia suitable for oil bioremediation in situ, without need for nitrogen supplementation. This was confirmed in bench-scale experiments in which unfertilized oily seawater was bioremediated by epilithon-coated gravel particles.

Engineering Escherichia coli coculture systems for the production of biochemical products

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

Zhang, Haoran; Pereira, Brian; Li, Zhengjun

Engineering microbial consortia to express complex biosynthetic pathways efficiently for the production of valuable compounds is a promising approach for metabolic engineering and synthetic biology. Here, we report the design, optimization, and scale-up of an Escherichia coli-E. coli coculture that successfully overcomes fundamental microbial production limitations, such as high-level intermediate secretion and low-efficiency sugar mixture utilization. For the production of the important chemical cis,cis-muconic acid, we show that the coculture approach achieves a production yield of 0.35 g/g from a glucose/xylose mixture, which is significantly higher than reported in previous reports. Furthermore, by efficiently producing another compound, 4-hydroxybenzoic acid, wemore » also demonstrate that the approach is generally applicable for biosynthesis of other important industrial products.« less

Engineering Escherichia coli coculture systems for the production of biochemical products

DOE PAGES

Zhang, Haoran; Pereira, Brian; Li, Zhengjun; ...

2015-06-25

Engineering microbial consortia to express complex biosynthetic pathways efficiently for the production of valuable compounds is a promising approach for metabolic engineering and synthetic biology. Here, we report the design, optimization, and scale-up of an Escherichia coli-E. coli coculture that successfully overcomes fundamental microbial production limitations, such as high-level intermediate secretion and low-efficiency sugar mixture utilization. For the production of the important chemical cis,cis-muconic acid, we show that the coculture approach achieves a production yield of 0.35 g/g from a glucose/xylose mixture, which is significantly higher than reported in previous reports. Furthermore, by efficiently producing another compound, 4-hydroxybenzoic acid, wemore » also demonstrate that the approach is generally applicable for biosynthesis of other important industrial products.« less

Suppressive composts: microbial ecology links between abiotic environments and healthy plants.

PubMed

Hadar, Yitzhak; Papadopoulou, Kalliope K

2012-01-01

Suppressive compost provides an environment in which plant disease development is reduced, even in the presence of a pathogen and a susceptible host. Despite the numerous positive reports, its practical application is still limited. The main reason for this is the lack of reliable prediction and quality control tools for evaluation of the level and specificity of the suppression effect. Plant disease suppression is the direct result of the activity of consortia of antagonistic microorganisms that naturally recolonize the compost during the cooling phase of the process. Thus, it is imperative to increase the level of understanding of compost microbial ecology and population dynamics. This may lead to the development of an ecological theory for complex ecosystems as well as favor the establishment of hypothesis-driven studies.

Microbial Fuel Cells and Microbial Ecology: Applications in Ruminant Health and Production Research

PubMed Central

Osterstock, Jason B.; Pinchak, William E.; Ishii, Shun’ichi; Nelson, Karen E.

2009-01-01

Microbial fuel cell (MFC) systems employ the catalytic activity of microbes to produce electricity from the oxidation of organic, and in some cases inorganic, substrates. MFC systems have been primarily explored for their use in bioremediation and bioenergy applications; however, these systems also offer a unique strategy for the cultivation of synergistic microbial communities. It has been hypothesized that the mechanism(s) of microbial electron transfer that enable electricity production in MFCs may be a cooperative strategy within mixed microbial consortia that is associated with, or is an alternative to, interspecies hydrogen (H2) transfer. Microbial fermentation processes and methanogenesis in ruminant animals are highly dependent on the consumption and production of H2in the rumen. Given the crucial role that H2 plays in ruminant digestion, it is desirable to understand the microbial relationships that control H2 partial pressures within the rumen; MFCs may serve as unique tools for studying this complex ecological system. Further, MFC systems offer a novel approach to studying biofilms that form under different redox conditions and may be applied to achieve a greater understanding of how microbial biofilms impact animal health. Here, we present a brief summary of the efforts made towards understanding rumen microbial ecology, microbial biofilms related to animal health, and how MFCs may be further applied in ruminant research. PMID:20024685

Microbial consortia: a critical look at microalgae co-cultures for enhanced biomanufacturing.

PubMed

Padmaperuma, Gloria; Kapoore, Rahul Vijay; Gilmour, Daniel James; Vaidyanathan, Seetharaman

2018-08-01

Monocultures have been the preferred production route in the bio-industry, where contamination has been a major bottleneck. In nature, microorganisms usually exist as part of organized communities and consortia, gaining benefits from co-habitation, keeping invaders at bay. There is increasing interest in the use of co-cultures to tackle contamination issues, and simultaneously increase productivity and product diversity. The feasibility of extending the natural phenomenon of co-habitation to the biomanufacturing industry in the form of co-cultures requires careful and systematic consideration of several aspects. This article will critically examine and review current work on microbial co-cultures, with the intent of examining the concept and proposing a design pipeline that can be developed in a biomanufacturing context.

Comparative proteomic analysis in pea treated with microbial consortia of beneficial microbes reveals changes in the protein network to enhance resistance against Sclerotinia sclerotiorum.

PubMed

Jain, Akansha; Singh, Akanksha; Singh, Surendra; Singh, Vinay; Singh, Harikesh Bahadur

2015-06-15

Microbial consortia may provide protection against pathogenic ingress via enhancing plant defense responses. Pseudomonas aeruginosa PJHU15, Trichoderma harzianum TNHU27 and Bacillus subtilis BHHU100 were used either singly or in consortia in the pea rhizosphere to observe proteome level changes upon Sclerotinia sclerotiorum challenge. Thirty proteins were found to increase or decrease differentially in 2-DE gels of pea leaves, out of which 25 were identified by MALDI-TOF MS or MS/MS. These proteins were classified into several functional categories including photosynthesis, respiration, phenylpropanoid metabolism, protein synthesis, stress regulation, carbohydrate and nitrogen metabolism and disease/defense-related processes. The respective homologue of each protein identified was trapped in Pisum sativum and a phylogenetic tree was constructed to check the ancestry. The proteomic view of the defense response to S. sclerotiorum in pea, in the presence of beneficial microbes, highlights the enhanced protection that can be provided by these microbes in challenged plants. Copyright © 2015 Elsevier GmbH. All rights reserved.

Genomic insights into the metabolic potential and interactions between marine methanotrophic ANME archaea and associated bacteria

NASA Astrophysics Data System (ADS)

Orphan, V. J.; Skennerton, C.; Chadwick, G.; Haroon, F.; Tyson, G. W.; Leu, A.; Hatzenpichler, R.; Woyke, T.; Malmstrom, R.; Yu, H.; Scheller, S.

2015-12-01

Cooperative metabolic interactions between multiple groups of methanotrophic 'ANME' archaea and sulfate-reducing bacteria represent the primary sink for methane within continental margin sediments. These syntrophic associations are frequently observed as structured multi-celled consortia in methane seeps, often comprising a substantial proportion of the microbial biomass within near seafloor seep sediments. Since their discovery nearly 15 years ago, a number of distinct ANME groups and multiple sulfate-reducing bacterial partners have been described from seep environments worldwide. Attempts to reconstruct the genomes of some ANME organisms have been reported, however the ecological physiology and metabolic interactions of distinct ANME lineages and their bacterial partners remains poorly understood. Here, we used a fluorescence azide-alkyne click chemistry technique known as BONCAT combined with FAC sorting to examine patterns in microbial membership and the genomes of single, metabolically active ANME-bacterial consortia recovered from methane seep sediments. This targeted consortia-level sequencing approach revealed significant diversity in the ANME-bacterial associations in situ as well as insights into the potential syntrophic mechanisms underpinning these enigmatic methane-fueled partnerships.

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

Identification and Resolution of Microdiversity through Metagenomic Sequencing of Parallel Consortia

PubMed Central

Maezato, Yukari; Wu, Yu-Wei; Romine, Margaret F.; Lindemann, Stephen R.

2015-01-01

To gain a predictive understanding of the interspecies interactions within microbial communities that govern community function, the genomic complement of every member population must be determined. Although metagenomic sequencing has enabled the de novo reconstruction of some microbial genomes from environmental communities, microdiversity confounds current genome reconstruction techniques. To overcome this issue, we performed short-read metagenomic sequencing on parallel consortia, defined as consortia cultivated under the same conditions from the same natural community with overlapping species composition. The differences in species abundance between the two consortia allowed reconstruction of near-complete (at an estimated >85% of gene complement) genome sequences for 17 of the 20 detected member species. Two Halomonas spp. indistinguishable by amplicon analysis were found to be present within the community. In addition, comparison of metagenomic reads against the consensus scaffolds revealed within-species variation for one of the Halomonas populations, one of the Rhodobacteraceae populations, and the Rhizobiales population. Genomic comparison of these representative instances of inter- and intraspecies microdiversity suggests differences in functional potential that may result in the expression of distinct roles in the community. In addition, isolation and complete genome sequence determination of six member species allowed an investigation into the sensitivity and specificity of genome reconstruction processes, demonstrating robustness across a wide range of sequence coverage (9× to 2,700×) within the metagenomic data set. PMID:26497460

Identification and Resolution of Microdiversity through Metagenomic Sequencing of Parallel Consortia

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

Nelson, William C.; Maezato, Yukari; Wu, Yu-Wei

2015-10-23

To gain a predictive understanding of the interspecies interactions within microbial communities that govern community function, the genomic complement of every member population must be determined. Although metagenomic sequencing has enabled thede novoreconstruction of some microbial genomes from environmental communities, microdiversity confounds current genome reconstruction techniques. To overcome this issue, we performed short-read metagenomic sequencing on parallel consortia, defined as consortia cultivated under the same conditions from the same natural community with overlapping species composition. The differences in species abundance between the two consortia allowed reconstruction of near-complete (at an estimated >85% of gene complement) genome sequences for 17 ofmore » the 20 detected member species. TwoHalomonasspp. indistinguishable by amplicon analysis were found to be present within the community. In addition, comparison of metagenomic reads against the consensus scaffolds revealed within-species variation for one of theHalomonaspopulations, one of theRhodobacteraceaepopulations, and theRhizobialespopulation. Genomic comparison of these representative instances of inter- and intraspecies microdiversity suggests differences in functional potential that may result in the expression of distinct roles in the community. In addition, isolation and complete genome sequence determination of six member species allowed an investigation into the sensitivity and specificity of genome reconstruction processes, demonstrating robustness across a wide range of sequence coverage (9× to 2,700×) within the metagenomic data set.« less

Short communication: culture-independent detection of lactic Acid bacteria bacteriocin genes in two traditional slovenian raw milk cheeses and their microbial consortia.

PubMed

Trmcić, A; Obermajer, T; Rogelj, I; Bogovic Matijasić, B

2008-12-01

Two Slovenian traditional raw milk cheeses, Tolminc (from cows' milk) and Kraski (from ewes' milk), were examined for the presence of 19 lactic acid bacteria bacteriocin genes by PCR analysis of total DNA extracts from 9 cheeses and from consortia of strains isolated from these cheeses. Eleven bacteriocin genes were detected in at least one cheese or consortium, or from both. Different cheeses or consortia contained 3 to 9 bacteriocin determinants. Plantaricin A gene determinants were found in all cheese and consortia DNA extracts. Genes for enterocins A, B, P, L50A, and L50B, and the bacteriocin cytolysin were commonly detected, as were genes for nisin. These results indicate that bacteriocinogenic strains of Lactobacillus, Enterococcus, and Lactococcus genera with protective potential are common members of indigenous microbiota of raw milk cheeses, which can be a good source of new protective strains.

Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulphidic marine sediments

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

Glass, DR. Jennifer; Yu, DR. Hang; Steele, Joshua

2013-01-01

Microbes have obligate requirements for trace metals in metalloenzymes that catalyse important biogeochemical reactions. In anoxic methane- and sulphiderich environments, microbes may have unique adaptations for metal acquisition and utilization because of decreased bioavailability as a result of metal sulphide precipitation. However, micronutrient cycling is largely unexplored in cold ( 10 C) and sulphidic (> 1 mM H2S) deep-sea methane seep ecosystems. We investigated trace metal geochemistry and microbial metal utilization in methane seeps offshore Oregon and California, USA, and report dissolved concentrations of nickel (0.5 270 nM), cobalt (0.5 6 nM), molybdenum (10 5600 nM) and tungsten (0.3 8more » nM) in Hydrate Ridge sediment porewaters. Despite low levels of cobalt and tungsten, metagenomic and metaproteomic data suggest that microbial consortia catalysing anaerobic oxidation of methane (AOM) utilize both scarce micronutrients in addition to nickel and molybdenum. Genetic machinery for cobalt-containing vitamin B12 biosynthesis was present in both anaerobic methanotrophic archaea (ANME) and sulphate-reducing bacteria. Proteins affiliated with the tungsten-containing form of formylmethanofuran dehydrogenase were expressed in ANME from two seep ecosystems, the first evidence for expression of a tungstoenzyme in psychrophilic microorganisms. Overall, our data suggest that AOM consortia use specialized biochemical strategies to overcome the challenges of metal availability in sulphidic environments.« less

Wine microbiome: A dynamic world of microbial interactions.

PubMed

Liu, Youzhong; Rousseaux, Sandrine; Tourdot-Maréchal, Raphaëlle; Sadoudi, Mohand; Gougeon, Régis; Schmitt-Kopplin, Philippe; Alexandre, Hervé

2017-03-04

Most fermented products are generated by a mixture of microbes. These microbial consortia perform various biological activities responsible for the nutritional, hygienic, and aromatic qualities of the product. Wine is no exception. Substantial yeast and bacterial biodiversity is observed on grapes, and in both must and wine. The diverse microorganisms present interact throughout the winemaking process. The interactions modulate the hygienic and sensorial properties of the wine. Many studies have been conducted to elucidate the nature of these interactions, with the aim of establishing better control of the two fermentations occurring during wine processing. However, wine is a very complex medium making such studies difficult. In this review, we present the current state of research on microbial interactions in wines. We consider the different kinds of interactions between different microorganisms together with the consequences of these interactions. We underline the major challenges to obtaining a better understanding of how microbes interact. Finally, strategies and methodologies that may help unravel microbe interactions in wine are suggested.

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

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

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

Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A.

The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earth's biogeochemical cycles. However, little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics to aquifer sediments and groundwater, and reconstruct 2,540 draft-quality, near-complete and complete strain-resolved genomes that represent the majority of known bacterial phyla as well as 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity and representing up to 36% of organisms detected in the system are used to documentmore » the distribution of pathways in coexisting organisms. Consistent with prior findings indicating metabolic handoffs in simple consortia, we find that few organisms within the community can conduct multiple sequential redox transformations. As environmental conditions change, different assemblages of organisms are selected for, altering linkages among the major biogeochemical cycles.« less

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

DOE PAGES

Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A.; ...

2016-10-24

The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earth's biogeochemical cycles. However, little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics to aquifer sediments and groundwater, and reconstruct 2,540 draft-quality, near-complete and complete strain-resolved genomes that represent the majority of known bacterial phyla as well as 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity and representing up to 36% of organisms detected in the system are used to documentmore » the distribution of pathways in coexisting organisms. Consistent with prior findings indicating metabolic handoffs in simple consortia, we find that few organisms within the community can conduct multiple sequential redox transformations. As environmental conditions change, different assemblages of organisms are selected for, altering linkages among the major biogeochemical cycles.« less

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

PubMed Central

Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A.; Sharon, Itai; Castelle, Cindy J.; Probst, Alexander J.; Thomas, Brian C.; Singh, Andrea; Wilkins, Michael J.; Karaoz, Ulas; Brodie, Eoin L.; Williams, Kenneth H.; Hubbard, Susan S.; Banfield, Jillian F.

2016-01-01

The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earth's biogeochemical cycles. However, little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics to aquifer sediments and groundwater, and reconstruct 2,540 draft-quality, near-complete and complete strain-resolved genomes that represent the majority of known bacterial phyla as well as 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity and representing up to 36% of organisms detected in the system are used to document the distribution of pathways in coexisting organisms. Consistent with prior findings indicating metabolic handoffs in simple consortia, we find that few organisms within the community can conduct multiple sequential redox transformations. As environmental conditions change, different assemblages of organisms are selected for, altering linkages among the major biogeochemical cycles. PMID:27774985

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

NASA Astrophysics Data System (ADS)

Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A.; Sharon, Itai; Castelle, Cindy J.; Probst, Alexander J.; Thomas, Brian C.; Singh, Andrea; Wilkins, Michael J.; Karaoz, Ulas; Brodie, Eoin L.; Williams, Kenneth H.; Hubbard, Susan S.; Banfield, Jillian F.

2016-10-01

The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earth's biogeochemical cycles. However, little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics to aquifer sediments and groundwater, and reconstruct 2,540 draft-quality, near-complete and complete strain-resolved genomes that represent the majority of known bacterial phyla as well as 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity and representing up to 36% of organisms detected in the system are used to document the distribution of pathways in coexisting organisms. Consistent with prior findings indicating metabolic handoffs in simple consortia, we find that few organisms within the community can conduct multiple sequential redox transformations. As environmental conditions change, different assemblages of organisms are selected for, altering linkages among the major biogeochemical cycles.

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.

Simplification of a complex microbial antilisterial consortium to evaluate the contribution of its flora in uncooked pressed cheese.

PubMed

Callon, Cécile; Saubusse, Marjorie; Didienne, Robert; Buchin, Solange; Montel, Marie-Christine

2011-02-28

A complex microbial consortium derived from raw milk and composed of populations classified in 4 groups (lactic acid bacteria (A), Gram positive catalase positive bacteria (B), Gram negative bacteria (C) and yeasts (D)) can contribute to the inhibition of Listeria monocytogenes in the core of an uncooked pressed cheese. To identify what groups may be involved in the inhibition, the consortium was simplified by successively omitting one group at a time. Pasteurized milk was inoculated with these more or less complex consortia and their effects on L. monocytogenes count, pH, acids and volatile compounds in the core of uncooked pressed cheese were evaluated. The growth of L. monocytogenes was the highest in cheeses prepared with pasteurized milk and only St. thermophilus. Inhibition in other cheeses was expressed by comparison with growth in these ones. All the consortia containing both lactic acid bacteria (group A) and Gram positive catalase positive bacteria (group B)--ABCD, ABD, ABC, AB--were more inhibitory than those containing lactic acid bacteria on its own (A) or associated only with yeasts (AD) or/and Gram negative (ADC). Consortia without lactic acid bacteria were weakly inhibitory or had no effect. Gram positive catalase positive bacteria alone were not inhibitory although most of the species became established in the cheeses. The Lactobacillus population (Lb. casei, Lb. plantarum, Lb. curvatus and Lb. farciminis) was predominant in cheeses (9 log CFU/g) with a higher count than Leuconostoc (7 log CFU/g) and Enterococcus (7 log CFU/g). Lactobacillus counts were negatively correlated with those of L. monocytogenes (r=-0.84 at 18 days) and with the level of D-lactic acid. There was no correlation between L. monocytogenes and Leuconostoc or Enterococcus counts. Complex consortium ABCD and AB not only had a stronger inhibitory power in cheeses than consortium AD, they were also associated with the highest levels of L-lactic and acetic acids. All cheeses inoculated with lactic acid bacteria differed from those without by higher levels of ethyl formiate, pentane and alcohols (2-butanol, 2-pentanol), and lower levels of ketones (2-hexanone, 2,3-butanedione) and aldehydes (2-methyl-butanal). Levels of 2-methyl-butanal, 2-butanol and 2-pentanol were higher in ABCD and AB cheeses than in AD cheeses. Beside their contribution to the inhibition, their effect on cheese flavour must be evaluated. Published by Elsevier B.V.

Adaptation of Methanogenic Inocula to Anaerobic Digestion of Maize Silage

PubMed Central

Wojcieszak, Martyna; Pyzik, Adam; Poszytek, Krzysztof; Krawczyk, Pawel S.; Sobczak, Adam; Lipinski, Leszek; Roubinek, Otton; Palige, Jacek; Sklodowska, Aleksandra; Drewniak, Lukasz

2017-01-01

A well-balanced microbial consortium is crucial for efficient biogas production. In turn, one of a major factor that influence on the structure of anaerobic digestion (AD) consortium is a source of microorganisms which are used as an inoculum. This study evaluated the influence of inoculum sources (with various origin) on adaptation of a biogas community and the efficiency of the biomethanization of maize silage. As initial inocula for AD of maize silage the samples from: (i) an agricultural biogas plant (ABP) which utilizes maize silage as a main substrate, (ii) cattle slurry (CS), which contain elevated levels of lignocelluloses materials, and (iii) raw sewage sludge (RSS) with low content of plant origin materials were used. The adaptation of methanogenic consortia was monitored during a series of passages, and the functionality of the adapted consortia was verified through start-up operation of AD in two-stage reactors. During the first stages of the adaptation phase, methanogenic consortia occurred very slowly, and only after several passages did the microbial community adapts to allow production of biogas with high methane content. The ABP consortium revealed highest biogas production in the adaptation and in the start-up process. The biodiversity dynamics monitored during adaptation and start-up process showed that community profile changed in a similar direction in three studied consortia. Native communities were very distinct to each other, while at the end of the Phase II of the start-up process microbial diversity profile was similar in all consortia. All adopted bacterial communities were dominated by representatives of Porphyromonadaceae, Rikenellaceae, Ruminococcaceae, and Synergistaceae. A shift from low acetate-preferring acetoclastic Methanosaetaceae (ABP and RSS) and/or hydrogenotrophic Archaea, e.g., Methanomicrobiaceae (CS) prevailing in the inoculum samples to larger populations of high acetate-preferring acetoclastic Methanosarcinaceae was observed by the end of the experiment. As a result, three independent, functional communities that syntrophically produced methane from acetate (primarily) and H2/CO2, methanol and methylamines were adapted. This study provides new insights into the specific process by which different inocula sampled from typical methanogenic environments that are commonly used to initiate industrial installations gradually adapted to allow biogas production from maize silage. PMID:29033919

Polyhydroxybutyrate synthesis on biodiesel wastewater using mixed microbial consortia.

PubMed

Dobroth, Zachary T; Hu, Shengjun; Coats, Erik R; McDonald, Armando G

2011-02-01

Crude glycerol (CG), a by-product of biodiesel production, is an organic carbon-rich substrate with potential as feedstock for polyhydroxyalkanoate (PHA) production. PHA is a biodegradable thermoplastic synthesized by microorganisms as an intracellular granule. In this study we investigated PHA production on CG using mixed microbial consortia (MMC) and determined that the enriched MMC produced exclusively polyhydroxybutyrate (PHB) utilizing the methanol fraction. PHB synthesis appeared to be stimulated by a macronutrient deficiency. Intracellular concentrations remained relatively constant over an operational cycle, with microbial growth occurring concurrent with polymer synthesis. PHB average molecular weights ranged from 200-380 kDa, while thermal properties compared well with commercial PHB. The resulting PHB material properties and characteristics would be suitable for many commercial uses. Considering full-scale process application, it was estimated that a 38 million L (10 million gallon) per year biodiesel operation could potentially produce up to 19 metric ton (20.9t on) of PHB per year. Copyright © 2010 Elsevier Ltd. All rights reserved.

Crude oil degradation by bacterial consortia under four different redox and temperature conditions.

PubMed

Xiong, Shunzi; Li, Xia; Chen, Jianfa; Zhao, Liping; Zhang, Hui; Zhang, Xiaojun

2015-02-01

There is emerging interest in the anaerobic degradation of crude oil. However, there is limited knowledge about the geochemical effects and microbiological activities for it. A mixture of anaerobic sludge and the production water from an oil well was used as an inoculum to construct four consortia, which were incubated under sulfate-reducing or methanogenic conditions at either mesophilic or thermophilic temperatures. Significant degradation of saturated and aromatic hydrocarbons and the changing quantities of some marker compounds, such as pristane, phytane, hopane and norhopane, and their relative quantities, suggested the activity of microorganisms in the consortia. Notably, the redox conditions and temperature strongly affected the diversity and structure of the enriched microbial communities and the oil degradation. Although some specific biomarker showed larger change under methanogenic condition, the degradation efficiencies for total aromatic and saturated hydrocarbon were higher under sulfate-reducing condition. After the 540-day incubation, bacteria of unknown classifications were dominant in the thermophilic methanogenic consortia, whereas Clostridium dominated the mesophilic methanogenic consortia. With the exception of the dominant phylotypes that were shared with the methanogenic consortia, the sulfate-reducing consortia were predominantly composed of Thermotogae, Deltaproteobacteria, Spirochaeta, and Synergistetes phyla. In conclusion, results in this study demonstrated that the different groups of degraders were responsible for degradation in the four constructed crude oil degrading consortia and consequently led to the existence of different amount of marker compounds under these distinct conditions. There might be distinct metabolic mechanism for degrading crude oil under sulfate-reducing and methanogenic conditions.

Degradation of organic pollutants by methane grown microbial consortia.

PubMed

Hesselsoe, Martin; Boysen, Susanne; Iversen, Niels; Jørgensen, Lars; Murrell, J Colin; McDonald, Ian; Radajewski, Stefan; Thestrup, Helle; Roslev, Peter

2005-10-01

Microbial consortia were enriched from various environmental samples with methane as the sole carbon and energy source. Selected consortia that showed a capacity for co-oxidation of naphthalene were screened for their ability to degrade methyl-tert-butyl-ether (MTBE), phthalic acid esters (PAE), benzene, xylene and toluene (BTX). MTBE was not removed within 24 h by any of the consortia examined. One consortium enriched from activated sludge ("AAE-A2"), degraded PAE, including (butyl-benzyl)phthalate (BBP), and di-(butyl)phthalate (DBP). PAE have not previously been described as substrates for methanotrophic consortia. The apparent Km and Vmax for DBP degradation by AAE-A2 at 20 degrees C was 3.1 +/- 1.2 mg l(-1) and 8.7 +/- 1.1 mg DBP (g protein x h)(-1), respectively. AAE-A2 also showed fast degradation of BTX (230 +/- 30 nmol benzene (mg protein x h)(-1) at 20 degrees C). Additionally, AAE-A2 degraded benzene continuously for 2 weeks. In contrast, a pure culture of the methanotroph Methylosinus trichosporium OB3b ceased benzene degradation after only 2 days. Experiments with methane mono-oxygenase inhibitors or competitive substrates suggested that BTX degradation was carried out by methane-oxidizing bacteria in the consortium, whereas the degradation of PAE was carried out by non-methanotrophic bacteria co-existing with methanotrophs. The composition of the consortium (AAE-A2) based on polar lipid fatty acid (PLFA) profiles showed dominance of type II methanotrophs (83-92% of biomass). Phylogeny based on a 16S-rRNA gene clone library revealed that the dominating methanotrophs belonged to Methylosinus/Methylocystis spp. and that members of at least 4 different non-methanotrophic genera were present (Pseudomonas, Flavobacterium, Janthinobacterium and Rubivivax).

The diversity and origins of toxins in ciguatera fish poisoning.

PubMed

Tosteson, T R

1995-06-01

The source of the diversity of phytotoxins found in the marine food web is not well understood. It is not clear what roles these secondary metabolites might have in the phytoplankton that produce them. The phytotoxins do not appear to be deterrents of predation, although the production of antibiotics by marine macroalgae might be considered in this light (86). It is equally doubtful that the production and/or presence of these toxins confers a selective advantage on the phytoplankton producers, when in fact the diversity of naturally occurring phytoplankton species may well be maintained by lytic viral infections (22,64). On the other hand, these multiple, diverse toxins may be the products of the different adaptations and interactions that take place between microalgal vectors and the highly variable spectrum of their microbial symbionts. We do not know what selective signals these toxic products may be providing in the maintenance of the symbiont-host consortia in which they are produced, however, their diversity most likely reflects the diversity of symbiotic interactions that exist in these consortia. Woven into the very fabric of the traditional marine food web is an invisible empire of marine micro-organisms, that by its very existence may determine the intense diversity of toxins found in marine biota. Marine bacteria are very likely the most abundant organisms in the sea and to a large degree maintain a food web of their own, often referred to as the microbial loop (64). This microbial web sustains the biogeochemical cycles in the sea. Much of the food produced by phytoplankton and cyanobacteria is consumed by bacteria in the microbial loop and may never enter the food web of larger invertebrates and fishes. Traditionally, the marine food web has been viewed, so to speak, from the top, however, it is now clear that there is an enormous marine microbial food web from which the food web of larger invertebrates and fishes emanates (Figure 13). In many respects the phytotoxins are biomarkers of the interactions between these two food webs. In their very diversity these toxins reflect an amalgam of interacting collaborating forms of life, a complex of phytoplankton hosts and their microbial symbionts producing multiple toxins and their derivatives that ultimately result in the complex medical symptoms they produce in human consumers of poisoned seafood. The term ciguatera has been employed to describe the syndrome of the illness contracted by persons who have eaten tropical and semitropical finfish poisoned by ciguatoxin.(ABSTRACT TRUNCATED AT 400 WORDS)

Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities.

PubMed

Narayanasamy, Shaman; Muller, Emilie E L; Sheik, Abdul R; Wilmes, Paul

2015-05-01

Biological wastewater treatment plants harbour diverse and complex microbial communities which prominently serve as models for microbial ecology and mixed culture biotechnological processes. Integrated omic analyses (combined metagenomics, metatranscriptomics, metaproteomics and metabolomics) are currently gaining momentum towards providing enhanced understanding of community structure, function and dynamics in situ as well as offering the potential to discover novel biological functionalities within the framework of Eco-Systems Biology. The integration of information from genome to metabolome allows the establishment of associations between genetic potential and final phenotype, a feature not realizable by only considering single 'omes'. Therefore, in our opinion, integrated omics will become the future standard for large-scale characterization of microbial consortia including those underpinning biological wastewater treatment processes. Systematically obtained time and space-resolved omic datasets will allow deconvolution of structure-function relationships by identifying key members and functions. Such knowledge will form the foundation for discovering novel genes on a much larger scale compared with previous efforts. In general, these insights will allow us to optimize microbial biotechnological processes either through better control of mixed culture processes or by use of more efficient enzymes in bioengineering applications. © 2015 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Biosurfactant production from marine hydrocarbon-degrading consortia and pure bacterial strains using crude oil as carbon source

PubMed Central

Antoniou, Eleftheria; Fodelianakis, Stilianos; Korkakaki, Emmanouela; Kalogerakis, Nicolas

2015-01-01

Biosurfactants (BSs) are “green” amphiphilic molecules produced by microorganisms during biodegradation, increasing the bioavailability of organic pollutants. In this work, the BS production yield of marine hydrocarbon degraders isolated from Elefsina bay in Eastern Mediterranean Sea has been investigated. The drop collapse test was used as a preliminary screening test to confirm BS producing strains or mixed consortia. The community structure of the best consortia based on the drop collapse test was determined by 16S-rDNA pyrotag screening. Subsequently, the effect of incubation time, temperature, substrate and supplementation with inorganic nutrients, on BS production, was examined. Two types of BS – lipid mixtures were extracted from the culture broth; the low molecular weight BS Rhamnolipids and Sophorolipids. Crude extracts were purified by silica gel column chromatography and then identified by thin layer chromatography and Fourier transform infrared spectroscopy. Results indicate that BS production yield remains constant and low while it is independent of the total culture biomass, carbon source, and temperature. A constant BS concentration in a culture broth with continuous degradation of crude oil (CO) implies that the BS producing microbes generate no more than the required amount of BSs that enables biodegradation of the CO. Isolated pure strains were found to have higher specific production yields than the complex microbial marine community-consortia. The heavy oil fraction of CO has emerged as a promising substrate for BS production (by marine BS producers) with fewer impurities in the final product. Furthermore, a particular strain isolated from sediments, Paracoccus marcusii, may be an optimal choice for bioremediation purposes as its biomass remains trapped in the hydrocarbon phase, not suffering from potential dilution effects by sea currents. PMID:25904907

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.

Underlying mechanisms for syntrophic metabolism of essential enzyme cofactors in microbial communities

PubMed Central

Romine, Margaret F; Rodionov, Dmitry A; Maezato, Yukari; Osterman, Andrei L; Nelson, William C

2017-01-01

Many microorganisms are unable to synthesize essential B vitamin-related enzyme cofactors de novo. The underlying mechanisms by which such microbes survive in multi-species communities are largely unknown. We previously reported the near-complete genome sequence of two ~18-member unicyanobacterial microbial consortia that maintain stable membership on defined medium lacking vitamins. Here we have used genome analysis and growth studies on isolates derived from the consortia to reconstruct pathways for biogenesis of eight essential cofactors and predict cofactor usage and precursor exchange in these communities. Our analyses revealed that all but the two Halomonas and cyanobacterial community members were auxotrophic for at least one cofactor. We also observed a mosaic distribution of salvage routes for a variety of cofactor precursors, including those produced by photolysis. Potentially bidirectional transporters were observed to be preferentially in prototrophs, suggesting a mechanism for controlled precursor release. Furthermore, we found that Halomonas sp. do not require cobalamin nor control its synthesis, supporting the hypothesis that they overproduce and export vitamins. Collectively, these observations suggest that the consortia rely on syntrophic metabolism of cofactors as a survival strategy for optimization of metabolic exchange within a shared pool of micronutrients. PMID:28186498

An investigation of anaerobic methane oxidation by consortia of methanotrophic archaea and bacterial partners using nanoSIMS and process-based modeling

NASA Astrophysics Data System (ADS)

Shi, Y.; Kempes, C.; Chadwick, G.; McGlynn, S.; He, X.; Orphan, V. J.; Meile, C. D.

2016-02-01

The anaerobic oxidation of methane in marine sediments plays an important role in the global methane cycle. Mediated by a microbial consortium consisting of archaea and bacteria, it is estimated that almost 80% of all the methane that arises from marine sediments is oxidized anaerobically by this process (Reeburgh 2007, Chemical Reviews 107, 486-513). We used reactive transport modeling to compare and contrast potential mechanisms of methane oxidation. This included acetate, hydrogen, formate, and disulfide acting as intermediates that are exchanged between archaea and bacteria. Moreover, we investigated electron transport through nanowires, facilitating the electron exchange between the microbial partners. It was shown that reaction kinetics, transport intensities, and energetic considerations all could decisively impact the overall rate of methane consumption. Informed by observed microbial cell distribution, we applied the model to a range of spatial distribution patterns of archaea and bacteria. We found that a consortium with evenly distributed archaeal and bacterial cells has the potential to more efficiently oxidize methane, because the vicinity of bacteria and archaea counteracts the build up of products and therefore prevents the thermodynamic shutdown of microbial metabolism. Single cell stable isotope enrichment in archaeal-bacterial consortia observed by nanoSIMS revealed rather uniform levels of anabolic activity within consortia with different spatial distribution patterns. Comparison to model simulation illustrates that efficient exchange is necessary to reproduce such observations and prevent conditions that are energetically unfavorable for methane oxidation to take place. Model simulations indicate that a recently described mechanism of direct interspecies electron transport between the methanotrophic archaea and its bacterial partner through a conductive matrix (McGlynn et al. 2015, Nature, 10.1038/nature15512) is consistent with observations.

Enhanced biodegradation of hydrocarbons in petroleum tank bottom oil sludge and characterization of biocatalysts and biosurfactants.

PubMed

Suganthi, S Hepziba; Murshid, Shabnam; Sriram, Sriswarna; Ramani, K

2018-08-15

Petroleum hydrocarbon removal from tank bottom oil sludge is a major issue due to its properties. Conventional physicochemical treatment techniques are less effective. Though the bioremediation is considered for the hydrocarbon removal from tank bottom oil sludge, the efficiency is low and time taking due to the low yield of biocatalysts and biosurfactants. The focal theme of the present investigation is to modify the process by introducing the intermittent inoculation for the enhanced biodegradation of hydrocarbons in the tank bottom oil sludge by maintaining a constant level of biocatalysts such as oxidoreductase, catalase, and lipase as well as biosurfactants. In addition, the heavy metal removal was also addressed. The microbial consortia comprising Shewanalla chilikensis, Bacillus firmus, and Halomonas hamiltonii was used for the biodegradation of oil sludge. One variable at a time approach was used for the optimum of culture conditions. The bacterial consortia degraded the oil sludge by producing biocatalysts such as lipase (80 U/ml), catalase (46 U/ml), oxidoreductase (68 U/ml) along with the production of lipoprotein biosurfactant (152 mg/g of oil sludge) constantly and achieved 96% reduction of total petroleum hydrocarbon. The crude enzymes were characterized by FT-IR and the biosurfactant was characterized by surface tension reduction, emulsification index, FT-IR, TLC, and SDS-PAGE. GC-MS and NMR also revealed that the hydrocarbons present in the oil sludge were effectively degraded by the microbial consortia. The ICP-OES result indicated that the microbial consortium is also effective in removing the heavy metals. Hence, bioremediation using the hydrocarbonoclastic microbial consortium can be considered as an environmentally friendly process for disposal of tank bottom oil sludge from petroleum oil refining industry. Copyright © 2018 Elsevier Ltd. All rights reserved.

From data to knowledge: The future of multi-omics data analysis for the rhizosphere

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

Allen White, Richard; Borkum, Mark I.; Rivas-Ubach, Albert

The rhizosphere is the interface between a plant's roots and its surrounding soil. The rhizosphere microbiome, a complex microbial ecosystem, nourishes the terrestrial biosphere. Integrated multi-omics is a modern approach to systems biology that analyzes and interprets the datasets of multiple -omes of both individual organisms and multi-organism communities and consortia. The successful usage and application of integrated multi-omics to rhizospheric science is predicated upon the availability of rhizosphere-specific data, metadata and software. This review analyzes the availability of multi-omics data, metadata and software for rhizospheric science, identifying potential issues, challenges and opportunities.

Single cell activity reveals direct electron transfer in methanotrophic consortia

NASA Astrophysics Data System (ADS)

McGlynn, Shawn E.; Chadwick, Grayson L.; Kempes, Christopher P.; Orphan, Victoria J.

2015-10-01

Multicellular assemblages of microorganisms are ubiquitous in nature, and the proximity afforded by aggregation is thought to permit intercellular metabolic coupling that can accommodate otherwise unfavourable reactions. Consortia of methane-oxidizing archaea and sulphate-reducing bacteria are a well-known environmental example of microbial co-aggregation; however, the coupling mechanisms between these paired organisms is not well understood, despite the attention given them because of the global significance of anaerobic methane oxidation. Here we examined the influence of interspecies spatial positioning as it relates to biosynthetic activity within structurally diverse uncultured methane-oxidizing consortia by measuring stable isotope incorporation for individual archaeal and bacterial cells to constrain their potential metabolic interactions. In contrast to conventional models of syntrophy based on the passage of molecular intermediates, cellular activities were found to be independent of both species intermixing and distance between syntrophic partners within consortia. A generalized model of electric conductivity between co-associated archaea and bacteria best fit the empirical data. Combined with the detection of large multi-haem cytochromes in the genomes of methanotrophic archaea and the demonstration of redox-dependent staining of the matrix between cells in consortia, these results provide evidence for syntrophic coupling through direct electron transfer.

Isolation of Paenibacillus sp. and Variovorax sp. strains from decaying woods and characterization of their potential for cellulose deconstruction.

PubMed

Ghio, Silvina; Lorenzo, Gonzalo Sabarís Di; Lia, Verónica; Talia, Paola; Cataldi, Angel; Grasso, Daniel; Campos, Eleonora

2012-01-01

Prospection of cellulose-degrading bacteria in natural environments allows the identification of novel cellulases and hemicellulases that could be useful in second-generation bioethanol production. In this work, cellulolytic bacteria were isolated from decaying native forest soils by enrichment on cellulose as sole carbon source. There was a predominance of Gram positive isolates that belonged to the phyla Proteobacteria and Firmicutes. Many primary isolates with cellulolytic activity were not pure cultures. From these consortia, isolation of pure constituents was attempted in order to test the hypothesis whether microbial consortia are needed for full degradation of complex substrates. Two isolates, CB1-2-A-5 and VG-4-A-2, were obtained as the pure constituents of CB1-2 and VG-4 consortia, respectively. Based on 16S RNA sequence, they could be classified as Variovorax paradoxus and Paenibacillus alvei. Noteworthy, only VG-4 consortium showed measurable xylan degrading capacity and signs of filter paper degradation. However, no xylan or filter paper degrading capacities were observed for the pure cultures isolated from it, suggesting that other members of this consortium were necessary for these hydrolyzing activities. Our results indicated that Paenibacillus sp. and Variovorax sp. as well as VG-4 consortium, might be a useful source of hydrolytic enzymes. Moreover, although Variovorax sp. had been previously identified in metagenomic studies of cellulolytic communities, this is the first report on the isolation and characterization of this microorganism as a cellulolytic genus.

Isolation of Paenibacillus sp. and Variovorax sp. strains from decaying woods and characterization of their potential for cellulose deconstruction

PubMed Central

Ghio, Silvina; Lorenzo, Gonzalo Sabarís Di; Lia, Verónica; Talia, Paola; Cataldi, Angel; Grasso, Daniel; Campos, Eleonora

2012-01-01

Prospection of cellulose-degrading bacteria in natural environments allows the identification of novel cellulases and hemicellulases that could be useful in second-generation bioethanol production. In this work, cellulolytic bacteria were isolated from decaying native forest soils by enrichment on cellulose as sole carbon source. There was a predominance of Gram positive isolates that belonged to the phyla Proteobacteria and Firmicutes. Many primary isolates with cellulolytic activity were not pure cultures. From these consortia, isolation of pure constituents was attempted in order to test the hypothesis whether microbial consortia are needed for full degradation of complex substrates. Two isolates, CB1-2-A-5 and VG-4-A-2, were obtained as the pure constituents of CB1-2 and VG-4 consortia, respectively. Based on 16S RNA sequence, they could be classified as Variovorax paradoxus and Paenibacillus alvei. Noteworthy, only VG-4 consortium showed measurable xylan degrading capacity and signs of filter paper degradation. However, no xylan or filter paper degrading capacities were observed for the pure cultures isolated from it, suggesting that other members of this consortium were necessary for these hydrolyzing activities. Our results indicated that Paenibacillus sp. and Variovorax sp. as well as VG-4 consortium, might be a useful source of hydrolytic enzymes. Moreover, although Variovorax sp. had been previously identified in metagenomic studies of cellulolytic communities, this is the first report on the isolation and characterization of this microorganism as a cellulolytic genus. PMID:23301200

Constraints on mechanisms and rates of anaerobic oxidation of methane by microbial consortia: process-based modeling of ANME-2 archaea and sulfate reducing bacteria interactions

NASA Astrophysics Data System (ADS)

Orcutt, B.; Meile, C.

2008-05-01

Anaerobic oxidation of methane (AOM) is the main process responsible for the removal of methane generated in Earth's marine subsurface environments. However, the biochemical mechanism of AOM remains elusive. By explicitly resolving the observed spatial arrangement of methanotrophic archaea and sulfate reducing bacteria found in consortia mediating AOM, potential intermediates involved in the electron transfer between the methane oxidizing and sulfate reducing partners were investigated via a consortium-scale reaction transport model that integrates the effect of diffusional transport with thermodynamic and kinetic controls on microbial activity. Model simulations were used to assess the impact of poorly constrained microbial characteristics such as minimum energy requirements to sustain metabolism, substrate affinity and cell specific rates. The role of environmental conditions such as the influence of methane levels on the feasibility of H2, formate and acetate as intermediate species, and the impact of the abundance of intermediate species on pathway reversal was examined. The results show that higher production rates of intermediates via AOM lead to increased diffusive fluxes from the methane oxidizing archaea to sulfate reducing bacteria, but the build-up of the exchangeable species causes the energy yield of AOM to drop below that required for ATP production. Comparison to data from laboratory experiments shows that under the experimental conditions of Nauhaus et al. (2007), neither hydrogen nor formate is exchanged fast enough between the consortia partners to achieve measured rates of metabolic activity, but that acetate exchange might support rates that approach those observed.

The Application of Magnetic Bead Selection to Investigate Interactions between the Oral Microbiota and Salivary Immunoglobulins.

PubMed

Madhwani, Tejal; McBain, Andrew J

2016-01-01

The effect of humoral immunity on the composition of the oral microbiota is less intensively investigated than hygiene and diet, in part due to a lack of simple and robust systems for investigating interactions between salivary immunoglobulins and oral bacteria. Here we report the application of an ex situ method to investigate the specificity of salivary immunoglobulins for salivary bacteria. Saliva collected from six volunteers was separated into immunoglobulin and microbial fractions, and the microbial fractions were then directly exposed to salivary immunoglobulins of "self" and "non-self" origin. Antibody-selected bacteria were separated from their congeners using a magnetic bead system, selective for IgA or IgG isotypes. The positively selected fractions were then characterized using gel-based eubacterial-specific DNA profiling. The eubacterial profiles of positively selected fractions diverged significantly from profiles of whole salivary consortia based on volunteer (P≤ 0.001%) and immunoglobulin origin (P≤ 0.001%), but not immunoglobulin isotype (P = 0.2). DNA profiles of separated microbial fractions were significantly (p≤ 0.05) less diverse than whole salivary consortia and included oral and environmental bacteria. Consortia selected using self immunoglobulins were generally less diverse than those selected with immunoglobulins of non-self origin. Magnetic bead separation facilitated the testing of interactions between salivary antibodies and oral bacteria, showing that these interactions are specific and may reflect differences in recognition by self and non-self immunoglobulins. Further development of this system could improve understanding of the relationship between the oral microbiota and the host immune system and of mechanisms underlying the compositional stability of the oral microbiota.

The genome sequence of Dyella jiangningensis FCAV SCS01 from a lignocellulose-decomposing microbial consortium metagenome reveals potential for biotechnological applications.

PubMed

Desiderato, Joana G; Alvarenga, Danillo O; Constancio, Milena T L; Alves, Lucia M C; Varani, Alessandro M

2018-05-14

Cellulose and its associated polymers are structural components of the plant cell wall, constituting one of the major sources of carbon and energy in nature. The carbon cycle is dependent on cellulose- and lignin-decomposing microbial communities and their enzymatic systems acting as consortia. These microbial consortia are under constant exploration for their potential biotechnological use. Herein, we describe the characterization of the genome of Dyella jiangningensis FCAV SCS01, recovered from the metagenome of a lignocellulose-degrading microbial consortium, which was isolated from a sugarcane crop soil under mechanical harvesting and covered by decomposing straw. The 4.7 Mbp genome encodes 4,194 proteins, including 36 glycoside hydrolases (GH), supporting the hypothesis that this bacterium may contribute to lignocellulose decomposition. Comparative analysis among fully sequenced Dyella species indicate that the genome synteny is not conserved, and that D. jiangningensis FCAV SCS01 carries 372 unique genes, including an alpha-glucosidase and maltodextrin glucosidase coding genes, and other potential biomass degradation related genes. Additional genomic features, such as prophage-like, genomic islands and putative new biosynthetic clusters were also uncovered. Overall, D. jiangningensis FCAV SCS01 represents the first South American Dyella genome sequenced and shows an exclusive feature among its genus, related to biomass degradation.

Passive treatment of wastewater and contaminated groundwater

DOEpatents

Phifer, Mark A.; Sappington, Frank C.; Millings, Margaret R.; Turick, Charles E.; McKinsey, Pamela C.

2007-11-06

A bioremediation system using inorganic oxide-reducing microbial consortia for the treatment of, inter alia coal mine and coal yard runoff uses a containment vessel for contaminated water and a second, floating phase for nutrients. Biodegradable oils are preferred nutrients.

Passive treatment of wastewater and contaminated groundwater

DOEpatents

Phifer, Mark A.; Sappington, Frank C.; Millings, Margaret R.; Turick, Charles E.; McKinsey, Pamela C.

2006-12-12

A bioremediation system using inorganic oxide-reducing microbial consortia for the treatment of, inter alia coal mine and coal yard runoff uses a containment vessel for contaminated water and a second, floating phase for nutrients. Biodegradable oils are preferred nutrients.

Metagenome enrichment approach used for selection of oil-degrading bacteria consortia for drill cutting residue bioremediation.

PubMed

Guerra, Alaine B; Oliveira, Jorge S; Silva-Portela, Rita C B; Araújo, Wydemberg; Carlos, Aline C; Vasconcelos, Ana Tereza R; Freitas, Ana Teresa; Domingos, Yldeney Silva; de Farias, Mirna Ferreira; Fernandes, Glauber José Turolla; Agnez-Lima, Lucymara F

2018-04-01

Drill cuttings leave behind thousands of tons of residues without adequate treatment, generating a large environmental liability. Therefore knowledge about the microbial community of drilling residue may be useful for developing bioremediation strategies. In this work, samples of drilling residue were enriched in different culture media in the presence of petroleum, aiming to select potentially oil-degrading bacteria and biosurfactant producers. Total DNA was extracted directly from the drill cutting samples and from two enriched consortia and sequenced using the Ion Torrent platform. Taxonomic analysis revealed the predominance of Proteobacteria in the metagenome from the drill cuttings, while Firmicutes was enriched in consortia samples. Functional analysis using the Biosurfactants and Biodegradation Database (BioSurfDB) revealed a similar pattern among the three samples regarding hydrocarbon degradation and biosurfactants production pathways. However, some statistical differences were observed between samples. Namely, the pathways related to the degradation of fatty acids, chloroalkanes, and chloroalkanes were enriched in consortia samples. The degradation colorimetric assay using dichlorophenolindophenol as an indicator was positive for several hydrocarbon substrates. The consortia were also able to produce biosurfactants, with biosynthesis of iturin, lichnysin, and surfactin among the more abundant pathways. A microcosms assay followed by gas chromatography analysis showed the efficacy of the consortia in degrading alkanes, as we observed a reduction of around 66% and 30% for each consortium in total alkanes. These data suggest the potential use of these consortia in the bioremediation of drilling residue based on autochthonous bioaugmentation. Copyright © 2018 Elsevier Ltd. All rights reserved.

Replicating the microbial community and water quality performance of full-scale slow sand filters in laboratory-scale filters.

PubMed

Haig, Sarah-Jane; Quince, Christopher; Davies, Robert L; Dorea, Caetano C; Collins, Gavin

2014-09-15

Previous laboratory-scale studies to characterise the functional microbial ecology of slow sand filters have suffered from methodological limitations that could compromise their relevance to full-scale systems. Therefore, to ascertain if laboratory-scale slow sand filters (L-SSFs) can replicate the microbial community and water quality production of industrially operated full-scale slow sand filters (I-SSFs), eight cylindrical L-SSFs were constructed and were used to treat water from the same source as the I-SSFs. Half of the L-SSFs sand beds were composed of sterilized sand (sterile) from the industrial filters and the other half with sand taken directly from the same industrial filter (non-sterile). All filters were operated for 10 weeks, with the microbial community and water quality parameters sampled and analysed weekly. To characterize the microbial community phyla-specific qPCR assays and 454 pyrosequencing of the 16S rRNA gene were used in conjunction with an array of statistical techniques. The results demonstrate that it is possible to mimic both the water quality production and the structure of the microbial community of full-scale filters in the laboratory - at all levels of taxonomic classification except OTU - thus allowing comparison of LSSF experiments with full-scale units. Further, it was found that the sand type composing the filter bed (non-sterile or sterile), the water quality produced, the age of the filters and the depth of sand samples were all significant factors in explaining observed differences in the structure of the microbial consortia. This study is the first to the authors' knowledge that demonstrates that scaled-down slow sand filters can accurately reproduce the water quality and microbial consortia of full-scale slow sand filters. Copyright © 2014 Elsevier Ltd. All rights reserved.

Understanding complex host-microbe interactions in Hydra

PubMed Central

Bosch, Thomas C.G.

2012-01-01

Any multicellular organism may be considered a metaorganism or holobiont—comprised of the macroscopic host and synergistic interdependence with bacteria, archaea, fungi, viruses, and numerous other microbial and eukaryotic species including algal symbionts. Defining the individual microbe-host conversations in these consortia is a challenging but necessary step on the path to understanding the function of the associations as a whole. Dissecting the fundamental principles that underlie all host-microbe interactions requires simple animal models with only a few specific bacterial species. Here I present Hydra as such a model with one of the simplest epithelia in the animal kingdom, with the availability of a fully sequenced genome and numerous genomic tools, and with few associated bacterial species. PMID:22688725

Soil amendments improve microbial ecology parameters of "topsoil inoculum" used in post-mining restoration

NASA Astrophysics Data System (ADS)

Kumaresan, Deepak; Munoz-Rojas, Miriam; Moreira-Grez, Benjamin; Kariman, Khalil; Whiteley, Andrew

2017-04-01

Mine operations generate substantial volumes of waste substrates, which are crushed and/or chemically treated waste rock from which ores are extracted. Establishment of rehabilitated landforms using post-mining substrates (i.e. waste rocks, tailings) that typically exhibit extreme conditions (such as high pH, nutrient deficiency, excessive salinity and metal toxicity) can be a major environmental problem and a critical issue during mine closure operations. More importantly, mine sites are located predominantly in arid or semi-arid lands where our understanding of basic ecosystem processes and microbial interactions with native plants (e.g. Eucalyptus spp., Acacia spp., Grevillea spp. in Western Australia) are limited. Despite the wide acknowledgement on the impact of microbial functional diversity on overall soil and plant health, no detailed attention has been paid to understand the role of belowground microbial functional diversity in the context of mine rehabilitation strategies. In this research, we investigated the role of nitrogen-based and microbial consortia amendments on improving the microbial ecology parameters of "topsoil inoculum" and subsequently its cascading effect on seedling establishment and plant morphology of Acacia ancistrocarpa, a legume native to the Pilbara and other regions of Western Australia and commonly used in arid zone restoration. The study was conducted under controlled environmental conditions in potted plants using topsoil retrieved from previously stockpiled material as growth media. A morphological assessment was undertaken to measure shoot length, shoot weight, root length, root area and root weight. Soil chemical properties, e.g. carbon, nitrogen and trace metals concentrations were determined Microbial activity was measured with the 1-day CO2 test, which determines soil microbial respiration rate based on the measurement of the CO2 burst produced after moistening dry soil (Muñoz-Rojas et al., 2016). Bacterial and archaeal community composition was assessed using high-throughput sequencing of the 16S rRNA marker gene analysis (Whiteley et al., 2012). Our results showed significant (P <0.05) larger rates of microbial activity and shoot:root ratio in those pots amended with both N and microbial consortia. Both amendments significantly influenced the chemical and bacterial-archaeal community composition in the topsoil inoculum. Topsoil amended with inorganic nitrogen revealed higher relative abundance of 16S rRNA gene sequences related to phylum Nitrospira, Planctomycetes, Gemmatimonadetes and Cyanobacteria/Chloroplast in comparison to "water-only" (control) and "microbial consortia" treatment. Addition of microbial consortia to topsoil significantly increased the concentrations of soil potassium, iron, copper and manganese. Interestingly, a large proportion of sequences that can only be assigned at the domain level (either Bacteria or Archaea) were detected in the control samples suggesting the presence of novel taxa/lineages in the native soil and their relative abundances are significantly influenced by the addition of amendments. Our data indicates that whilst amendments results significant improvement of plant growth and establishment at early stages it also results in considerable phylogenetic divergence within soil bacterial/archaeal communities, in particular loss of indigenous taxa/lineages that could have above-below ground feedback with native plants. Muñoz-Rojas M, Erickson TE, Martini D, Dixon KW, Merritt DJ. 2016. Soil physicochemical and microbiological indicators of short, medium and long term post-fire recovery in semi-arid ecosystems. Ecological indicators 63, 14-22.DOI: 10.1016/j.ecolind.2015.11.038 Whiteley AS, Jenkins S, Waite I, Kresoje N, Payne H, Mullan B, Allcock R, O'Donnell AG. Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform. J Microbiol Methods 91, 80-88, doi:10.1016/j.mimet.2012.07.008 (2012).

Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics

PubMed Central

Harcombe, William R.; Riehl, William J.; Dukovski, Ilija; Granger, Brian R.; Betts, Alex; Lang, Alex H.; Bonilla, Gracia; Kar, Amrita; Leiby, Nicholas; Mehta, Pankaj; Marx, Christopher J.; Segrè, Daniel

2014-01-01

Summary The inter-species exchange of metabolites plays a key role in the spatio-temporal dynamics of microbial communities. This raises the question whether ecosystem-level behavior of structured communities can be predicted using genome-scale models of metabolism for multiple organisms. We developed a modeling framework that integrates dynamic flux balance analysis with diffusion on a lattice, and applied it to engineered consortia. First, we predicted, and experimentally confirmed, the species-ratio to which a 2-species mutualistic consortium converges, and the equilibrium composition of a newly engineered 3-member community. We next identified a specific spatial arrangement of colonies, which gives rise to what we term the “eclipse dilemma”: does a competitor placed between a colony and its cross-feeding partner benefit or hurt growth of the original colony? Our experimentally validated finding, that the net outcome is beneficial, highlights the complex nature of metabolic interactions in microbial communities, while at the same time demonstrating their predictability. PMID:24794435

The Application of Magnetic Bead Selection to Investigate Interactions between the Oral Microbiota and Salivary Immunoglobulins

PubMed Central

Madhwani, Tejal

2016-01-01

The effect of humoral immunity on the composition of the oral microbiota is less intensively investigated than hygiene and diet, in part due to a lack of simple and robust systems for investigating interactions between salivary immunoglobulins and oral bacteria. Here we report the application of an ex situ method to investigate the specificity of salivary immunoglobulins for salivary bacteria. Saliva collected from six volunteers was separated into immunoglobulin and microbial fractions, and the microbial fractions were then directly exposed to salivary immunoglobulins of “self” and “non-self” origin. Antibody-selected bacteria were separated from their congeners using a magnetic bead system, selective for IgA or IgG isotypes. The positively selected fractions were then characterized using gel-based eubacterial-specific DNA profiling. The eubacterial profiles of positively selected fractions diverged significantly from profiles of whole salivary consortia based on volunteer (P≤ 0.001%) and immunoglobulin origin (P≤ 0.001%), but not immunoglobulin isotype (P = 0.2). DNA profiles of separated microbial fractions were significantly (p≤ 0.05) less diverse than whole salivary consortia and included oral and environmental bacteria. Consortia selected using self immunoglobulins were generally less diverse than those selected with immunoglobulins of non-self origin. Magnetic bead separation facilitated the testing of interactions between salivary antibodies and oral bacteria, showing that these interactions are specific and may reflect differences in recognition by self and non-self immunoglobulins. Further development of this system could improve understanding of the relationship between the oral microbiota and the host immune system and of mechanisms underlying the compositional stability of the oral microbiota. PMID:27483159

Microbial Life in Soil - Linking Biophysical Models with Observations

NASA Astrophysics Data System (ADS)

Or, Dani; Tecon, Robin; Ebrahimi, Ali; Kleyer, Hannah; Ilie, Olga; Wang, Gang

2015-04-01

Microbial life in soil occurs within fragmented aquatic habitats formed in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools that enable new mechanistic insights into how differences in substrate affinities among microbial species and soil micro-hydrological conditions may give rise to a remarkable spatial and functional order in an extremely heterogeneous soil microbial world

Microbial Life in Soil - Linking Biophysical Models with Observations

NASA Astrophysics Data System (ADS)

Or, D.; Tecon, R.; Ebrahimi, A.; Kleyer, H.; Ilie, O.; Wang, G.

2014-12-01

Microbial life in soil occurs within fragmented aquatic habitats in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools that enable new mechanistic insights into how differences in substrate affinities among microbial species and soil micro-hydrological conditions may give rise to a remarkable spatial and functional order in an extremely heterogeneous soil microbial world.

Synergistic Interactions in Microbial Biofilms Facilitate the Establishment of Opportunistic Pathogenic Fungi in Household Dishwashers.

PubMed

Zupančič, Jerneja; Raghupathi, Prem K; Houf, Kurt; Burmølle, Mette; Sørensen, Søren J; Gunde-Cimerman, Nina

2018-01-01

Biofilms formed on rubber seals in dishwashers harbor diverse microbiota. In this study, we focussed on the microbial composition of bacteria and fungi, isolated from a defined area of one square centimeter of rubber from four domestic dishwashers and assessed their abilities to in vitro multispecies biofilm formation. A total of 80 isolates (64 bacterial and 16 fungal) were analyzed. Multiple combinations of bacterial isolates from each dishwasher were screened for synergistic interactions. 32 out of 140 tested (23%) four-species bacterial combinations displayed consistent synergism leading to an overall increase in biomass, in all experimental trails. Bacterial isolates from two of the four dishwashers generated a high number of synergistically interacting four-species consortia. Network based correlation analyses also showed higher co-occurrence patterns observed between bacterial members in the same two dishwasher samples, indicating cooperative effects. Furthermore, two synergistic four-species bacterial consortia were tested for their abilities to incorporate an opportunistic fungal pathogen, Exophiala dermatitidis and their establishment as biofilms on sterile ethylene propylene diene monomer M-class (EPDM) rubber and polypropylene (PP) surfaces. When the bacterial consortia included E. dermatitidis , the overall cell numbers of both bacteria and fungi increased and a substantial increase in biofilm biomass was observed. These results indicate a novel phenomenon of cross kingdom synergy in biofilm formation and these observations could have potential implications for human health.

Synergistic Interactions in Microbial Biofilms Facilitate the Establishment of Opportunistic Pathogenic Fungi in Household Dishwashers

PubMed Central

Zupančič, Jerneja; Raghupathi, Prem K.; Houf, Kurt; Burmølle, Mette; Sørensen, Søren J.; Gunde-Cimerman, Nina

2018-01-01

Biofilms formed on rubber seals in dishwashers harbor diverse microbiota. In this study, we focussed on the microbial composition of bacteria and fungi, isolated from a defined area of one square centimeter of rubber from four domestic dishwashers and assessed their abilities to in vitro multispecies biofilm formation. A total of 80 isolates (64 bacterial and 16 fungal) were analyzed. Multiple combinations of bacterial isolates from each dishwasher were screened for synergistic interactions. 32 out of 140 tested (23%) four-species bacterial combinations displayed consistent synergism leading to an overall increase in biomass, in all experimental trails. Bacterial isolates from two of the four dishwashers generated a high number of synergistically interacting four-species consortia. Network based correlation analyses also showed higher co-occurrence patterns observed between bacterial members in the same two dishwasher samples, indicating cooperative effects. Furthermore, two synergistic four-species bacterial consortia were tested for their abilities to incorporate an opportunistic fungal pathogen, Exophiala dermatitidis and their establishment as biofilms on sterile ethylene propylene diene monomer M-class (EPDM) rubber and polypropylene (PP) surfaces. When the bacterial consortia included E. dermatitidis, the overall cell numbers of both bacteria and fungi increased and a substantial increase in biofilm biomass was observed. These results indicate a novel phenomenon of cross kingdom synergy in biofilm formation and these observations could have potential implications for human health. PMID:29441043

Proliferation of antibiotic resistance genes in microbial consortia of sequencing batch reactors (SBRs) upon exposure to trace erythromycin or erythromycin-H2O.

PubMed

Fan, Caian; He, Jianzhong

2011-05-01

A variety of antibiotics and their metabolites at sub-inhibitory level concentrations are suspected to expand resistance genes in the environment. However, knowledge is limited on the causal correlation of trace antibiotics or their metabolites with resistance proliferation. In this study, erythromycin (ERY) resistance genes were screened on microbial consortia of sequencing batch reactors (SBRs) after one year acclimation to ERY (100 μg/L) or dehydrated erythromycin (ERY-H(2)O, 50 μg/L). The identified esterase gene ereA explains that ERY could be degraded to six products by microbes acclimated to ERY (100 μg/L). However, ERY could not be degraded by microbes acclimated to ERY-H(2)O (50 μg/L), which may be due to the less proliferated ereA gene. Biodegradation of ERY required the presence of exogenous carbon source (e.g., glucose) and nutrients (e.g., nitrogen, phosphorus) for assimilation, but overdosed ammonium-N (>40 mg/L) inhibited degradation of ERY. Zoogloea, a kind of biofilm formation bacteria, became predominant in the ERY degradation consortia, suggesting that the input of ERY could induce biofilm resistance to antibiotics. Our study highlights that lower μg/L level of ERY or ERY-H(2)O in the environment encourages expansion of resistance genes in microbes. Copyright © 2011 Elsevier Ltd. All rights reserved.

Metabolism and biotransformation of azo dye by bacterial consortium studied in a bioreaction calorimeter.

PubMed

Shanmugam, Bhuvanesh Kumar; Mahadevan, Surianarayanan

2015-11-01

Effluents from leather and textile industries are difficult for treatment owing to its recalcitrant nature. Since the volume of effluent generated are high, a robust and active microbial consortia is required for effective treatment. The focus in the present study is the calorimetric traceability of the metabolic behaviors of mixed microbial consortia, while it grows and degrades recalcitrant substance such as an azo dye acid blue 113. The consortium exhibited a syntrophic division of substrate and was effective in degrading dye up to 0.8g/l. Notably, it was able to degrade 93.7% of the azo dye in 12-16h whereas its monocultures required 48-72h to reach 82.1%. The products of biodegradation were analyzed and the chemical pathway substantiated using chemical thermodynamic and energy release patterns. MTT assay confirmed that emanates are eco-friendly. Heat profile pattern and bioenergetics provide fundamental data for a feasible application in commercial level. Copyright © 2015 Elsevier Ltd. All rights reserved.

Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulfidic marine sediments

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

Glass, DR. Jennifer; Yu, DR. Hang; Steele, Joshua

Microbes have obligate requirements for trace metals in metalloenzymes that catalyze important biogeochemical reactions. In anoxic methane- and sulfide-rich environments, microbes may have unique adaptations for metal acquisition and utilization due to decreased bioavailability as a result of metal sulfide precipitation. However, micronutrient cycling is largely unexplored in cold ( 10 C) and sulfidic (>1 mM H2S) deep-sea methane seep ecosystems. We investigated trace metal geochemistry and microbial metal utilization in methane seeps offshore Oregon and California, USA, and report dissolved concentrations of nickel (0.5-270 nM), cobalt (0.5-6 nM), molybdenum (10-5,600 nM) and tungsten (0.3-8 nM) in Hydrate Ridge sedimentmore » porewaters. Despite low levels of cobalt and tungsten, metagenomic and metaproteomic data suggest that microbial consortia catalyzing anaerobic oxidation of methane utilize both scarce micronutrients in addition to nickel and molybdenum. Genetic machinery for cobalt-containing vitamin B12 biosynthesis was present in both anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB). Proteins affiliated with the tungsten-containing form of formylmethanofuran dehydrogenase were expressed in ANME from two seep ecosystems, the first evidence for expression of a tungstoenzyme in psychrotolerant microorganisms. Finally, our data suggest that chemical speciation of metals in highly sulfidic porewaters may exert a stronger influence on microbial bioavailability than total concentration« less

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

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

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

1999-06-01

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

Identification, visualization, and sorting of translationally active microbial consortia from deep-sea methane seeps

NASA Astrophysics Data System (ADS)

Hatzenpichler, R.; Connon, S. A.; Goudeau, D.; Malmstrom, R.; Woyke, T.; Orphan, V. J.

2015-12-01

Within the past few years, great progress has been made in tapping the genomes of individual cells separated from environmental samples. Unfortunately, however, most often these efforts have been target blind, as they did not pre-select for taxa of interest or focus on metabolically active cells that could be considered key species of the system at the time. This problem is particularly pronounced in low-turnover systems such as deep sea sediments. In an effort to tap the genetic potential hidden within functionally active cells, we have recently developed an approach for the in situ fluorescent tracking of protein synthesis in uncultured cells via bioorthogonal non-canonical amino acid-tagging (BONCAT). This technique depends on the incorporation of synthetic amino acids that carry chemically modifiable tags into newly made proteins, which later can be visualized via click chemistry-mediated fluorescence-labeling. BONCAT is thus able to specifically target proteins that have been expressed in reaction to an experimental condition. We are particularly interested in using BONCAT to understand the functional potential of slow-growing syntrophic consortia of anaerobic methanotrophic archaea and sulfate-reducing bacteria which together catalyze the anaerobic oxidation of methane (AOM) in marine methane seeps. In order to specifically target consortia that are active under varying environmental regimes, we are studying different subpopulations of these inter-domain consortia via a combination of BONCAT with rRNA-targeted FISH. We then couple the BONCAT-enabled staining of active consortia with their separation from inactive members of the community via fluorescence-activated cell-sorting (FACS) and metagenomic sequencing of individual consortia. Using this approach, we were able to identify previously unrecognized AOM-partnerships. By comparing the mini-metagenomes obtained from individual consortia with each other we are starting to gain a more hollistic understanding of the genetic similarities and niche-determining characteristics of a range of functional and taxonomic clades of AOM-consortia.

Microbial Metabolic Roles in Bedrock Degradation and the Genesis of Biomineral and Biopattern Biosignatures in Caves and Mines

NASA Astrophysics Data System (ADS)

Boston, P. J.

2016-12-01

In subsurface environments like natural or anthropogenic caves (aka mines), microorganisms facilitate considerable bedrock degradation under a variety of circumstances. Mobilization of materials from these processes frequently produces distinctive biominerals, identifiable biotextures, and unique biopatterns. Microbial activities can even determine the form of speleothems (secondary mineral cave decorations), thus providing highly conspicuous macroscopic biosignatures. It is critical to understand microbial-mineral interactions, recognizing that while the lithology controls important aspects of the environment, in turn, the geochemistry is greatly affected by the biology. Microbial communities can contribute to the actual formation of cavities (speleogenesis), and subsequent enlargement of caves and vugs and the mineral deposits that enrich many subterranean spaces. A major challenge is to quantify such influences. Genetic analysis is revealing a vast but highly partitioned biodiversity in the overall rock fracture habitat of Earth's crust especially in caves and mines where the three phases of matter (solid rock, fluids, and gases) typically interact producing high niche richness. Lessons learned from the microbial/geochemical systems that we have studied include: 1) significant similarities in metabolic functions between different geochemical systems, 2) ubiquity of metal oxidation for energy, 3) ubiquity of biofilms, some highly mineralized, 4) highly interdependent, multi-species communities that can only transform materials in consortia, 5) complex ecological succession including characteristic pioneer species, 6) often very slow growth rates in culture, 7) prevalence of very small cell sizes, ( 100 - 500 nm diam.), 8) mineral reprecipitation of mobilized materials, often dependent on the presence of live microbial communities to produce initial amorphous compounds followed by gradual crystallization, and 9) resultant in situ self-fossilization. Microbial metabolism occurs against a complex backdrop of hydrology, geochemistry, and geological structures of subsurface environments. These are not static but change in response to both short term and much longer geological time scales thus presenting significant challenges in interpretation.

Monitoring of microbial communities in anaerobic digestion sludge for biogas optimisation.

PubMed

Lim, Jun Wei; Ge, Tianshu; Tong, Yen Wah

2018-01-01

This study characterised and compared the microbial communities of anaerobic digestion (AD) sludge using three different methods - (1) Clone library; (2) Pyrosequencing; and (3) Terminal restriction fragment length polymorphism (T-RFLP). Although high-throughput sequencing techniques are becoming increasingly popular and affordable, the reliance of such techniques for frequent monitoring of microbial communities may be a financial burden for some. Furthermore, the depth of microbial analysis revealed by high-throughput sequencing may not be required for monitoring purposes. This study aims to develop a rapid, reliable and economical approach for the monitoring of microbial communities in AD sludge. A combined approach where genetic information of sequences from clone library was used to assign phylogeny to T-RFs determined experimentally was developed in this study. In order to assess the effectiveness of the combined approach, microbial communities determined by the combined approach was compared to that characterised by pyrosequencing. Results showed that both pyrosequencing and clone library methods determined the dominant bacteria phyla to be Proteobacteria, Firmicutes, Bacteroidetes, and Thermotogae. Both methods also found that sludge A and B were predominantly dominated by acetogenic methanogens followed by hydrogenotrophic methanogens. The number of OTUs detected by T-RFLP was significantly lesser than that detected by the clone library. In this study, T-RFLP analysis identified majority of the dominant species of the archaeal consortia. However, many of the more highly diverse bacteria consortia were missed. Nevertheless, the combined approach developed in this study where clone sequences from the clone library were used to assign phylogeny to T-RFs determined experimentally managed to accurately predict the same dominant microbial groups for both sludge A and sludge B, as compared to the pyrosequencing results. Results showed that the combined approach of clone library and T-RFLP accurately predicted the dominant microbial groups and thus is a reliable and more economical way to monitor the evolution of microbial systems in AD sludge. Copyright © 2017 Elsevier Ltd. All rights reserved.

Characterization of bacterial consortia capable of degrading 4-chlorobenzoate and 4-bromobenzoate under denitrifying conditions.

PubMed

Song, Bongkeun; Kerkhof, Lee J; Häggblom, Max M

2002-08-06

4-Chlorobenzoate and 4-bromobenzoate were readily degraded in denitrifying enrichment cultures established with river sediment, estuarine sediment or agricultural soil as inoculum. Stable denitrifying consortia were obtained and maintained by serial dilution and repeated feeding of substrates. Microbial community analyses were performed to characterize the 4-chlorobenzoate and 4-bromobenzoate degrading consortia with terminal restriction fragment length polymorphism (T-RFLP) and cloning of 16S rRNA genes from the cultures. Interestingly, two major terminal restriction fragments (T-RFs) in the 4-chlorobenzoate degrading consortia and one T-RF in the 4-bromobenzoate utilizing consortium were observed from T-RFLP analysis regardless of their geographical and ecological origins. The two T-RFs (clones 4CB1 and 4CB2) in 4-chlorobenzoate degrading consortia were identified as members of the beta-subunit of the Proteobacteria on the basis of 16S rRNA sequencing analysis. Phylogenetic analysis of 16S rRNA genes showed that clone 4CB1 was closely related to Thauera aromatica while clone 4CB2 was distantly related to the genera Limnobacter and Ralstonia. The 4-bromobenzoate utilizing consortium mainly consisted of one T-RF, which was identical to clone 4CB2 in spite of different enrichment substrate. This suggests that degradation of 4-chlorobenzoate and 4-bromobenzoate under denitrifying conditions was mediated by bacteria belonging to the beta-subunit of the Proteobacteria.

Responses of mixed methanotrophic consortia to variable Cu2+/Fe2+ ratios.

PubMed

Chidambarampadmavathy, Karthigeyan; Karthikeyan, Obulisamy Parthiba; Huerlimann, Roger; Maes, Gregory E; Heimann, Kirsten

2017-07-15

Methane mitigation in landfill top cover soils is mediated by methanotrophs whose optimal methane (CH 4 ) oxidation capacity is governed by environmental and complex microbial community interactions. Optimization of CH 4 remediating bio-filters need to take microbial responses into account. Divalent copper (Cu 2+ ) and iron (Fe 2+ ) are present in landfills at variable ratios and play a vital role in methane oxidation capacity and growth of methanotrophs. This study, as a first of its kind, therefore quantified effects of variable Cu 2+ and Fe 2+ (5:5, 5:25 and 5:50 μM) ratios on mixed methanotrophic communities enriched from landfill top cover (LB) and compost soils (CB). CH 4 oxidation capacity, CH 4 removal efficiencies, fatty acids content/profiles and polyhydroxybutyrate (PHB; a biopolymer) contents were also analysed to quantify performance and potential co-product development. Mixed methanotroph cultures were raised in 10 L continuous stirred tank reactors (CSTRs, Bioflo ® & Celligen ® 310 Fermentor/Bioreactor; John Morris Scientific, Chatswood, NSW, Australia). Community structure was determined by amplifying the V3-V4 region of 16s rRNA gene. Community structure and, consequently, fatty acid-profiles changed significantly with increasing Cu 2+ /Fe 2+ ratios, and responses were different for LB and CB. Effects on methane oxidation capacities and PHB content were similar in the LB- and CB-CSTR, decreasing with increasing Cu 2+ /Fe 2+ ratios, while biomass growth was unaffected. In general, high Fe 2+ concentration favored growth of the type -II methanotroph Methylosinus in the CB-CSTR, but methanotroph abundances decreased in the LB-CSTR. Increase in Cu 2+ /Fe 2+ ratio increased the growth of Sphingopyxis in both systems, while Azospirllum was co-dominant in the LB- but absent in the CB-CSTR. After 13 days, methane oxidation capacities and PHB content decreased by ∼50% and more in response to increasing Fe 2+ concentrations. Although methanotroph abundance was ∼2% in the LB- (compared to >50% in CB-CSTR), methane oxidation capacities were comparable in the two systems, suggesting that methane oxidation capacity was maintained by the dominant Azospirllum and Sphingopyxis in the LB-CSTR. Despite similar methanotroph inoculum community composition and controlled environmental variables, increasing Cu 2+ /Fe 2+ ratios resulted in significantly different microbial community structures in the LB- and CB-CSTR, indicative of complex microbial interactions. In summary, our results suggest that a detailed understanding of allelopathic interactions in mixed methanotrophic consortia is vital for constructing robust bio-filters for CH 4 emission abatement. Copyright © 2017 Elsevier Ltd. All rights reserved.

Strategies for enhancing the effectiveness of metagenomic-based enzyme discovery in lignocellulytic microbial communities

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

DeAngelis, K.M.; Gladden, J.G.; Allgaier, M.

2010-03-01

Producing cellulosic biofuels from plant material has recently emerged as a key U.S. Department of Energy goal. For this technology to be commercially viable on a large scale, it is critical to make production cost efficient by streamlining both the deconstruction of lignocellulosic biomass and fuel production. Many natural ecosystems efficiently degrade lignocellulosic biomass and harbor enzymes that, when identified, could be used to increase the efficiency of commercial biomass deconstruction. However, ecosystems most likely to yield relevant enzymes, such as tropical rain forest soil in Puerto Rico, are often too complex for enzyme discovery using current metagenomic sequencing technologies.more » One potential strategy to overcome this problem is to selectively cultivate the microbial communities from these complex ecosystems on biomass under defined conditions, generating less complex biomass-degrading microbial populations. To test this premise, we cultivated microbes from Puerto Rican soil or green waste compost under precisely defined conditions in the presence dried ground switchgrass (Panicum virgatum L.) or lignin, respectively, as the sole carbon source. Phylogenetic profiling of the two feedstock-adapted communities using SSU rRNA gene amplicon pyrosequencing or phylogenetic microarray analysis revealed that the adapted communities were significantly simplified compared to the natural communities from which they were derived. Several members of the lignin-adapted and switchgrass-adapted consortia are related to organisms previously characterized as biomass degraders, while others were from less well-characterized phyla. The decrease in complexity of these communities make them good candidates for metagenomic sequencing and will likely enable the reconstruction of a greater number of full length genes, leading to the discovery of novel lignocellulose-degrading enzymes adapted to feedstocks and conditions of interest.« less

Comparative Fecal Metagenomics Unveils Unique Functional Capacity of the Swine Gut

EPA Science Inventory

Uncovering the taxonomic composition and functional capacity within the swine gut microbial consortia is of great importance to animal physiology and health and to food and water safety due to the presence of human pathogens in pig feces. Limited information on the physiological...

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

PubMed

Alvaro, J J; Clausen, S

2010-03-01

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

Synthetic photosynthetic consortia define interactions leading to robustness and photoproduction

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

Hays, Stephanie G.; Yan, Leo L. W.; Silver, Pamela A.

In this study, microbial consortia composed of autotrophic and heterotrophic species abound in nature, yet examples of synthetic communities with mixed metabolism are limited in the laboratory. We previously engineered a model cyanobacterium, Synechococcus elongatus PCC 7942, to secrete the bulk of the carbon it fixes as sucrose, a carbohydrate that can be utilized by many other microbes. Here, we tested the capability of sucrose-secreting cyanobacteria to act as a flexible platform for the construction of synthetic, light-driven consortia by pairing them with three disparate heterotrophs: Bacillus subtilis, Escherichia coli, or Saccharomyces cerevisiae. The comparison of these different co-culture dyadsmore » reveals general design principles for the construction of robust autotroph/heterotroph consortia. As a result, we observed heterotrophic growth dependent upon cyanobacterial photosynthate in each co-culture pair. Furthermore, these synthetic consortia could be stabilized over the long-term (weeks to months) and both species could persist when challenged with specific perturbations. Stability and productivity of autotroph/heterotroph co-cultures was dependent on heterotroph sucrose utilization, as well as other species-independent interactions that we observed across all dyads. One destabilizing interaction we observed was that non-sucrose byproducts of oxygenic photosynthesis negatively impacted heterotroph growth. Conversely, inoculation of each heterotrophic species enhanced cyanobacterial growth in comparison to axenic cultures. Finally, these consortia can be flexibly programmed for photoproduction of target compounds and proteins; by changing the heterotroph in co-culture to specialized strains of B. subtilis or E. coli we demonstrate production of alpha-amylase and polyhydroxybutyrate, respectively. In conclusion, enabled by the unprecedented flexibility of this consortia design, we uncover species-independent design principles that influence cyanobacteria/heterotroph consortia robustness. The modular nature of these communities and their unusual robustness exhibits promise as a platform for highly-versatile photoproduction strategies that capitalize on multi-species interactions and could be utilized as a tool for the study of nascent symbioses. Further consortia improvements via engineered interventions beyond those we show here (i.e., increased efficiency growing on sucrose) could improve these communities as production platforms.« less

Synthetic photosynthetic consortia define interactions leading to robustness and photoproduction

DOE PAGES

Hays, Stephanie G.; Yan, Leo L. W.; Silver, Pamela A.; ...

2017-01-23

In this study, microbial consortia composed of autotrophic and heterotrophic species abound in nature, yet examples of synthetic communities with mixed metabolism are limited in the laboratory. We previously engineered a model cyanobacterium, Synechococcus elongatus PCC 7942, to secrete the bulk of the carbon it fixes as sucrose, a carbohydrate that can be utilized by many other microbes. Here, we tested the capability of sucrose-secreting cyanobacteria to act as a flexible platform for the construction of synthetic, light-driven consortia by pairing them with three disparate heterotrophs: Bacillus subtilis, Escherichia coli, or Saccharomyces cerevisiae. The comparison of these different co-culture dyadsmore » reveals general design principles for the construction of robust autotroph/heterotroph consortia. As a result, we observed heterotrophic growth dependent upon cyanobacterial photosynthate in each co-culture pair. Furthermore, these synthetic consortia could be stabilized over the long-term (weeks to months) and both species could persist when challenged with specific perturbations. Stability and productivity of autotroph/heterotroph co-cultures was dependent on heterotroph sucrose utilization, as well as other species-independent interactions that we observed across all dyads. One destabilizing interaction we observed was that non-sucrose byproducts of oxygenic photosynthesis negatively impacted heterotroph growth. Conversely, inoculation of each heterotrophic species enhanced cyanobacterial growth in comparison to axenic cultures. Finally, these consortia can be flexibly programmed for photoproduction of target compounds and proteins; by changing the heterotroph in co-culture to specialized strains of B. subtilis or E. coli we demonstrate production of alpha-amylase and polyhydroxybutyrate, respectively. In conclusion, enabled by the unprecedented flexibility of this consortia design, we uncover species-independent design principles that influence cyanobacteria/heterotroph consortia robustness. The modular nature of these communities and their unusual robustness exhibits promise as a platform for highly-versatile photoproduction strategies that capitalize on multi-species interactions and could be utilized as a tool for the study of nascent symbioses. Further consortia improvements via engineered interventions beyond those we show here (i.e., increased efficiency growing on sucrose) could improve these communities as production platforms.« less

Using federal technology policy to strength the US microelectronics industry

NASA Astrophysics Data System (ADS)

Gover, J. E.; Gwyn, C. W.

1994-07-01

A review of US and Japanese experiences with using microelectronics consortia as a tool for strengthening their respective industries reveals major differences. Japan has established catch-up consortia with focused goals. These consortia have a finite life targeted from the beginning, and emphasis is on work that supports or leads to product and process-improvement-driven commercialization. Japan's government has played a key role in facilitating the development of consortia and has used consortia promote domestic competition. US consortia, on the other hand, have often emphasized long-range research with considerably less focus than those in Japan. The US consortia have searched for and often made revolutionary technology advancements. However, technology transfer to their members has been difficult. Only SEMATECH has assisted its members with continuous improvements, compressing product cycles, establishing relationships, and strengthening core competencies. The US government has not been a catalyst nor provided leadership in consortia creation and operation. We propose that in order to regain world leadership in areas where US companies lag foreign competition, the US should create industry-wide, horizontal-vertical, catch-up consortia or continue existing consortia in the six areas where the US lags behind Japan -- optoelectronics, displays, memories, materials, packaging, and manufacturing equipment. In addition, we recommend that consortia be established for special government microelectronics and microelectronics research integration and application. We advocate that these consortia be managed by an industry-led Microelectronics Alliance, whose establishment would be coordinated by the Department of Commerce. We further recommend that the Semiconductor Research Corporation, the National Science Foundation Engineering Research Centers, and relevant elements of other federal programs be integrated into this consortia complex.

Using federal technology policy to strength the US microelectronics industry

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

Gover, J.E.; Gwyn, C.W.

1994-07-01

A review of US and Japanese experiences with using microelectronics consortia as a tool for strengthening their respective industries reveals major differences. Japan has established catch-up consortia with focused goals. These consortia have a finite life targeted from the beginning, and emphasis is on work that supports or leads to product and process-improvement-driven commercialization. Japan`s government has played a key role in facilitating the development of consortia and has used consortia promote domestic competition. US consortia, on the other hand, have often emphasized long-range research with considerably less focus than those in Japan. The US consortia have searched for andmore » often made revolutionary technology advancements. However, technology transfer to their members has been difficult. Only SEMATECH has assisted its members with continuous improvements, compressing product cycles, establishing relationships, and strengthening core competencies. The US government has not been a catalyst nor provided leadership in consortia creation and operation. We propose that in order to regain world leadership in areas where US companies lag foreign competition, the US should create industry-wide, horizontal-vertical, catch-up consortia or continue existing consortia in the six areas where the US lags behind Japan -- optoelectronics, displays, memories, materials, packaging, and manufacturing equipment. In addition, we recommend that consortia be established for special government microelectronics and microelectronics research integration and application. We advocate that these consortia be managed by an industry-led Microelectronics Alliance, whose establishment would be coordinated by the Department of Commerce. We further recommend that the Semiconductor Research Corporation, the National Science Foundation Engineering Research Centers, and relevant elements of other federal programs be integrated into this consortia complex.« less

Bacteria of an anaerobic 1,2-dichloropropane-dechlorinating mixed culture are phylogenetically related to those of other anaerobic dechlorinating consortia.

PubMed

Schlötelburg, C; von Wintzingerode, F; Hauck, R; Hegemann, W; Göbel, U B

2000-07-01

A 16S-rDNA-based molecular study was performed to determine the bacterial diversity of an anaerobic, 1,2-dichloropropane-dechlorinating bioreactor consortium derived from sediment of the River Saale, Germany. Total community DNA was extracted and bacterial 16S rRNA genes were subsequently amplified using conserved primers. A clone library was constructed and analysed by sequencing the 16S rDNA inserts of randomly chosen clones followed by dot blot hybridization with labelled polynucleotide probes. The phylogenetic analysis revealed significant sequence similarities of several as yet uncultured bacterial species in the bioreactor to those found in other reductively dechlorinating freshwater consortia. In contrast, no close relationship was obtained with as yet uncultured bacteria found in reductively dechlorinating consortia derived from marine habitats. One rDNA clone showed >97% sequence similarity to Dehalobacter species, known for reductive dechlorination of tri- and tetrachloroethene. These results suggest that reductive dechlorination in microbial freshwater habitats depends upon a specific bacterial community structure.

In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study

PubMed Central

2009-01-01

Background Three methods were developed for the application of stoichiometry-based network analysis approaches including elementary mode analysis to the study of mass and energy flows in microbial communities. Each has distinct advantages and disadvantages suitable for analyzing systems with different degrees of complexity and a priori knowledge. These approaches were tested and compared using data from the thermophilic, phototrophic mat communities from Octopus and Mushroom Springs in Yellowstone National Park (USA). The models were based on three distinct microbial guilds: oxygenic phototrophs, filamentous anoxygenic phototrophs, and sulfate-reducing bacteria. Two phases, day and night, were modeled to account for differences in the sources of mass and energy and the routes available for their exchange. Results The in silico models were used to explore fundamental questions in ecology including the prediction of and explanation for measured relative abundances of primary producers in the mat, theoretical tradeoffs between overall productivity and the generation of toxic by-products, and the relative robustness of various guild interactions. Conclusion The three modeling approaches represent a flexible toolbox for creating cellular metabolic networks to study microbial communities on scales ranging from cells to ecosystems. A comparison of the three methods highlights considerations for selecting the one most appropriate for a given microbial system. For instance, communities represented only by metagenomic data can be modeled using the pooled method which analyzes a community's total metabolic potential without attempting to partition enzymes to different organisms. Systems with extensive a priori information on microbial guilds can be represented using the compartmentalized technique, employing distinct control volumes to separate guild-appropriate enzymes and metabolites. If the complexity of a compartmentalized network creates an unacceptable computational burden, the nested analysis approach permits greater scalability at the cost of more user intervention through multiple rounds of pathway analysis. PMID:20003240

Schrödinger's microbes: Tools for distinguishing the living from the dead in microbial ecosystems.

PubMed

Emerson, Joanne B; Adams, Rachel I; Román, Clarisse M Betancourt; Brooks, Brandon; Coil, David A; Dahlhausen, Katherine; Ganz, Holly H; Hartmann, Erica M; Hsu, Tiffany; Justice, Nicholas B; Paulino-Lima, Ivan G; Luongo, Julia C; Lymperopoulou, Despoina S; Gomez-Silvan, Cinta; Rothschild-Mancinelli, Brooke; Balk, Melike; Huttenhower, Curtis; Nocker, Andreas; Vaishampayan, Parag; Rothschild, Lynn J

2017-08-16

While often obvious for macroscopic organisms, determining whether a microbe is dead or alive is fraught with complications. Fields such as microbial ecology, environmental health, and medical microbiology each determine how best to assess which members of the microbial community are alive, according to their respective scientific and/or regulatory needs. Many of these fields have gone from studying communities on a bulk level to the fine-scale resolution of microbial populations within consortia. For example, advances in nucleic acid sequencing technologies and downstream bioinformatic analyses have allowed for high-resolution insight into microbial community composition and metabolic potential, yet we know very little about whether such community DNA sequences represent viable microorganisms. In this review, we describe a number of techniques, from microscopy- to molecular-based, that have been used to test for viability (live/dead determination) and/or activity in various contexts, including newer techniques that are compatible with or complementary to downstream nucleic acid sequencing. We describe the compatibility of these viability assessments with high-throughput quantification techniques, including flow cytometry and quantitative PCR (qPCR). Although bacterial viability-linked community characterizations are now feasible in many environments and thus are the focus of this critical review, further methods development is needed for complex environmental samples and to more fully capture the diversity of microbes (e.g., eukaryotic microbes and viruses) and metabolic states (e.g., spores) of microbes in natural environments.

Sulfate-reducing bacteria mediate thionation of diphenylarsinic acid under anaerobic conditions.

PubMed

Guan, Ling; Shiiya, Ayaka; Hisatomi, Shihoko; Fujii, Kunihiko; Nonaka, Masanori; Harada, Naoki

2015-02-01

Diphenylarsinic acid (DPAA) is often found as a toxic intermediate metabolite of diphenylchloroarsine or diphenylcyanoarsine that were produced as chemical warfare agents and were buried in soil after the World Wars. In our previous study Guan et al. (J Hazard Mater 241-242:355-362, 2012), after application of sulfate and carbon sources, anaerobic transformation of DPAA in soil was enhanced with the production of diphenylthioarsinic acid (DPTAA) as a main metabolite. This study aimed to isolate and characterize anaerobic soil microorganisms responsible for the metabolism of DPAA. First, we obtained four microbial consortia capable of transforming DPAA to DPTAA at a high transformation rate of more than 80% after 4 weeks of incubation. Sequencing for the bacterial 16S rRNA gene clone libraries constructed from the consortia revealed that all the positive consortia contained Desulfotomaculum acetoxidans species. In contrast, the absence of dissimilatory sulfite reductase gene (dsrAB) which is unique to sulfate-reducing bacteria was confirmed in the negative consortia showing no DPAA reduction. Finally, strain DEA14 showing transformation of DPAA to DPTAA was isolated from one of the positive consortia. The isolate was assigned to D. acetoxidans based on the partial 16S rDNA sequence analysis. Thionation of DPAA was also carried out in a pure culture of a known sulfate-reducing bacterial strain, Desulfovibrio aerotolerans JCM 12613(T). These facts indicate that sulfate-reducing bacteria are microorganisms responsible for the transformation of DPAA to DPTAA under anaerobic conditions.

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

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

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

1999-06-01

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

Focusing on Environmental Biofilms With Variable-Pressure Scanning Electron Microscopy

NASA Astrophysics Data System (ADS)

Joubert, L.; Wolfaardt, G. M.; Du Plessis, K.

2006-12-01

Since the term biofilm has been coined almost 30 years ago, visualization has formed an integral part of investigations on microbial attachment. Electron microscopic (EM) biofilm studies, however, have been limited by the hydrated extracellular matrix which loses structural integrity with conventional preparative techniques, and under required high-vacuum conditions, resulting in a loss of information on spatial relationships and distribution of biofilm microbes. Recent advances in EM technology enable the application of Variable Pressure Scanning Electron Microscopy (VP SEM) to biofilms, allowing low vacuum and hydrated chamber atmosphere during visualization. Environmental biofilm samples can be viewed in situ, unfixed and fully hydrated, with application of gold-sputter-coating only, to increase image resolution. As the impact of microbial biofilms can be both hazardous and beneficial to man and his environment, recognition of biofilms as a natural form of microbial existence is needed to fully assess the potential role of microbial communities on technology. The integration of multiple techniques to elucidate biofilm processes has become imperative for unraveling complex phenotypic adaptations of this microbial lifestyle. We applied VP SEM as integrative technique with traditional and novel analytical techniques to (1)localize lignocellulosic microbial consortia applied for producing alternative bio-energy sources in the mining wastewater industry, (2) characterize and visualize wetland microbial communities in the treatment of winery wastewater, and (3)determine the impact of recombinant technology on yeast biofilm behavior. Visualization of microbial attachment to a lignocellulose substrate, and degradation of exposed plant tissue, gave insight into fiber degradation and volatile fatty acid production for biological sulphate removal from mining wastewater. Also, the 3D-architecture of complex biofilms developing in constructed wetlands was correlated with molecular fingerprints of wetland communities using tRFLP (Terminal Restriction Fragment Length Polymorphism) - and gave evidence of temporal and spatial variation in a wetland system, to potentially be applied as management tool in wastewater treatment. Visualization of differences in biofilm development by wild and recombinant yeast strains furthermore supported real-time quantitative data of biofilm development by Cryptococcus laurentii and Saccharomyces yeast strains. In all cases VP SEM allowed a more holistic interpretation of biofilm processes than afforded by quantitative empirical data only.

Microbially assisted phytoremediation approaches for two multi-element contaminated sites.

PubMed

Langella, Francesca; Grawunder, Anja; Stark, Romy; Weist, Aileen; Merten, Dirk; Haferburg, Götz; Büchel, Georg; Kothe, Erika

2014-01-01

Phytoremediation is an environmental friendly, cost-effective technology for a soft restoration of abandoned mine sites. The grasses Agrostis capillaris, Deschampsia flexuosa and Festuca rubra, and the annual herb Helianthus annuus were combined with microbial consortia in pot experiments on multi-metal polluted substrates collected at a former uranium mine near Ronneburg, Germany, and a historic copper mine in Kopparberg, Sweden, to test for phytoextraction versus phytostabilization abilities. Metal uptake into plant biomass was evaluated to identify optimal plant-microbe combinations for each substrate. Metal bioavailability was found to be plant species and element specific, and influenced by the applied bacterial consortia of 10 strains, each isolated from the same soil to which it was applied. H. annuus showed high extraction capacity for several metals on the German soil independent of inoculation. Our study could also show a significant enhancement of extraction for F. rubra and A. capillaris when combined with the bacterial consortium, although usually grasses are considered metal excluder species. On the Swedish mixed substrate, due to its toxicity, with 30 % bark compost, A. capillaris inoculated with the respective consortium was able to extract multi-metal contaminants.

Big and disparate data: considerations for pediatric consortia.

PubMed

Stingone, Jeanette A; Mervish, Nancy; Kovatch, Patricia; McGuinness, Deborah L; Gennings, Chris; Teitelbaum, Susan L

2017-04-01

Increasingly, there is a need for examining exposure disease associations in large, diverse datasets to understand the complex determinants of pediatric disease and disability. Recognizing that children's health research consortia will be important sources of big data, it is crucial for the pediatric research community to be knowledgeable about the challenges and opportunities that they will face. The present review will provide examples of existing children's health consortia, highlight recent pooled analyses conducted by children's health research consortia, address common challenges of pooled analyses, and provide recommendations to advance collective research efforts in pediatric research. Formal consortia and other collective-science initiatives are increasingly being created to share individual data from a set of relevant epidemiological studies to address a common research topic under the concept that the joint effort of many individual groups can accomplish far more than working alone. There are practical challenges to the participation of investigators within consortia that need to be addressed in order for them to work. Researchers who access consortia with data centers will be able to go far beyond their initial hypotheses and potentially accomplish research that was previously thought infeasible or too costly.

Functional Stability of a Mixed Microbial Consortium Producing PHA From Waste Carbon Sources

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

David N. Thompson; Erik R. Coats; William A. Smith

2006-04-01

Polyhydroxyalkanoates (PHAs) represent an environmentally-effective alternative to synthetic thermoplastics; however, current production practices are not sustainable. In this study, PHA production was accomplished in sequencing batch bioreactors utilizing real wastewaters and mixed microbial consortia from municipal activated sludge as inoculum. Polymer production reached 85%, 53%, and 10% of the cell dry weight from methanol-enriched pulp-and-paper mill foul condensate, fermented municipal primary solids, and biodiesel wastewater, respectively. Employing denaturing gradient gel electrophoresis of 16S-rDNA from PCR-amplified DNA extracts, distinctly different communities were observed between and within wastewaters following enrichment. Most importantly, functional stability was maintained despite differing and contrasting microbial populations.

Functional Stability of a Mixed Microbial Consortium Producing PHA From Waste Carbon Sources

NASA Astrophysics Data System (ADS)

Coats, Erik R.; Loge, Frank J.; Smith, William A.; Thompson, David N.; Wolcott, Michael P.

Polyhydroxyalkanoates (PHAs) represent an environmentally effective alternative to synthetic thermoplastics; however, current production practices are not sustainable. In this study, PHA production was accomplished in sequencing batch bioreactors utilizing real wastewaters and mixed microbial consortia from municipal activated sludge as inoculum. Polymer production reached 85, 53, and 10% of the cell dry weight from methanol-enriched pulp and paper mill foul condensate, fermented municipal primary solids, and biodiesel wastewater, respectively. Using denaturing gradient gel electrophoresis of 16S-rDNA from polymerase chain reaction-amplified DNA extracts, distinctly different communities were observed between and within wastewaters following enrichment. Most importantly, functional stability was maintained despite differing and contrasting microbial populations.

Developing a model for cystic fibrosis sociomicrobiology based on antibiotic and environmental stress.

PubMed

Lopes, Susana Patrícia; Azevedo, Nuno Filipe; Pereira, Maria Olívia

2017-12-01

Cystic fibrosis (CF) infections are invariably biofilm-mediated and polymicrobial, being safe to assume that a myriad of factors affects the sociomicrobiology within the CF infection site and modulate the CF community dynamics, by shaping their social activities, overall functions, virulence, ultimately affecting disease outcome. This work aimed to assess changes in the dynamics (particularly on the microbial composition) of dual-/three-species biofilms involving CF-classical (Pseudomonas aeruginosa) and unusual species (Inquilinus limosus and Dolosigranulum pigrum), according to variable oxygen conditions and antibiotic exposure. Low fluctuations in biofilm compositions were observed across distinct oxygen environments, with dual-species biofilms exhibiting similar relative proportions and P. aeruginosa and/or D. pigrum populations dominating three-species consortia. Once exposed to antibiotics, biofilms displayed high resistance profiles, and microbial compositions, distributions, and microbial interactions significantly challenged. The antibiotic/oxygen environment supported such fluctuations, which enhanced for three-species communities. In conclusion, antibiotic therapy hugely disturbed CF communities' dynamics, inducing significant compositional changes on multispecies consortia. Clearly, multiple perturbations may disturb this dynamic, giving rise to various microbiological scenarios in vivo, and affecting disease phenotype. Therefore, an appreciation of the ecological/evolutionary nature within CF communities will be useful for the optimal use of current therapies and for newer breakthroughs on CF antibiotherapy. Copyright © 2017 Elsevier GmbH. All rights reserved.

Roles of microorganisms other than Clostridium and Enterobacter in anaerobic fermentative biohydrogen production systems--a review.

PubMed

Hung, Chun-Hsiung; Chang, Yi-Tang; Chang, Yu-Jie

2011-09-01

Anaerobic fermentative biohydrogen production, the conversion of organic substances especially from organic wastes to hydrogen gas, has become a viable and promising means of producing sustainable energy. Successful biological hydrogen production depends on the overall performance (results of interactions) of bacterial communities, i.e., mixed cultures in reactors. Mixed cultures might provide useful combinations of metabolic pathways for the processing of complex waste material ingredients, thereby supporting the more efficient decomposition and hydrogenation of biomass than pure bacteria species would. Therefore, understanding the relationships between variations in microbial composition and hydrogen production efficiency is the first step in constructing more efficient hydrogen-producing consortia, especially when complex and non-sterilized organic wastes are used as feeding substrates. In this review, we describe recent discoveries on bacterial community composition obtained from dark fermentation biohydrogen production systems, with emphasis on the possible roles of microorganisms that co-exist with common hydrogen producers. Copyright © 2011 Elsevier Ltd. All rights reserved.

Comparative metagenomic analysis of microcosm structures and lignocellulolytic enzyme systems of symbiotic biomass-degrading consortia.

PubMed

Wongwilaiwalin, Sarunyou; Laothanachareon, Thanaporn; Mhuantong, Wuttichai; Tangphatsornruang, Sithichoke; Eurwilaichitr, Lily; Igarashi, Yasuo; Champreda, Verawat

2013-10-01

Decomposition of lignocelluloses by cooperative microbial actions is an essential process of carbon cycling in nature and provides a basis for biomass conversion to fuels and chemicals in biorefineries. In this study, structurally stable symbiotic aero-tolerant lignocellulose-degrading microbial consortia were obtained from biodiversified microflora present in industrial sugarcane bagasse pile (BGC-1), cow rumen fluid (CRC-1), and pulp mill activated sludge (ASC-1) by successive subcultivation on rice straw under facultative anoxic conditions. Tagged 16S rRNA gene pyrosequencing revealed that all isolated consortia originated from highly diverse environmental microflora shared similar composite phylum profiles comprising mainly Firmicutes, reflecting convergent adaptation of microcosm structures, however, with substantial differences at refined genus level. BGC-1 comprising cellulolytic Clostridium and Acetanaerobacterium in stable coexistence with ligninolytic Ureibacillus showed the highest capability on degradation of agricultural residues and industrial pulp waste with CMCase, xylanase, and β-glucanase activities in the supernatant. Shotgun pyrosequencing of the BGC-1 metagenome indicated a markedly high relative abundance of genes encoding for glycosyl hydrolases, particularly for lignocellulytic enzymes in 26 families. The enzyme system comprised a unique composition of main-chain degrading and side-chain processing hydrolases, dominated by GH2, 3, 5, 9, 10, and 43, reflecting adaptation of enzyme profiles to the specific substrate. Gene mapping showed metabolic potential of BGC-1 for conversion of biomass sugars to various fermentation products of industrial importance. The symbiotic consortium is a promising simplified model for study of multispecies mechanisms on consolidated bioprocessing and a platform for discovering efficient synergistic enzyme systems for biotechnological application.

Magnetite production and transformation in the methanogenic consortia from coastal riverine sediments.

PubMed

Zheng, Shiling; Wang, Bingchen; Liu, Fanghua; Wang, Oumei

2017-11-01

Minerals that contain ferric iron, such as amorphous Fe(III) oxides (A), can inhibit methanogenesis by competitively accepting electrons. In contrast, ferric iron reduced products, such as magnetite (M), can function as electrical conductors to stimulate methanogenesis, however, the processes and effects of magnetite production and transformation in the methanogenic consortia are not yet known. Here we compare the effects on methanogenesis of amorphous Fe (III) oxides (A) and magnetite (M) with ethanol as the electron donor. RNA-based terminal restriction fragment length polymorphism with a clone library was used to analyse both bacterial and archaeal communities. Iron (III)-reducing bacteria including Geobacteraceae and methanogens such as Methanosarcina were enriched in iron oxide-supplemented enrichment cultures for two generations with ethanol as the electron donor. The enrichment cultures with A and non-Fe (N) dominated by the active bacteria belong to Veillonellaceae, and archaea belong to Methanoregulaceae and Methanobacteriaceae, Methanosarcinaceae (Methanosarcina mazei), respectively. While the enrichment cultures with M, dominated by the archaea belong to Methanosarcinaceae (Methanosarcina barkeri). The results also showed that methanogenesis was accelerated in the transferred cultures with ethanol as the electron donor during magnetite production from A reduction. Powder X-ray diffraction analysis indicated that magnetite was generated from microbial reduction of A and M was transformed into siderite and vivianite with ethanol as the electron donor. Our data showed the processes and effects of magnetite production and transformation in the methanogenic consortia, suggesting that significantly different effects of iron minerals on microbial methanogenesis in the iron-rich coastal riverine environment were present.

Invited review: Microbial evolution in raw-milk, long-ripened cheeses produced using undefined natural whey starters.

PubMed

Gatti, Monica; Bottari, Benedetta; Lazzi, Camilla; Neviani, Erasmo; Mucchetti, Germano

2014-02-01

The robustness of the starter culture during cheese fermentation is enhanced by the presence of a rich consortium of microbes. Natural starters are consortia of microbes undoubtedly richer than selected starters. Among natural starters, natural whey starters (NWS) are the most common cultures currently used to produce different varieties of cheeses. Undefined NWS are typically used for Italian cooked, long-ripened, extra-hard, raw milk cheeses, such as Parmigiano Reggiano and Grana Padano. Together with raw milk microbiota, NWS are responsible for most cheese characteristics. The microbial ecology of these 2 cheese varieties is based on a complex interaction among starter lactic acid bacteria (SLAB) and nonstarter lactic acid bacteria (NSLAB), which are characterized by their different abilities to grow in a changing substrate. This review aims to summarize the latest findings on Parmigiano Reggiano and Grana Padano to better understand the dynamics of SLAB, which mainly arise from NWS, and NSLAB, which mainly arise from raw milk, and their possible role in determining the characteristics of these cheeses. The review is presented in 4 main sections. The first summarizes the main microbiological and chemical properties of the ripened cheese as determined by cheese-making process variables, as these variables may affect microbial growth. The second describes the microbiota of raw milk as affected by specific milk treatments, from milking to the filling of the cheese milk vat. The third describes the microbiota of NWS, and the fourth reviews the knowledge available on microbial dynamics from curd to ripened cheese. As the dynamics and functionality of complex undefined NWS is one of the most important areas of focus in current food microbiology research, this review may serve as a good starting point for implementing future studies on microbial diversity and functionality of undefined cheese starter cultures. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Assessing the role of spatial structure on cell-specific activity and interactions within uncultured methane-oxidizing syntrophic consortia (Invited)

NASA Astrophysics Data System (ADS)

Orphan, V. J.; McGlynn, S.; Chadwick, G.; Dekas, A.; Green-Saxena, A.

2013-12-01

Sulfate-coupled anaerobic oxidation of methane is catalysed through symbiotic associations between archaea and sulphate-reducing bacteria and represents the dominant sink for methane in the oceans. These methane-oxidizing symbiotic consortia form well-structured multi-celled aggregations in marine methane seeps, where close spatial proximity is believed to be essential for efficient exchange of substrates between syntrophic partners. The nature of this interspecies metabolic relationship is still unknown however there are a number of hypotheses regarding the electron carrying intermediate and ecophysiology of the partners, each of which should be affected by, and influence, the spatial arrangement of archaeal and bacterial cells within aggregates. To advance our understanding of the role of spatial structure within naturally occurring environmental consortia, we are using spatial statistical methods combined with fluorescence in situ hybridization and high-resolution nanoscale secondary ion mass spectrometry (FISH-nanoSIMS) to quantify the effect of spatial organization and intra- and inter-species interactions on cell-specific microbial activity within these diverse archaeal-bacterial partnerships.

Synthetic Ecology of Microbes: Mathematical Models and Applications

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

Zomorrodi, Ali R.; Segre, Daniel

As the indispensable role of natural microbial communities in many aspects of life on Earth is uncovered, the bottom-up engineering of synthetic microbial consortia with novel functions is becoming an attractive alternative to engineering single-species systems. Here, we summarize recent work on synthetic microbial communities with a particular emphasis on open challenges and opportunities in environmental sustainability and human health. We next provide a critical overview of mathematical approaches, ranging from phenomenological to mechanistic, to decipher the principles that govern the function, dynamics and evolution of microbial ecosystems. Lastly, we present our outlook on key aspects of microbial ecosystems andmore » synthetic ecology that require further developments, including the need for more efficient computational algorithms, a better integration of empirical methods and model-driven analysis, the importance of improving gene function annotation, and the value of a standardized library of well-characterized organisms to be used as building blocks of synthetic communities.« less

Synthetic Ecology of Microbes: Mathematical Models and Applications

DOE PAGES

Zomorrodi, Ali R.; Segre, Daniel

2015-11-11

As the indispensable role of natural microbial communities in many aspects of life on Earth is uncovered, the bottom-up engineering of synthetic microbial consortia with novel functions is becoming an attractive alternative to engineering single-species systems. Here, we summarize recent work on synthetic microbial communities with a particular emphasis on open challenges and opportunities in environmental sustainability and human health. We next provide a critical overview of mathematical approaches, ranging from phenomenological to mechanistic, to decipher the principles that govern the function, dynamics and evolution of microbial ecosystems. Lastly, we present our outlook on key aspects of microbial ecosystems andmore » synthetic ecology that require further developments, including the need for more efficient computational algorithms, a better integration of empirical methods and model-driven analysis, the importance of improving gene function annotation, and the value of a standardized library of well-characterized organisms to be used as building blocks of synthetic communities.« less

A Diverse Community To Study Communities: Integration of Experiments and Mathematical Models To Study Microbial Consortia.

PubMed

Succurro, Antonella; Moejes, Fiona Wanjiku; Ebenhöh, Oliver

2017-08-01

The last few years have seen the advancement of high-throughput experimental techniques that have produced an extraordinary amount of data. Bioinformatics and statistical analyses have become instrumental to interpreting the information coming from, e.g., sequencing data and often motivate further targeted experiments. The broad discipline of "computational biology" extends far beyond the well-established field of bioinformatics, but it is our impression that more theoretical methods such as the use of mathematical models are not yet as well integrated into the research studying microbial interactions. The empirical complexity of microbial communities presents challenges that are difficult to address with in vivo / in vitro approaches alone, and with microbiology developing from a qualitative to a quantitative science, we see stronger opportunities arising for interdisciplinary projects integrating theoretical approaches with experiments. Indeed, the addition of in silico experiments, i.e., computational simulations, has a discovery potential that is, unfortunately, still largely underutilized and unrecognized by the scientific community. This minireview provides an overview of mathematical models of natural ecosystems and emphasizes that one critical point in the development of a theoretical description of a microbial community is the choice of problem scale. Since this choice is mostly dictated by the biological question to be addressed, in order to employ theoretical models fully and successfully it is vital to implement an interdisciplinary view at the conceptual stages of the experimental design. Copyright © 2017 Succurro et al.

Waste treatment integration in space

NASA Technical Reports Server (NTRS)

Baresi, L.; Kern, R.

1991-01-01

The circumstances and criteria for space-based waste treatment bioregenerative life-support systems differ in many ways from those needed in terrestrial applications. In fact, the term "waste" may not even be appropriate in the context of nearly closed, cycling, ecosystems such as those under consideration. Because of these constraints there is a need for innovative approaches to the problem of "materials recycling". Hybrid physico-chemico-biological systems offer advantages over both strictly physico-chemico or biological approaches that would be beneficial to material recycling. To effectively emulate terrestrial cycling, the use of various microbial consortia ("assemblies of interdependent microbes") should be seriously considered for the biological components of such systems. This paper will examine the use of consortia in the context of a hybrid-system for materials recycling in space.

Endotoxins in Environmental and Clinical Samples Assessed by GC-Tandem MS

NASA Astrophysics Data System (ADS)

Szponar, Bogumila

Bacteria appeared on the Earth millions years before us and human evolution was triggered by the constant presence of pathogenic and symbiotic microorganisms in our surroundings. Interplay occurred between higher organism and microbial consortia residing in the host organs and on the epithelial surfaces; another natural space of bacteria-human interaction is the indoor environment where we spend the majority of our lifetime. Indoor microbial exposure affects our well-being and can result in respiratory symptoms, such as allergies and asthma, since both dead and live microorganisms and their cell constituents, including lipopolysaccharides (LPS, endotoxins), interact with our immune system. Thus, there is a demand for robust tools for qualitative and quantitative determination of the microbial communities that we are exposed to.

Construction and screening of marine metagenomic libraries.

PubMed

Weiland, Nancy; Löscher, Carolin; Metzger, Rebekka; Schmitz, Ruth

2010-01-01

Marine microbial communities are highly diverse and have evolved during extended evolutionary processes of physiological adaptations under the influence of a variety of ecological conditions and selection pressures. They harbor an enormous diversity of microbes with still unknown and probably new physiological characteristics. Besides, the surfaces of marine multicellular organisms are typically covered by a consortium of epibiotic bacteria and act as barriers, where diverse interactions between microorganisms and hosts take place. Thus, microbial diversity in the water column of the oceans and the microbial consortia on marine tissues of multicellular organisms are rich sources for isolating novel bioactive compounds and genes. Here we describe the sampling, construction of large-insert metagenomic libraries from marine habitats and exemplarily one function based screen of metagenomic clones.

Metagenomic Analyses Reveal the Involvement of Syntrophic Consortia in Methanol/Electricity Conversion in Microbial Fuel Cells

PubMed Central

Yamamuro, Ayaka; Kouzuma, Atsushi; Abe, Takashi; Watanabe, Kazuya

2014-01-01

Methanol is widely used in industrial processes, and as such, is discharged in large quantities in wastewater. Microbial fuel cells (MFCs) have the potential to recover electric energy from organic pollutants in wastewater; however, the use of MFCs to generate electricity from methanol has not been reported. In the present study, we developed single-chamber MFCs that generated electricity from methanol at the maximum power density of 220 mW m−2 (based on the projected area of the anode). In order to reveal how microbes generate electricity from methanol, pyrosequencing of 16S rRNA-gene amplicons and Illumina shotgun sequencing of metagenome were conducted. The pyrosequencing detected in abundance Dysgonomonas, Sporomusa, and Desulfovibrio in the electrolyte and anode and cathode biofilms, while Geobacter was detected only in the anode biofilm. Based on known physiological properties of these bacteria, it is considered that Sporomusa converts methanol into acetate, which is then utilized by Geobacter to generate electricity. This speculation is supported by results of shotgun metagenomics of the anode-biofilm microbes, which reconstructed relevant catabolic pathways in these bacteria. These results suggest that methanol is anaerobically catabolized by syntrophic bacterial consortia with electrodes as electron acceptors. PMID:24852573

Metagenomic analyses reveal the involvement of syntrophic consortia in methanol/electricity conversion in microbial fuel cells.

PubMed

Yamamuro, Ayaka; Kouzuma, Atsushi; Abe, Takashi; Watanabe, Kazuya

2014-01-01

Methanol is widely used in industrial processes, and as such, is discharged in large quantities in wastewater. Microbial fuel cells (MFCs) have the potential to recover electric energy from organic pollutants in wastewater; however, the use of MFCs to generate electricity from methanol has not been reported. In the present study, we developed single-chamber MFCs that generated electricity from methanol at the maximum power density of 220 mW m(-2) (based on the projected area of the anode). In order to reveal how microbes generate electricity from methanol, pyrosequencing of 16S rRNA-gene amplicons and Illumina shotgun sequencing of metagenome were conducted. The pyrosequencing detected in abundance Dysgonomonas, Sporomusa, and Desulfovibrio in the electrolyte and anode and cathode biofilms, while Geobacter was detected only in the anode biofilm. Based on known physiological properties of these bacteria, it is considered that Sporomusa converts methanol into acetate, which is then utilized by Geobacter to generate electricity. This speculation is supported by results of shotgun metagenomics of the anode-biofilm microbes, which reconstructed relevant catabolic pathways in these bacteria. These results suggest that methanol is anaerobically catabolized by syntrophic bacterial consortia with electrodes as electron acceptors.

Microbial consortia of gorgonian corals from the Aleutian islands

USGS Publications Warehouse

Gray, Michael A.; Stone, R.P.; McLaughlin, M.R.; Kellogg, C.A.

2011-01-01

Gorgonians make up the majority of corals in the Aleutian archipelago and provide critical fish habitat in areas of economically important fisheries. The microbial ecology of the deep-sea gorgonian corals Paragorgea arborea, Plumarella superba, and Cryogorgia koolsae was examined with culture-based and 16S rRNA gene-based techniques. Six coral colonies (two per species) were collected. Samples from all corals were cultured, and clone libraries were constructed from P. superba and C. koolsae. Cultured bacteria were dominated by the Gammaproteobacteria, especially Vibrionaceae, with other phyla comprising <6% of the isolates. The clone libraries showed dramatically different bacterial communities between corals of the same species collected at different sites, with no clear pattern of conserved bacterial consortia. Two of the clone libraries (one from each coral species) were dominated by Tenericutes, with Alphaproteobacteria dominating the remaining sequences. The other libraries were more diverse and had a more even distribution of bacterial phyla, showing more similarity between genera than within coral species. Here we report the first microbiological characterization of P. arborea, P. superba, and C. koolsae. FEMS Microbiology Ecology ?? 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. No claim to original US government works.

Stable isotope fractionation of selenium by natural microbial consortia

USGS Publications Warehouse

Ellis, A.S.; Johnson, T.M.; Herbel, M.J.; Bullen, T.D.

2003-01-01

The mobility and bioavailability of Se depend on its redox state, and reduction of Se oxyanions to less mobile, reduced species controls transport of this potentially toxic element in the environment. Stable isotope fractionation of Se is currently being developed as an indicator of Se immobilization through reduction. In this study, Se isotope fractionation resulting from reduction of Se(VI) and Se(IV) oxyanions by natural microbial consortia was measured in sediment slurry experiments under nearly natural conditions, with no substrate added. Experiments were conducted with a wide range of initial Se concentrations and with sediment and water from three locations with contrasting environmental settings. The products of Se(VI) and Se(IV) reduction were enriched in the lighter isotopes relative to the reactants. Shifts of -2.60/00 to -3.10/00 and -5.50/00 to -5.70/00, respectively, were observed in the 80Se/76Se ratio. These isotopic fractionations did not depend significantly on initial Se concentrations, which were varied from 22 μg/l to 8 mg/l, or on geochemical differences among the sediments. These results provide estimates of Se isotope fractionation in organic-rich wetland environments but may not be appropriate for substrate-poor aquifers and marine sediments.

Microbial consortia of gorgonian corals from the Aleutian islands.

PubMed

Gray, Michael A; Stone, Robert P; McLaughlin, Molly R; Kellogg, Christina A

2011-04-01

Gorgonians make up the majority of corals in the Aleutian archipelago and provide critical fish habitat in areas of economically important fisheries. The microbial ecology of the deep-sea gorgonian corals Paragorgea arborea, Plumarella superba, and Cryogorgia koolsae was examined with culture-based and 16S rRNA gene-based techniques. Six coral colonies (two per species) were collected. Samples from all corals were cultured, and clone libraries were constructed from P. superba and C. koolsae. Cultured bacteria were dominated by the Gammaproteobacteria, especially Vibrionaceae, with other phyla comprising <6% of the isolates. The clone libraries showed dramatically different bacterial communities between corals of the same species collected at different sites, with no clear pattern of conserved bacterial consortia. Two of the clone libraries (one from each coral species) were dominated by Tenericutes, with Alphaproteobacteria dominating the remaining sequences. The other libraries were more diverse and had a more even distribution of bacterial phyla, showing more similarity between genera than within coral species. Here we report the first microbiological characterization of P. arborea, P. superba, and C. koolsae. FEMS Microbiology Ecology © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. No claim to original US government works.

Biodegradation of oil tank bottom sludge using microbial consortia.

PubMed

Gallego, José Luis R; García-Martínez, María Jesús; Llamas, Juan F; Belloch, Carmen; Peláez, Ana I; Sánchez, Jesús

2007-06-01

We present a rationale for the selection of a microbial consortia specifically adapted to degrade toxic components of oil refinery tank bottom sludge (OTBS). Sources such as polluted soils, petrochemical waste, sludge from refinery-wastewater plants, and others were used to obtain a collection of eight microorganisms, which were individually tested and characterized to analyze their degradative capabilities on different hydrocarbon families. After initial experiments using mixtures of these strains, we developed a consortium consisting of four microorganisms (three bacteria and one yeast) selected in the basis of their cometabolic effects, emulsification properties, colonization of oil components, and degradative capabilities. Although the specific contribution each of the former parameters makes is not clearly understood, the activity of the four-member consortium had a strong impact not only on linear alkane degradation (100%), but also on the degradation of cycloalkanes (85%), branched alkanes (44%), and aromatic and sulphur-aromatic compounds (31-55%). The effectiveness of this consortium was significantly superior to that obtained by individual strains, commercial inocula or an undefined mixture of culturable and non-culturable microorganisms obtained from OTBS-polluted soil. However, results were similar when another consortium of four microorganisms, previously isolated in the same OTBS-polluted soil, was assayed.

Effect of rhizobacterial consortia from undisturbed arid- and agro-ecosystems on wheat growth under different conditions.

PubMed

Inostroza, N G; Barra, P J; Wick, L Y; Mora, M L; Jorquera, M A

2017-02-01

Plant growth-promoting rhizobacteria (PGPR) are studied as complements/alternatives to chemical fertilizers used in agriculture. However, poor information exists on the potential of PGPR from undisturbed ecosystems. Here, we have evaluated the plant growth-promoting (PGP) effect of rhizobacterial consortia from undisturbed Chilean arid ecosystems (Consortium C1) and agro-ecosystems (Consortium C2) on plant biomass production. The PGP effects of C1 and C2 were assayed in wheat seedlings (Triticum aestivum L.) grown in pots under growth chamber conditions and in pots placed in an open greenhouse under natural conditions, using two different Chilean Andisols (Piedras Negras and Freire series) kept either at 30 or 60% of their maximum water holding capacity (MWHC). PGP effects depended on the soil type, MWHC and the growth conditions tested. Although both consortia showed PGB effects in artificial soils relative to controls in growth chambers, only C1 provoked a PGP effect at 60% MWHC in phosphorus-poor soil of the 'Piedras Negras' series. At natural conditions, however, only C1 exhibited statistically significant PGP effects at 30% MWHC in 'Piedras Negras', yet and most importantly allowed to maintain similar plant biomass as at 60% MWHC. Our results support possible applications of rhizobacterial consortia from arid ecosystems to improve wheat growth in Chilean Andisols under water shortage conditions. Wheat seedling inoculated with rhizobacterial consortia obtained from an undisturbed Chilean arid ecosystem showed improved growth in phosphorus-poor and partly dry soil. Arid ecosystems should be considered in further studies as an alternative source of microbial inoculants for agro-ecosystems subjected to stressful conditions by low nutrients and/or adverse climate events. © 2016 The Society for Applied Microbiology.

Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments

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

Trembath-Reichert, Elizabeth; Case, David H.; Orphan, Victoria J.

Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range ofDeltaproteobacteriadiversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seepmore » sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. In addition, many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co-occurrences containing putatively heterotrophic, candidate phyla such as OD1, Atribacteria, MBG-B, and Hyd24-12 and the potential for complex sulfur cycling involving Epsilon-, Delta-, and Gammaproteobacteria in methane seep ecosystems.« less

Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments

DOE PAGES

Trembath-Reichert, Elizabeth; Case, David H.; Orphan, Victoria J.

2016-04-18

Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range ofDeltaproteobacteriadiversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seepmore » sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. In addition, many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co-occurrences containing putatively heterotrophic, candidate phyla such as OD1, Atribacteria, MBG-B, and Hyd24-12 and the potential for complex sulfur cycling involving Epsilon-, Delta-, and Gammaproteobacteria in methane seep ecosystems.« less

Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments.

PubMed

Trembath-Reichert, Elizabeth; Case, David H; Orphan, Victoria J

2016-01-01

Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. Many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co-occurrences containing putatively heterotrophic, candidate phyla such as OD1, Atribacteria, MBG-B, and Hyd24-12 and the potential for complex sulfur cycling involving Epsilon-, Delta-, and Gammaproteobacteria in methane seep ecosystems.

Constraints on mechanisms and rates of anaerobic oxidation of methane by microbial consortia: process-based modeling of ANME-2 archaea and sulfate reducing bacteria interactions

NASA Astrophysics Data System (ADS)

Orcutt, B.; Meile, C.

2008-11-01

Anaerobic oxidation of methane (AOM) is the main process responsible for the removal of methane generated in Earth's marine subsurface environments. However, the biochemical mechanism of AOM remains elusive. By explicitly resolving the observed spatial arrangement of methanotrophic archaea and sulfate reducing bacteria found in consortia mediating AOM, potential intermediates involved in the electron transfer between the methane oxidizing and sulfate reducing partners were investigated via a consortium-scale reaction transport model that integrates the effect of diffusional transport with thermodynamic and kinetic controls on microbial activity. Model simulations were used to assess the impact of poorly constrained microbial characteristics such as minimum energy requirements to sustain metabolism and cell specific rates. The role of environmental conditions such as the influence of methane levels on the feasibility of H2, formate and acetate as intermediate species, and the impact of the abundance of intermediate species on pathway reversal were examined. The results show that higher production rates of intermediates via AOM lead to increased diffusive fluxes from the methane oxidizing archaea to sulfate reducing bacteria, but the build-up of the exchangeable species can cause the energy yield of AOM to drop below that required for ATP production. Comparison to data from laboratory experiments shows that under the experimental conditions of Nauhaus et al. (2007), none of the potential intermediates considered here is able to support metabolic activity matching the measured rates.

Temperature, inocula and substrate: Contrasting electroactive consortia, diversity and performance in microbial fuel cells.

PubMed

Heidrich, E S; Dolfing, J; Wade, M J; Sloan, W T; Quince, C; Curtis, T P

2018-02-01

The factors that affect microbial community assembly and its effects on the performance of bioelectrochemical systems are poorly understood. Sixteen microbial fuel cell (MFC) reactors were set up to test the importance of inoculum, temperature and substrate: Arctic soil versus wastewater as inoculum; warm (26.5°C) versus cold (7.5°C) temperature; and acetate versus wastewater as substrate. Substrate was the dominant factor in determining performance and diversity: unexpectedly the simple electrogenic substrate delivered a higher diversity than a complex wastewater. Furthermore, in acetate fed reactors, diversity did not correlate with performance, yet in wastewater fed ones it did, with greater diversity sustaining higher power densities and coulombic efficiencies. Temperature had only a minor effect on power density, (Q 10 : 2 and 1.2 for acetate and wastewater respectively): this is surprising given the well-known temperature sensitivity of anaerobic bioreactors. Reactors were able to operate at low temperature with real wastewater without the need for specialised inocula; it is speculated that MFC biofilms may have a self-heating effect. Importantly, the warm acetate fed reactors in this study did not act as direct model for cold wastewater fed systems. Application of this technology will encompass use of real wastewater at ambient temperatures. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Syntrophic interactions and mechanisms underpinning anaerobic methane oxidation: targeted metaproteogenomics, single-cell protein detection and quantitative isotope imaging of microbial consortia

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

Orphan, Victoria Jeanne

2014-11-26

Syntrophy and mutualism play a central role in carbon and nutrient cycling by microorganisms. Yet, our ability to effectively study symbionts in culture has been hindered by the inherent interdependence of syntrophic associations, their dynamic behavior, and their frequent existence at thermodynamic limits. Now solutions to these challenges are emerging in the form of new methodologies. Developing strategies that establish links between the identity of microorganisms and their metabolic potential, as well as techniques that can probe metabolic networks on a scale that captures individual molecule exchange and processing, is at the forefront of microbial ecology. Understanding the interactions betweenmore » microorganisms on this level, at a resolution previously intractable, will lead to our greater understanding of carbon turnover and microbial community resilience to environmental perturbations. In this project, we studied an enigmatic syntrophic association between uncultured methane-oxidizing archaea and sulfate-reducing bacteria. This environmental archaeal-bacterial partnership represents a globally important sink for methane in anoxic environments. The specific goals of this project were organized into 3 major tasks designed to address questions relating to the ecophysiology of these syntrophic organisms under changing environmental conditions (e.g. different electron acceptors and nutrients), primarily through the development of microanalytical imaging methods which enable the visualization of the spatial distribution of the partners within aggregates, consumption and exchange of isotopically labeled substrates, and expression of targeted proteins identified via metaproteomics. The advanced tool set developed here to collect, correlate, and analyze these high resolution image and isotope-based datasets from methane-oxidizing consortia has the potential to be widely applicable for studying and modeling patterns of activity and interactions across a broad range of spatially structured microbial partnerships, including other syntrophic associations, microbial mats, biofilms, and plant-microbe or animal-microbe symbioses in nature.« less

The process-related dynamics of microbial community during a simulated fermentation of Chinese strong-flavored liquor.

PubMed

Zhang, Yanyan; Zhu, Xiaoyu; Li, Xiangzhen; Tao, Yong; Jia, Jia; He, Xiaohong

2017-09-15

Famous Chinese strong-flavored liquor (CSFL) is brewed by microbial consortia in a special fermentation pit (FT). However, the fermentation process was not fully understood owing to the complicate community structure and metabolism. In this study, the process-related dynamics of microbial communities and main flavor compounds during the 70-day fermentation process were investigated in a simulated fermentation system. A three-phase model was proposed to characterize the process of the CSFL fermentation. (i) In the early fermentation period (1-23 days), glucose was produced from macromolecular carbohydrates (e.g., starch). The prokaryotic diversity decreased significantly. The Lactobacillaceae gradually predominated in the prokaryotic community. In contrast, the eukaryotic diversity rose remarkably in this stage. Thermoascus, Aspergillus, Rhizopus and unidentified Saccharomycetales were dominant eukaryotic members. (ii) In the middle fermentation period (23-48 days), glucose concentration decreased while lactate acid and ethanol increased significantly. Prokaryotic community was almost dominated by the Lactobacillus, while eukaryotic community was mainly comprised of Thermoascus, Emericella and Aspergillus. (iii) In the later fermentation period (48-70 days), the concentrations of ethyl esters, especially ethyl caproate, increased remarkably. The CSFL fermentation could undergo three stages: saccharification, glycolysis and esterification. Saccharomycetales, Monascus, and Rhizopus were positively correlated to glucose concentration (P < 0.05), highlighting their important roles in the starch saccharification. The Lactobacillaceae, Bacilli, Botryotinia, Aspergillus, unidentified Pleosporales and Capnodiales contributed to the glycolysis and esterification, because they were positively correlated to most organic acids and ethyl esters (P < 0.05). Additionally, four genera, including Emericella, Suillus, Mortierella and Botryotinia, that likely played key roles in fermentation, were observed firstly. This study observed comprehensive dynamics of microbial communities during the CSFL fermentation, and it further revealed the correlations between some crucial microorganisms and flavoring chemicals (FCs). The results from this study help to design effective strategies to manipulate microbial consortia for fermentation process optimization in the CSFL brew practice.

Biomass, community structure and nutritional status attributes of the deep subsurface microbiota---at Idaho and Hanford sites

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

White, D.C.; Ringelberg, D.B.

1991-10-28

The signature lipid biomarker technique based on phospholipid ester-linked fatty acid pattern analysis (PLFA) provides data on the total viable or potentially viable communities without the necessity of: (1) Quantitative recovery from the sediments or (2) The ability to culture the organisms. Analysis of PLFA provides evidence for the nutritional status (starvation and/or unbalanced growth) in situ. PLFA analysis of SSP samples from the INEL and PNL sites vadose zones showed higher biomass at the surface with prominent Actinomyces biomarkers with lower biomasses of stressed microbiota at progressively greater depth. The biomass and community diversity increased at the water tablemore » at both sites. Both these Western sites showed lower viable microbial biomasses than the WSRS samples. Cluster analysis of the total patterns from various sedimentary horizons showed three major consortia of microbes, with surface microbiota related at both sites, low viable biomass sites closely related at both sites, with anaerobic desaturase pathway being predominant at INEL and consortia utilizing predominantly branched saturated and the aerobic desaturase pathway at both sites. Preliminary examination of the consortia recovered from NTS show a clear relationship to water level.« less

Microstencils to generate defined, multi-species patterns of bacteria

DOE PAGES

Timm, Collin M.; Hansen, Ryan R.; Doktycz, Mitchel J.; ...

2015-11-12

Microbial communities are complex heterogeneous systems that are influenced by physical and chemical interactions with their environment, host, and community members. Techniques that facilitate the quantitative evaluation of how microscale organization influences the morphogenesis of multispecies communities could provide valuable insights into the dynamic behavior and organization of natural communities, the design of synthetic environments for multispecies culture, and the engineering of artificial consortia. In this work, we demonstrate a method for patterning microbes into simple arrangements that allow the quantitative measurement of growth dynamics as a function of their proximity to one another. The method combines parylene-based liftoff techniquesmore » with microfluidic delivery to simultaneously pattern multiple bacterial species with high viability using low-cost, customizable methods. Furthermore, quantitative measurements of bacterial growth for two competing isolates demonstrate that spatial coordination can play a critical role in multispecies growth and structure.« less

Cell-Free and In Vivo Characterization of Lux, Las, and Rpa Quorum Activation Systems in E. coli.

PubMed

Halleran, Andrew D; Murray, Richard M

2018-02-16

Synthetic biologists have turned toward quorum systems as a path for building sophisticated microbial consortia that exhibit group decision making. Currently, however, even the most complex consortium circuits rely on only one or two quorum sensing systems, greatly restricting the available design space. High-throughput characterization of available quorum sensing systems is useful for finding compatible sets of systems that are suitable for a defined circuit architecture. Recently, cell-free systems have gained popularity as a test-bed for rapid prototyping of genetic circuitry. We take advantage of the transcription-translation cell-free system to characterize three commonly used Lux-type quorum activators, Lux, Las, and Rpa. We then compare the cell-free characterization to results obtained in vivo. We find significant genetic crosstalk in both the Las and Rpa systems and substantial signal crosstalk in Lux activation. We show that cell-free characterization predicts crosstalk observed in vivo.

Microstencils to generate defined, multi-species patterns of bacteria

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

Timm, Collin M.; Hansen, Ryan R.; Doktycz, Mitchel J.

Microbial communities are complex heterogeneous systems that are influenced by physical and chemical interactions with their environment, host, and community members. Techniques that facilitate the quantitative evaluation of how microscale organization influences the morphogenesis of multispecies communities could provide valuable insights into the dynamic behavior and organization of natural communities, the design of synthetic environments for multispecies culture, and the engineering of artificial consortia. In this work, we demonstrate a method for patterning microbes into simple arrangements that allow the quantitative measurement of growth dynamics as a function of their proximity to one another. The method combines parylene-based liftoff techniquesmore » with microfluidic delivery to simultaneously pattern multiple bacterial species with high viability using low-cost, customizable methods. Furthermore, quantitative measurements of bacterial growth for two competing isolates demonstrate that spatial coordination can play a critical role in multispecies growth and structure.« less

Production-related petroleum microbiology: progress and prospects.

PubMed

Voordouw, Gerrit

2011-06-01

Microbial activity in oil reservoirs is common. Methanogenic consortia hydrolyze low molecular weight components to methane and CO2, transforming light oil to heavy oil to bitumen. The presence of sulfate in injection water causes sulfate-reducing bacteria to produce sulfide. This souring can be reversed by nitrate, stimulating nitrate-reducing bacteria. Removing biogenic sulfide is important, because it contributes to pitting corrosion and resulting pipeline failures. Increased water production eventually makes oil production uneconomic. Microbial fermentation products can lower oil viscosity or interfacial tension and produced biomass can block undesired flow paths to produce more oil. These biotechnologies benefit from increased understanding of reservoir microbial ecology through new sequence technologies and help to decrease the environmental impact of oil production. Copyright © 2010 Elsevier Ltd. All rights reserved.

Comparative performances of microbial capacitive deionization cell and microbial fuel cell fed with produced water from the Bakken shale.

PubMed

Shrestha, Namita; Chilkoor, Govinda; Wilder, Joseph; Ren, Zhiyong Jason; Gadhamshetty, Venkataramana

2018-06-01

This study evaluates and compares the performance of microbial fuel cells (MFCs) and microbial capacitive deionization cells (MCDCs) fed with wastewater produced from the Bakken shale. The produced water was characterized by high levels of dissolved solids and chemical oxygen demand (COD). Two-compartment MFCs and three-compartment MCDCs were evaluated under batch-fed mode using mixed microbial consortia in the anode, ferricyanide in the cathode, and produced water as the electrolyte in the anode and capacitive deionization units. COD removal in the MFCs was 88%, while that in the MCDCs was limited to 76%. The lower performance of the MCDCs was due to the large impedance (6600 Ω cm 2 ) compared with the MFCs (870 Ω cm 2 ). However, the MCDCs achieved two-fold higher removal of dissolved solids. Both the MFCs and MCDCs suffered from a higher impedance induced by fouling in the latter stages of the operation. Copyright © 2018 Elsevier B.V. All rights reserved.

Microbial technology with major potentials for the urgent environmental needs of the next decades.

PubMed

Verstraete, Willy; De Vrieze, Jo

2017-09-01

Several needs in the context of the water-energy-food nexus will become more prominent in the next decades. It is crucial to delineate these challenges and to find opportunities for innovative microbial technologies in the framework of sustainability and climate change. Here, we focus on four key issues, that is the imbalance in the nitrogen cycle, the diffuse emission of methane, the necessity for carbon capture and the deterioration of freshwater reserves. We suggest a set of microbial technologies to deal with each of these issues, such as (i) the production of microbial protein as food and feed, (ii) the control of methanogenic archaea and better use of methanotrophic consortia, (iii) the avoidance of nitrification and (iv) the upgrading of CO 2 to microbial bioproducts. The central message is that instead of using crude methods to exploit microorganisms for degradations, the potentials of the microbiomes should be used to create processes and products that fit the demands of the cyclic market economy. © 2017 The Authors. Microbial Biotechnology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Anodic microbial community diversity as a predictor of the power output of microbial fuel cells.

PubMed

Stratford, James P; Beecroft, Nelli J; Slade, Robert C T; Grüning, André; Avignone-Rossa, Claudio

2014-03-01

The relationship between the diversity of mixed-species microbial consortia and their electrogenic potential in the anodes of microbial fuel cells was examined using different diversity measures as predictors. Identical microbial fuel cells were sampled at multiple time-points. Biofilm and suspension communities were analysed by denaturing gradient gel electrophoresis to calculate the number and relative abundance of species. Shannon and Simpson indices and richness were examined for association with power using bivariate and multiple linear regression, with biofilm DNA as an additional variable. In simple bivariate regressions, the correlation of Shannon diversity of the biofilm and power is stronger (r=0.65, p=0.001) than between power and richness (r=0.39, p=0.076), or between power and the Simpson index (r=0.5, p=0.018). Using Shannon diversity and biofilm DNA as predictors of power, a regression model can be constructed (r=0.73, p<0.001). Ecological parameters such as the Shannon index are predictive of the electrogenic potential of microbial communities. Copyright © 2014 Elsevier Ltd. All rights reserved.

Characterization of Explosives Processing Waste Decomposition Due to Composting

DTIC Science & Technology

1991-11-01

volume % of soil in the compost. The amendment mixture was 30% sawdust, 15% apple pomace, 20% chicken manure, and 35% chopped potato waste. The negative...experiments. 3.3 Dkictiion Naturally occurring soil- and sediment-dwelling microbes produce a diverse array of exo- and endoenzymes that can degrade...consortia of microbes . Additionally, the loss of TNT by microbial processes was accompanied by commensurate reductions in compost leachate toxicity and

Microbial Fuels Cell-Based Biosensor for Toxicity Detection: A Review

PubMed Central

Zhou, Tuoyu; Han, Huawen; Liu, Pu; Xiong, Jian; Tian, Fake; Li, Xiangkai

2017-01-01

With the unprecedented deterioration of environmental quality, rapid recognition of toxic compounds is paramount for performing in situ real-time monitoring. Although several analytical techniques based on electrochemistry or biosensors have been developed for the detection of toxic compounds, most of them are time-consuming, inaccurate, or cumbersome for practical applications. More recently, microbial fuel cell (MFC)-based biosensors have drawn increasing interest due to their sustainability and cost-effectiveness, with applications ranging from the monitoring of anaerobic digestion process parameters (VFA) to water quality detection (e.g., COD, BOD). When a MFC runs under correct conditions, the voltage generated is correlated with the amount of a given substrate. Based on this linear relationship, several studies have demonstrated that MFC-based biosensors could detect heavy metals such as copper, chromium, or zinc, as well as organic compounds, including p-nitrophenol (PNP), formaldehyde and levofloxacin. Both bacterial consortia and single strains can be used to develop MFC-based biosensors. Biosensors with single strains show several advantages over systems integrating bacterial consortia, such as selectivity and stability. One of the limitations of such sensors is that the detection range usually exceeds the actual pollution level. Therefore, improving their sensitivity is the most important for widespread application. Nonetheless, MFC-based biosensors represent a promising approach towards single pollutant detection. PMID:28956857

Microbial Fuels Cell-Based Biosensor for Toxicity Detection: A Review.

PubMed

Zhou, Tuoyu; Han, Huawen; Liu, Pu; Xiong, Jian; Tian, Fake; Li, Xiangkai

2017-09-28

With the unprecedented deterioration of environmental quality, rapid recognition of toxic compounds is paramount for performing in situ real-time monitoring. Although several analytical techniques based on electrochemistry or biosensors have been developed for the detection of toxic compounds, most of them are time-consuming, inaccurate, or cumbersome for practical applications. More recently, microbial fuel cell (MFC)-based biosensors have drawn increasing interest due to their sustainability and cost-effectiveness, with applications ranging from the monitoring of anaerobic digestion process parameters (VFA) to water quality detection (e.g., COD, BOD). When a MFC runs under correct conditions, the voltage generated is correlated with the amount of a given substrate. Based on this linear relationship, several studies have demonstrated that MFC-based biosensors could detect heavy metals such as copper, chromium, or zinc, as well as organic compounds, including p -nitrophenol (PNP), formaldehyde and levofloxacin. Both bacterial consortia and single strains can be used to develop MFC-based biosensors. Biosensors with single strains show several advantages over systems integrating bacterial consortia, such as selectivity and stability. One of the limitations of such sensors is that the detection range usually exceeds the actual pollution level. Therefore, improving their sensitivity is the most important for widespread application. Nonetheless, MFC-based biosensors represent a promising approach towards single pollutant detection.

Corexit 9500 Enhances Oil Biodegradation and Changes ...

EPA Pesticide Factsheets

While COREXIT 9500 is widely applied after oil spills for its reported dispersing activity, there is still a debate on the effectiveness on enhancing oil biodegradation and its potential toxic effect on microbial communities. To better understand the impact of COREXIT 9500 on the structure and activity levels of hydrocarbon degrading microbial communities, we analyzed next-generation 16S rRNA gene sequencing libraries of hydrocarbon enrichments grown at cryophilic and mesophilic conditions and using both DNA and RNA extracts as sequencing templates. Oil biodegradation patterns in both cryophilic and mesophilic enrichments were consistent with those reported in the literature (i.e., aliphatics were degraded faster than aromatics). A slight increase in biodegradation was observed in the presence of COREXIT at both 25°C and 5°C experiments. Differences in community structure were observed between treatment conditions in the DNA-based libraries. The 25°C consortia was dominated by unclassified members of the Vibrio, Pseudoidiomarina, Marinobacter, Alcanivorax, and Thallassospira species, while the 5°C consortia were dominated by several genera of Flavobacteria, Alcanivorax and Oleispira. With the exception of Vibrio-like species, members of these genera have been linked to hydrocarbon degradation and have been observed after oil spills. Colwellia and Cycloclasticus, known aromatic degraders, was also found in these enrichments. RNA-based sequencing of 25°C

Control of Clostridium difficile infection by defined microbial communities

PubMed Central

Collins, James

2017-01-01

Summary Each year in the United States, billions of dollars are spent combating almost half a million Clostridium difficile infections (CDI) and trying to reduce the ~29,000 patient deaths where C. difficile has an attributed role (1). In Europe, disease prevalence varies by country and level of surveillance, though yearly costs are estimated at €3 billion (2). One factor contributing to the significant healthcare burden of C. difficile is the relatively high frequency of recurrent C. difficile infections(3). Recurrent C. difficile infection (rCDI), i.e., a second episode of symptomatic CDI occurring within eight weeks of successful initial CDI treatment, occurs in ~25% of patients with 35-65% of these patients experiencing multiple episodes of recurrent disease(4, 5). Using microbial communities to treat rCDI, either as whole fecal transplants or as defined consortia of bacterial isolates have shown great success (in the case of fecal transplants) or potential promise (in the case of defined consortia of isolates). This review will briefly summarize the epidemiology and physiology of C. difficile infection, describe our current understanding of how fecal microbiota transplants treat recurrent CDI, and outline potential ways through which that knowledge can be used to rationally-design and test alternative microbe-based therapeutics. PMID:28936948

Combined polyhydroxyalkanoates (PHA) and 1,3-propanediol production from crude glycerol: Selective conversion of volatile fatty acids into PHA by mixed microbial consortia.

PubMed

Burniol-Figols, Anna; Varrone, Cristiano; Le, Simone Balzer; Daugaard, Anders Egede; Skiadas, Ioannis V; Gavala, Hariklia N

2018-06-01

Crude glycerol is an important by-product of the biodiesel industry, which can be converted into volatile fatty acids (VFA) and/or 1,3-propanediol (1,3-PDO) by fermentation. In this study, a selective conversion of VFA to polyhydroxyalkanoates (PHA) was attained while leaving 1,3-PDO in the supernatant by means of mixed microbial consortia selection strategies. The process showed highly reproducible results in terms of PHA yield, 0.99 ± 0.07 C mol PHA/C mol S (0.84 g COD PHA/g COD S), PHA content (76 ± 3.1 g PHA/100 g TSS) and 1,3-PDO recovery (99 ± 2.1%). The combined process had an ultimate yield from crude glycerol of 0.19 g COD PHA and 0.42 g COD 1,3-PDO per g of input COD. The novel enrichment strategy applied for selectively transforming fermentation by-products into a high value product (PHA) demonstrates the significance of the enrichment process for targeting specific bio-transformations and could potentially prove valuable for other biotechnological applications as well. Copyright © 2018 Elsevier Ltd. All rights reserved.

Polyhydroxyalkanoate synthesis by mixed microbial consortia cultured on fermented dairy manure: Effect of aeration on process rates/yields and the associated microbial ecology.

PubMed

Coats, Erik R; Watson, Benjamin S; Brinkman, Cynthia K

2016-12-01

Polyhydroxyalkanoates (PHAs) are biodegradable polymers that can substitute for petroleum-based plastics in a variety of applications. One avenue to commercial PHA production involves coupling waste-based synthesis with the use of mixed microbial consortia (MMC). In this regard, production requires maximizing the enrichment of a MMC capable of feast-famine PHA synthesis, with the metabolic response induced through imposition of aerobic-dynamic feeding (ADF) conditions. However, the concept of PHA production in complex matrices remains unrefined; process operational improvements are needed, along with an enhanced understanding of the MMC. Research presented herein investigated the effect of aeration on feast-famine PHA synthesis, with four independent aeration state systems studied; MMC were fed volatile fatty acid (VFA)-rich fermented dairy manure. Regardless of the aeration state, all MMC exhibited a feast-famine response based on observed carbon cycling. Moreover, there was no statistical difference in PHA synthesis rates, with q PHA ranging from 0.10 to 0.19 CmmolPHA gVSS -1 min -1 ; VFA uptake rates exhibited similar statistical indifferences. PHA production assessments on the enriched MMC resulted in maximum intracellular concentrations ranging from 22.5 to 90.7% (mgPHA mgVSS -1 ); at maximum concentration, the mean hydroxyvalerate mol content was 73 ± 0.6%. While a typical feast-famine dissolved oxygen (DO) pattern was observed at maximum aeration, less resolution was observed at decreasing aeration rates, suggesting that DO may not be an optimal process monitoring parameter. At lower aeration states, nitrogen cycling patterns, supported by molecular investigations targeting AOBs and NOBs, indicate that NO 2 and NO 3 sustained feast-famine PHA synthesis. Next-generation sequencing analysis of the respective MMC revealed numerous and diverse genera exhibiting the potential to achieve PHA synthesis, suggesting functional redundancy embedded in the diverse MMC. Ultimately, results demonstrate that aeration can be controlled in waste-based ADF systems to sustain PHA production potential, while enriching for a diverse MMC that exhibits potential functional redundancy. Reduced aeration could also enhance cost competitiveness of waste-based PHA production, with potential further benefits associated with nitrogen treatment. Copyright © 2016 Elsevier Ltd. All rights reserved.

A Metagenomic Approach to Cyanobacterial Genomics

PubMed Central

Alvarenga, Danillo O.; Fiore, Marli F.; Varani, Alessandro M.

2017-01-01

Cyanobacteria, or oxyphotobacteria, are primary producers that establish ecological interactions with a wide variety of organisms. Although their associations with eukaryotes have received most attention, interactions with bacterial and archaeal symbionts have also been occurring for billions of years. Due to these associations, obtaining axenic cultures of cyanobacteria is usually difficult, and most isolation efforts result in unicyanobacterial cultures containing a number of associated microbes, hence composing a microbial consortium. With rising numbers of cyanobacterial blooms due to climate change, demand for genomic evaluations of these microorganisms is increasing. However, standard genomic techniques call for the sequencing of axenic cultures, an approach that not only adds months or even years for culture purification, but also appears to be impossible for some cyanobacteria, which is reflected in the relatively low number of publicly available genomic sequences of this phylum. Under the framework of metagenomics, on the other hand, cumbersome techniques for achieving axenic growth can be circumvented and individual genomes can be successfully obtained from microbial consortia. This review focuses on approaches for the genomic and metagenomic assessment of non-axenic cyanobacterial cultures that bypass requirements for axenity. These methods enable researchers to achieve faster and less costly genomic characterizations of cyanobacterial strains and raise additional information about their associated microorganisms. While non-axenic cultures may have been previously frowned upon in cyanobacteriology, latest advancements in metagenomics have provided new possibilities for in vitro studies of oxyphotobacteria, renewing the value of microbial consortia as a reliable and functional resource for the rapid assessment of bloom-forming cyanobacteria. PMID:28536564

Implementation of Complex Biological Logic Circuits Using Spatially Distributed Multicellular Consortia

PubMed Central

Urrios, Arturo; de Nadal, Eulàlia; Solé, Ricard; Posas, Francesc

2016-01-01

Engineered synthetic biological devices have been designed to perform a variety of functions from sensing molecules and bioremediation to energy production and biomedicine. Notwithstanding, a major limitation of in vivo circuit implementation is the constraint associated to the use of standard methodologies for circuit design. Thus, future success of these devices depends on obtaining circuits with scalable complexity and reusable parts. Here we show how to build complex computational devices using multicellular consortia and space as key computational elements. This spatial modular design grants scalability since its general architecture is independent of the circuit’s complexity, minimizes wiring requirements and allows component reusability with minimal genetic engineering. The potential use of this approach is demonstrated by implementation of complex logical functions with up to six inputs, thus demonstrating the scalability and flexibility of this method. The potential implications of our results are outlined. PMID:26829588

Deep-Sea Archaea Fix and Share Nitrogen in Methane-Consuming Microbial Consortia

NASA Astrophysics Data System (ADS)

Dekas, Anne E.; Poretsky, Rachel S.; Orphan, Victoria J.

2009-10-01

Nitrogen-fixing (diazotrophic) microorganisms regulate productivity in diverse ecosystems; however, the identities of diazotrophs are unknown in many oceanic environments. Using single-cell-resolution nanometer secondary ion mass spectrometry images of 15N incorporation, we showed that deep-sea anaerobic methane-oxidizing archaea fix N2, as well as structurally similar CN-, and share the products with sulfate-reducing bacterial symbionts. These archaeal/bacterial consortia are already recognized as the major sink of methane in benthic ecosystems, and we now identify them as a source of bioavailable nitrogen as well. The archaea maintain their methane oxidation rates while fixing N2 but reduce their growth, probably in compensation for the energetic burden of diazotrophy. This finding extends the demonstrated lower limits of respiratory energy capable of fueling N2 fixation and reveals a link between the global carbon, nitrogen, and sulfur cycles.

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

NONE

ARCTECH has developed a novel process (MicGAS) for direct, anaerobic biomethanation of coals. Biomethanation potential of coals of different ranks (Anthracite, bitumious, sub-bitumious, and lignites of different types), by various microbial consortia, was investigated. Studies on biogasification of Texas Lignite (TxL) were conducted with a proprietary microbial consortium, Mic-1, isolated from hind guts of soil eating termites (Zootermopsis and Nasutitermes sp.) and further improved at ARCTECH. Various microbial populations of the Mic-1 consortium carry out the multi-step MicGAS Process. First, the primary coal degraders, or hydrolytic microbes, degrade the coal to high molecular weight (MW) compounds. Then acedogens ferment themore » high MW compounds to low MW volatile fatty acids. The volatile fatty acids are converted to acetate by acetogens, and the methanogens complete the biomethanation by converting acetate and CO{sub 2} to methane.« less

Mineralized remains of morphotypes of filamentous cyanobacteria in carbonaceous meteorites

NASA Astrophysics Data System (ADS)

Hoover, Richard B.

2005-09-01

The quest for conclusive evidence of microfossils in meteorites has been elusive. Abiotic microstructures, mineral grains, and even coating artifacts may mimic unicellular bacteria, archaea and nanobacteria with simple spherical or rod morphologies (i.e., cocci, diplococci, bacilli, etc.). This is not the case for the larger and more complex microorganisms, colonies and microbial consortia and ecosystems. Microfossils of algae, cyanobacteria, and cyanobacterial and microbial mats have been recognized and described from many of the most ancient rocks on Earth. The filamentous cyanobacteria and sulphur-bacteria have very distinctive size ranges, complex and recognizable morphologies and visibly differentiated cellular microstructures. The taphonomic modes of fossilization and the life habits and processes of these microorganisms often result in distinctive chemical biosignatures associated with carbonization, silicification, calcification, phosphatization and metal-binding properties of their cell-walls, trichomes, sheaths and extracellular polymeric substances (EPS). Valid biogenicity is provided by the combination of a suite of known biogenic elements (that differ from the meteorite matrix) found in direct association with recognizable and distinct biological features and microstructures (e.g., uniseriate or multiseriate filaments, trichomes, sheaths and cells of proper size/size range); specialized cells (e.g., basal or apical cells, hormogonia, akinetes, and heterocysts); and evidence of growth characteristics (e.g., spiral filaments, robust or thin sheaths, laminated sheaths, true or false branching of trichomes, tapered or uniform filaments) and evidence of locomotion (e.g. emergent cells and trichomes, coiling hormogonia, and hollow or flattened and twisted sheaths). Since 1997 we have conducted Environmental and Field Emission Scanning Electron Microscopy (ESEM and FESEM) studies of freshly fractured interior surfaces of carbonaceous meteorites, terrestrial rocks, living, cryopreserved and fossilized extremophiles and cyanobacteria. These studies have resulted in the detection of mineralized remains of morphotypes of filamentous cyanobacteria, mats and consortia in many carbonaceous meteorites. These well-preserved and embedded microfossils are consistent with the size, morphology and ultra-microstructure of filamentous trichomic prokaryotes and degraded remains of microfibrils of cyanobacterial sheaths. EDAX elemental studies reveal that the forms in the meteorites often have highly carbonized sheaths in close association with permineralized filaments, trichomes, and microbial cells. The eextensive protocols and methodologies that have been developed to protect the samples from contamination and to distinguish recent contaminants from indigenous microfossils are described recent bio-contaminants. Ratios of critical bioelements (C:O, C:N, C:P, and C:S) reveal dramatic differences between microfossils in Earth rocks and meteorites and in the cells, filaments, trichomes, and hormogonia of recently living cyanobacteria. The results of comparative optical, ESEM and FESEM studies and EDAX elemental analyses of recent cyanobacteria (e.g. Calothrix, Oscillatoria, and Lyngbya) of similar size, morphology and microstructure to microfossils found embedded in the Murchison CM2 and the Orgueil CI1 carbonaceous meteorites are presented

Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

PubMed Central

Bokulich, Nicholas A.; Thorngate, John H.; Richardson, Paul M.; Mills, David A.

2014-01-01

Wine grapes present a unique biogeography model, wherein microbial biodiversity patterns across viticultural zones not only answer questions of dispersal and community maintenance, they are also an inherent component of the quality, consumer acceptance, and economic appreciation of a culturally important food product. On their journey from the vineyard to the wine bottle, grapes are transformed to wine through microbial activity, with indisputable consequences for wine quality parameters. Wine grapes harbor a wide range of microbes originating from the surrounding environment, many of which are recognized for their role in grapevine health and wine quality. However, determinants of regional wine characteristics have not been identified, but are frequently assumed to stem from viticultural or geological factors alone. This study used a high-throughput, short-amplicon sequencing approach to demonstrate that regional, site-specific, and grape-variety factors shape the fungal and bacterial consortia inhabiting wine-grape surfaces. Furthermore, these microbial assemblages are correlated to specific climatic features, suggesting a link between vineyard environmental conditions and microbial inhabitation patterns. Taken together, these factors shape the unique microbial inputs to regional wine fermentations, posing the existence of nonrandom “microbial terroir” as a determining factor in regional variation among wine grapes. PMID:24277822

Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate.

PubMed

Bokulich, Nicholas A; Thorngate, John H; Richardson, Paul M; Mills, David A

2014-01-07

Wine grapes present a unique biogeography model, wherein microbial biodiversity patterns across viticultural zones not only answer questions of dispersal and community maintenance, they are also an inherent component of the quality, consumer acceptance, and economic appreciation of a culturally important food product. On their journey from the vineyard to the wine bottle, grapes are transformed to wine through microbial activity, with indisputable consequences for wine quality parameters. Wine grapes harbor a wide range of microbes originating from the surrounding environment, many of which are recognized for their role in grapevine health and wine quality. However, determinants of regional wine characteristics have not been identified, but are frequently assumed to stem from viticultural or geological factors alone. This study used a high-throughput, short-amplicon sequencing approach to demonstrate that regional, site-specific, and grape-variety factors shape the fungal and bacterial consortia inhabiting wine-grape surfaces. Furthermore, these microbial assemblages are correlated to specific climatic features, suggesting a link between vineyard environmental conditions and microbial inhabitation patterns. Taken together, these factors shape the unique microbial inputs to regional wine fermentations, posing the existence of nonrandom "microbial terroir" as a determining factor in regional variation among wine grapes.

Rapid enrichment of (homo)acetogenic consortia from animal feces using a high mass-transfer gas-lift reactor fed with syngas.

PubMed

Park, Shinyoung; Yasin, Muhammad; Kim, Daehee; Park, Hee-Deung; Kang, Chang Min; Kim, Duk Jin; Chang, In Seop

2013-09-01

A gas-lift reactor having a high mass transfer coefficient (k(L)a = 80.28 h(-1)) for a relatively insoluble gas (carbon monoxide; CO) was used to enrich (homo)acetogens from animal feces. Samples of fecal matter from cow, rabbit, chicken, and goat were used as sources of inoculum for the enrichment of CO and H(2) utilizing microbial consortia. To confirm the successful enrichment, the Hungate roll tube technique was employed to count and then isolate putative CO utilizers. The results of this work showed that CO and H(2) utilizing consortia were established for each inoculum source after 8 days. The number of colony-forming units in cow, rabbit, chicken, and goat fecal samples were 3.83 × 10(9), 1.03 × 10(9), 8.3 × 10(8), and 3.25 × 10(8) cells/ml, respectively. Forty-two colonies from the animal fecal samples were screened for the ability to utilize CO/H(2). Ten of these 42 colonies were capable of utilizing CO/H(2). Five isolates from cow feces (samples 5, 6, 8, 16, and 22) were highly similar to previously unknown (homo)acetogen, while cow-7 has shown 99 % similarity with Acetobacterium sp. as acetogens. On the other hand, four isolates from chicken feces (samples 3, 8, 10, and 11) have also shown high CO/H(2) utilizing activity. Hence, it is expected that this research could be used as the basis for the rapid enrichment of (homo)acetogenic consortia from various environmental sources.

Biodiversity, ecological determinants, and metabolic exploitation of sourdough microbiota.

PubMed

De Vuyst, L; Vrancken, G; Ravyts, F; Rimaux, T; Weckx, S

2009-10-01

Sourdough is a microbial ecosystem of lactic acid bacteria (LAB) and yeasts in a matrix of mainly cereal flour and water. Culture-dependent and culture-independent microbiological analysis together with metabolite target analyses of different sourdoughs enabled to understand this complex fermentation process. It is difficult to link the species diversity of the sourdough microbiota with the (geographical) type of sourdough and the flour used, although the type and quality of the latter is the main source of autochthonous LAB in spontaneous sourdough fermentations and plays a key role in establishing stable microbial consortia within a short time. Carbohydrate fermentation targeted towards maltose catabolism, the use of external alternative electron acceptors, amino acid transamination reactions, and/or the arginine deiminase pathway are metabolic activities that favour energy production, cofactor (re)cycling, and/or tolerance towards acid stress, and hence contribute to the competitiveness and dominance of certain species of LAB found in sourdoughs. Also, microbial interactions play an important role. The availability of genome sequences for several LAB species that are of importance in sourdough as well as technological advances in the fields of functional genomics, transcriptomics, and proteomics enable new approaches to study sourdough fermentations beyond the single species level and will allow an integral analysis of the metabolic activities and interactions taking place in sourdough. Finally, the implementation of selected starter cultures in sourdough technology is of pivotal importance for the industrial production of sourdoughs to be used as flavour carrier, texture-improving, or health-promoting dough ingredient.

Isotopomer analysis of production and consumption mechanisms of N2O and CH4 in an advanced wastewater treatment system.

PubMed

Toyoda, Sakae; Suzuki, Yuuri; Hattori, Shohei; Yamada, Keita; Fujii, Ayako; Yoshida, Naohiro; Kouno, Rina; Murayama, Kouki; Shiomi, Hiroshi

2011-02-01

Wastewater treatment processes are believed to be anthropogenic sources of nitrous oxide (N(2)O) and methane (CH(4)). However, few studies have examined the mechanisms and controlling factors in production of these greenhouse gases in complex bacterial systems. To elucidate production and consumption mechanisms of N(2)O and CH(4) in microbial consortia during wastewater treatment and to characterize human waste sources, we measured their concentrations and isotopomer ratios (elemental isotope ratios and site-specific N isotope ratios in asymmetric molecules of NNO) in water and gas samples collected by an advanced treatment system in Tokyo. Although the estimated emissions of N(2)O and CH(4) from the system were found to be lower than those from the typical treatment systems reported before, water in biological reaction tanks was supersaturated with both gases. The concentration of N(2)O, produced mainly by nitrifier-denitrification as indicated by isotopomer ratios, was highest in the oxic tank (ca. 4000% saturation). The dissolved CH(4) concentration was highest in in-flow water (ca. 3000% saturation). It decreased gradually during treatment. Its carbon isotope ratio indicated that the decrease resulted from bacterial CH(4) oxidation and that microbial CH(4) production can occur in anaerobic and settling tanks.

Community structure and succession regulation of fungal consortia in the lignocellulose-degrading process on natural biomass.

PubMed

Tian, Baoyu; Wang, Chunxiang; Lv, Ruirui; Zhou, Junxiong; Li, Xin; Zheng, Yi; Jin, Xiangyu; Wang, Mengli; Ye, Yongxia; Huang, Xinyi; Liu, Ping

2014-01-01

The study aims to investigate fungal community structures and dynamic changes in forest soil lignocellulose-degrading process. rRNA gene clone libraries for the samples collected in different stages of lignocellulose degradation process were constructed and analyzed. A total of 26 representative RFLP types were obtained from original soil clone library, including Mucoromycotina (29.5%), unclassified Zygomycetes (33.5%), Ascomycota (32.4%), and Basidiomycota (4.6%). When soil accumulated with natural lignocellulose, 16 RFLP types were identified from 8-day clone library, including Basidiomycota (62.5%), Ascomycota (36.1%), and Fungi incertae sedis (1.4%). After enrichment for 15 days, identified 11 RFLP types were placed in 3 fungal groups: Basidiomycota (86.9%), Ascomycota (11.5%), and Fungi incertae sedis (1.6%). The results showed richer, more diversity and abundance fungal groups in original forest soil. With the degradation of lignocellulose, fungal groups Mucoromycotina and Ascomycota decreased gradually, and wood-rotting fungi Basidiomycota increased and replaced the opportunist fungi to become predominant group. Most of the fungal clones identified in sample were related to the reported lignocellulose-decomposing strains. Understanding of the microbial community structure and dynamic change during natural lignocellulose-degrading process will provide us with an idea and a basis to construct available commercial lignocellulosic enzymes or microbial complex.

A Hydroponic Co-cultivation System for Simultaneous and Systematic Analysis of Plant/Microbe Molecular Interactions and Signaling.

PubMed

Nathoo, Naeem; Bernards, Mark A; MacDonald, Jacqueline; Yuan, Ze-Chun

2017-07-22

An experimental design mimicking natural plant-microbe interactions is very important to delineate the complex plant-microbe signaling processes. Arabidopsis thaliana-Agrobacterium tumefaciens provides an excellent model system to study bacterial pathogenesis and plant interactions. Previous studies of plant-Agrobacterium interactions have largely relied on plant cell suspension cultures, the artificial wounding of plants, or the artificial induction of microbial virulence factors or plant defenses by synthetic chemicals. However, these methods are distinct from the natural signaling in planta, where plants and microbes recognize and respond in spatial and temporal manners. This work presents a hydroponic cocultivation system where intact plants are supported by metal mesh screens and cocultivated with Agrobacterium. In this cocultivation system, no synthetic phytohormone or chemical that induces microbial virulence or plant defense is supplemented. The hydroponic cocultivation system closely resembles natural plant-microbe interactions and signaling homeostasis in planta. Plant roots can be separated from the medium containing Agrobacterium, and the signaling and responses of both the plant hosts and the interacting microbes can be investigated simultaneously and systematically. At any given timepoint/interval, plant tissues or bacteria can be harvested separately for various "omics" analyses, demonstrating the power and efficacy of this system. The hydroponic cocultivation system can be easily adapted to study: 1) the reciprocal signaling of diverse plant-microbe systems, 2) signaling between a plant host and multiple microbial species (i.e. microbial consortia or microbiomes), 3) how nutrients and chemicals are implicated in plant-microbe signaling, and 4) how microbes interact with plant hosts and contribute to plant tolerance to biotic or abiotic stresses.

The Green Berry Consortia of the Sippewissett Salt Marsh: Millimeter-Sized Aggregates of Diazotrophic Unicellular Cyanobacteria.

PubMed

Wilbanks, Elizabeth G; Salman-Carvalho, Verena; Jaekel, Ulrike; Humphrey, Parris T; Eisen, Jonathan A; Buckley, Daniel H; Zinder, Stephen H

2017-01-01

Microbial interactions driving key biogeochemical fluxes often occur within multispecies consortia that form spatially heterogeneous microenvironments. Here, we describe the "green berry" consortia of the Sippewissett salt marsh (Falmouth, MA, United States): millimeter-sized aggregates dominated by an uncultured, diazotrophic unicellular cyanobacterium of the order Chroococcales (termed GB-CYN1). We show that GB-CYN1 is closely related to Crocosphaera watsonii (UCYN-B) and " Candidatus Atelocyanobacterium thalassa" (UCYN-A), two groups of unicellular diazotrophic cyanobacteria that play an important role in marine primary production. Other green berry consortium members include pennate diatoms and putative heterotrophic bacteria from the Alphaproteobacteria and Bacteroidetes . Tight coupling was observed between photosynthetic oxygen production and heterotrophic respiration. When illuminated, the green berries became supersaturated with oxygen. From the metagenome, we observed that GB-CYN1 encodes photosystem II genes and thus has the metabolic potential for oxygen production unlike UCYN-A. In darkness, respiratory activity rapidly depleted oxygen creating anoxia within the aggregates. Metagenomic data revealed a suite of nitrogen fixation genes encoded by GB-CYN1, and nitrogenase activity was confirmed at the whole-aggregate level by acetylene reduction assays. Metagenome reads homologous to marker genes for denitrification were observed and suggest that heterotrophic denitrifiers might co-occur in the green berries, although the physiology and activity of facultative anaerobes in these aggregates remains uncharacterized. Nitrogen fixation in the surface ocean was long thought to be driven by filamentous cyanobacterial aggregates, though recent work has demonstrated the importance of unicellular diazotrophic cyanobacteria (UCYN) from the order Chroococcales. The green berries serve as a useful contrast to studies of open ocean UCYN and may provide a tractable model system to investigate microbial dynamics within phytoplankton aggregates, a phenomenon of global importance to the flux of particulate organic carbon and nitrogen in surface waters.

The Green Berry Consortia of the Sippewissett Salt Marsh: Millimeter-Sized Aggregates of Diazotrophic Unicellular Cyanobacteria

PubMed Central

Wilbanks, Elizabeth G.; Salman-Carvalho, Verena; Jaekel, Ulrike; Humphrey, Parris T.; Eisen, Jonathan A.; Buckley, Daniel H.; Zinder, Stephen H.

2017-01-01

Microbial interactions driving key biogeochemical fluxes often occur within multispecies consortia that form spatially heterogeneous microenvironments. Here, we describe the “green berry” consortia of the Sippewissett salt marsh (Falmouth, MA, United States): millimeter-sized aggregates dominated by an uncultured, diazotrophic unicellular cyanobacterium of the order Chroococcales (termed GB-CYN1). We show that GB-CYN1 is closely related to Crocosphaera watsonii (UCYN-B) and “Candidatus Atelocyanobacterium thalassa” (UCYN-A), two groups of unicellular diazotrophic cyanobacteria that play an important role in marine primary production. Other green berry consortium members include pennate diatoms and putative heterotrophic bacteria from the Alphaproteobacteria and Bacteroidetes. Tight coupling was observed between photosynthetic oxygen production and heterotrophic respiration. When illuminated, the green berries became supersaturated with oxygen. From the metagenome, we observed that GB-CYN1 encodes photosystem II genes and thus has the metabolic potential for oxygen production unlike UCYN-A. In darkness, respiratory activity rapidly depleted oxygen creating anoxia within the aggregates. Metagenomic data revealed a suite of nitrogen fixation genes encoded by GB-CYN1, and nitrogenase activity was confirmed at the whole-aggregate level by acetylene reduction assays. Metagenome reads homologous to marker genes for denitrification were observed and suggest that heterotrophic denitrifiers might co-occur in the green berries, although the physiology and activity of facultative anaerobes in these aggregates remains uncharacterized. Nitrogen fixation in the surface ocean was long thought to be driven by filamentous cyanobacterial aggregates, though recent work has demonstrated the importance of unicellular diazotrophic cyanobacteria (UCYN) from the order Chroococcales. The green berries serve as a useful contrast to studies of open ocean UCYN and may provide a tractable model system to investigate microbial dynamics within phytoplankton aggregates, a phenomenon of global importance to the flux of particulate organic carbon and nitrogen in surface waters. PMID:28928719

The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota.

PubMed

Milani, Christian; Duranti, Sabrina; Bottacini, Francesca; Casey, Eoghan; Turroni, Francesca; Mahony, Jennifer; Belzer, Clara; Delgado Palacio, Susana; Arboleya Montes, Silvia; Mancabelli, Leonardo; Lugli, Gabriele Andrea; Rodriguez, Juan Miguel; Bode, Lars; de Vos, Willem; Gueimonde, Miguel; Margolles, Abelardo; van Sinderen, Douwe; Ventura, Marco

2017-12-01

The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult health conditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbial players of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and disease. Copyright © 2017 American Society for Microbiology.

Corexit 9500 Enhances Oil Biodegradation and Changes Active Bacterial Community Structure of Oil-Enriched Microcosms.

PubMed

Techtmann, Stephen M; Zhuang, Mobing; Campo, Pablo; Holder, Edith; Elk, Michael; Hazen, Terry C; Conmy, Robyn; Santo Domingo, Jorge W

2017-05-15

To better understand the impacts of Corexit 9500 on the structure and activity levels of hydrocarbon-degrading microbial communities, we analyzed next-generation 16S rRNA gene sequencing libraries of hydrocarbon enrichments grown at 5 and 25°C using both DNA and RNA extracts as the sequencing templates. Oil biodegradation patterns in both 5 and 25°C enrichments were consistent with those reported in the literature (i.e., aliphatics were degraded faster than aromatics). Slight increases in biodegradation were observed in the presence of Corexit at both temperatures. Differences in community structure were observed between treatment conditions in the DNA-based libraries. The 25°C consortia were dominated by Vibrio , Idiomarina , Marinobacter , Alcanivorax , and Thalassospira species, while the 5°C consortia were dominated by several species of the genera Flavobacterium , Alcanivorax , and Oleispira Most of these genera have been linked to hydrocarbon degradation and have been observed after oil spills. Colwellia and Cycloclasticus , known aromatic degraders, were also found in these enrichments. The addition of Corexit did not have an effect on the active bacterial community structure of the 5°C consortia, while at 25°C, a decrease in the relative abundance of Marinobacter was observed. At 25°C, Thalassospira , Marinobacter , and Idiomarina were present at higher relative abundances in the RNA than DNA libraries, suggesting that they were active in degradation. Similarly, Oleispira was greatly stimulated by the addition of oil at 5°C. IMPORTANCE While dispersants such as Corexit 9500 can be used to treat oil spills, there is still debate on the effectiveness on enhancing oil biodegradation and its potential toxic effect on oil-degrading microbial communities. The results of this study provide some insights on the microbial dynamics of hydrocarbon-degrading bacterial populations in the presence of Corexit 9500. Operational taxonomic unit (OTU) analyses indicated that several OTUs were inhibited by the addition of Corexit. Conversely, a number of OTUs were stimulated by the addition of the dispersant, many of which were identified as known hydrocarbon-degrading bacteria. The results highlight the value of using RNA-based methods to further understand the impact of dispersant on the overall activity of different hydrocarbon-degrading bacterial groups. Copyright © 2017 American Society for Microbiology.

Corexit 9500 Enhances Oil Biodegradation and Changes Active Bacterial Community Structure of Oil-Enriched Microcosms

PubMed Central

Zhuang, Mobing; Campo, Pablo; Holder, Edith; Elk, Michael; Conmy, Robyn

2017-01-01

ABSTRACT To better understand the impacts of Corexit 9500 on the structure and activity levels of hydrocarbon-degrading microbial communities, we analyzed next-generation 16S rRNA gene sequencing libraries of hydrocarbon enrichments grown at 5 and 25°C using both DNA and RNA extracts as the sequencing templates. Oil biodegradation patterns in both 5 and 25°C enrichments were consistent with those reported in the literature (i.e., aliphatics were degraded faster than aromatics). Slight increases in biodegradation were observed in the presence of Corexit at both temperatures. Differences in community structure were observed between treatment conditions in the DNA-based libraries. The 25°C consortia were dominated by Vibrio, Idiomarina, Marinobacter, Alcanivorax, and Thalassospira species, while the 5°C consortia were dominated by several species of the genera Flavobacterium, Alcanivorax, and Oleispira. Most of these genera have been linked to hydrocarbon degradation and have been observed after oil spills. Colwellia and Cycloclasticus, known aromatic degraders, were also found in these enrichments. The addition of Corexit did not have an effect on the active bacterial community structure of the 5°C consortia, while at 25°C, a decrease in the relative abundance of Marinobacter was observed. At 25°C, Thalassospira, Marinobacter, and Idiomarina were present at higher relative abundances in the RNA than DNA libraries, suggesting that they were active in degradation. Similarly, Oleispira was greatly stimulated by the addition of oil at 5°C. IMPORTANCE While dispersants such as Corexit 9500 can be used to treat oil spills, there is still debate on the effectiveness on enhancing oil biodegradation and its potential toxic effect on oil-degrading microbial communities. The results of this study provide some insights on the microbial dynamics of hydrocarbon-degrading bacterial populations in the presence of Corexit 9500. Operational taxonomic unit (OTU) analyses indicated that several OTUs were inhibited by the addition of Corexit. Conversely, a number of OTUs were stimulated by the addition of the dispersant, many of which were identified as known hydrocarbon-degrading bacteria. The results highlight the value of using RNA-based methods to further understand the impact of dispersant on the overall activity of different hydrocarbon-degrading bacterial groups. PMID:28283527

IgA Function in Relation to the Intestinal Microbiota.

PubMed

Macpherson, Andrew J; Yilmaz, Bahtiyar; Limenitakis, Julien P; Ganal-Vonarburg, Stephanie C

2018-04-26

IgA is the dominant immunoglobulin isotype produced in mammals, largely secreted across the intestinal mucosal surface. Although induction of IgA has been a hallmark feature of microbiota colonization following colonization in germ-free animals, until recently appreciation of the function of IgA in host-microbial mutualism has depended mainly on indirect evidence of alterations in microbiota composition or penetration of microbes in the absence of somatic mutations in IgA (or compensatory IgM). Highly parallel sequencing techniques that enable high-resolution analysis of either microbial consortia or IgA sequence diversity are now giving us new perspectives on selective targeting of microbial taxa and the trajectory of IgA diversification according to induction mechanisms, between different individuals and over time. The prospects are to link the range of diversified IgA clonotypes to specific antigenic functions in modulating the microbiota composition, position and metabolism to ensure host mutualism.

Sociomicrobiology and Pathogenic Bacteria.

PubMed

Xavier, Joao B

2016-06-01

The study of microbial pathogenesis has been primarily a reductionist science since Koch's principles. Reductionist approaches are essential to identify the causal agents of infectious disease, their molecular mechanisms of action, and potential drug targets, and much of medicine's success in the treatment of infectious disease stems from that approach. But many bacteria-caused diseases cannot be explained by a single bacterium. Several aspects of bacterial pathogenesis will benefit from a more holistic approach that takes into account social interaction among bacteria of the same species and between species in consortia such as the human microbiome. The emerging discipline of sociomicrobiology provides a framework to dissect microbial interactions in single and multi-species communities without compromising mechanistic detail. The study of bacterial pathogenesis can benefit greatly from incorporating concepts from other disciplines such as social evolution theory and microbial ecology, where communities, their interactions with hosts, and with the environment play key roles.

Evolution of microbial markets.

PubMed

Werner, Gijsbert D A; Strassmann, Joan E; Ivens, Aniek B F; Engelmoer, Daniel J P; Verbruggen, Erik; Queller, David C; Noë, Ronald; Johnson, Nancy Collins; Hammerstein, Peter; Kiers, E Toby

2014-01-28

Biological market theory has been used successfully to explain cooperative behavior in many animal species. Microbes also engage in cooperative behaviors, both with hosts and other microbes, that can be described in economic terms. However, a market approach is not traditionally used to analyze these interactions. Here, we extend the biological market framework to ask whether this theory is of use to evolutionary biologists studying microbes. We consider six economic strategies used by microbes to optimize their success in markets. We argue that an economic market framework is a useful tool to generate specific and interesting predictions about microbial interactions, including the evolution of partner discrimination, hoarding strategies, specialized versus diversified mutualistic services, and the role of spatial structures, such as flocks and consortia. There is untapped potential for studying the evolutionary dynamics of microbial systems. Market theory can help structure this potential by characterizing strategic investment of microbes across a diversity of conditions.

The Sponge Hologenome

PubMed Central

Thomas, Torsten

2016-01-01

ABSTRACT A paradigm shift has recently transformed the field of biological science; molecular advances have revealed how fundamentally important microorganisms are to many aspects of a host’s phenotype and evolution. In the process, an era of “holobiont” research has emerged to investigate the intricate network of interactions between a host and its symbiotic microbial consortia. Marine sponges are early-diverging metazoa known for hosting dense, specific, and often highly diverse microbial communities. Here we synthesize current thoughts about the environmental and evolutionary forces that influence the diversity, specificity, and distribution of microbial symbionts within the sponge holobiont, explore the physiological pathways that contribute to holobiont function, and describe the molecular mechanisms that underpin the establishment and maintenance of these symbiotic partnerships. The collective genomes of the sponge holobiont form the sponge hologenome, and we highlight how the forces that define a sponge’s phenotype in fact act on the genomic interplay between the different components of the holobiont. PMID:27103626

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.

Evolution of microbial markets

PubMed Central

Werner, Gijsbert D. A.; Strassmann, Joan E.; Ivens, Aniek B. F.; Engelmoer, Daniel J. P.; Verbruggen, Erik; Queller, David C.; Noë, Ronald; Johnson, Nancy Collins; Hammerstein, Peter; Kiers, E. Toby

2014-01-01

Biological market theory has been used successfully to explain cooperative behavior in many animal species. Microbes also engage in cooperative behaviors, both with hosts and other microbes, that can be described in economic terms. However, a market approach is not traditionally used to analyze these interactions. Here, we extend the biological market framework to ask whether this theory is of use to evolutionary biologists studying microbes. We consider six economic strategies used by microbes to optimize their success in markets. We argue that an economic market framework is a useful tool to generate specific and interesting predictions about microbial interactions, including the evolution of partner discrimination, hoarding strategies, specialized versus diversified mutualistic services, and the role of spatial structures, such as flocks and consortia. There is untapped potential for studying the evolutionary dynamics of microbial systems. Market theory can help structure this potential by characterizing strategic investment of microbes across a diversity of conditions. PMID:24474743

Metagenomic assessment of the microbial diversity in ground pork products from markets in the North Central Region of South Korea.

PubMed

Koo, Ok-Kyung; Baker, Christopher A; Kim, Hyun-Jung; Park, Si Hong; Ricke, Steven C

2016-09-01

The purpose of this study was to characterize the microbial community in ground pork using molecular approaches. Forty six ground pork products were purchased from local stores in the north central area of South Korea. Aerobic plate counts varied 4.23 ± 5.14 × 10(5) CFU/g with the range between 5.00 × 10(3) and 1.85 × 10(6) CFU/g for ground pork samples. Four ground meat samples were further processed for metagenomic analysis. Pseudomonas species was the most relative abundant with a wide range occurring (1.72 to 77.7%) as part of the microbial genera in ground pork. Bacteria such as Carnobacterium, Yersinia, Photobacterium were also identified in ground pork. Despite the prominence of certain genera across all samples there was still extensive microbial diversity among ground pork products that originated from different slaughter houses and were processed in different markets. Such diversity indicates that designing interventions to extend shelf life may be hampered by the extensive variability in the microbial consortia associated with pork products. However, this diversity may be useful for developing microbial traceability signatures unique to a slaughter house or a particular market.

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

PubMed

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

2015-10-01

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

Parallel characterization of anaerobic toluene- and ethylbenzene-degrading microbial consortia by PCR-denaturing gradient gel electrophoresis, RNA-DNA membrane hybridization, and DNA microarray technology

NASA Technical Reports Server (NTRS)

Koizumi, Yoshikazu; Kelly, John J.; Nakagawa, Tatsunori; Urakawa, Hidetoshi; El-Fantroussi, Said; Al-Muzaini, Saleh; Fukui, Manabu; Urushigawa, Yoshikuni; Stahl, David A.

2002-01-01

A mesophilic toluene-degrading consortium (TDC) and an ethylbenzene-degrading consortium (EDC) were established under sulfate-reducing conditions. These consortia were first characterized by denaturing gradient gel electrophoresis (DGGE) fingerprinting of PCR-amplified 16S rRNA gene fragments, followed by sequencing. The sequences of the major bands (T-1 and E-2) belonging to TDC and EDC, respectively, were affiliated with the family Desulfobacteriaceae. Another major band from EDC (E-1) was related to an uncultured non-sulfate-reducing soil bacterium. Oligonucleotide probes specific for the 16S rRNAs of target organisms corresponding to T-1, E-1, and E-2 were designed, and hybridization conditions were optimized for two analytical formats, membrane and DNA microarray hybridization. Both formats were used to characterize the TDC and EDC, and the results of both were consistent with DGGE analysis. In order to assess the utility of the microarray format for analysis of environmental samples, oil-contaminated sediments from the coast of Kuwait were analyzed. The DNA microarray successfully detected bacterial nucleic acids from these samples, but probes targeting specific groups of sulfate-reducing bacteria did not give positive signals. The results of this study demonstrate the limitations and the potential utility of DNA microarrays for microbial community analysis.

Parallel Characterization of Anaerobic Toluene- and Ethylbenzene-Degrading Microbial Consortia by PCR-Denaturing Gradient Gel Electrophoresis, RNA-DNA Membrane Hybridization, and DNA Microarray Technology

PubMed Central

Koizumi, Yoshikazu; Kelly, John J.; Nakagawa, Tatsunori; Urakawa, Hidetoshi; El-Fantroussi, Saïd; Al-Muzaini, Saleh; Fukui, Manabu; Urushigawa, Yoshikuni; Stahl, David A.

2002-01-01

A mesophilic toluene-degrading consortium (TDC) and an ethylbenzene-degrading consortium (EDC) were established under sulfate-reducing conditions. These consortia were first characterized by denaturing gradient gel electrophoresis (DGGE) fingerprinting of PCR-amplified 16S rRNA gene fragments, followed by sequencing. The sequences of the major bands (T-1 and E-2) belonging to TDC and EDC, respectively, were affiliated with the family Desulfobacteriaceae. Another major band from EDC (E-1) was related to an uncultured non-sulfate-reducing soil bacterium. Oligonucleotide probes specific for the 16S rRNAs of target organisms corresponding to T-1, E-1, and E-2 were designed, and hybridization conditions were optimized for two analytical formats, membrane and DNA microarray hybridization. Both formats were used to characterize the TDC and EDC, and the results of both were consistent with DGGE analysis. In order to assess the utility of the microarray format for analysis of environmental samples, oil-contaminated sediments from the coast of Kuwait were analyzed. The DNA microarray successfully detected bacterial nucleic acids from these samples, but probes targeting specific groups of sulfate-reducing bacteria did not give positive signals. The results of this study demonstrate the limitations and the potential utility of DNA microarrays for microbial community analysis. PMID:12088997

Evaluating the Metal Tolerance Capacity of Microbial Communities Isolated from Alberta Oil Sands Process Water

PubMed Central

Frankel, Mathew L.; Demeter, Marc A.; Lemire, Joe A.; Turner, Raymond J.

2016-01-01

Anthropogenic activities have resulted in the intensified use of water resources. For example, open pit bitumen extraction by Canada’s oil sands operations uses an estimated volume of three barrels of water for every barrel of oil produced. The waste tailings–oil sands process water (OSPW)–are stored in holding ponds, and present an environmental concern as they are comprised of residual hydrocarbons and metals. Following the hypothesis that endogenous OSPW microbial communities have an enhanced tolerance to heavy metals, we tested the capacity of planktonic and biofilm populations from OSPW to withstand metal ion challenges, using Cupriavidus metallidurans, a known metal-resistant organism, for comparison. The toxicity of the metals toward biofilm and planktonic bacterial populations was determined by measuring the minimum biofilm inhibitory concentrations (MBICs) and planktonic minimum inhibitory concentrations (MICs) using the MBEC ™ assay. We observed that the OSPW community and C. metallidurans had similar tolerances to 22 different metals. While thiophillic elements (Te, Ag, Cd, Ni) were found to be most toxic, the OSPW consortia demonstrated higher tolerance to metals reported in tailings ponds (Al, Fe, Mo, Pb). Metal toxicity correlated with a number of physicochemical characteristics of the metals. Parameters reflecting metal-ligand affinities showed fewer and weaker correlations for the community compared to C. metallidurans, suggesting that the OSPW consortia may have developed tolerance mechanisms toward metals present in their environment. PMID:26849649

Microbial consortia in meat processing environments

NASA Astrophysics Data System (ADS)

Alessandria, V.; Rantsiou, K.; Cavallero, M. C.; Riva, S.; Cocolin, L.

2017-09-01

Microbial contamination in food processing plants can play a fundamental role in food quality and safety. The description of the microbial consortia in the meat processing environment is important since it is a first step in understanding possible routes of product contamination. Furthermore, it may contribute in the development of sanitation programs for effective pathogen removal. The purpose of this study was to characterize the type of microbiota in the environment of meat processing plants: the microbiota of three different meat plants was studied by both traditional and molecular methods (PCR-DGGE) in two different periods. Different levels of contamination emerged between the three plants as well as between the two sampling periods. Conventional methods of killing free-living bacteria through antimicrobial agents and disinfection are often ineffective against bacteria within a biofilm. The use of gas-discharge plasmas potentially can offer a good alternative to conventional sterilization methods. The purpose of this study was to measure the effectiveness of Atmospheric Pressure Plasma (APP) surface treatments against bacteria in biofilms. Biofilms produced by three different L. monocytogenes strains on stainless steel surface were subjected to three different conditions (power, exposure time) of APP. Our results showed how most of the culturable cells are inactivated after the Plasma exposure but the RNA analysis by qPCR highlighted the entrance of the cells in the viable-but non culturable (VBNC) state, confirming the hypothesis that cells are damaged after plasma treatment, but in a first step, still remain alive. The understanding of the effects of APP on the L. monocytogenes biofilm can improve the development of sanitation programs with the use of APP for effective pathogen removal.

Ecosystem services and plant physiological status during endophyte-assisted phytoremediation of metal contaminated soil.

PubMed

Burges, Aritz; Epelde, Lur; Blanco, Fernando; Becerril, José M; Garbisu, Carlos

2017-04-15

Mining sites shelter a characteristic biodiversity with large potential for the phytoremediation of metal contaminated soils. Endophytic plant growth-promoting bacteria were isolated from two metal-(hyper)accumulator plant species growing in a metal contaminated mine soil. After characterizing their plant growth-promoting traits, consortia of putative endophytes were used to carry out an endophyte-assisted phytoextraction experiment using Noccaea caerulescens and Rumex acetosa (singly and in combination) under controlled conditions. We evaluated the influence of endophyte-inoculated plants on soil physicochemical and microbial properties, as well as plant physiological parameters and metal concentrations. Data interpretation through the grouping of soil properties within a set of ecosystem services was also carried out. When grown together, we observed a 41 and 16% increase in the growth of N. caerulescens and R. acetosa plants, respectively, as well as higher values of Zn phytoextraction and soil microbial biomass and functional diversity. Inoculation of the consortia of putative endophytes did not lead to higher values of plant metal uptake, but it improved the plants' physiological status, by increasing the content of chlorophylls and carotenoids by up to 28 and 36%, respectively, indicating a reduction in the stress level of plants. Endophyte-inoculation also stimulated soil microbial communities: higher values of acid phosphatase activity (related to the phosphate solubilising traits of the endophytes), bacterial and fungal abundance, and structural diversity. The positive effects of plant growth and endophyte inoculation on soil properties were reflected in an enhancement of some ecosystem services (biodiversity, nutrient cycling, water flow regulation, water purification and contamination control). Copyright © 2016 Elsevier B.V. All rights reserved.

Development of tailored indigenous marine consortia for the degradation of naturally weathered polyethylene films

PubMed Central

Syranidou, Evdokia; Karkanorachaki, Katerina; Amorotti, Filippo; Repouskou, Eftychia; Kroll, Kevin; Kolvenbach, Boris; Corvini, Philippe F-X; Fava, Fabio

2017-01-01

This study investigated the potential of bacterial-mediated polyethylene (PE) degradation in a two-phase microcosm experiment. During phase I, naturally weathered PE films were incubated for 6 months with the indigenous marine community alone as well as bioaugmented with strains able to grow in minimal medium with linear low-density polyethylene (LLDPE) as the sole carbon source. At the end of phase I the developed biofilm was harvested and re-inoculated with naturally weathered PE films. Bacteria from both treatments were able to establish an active population on the PE surfaces as the biofilm community developed in a time dependent way. Moreover, a convergence in the composition of these communities was observed towards an efficient PE degrading microbial network, comprising of indigenous species. In acclimated communities, genera affiliated with synthetic (PE) and natural (cellulose) polymer degraders as well as hydrocarbon degrading bacteria were enriched. The acclimated consortia (indigenous and bioaugmented) reduced more efficiently the weight of PE films in comparison to non-acclimated bacteria. The SEM images revealed a dense and compact biofilm layer and signs of bio-erosion on the surface of the films. Rheological results suggest that the polymers after microbial treatment had wider molecular mass distribution and a marginally smaller average molar mass suggesting biodegradation as opposed to abiotic degradation. Modifications on the surface chemistry were observed throughout phase II while the FTIR profiles of microbially treated films at month 6 were similar to the profiles of virgin PE. Taking into account the results, we can suggest that the tailored indigenous marine community represents an efficient consortium for degrading weathered PE plastics. PMID:28841722

Clonality of bacterial consortia in root canals and subjacent gingival crevices.

PubMed

Parahitiyawa, Nipuna B; Chu, Frederick C S; Leung, Wai K; Yam, Wing C; Jin, Li Jian; Samaranayake, Lakshman P

2015-02-01

No oral niche can be considered to be segregated from the subjacent milieu because of the complex community behavior and nature of the oral biofilms. The aim of this study was to address the paucity of information on how these species are clonally related to the subjacent gingival crevice bacteria. We utilized a metagenomic approach of amplifying 16S rDNA from genomic DNA, cloning, sequencing and analysis using LIBSHUFF software to assess the genetic homogeneity of the bacterial species from two infected root canals and subjacent gingival crevices. The four niches studied yielded 186 clones representing 54 phylotypes. Clone library comparisons using LIBSHUFF software indicated that each niche was inhabited by a unique flora. Further, 42% of the clones were of hitherto unknown phylotypes indicating the extent of bacterial diversity, especially in infected root canals and subjacent gingival crevices. We believe data generated through this novel analytical tool shed new light on understanding oral microbial ecosystems. © 2014 Wiley Publishing Asia Pty Ltd.

Microbial Extremophiles in Aspect of Limits of Life

NASA Technical Reports Server (NTRS)

Pikuta, Elena V.; Hoover, Richard B.; Tang, Jane

2007-01-01

During Earth's evolution accompanied by geophysical and climatic changes a number of ecosystems have been formed. These ecosystems differ by the broad variety of physicochemical and biological factors composing our environment. Traditionally, pH and salinity are considered as geochemical extremes, as opposed to the temperature, pressure and radiation that are referred to as physical extremes (Van den Burg, 2003). Life inhabits all possible places on Earth interacting with the environment and within itself (cross species relations). In nature it is very rare when an ecotope is inhabited by a single species. As a rule, most ecosystems contain the functionally related and evolutionarily adjusted communities (consortia and populations). In contrast to the multicellular structure of eukaryotes (tissues, organs, systems of organs, whole organism), the highest organized form of prokaryotic life in nature is the benthic colonization in biofilms and microbial mats. In these complex structures all microbial cells of different species are distributed in space and time according to their functions and to physicochemical gradients that allow more effective system support, self-protection, and energy distribution. In vitro, of course, the most primitive organized structure for bacterial and archaeal cultures is the colony, the size, shape, color, consistency, and other characteristics of which could carry varies specifics on species or subspecies levels. In table 1 all known types of microbial communities are shown (Pikuta et a]., 2005). In deep underground (lithospheric) and deep-sea ecosystems an additional factor - pressure, and irradiation - could also be included in the list of microbial communities. Currently the beststudied ecosystems are: human body (due to the medical importance), and fresh water and marine ecosystems (due to the reason of an environmental safety). For a long time, extremophiles were terra incognita, since the environments with aggressive parameters (compared to the human body temperature, pH, mineralization, and pressure) were considered a priori as a dead zone.

Anaerobic bioprocessing of low-rank coals. [Veillonella alcalescens and Propionibacterium acidipropionici

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

Jain, M.K.; Narayan, R.; Han, O.

1992-01-30

The overall goal of this project is to find biological methods to remove carboxylic functionalities from low-rank coals under ambient conditions and to assess the properties of these modified coals towards coal liquefaction. The main objectives of this quarter were: (1) continuation of microbial consortia development, (2) evaluation of the isolated organisms for decarboxylation, (3) selection of best performing culture (known cultures vs. new isolates), and (4) coal decarboxylation using activated carbon as blanks. The project began on September 12, 1990.

Design and performance of a trickling air biofilter for chlorobenzene and o-dichlorobenzene vapors.

PubMed Central

Oh, Y S; Bartha, R

1994-01-01

From contaminated industrial sludge, two stable multistrain microbial enrichments (consortia) that were capable of rapidly utilizing chlorobenzene and o-dichlorobenzene, respectively, were obtained. These consortia were characterized as to their species composition, tolerance range, and activity maxima in order to establish and maintain the required operational parameters during their use in biofilters for the removal of chlorobenzene contaminants from air. The consortia were immobilized on a porous perlite support packed into filter columns. Metered airstreams containing the contaminant vapors were partially humidified and passed through these columns. The vapor concentrations prior to and after biofiltration were measured by gas chromatography. Liquid was circulated concurrently with the air, and the device was operated in the trickling air biofilter mode. The experimental arrangement allowed the independent variation of liquid flow, airflow, and solvent vapor concentrations. Bench-scale trickling air biofilters removed monochlorobenzene, o-dichlorobenzene, and their mixtures at rates of up to 300 g of solvent vapor h(-1) m(-3) filter volume. High liquid recirculation rates and automated pH control were critical for stable filtration performance. When the accumulating NaCl was periodically diluted, the trickling air biofilters continued to remove chlorobenzenes for several months with no loss of activity. The demonstrated high performance and stability of the described trickling air biofilters favor their use in industrial-scale air pollution control. PMID:8085815

Membrane lipid patterns typify distinct anaerobic methanotrophic consortia

PubMed Central

Blumenberg, Martin; Seifert, Richard; Reitner, Joachim; Pape, Thomas; Michaelis, Walter

2004-01-01

The anaerobic oxidation of methane (AOM) is one of the major sinks of this substantial greenhouse gas in marine environments. Recent investigations have shown that diverse communities of anaerobic archaea and sulfate-reducing bacteria are involved in AOM. Most of the relevant archaea are assigned to two distinct phylogenetic clusters, ANME-1 and ANME-2. A suite of specific 13C-depleted lipids demonstrating the presence of consortia mediating AOM in fossil and recent environments has been established. Here we report on substantial differences in the lipid composition of microbial consortia sampled from distinct compartments of AOM-driven carbonate reefs growing in the northwestern Black Sea. Communities in which the dominant archaea are from the ANME-1 cluster yield internally cyclized tetraether lipids typical of thermophiles. Those in which ANME-2 archaea are dominant yield sn-2-hydroxyarchaeol accompanied by crocetane and crocetenes. The bacterial lipids from these communities are also distinct even though the sulfate-reducing bacteria all belong to the Desulfosarcina/Desulfococcus group. Nonisoprenoidal glycerol diethers are predominantly associated with ANME-1-dominated communities. Communities with ANME-2 yield mainly conventional, ester-linked diglycerides. ANME-1 archaea and associated sulfate-reducing bacteria seem to be enabled to use low concentrations of methane and to grow within a broad range of temperatures. Our results offer a tool for the study of recent and especially of fossil methane environments. PMID:15258285

Identification of Uncultured Bacterial Species from Firmicutes, Bacteroidetes and CANDIDATUS Saccharibacteria as Candidate Cellulose Utilizers from the Rumen of Beef Cows

PubMed Central

Opdahl, Lee James; Gonda, Michael G.

2018-01-01

The ability of ruminants to utilize cellulosic biomass is a result of the metabolic activities of symbiotic microbial communities that reside in the rumen. To gain further insight into this complex microbial ecosystem, a selection-based batch culturing approach was used to identify candidate cellulose-utilizing bacterial consortia. Prior to culturing with cellulose, rumen contents sampled from three beef cows maintained on a forage diet shared 252 Operational Taxonomic Units (OTUs), accounting for 41.6–50.0% of bacterial 16S rRNA gene sequences in their respective samples. Despite this high level of overlap, only one OTU was enriched in cellulose-supplemented cultures from all rumen samples. Otherwise, each set of replicate cellulose supplemented cultures originating from a sampled rumen environment was found to have a distinct bacterial composition. Two of the seven most enriched OTUs were closely matched to well-established rumen cellulose utilizers (Ruminococcus flavefaciens and Fibrobacter succinogenes), while the others did not show high nucleotide sequence identity to currently defined bacterial species. The latter were affiliated to Prevotella (1 OTU), Ruminococcaceae (3 OTUs), and the candidate phylum Saccharibacteria (1 OTU), respectively. While further investigations will be necessary to elucidate the metabolic function(s) of each enriched OTU, these results together further support cellulose utilization as a ruminal metabolic trait shared across vast phylogenetic distances, and that the rumen is an environment conducive to the selection of a broad range of microbial adaptations for the digestion of plant structural polysaccharides. PMID:29495256

Relationships between water and gas chemistry in mature coalbed methane reservoirs of the Black Warrior Basin

USGS Publications Warehouse

Pashin, Jack C.; McIntyre-Redden, Marcella R.; Mann, Steven D.; Kopaska-Merkel, David C.; Varonka, Matthew S.; Orem, William H.

2014-01-01

Water and gas chemistry in coalbed methane reservoirs of the Black Warrior Basin reflects a complex interplay among burial processes, basin hydrodynamics, thermogenesis, and late-stage microbial methanogenesis. These factors are all important considerations for developing production and water management strategies. Produced water ranges from nearly potable sodium-bicarbonate water to hypersaline sodium-chloride brine. The hydrodynamic framework of the basin is dominated by structurally controlled fresh-water plumes that formed by meteoric recharge along the southeastern margin of the basin. The produced water contains significant quantities of hydrocarbons and nitrogen compounds, and the produced gas appears to be of mixed thermogenic-biogenic origin.Late-stage microbial methanogenesis began following unroofing of the basin, and stable isotopes in the produced gas and in mineral cements indicate that late-stage methanogenesis occurred along a CO2-reduction metabolic pathway. Hydrocarbons, as well as small amounts of nitrate in the formation water, probably helped nourish the microbial consortia, which were apparently active in fresh to hypersaline water. The produced water contains NH4+ and NH3, which correlate strongly with brine concentration and are interpreted to be derived from silicate minerals. Denitrification reactions may have generated some N2, which is the only major impurity in the coalbed gas. Carbon dioxide is a minor component of the produced gas, but significant quantities are dissolved in the formation water. Degradation of organic compounds, augmented by deionization of NH4+, may have been the principal sources of hydrogen facilitating late-stage CO2 reduction.

Identification of Uncultured Bacterial Species from Firmicutes, Bacteroidetes and CANDIDATUS Saccharibacteria as Candidate Cellulose Utilizers from the Rumen of Beef Cows.

PubMed

Opdahl, Lee James; Gonda, Michael G; St-Pierre, Benoit

2018-02-24

The ability of ruminants to utilize cellulosic biomass is a result of the metabolic activities of symbiotic microbial communities that reside in the rumen. To gain further insight into this complex microbial ecosystem, a selection-based batch culturing approach was used to identify candidate cellulose-utilizing bacterial consortia. Prior to culturing with cellulose, rumen contents sampled from three beef cows maintained on a forage diet shared 252 Operational Taxonomic Units (OTUs), accounting for 41.6-50.0% of bacterial 16S rRNA gene sequences in their respective samples. Despite this high level of overlap, only one OTU was enriched in cellulose-supplemented cultures from all rumen samples. Otherwise, each set of replicate cellulose supplemented cultures originating from a sampled rumen environment was found to have a distinct bacterial composition. Two of the seven most enriched OTUs were closely matched to well-established rumen cellulose utilizers ( Ruminococcus flavefaciens and Fibrobacter succinogenes ), while the others did not show high nucleotide sequence identity to currently defined bacterial species. The latter were affiliated to Prevotella (1 OTU), Ruminococcaceae (3 OTUs), and the candidate phylum Saccharibacteria (1 OTU), respectively. While further investigations will be necessary to elucidate the metabolic function(s) of each enriched OTU, these results together further support cellulose utilization as a ruminal metabolic trait shared across vast phylogenetic distances, and that the rumen is an environment conducive to the selection of a broad range of microbial adaptations for the digestion of plant structural polysaccharides.

HIPPARCOS - Activities of the data reduction consortia

NASA Astrophysics Data System (ADS)

Lindegren, L.; Kovalevsky, J.

The complete reduction of data from the ESA astrometry satellite Hipparcos, from some 1012bits of photon counts and ancillary data to a catalogue of astrometric parameters and magnitudes for the 100,000 programme stars, will be independently undertaken by two scientific consortia, NDAC and FAST. This approach is motivated by the size and complexity of the reductions and to ensure the validity of the results. The end product will be a single, agreed-upon catalogue. This paper describes briefly the principles of reduction and the organisation and status within each consortium.

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.

Aspergillus oryzae–Saccharomyces cerevisiae Consortium Allows Bio-Hybrid Fuel Cell to Run on Complex Carbohydrates

PubMed Central

Jahnke, Justin P.; Hoyt, Thomas; LeFors, Hannah M.; Sumner, James J.; Mackie, David M.

2016-01-01

Consortia of Aspergillus oryzae and Saccharomyces cerevisiae are examined for their abilities to turn complex carbohydrates into ethanol. To understand the interactions between microorganisms in consortia, Fourier-transform infrared spectroscopy is used to follow the concentrations of various metabolites such as sugars (e.g., glucose, maltose), longer chain carbohydrates, and ethanol to optimize consortia conditions for the production of ethanol. It is shown that with proper design A. oryzae can digest food waste simulants into soluble sugars that S. cerevisiae can ferment into ethanol. Depending on the substrate and conditions used, concentrations of 13% ethanol were achieved in 10 days. It is further shown that a direct alcohol fuel cell (FC) can be coupled with these A. oryzae-enabled S. cerevisiae fermentations using a reverse osmosis membrane. This “bio-hybrid FC” continually extracted ethanol from an ongoing consortium, enhancing ethanol production and allowing the bio-hybrid FC to run for at least one week. Obtained bio-hybrid FC currents were comparable to those from pure ethanol—water mixtures, using the same FC. The A. oryzae–S. cerevisiae consortium, coupled to a bio-hybrid FC, converted food waste simulants into electricity without any pre- or post-processing. PMID:27681904

Aspergillus oryzae-Saccharomyces cerevisiae Consortium Allows Bio-Hybrid Fuel Cell to Run on Complex Carbohydrates.

PubMed

Jahnke, Justin P; Hoyt, Thomas; LeFors, Hannah M; Sumner, James J; Mackie, David M

2016-02-04

Consortia of Aspergillus oryzae and Saccharomyces cerevisiae are examined for their abilities to turn complex carbohydrates into ethanol. To understand the interactions between microorganisms in consortia, Fourier-transform infrared spectroscopy is used to follow the concentrations of various metabolites such as sugars (e.g., glucose, maltose), longer chain carbohydrates, and ethanol to optimize consortia conditions for the production of ethanol. It is shown that with proper design A. oryzae can digest food waste simulants into soluble sugars that S. cerevisiae can ferment into ethanol. Depending on the substrate and conditions used, concentrations of 13% ethanol were achieved in 10 days. It is further shown that a direct alcohol fuel cell (FC) can be coupled with these A. oryzae-enabled S. cerevisiae fermentations using a reverse osmosis membrane. This "bio-hybrid FC" continually extracted ethanol from an ongoing consortium, enhancing ethanol production and allowing the bio-hybrid FC to run for at least one week. Obtained bio-hybrid FC currents were comparable to those from pure ethanol-water mixtures, using the same FC. The A. oryzae-S. cerevisiae consortium, coupled to a bio-hybrid FC, converted food waste simulants into electricity without any pre- or post-processing.

Electricity generation from an inorganic sulfur compound containing mining wastewater by acidophilic microorganisms.

PubMed

Ni, Gaofeng; Christel, Stephan; Roman, Pawel; Wong, Zhen Lim; Bijmans, Martijn F M; Dopson, Mark

2016-09-01

Sulfide mineral processing often produces large quantities of wastewaters containing acid-generating inorganic sulfur compounds. If released untreated, these wastewaters can cause catastrophic environmental damage. In this study, microbial fuel cells were inoculated with acidophilic microorganisms to investigate whether inorganic sulfur compound oxidation can generate an electrical current. Cyclic voltammetry suggested that acidophilic microorganisms mediated electron transfer to the anode, and that electricity generation was catalyzed by microorganisms. A cation exchange membrane microbial fuel cell, fed with artificial wastewater containing tetrathionate as electron donor, reached a maximum whole cell voltage of 72 ± 9 mV. Stepwise replacement of the artificial anolyte with real mining process wastewater had no adverse effect on bioelectrochemical performance and generated a maximum voltage of 105 ± 42 mV. 16S rRNA gene sequencing of the microbial consortia resulted in sequences that aligned within the genera Thermoplasma, Ferroplasma, Leptospirillum, Sulfobacillus and Acidithiobacillus. This study opens up possibilities to bioremediate mining wastewater using microbial fuel cell technology. Copyright © 2016 The Authors. Published by Elsevier Masson SAS.. All rights reserved.

Functional and taxonomic dynamics of an electricity-consuming methane-producing microbial community.

PubMed

Bretschger, Orianna; Carpenter, Kayla; Phan, Tony; Suzuki, Shino; Ishii, Shun'ichi; Grossi-Soyster, Elysse; Flynn, Michael; Hogan, John

2015-11-01

The functional and taxonomic microbial dynamics of duplicate electricity-consuming methanogenic communities were observed over a 6 months period to characterize the reproducibility, stability and recovery of electromethanogenic consortia. The highest rate of methanogenesis was 0.72 mg-CH4/L/day, which occurred during the third month of enrichment when multiple methanogenic phylotypes and associated Desulfovibrionaceae phylotypes were present in the electrode-associated microbial community. Results also suggest that electromethanogenic microbial communities are very sensitive to electron donor-limiting open-circuit conditions. A 45 min exposure to open-circuit conditions induced an 87% drop in volumetric methane production rates. Methanogenic performance recovered after 4 months to a maximum value of 0.30 mg-CH4/L/day under set potential operation (-700 mV vs Ag/AgCl); however, current consumption and biomass production was variable over time. Long-term functional and taxonomic analyses from experimental replicates provide new knowledge toward understanding how to enrich electromethanogenic communities and operate bioelectrochemical systems for stable and reproducible performance. Copyright © 2015 Elsevier Ltd. All rights reserved.

Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics

PubMed Central

Bokulich, Nicholas A.; Collins, Thomas S.; Masarweh, Chad; Allen, Greg; Heymann, Hildegarde; Ebeler, Susan E.

2016-01-01

ABSTRACT Regionally distinct wine characteristics (terroir) are an important aspect of wine production and consumer appreciation. Microbial activity is an integral part of wine production, and grape and wine microbiota present regionally defined patterns associated with vineyard and climatic conditions, but the degree to which these microbial patterns associate with the chemical composition of wine is unclear. Through a longitudinal survey of over 200 commercial wine fermentations, we demonstrate that both grape microbiota and wine metabolite profiles distinguish viticultural area designations and individual vineyards within Napa and Sonoma Counties, California. Associations among wine microbiota and fermentation characteristics suggest new links between microbiota, fermentation performance, and wine properties. The bacterial and fungal consortia of wine fermentations, composed from vineyard and winery sources, correlate with the chemical composition of the finished wines and predict metabolite abundances in finished wines using machine learning models. The use of postharvest microbiota as an early predictor of wine chemical composition is unprecedented and potentially poses a new paradigm for quality control of agricultural products. These findings add further evidence that microbial activity is associated with wine terroir. PMID:27302757

Substrate removal and electricity generation in a membrane-less microbial fuel cell for biological treatment of wastewater.

PubMed

Wang, Haiping; Jiang, Sunny C; Wang, Yun; Xiao, Bo

2013-06-01

Microbial fuel cells have gained popularity in recent years due to its promise in converting organic wastewater into renewable electrical energy. In this study, a membrane-less MFC with a biocathode was developed to evaluate its performance in electricity generation while simultaneously treating wastewater. The MFC fed with a continuous flow of 2g/day acetate produced a power density of 30 mW/m(2) and current density of 245 mA/m(2). A substrate degradation efficiency (SDE) of 75.9% was achieved with 48.7% attributed to the anaerobic process and 27.2% to the aerobic process. Sequencing analysis of the microbial consortia using 16S rDNA pryosequencing showed the predominance of Bacteroidia in the anode after one month of operation, while the microbial community in the cathode chamber was dominated by Gamma-proteobacteria and Beta-proteobacteria. Coulombic efficiencies varied from 19.8% to 58.1% using different acetate concentrations, indicating power density can be further improved through the accumulation of electron-transferring bacteria. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2016-07-01

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

Application of clone library analysis and real-time PCR for comparison of microbial communities in a low-grade copper sulfide ore bioheap leachate.

PubMed

Bowei, Chen; Xingyu, Liu; Wenyan, Liu; Jiankang, Wen

2009-11-01

The microbial communities of leachate from a bioleaching heap located in China were analyzed using the 16S rRNA gene clone library and real-time quantitative PCR. Both methods showed that Leptospirillum spp. were the dominant bacteria, and Ferroplasma acidiphilum were the only archaea detected in the leachate. Clone library results indicated that nine operational taxonomic units (OTUs) were obtained, which fell into four divisions, the Nitrospirae (74%), the gamma-Proteobacteria (14%), the Actinobacteria (6%) and the Euryarchaeota (6%). The results obtained by real-time PCR in some ways were the same as clone library analysis. Furthermore, Sulfobacillus spp., detected only by real-time PCR, suggests that real-time PCR was a reliable technology to study the microbial communities in bioleaching environments. It is a useful tool to assist clone library analysis, to further understand microbial consortia and to have comprehensive and exact microbiological information about bioleaching environments. Finally, the interactions among the microorganisms detected in the leachate were summarized according to the characteristics of these species.

Biomining Microorganisms: Molecular Aspects and Applications in Biotechnology and Bioremediation

NASA Astrophysics Data System (ADS)

Jerez, Carlos A.

The microbial solubilization of metals using chemolithoautotrophic microorganisms has successfully been used in industrial processes called biomining to extract metals such as copper, gold, uranium and others. The most studied leaching bacteria are from the genus Acidithiobacillus belonging to the Gram-negative γ-proteobacteria. Acidithiobacillus spp. obtain their energy from the oxidation of ferrous iron, elemental sulfur, or partially oxidized sulfur compounds. Other thermophilic archaeons capable of oxidizing sulfur and iron (II) have also been known for many years, and they are mainly from the genera Sulfolobus, Acidianus, Metallosphaera and Sulfurisphaera. Recently, some mesophilic iron (II)-oxidizing archaeons such as Ferroplasma acidiphilium and F. acidarmanus belonging to the Thermoplasmales have also been isolated and characterized. Recent studies of microorganisms consider them in their consortia, integrating fundamental biological knowledge with metagenomics, metaproteomics, and other data to obtain a global picture of how a microbial community functions. The understanding of microbial growth and activities in oxidizing metal ions will be useful for improving applied microbial biotechnologies such as biomining, bioshrouding, biomonitoring and bioremediation of metals in acidic environments.

Determination of natural organic matter and iron binding capacity in fen samples

NASA Astrophysics Data System (ADS)

Kügler, Stefan; Cooper, Rebecca E.; Frieder Mohr, Jan; Wichard, Thomas; Küsel, Kirsten

2017-04-01

Natural organic matter (NOM) plays an important role in ecosystem processes such as soil carbon stabilization, nutrient availability and metal complexation. Iron-NOM-complexes, for example, are known to increase the solubility and, as a result, the bioavailability of iron in natural environments leading to several effects on the microbial community. Due to the various functions of NOM in natural environments, there is a high level of interest in the characterization of the molecular composition. The complexity of NOM presents a significant challenge in the elucidation of its composition. However, the development and utilization of high resolution mass spectrometry (HR-MS) as a tool to detect single compounds in complex samples has spearheaded the effort to elucidate the composition of NOM. Over the past years, the accuracy of ion cyclotron- or Orbitrap mass spectrometers has increased dramatically resulting in the possibility to obtain a mass differentiation of the large number of compounds in NOM. Together these tools provide significant and powerful insight into the molecular composition of NOM. In the current study, we aim to understand abiotic and biotic interactions between NOM and metals, such as iron, found in the Schlöppnerbrunnen fen (Fichtelgebirge, Germany) and how these interactions impact the microbial consortia. We characterized the dissolved organic matter (DOM) as well as basic chemical parameters in the iron-rich (up to 20 mg (g wt peat)-1), slightly acidic (pH 4.8) fen to gain more information about DOM-metal interactions. This minerotrophic peatland connected to the groundwater has received Fe(II) released from the surrounding soils in the Lehstenbach catchment. Absorption spectroscopy (AAS), differential pulse polarography (DPP) and high resolution electrospray ionization mass spectrometry (HR-ESI-Orbitrap-MS) was applied to characterize the molecular composition of DOM in the peat water extract (PWE). We identified typical patterns for DOM illustrated by van Krevelen plots, which indicate the presence of different substance classes including condensed aromatics, lignins and tannins known to complex iron. Our results indicate a variety of potential Fe-DOM-complexes present in the PWE samples when iron is incorporated into the elemental composition search. Using DPP we determine the complexation capacity of iron in the natural matrix of the fen along with the identification of ligands in order to estimate the iron bioavailability for bacteria. As the microbial redox system of the fen is impacted by other metals in the environment, we perform comprehensive analysis of the entirety of metal ions and concentrations in the water samples. Dialysis chambers are currently installed in the iron-rich fen from which pore water samples will be collected at 1 cm increments between 0-20 cm depth to determine the depth profiles of Fe(II)- and Fe(III)-concentration and evaluate the influence of the depth profiles on the interplay between microorganism comprising the natural microbial redox system of the fen. We have shown that metal-DOM-pH interactions affect the bioavailable metal concentration in fen water systems. This information will pave the way for a better understanding of the bacterial recruitment of trace elements and microbial redox reactions.

Insights into the microbial diversity and community dynamics of Chinese traditional fermented foods from using high-throughput sequencing approaches*

PubMed Central

He, Guo-qing; Liu, Tong-jie; Sadiq, Faizan A.; Gu, Jing-si; Zhang, Guo-hua

2017-01-01

Chinese traditional fermented foods have a very long history dating back thousands of years and have become an indispensable part of Chinese dietary culture. A plethora of research has been conducted to unravel the composition and dynamics of microbial consortia associated with Chinese traditional fermented foods using culture-dependent as well as culture-independent methods, like different high-throughput sequencing (HTS) techniques. These HTS techniques enable us to understand the relationship between a food product and its microbes to a greater extent than ever before. Considering the importance of Chinese traditional fermented products, the objective of this paper is to review the diversity and dynamics of microbiota in Chinese traditional fermented foods revealed by HTS approaches. PMID:28378567

Applications of methylotrophs: can single carbon be harnessed for biotechnology?

PubMed

Chistoserdova, Ludmila

2018-04-01

This review summarizes developments in the field of applied research involving microbial conversion of single carbon compounds (methane, methanol, CO 2 ). The potential of the microorganisms involved in biotechnological applications could be realized via engineering native C1 utilizers toward higher output of value-added compounds, including biofuels, or via production of value chemicals as parts of novel, heterologously expressed biochemical pathways. Alternatively, C1 metabolism could be implemented in traditional industrial platforms (Escherichia coli, yeast), via introduction of specific metabolic modules. Most recent research spanning both approaches is covered. The potential of C1 utilizers in biomining of rare Earth elements, as well as the potential of C1 consuming microbial consortia in industrial applications are discussed. Copyright © 2018 Elsevier Ltd. All rights reserved.

Multispecies Biofilms Transform Selenium Oxyanions into Elemental Selenium Particles: Studies Using Combined Synchrotron X-ray Fluorescence Imaging and Scanning Transmission X-ray Microscopy.

PubMed

Yang, Soo In; George, Graham N; Lawrence, John R; Kaminskyj, Susan G W; Dynes, James J; Lai, Barry; Pickering, Ingrid J

2016-10-04

Selenium (Se) is an element of growing environmental concern, because low aqueous concentrations can lead to biomagnification through the aquatic food web. Biofilms, naturally occurring microbial consortia, play numerous important roles in the environment, especially in biogeochemical cycling of toxic elements in aquatic systems. The complexity of naturally forming multispecies biofilms presents challenges for characterization because conventional microscopic techniques require chemical and physical modifications of the sample. Here, multispecies biofilms biotransforming selenium oxyanions were characterized using X-ray fluorescence imaging (XFI) and scanning transmission X-ray microscopy (STXM). These complementary synchrotron techniques required minimal sample preparation and were applied correlatively to the same biofilm areas. Sub-micrometer XFI showed distributions of Se and endogenous metals, while Se K-edge X-ray absorption spectroscopy indicated the presence of elemental Se (Se 0 ). Nanoscale carbon K-edge STXM revealed the distributions of microbial cells, extracellular polymeric substances (EPS), and lipids using the protein, saccharide, and lipid signatures, respectively, together with highly localized Se 0 using the Se L III edge. Transmission electron microscopy showed the electron-dense particle diameter to be 50-700 nm, suggesting Se 0 nanoparticles. The intimate association of Se 0 particles with protein and polysaccharide biofilm components has implications for the bioavailability of selenium in the environment.

Multispecies Biofilms Transform Selenium Oxyanions into Elemental Selenium Particles: Studies Using Combined Synchrotron X-ray Fluorescence Imaging and Scanning Transmission X-ray Microscopy

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

Yang, Soo In; George, Graham N.; Lawrence, John R.

2016-10-04

Selenium (Se) is an element of growing environmental concern, because low aqueous concentrations can lead to biomagnification through the aquatic food web. Biofilms, naturally occurring microbial consortia, play numerous important roles in the environment, especially in biogeochemical cycling of toxic elements in aquatic systems. The complexity of naturally forming multispecies biofilms presents challenges for characterization because conventional microscopic techniques require chemical and physical modifications of the sample. Here, multispecies biofilms biotransforming selenium oxyanions were characterized using X-ray fluorescence imaging (XFI) and scanning transmission X-ray microscopy (STXM). These complementary synchrotron techniques required minimal sample preparation and were applied correlatively to themore » same biofilm areas. Sub-micrometer XFI showed distributions of Se and endogenous metals, while Se K-edge X-ray absorption spectroscopy indicated the presence of elemental Se (Se0). Nanoscale carbon K-edge STXM revealed the distributions of microbial cells, extracellular polymeric substances (EPS), and lipids using the protein, saccharide, and lipid signatures, respectively, together with highly localized Se0 using the Se LIII edge. Transmission electron microscopy showed the electron-dense particle diameter to be 50–700 nm, suggesting Se0 nanoparticles. The intimate association of Se0 particles with protein and polysaccharide biofilm components has implications for the bioavailability of selenium in the environment.« less

Distinct succession patterns of abundant and rare bacteria in temporal microcosms with pollutants.

PubMed

Jiao, Shuo; Luo, Yantao; Lu, Mingmei; Xiao, Xiao; Lin, Yanbing; Chen, Weimin; Wei, Gehong

2017-06-01

Elucidating the driving forces behind the temporal dynamics of abundant and rare microbes is essential for understanding the assembly and succession of microbial communities. Here, we explored the successional trajectories and mechanisms of abundant and rare bacteria via soil-enrichment subcultures in response to various pollutants (phenanthrene, n-octadecane, and CdCl 2 ) using time-series Illumina sequencing datasets. The results reveal different successional patterns of abundant and rare sub-communities in eighty pollutant-degrading consortia and two original soil samples. A temporal decrease in α-diversity and high turnover rate for β-diversity indicate that deterministic processes are the main drivers of the succession of the abundant sub-community; however, the high cumulative species richness indicates that stochastic processes drive the succession of the rare sub-community. A functional prediction showed that abundant bacteria contribute primary functions to the pollutant-degrading consortia, such as amino acid metabolism, cellular responses to stress, and hydrocarbon degradation. Meanwhile, rare bacteria contribute a substantial fraction of auxiliary functions, such as carbohydrate-active enzymes, fermentation, and homoacetogenesis, which indicates their roles as a source of functional diversity. Our study suggests that the temporal succession of microbes in polluted microcosms is mainly associated with abundant bacteria rather than the high proportion of rare taxa. The major forces (i.e., stochastic or deterministic processes) driving microbial succession could be dependent on the low- or high-abundance community members in temporal microcosms with pollutants. Copyright © 2017 Elsevier Ltd. All rights reserved.

Pandemic pharmaceutical dosing effects on wastewater treatment: no adaptation of activated sludge bacteria to degrade the antiviral drug oseltamivir (Tamiflu®) and loss of nutrient removal performance.

PubMed

Slater, Frances R; Singer, Andrew C; Turner, Susan; Barr, Jeremy J; Bond, Philip L

2011-02-01

The 2009-2010 influenza pandemic saw many people treated with antivirals and antibiotics. High proportions of both classes of drugs are excreted and enter wastewater treatment plants (WWTPs) in biologically active forms. To date, there has been no study into the potential for influenza pandemic-scale pharmaceutical use to disrupt WWTP function. Furthermore, there is currently little indication as to whether WWTP microbial consortia can degrade antiviral neuraminidase inhibitors when exposed to pandemic-scale doses. In this study, we exposed an aerobic granular sludge sequencing batch reactor, operated for enhanced biological phosphorus removal (EBPR), to a simulated influenza-pandemic dosing of antibiotics and antivirals for 8 weeks. We monitored the removal of the active form of Tamiflu(®), oseltamivir carboxylate (OC), bacterial community structure, granule structure and changes in EBPR and nitrification performance. There was little removal of OC by sludge and no evidence that the activated sludge community adapted to degrade OC. There was evidence of changes to the bacterial community structure and disruption to EBPR and nitrification during and after high-OC dosing. This work highlights the potential for the antiviral contamination of receiving waters and indicates the risk of destabilizing WWTP microbial consortia as a result of high concentrations of bioactive pharmaceuticals during an influenza pandemic. © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Biochemical and biophysical characterization of novel GH10 xylanase prospected from a sugar cane bagasse compost-derived microbial consortia.

PubMed

Evangelista, Danilo Elton; Kadowaki, Marco Antonio Seiki; Mello, Bruno Luan; Polikarpov, Igor

2018-04-01

Environmental issues are promoting the development of innovative technologies for the production of renewable energy and "green products" from plant biomass residues. These technologies rely on the conversion of the plant cell wall (PCW) polysaccharides into simple sugars, which involve synergistic activities of different PCW degrading enzymes, including xylanases; these are widely applied in food and feed sectors, paper and textile industries, among others. We cloned, expressed and biochemically characterized a novel xylanase (Xyn10) from the GH10 identified in a metatranscriptome of compost-derived microbial consortia and determined its low-resolution SAXS molecular envelope in solution. Our results reveal that Xyn10 is a monomeric flexible globular enzyme, with high stability with a broad pH range from 4 to 10 and optimal activity conditions at pH 7 and 40 °C. Only 10% of activity loss was observed after the enzyme was incubated for 30 h at 40 °C with a pH ranging from 5 to 10. Moreover, Xyn10 maintained 100% of its initial activity after incubation for 120 h at 40 °C and 51% after incubation for 24 h at 50 °C (pH = 7.0). Xyn10 shows endocatalytic activity towards xylan and arabinoxylan, liberating xylose, xylobiose, 1,2-α-d-methylglucuronic acid decorated xylotriose, and 1,3-α-l-arabinofuranose decorated xylobiose and xylotriose oligosaccharides. Copyright © 2017 Elsevier B.V. All rights reserved.

Phylogenetic and functional diversity within toluene-degrading, sulphate-reducing consortia enriched from a contaminated aquifer.

PubMed

Kuppardt, Anke; Kleinsteuber, Sabine; Vogt, Carsten; Lüders, Tillmann; Harms, Hauke; Chatzinotas, Antonis

2014-08-01

Three toluene-degrading microbial consortia were enriched under sulphate-reducing conditions from different zones of a benzene, toluene, ethylbenzene and xylenes (BTEX) plume of two connected contaminated aquifers. Two cultures were obtained from a weakly contaminated zone of the lower aquifer, while one culture originated from the highly contaminated upper aquifer. We hypothesised that the different habitat characteristics are reflected by distinct degrader populations. Degradation of toluene with concomitant production of sulphide was demonstrated in laboratory microcosms and the enrichment cultures were phylogenetically characterised. The benzylsuccinate synthase alpha-subunit (bssA) marker gene, encoding the enzyme initiating anaerobic toluene degradation, was targeted to characterise the catabolic diversity within the enrichment cultures. It was shown that the hydrogeochemical parameters in the different zones of the plume determined the microbial composition of the enrichment cultures. Both enrichment cultures from the weakly contaminated zone were of a very similar composition, dominated by Deltaproteobacteria with the Desulfobulbaceae (a Desulfopila-related phylotype) as key players. Two different bssA sequence types were found, which were both affiliated to genes from sulphate-reducing Deltaproteobacteria. In contrast, the enrichment culture from the highly contaminated zone was dominated by Clostridia with a Desulfosporosinus-related phylotype as presumed key player. A distinct bssA sequence type with high similarity to other recently detected sequences from clostridial toluene degraders was dominant in this culture. This work contributes to our understanding of the niche partitioning between degrader populations in distinct compartments of BTEX-contaminated aquifers.

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

The oral microbiome and the immunobiology of periodontal disease and caries

PubMed Central

Costalonga, Massimo; Herzberg, Mark C.

2015-01-01

The composition of the oral microbiome differs from one intraoral site to another, reflecting in part the host response and immune capacity at each site. By focusing on two major oral infections, periodontal disease and caries, new principles of disease emerge. Periodontal disease affects the soft tissues and bone that support the teeth. Caries is a unique infection of the dental hard tissues. The initiation of both diseases is marked by an increase in the complexity of the microbiome. In periodontitis, pathobionts and keystone pathogens such as Porphyromonas gingivalis appear in greater proportion than in health. As a keystone pathogen, P. gingivalis impairs host immune responses and appears necessary but not sufficient to cause periodontitis. Historically, dental caries had been causally linked to Streptococcus mutans. Contemporary microbiome studies now indicate that singular pathogens are not obvious in either caries or periodontitis. Both diseases appear to result from a perturbation among relatively minor constituents in local microbial communities resulting in dysbiosis. Emergent consortia of the minor members of the respective microbiomes act synergistically to stress the ability of the host to respond and protect. In periodontal disease, host protection first occurs at the level of innate gingival epithelial immunity. Secretory IgA antibody and other salivary antimicrobial systems also act against periodontopathic and cariogenic consortia. When the gingival immune response is impaired, periodontal tissue pathology results when matrix metalloproteinases are released from neutrophils and T cells mediate alveolar bone loss. In caries, several species are acidogenic and aciduric and appear to work synergistically to promote demineralization of the enamel and dentin. Whereas technically possible, particularly for caries, vaccines are unlikely to be commercialized in the near future because of the low morbidity of caries and periodontitis. PMID:25447398

The oral microbiome and the immunobiology of periodontal disease and caries.

PubMed

Costalonga, Massimo; Herzberg, Mark C

2014-12-01

The composition of the oral microbiome differs from one intraoral site to another, reflecting in part the host response and immune capacity at each site. By focusing on two major oral infections, periodontal disease and caries, new principles of disease emerge. Periodontal disease affects the soft tissues and bone that support the teeth. Caries is a unique infection of the dental hard tissues. The initiation of both diseases is marked by an increase in the complexity of the microbiome. In periodontitis, pathobionts and keystone pathogens such as Porphyromonas gingivalis appear in greater proportion than in health. As a keystone pathogen, P. gingivalis impairs host immune responses and appears necessary but not sufficient to cause periodontitis. Historically, dental caries had been causally linked to Streptococcus mutans. Contemporary microbiome studies now indicate that singular pathogens are not obvious in either caries or periodontitis. Both diseases appear to result from a perturbation among relatively minor constituents in local microbial communities resulting in dysbiosis. Emergent consortia of the minor members of the respective microbiomes act synergistically to stress the ability of the host to respond and protect. In periodontal disease, host protection first occurs at the level of innate gingival epithelial immunity. Secretory IgA antibody and other salivary antimicrobial systems also act against periodontopathic and cariogenic consortia. When the gingival immune response is impaired, periodontal tissue pathology results when matrix metalloproteinases are released from neutrophils and T cells mediate alveolar bone loss. In caries, several species are acidogenic and aciduric and appear to work synergistically to promote demineralization of the enamel and dentin. Whereas technically possible, particularly for caries, vaccines are unlikely to be commercialized in the near future because of the low morbidity of caries and periodontitis. Copyright © 2014. Published by Elsevier B.V.

Fully reversible current driven by a dual marine photosynthetic microbial community.

PubMed

Darus, Libertus; Lu, Yang; Ledezma, Pablo; Keller, Jürg; Freguia, Stefano

2015-11-01

The electrochemical activity of two seawater microbial consortia were investigated in three-electrode bioelectrochemical cells. Two seawater inocula - from the Sunshine Coast (SC) and Gold Coast (GC) shores of Australia - were enriched at +0.6 V vs. SHE using 12/12 h day/night cycles. After re-inoculation, the SC consortium developed a fully-reversible cathodic/anodic current, with a max. of -62 mA m(-2) during the day and +110 mA m(-2) at night, while the GC exhibited negligible daytime output but +98 mA m(-2) at night. Community analysis revealed that both enrichments were dominated by cyanobacteria, indicating their potential as biocatalysts for indirect light conversion to electricity. Moreover, the presence of γ-proteobacterium Congregibacter in SC biofilm was likely related to the cathodic reductive current, indicating its effectiveness at catalysing cathodic oxygen reduction at a surprisingly high potential. For the first time a correlation between a dual microbial community and fully reversible current is reported. 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.

An Enrichment of CRISPR and Other Defense-Related Features in Marine Sponge-Associated Microbial Metagenomes

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

Horn, Hannes; Slaby, Beate M.; Jahn, Martin T.

Many marine sponges are populated by dense and taxonomically diverse microbial consortia. We employed a metagenomics approach to unravel the differences in the functional gene repertoire among three Mediterranean sponge species, Petrosia ficiformis, Sarcotragus foetidus, Aplysina aerophoba and seawater. Different signatures were observed between sponge and seawater metagenomes with regard to microbial community composition, GC content, and estimated bacterial genome size. Our analysis showed further a pronounced repertoire for defense systems in sponge metagenomes. Specifically, clustered regularly interspaced short palindromic repeats, restriction modification, DNA phosphorothioation and phage growth limitation systems were enriched in sponge metagenomes. These data suggest that defensemore » is an important functional trait for an existence within sponges that requires mechanisms to defend against foreign DNA from microorganisms and viruses. Furthermore, this study contributes to an understanding of the evolutionary arms race between viruses/phages and bacterial genomes and it sheds light on the bacterial defenses that have evolved in the context of the sponge holobiont.« less

An Enrichment of CRISPR and Other Defense-Related Features in Marine Sponge-Associated Microbial Metagenomes

DOE PAGES

Horn, Hannes; Slaby, Beate M.; Jahn, Martin T.; ...

2016-11-08

Many marine sponges are populated by dense and taxonomically diverse microbial consortia. We employed a metagenomics approach to unravel the differences in the functional gene repertoire among three Mediterranean sponge species, Petrosia ficiformis, Sarcotragus foetidus, Aplysina aerophoba and seawater. Different signatures were observed between sponge and seawater metagenomes with regard to microbial community composition, GC content, and estimated bacterial genome size. Our analysis showed further a pronounced repertoire for defense systems in sponge metagenomes. Specifically, clustered regularly interspaced short palindromic repeats, restriction modification, DNA phosphorothioation and phage growth limitation systems were enriched in sponge metagenomes. These data suggest that defensemore » is an important functional trait for an existence within sponges that requires mechanisms to defend against foreign DNA from microorganisms and viruses. Furthermore, this study contributes to an understanding of the evolutionary arms race between viruses/phages and bacterial genomes and it sheds light on the bacterial defenses that have evolved in the context of the sponge holobiont.« less

Microbiome Therapeutics – Advances and Challenges

PubMed Central

Mimee, Mark; Citorik, Robert J.; Lu, Timothy K.

2016-01-01

The microbial community that lives on and in the human body exerts a major impact on human health, from metabolism to immunity. In order to leverage the close associations between microbes and their host, development of therapeutics targeting the microbiota has surged in recent years. Here, we discuss current additive and subtractive strategies to manipulate the microbiota, focusing on bacteria engineered to produce therapeutic payloads, consortia of natural organisms and selective antimicrobials. Further, we present challenges faced by the community in the development of microbiome therapeutics, including designing microbial therapies that are adapted for specific geographies in the body, stable colonization with microbial therapies, discovery of clinically relevant biosensors, robustness of engineered synthetic gene circuits and addressing safety and biocontainment concerns. Moving forward, collaboration between basic and applied researchers and clinicians to address these challenges will poise the field to herald an age of next-generation, cellular therapies that draw on novel findings in basic research to inform directed augmentation of the human microbiota. PMID:27158095

Microbiome therapeutics - Advances and challenges.

PubMed

Mimee, Mark; Citorik, Robert J; Lu, Timothy K

2016-10-01

The microbial community that lives on and in the human body exerts a major impact on human health, from metabolism to immunity. In order to leverage the close associations between microbes and their host, development of therapeutics targeting the microbiota has surged in recent years. Here, we discuss current additive and subtractive strategies to manipulate the microbiota, focusing on bacteria engineered to produce therapeutic payloads, consortia of natural organisms and selective antimicrobials. Further, we present challenges faced by the community in the development of microbiome therapeutics, including designing microbial therapies that are adapted for specific geographies in the body, stable colonization with microbial therapies, discovery of clinically relevant biosensors, robustness of engineered synthetic gene circuits and addressing safety and biocontainment concerns. Moving forward, collaboration between basic and applied researchers and clinicians to address these challenges will poise the field to herald an age of next-generation, cellular therapies that draw on novel findings in basic research to inform directed augmentation of the human microbiota. Copyright © 2016. 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.

Methane Seep in Shallow-Water Permeable Sediment Harbors High Diversity of Anaerobic Methanotrophic Communities, Elba, Italy

PubMed Central

Ruff, S. Emil; Kuhfuss, Hanna; Wegener, Gunter; Lott, Christian; Ramette, Alban; Wiedling, Johanna; Knittel, Katrin; Weber, Miriam

2016-01-01

The anaerobic oxidation of methane (AOM) is a key biogeochemical process regulating methane emission from marine sediments into the hydrosphere. AOM is largely mediated by consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB), and has mainly been investigated in deep-sea sediments. Here we studied methane seepage at four spots located at 12 m water depth in coastal, organic carbon depleted permeable sands off the Island of Elba (Italy). We combined biogeochemical measurements, sequencing-based community analyses and in situ hybridization to investigate the microbial communities of this environment. Increased alkalinity, formation of free sulfide and nearly stoichiometric methane oxidation and sulfate reduction rates up to 200 nmol g-1 day-1 indicated the predominance of sulfate-coupled AOM. With up to 40 cm thickness the zones of AOM activity were unusually large and occurred in deeper sediment horizons (20–50 cm below seafloor) as compared to diffusion-dominated deep-sea seeps, which is likely caused by advective flow of pore water due to the shallow water depth and permeability of the sands. Hydrodynamic forces also may be responsible for the substantial phylogenetic and unprecedented morphological diversity of AOM consortia inhabiting these sands, including the clades ANME-1a/b, ANME-2a/b/c, ANME-3, and their partner bacteria SEEP-SRB1a and SEEP-SRB2. High microbial dispersal, the availability of diverse energy sources and high habitat heterogeneity might explain that the emission spots shared few microbial taxa, despite their physical proximity. Although the biogeochemistry of this shallow methane seep was very different to that of deep-sea seeps, their key functional taxa were very closely related, which supports the global dispersal of key taxa and underlines strong selection by methane as the predominant energy source. Mesophilic, methane-fueled ecosystems in shallow-water permeable sediments may comprise distinct microbial habitats due to their unique biogeochemical and physical characteristics. To link AOM phylotypes with seep habitats and to enable future meta-analyses we thus propose that seep environment ontology needs to be further specified. PMID:27065954

Methane Seep in Shallow-Water Permeable Sediment Harbors High Diversity of Anaerobic Methanotrophic Communities, Elba, Italy.

PubMed

Ruff, S Emil; Kuhfuss, Hanna; Wegener, Gunter; Lott, Christian; Ramette, Alban; Wiedling, Johanna; Knittel, Katrin; Weber, Miriam

2016-01-01

The anaerobic oxidation of methane (AOM) is a key biogeochemical process regulating methane emission from marine sediments into the hydrosphere. AOM is largely mediated by consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB), and has mainly been investigated in deep-sea sediments. Here we studied methane seepage at four spots located at 12 m water depth in coastal, organic carbon depleted permeable sands off the Island of Elba (Italy). We combined biogeochemical measurements, sequencing-based community analyses and in situ hybridization to investigate the microbial communities of this environment. Increased alkalinity, formation of free sulfide and nearly stoichiometric methane oxidation and sulfate reduction rates up to 200 nmol g(-1) day(-1) indicated the predominance of sulfate-coupled AOM. With up to 40 cm thickness the zones of AOM activity were unusually large and occurred in deeper sediment horizons (20-50 cm below seafloor) as compared to diffusion-dominated deep-sea seeps, which is likely caused by advective flow of pore water due to the shallow water depth and permeability of the sands. Hydrodynamic forces also may be responsible for the substantial phylogenetic and unprecedented morphological diversity of AOM consortia inhabiting these sands, including the clades ANME-1a/b, ANME-2a/b/c, ANME-3, and their partner bacteria SEEP-SRB1a and SEEP-SRB2. High microbial dispersal, the availability of diverse energy sources and high habitat heterogeneity might explain that the emission spots shared few microbial taxa, despite their physical proximity. Although the biogeochemistry of this shallow methane seep was very different to that of deep-sea seeps, their key functional taxa were very closely related, which supports the global dispersal of key taxa and underlines strong selection by methane as the predominant energy source. Mesophilic, methane-fueled ecosystems in shallow-water permeable sediments may comprise distinct microbial habitats due to their unique biogeochemical and physical characteristics. To link AOM phylotypes with seep habitats and to enable future meta-analyses we thus propose that seep environment ontology needs to be further specified.

Intermunicipal health care consortia in Brazil: strategic behavior, incentives and sustainability.

PubMed

Teixeira, Luciana; Bugarin, Mauricio; Dourado, Maria Cristina

2006-01-01

This article studies strategic behavior in municipal health care consortia where neighboring municipalities form a partnership to supply high-complexity health care. Each municipality partially funds the organization. Depending on the partnership contract, a free rider problem may jeopardize the organization. A municipality will default its payments if it can still benefit from the services, especially when political pressures for competing expenditure arise. The main result is that the partnership sustainability depends on punishment mechanisms to a defaulting member, the gains from joint provision of services and the overall economic environment. Possible solutions to the incentive problem are discussed.

Expanding diversity of potential bacterial partners of the methanotrophic ANME archaea using Magneto-FISH

NASA Astrophysics Data System (ADS)

Trembath-Reichert, E.; Green-Saxena, A.; Steele, J. A.; Orphan, V. J.

2012-12-01

Sulfate-coupled anaerobic oxidation of methane (AOM) in marine sediments is the major sink for methane in the oceans. This process is believed to be catalyzed by as yet uncultured syntrophic consortia of ANME archaea (affiliated with the Methanosarcinales) and sulfate-reducing bacteria belonging to the Desulfosarcina/Desulfococcus and Desulfobulbaceae. These syntrophic consortia have been described from methane-rich habitats worldwide and appear to be most concentrated in areas of high methane flux, such as cold seeps along continental margins. The extent of the diversity and ecophysiological potential of these microbial associations is still poorly constrained. In an effort to better characterize the diversity of microorganisms forming associations with different clades of methanotrophic ANME archaea (ANME-1, ANME-2a/b/c, ANME-3) and link these organisms to potentially diagnostic metabolic genes (e.g. mcrA, dsrAB, aprA), we employed a unique culture-independent whole cell capture technique which combines Fluorescence In Situ Hybridization with immuno-magnetic cell capture (Magneto-FISH). We used Magneto-FISH for targeted enrichment of specific ANME groups and their associated bacteria directly from formalin- and ethanol-fixed methane seep sediment. The identity and metabolic gene diversity of captured microorganisms were then assessed by clone library construction and sequencing. Diversity recovered from Magneto-FISH experiments using general and clade-specific ANME targeted probes show both the expected selectivity of the FISH probes (i.e. predominately ANME-2c subclade captured with an ANME-2c probe and multiple ANME groups recovered with the general probe targeting most ANME). Follow up FISH experiments were conducted to confirm physical associations between ANME and unique bacterial members (deltaproteobacteria and other non-sulfate reducing groups) that were common to multiple Magneto-FISH capture experiments. Analyses of metabolic gene diversity for archaeal (mcrA) and sulfate-reducing (aprA and dsrAB) members of the consortia were generally consistent with the diversity observed by 16S rRNA from individual Magneto-FISH experiments. Together, this data indicates a role for the involvement of additional microbial groups in the AOM symbioses at methane seeps.

Thermodynamic and Kinetic Requirements in Anaerobic Methane Oxidizing Consortia Exclude Hydrogen, Acetate, and Methanol as Possible Electron Shuttles.

PubMed

Sørensen, K.B.; Finster, K.; Ramsing, N.B.

2001-07-01

Anaerobic methane oxidation (AMO) has long remained an enigma in microbial ecology. In the process the net reaction appears to be an oxidation of methane with sulfate as electron acceptor. In order to explain experimental data such as effects of inhibitors and isotopic signals in biomarkers it has been suggested that the process is carried out by a consortium of bacteria using an unknown compound to shuttle electrons between the participants. The overall change in free energy during AMO with sulfate is very small (?22 kJ mol-1) at in situ concentrations of methane and sulfate. In order to share the available free energy between the members of the consortium, the concentration of the intermediate electron shuttle compound becomes crucial. Diffusive flux of a substrate (i.e, the electron shuttle) between bacteria requires a stable concentration gradient where the concentration is higher in the producing organism than in the consuming organism. Since changes in concentrations cause changes in reaction free energies, the diffusive flux of a catabolic product/substrate between bacteria is associated with a net loss of available energy. This restricts maximal inter-bacterial distances in consortia composed of stationary bacteria. A simple theoretical model was used to describe the relationship between inter-bacterial distances and the energy lost due to concentration differences in consortia. Key parameters turned out to be the permissible concentration range of the electron shuttle in the consortium (i.e., the concentration range that allows both participants to gain sufficient energy) and the stoichiometry of the partial reactions. The model was applied to two known consortia degrading ethanol and butyrate and to four hypothetical methane-oxidizing consortia (MOC) based on interspecies transfer of hydrogen, methanol, acetate, or formate, respectively. In the first three MOCs the permissible distances between producers and consumers of the transferred compounds were less than two times prokaryotic cell wall diameters. Consequently, it is not possible that a MOC can be based on inter-species transfer of hydrogen, methanol, or acetate. Formate, on the other hand, is a possible shuttle candidate provided the bacteria are attached to one another. In general the model predicts that members of consortia thriving on low energy such as the MOC must adhere to each other and utilize a compound for the exchange of electrons that has a high permissible concentration range and a high diffusion coefficient and transfers as many electrons as possible per molecule.

Parallel Mutations Result in a Wide Range of Cooperation and Community Consequences in a Two-Species Bacterial Consortium

DOE PAGES

Douglas, Sarah M.; Chubiz, Lon M.; Harcombe, William R.; ...

2016-09-12

Multi-species microbial communities play a critical role in human health, industry, and waste remediation. Recently, the evolution of synthetic consortia in the laboratory has enabled adaptation to be addressed in the context of interacting species. Using an engineered bacterial consortium,we repeatedly evolved cooperative genotypes and examined both the predictability of evolution and the phenotypes that determinecommunity dynamics. Eight Salmonella enterica serovar Typhimurium strains evolved methionine excretion sufficient to support growth of an Escherichia coli methionine auxotroph, from whom they required excreted growth substrates. Non-synonymousmutations in metA, encoding homoserine trans-succinylase (HTS), were detected in each evolved S. enterica methionine cooperator andmore » were shown to be necessary for cooperative consortia growth. Molecular modeling was used to predict that most of the non-synonymous mutations slightly increase the binding affinity for HTS homodimer formation. Despite this genetic parallelism and trend of increasing protein binding stability, these metA alleles gave rise to a wide range of phenotypic diversity in termsof individual versus group benefit. The cooperators with the highest methionine excretion permitted nearly two-fold faster consortia growth and supported the highest fraction of E. coli, yet also had the slowest individual growth rates compared to less cooperative strains. Thus, although the genetic basis of adaptation was quite similar across independent origins of cooperative phenotypes, quantitative measurements of metabolite production were required to predict either the individual-level growth consequences or how these propagate to community-level behavior.« less

The long-term effect of uranium and pH on the community composition of an artificial consortium.

PubMed

Brzoska, Ryann M; Bollmann, Annette

2016-01-01

In the environment, microorganisms are living in diverse communities, which are impacted by the prevailing environmental conditions. Here, we present a study investigating the effect of low pH and elevated uranium concentration on the dynamics of an artificial microbial consortium. The members (Caulobacter sp. OR37, Asinibacterium sp. OR53, Ralstonia sp. OR214 and Rhodanobacter sp. OR444) were isolated from a uranium contaminated and acidic subsurface sediment. In pure culture, Ralstonia sp. OR214 had the highest growth rate at neutral and low pH and only Caulobacter sp. OR37 and Asinibacterium sp. OR53 grew in the presence uranium. The four strains were mixed in equal ratios, incubated at neutral and low pH and in the presence uranium and transferred to fresh medium once per week for 30 weeks. After 30 weeks, Ralstonia sp. OR214 was dominant at low and neutral pH and Caulobacter sp. OR37 and Asinibacterium sp. OR53 were dominant in the presence of uranium. After 12 weeks, the cultures were also transferred to new conditions to access the response of the consortia to changing conditions. The transfers showed an irreversible effect of uranium, but not of low pH on the consortia. Overall, the strains initially tolerant to the respective conditions persisted over time in high abundances in the consortia. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Parallel Mutations Result in a Wide Range of Cooperation and Community Consequences in a Two-Species Bacterial Consortium

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

Douglas, Sarah M.; Chubiz, Lon M.; Harcombe, William R.

Multi-species microbial communities play a critical role in human health, industry, and waste remediation. Recently, the evolution of synthetic consortia in the laboratory has enabled adaptation to be addressed in the context of interacting species. Using an engineered bacterial consortium,we repeatedly evolved cooperative genotypes and examined both the predictability of evolution and the phenotypes that determinecommunity dynamics. Eight Salmonella enterica serovar Typhimurium strains evolved methionine excretion sufficient to support growth of an Escherichia coli methionine auxotroph, from whom they required excreted growth substrates. Non-synonymousmutations in metA, encoding homoserine trans-succinylase (HTS), were detected in each evolved S. enterica methionine cooperator andmore » were shown to be necessary for cooperative consortia growth. Molecular modeling was used to predict that most of the non-synonymous mutations slightly increase the binding affinity for HTS homodimer formation. Despite this genetic parallelism and trend of increasing protein binding stability, these metA alleles gave rise to a wide range of phenotypic diversity in termsof individual versus group benefit. The cooperators with the highest methionine excretion permitted nearly two-fold faster consortia growth and supported the highest fraction of E. coli, yet also had the slowest individual growth rates compared to less cooperative strains. Thus, although the genetic basis of adaptation was quite similar across independent origins of cooperative phenotypes, quantitative measurements of metabolite production were required to predict either the individual-level growth consequences or how these propagate to community-level behavior.« less

Microbial growth under a high-pressure CO2 environment

NASA Astrophysics Data System (ADS)

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

2009-12-01

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

Comparative Demonstration of Active and Semi-Passive In Situ Bioremediation Approaches for Perchlorate Impacted Groundwater: Active In Situ Bioremediation Demonstration (Aerojet Facility)

DTIC Science & Technology

2012-12-01

non-pathogenic microbial consortia that are capable of mediating complete dechlorination of TCE to ethene. For example, the General Electric Company...Piezometric Surface """""" ’"’"’ 16" Normal Resistivity Log Notes: 1. Water levels w:re measured October 2001, except EW-1, EW-2, and RW- 1, wh1ch...Wells by GeoTrans or Kleinfelder. Aerojet utilized various contractors for the installation of piping and electrical controls between the wells

Polymerase Chain Reaction (PCR) Analysis of Microbial Consortia on Wastewater Treatment Processes for High Explosives

DTIC Science & Technology

2009-09-01

Phyluma Raw Sewage GLBR Sp.b Clone (%)c Sp. Clone (%)d Actinobacteria 0 0 2 3.5 Bacteroidetes 6 28.2 7 8.2 Chloroflexi 2 11.3 2 3.5 Firmicutes 7...and 2,4,6-trinitrotoluene (TNT) based on 16S rDNA clone distribution. Phyluma Sp.b Clone (%)c Acidobacteria 1 1.1 Actinobacteria 1 8.7...distribution, established that the culture was enriched in both Actinobacteria and Proteobacteria, suggesting involvement of both phyla in 2,4-DNP degradation

Microbial Methanogenesis In Laboratory Incubations Of Coal: Implications For A Sustainable Energy Resource In Subsurface Coalbeds

NASA Astrophysics Data System (ADS)

Harris, S. H.; Barker, C. E.; Smith, R. L.

2005-12-01

Methane desorbed from subsurface coalseams contributes about 8% of the total natural gas produced in the US. This value is expected to increase over the next several years as a growing proportion of energy demands are supplied from unconventional reservoirs. Isotopic analyses of gas samples from several geographically separate coalbeds indicates a substantial proportion of the sorbed methane is biogenic in origin. Furthermore, previous studies have shown the ability of microbial consortia to degrade coal in aerobic laboratory incubations. These findings suggests the stimulation of microbial methane production in subsurface coals may provide a sustainable source of domestic energy. To address this prospect, we assessed the ability of indigenous microbial populations to produce methane in coal maintained under anaerobic conditions in the laboratory and investigated factors that influenced the rate and extent of the process. Several freshly collected coals of different rank were examined for their ability to support methanogenesis in mineral medium alone or amended with different nutrients such as hydrogen (4 kPa), formate (20 mM), or acetate (25mM). Microbial methane production was distinguished from abiotic desorption by subtracting methane generated in replicate incubations that contained bromoethanesulfonic acid (5 mM), an inhibitor of methanogenesis. The extent and rate of methane production varied among the different coals. A relatively shallow (400 m), immature coal exhibited a rate of 700 nmole CH4*day-1*g coal-1, a value comparable to previous observations of contaminated sediments. Methane production was negligible in a deeper, relatively mature (650 m) coal obtained from the same borehole although the same material exhibited a rate of about 80 nmole CH4*day-1*g coal-1 after a formate amendment. In contrast, hydrogen proved to be ineffective as a methanogenic substrate, although this electron donor was rapidly consumed in coal incubations. A filter-sterilized warm water extract of spent coal renewed methanogenesis in incubations no longer generating methane, suggesting the cessation of methane production was not due to moribund cells or the accumulation of an inhibitory compound, but rather the lack of suitable electron donor. Viable methanogenic consortia were present in most of the coal samples examined in this study and their activity could be enhanced by electron donor amendment, which presumably supports microbial growth. Furthermore, the observation of rapid hydrogen consumption uncoupled from methanogenesis suggests competition exists for this compound. The success of efforts to stimulate methanogenesis in subsurface coalbeds will likely be influenced by the nature of the electron donor.

Tracking microbial interactions with NanoSIMS

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

Musat, Niculina; Musat, Florin; Weber, Peter Kilian

The combination of stable isotope probing (SIP), NanoSIMS imaging and microbe identification via fluorescence in situ hybridization (FISH) is often used to link identity to function at the cellular level in microbial communities. Many opportunities remain for nanoSIP to identify metabolic interactions and nutrient fluxes within syntrophic associations and obligate symbioses where exchanges can be extremely rapid. However, additional data, such as genomic potential, gene expression or other imaging modalities are often critical to deciphering the mechanisms underlying specific interactions, and researchers must keep sample preparation artefacts in mind. Here we focus on recent applications of nanoSIP, particularly where usedmore » to track exchanges of isotopically labelled molecules between organisms. Here, we highlight metabolic interactions within syntrophic consortia, carbon/nitrogen fluxes between phototrophs and their heterotrophic partners, and symbiont–host nutrient sharing.« less

Tracking microbial interactions with NanoSIMS

DOE PAGES

Musat, Niculina; Musat, Florin; Weber, Peter Kilian; ...

2016-07-12

The combination of stable isotope probing (SIP), NanoSIMS imaging and microbe identification via fluorescence in situ hybridization (FISH) is often used to link identity to function at the cellular level in microbial communities. Many opportunities remain for nanoSIP to identify metabolic interactions and nutrient fluxes within syntrophic associations and obligate symbioses where exchanges can be extremely rapid. However, additional data, such as genomic potential, gene expression or other imaging modalities are often critical to deciphering the mechanisms underlying specific interactions, and researchers must keep sample preparation artefacts in mind. Here we focus on recent applications of nanoSIP, particularly where usedmore » to track exchanges of isotopically labelled molecules between organisms. Here, we highlight metabolic interactions within syntrophic consortia, carbon/nitrogen fluxes between phototrophs and their heterotrophic partners, and symbiont–host nutrient sharing.« less

Metaproteome analysis to determine the metabolically active part of a thermophilic microbial community producing biogas from agricultural biomass.

PubMed

Hanreich, Angelika; Heyer, Robert; Benndorf, Dirk; Rapp, Erdmann; Pioch, Markus; Reichl, Udo; Klocke, Michael

2012-07-01

Complex consortia of microorganisms are responsible for biogas production. A lot of information about the taxonomic structure and enzymatic potential of such communities has been collected by a variety of gene-based approaches, yet little is known about which of all the assumable metabolic pathways are active throughout the process of biogas formation. To tackle this problem, we established a protocol for the metaproteomic analysis of samples taken from biogas reactors fed with agricultural biomass. In contrast to previous studies where an anaerobic digester was fed with synthetic wastewater, the complex matrix in this study required the extraction of proteins with liquid phenol and the application of paper bridge loading for 2-dimensional gel electrophoresis. Proteins were subjected to nanoHPLC (high-performance liquid chromatography) coupled to tandem mass spectrometry for characterization. Several housekeeping proteins as well as methanogenesis-related enzymes were identified by a MASCOT search and de novo sequencing, which proved the feasibility of our approach. The establishment of such an approach is the basis for further metaproteomic studies of biogas-producing communities. In particular, the apparent status of metabolic activities within the communities can be monitored. The knowledge collected from such experiments could lead to further improvements of biogas production.

Nanobarium Titanate As Supplement To Accelerate Plastic Waste Biodegradation By Indigenous Bacterial Consortia

NASA Astrophysics Data System (ADS)

Kapri, Anil; Zaidi, M. G. H.; Goel, Reeta

2009-06-01

Plastic waste biodegradation studies have seen several developmental phases from the discovery of potential microbial cultures, inclusion of photo-oxidizable additives into the polymer chain, to the creation of starch-embedded biodegradable plastics. The present study deals with the supplementation of nanobarium titanate (NBT) in the minimal broth in order to alter the growth-profiles of the Low-density polyethylene (LDPE) degrading consortia. The pro-bacterial influence of the nanoparticles could be seen by substantial changes such as shortening of the lag phase and elongation of the exponential as well as stationary growth phases, respectively, which eventually increase the biodegradation efficiency. In-vitro biodegradation studies revealed better dissolution of LDPE in the presence of NBT as compared to control. Significant shifting in λ-max values was observed in the treated samples through UV-Vis spectroscopy, while Fourier transform infrared spectroscopy (FTIR) and simultaneous thermogravimetric-differential thermogravimetry-differential thermal analysis (TG-DTG-DTA) further confirmed the breakage and formation of bonds in the polymer backbone. Therefore, this study suggests the implementation of NBT as nutritional additive for plastic waste management through bacterial growth acceleration.

Microbial anodic consortia fed with fermentable substrates in microbial electrolysis cells: Significance of microbial structures.

PubMed

Flayac, Clément; Trably, Eric; Bernet, Nicolas

2018-05-28

Microbial community structure of anodic biofilms plays a key role in bioelectrochemical systems (BESs). When ecosystems are used as inocula, many bacterial species having interconnected ecological interactions are present. The aim of the present study was to identify these interactions for the conversion of single substrates into electrical current. Dual-chamber reactors were inoculated with activated sludge and fed in batch mode with acetate, lactate, butyrate and propionate at 80 mMe - equivalents in quadruplicate. Analyses of biofilms and planktonic microbial communities showed that the anodic biofilms were mainly dominated by the Geobacter genus (62.4% of the total sequences). At the species level, Geobacter sulfurreducens was dominant in presence of lactate and acetate, while Geobacter toluenoxydans and Geobacter pelophilus were dominant with butyrate and propionate as substrates. These results indicate for the first time a specificity within the Geobacter genus towards the electron donor, suggesting a competitive process for electrode colonization and the implementations of syntrophic interactions for complete oxidation of substrates such as propionate and butyrate. All together, these results provide a new insight into the ecological relationships within electroactive biofilms and suggest eco-engineering perspectives to improve the performances of BESs. Copyright © 2018 Elsevier B.V. All rights reserved.

Effects of uranium concentration on microbial community structure and functional potential.

PubMed

Sutcliffe, Brodie; Chariton, Anthony A; Harford, Andrew J; Hose, Grant C; Greenfield, Paul; Elbourne, Liam D H; Oytam, Yalchin; Stephenson, Sarah; Midgley, David J; Paulsen, Ian T

2017-08-01

Located in the Northern Territory of Australia, Ranger uranium mine is directly adjacent to the UNESCO World Heritage listed Kakadu National Park, with rehabilitation targets needed to ensure the site can be incorporated into the park following the mine's closure in 2026. This study aimed to understand the impact of uranium concentration on microbial communities, in order to identify and describe potential breakpoints in microbial ecosystem services. This is the first study to report in situ deployment of uranium-spiked sediments along a concentration gradient (0-4000 mg U kg -1 ), with the study design maximising the advantages of both field surveys and laboratory manipulative studies. Changes to microbial communities were characterised through the use of amplicon and shotgun metagenomic next-generation sequencing. Significant changes to taxonomic and functional community assembly occurred at a concentration of 1500 mg U kg -1 sediment and above. At uranium concentrations of ≥ 1500 mg U kg -1 , genes associated with methanogenic consortia and processes increased in relative abundance, while numerous significant changes were also seen in the relative abundances of genes involved in nitrogen cycling. Such alterations in carbon and nitrogen cycling pathways suggest that taxonomic and functional changes to microbial communities may result in changes in ecosystem processes and resilience. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology.

PubMed

von Bergen, Martin; Jehmlich, Nico; Taubert, Martin; Vogt, Carsten; Bastida, Felipe; Herbst, Florian-Alexander; Schmidt, Frank; Richnow, Hans-Hermann; Seifert, Jana

2013-10-01

The recent development of metaproteomics has enabled the direct identification and quantification of expressed proteins from microbial communities in situ, without the need for microbial enrichment. This became possible by (1) significant increases in quality and quantity of metagenome data and by improvements of (2) accuracy and (3) sensitivity of modern mass spectrometers (MS). The identification of physiologically relevant enzymes can help to understand the role of specific species within a community or an ecological niche. Beside identification, relative and absolute quantitation is also crucial. We will review label-free and label-based methods of quantitation in MS-based proteome analysis and the contribution of quantitative proteome data to microbial ecology. Additionally, approaches of protein-based stable isotope probing (protein-SIP) for deciphering community structures are reviewed. Information on the species-specific metabolic activity can be obtained when substrates or nutrients are labeled with stable isotopes in a protein-SIP approach. The stable isotopes ((13)C, (15)N, (36)S) are incorporated into proteins and the rate of incorporation can be used for assessing the metabolic activity of the corresponding species. We will focus on the relevance of the metabolic and phylogenetic information retrieved with protein-SIP studies and for detecting and quantifying the carbon flux within microbial consortia. Furthermore, the combination of protein-SIP with established tools in microbial ecology such as other stable isotope probing techniques are discussed.

Cd and proton adsorption onto bacterial consortia grown from industrial wastes and contaminated geologic settings.

PubMed

Borrok, David M; Fein, Jeremy B; Kulpa, Charles F

2004-11-01

To model the effects of bacterial metal adsorption in contaminated environments, results from metal adsorption experiments involving individual pure stains of bacteria must be extrapolated to systems in which potentially dozens of bacterial species are present. This extrapolation may be made easier because bacterial consortia from natural environments appear to exhibit similar metal binding properties. However, bacteria that thrive in highly perturbed contaminated environments may exhibit significantly different adsorptive behavior. Here we measure proton and Cd adsorption onto a range of bacterial consortia grown from heavily contaminated industrial wastes, groundwater, and soils. We model the results using a discrete site surface complexation approach to determine binding constants and site densities for each consortium. The results demonstrate that bacterial consortia from different contaminated environments exhibit a range of total site densities (approximately a 3-fold difference) and Cd-binding constants (approximately a 10-fold difference). These ranges for Cd binding constants may be small enough to suggest that bacteria-metal adsorption in contaminated environments can be described using relatively few "averaged" bacteria-metal binding constants (in conjunction with the necessary binding constants for competing surfaces and ligands). However, if additional precision is necessary, modeling parameters must be developed separately for each contaminated environment of interest.

Biodiversity maintenance in food webs with regulatory environmental feedbacks.

PubMed

Bagdassarian, Carey K; Dunham, Amy E; Brown, Christopher G; Rauscher, Daniel

2007-04-21

Although the food web is one of the most fundamental and oldest concepts in ecology, elucidating the strategies and structures by which natural communities of species persist remains a challenge to empirical and theoretical ecologists. We show that simple regulatory feedbacks between autotrophs and their environment when embedded within complex and realistic food-web models enhance biodiversity. The food webs are generated through the niche-model algorithm and coupled with predator-prey dynamics, with and without environmental feedbacks at the autotroph level. With high probability and especially at lower, more realistic connectance levels, regulatory environmental feedbacks result in fewer species extinctions, that is, in increased species persistence. These same feedback couplings, however, also sensitize food webs to environmental stresses leading to abrupt collapses in biodiversity with increased forcing. Feedback interactions between species and their material environments anchor food-web persistence, adding another dimension to biodiversity conservation. We suggest that the regulatory features of two natural systems, deep-sea tubeworms with their microbial consortia and a soil ecosystem manifesting adaptive homeostatic changes, can be embedded within niche-model food-web dynamics.

Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches.

PubMed

Malla, Muneer A; Dubey, Anamika; Yadav, Shweta; Kumar, Ashwani; Hashem, Abeer; Abd Allah, Elsayed Fathi

2018-01-01

Rapid industrialization and population explosion has resulted in the generation and dumping of various contaminants into the environment. These harmful compounds deteriorate the human health as well as the surrounding environments. Current research aims to harness and enhance the natural ability of different microbes to metabolize these toxic compounds. Microbial-mediated bioremediation offers great potential to reinstate the contaminated environments in an ecologically acceptable approach. However, the lack of the knowledge regarding the factors controlling and regulating the growth, metabolism, and dynamics of diverse microbial communities in the contaminated environments often limits its execution. In recent years the importance of advanced tools such as genomics, proteomics, transcriptomics, metabolomics, and fluxomics has increased to design the strategies to treat these contaminants in ecofriendly manner. Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches in microbial-mediated bioremediation. Additionally, we discussed how the multi-omics approaches help to comprehend and explore the structural and functional aspects of the microbial consortia in response to the different environmental pollutants and presented some success stories by using these approaches.

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

PubMed

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

2016-09-30

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

Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches

PubMed Central

Malla, Muneer A.; Dubey, Anamika; Yadav, Shweta; Kumar, Ashwani; Hashem, Abeer; Abd_Allah, Elsayed Fathi

2018-01-01

Rapid industrialization and population explosion has resulted in the generation and dumping of various contaminants into the environment. These harmful compounds deteriorate the human health as well as the surrounding environments. Current research aims to harness and enhance the natural ability of different microbes to metabolize these toxic compounds. Microbial-mediated bioremediation offers great potential to reinstate the contaminated environments in an ecologically acceptable approach. However, the lack of the knowledge regarding the factors controlling and regulating the growth, metabolism, and dynamics of diverse microbial communities in the contaminated environments often limits its execution. In recent years the importance of advanced tools such as genomics, proteomics, transcriptomics, metabolomics, and fluxomics has increased to design the strategies to treat these contaminants in ecofriendly manner. Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches in microbial-mediated bioremediation. Additionally, we discussed how the multi-omics approaches help to comprehend and explore the structural and functional aspects of the microbial consortia in response to the different environmental pollutants and presented some success stories by using these approaches. PMID:29915565

Deciphering microbial interactions in synthetic human gut microbiome communities.

PubMed

Venturelli, Ophelia S; Carr, Alex C; Fisher, Garth; Hsu, Ryan H; Lau, Rebecca; Bowen, Benjamin P; Hromada, Susan; Northen, Trent; Arkin, Adam P

2018-06-21

The ecological forces that govern the assembly and stability of the human gut microbiota remain unresolved. We developed a generalizable model-guided framework to predict higher-dimensional consortia from time-resolved measurements of lower-order assemblages. This method was employed to decipher microbial interactions in a diverse human gut microbiome synthetic community. We show that pairwise interactions are major drivers of multi-species community dynamics, as opposed to higher-order interactions. The inferred ecological network exhibits a high proportion of negative and frequent positive interactions. Ecological drivers and responsive recipient species were discovered in the network. Our model demonstrated that a prevalent positive and negative interaction topology enables robust coexistence by implementing a negative feedback loop that balances disparities in monospecies fitness levels. We show that negative interactions could generate history-dependent responses of initial species proportions that frequently do not originate from bistability. Measurements of extracellular metabolites illuminated the metabolic capabilities of monospecies and potential molecular basis of microbial interactions. In sum, these methods defined the ecological roles of major human-associated intestinal species and illuminated design principles of microbial communities. © 2018 The Authors. Published under the terms of the CC BY 4.0 license.

[Mycotrophic capacity and efficiency of microbial consortia of arbuscular mycorrhizal fungi native of soils from Buenos Aires province under contrasting management].

PubMed

Thougnon Islas, Andrea J; Eyherabide, Mercedes; Echeverría, Hernán E; Sainz Rozas, Hernán R; Covacevich, Fernanda

2014-01-01

We characterized the infective and sporulation capacities of microbial consortia of arbuscular mycorrhizal fungi (AMF) native of Buenos Aires province (Argentina) and determined if some soil characteristics and mycorrhizal parameters could allow to select potentially beneficial inocula. Soil samples were selected from seven locations in Buenos Aires province all under agricultural (A) and pristine (P) conditions. The AMF were multiplied and mycorrhizal root colonization of trap plants was observed at 10 weeks of growth. Spore number in field was low; however, after multiplication spore density accounted for 80-1175 spores per 100g of soil. The principal component analysis showed that the P and Fe soil contents are the main modulators of infectivity and sporulation capacity. The mycorrhizal potential was determined in three locations, being high in Pristine Lobería and Agricultural Trenque Lauquen and low in Junín. Agricultural Lobería (AL) and Pristine Lobería (PL) inocula were selected and their efficiency was evaluated under controlled conditions. Even though shoot dry matter increases after inoculation was not significant (p>0.05) mycorrhizal response was greater than 40% for tomato and 25% for corn, particularly after inoculation with inocula from the agricultural management. These results could be associated to the incipient development of mycorrhizae in both species. Additional research should be conducted to further develop our findings in order to determine the factors involved in the selection of efficient inocula. Copyright © 2014 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.

Modeling the survival responses of a multi-component biofilm to environmental stress

NASA Astrophysics Data System (ADS)

Carles Brangarí, Albert; Manzoni, Stefano; Sanchez-Vila, Xavier; Fernàndez-Garcia, Daniel

2017-04-01

Biofilms are consortia of microorganisms embedded in self-produced matrices of biopolymers. The survival of such communities depends on their capacity to improve the environmental conditions of their habitat by mitigating, or even benefitting from some adverse external factors. The mechanisms by which the microbial habitat is regulated remain mostly unknown. However, many studies have reported physiological responses to environmental stresses that include the release of extracellular polymeric substances (EPS) and the induction of a dormancy state. A sound understanding of these capacities is required to enhance the knowledge of the microbial dynamics in soils and its potential role in the carbon cycle, with significant implications for the degradation of contaminants and the emission of greenhouse gases, among others. We present a numerical analysis of the dynamics of soil microbes and their responses to environmental stresses. The conceptual model considers a multi-component heterotrophic biofilm made up of active cells, dormant cells, EPS, and extracellular enzymes. Biofilm distribution and properties are defined at the pore-scale and used to determine nutrient availability and water saturation via feedbacks of biofilm on soil hydraulic properties. The pore space micro-habitat is modeled as a simplified pore-network of cylindrical tubes in which biofilms proliferate. Microbial compartments and most of the carbon fluxes are defined at the bulk level. Microbial processes include the synthesis, decay and detachment of biomass, the activation/deactivation of cells, and the release and reutilization of EPS. Results suggest that the release of EPS and the capacity to enter a dormant state offer clear evolutionary advantages in scenarios characterized by environmental stress. On the contrary, when the conditions are favorable, the diversion of carbon into the production of the aforementioned survival mechanisms does not confer any additional benefit and the population of active cells decline. The proposed model (including complex relations between active biomass and biofilm) has been proved useful to capture the most relevant processes involved in biofilm proliferation and its adaptation to environmental conditions. These aspects are largely neglected in biogeochemical models, but could be relevant in soils where strong feedbacks of microbial activity on hydraulic properties emerge.

Rapid Formation of Microbe-Oil Aggregates and Changes in Community Composition in Coastal Surface Water Following Exposure to Oil and the Dispersant Corexit.

PubMed

Doyle, Shawn M; Whitaker, Emily A; De Pascuale, Veronica; Wade, Terry L; Knap, Anthony H; Santschi, Peter H; Quigg, Antonietta; Sylvan, Jason B

2018-01-01

During the Deepwater Horizon (DWH) oil spill, massive quantities of oil were deposited on the seafloor via a large-scale marine oil-snow sedimentation and flocculent accumulation (MOSSFA) event. The role of chemical dispersants (e.g., Corexit) applied during the DWH oil spill clean-up in helping or hindering the formation of this MOSSFA event are not well-understood. Here, we present the first experiment related to the DWH oil spill to specifically investigate the relationship between microbial community structure, oil and Corexit®, and marine oil-snow in coastal surface waters. We observed the formation of micron-scale aggregates of microbial cells around droplets of oil and dispersant and found that their rate of formation was directly related to the concentration of oil within the water column. These micro-aggregates are potentially important precursors to the formation of larger marine oil-snow particles. Therefore, our observation that Corexit® significantly enhanced their formation suggests dispersant application may play a role in the development of MOSSFA events. We also observed that microbial communities in marine surface waters respond to oil and oil plus Corexit® differently and much more rapidly than previously measured, with major shifts in community composition occurring within only a few hours of experiment initiation. In the oil-amended treatments without Corexit®, this manifested as an increase in community diversity due to the outgrowth of several putative aliphatic- and aromatic-hydrocarbon degrading genera, including phytoplankton-associated taxa. In contrast, microbial community diversity was reduced in mesocosms containing chemically dispersed oil. Importantly, different consortia of hydrocarbon degrading bacteria responded to oil and chemically dispersed oil, indicating that functional redundancy in the pre-spill community likely results in hydrocarbon consumption in both undispersed and dispersed oils, but by different bacterial taxa. Taken together, these data improve our understanding of how dispersants influence the degradation and transport of oil in marine surface waters following an oil spill and provide valuable insight into the early response of complex microbial communities to oil exposure.

Rapid Formation of Microbe-Oil Aggregates and Changes in Community Composition in Coastal Surface Water Following Exposure to Oil and the Dispersant Corexit

PubMed Central

Doyle, Shawn M.; Whitaker, Emily A.; De Pascuale, Veronica; Wade, Terry L.; Knap, Anthony H.; Santschi, Peter H.; Quigg, Antonietta; Sylvan, Jason B.

2018-01-01

During the Deepwater Horizon (DWH) oil spill, massive quantities of oil were deposited on the seafloor via a large-scale marine oil-snow sedimentation and flocculent accumulation (MOSSFA) event. The role of chemical dispersants (e.g., Corexit) applied during the DWH oil spill clean-up in helping or hindering the formation of this MOSSFA event are not well-understood. Here, we present the first experiment related to the DWH oil spill to specifically investigate the relationship between microbial community structure, oil and Corexit®, and marine oil-snow in coastal surface waters. We observed the formation of micron-scale aggregates of microbial cells around droplets of oil and dispersant and found that their rate of formation was directly related to the concentration of oil within the water column. These micro-aggregates are potentially important precursors to the formation of larger marine oil-snow particles. Therefore, our observation that Corexit® significantly enhanced their formation suggests dispersant application may play a role in the development of MOSSFA events. We also observed that microbial communities in marine surface waters respond to oil and oil plus Corexit® differently and much more rapidly than previously measured, with major shifts in community composition occurring within only a few hours of experiment initiation. In the oil-amended treatments without Corexit®, this manifested as an increase in community diversity due to the outgrowth of several putative aliphatic- and aromatic-hydrocarbon degrading genera, including phytoplankton-associated taxa. In contrast, microbial community diversity was reduced in mesocosms containing chemically dispersed oil. Importantly, different consortia of hydrocarbon degrading bacteria responded to oil and chemically dispersed oil, indicating that functional redundancy in the pre-spill community likely results in hydrocarbon consumption in both undispersed and dispersed oils, but by different bacterial taxa. Taken together, these data improve our understanding of how dispersants influence the degradation and transport of oil in marine surface waters following an oil spill and provide valuable insight into the early response of complex microbial communities to oil exposure. PMID:29696005

Worldwide exploration of the microbiome harbored by the cnidarian model, Exaiptasia pallida (Agassiz in Verrill, 1864) indicates a lack of bacterial association specificity at a lower taxonomic rank

PubMed Central

Brown, Tanya; Otero, Christopher; Grajales, Alejandro; Rodriguez, Estefania

2017-01-01

Examination of host-microbe interactions in early diverging metazoans, such as cnidarians, is of great interest from an evolutionary perspective to understand how host-microbial consortia have evolved. To address this problem, we analyzed whether the bacterial community associated with the cosmopolitan and model sea anemone Exaiptasia pallida shows specific patterns across worldwide populations ranging from the Caribbean Sea, and the Atlantic and Pacific oceans. By comparing sequences of the V1–V3 hypervariable regions of the bacterial 16S rRNA gene, we revealed that anemones host a complex and diverse microbial community. When examined at the phylum level, bacterial diversity and abundance associated with E. pallida are broadly conserved across geographic space with samples, containing largely Proteobacteria and Bacteroides. However, the species-level makeup within these phyla differs drastically across space suggesting a high-level core microbiome with local adaptation of the constituents. Indeed, no bacterial OTU was ubiquitously found in all anemones samples. We also revealed changes in the microbial community structure after rearing anemone specimens in captivity within a period of four months. Furthermore, the variation in bacterial community assemblages across geographical locations did not correlate with the composition of microalgal Symbiodinium symbionts. Our findings contrast with the postulation that cnidarian hosts might actively select and maintain species-specific microbial communities that could have resulted from an intimate co-evolution process. The fact that E. pallida is likely an introduced species in most sampled localities suggests that this microbial turnover is a relatively rapid process. Our findings suggest that environmental settings, not host specificity, seem to dictate bacterial community structure associated with this sea anemone. More than maintaining a specific composition of bacterial species some cnidarians associate with a wide range of bacterial species as long as they provide the same physiological benefits towards the maintenance of a healthy host. The examination of the previously uncharacterized bacterial community associated with the cnidarian sea anemone model E. pallida is the first global-scale study of its kind. PMID:28533949

The effects of group size and group economic factors on collaboration: a study of the financial performance of rural hospitals in consortia.

PubMed

Chan, B; Feldman, R; Manning, W G

1999-04-01

To determine factors that distinguish effective rural hospital consortia from ineffective ones in terms of their ability to improve members' financial performance. Two questions in particular were addressed: (1) Do large consortia have a greater collective impact on their members? (2) Does a consortium's economic environment determine the degree of collective impact on members? Based on the hospital survey conducted during February 1992 by the Robert Wood Johnson Hospital-Based Rural Health Care project of rural hospital consortia. The survey data were augmented with data from Medicare Cost Reports (1985-1991), AHA Annual Surveys (1985-1991), and other secondary data. Dependent variables were total operating profit, cost per adjusted admission, and revenue per adjusted admission. Control variables included degree of group formalization, degree of inequality of resources among members (group asymmetry), affiliation with other consortium group(s), individual economic environment, common hospital characteristics (bed size, ownership type, system affiliation, case mix, etc.), year (1985-1991), and census region dummies. All dependent variables have a curvilinear association with group size. The optimum group size is somewhere in the neighborhood of 45. This reveals the benefits of collective action (i.e., scale economies and/or synergy effects) and the issue of complexity as group size increases. Across analyses, no strong evidence exists of group economic environment impacts, and the environmental influences come mainly from the local economy rather than from the group economy. There may be some success stories of collaboration among hospitals in consortia, and consortium effects vary across different collaborations. When studying consortia, it makes sense to develop a typology of groups based on some performance indicators. The results of this study imply that government, rural communities, and consortium staff and steering committees should forge the consortium concept by expanding membership in order to gain greater financial benefits for individual hospitals.

Saliva and dental plaque.

PubMed

Rudney, J D

2000-12-01

Dental plaque is being redefined as oral biofilm. Diverse overlapping microbial consortia are present on all oral tissues. Biofilms are structured, displaying features like channels and projections. Constituent species switch back and forth between sessile and planktonic phases. Saliva is the medium for planktonic suspension. Several major functions can be defined for saliva in relation to oral biofilm. It serves as a medium for transporting planktonic bacteria within and between mouths. Bacteria in transit may be vulnerable to negative selection. Salivary agglutinins may prevent reattachment to surfaces. Killing by antimicrobial proteins may lead to attachment of dead cells. Salivary proteins form conditioning films on all oral surfaces. This contributes to positive selection for microbial adherence. Saliva carries chemical messengers which allow live adherent cells to sense a critical density of conspecifics. Growth begins, and thick biofilms may become resistant to antimicrobial substances. Salivary macromolecules may be catabolized, but salivary flow also may clear dietary substrates. Salivary proteins act in ways that benefit both host and microbe. All have multiple functions, and many do the same job. They form heterotypic complexes, which may exist in large micelle-like structures. These issues make it useful to compare subjects whose saliva functions differently. We have developed a simultaneous assay for aggregation, killing, live adherence, and dead adherence of oral species. Screening of 149 subjects has defined high killing/low adherence, low killing/high adherence, high killing/high adherence, and low killing/low adherence groups. These will be evaluated for differences in their flora.

Quantifying Microbial Utilization of Petroleum Hydrocarbons in Salt Marsh Sediments by Using the 13C Content of Bacterial rRNA▿

PubMed Central

Pearson, Ann; Kraunz, Kimberly S.; Sessions, Alex L.; Dekas, Anne E.; Leavitt, William D.; Edwards, Katrina J.

2008-01-01

Natural remediation of oil spills is catalyzed by complex microbial consortia. Here we took a whole-community approach to investigate bacterial incorporation of petroleum hydrocarbons from a simulated oil spill. We utilized the natural difference in carbon isotopic abundance between a salt marsh ecosystem supported by the 13C-enriched C4 grass Spartina alterniflora and 13C-depleted petroleum to monitor changes in the 13C content of biomass. Magnetic bead capture methods for selective recovery of bacterial RNA were used to monitor the 13C content of bacterial biomass during a 2-week experiment. The data show that by the end of the experiment, up to 26% of bacterial biomass was derived from consumption of the freshly spilled oil. The results contrast with the inertness of a nearby relict spill, which occurred in 1969 in West Falmouth, MA. Sequences of 16S rRNA genes from our experimental samples also were consistent with previous reports suggesting the importance of Gamma- and Deltaproteobacteria and Firmicutes in the remineralization of hydrocarbons. The magnetic bead capture approach makes it possible to quantify uptake of petroleum hydrocarbons by microbes in situ. Although employed here at the domain level, RNA capture procedures can be highly specific. The same strategy could be used with genus-level specificity, something which is not currently possible using the 13C content of biomarker lipids. PMID:18083852

Sensitive and substrate-specific detection of metabolically active microorganisms in natural microbial consortia using community isotope arrays.

PubMed

Tourlousse, Dieter M; Kurisu, Futoshi; Tobino, Tomohiro; Furumai, Hiroaki

2013-05-01

The goal of this study was to develop and validate a novel fosmid-clone-based metagenome isotope array approach - termed the community isotope array (CIArray) - for sensitive detection and identification of microorganisms assimilating a radiolabeled substrate within complex microbial communities. More specifically, a sample-specific CIArray was used to identify anoxic phenol-degrading microorganisms in activated sludge treating synthetic coke-oven wastewater in a single-sludge predenitrification-nitrification process. Hybridization of the CIArray with DNA from the (14) C-phenol-amended sample indicated that bacteria assimilating (14) C-atoms, presumably directly from phenol, under nitrate-reducing conditions were abundant in the reactor, and taxonomic assignment of the fosmid clone end sequences suggested that they belonged to the Gammaproteobacteria. The specificity of the CIArray was validated by quantification of fosmid-clone-specific DNA in density-resolved DNA fractions from samples incubated with (13) C-phenol, which verified that all CIArray-positive probes stemmed from microorganisms that assimilated isotopically labeled carbon. This also demonstrated that the CIArray was more sensitive than DNA-SIP, as the former enabled positive detection at a phenol concentration that failed to yield a 'heavy' DNA fraction. Finally, two operational taxonomic units distantly related to marine Gammaproteobacteria were identified to account for more than half of 16S rRNA gene clones in the 'heavy' DNA library, corroborating the CIArray-based identification. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Molecular and Microscopical Investigation of the Microflora Inhabiting a Deteriorated Italian Manuscript Dated from the Thirteenth Century

PubMed Central

Michaelsen, Astrid; Piñar, Guadalupe

2010-01-01

This case study shows the application of nontraditional diagnostic methods to investigate the microbial consortia inhabiting an ancient manuscript. The manuscript was suspected to be biologically deteriorated and SEM observations showed the presence of fungal spores attached to fibers, but classic culturing methods did not succeed in isolating microbial contaminants. Therefore, molecular methods, including PCR, denaturing gradient gel electrophoresis (DGGE), and clone libraries, were used as a sensitive alternative to conventional cultivation techniques. DGGE fingerprints revealed a high biodiversity of both bacteria and fungi inhabiting the manuscript. DNA sequence analysis confirmed the existence of fungi and bacteria in manuscript samples. A number of fungal clones identified on the manuscript showed similarity to fungal species inhabiting dry or saline environments, suggesting that the manuscript environment selects for osmophilic or xerophilic fungal species. Most of the bacterial sequences retrieved from the manuscript belong to phylotypes with cellulolytic activities. PMID:20449583

Formulation of bacterial consortium as whole cell biocatalyst for degradation of oil compounds

NASA Astrophysics Data System (ADS)

Yetti, Elvi; A'la, Amalia; Luthfiyah, Nailul; Wijaya, Hans; Thontowi, Ahmad; Yopi

2017-11-01

In this research, weaim to investigateformulation of bacterial consortium as whole cell biocatalyst for degradation of oil compounds. We constructed microbial consortium from 4 (four) selected marine oil bacteria to become 15 (twelve) combination culture. Those bacteria were from collection of Laboratory of Biocatalyst and Fermentation, Research Center for Biotechnology, Indonesian Institutes of Sciences and designated as Labrenzia sp. MBTDCMFRIMab26, Labrenzia aggregata strasin HQB397, Novosphingobium pentaromativorans strain PQ-3 16S, and Novosphingobium pentaromativorans strain US6-1. The mixture or bacteria consortia, denoted as F1, F2, …F15 consisted of 1, 2, 3 and 4 bacterial strains, respectively. The strains were selected based on the criteria that they were able to display good growth in crude oil containing media. Five bacterialformulationsshowed good potentialas candidates for microbial consortium. We will optimize these consortium with carrier matrix choosed from biomass materials and also carry out oil content analysis.

Construction and Screening of Marine Metagenomic Large Insert Libraries.

PubMed

Weiland-Bräuer, Nancy; Langfeldt, Daniela; Schmitz, Ruth A

2017-01-01

The marine environment covers more than 70 % of the world's surface. Marine microbial communities are highly diverse and have evolved during extended evolutionary processes of physiological adaptations under the influence of a variety of ecological conditions and selection pressures. They harbor an enormous diversity of microbes with still unknown and probably new physiological characteristics. In the past, marine microbes, mostly bacteria of microbial consortia attached to marine tissues of multicellular organisms, have proven to be a rich source of highly potent bioactive compounds, which represent a considerable number of drug candidates. However, to date, the biodiversity of marine microbes and the versatility of their bioactive compounds and metabolites have not been fully explored. This chapter describes sampling in the marine environment, construction of metagenomic large insert libraries from marine habitats, and exemplarily one function based screen of metagenomic clones for identification of quorum quenching activities.

Biodiesel production from microbial granules in sequencing batch reactor.

PubMed

Liu, Lin; Hong, Yuling; Ye, Xin; Wei, Lili; Liao, Jie; Huang, Xu; Liu, Chaoxiang

2018-02-01

Effect of reaction variables of in situ transesterification on the biodiesel production, and the characteristic differences of biodiesel obtained from aerobic granular sludge (AG) and algae-bacteria granular consortia (AAG) were investigated. The results indicated that the effect of variables on the biodiesel yield decreased in the order of methanol quantity > catalyst concentration > reaction time, yet the parameters change will not significantly affect biodiesel properties. The maximum biodiesel yield of AAG was 66.21 ± 1.08 mg/g SS, what is significant higher than that of AG (35.44 ± 0.92 mg/g SS). Although methyl palmitate was the dominated composition of biodiesel obtained from both granules, poly-unsaturated fatty acid in the AAG showed a higher percentage (21.86%) than AG (1.2%) due to Scenedesmus addition. Further, microbial analysis confirmed that the composition of biodiesel obtained from microbial granules was also determined by bacterial community, and Xanthomonadaceae and Rhodobacteraceae were the dominant bacteria of AG and AAG, respectively. Copyright © 2017 Elsevier Ltd. All rights reserved.

Archaeal and bacterial diversity in two hot spring microbial mats from a geothermal region in Romania.

PubMed

Coman, Cristian; Drugă, Bogdan; Hegedus, Adriana; Sicora, Cosmin; Dragoş, Nicolae

2013-05-01

The diversity of archaea and bacteria was investigated in two slightly alkaline, mesophilic hot springs from the Western Plain of Romania. Phylogenetic analysis showed a low diversity of Archaea, only three Euryarchaeota taxa being detected: Methanomethylovorans thermophila, Methanomassiliicoccus luminyensis and Methanococcus aeolicus. Twelve major bacterial groups were identified, both springs being dominated by Cyanobacteria, Chloroflexi and Proteobacteria. While at the phylum/class-level the microbial mats share a similar biodiversity; at the species level the geothermal springs investigated seem to be colonized by specific consortia. The dominant taxa were filamentous heterocyst-containing Fischerella, at 45 °C and non-heterocyst Leptolyngbya and Geitlerinema, at 55 °C. Other bacterial taxa (Thauera sp., Methyloversatilis universalis, Pannonibacter phragmitetus, Polymorphum gilvum, Metallibacterium sp. and Spartobacteria) were observed for the first time in association with a geothermal habitat. Based on their bacterial diversity the two mats were clustered together with other similar habitats from Europe and part of Asia, most likely the water temperature playing a major role in the formation of specific microbial communities that colonize the investigated thermal springs.

Comparative metagenomics reveals different hydrocarbon degradative abilities from enriched oil-drilling waste.

PubMed

Napp, Amanda P; Pereira, José Evandro S; Oliveira, Jorge S; Silva-Portela, Rita C B; Agnez-Lima, Lucymara F; Peralba, Maria C R; Bento, Fátima M; Passaglia, Luciane M P; Thompson, Claudia E; Vainstein, Marilene H

2018-06-11

The oil drilling process generates large volumes of waste with inadequate treatments. Here, oil drilling waste (ODW) microbial communities demonstrate different hydrocarbon degradative abilities when exposed to distinct nutrient enrichments as revealed by comparative metagenomics. The ODW was enriched in Luria Broth (LBE) and Potato Dextrose (PDE) media to examine the structure and functional variations of microbial consortia. Two metagenomes were sequenced on Ion Torrent platform and analyzed using MG-RAST. The STAMP software was used to analyze statistically significant differences amongst different attributes of metagenomes. The microbial diversity presented in the different enrichments was distinct and heterogeneous. The metabolic pathways and enzymes were mainly related to the aerobic hydrocarbons degradation. Moreover, our results showed efficient biodegradation after 15 days of treatment for aliphatic hydrocarbons (C8-C33) and polycyclic aromatic hydrocarbons (PAHs), with a total of about 50.5% and 46.4% for LBE and 44.6% and 37.9% for PDE, respectively. The results obtained suggest the idea that the enzymatic apparatus have the potential to degrade petroleum compounds. Copyright © 2018 Elsevier Ltd. All rights reserved.

DEVELOPMENT OF AN ENVIRONMENTALLY BENIGN MICROBIAL INHIBITOR TO CONTROL INTERNAL PIPELINE CORROSION

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

Kristine L. Lowe; Bill W. Bogan; Wendy R. Sullivan

2004-07-30

The overall program objective is to develop and evaluate environmentally benign agents or products that are effective in the prevention, inhibition, and mitigation of microbially influenced corrosion (MIC) in the internal surfaces of metallic natural gas pipelines. The goal is to develop one or more environmentally benign (a.k.a. ''green'') products that can be applied to maintain the structure and dependability of the natural gas infrastructure. Previous testing indicated that the growth, and the metal corrosion caused by pure cultures of sulfate reducing bacteria were inhibited by hexane extracts of some pepper plants. This quarter tests were performed with mixed bacterialmore » cultures obtained from natural gas pipelines. Treatment with the pepper extracts affected the growth and metabolic activity of the microbial consortia. Specifically, the growth and metabolism of sulfate reducing bacteria was inhibited. The demonstration that pepper extracts can inhibit the growth and metabolism of sulfate reducing bacteria in mixed cultures is a significant observation validating a key hypothesis of the project. Future tests to determine the effects of pepper extracts on mature/established biofilms will be performed next.« less

Biogeographical distribution analysis of hydrocarbon degrading and biosurfactant producing genes suggests that near-equatorial biomes have higher abundance of genes with potential for bioremediation.

PubMed

Oliveira, Jorge S; Araújo, Wydemberg J; Figueiredo, Ricardo M; Silva-Portela, Rita C B; de Brito Guerra, Alaine; da Silva Araújo, Sinara Carla; Minnicelli, Carolina; Carlos, Aline Cardoso; de Vasconcelos, Ana Tereza Ribeiro; Freitas, Ana Teresa; Agnez-Lima, Lucymara F

2017-07-27

Bacterial and Archaeal communities have a complex, symbiotic role in crude oil bioremediation. Their biosurfactants and degradation enzymes have been in the spotlight, mainly due to the awareness of ecosystem pollution caused by crude oil accidents and their use. Initially, the scientific community studied the role of individual microbial species by characterizing and optimizing their biosurfactant and oil degradation genes, studying their individual distribution. However, with the advances in genomics, in particular with the use of New-Generation-Sequencing and Metagenomics, it is now possible to have a macro view of the complex pathways related to the symbiotic degradation of hydrocarbons and surfactant production. It is now possible, although more challenging, to obtain the DNA information of an entire microbial community before automatically characterizing it. By characterizing and understanding the interconnected role of microorganisms and the role of degradation and biosurfactant genes in an ecosystem, it becomes possible to develop new biotechnological approaches for bioremediation use. This paper analyzes 46 different metagenome samples, spanning 20 biomes from different geographies obtained from different research projects. A metagenomics bioinformatics pipeline, focused on the biodegradation and biosurfactant-production pathways, genes and organisms, was applied. Our main results show that: (1) surfactation and degradation are correlated events, and therefore should be studied together; (2) terrestrial biomes present more degradation genes, especially cyclic compounds, and less surfactation genes, when compared to water biomes; and (3) latitude has a significant influence on the diversity of genes involved in biodegradation and biosurfactant production. This suggests that microbiomes found near the equator are richer in genes that have a role in these processes and thus have a higher biotechnological potential. In this work we have focused on the biogeographical distribution of hydrocarbon degrading and biosurfactant producing genes. Our principle results can be seen as an important step forward in the application of bioremediation techniques, by considering the biostimulation, optimization or manipulation of a starting microbial consortia from the areas with higher degradation and biosurfactant producing genetic diversity.

Ceramic Proppant Design for In-situ Microbially Enhanced Methane Recovery

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

Sparks, Taylor D.; Mclennan, John; Fuertez, John

This project designed a new type of multi-functional lightweight proppant. The proppant is utilized as the conventional lightweight proppant but also transports microorganisms to coalbed reservoirs. The proppant is coated with a polymer which protects the methanogenic microorganisms and serves as a time-release delivery for methane generation. To produce the multifunctional proppant, we assigned five tasks: 1) culturing methanogenic microbes from natural carbon sources; 2) identifying optimized growth and methanogenesis conditions for the microbial consortia; 3) synthesizing the lightweight ceramic proppant; 4) encapsulating the consortia and proppant; and 5) demonstrating lab scale simulated performance by monitoring in-situ methane generation andmore » hydraulic conductivity. Task 1) To evaluate the feasibility of ex-situ cultivation, natural microbial populations were collected from various hydrocarbon-rich environments and locations characterized by natural methanogenesis. Different rank coals, complex hydrocarbon sources, hydrocarbon seeps, and natural biogenic environments were incorporated in the sampling. Three levels of screening allowed selection of microbial populations, favorable nutrient amendments, sources of the microbial community, and quantification of methane produced from various coal types. Incubation periods of up to 24 weeks were evaluated at 23°C. Headspace concentrations of CH 4 and CO 2 were analyzed by gas chromatography. After a two-week incubation period of the most promising microbes, generated headspace gas concentrations reached 873,400 ppm for methane and 176,370 ppm for carbon dioxide. Task 2) A central composite design (CCD) was used to explore a broad range of operational conditions, examine the effects of the important environmental factors, such as temperature, pH and salt concentration, and query a feasible region of operation to maximize methane production from coal. Coal biogasification was optimal for this consortium at an initial pH value of 5.5, at 30 °C, and at a NaCl concentration 3.7 mg/cm 3 (i.e., 145,165 ppm). Task 3) To create the lightweight ceramic proppant, the kaolinite and iron oxide (Fe 2O 3) mixture were sintered under reducing atmosphere varying partial pressures of oxygen from 1.7×10 -13 atm to 1.8×10-11 atm. The Fe 2O 3 reduces to FeO and reacts with kaolinite decomposed to mullite to form Fe 2SiO 4, FeSiO 3, and FeAl 2O 4. As a result the proppant develops large pores (~100 µm), giving it a low bulk density (1.43 g/cm 3), and high porosity (45.2 vol%) at P_(O_2 )of 1.8×10 -11 atm. The proppant sintered at P_(O_2 )of 1.7×10 -13 atm is characterized by smaller pores (26 µm), higher density (1.72 g/cm3) and lower porosity (37.5 vol%). Crush resistance testing at 9,000 psi yields 6.8 wt% fine particles increasing to 17.7 wt% in porous samples. Acid solubility varies from 5.5 wt% loss increasing to 12.9 wt% in porous samples. Task 4 and 5) The microbial consortia obtained from the optimized condition and lightweight proppant were encapsulated by calcium-alginate polymer. The encapsulation system, including microbes and a proppant, was stored at 20°C and 36°C. The sample stored at 36°C generated 7.1×[10] 3 ppm of methane at 670 h, whereas the sample incubated at 20°C generated 1.1×[10] 3 ppm of methane. Benchtop lab-scale bioreactors were constructed and showed with real-time measurements that, as the microbes produced methane, the pH decreased, and hydrogen and carbon dioxide gases were consumed. A calcium ion-selective sensor revealed the release mechanism of the microbes from encapsulation. The calcium ions interconnecting the alginate monomers were disassociated by counter cations such as protons and potassium ions. The counter cations bound to the carboxyl group on the alginate monomer, which thus lost its ionic interactions with the calcium ions, resulting in decomposition of the hydrogel structure. Furthermore, the conductivity was increased to ~700 mD-ft from ~530 mD-ft once the encapsulated sample was applied to the coal pack. The particle size of coal was reduced when the encapsulated sample was added to the coal. The reduced coal size implied that the microbes would consume the hydrocarbon in coal.« less

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

Karpinets, Tatiana V; Pelletier, Dale A; Pan, Chongle

Understanding of cellular processes involved in the anaerobic degradation of complex organic compounds by microorganisms is crucial for development of innovative biotechnologies for bioethanol production and for efficient degradation of toxic organic compounds. In natural environment the degradation is usually accomplished by syntrophic consortia comprised of different bacterial species. Here we show that the metabolically versatile phototrophic bacterium Rhodopseudomonas palustris may form its own syntrophic consortia, when it grows anaerobically on p-coumarate or benzoate as a sole carbon source. In the study we reveal the consortia from a comparison of large-scale measurements of mRNA and protein expressions under p-coumarate andmore » benzoate degrading conditions using a novel computational approach referred as phenotype fingerprinting. In this approach marker genes for known R. palustris phenotypes are employed to calculate their expression from the gene and protein expressions in each studied condition. Subpopulations of the consortia are inferred from the expression of phenotypes and known metabolic modes of the R. palustris growth. We find that p-coumarate degrading condition leads to at least three R. palustris subpopulations utilizing p-coumarate, benzoate, and CO2 and H2. Benzoate degrading condition also produces at least three subpopulations utilizing benzoate, CO2 and H2, and N2 and formate. Communication among syntrophs and inter-syntrophic dynamics in each consortium are indicated by up-regulation of transporters and genes involved in the curli formation and chemotaxis. The photoautotrphic subpopulation found in both consortia is characterized by activation of two cbb operons and the uptake hydrogenase system. A specificity of N2-fixing subpopulation in the benzoate degrading consortium is the preferential activation of the vanadium nitrogenase over the molybdenum nitrogenase. The N2-fixing subpopulation in the consortium is confirmed by consumption of dissolved nitrogen gas under the benzoate degrading conditions.« less

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.

Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River

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

Brown, Bonnie L.; LePrell, Rebecca V.; Franklin, Rima B.

Knowledge of the diversity and ecological function of the microbial consortia of James River in Virginia, USA, is essential to developing a more complete understanding of the ecology of this model river system. Metagenomic analysis of James River's planktonic microbial community was performed for the first time using an unamplified genomic library and a 16S rDNA amplicon library prepared and sequenced by Ion PGM and MiSeq, respectively. From the 0.46-Gb WGS library (GenBank:SRR1146621; MG-RAST:4532156.3), 4 x 10 6 reads revealed >3 x 10 6 genes, 240 families of prokaryotes, and 155 families of eukaryotes. From the 0.68-Gb 16S library (GenBank:SRR2124995;more » MG-RAST:4631271.3; EMB:2184), 4 x 10 6 reads revealed 259 families of eubacteria. Results of the WGS and 16S analyses were highly consistent and indicated that more than half of the bacterial sequences were Proteobacteria, predominantly Comamonadaceae. The most numerous genera in this group were Acidovorax (including iron oxidizers, nitrotolulene degraders, and plant pathogens), which accounted for 10 % of assigned bacterial reads. Polaromonas were another 6 % of all bacterial reads, with many assignments to groups capable of degrading polycyclic aromatic hydrocarbons. Albidiferax (iron reducers) and Variovorax (biodegraders of a variety of natural biogenic compounds as well as anthropogenic contaminants such as polycyclic aromatic hydrocarbons and endocrine disruptors) each accounted for an additional 3% of bacterial reads. Comparison of these data to other publically-available aquatic metagenomes revealed that this stretch of James River is highly similar to the upper Mississippi River, and that these river systems are more similar to aquaculture and sludge ecosystems than they are to lakes or to a pristine section of the upper Amazon River. Altogether, these analyses exposed previously unknown aspects of microbial biodiversity, documented the ecological responses of microbes to urban effects, and revealed the noteworthy presence of 22 human-pathogenic bacterial genera (e.g., Enterobacteriaceae, pathogenic Pseudomonadaceae, and ‘Vibrionales') and 6 pathogenic eukaryotic genera (e.g., Trypanosomatidae and Vahlkampfiidae). This information about pathogen diversity may be used to promote human epidemiological studies, enhance existing water quality monitoring efforts, and increase awareness of the possible health risks associated with recreational use of James River.« less

Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River

DOE PAGES

Brown, Bonnie L.; LePrell, Rebecca V.; Franklin, Rima B.; ...

2015-09-19

Knowledge of the diversity and ecological function of the microbial consortia of James River in Virginia, USA, is essential to developing a more complete understanding of the ecology of this model river system. Metagenomic analysis of James River's planktonic microbial community was performed for the first time using an unamplified genomic library and a 16S rDNA amplicon library prepared and sequenced by Ion PGM and MiSeq, respectively. From the 0.46-Gb WGS library (GenBank:SRR1146621; MG-RAST:4532156.3), 4 x 10 6 reads revealed >3 x 10 6 genes, 240 families of prokaryotes, and 155 families of eukaryotes. From the 0.68-Gb 16S library (GenBank:SRR2124995;more » MG-RAST:4631271.3; EMB:2184), 4 x 10 6 reads revealed 259 families of eubacteria. Results of the WGS and 16S analyses were highly consistent and indicated that more than half of the bacterial sequences were Proteobacteria, predominantly Comamonadaceae. The most numerous genera in this group were Acidovorax (including iron oxidizers, nitrotolulene degraders, and plant pathogens), which accounted for 10 % of assigned bacterial reads. Polaromonas were another 6 % of all bacterial reads, with many assignments to groups capable of degrading polycyclic aromatic hydrocarbons. Albidiferax (iron reducers) and Variovorax (biodegraders of a variety of natural biogenic compounds as well as anthropogenic contaminants such as polycyclic aromatic hydrocarbons and endocrine disruptors) each accounted for an additional 3% of bacterial reads. Comparison of these data to other publically-available aquatic metagenomes revealed that this stretch of James River is highly similar to the upper Mississippi River, and that these river systems are more similar to aquaculture and sludge ecosystems than they are to lakes or to a pristine section of the upper Amazon River. Altogether, these analyses exposed previously unknown aspects of microbial biodiversity, documented the ecological responses of microbes to urban effects, and revealed the noteworthy presence of 22 human-pathogenic bacterial genera (e.g., Enterobacteriaceae, pathogenic Pseudomonadaceae, and ‘Vibrionales') and 6 pathogenic eukaryotic genera (e.g., Trypanosomatidae and Vahlkampfiidae). This information about pathogen diversity may be used to promote human epidemiological studies, enhance existing water quality monitoring efforts, and increase awareness of the possible health risks associated with recreational use of James River.« less

Programmable removal of bacterial strains by use of genome-targeting CRISPR-Cas systems.

PubMed

Gomaa, Ahmed A; Klumpe, Heidi E; Luo, Michelle L; Selle, Kurt; Barrangou, Rodolphe; Beisel, Chase L

2014-01-28

CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems in bacteria and archaea employ CRISPR RNAs to specifically recognize the complementary DNA of foreign invaders, leading to sequence-specific cleavage or degradation of the target DNA. Recent work has shown that the accidental or intentional targeting of the bacterial genome is cytotoxic and can lead to cell death. Here, we have demonstrated that genome targeting with CRISPR-Cas systems can be employed for the sequence-specific and titratable removal of individual bacterial strains and species. Using the type I-E CRISPR-Cas system in Escherichia coli as a model, we found that this effect could be elicited using native or imported systems and was similarly potent regardless of the genomic location, strand, or transcriptional activity of the target sequence. Furthermore, the specificity of targeting with CRISPR RNAs could readily distinguish between even highly similar strains in pure or mixed cultures. Finally, varying the collection of delivered CRISPR RNAs could quantitatively control the relative number of individual strains within a mixed culture. Critically, the observed selectivity and programmability of bacterial removal would be virtually impossible with traditional antibiotics, bacteriophages, selectable markers, or tailored growth conditions. Once delivery challenges are addressed, we envision that this approach could offer a novel means to quantitatively control the composition of environmental and industrial microbial consortia and may open new avenues for the development of "smart" antibiotics that circumvent multidrug resistance and differentiate between pathogenic and beneficial microorganisms. Controlling the composition of microbial populations is a critical aspect in medicine, biotechnology, and environmental cycles. While different antimicrobial strategies, such as antibiotics, antimicrobial peptides, and lytic bacteriophages, offer partial solutions, what remains elusive is a generalized and programmable strategy that can distinguish between even closely related microorganisms and that allows for fine control over the composition of a microbial population. This study demonstrates that RNA-directed immune systems in bacteria and archaea called CRISPR-Cas systems can provide such a strategy. These systems can be employed to selectively and quantitatively remove individual bacterial strains based purely on sequence information, creating opportunities in the treatment of multidrug-resistant infections, the control of industrial fermentations, and the study of microbial consortia.

Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River.

PubMed

Brown, Bonnie L; LePrell, Rebecca V; Franklin, Rima B; Rivera, Maria C; Cabral, Francine M; Eaves, Hugh L; Gardiakos, Vicki; Keegan, Kevin P; King, Timothy L

2015-01-01

Knowledge of the diversity and ecological function of the microbial consortia of James River in Virginia, USA, is essential to developing a more complete understanding of the ecology of this model river system. Metagenomic analysis of James River's planktonic microbial community was performed for the first time using an unamplified genomic library and a 16S rDNA amplicon library prepared and sequenced by Ion PGM and MiSeq, respectively. From the 0.46-Gb WGS library (GenBank:SRR1146621; MG-RAST:4532156.3), 4 × 10(6) reads revealed >3 × 10(6) genes, 240 families of prokaryotes, and 155 families of eukaryotes. From the 0.68-Gb 16S library (GenBank:SRR2124995; MG-RAST:4631271.3; EMB:2184), 4 × 10(6) reads revealed 259 families of eubacteria. Results of the WGS and 16S analyses were highly consistent and indicated that more than half of the bacterial sequences were Proteobacteria, predominantly Comamonadaceae. The most numerous genera in this group were Acidovorax (including iron oxidizers, nitrotolulene degraders, and plant pathogens), which accounted for 10 % of assigned bacterial reads. Polaromonas were another 6 % of all bacterial reads, with many assignments to groups capable of degrading polycyclic aromatic hydrocarbons. Albidiferax (iron reducers) and Variovorax (biodegraders of a variety of natural biogenic compounds as well as anthropogenic contaminants such as polycyclic aromatic hydrocarbons and endocrine disruptors) each accounted for an additional 3 % of bacterial reads. Comparison of these data to other publically-available aquatic metagenomes revealed that this stretch of James River is highly similar to the upper Mississippi River, and that these river systems are more similar to aquaculture and sludge ecosystems than they are to lakes or to a pristine section of the upper Amazon River. Taken together, these analyses exposed previously unknown aspects of microbial biodiversity, documented the ecological responses of microbes to urban effects, and revealed the noteworthy presence of 22 human-pathogenic bacterial genera (e.g., Enterobacteriaceae, pathogenic Pseudomonadaceae, and 'Vibrionales') and 6 pathogenic eukaryotic genera (e.g., Trypanosomatidae and Vahlkampfiidae). This information about pathogen diversity may be used to promote human epidemiological studies, enhance existing water quality monitoring efforts, and increase awareness of the possible health risks associated with recreational use of James River.

Best Practices in Establishing and Sustaining Consortia in Pharmacy Education

PubMed Central

Hincapie, Ana; Baugh, Gina; Rice, Luke; Sy, Erin; Penm, Jonathan; Albano, Christian

2017-01-01

Objective. To describe best practices, necessary resources, and success or lessons learned from established consortia in pharmacy education. Methods. Using semi-structured interviews and qualitative analysis, interviews with members of established consortia in pharmacy education were conducted until saturation was reached. Themes were analyzed and meaningful descriptions of consortia characteristics were developed using systematic text condensation. Results. Thirteen interviews were conducted. The primary purpose for forming a consortium was identified as threefold: share ideas/best practices; facilitate collaboration; and perform shared problem-solving. For experiential education consortia, two additional purposes were found: share capacity for practice sites, and promote standardization across programs. When investigating best practices for established consortia, three main themes were identified. These included strategies for: (1) relationship building within consortia, (2) successful outcomes of consortia, and (3) sustainability. Successful outcomes included scholarship and, sometimes, program standardization. Sustainability was linked to structure/support and momentum. Respect was considered the foundation for collaborative relationships to flourish in these consortia. Conclusions. Pharmacy education consortia form through a process that involves relationship building to produce outcomes that promote sustainability, which benefits both pharmacy schools and individual faculty members. Consortium formation is a viable, productive, and often necessary institutional goal for pharmacy schools. PMID:28381887

Exploring Biogeochemistry and Microbial Diversity of Extant Microbialites in Mexico and Cuba

PubMed Central

Valdespino-Castillo, Patricia M.; Hu, Ping; Merino-Ibarra, Martín; López-Gómez, Luz M.; Cerqueda-García, Daniel; González-De Zayas, Roberto; Pi-Puig, Teresa; Lestayo, Julio A.; Holman, Hoi-Ying; Falcón, Luisa I.

2018-01-01

Microbialites are modern analogs of ancient microbial consortia that date as far back as the Archaean Eon. Microbialites have contributed to the geochemical history of our planet through their diverse metabolic capacities that mediate mineral precipitation. These mineral-forming microbial assemblages accumulate major ions, trace elements and biomass from their ambient aquatic environments; their role in the resulting chemical structure of these lithifications needs clarification. We studied the biogeochemistry and microbial structure of microbialites collected from diverse locations in Mexico and in a previously undescribed microbialite in Cuba. We examined their structure, chemistry and mineralogy at different scales using an array of nested methods including 16S rRNA gene high-throughput sequencing, elemental analysis, X-Ray fluorescence (XRF), X-Ray diffraction (XRD), Scanning Electron Microscopy-Energy Dispersive Spectroscopy (SEM-EDS), Fourier Transformed Infrared (FTIR) spectroscopy and Synchrotron Radiation-based Fourier Transformed Infrared (SR-FTIR) spectromicroscopy. The resulting data revealed high biological and chemical diversity among microbialites and specific microbe to chemical correlations. Regardless of the sampling site, Proteobacteria had the most significant correlations with biogeochemical parameters such as organic carbon (Corg), nitrogen and Corg:Ca ratio. Biogeochemically relevant bacterial groups (dominant phototrophs and heterotrophs) showed significant correlations with major ion composition, mineral type and transition element content, such as cadmium, cobalt, chromium, copper and nickel. Microbial-chemical relationships were discussed in reference to microbialite formation, microbial metabolic capacities and the role of transition elements as enzyme cofactors. This paper provides an analytical baseline to drive our understanding of the links between microbial diversity with the chemistry of their lithified precipitations. PMID:29666607

Exploring Biogeochemistry and Microbial Diversity of Extant Microbialites in Mexico and Cuba.

PubMed

Valdespino-Castillo, Patricia M; Hu, Ping; Merino-Ibarra, Martín; López-Gómez, Luz M; Cerqueda-García, Daniel; González-De Zayas, Roberto; Pi-Puig, Teresa; Lestayo, Julio A; Holman, Hoi-Ying; Falcón, Luisa I

2018-01-01

Microbialites are modern analogs of ancient microbial consortia that date as far back as the Archaean Eon. Microbialites have contributed to the geochemical history of our planet through their diverse metabolic capacities that mediate mineral precipitation. These mineral-forming microbial assemblages accumulate major ions, trace elements and biomass from their ambient aquatic environments; their role in the resulting chemical structure of these lithifications needs clarification. We studied the biogeochemistry and microbial structure of microbialites collected from diverse locations in Mexico and in a previously undescribed microbialite in Cuba. We examined their structure, chemistry and mineralogy at different scales using an array of nested methods including 16S rRNA gene high-throughput sequencing, elemental analysis, X-Ray fluorescence (XRF), X-Ray diffraction (XRD), Scanning Electron Microscopy-Energy Dispersive Spectroscopy (SEM-EDS), Fourier Transformed Infrared (FTIR) spectroscopy and Synchrotron Radiation-based Fourier Transformed Infrared (SR-FTIR) spectromicroscopy. The resulting data revealed high biological and chemical diversity among microbialites and specific microbe to chemical correlations. Regardless of the sampling site, Proteobacteria had the most significant correlations with biogeochemical parameters such as organic carbon (C org ), nitrogen and C org :Ca ratio. Biogeochemically relevant bacterial groups (dominant phototrophs and heterotrophs) showed significant correlations with major ion composition, mineral type and transition element content, such as cadmium, cobalt, chromium, copper and nickel. Microbial-chemical relationships were discussed in reference to microbialite formation, microbial metabolic capacities and the role of transition elements as enzyme cofactors. This paper provides an analytical baseline to drive our understanding of the links between microbial diversity with the chemistry of their lithified precipitations.

Bacterial community shift and hydrocarbon transformation during bioremediation of short-term petroleum-contaminated soil.

PubMed

Wu, Manli; Ye, Xiqiong; Chen, Kaili; Li, Wei; Yuan, Jing; Jiang, Xin

2017-04-01

A laboratory study was conducted to evaluate the impact of bioaugmentation plus biostimulation (BR, added both nutrients and bacterial consortia), and natural attenuation (NA) on hydrocarbon degradation efficiency and microflora characterization during remediation of a freshly contaminated soil. After 112 days of remediation, the initial level of total petroleum hydrocarbon (TPH) (61,000 mg/kg soil) was reduced by 4.5% and 5.0% in the NA and BR treatments, respectively. Bioremediation did not significantly enhance TPH biodegradation compared to natural attenuation. The degradation of the aliphatic fraction was the most active with the degradation rate of 30.3 and 28.7 mg/kg/day by the NA and BR treatments, respectively. Soil microbial activities and counts in soil were generally greater for bioremediation than for natural attenuation. MiSeq sequencing indicated that the diversity and structure of microbial communities were affected greatly by bioremediation. In response to bioremediation treatment, Promicromonospora, Pseudomonas, Microcella, Mycobacterium, Alkanibacter, and Altererythrobacter became dominant genera in the soil. The result indicated that combining bioaugmentation with biostimulation did not improve TPH degradation, but soil microbial activities and structure of microbial communities are sensitive to bioremediation in short-term and heavily oil-contaminated soil. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Synthetic Community System for Probing Microbial Interactions Driven by Exometabolites

PubMed Central

Chodkowski, John L.

2017-01-01

ABSTRACT Though most microorganisms live within a community, we have modest knowledge about microbial interactions and their implications for community properties and ecosystem functions. To advance understanding of microbial interactions, we describe a straightforward synthetic community system that can be used to interrogate exometabolite interactions among microorganisms. The filter plate system (also known as the Transwell system) physically separates microbial populations, but allows for chemical interactions via a shared medium reservoir. Exometabolites, including small molecules, extracellular enzymes, and antibiotics, are assayed from the reservoir using sensitive mass spectrometry. Community member outcomes, such as growth, productivity, and gene regulation, can be determined using flow cytometry, biomass measurements, and transcript analyses, respectively. The synthetic community design allows for determination of the consequences of microbiome diversity for emergent community properties and for functional changes over time or after perturbation. Because it is versatile, scalable, and accessible, this synthetic community system has the potential to practically advance knowledge of microbial interactions that occur within both natural and artificial communities. IMPORTANCE Understanding microbial interactions is a fundamental objective in microbiology and ecology. The synthetic community system described here can set into motion a range of research to investigate how the diversity of a microbiome and interactions among its members impact its function, where function can be measured as exometabolites. The system allows for community exometabolite profiling to be coupled with genome mining, transcript analysis, and measurements of member productivity and population size. It can also facilitate discovery of natural products that are only produced within microbial consortia. Thus, this synthetic community system has utility to address fundamental questions about a diversity of possible microbial interactions that occur in both natural and engineered ecosystems. Author Video: An author video summary of this article is available. PMID:29152587

Update on FMT 2015: Indications, Methodologies, Mechanisms and Outlook

PubMed Central

Kelly, Colleen R.; Kahn, Stacy; Kashyap, Purna; Laine, Loren; Rubin, David; Atreja, Ashish; Moore, Thomas; Wu, Gary

2016-01-01

The community of microorganisms within the human gut (or microbiota) is critical to health and functions with a level of complexity comparable to an organ system. Alterations of this ecology (or dysbiosis) has been implicated in a number of disease states, the prototypical example being Clostridium difficile infection (CDI). Fecal microbiota transplantation (FMT) has been demonstrated to durably alter the gut microbiota of the recipient and has shown efficacy in the treatment of recurrent CDI. There is hope that FMT may eventually prove beneficial for treatment of other disease associated with alterations in gut microbiota, such as inflammatory bowel disease, irritable bowel syndrome and the metabolic syndrome, to name a few. Although the basic principles that underlie the mechanisms by which FMT demonstrates therapeutic efficacy in CDI are becoming apparent, further research is needed to understand the possible role of FMT in these other conditions. Though relatively simple to perform, questions regarding both short- and long-term safety, as well as the complex and rapidly evolving regulatory landscape has limited widespread utilization. Future work will focus on establishing best practices and more robust safety data than exist currently, as well as refining FMT beyond current “whole stool” transplants to increase safety and tolerability. Encapsulated formulations, full spectrum stool-based products and defined microbial consortia are all in the immediate future. PMID:25982290

47 CFR 54.604 - Consortia, telecommunications services, and existing contracts.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 47 Telecommunication 3 2014-10-01 2014-10-01 false Consortia, telecommunications services, and existing contracts. 54.604 Section 54.604 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED... Telecommunications Program § 54.604 Consortia, telecommunications services, and existing contracts. (a) Consortia. (1...

47 CFR 54.604 - Consortia, telecommunications services, and existing contracts.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 47 Telecommunication 3 2013-10-01 2013-10-01 false Consortia, telecommunications services, and existing contracts. 54.604 Section 54.604 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED... Telecommunications Program § 54.604 Consortia, telecommunications services, and existing contracts. (a) Consortia. (1...

Low temperature S(0) biomineralization at a supraglacial spring system in the Canadian High Arctic.

PubMed

Gleeson, D F; Williamson, C; Grasby, S E; Pappalardo, R T; Spear, J R; Templeton, A S

2011-07-01

Elemental sulfur (S(0) ) is deposited each summer onto surface ice at Borup Fiord pass on Ellesmere Island, Canada, when high concentrations of aqueous H(2) S are discharged from a supraglacial spring system. 16S rRNA gene clone libraries generated from sulfur deposits were dominated by β-Proteobacteria, particularly Ralstonia sp. Sulfur-cycling micro-organisms such as Thiomicrospira sp., and ε-Proteobacteria such as Sulfuricurvales and Sulfurovumales spp. were also abundant. Concurrent cultivation experiments isolated psychrophilic, sulfide-oxidizing consortia, which produce S(0) in opposing gradients of Na(2) S and oxygen. 16S rRNA gene analyses of sulfur precipitated in gradient tubes show stable sulfur-biomineralizing consortia dominated by Marinobacter sp. in association with Shewanella, Loktanella, Rubrobacter, Flavobacterium, and Sphingomonas spp. Organisms closely related to cultivars appear in environmental 16S rRNA clone libraries; none currently known to oxidize sulfide. Once consortia were simplified to Marinobacter and Flavobacteria spp. through dilution-to-extinction and agar removal, sulfur biomineralization continued. Shewanella, Loktanella, Sphingomonas, and Devosia spp. were also isolated on heterotrophic media, but none produced S(0) alone when reintroduced to Na(2) S gradient tubes. Tubes inoculated with a Marinobacter and Shewanella spp. co-culture did show sulfur biomineralization, suggesting that Marinobacter may be the key sulfide oxidizer in laboratory experiments. Light, florescence and scanning electron microscopy of mineral aggregates produced in Marinobacter experiments revealed abundant cells, with filaments and sheaths variably mineralized with extracellular submicron sulfur grains; similar biomineralization was not observed in abiotic controls. Detailed characterization of mineral products associated with low temperature microbial sulfur-cycling may provide biosignatures relevant to future exploration of Europa and Mars. © 2011 Blackwell Publishing Ltd.

Nitrate-based niche differentiation by distinct sulfate-reducing bacteria involved in the anaerobic oxidation of methane

PubMed Central

Green-Saxena, A; Dekas, A E; Dalleska, N F; Orphan, V J

2014-01-01

Diverse associations between methanotrophic archaea (ANME) and sulfate-reducing bacterial groups (SRB) often co-occur in marine methane seeps; however, the ecophysiology of these different symbiotic associations has not been examined. Here, we applied a combination of molecular, geochemical and Fluorescence in situ hybridization (FISH) coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS) analyses of in situ seep sediments and methane-amended sediment incubations from diverse locations (Eel River Basin, Hydrate Ridge and Costa Rican Margin seeps) to investigate the distribution and physiology of a newly identified subgroup of the Desulfobulbaceae (seepDBB) found in consortia with ANME-2c archaea, and compared these with the more commonly observed associations between the same ANME partner and the Desulfobacteraceae (DSS). FISH analyses revealed aggregates of seepDBB cells in association with ANME-2 from both environmental samples and laboratory incubations that are distinct in their structure relative to co-occurring ANME/DSS consortia. ANME/seepDBB aggregates were most abundant in shallow sediment depths below sulfide-oxidizing microbial mats. Depth profiles of ANME/seepDBB aggregate abundance revealed a positive correlation with elevated porewater nitrate relative to ANME/DSS aggregates in all seep sites examined. This relationship with nitrate was supported by sediment microcosm experiments, in which the abundance of ANME/seepDBB was greater in nitrate-amended incubations relative to the unamended control. FISH-NanoSIMS additionally revealed significantly higher 15N-nitrate incorporation levels in individual aggregates of ANME/seepDBB relative to ANME/DSS aggregates from the same incubation. These combined results suggest that nitrate is a geochemical effector of ANME/seepDBB aggregate distribution, and provides a unique niche for these consortia through their utilization of a greater range of nitrogen substrates than the ANME/DSS. PMID:24008326

The Vocational-Technical Resource Consortia Serving Business and Industry in Ohio. Digest of Study: Operational Procedures for Successful Vocational-Technical Resource Consortia in Serving Business and Industry in Ohio.

ERIC Educational Resources Information Center

Frasier, James E.; Stanton, William

This publication reports the development of the vocational-technical resource consortia in Ohio and identifies the operational procedures associated with successful programs. Five exemplary consortia were studied in some depth; however, data were obtained from all of the 23 consortia in the state. The research indicates that the consortium is an…

A Reproducible Oral Microcosm Biofilm Model for Testing Dental Materials

PubMed Central

Rudney, J.D.; Chen, R.; Lenton, P.; Li, J.; Li, Y.; Jones, R.S.; Reilly, C.; Fok, A.S.; Aparicio, C.

2012-01-01

Aims Most studies of biofilm effects on dental materials use single-species biofilms, or consortia. Microcosm biofilms grown directly from saliva or plaque are much more diverse, but difficult to characterize. We used the Human Oral Microbial Identification Microarray (HOMIM) to validate a reproducible oral microcosm model. Methods and Results Saliva and dental plaque were collected from adults and children. Hydroxyapatite and dental composite disks were inoculated with either saliva or plaque, and microcosm biofilms were grown in a CDC biofilm reactor. In later experiments, the reactor was pulsed with sucrose. DNA from inoculums and microcosms were analyzed by HOMIM for 272 species. Microcosms included about 60% of species from the original inoculum. Biofilms grown on hydroxyapatite and composites were extremely similar. Sucrose-pulsing decreased diversity and pH, but increased the abundance of Streptococcus and Veilonella. Biofilms from the same donor, grown at different times, clustered together. Conclusions This model produced reproducible microcosm biofilms that were representative of the oral microbiota. Sucrose induced changes associated with dental caries. Significance and Impact of the Study This is the first use of HOMIM to validate an oral microcosm model that can be used to study the effects of complex biofilms on dental materials. PMID:22925110

Subgingival microbiota in health compared to periodontitis and the influence of smoking.

PubMed

Camelo-Castillo, Anny J; Mira, Alex; Pico, Alex; Nibali, Luigi; Henderson, Brian; Donos, Nikolaos; Tomás, Inmaculada

2015-01-01

The etiology of periodontitis has traditionally been associated to a consortium of three bacterial species-the so-called "red-complex" of periodontal disease-which has been the target for most diagnostic and therapeutic strategies. However, other species have also been found to correlate with disease severity. In addition, the influence of smoking on periodontal microbiota is poorly understood. In the current manuscript, the composition of the subgingival microbiota in healthy individuals vs. patients with chronic periodontitis has been investigated using 16S pyrosequencing and the influence of smoking on periodontal composition has been examined. Subgingival bacterial communities were sampled from 82 patients: 22 non-smoking healthy controls, 28 non-smoking periodontal patients, and 32 smoking periodontal patients. Bacterial diversity was higher in periodontal patients than in healthy subjects, which could be interpreted as the consequence of a nutritionally richer environment or a reduced immune competence. Periodontal patients showed a significantly higher prevalence/relative abundance of "established" periopathogens but also other taxa whose role is not well-established and that should be targets for future research. These include Anaeroglobus, Bulleidia, Desulfobulbus, Filifactor, Mogibacterium, Phocaeicola, Schwartzia or TM7. The microbial community of smoking-associated periodontitis is less diverse and distinct from that of non-smokers, indicating that smoking has an influence on periodontal ecology. Interestingly, the high sequencing coverage allowed the detection at low proportions of periodontal pathogens in all healthy individuals, indicating that chronic periodontitis cannot be strictly considered an infectious disease but the outcome of a polymicrobial dysbiosis, where changes in the proportions of microbial consortia trigger the inflammatory and tissue-degradation responses of the host.

The biogeochemical vertical structure renders a meromictic volcanic lake a trap for geogenic CO2 (Lake Averno, Italy)

PubMed Central

Fazi, Stefano; Rossetti, Simona; Pratesi, Paolo; Ceccotti, Marco; Cabassi, Jacopo; Capecchiacci, Francesco; Venturi, Stefania; Vaselli, Orlando

2018-01-01

Volcanic lakes are characterized by physicochemical favorable conditions for the development of reservoirs of C-bearing greenhouse gases that can be dispersed to air during occasional rollover events. By combining a microbiological and geochemical approach, we showed that the chemistry of the CO2- and CH4-rich gas reservoir hosted within the meromictic Lake Averno (Campi Flegrei, southern Italy) are related to the microbial niche differentiation along the vertical water column. The simultaneous occurrence of diverse functional groups of microbes operating under different conditions suggests that these habitats harbor complex microbial consortia that impact on the production and consumption of greenhouse gases. In the epilimnion, the activity of aerobic methanotrophic bacteria and photosynthetic biota, together with CO2 dissolution at relatively high pH, enhanced CO2- and CH4 consumption, which also occurred in the hypolimnion. Moreover, results from computations carried out to evaluate the dependence of the lake stability on the CO2/CH4 ratios, suggested that the water density vertical gradient was mainly controlled by salinity and temperature, whereas the effect of dissolved gases was minor, excepting if extremely high increases of CH4 are admitted. Therefore, biological processes, controlling the composition of CO2 and CH4, contributed to stabilize the lake stratification of the lake. Overall, Lake Averno, and supposedly the numerous worldwide distributed volcanic lakes having similar features (namely bio-activity lakes), acts as a sink for the CO2 supplied from the hydrothermal/magmatic system, displaying a significant influence on the local carbon budget. PMID:29509779

Chemical and microbiological characterization of an aged PCB-contaminated soil.

PubMed

Stella, T; Covino, S; Burianová, E; Filipová, A; Křesinová, Z; Voříšková, J; Větrovský, T; Baldrian, P; Cajthaml, T

2015-11-15

This study was aimed at complex characterization of three soil samples (bulk soil, topsoil and rhizosphere soil) from a site historically contaminated with polychlorinated biphenyls (PCB). The bulk soil was the most highly contaminated, with a PCB concentration of 705.95 mg kg(-1), while the rhizosphere soil was the least contaminated (169.36 mg kg(-1)). PCB degradation intermediates, namely chlorobenzoic acids (CBAs), were detected in all the soil samples, suggesting the occurrence of microbial transformation processes over time. The higher content of organic carbon in the topsoil and rhizosphere soil than in the bulk soil could be linked to the reduced bioaccessibility (bioavailability) of these chlorinated pollutants. However, different proportions of the PCB congener contents and different bioaccessibility of the PCB homologues indicate microbial biotransformation of the compounds. The higher content of organic carbon probably also promoted the growth of microorganisms, as revealed by phospholipid fatty acid (PFLA) quantification. Tag-encoded pyrosequencing analysis showed that the bacterial community structure was significantly similar among the three soils and was predominated by Proteobacteria (44-48%) in all cases. Moreover, analysis at lower taxonomic levels pointed to the presence of genera (Sphingomonas, Bulkholderia, Arthrobacter, Bacillus) including members with reported PCB removal abilities. The fungal community was mostly represented by Basidiomycota and Ascomycota, which accounted for >80% of all the sequences detected in the three soils. Fungal taxa with biodegradation potential (Paxillus, Cryptococcus, Phoma, Mortierella) were also found. These results highlight the potential of the indigenous consortia present at the site as a starting point for PCB bioremediation processes. Copyright © 2015 Elsevier B.V. All rights reserved.

Genome-Centric Analysis of a Thermophilic and Cellulolytic Bacterial Consortium Derived from Composting

PubMed Central

Lemos, Leandro N.; Pereira, Roberta V.; Quaggio, Ronaldo B.; Martins, Layla F.; Moura, Livia M. S.; da Silva, Amanda R.; Antunes, Luciana P.; da Silva, Aline M.; Setubal, João C.

2017-01-01

Microbial consortia selected from complex lignocellulolytic microbial communities are promising alternatives to deconstruct plant waste, since synergistic action of different enzymes is required for full degradation of plant biomass in biorefining applications. Culture enrichment also facilitates the study of interactions among consortium members, and can be a good source of novel microbial species. Here, we used a sample from a plant waste composting operation in the São Paulo Zoo (Brazil) as inoculum to obtain a thermophilic aerobic consortium enriched through multiple passages at 60°C in carboxymethylcellulose as sole carbon source. The microbial community composition of this consortium was investigated by shotgun metagenomics and genome-centric analysis. Six near-complete (over 90%) genomes were reconstructed. Similarity and phylogenetic analyses show that four of these six genomes are novel, with the following hypothesized identifications: a new Thermobacillus species; the first Bacillus thermozeamaize genome (for which currently only 16S sequences are available) or else the first representative of a new family in the Bacillales order; the first representative of a new genus in the Paenibacillaceae family; and the first representative of a new deep-branching family in the Clostridia class. The reconstructed genomes from known species were identified as Geobacillus thermoglucosidasius and Caldibacillus debilis. The metabolic potential of these recovered genomes based on COG and CAZy analyses show that these genomes encode several glycoside hydrolases (GHs) as well as other genes related to lignocellulose breakdown. The new Thermobacillus species stands out for being the richest in diversity and abundance of GHs, possessing the greatest potential for biomass degradation among the six recovered genomes. We also investigated the presence and activity of the organisms corresponding to these genomes in the composting operation from which the consortium was built, using compost metagenome and metatranscriptome datasets generated in a previous study. We obtained strong evidence that five of the six recovered genomes are indeed present and active in that composting process. We have thus discovered three (perhaps four) new thermophillic bacterial species that add to the increasing repertoire of known lignocellulose degraders, whose biotechnological potential can now be investigated in further studies. PMID:28469608

Complete Biosynthesis of Anthocyanins Using E. coli Polycultures.

PubMed

Jones, J Andrew; Vernacchio, Victoria R; Collins, Shannon M; Shirke, Abhijit N; Xiu, Yu; Englaender, Jacob A; Cress, Brady F; McCutcheon, Catherine C; Linhardt, Robert J; Gross, Richard A; Koffas, Mattheos A G

2017-06-06

Fermentation-based chemical production strategies provide a feasible route for the rapid, safe, and sustainable production of a wide variety of important chemical products, ranging from fuels to pharmaceuticals. These strategies have yet to find wide industrial utilization due to their inability to economically compete with traditional extraction and chemical production methods. Here, we engineer for the first time the complex microbial biosynthesis of an anthocyanin plant natural product, starting from sugar. This was accomplished through the development of a synthetic, 4-strain Escherichia coli polyculture collectively expressing 15 exogenous or modified pathway enzymes from diverse plants and other microbes. This synthetic consortium-based approach enables the functional expression and connection of lengthy pathways while effectively managing the accompanying metabolic burden. The de novo production of specific anthocyanin molecules, such as calistephin, has been an elusive metabolic engineering target for over a decade. The utilization of our polyculture strategy affords milligram-per-liter production titers. This study also lays the groundwork for significant advances in strain and process design toward the development of cost-competitive biochemical production hosts through nontraditional methodologies. IMPORTANCE To efficiently express active extensive recombinant pathways with high flux in microbial hosts requires careful balance and allocation of metabolic resources such as ATP, reducing equivalents, and malonyl coenzyme A (malonyl-CoA), as well as various other pathway-dependent cofactors and precursors. To address this issue, we report the design, characterization, and implementation of the first synthetic 4-strain polyculture. Division of the overexpression of 15 enzymes and transcription factors over 4 independent strain modules allowed for the division of metabolic burden and for independent strain optimization for module-specific metabolite needs. This study represents the most complex synthetic consortia constructed to date for metabolic engineering applications and provides a new paradigm in metabolic engineering for the reconstitution of extensive metabolic pathways in nonnative hosts. Copyright © 2017 Jones et al.

Pyrosequencing analysis of microbial communities reveals dominant cosmopolitan phylotypes in deep-sea sediments of the eastern Mediterranean Sea.

PubMed

Polymenakou, Paraskevi N; Christakis, Christos A; Mandalakis, Manolis; Oulas, Anastasis

2015-06-01

The deep eastern basin of the Mediterranean Sea is considered to be one of the world's most oligotrophic areas in the world. Here we performed pyrosequenicng analysis of bacterial and archaeal communities in oxic nutrient-poor sediments collected from the eastern Mediterranean at 1025-4393 m depth. Microbial communities were surveyed by targeting the hypervariable V5-V6 regions of the 16S ribosomal RNA gene using bar-coded pyrosequencing. With a total of 13,194 operational taxonomic units (OTUs) or phylotypes at 97% sequence similarities, the phylogenetic affiliation of microbes was assigned to 23 bacterial and 2 archaeal known phyla, 23 candidate divisions at the phylum level and distributed into 186 families. It was further revealed that the microbial consortia inhabiting all sampling sites were highly diverse, but dominated by phylotypes closely related to members of the genus Pseudomonas and Marine Group I archaea. Such pronounced and widespread enrichment probably manifests the cosmopolitan character of these species and raises questions about their metabolic adaptation to the physical stressors and low nutrient availability of the deep eastern Mediterranean Sea. Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Cellulase and xylanase production at pilot scale by solid-state fermentation from coffee husk using specialized consortia: The consistency of the process and the microbial communities involved.

PubMed

Cerda, Alejandra; Mejías, Laura; Gea, Teresa; Sánchez, Antoni

2017-11-01

Solid state fermentation is a promising technology however rising concerns related to scale up and reproducibility in a productive process. Coffee husk and a specialized inoculum were used in a 4.5L and then in 50L reactors to assess the reproducibility of a cellulase and hemicellulase production system. Fermentations were consistent in terms of cellulase production and microbial communities. The higher temperatures achieved when operating at 50L generated a shift on the microbial communities and a reduction of nearly 50% on cellulase production at pilot scale. In spite, an overall enzymatic production of 3.1±0.5FPUg -1 DM and 48±4Ug -1 DM for FPase and Xyl activities was obtained, respectively, with low deviation coefficients of 16 and 19% for FPase and Xyl production. Gaseous emissions assessment revealed an emission factor of 2.6·10 -3 kg volatile organic compounds per Mg of coffee husk and negligible NH 3 , CH 4 and N 2 O emissions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Reciprocal interaction of diet and microbiome in inflammatory bowel diseases.

PubMed

Schaubeck, Monika; Haller, Dirk

2015-11-01

Diet is an emerging but poorly defined disease modulator in inflammatory bowel diseases (IBDs). Dietary factors exert direct effects on epithelial and immune cells and indirectly modulate immune homeostasis by shaping the intestinal microbiota. The increase in IBD prevalence in industrialized countries is associated with lifestyle changes including diets rich in energy, saturated fats, meat and sugar. Despite the fact that the intestinal ecosystem shows high stability and resilience to short-term perturbations, long-term dietary habits have profound effects on composition and function eventually leading to dysbiosis, that is changes in microbial composition associated with deleterious effects to the host. High-throughput sequencing data generated deeper insights of the intestinal ecosystems related to health and disease. However, the available cohort-studies establish associative relationships between microbiota changes and disease, rather than causality. New mouse models of intestinal inflammation and the possibility to transfer disease-associated microbial consortia state an essential tool to unravel the potential of diet-induced microbial shifts. This review will discuss new insights of how nutrition or single dietary factors shape the intestinal ecosystem. Furthermore, we want to provide perspectives for clinical translation of this knowledge to treat or prevent IBD.

Opportunistic pathogens and faecal indicators in drinking water associated biofilms in Cluj, Romania.

PubMed

Farkas, A; Drăgan-Bularda, M; Ciatarâş, D; Bocoş, B; Tigan, S

2012-09-01

Biofouling occurs without exception in all water systems, with undesirable effects such as biocorrosion and deterioration of water quality. Drinking water associated biofilms represent a potential risk to human health by harbouring pathogenic or toxin-releasing microorganisms. This is the first study investigating the attached microbiota, with potential threat to human health, in a public water system in Romania. The presence and the seasonal variation of viable faecal indicators and opportunistic pathogens were investigated within naturally developed biofilms in a drinking water treatment plant. Bacterial frequencies were correlated with microbial loads in biofilms as well as with physical and chemical characteristics of biofilms and raw water. The biofilms assessed in the current study proved to be extremely active microbial consortia. High bacterial numbers were recovered by cultivation, including Pseudomonas aeruginosa, Escherichia coli, Aeromonas hydrophila, intestinal enterococci and Clostridium perfringens. There were no Legionella spp. detected in any biofilm sample. Emergence of opportunistic pathogens in biofilms was not significantly affected by the surface material, but by the treatment process. Implementation of a water safety plan encompassing measures to prevent microbial contamination and to control biofouling would be appropriate.

Applying functional metagenomics to search for novel lignocellulosic enzymes in a microbial consortium derived from a thermophilic composting phase of sugarcane bagasse and cow manure.

PubMed

Colombo, Lívia Tavares; de Oliveira, Marcelo Nagem Valério; Carneiro, Deisy Guimarães; de Souza, Robson Assis; Alvim, Mariana Caroline Tocantins; Dos Santos, Josenilda Carlos; da Silva, Cynthia Canêdo; Vidigal, Pedro Marcus Pereira; da Silveira, Wendel Batista; Passos, Flávia Maria Lopes

2016-09-01

Environments where lignocellulosic biomass is naturally decomposed are sources for discovery of new hydrolytic enzymes that can reduce the high cost of enzymatic cocktails for second-generation ethanol production. Metagenomic analysis was applied to discover genes coding carbohydrate-depleting enzymes from a microbial laboratory subculture using a mix of sugarcane bagasse and cow manure in the thermophilic composting phase. From a fosmid library, 182 clones had the ability to hydrolyse carbohydrate. Sequencing of 30 fosmids resulted in 12 contigs encoding 34 putative carbohydrate-active enzymes belonging to 17 glycosyl hydrolase (GH) families. One third of the putative proteins belong to the GH3 family, which includes β-glucosidase enzymes known to be important in the cellulose-deconstruction process but present with low activity in commercial enzyme preparations. Phylogenetic analysis of the amino acid sequences of seven selected proteins, including three β-glucosidases, showed low relatedness with protein sequences deposited in databases. These findings highlight microbial consortia obtained from a mixture of decomposing biomass residues, such as sugar cane bagasse and cow manure, as a rich resource of novel enzymes potentially useful in biotechnology for saccharification of lignocellulosic substrate.

Characterization of microbial consortia in a terephthalate-degrading anaerobic granular sludge system.

PubMed

Wu, J H; Liu, W T; Tseng, I C; Cheng, S S

2001-02-01

The microbial composition and spatial distribution in a terephthalate-degrading anaerobic granular sludge system were characterized using molecular techniques. 16S rDNA clone library and sequence analysis revealed that 78.5% of 106 bacterial clones belonged to the delta subclass of the class Proteobacteria; the remaining clones were assigned to the green non-sulfur bacteria (7.5%), Synergistes (0.9%) and unidentified divisions (13.1%). Most of the bacterial clones in the delta-Proteobacteria formed a novel group containing no known bacterial isolates. For the domain Archaea, 81.7% and 18.3% of 72 archaeal clones were affiliated with Methanosaeta and Methanospirillum, respectively. Spatial localization of microbial populations inside granules was determined by transmission electron microscopy and fluorescent in situ hybridization with oligonucleotide probes targeting the novel delta-proteobacterial group, the acetoclastic Methanosaeta, and the hydrogenotrophic Methanospirillum and members of Methanobacteriaceae. The novel group included at least two different populations with identical rod-shape morphology, which made up more than 87% of the total bacterial cells, and were closely associated with methanogenic populations to form a nonlayered granular structure. This novel group was presumed to be the primary bacterial population involved in the terephthalate degradation in the methanogenic granular consortium.

Microbial Community Succession During Lactate Amendment of Chromium Contaminated Groundwater Reveals a Predominance of Pelosinus spp.

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

Mosher, Jennifer J; Phelps, Tommy Joe; Drake, Meghan M

2012-01-01

Microbial community structure and metabolism in contaminated ecosystems are potentially controlled not only by the different populations within the community, but a myriad of dynamic physicochemical parameters as well. The goal of the current work was to determine the impact of organic acid enrichment, in this case lactate, on the succession of the native microbial community from a contaminated groundwater aquifer. Triplicate anaerobic, continuous-flow glass reactors were inoculated with Hanford 100-H groundwater and incubated for 95 days to obtain a stable, enriched community. The microbial community experienced a shift in the population dynamics over time to eventually form a communitymore » with far less diversity than the original. The final community was dominated by Pelosinus spp. and to a lesser degree, Acetobacterium spp. with small amounts of other bacteria and archaea including methanogens. The resultant diversity was far decreased from 63 genera within 12 phyla to 11 bacterial genera (from three phyla) and 2 archaeal genera (from one phylum). Isolation efforts were successful in attaining new species of Pelosinus and known members of Methanosarcina barkerii along with several sulfate- and Fe(III)- reducing consortia members. The continuous-flow reactors allowed for testing physiochemical factors with microbial community dynamics on a smaller, replicable, scale while also facilitating the isolation of several previously uncultured community members. These lab-scale simulations will presumably allow for a deeper understanding of the community metabolism with specific carbon amendments that can inform future in situ efforts.« less

Composition of Hydrothermal Vent Microbial Communities as Revealed by Analyses of Signature Lipids, Stable Carbon Isotopes and Aquificales Cultures

NASA Technical Reports Server (NTRS)

Jahnke, Linda L.; Eder, Wolfgang; Huber, Robert; Hinrichs, Kai-Uwe; Hayes, John M.; Cady, Sherry L.; DesMarais, David J.; Hope, Janet M.; Summons, Roger E.

2001-01-01

Extremely thermophilic microbial communities associated with the siliceous vent walls and outflow channel of Octopus Spring, Yellowstone National Park, have been examined for lipid biomarker and carbon isotopic signatures. These data were compared with that obtained from representatives of three Aquificales genera. Thermocrinis ruber, Thermocrinis sp. HI, Hydrogenobacter thermophilus, Aquifex pyrophilus and Aquifex aeolicus all contained phospholipids composed not only of the usual ester-linked fatty acids, but also ether-linked alkyl moieties. The fatty acids of all cultured organisms were dominated by very distinct pattern of n-C-20:1 and cy-C-21 compounds. The alkyl glycerol ethers were present primarily as C-18:0 monoethers with the exception of the Aquifex spp. in which dialkyl glycerol ethers with a boarder carbon-number distribution were also present. These Aquificales biomarker lipids were the major constituents in the lipid extracts of the Octopus Spring microbial samples. Two natural samples, a microbial biofilm growing in association with deposition of amorphous silica on the vent walls at 92 C, and the well-known "pink-streamer community" (PSC), siliceous filaments of a microbial consortia growing in the outflow channel at 87 C were analyzed. Both the biofilm and PSC samples contained mono- and dialkyl glycerol ethers with a prevalence of C-18 and C-20 alkyls. Phospholipid fatty acids were comprised of both the characteristic. Additional information is contained in the original extended abstract.

The microbial mats of Pavilion Lake microbialites: examining the relationship between photosynthesis and carbonate precipitation

NASA Astrophysics Data System (ADS)

Lim, D. S. S.; Hawes, I.; Mackey, T. J.; Brady, A. L.; Biddle, J.; Andersen, D. T.; Belan, M.; Slater, G.; Abercromby, A.; Squyres, S. W.; Delaney, M.; Haberle, C. W.; Cardman, Z.

2014-12-01

Pavilion Lake in British Columbia, Canada is an ultra-oligotrophic lake that has abundant microbialite growth. Recent research has shown that photoautotrophic microbial communities are important to modern microbialite development in Pavilion Lake. However, questions remain as to the relationship between changing light levels within the lake, variation in microbialite macro-structure, microbial consortia, and the preservation of associated biosignatures within the microbialite fabrics. The 2014 Pavilion Lake Research Project (PLRP) field program was focused on data gathering to understand these complex relationships by determining if a) light is the immediate limit to photosynthetic activity and, if so, if light is distributed around microbialites in ways that are consistent with emergent microbialite structure; and b) if at more local scales, the filamentous pink and green cyanobacterial nodular colonies identified in previous PLRP studies are centers of photosynthetic activity that create pH conditions suitable for carbonate precipitation. A diver-deployed pulse-amplitude modulated (PAM) fluorometer was used to collect synoptic in situ measurements of fluorescence yield and irradiance and across microbialites, focusing on comparing flat and vertical structural elements at a range of sites and depths. As well, we collected time series measurements of photosynthetic activity and irradiance at a set depth of 18 m across three different regions in Pavilion Lake. Our initial findings suggest that all microbialite surfaces are primarily light-limited regardless of depth or location within the lake. Shore based PAM fluorometry and microelectrode profiling of diver-collected samples suggest that pink and green nodules have different photosynthetic properties and pH profiles, and that nodular growth is likely to be the primary route of calcification due to the gelatinous covering the nodule creates. On-going tests for molecular signatures and isotopic shifts will allow for further examination of surface microvariation and the associated influence on microbialite development.

25 CFR 1000.438 - May Tribes/Consortia appeal Department decisions to a Federal court?

Code of Federal Regulations, 2013 CFR

2013-04-01

... 25 Indians 2 2013-04-01 2013-04-01 false May Tribes/Consortia appeal Department decisions to a... INDIAN SELF-DETERMINATION AND EDUCATION ACT Appeals § 1000.438 May Tribes/Consortia appeal Department decisions to a Federal court? Yes, Tribes/Consortia may appeal decisions of Department officials relating to...

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.

Ice Shelf Microbial Ecosystems in the High Arctic and Implications for Life on Snowball Earth

NASA Astrophysics Data System (ADS)

Vincent, W. F.; Gibson, J. A. E.; Pienitz, R.; Villeneuve, V.; Broady, P. A.; Hamilton, P. B.; Howard-Williams, C.

The Ward Hunt Ice Shelf (83°N, 74°W) is the largest remaining section of thick (>10m) landfast sea ice along the northern coastline of Ellesmere Island, Canada. Extensive meltwater lakes and streams occur on the surface of the ice and are colonized by photosynthetic microbial mat communities. This High Arctic cryo-ecosystem is similar in several of its physical, biological and geochemical features to the McMurdo Ice Shelf in Antarctica. The ice-mats in both polar regions are dominated by filamentous cyanobacteria but also contain diatoms, chlorophytes, flagellates, ciliates, nematodes, tardigrades and rotifers. The luxuriant Ward Hunt consortia also contain high concentrations (107-108cm-2) of viruses and heterotrophic bacteria. During periods of extensive ice cover, such as glaciations during the Proterozoic, cryotolerant mats of the type now found in these polar ice shelf ecosystems would have provided refugia for the survival, growth and evolution of a variety of organisms, including multicellular eukaryotes.

Strategies and Methodologies for Developing Microbial Detoxification Systems to Mitigate Mycotoxins

PubMed Central

Zhu, Yan; Hassan, Yousef I.; Lepp, Dion; Shao, Suqin; Zhou, Ting

2017-01-01

Mycotoxins, the secondary metabolites of mycotoxigenic fungi, have been found in almost all agricultural commodities worldwide, causing enormous economic losses in livestock production and severe human health problems. Compared to traditional physical adsorption and chemical reactions, interest in biological detoxification methods that are environmentally sound, safe and highly efficient has seen a significant increase in recent years. However, researchers in this field have been facing tremendous unexpected challenges and are eager to find solutions. This review summarizes and assesses the research strategies and methodologies in each phase of the development of microbiological solutions for mycotoxin mitigation. These include screening of functional microbial consortia from natural samples, isolation and identification of single colonies with biotransformation activity, investigation of the physiological characteristics of isolated strains, identification and assessment of the toxicities of biotransformation products, purification of functional enzymes and the application of mycotoxin decontamination to feed/food production. A full understanding and appropriate application of this tool box should be helpful towards the development of novel microbiological solutions on mycotoxin detoxification. PMID:28387743

Mosaic patterns of B-vitamin synthesis and utilization in a natural marine microbial community.

PubMed

Gómez-Consarnau, Laura; Sachdeva, Rohan; Gifford, Scott M; Cutter, Lynda S; Fuhrman, Jed A; Sañudo-Wilhelmy, Sergio A; Moran, Mary Ann

2018-04-16

Aquatic environments contain large communities of microorganisms whose synergistic interactions mediate the cycling of major and trace nutrients, including vitamins. B-vitamins are essential coenzymes that many organisms cannot synthesize. Thus, their exchange among de novo synthesizers and auxotrophs is expected to play an important role in the microbial consortia and explain some of the temporal and spatial changes observed in diversity. In this study, we analyzed metatranscriptomes of a natural marine microbial community, diel sampled quarterly over one year to try to identify the potential major B-vitamin synthesizers and consumers. Transcriptomic data showed that the best-represented taxa dominated the expression of synthesis genes for some B-vitamins but lacked transcripts for others. For instance, Rhodobacterales dominated the expression of vitamin-B 12 synthesis, but not of vitamin-B 7 , whose synthesis transcripts were mainly represented by Flavobacteria. In contrast, bacterial groups that constituted less than 4% of the community (e.g., Verrucomicrobia) accounted for most of the vitamin-B 1 synthesis transcripts. Furthermore, ambient vitamin-B 1 concentrations were higher in samples collected during the day, and were positively correlated with chlorophyll-a concentrations. Our analysis supports the hypothesis that the mosaic of metabolic interdependencies through B-vitamin synthesis and exchange are key processes that contribute to shaping microbial communities in nature. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Toward a "Common Definition of English Learner": Guidance for States and State Assessment Consortia in Defining and Addressing Policy and Technical Issues and Options

ERIC Educational Resources Information Center

Linquanti, Robert; Cook, H. Gary

2013-01-01

States participating in the four federally-funded assessment consortia are required to establish a "common definition of English Learner." This includes the two Race to the Top academic assessment consortia and the two Enhanced Assessment Grant English language proficiency (ELP) assessment consortia. This paper provides guidance that…

Metal-tolerant PAH-degrading bacteria: development of suitable test medium and effect of cadmium and its availability on PAH biodegradation.

PubMed

Thavamani, Palanisami; Megharaj, Mallavarapu; Naidu, Ravi

2015-06-01

The use of metal-tolerant polyaromatic hydrocarbon (PAH)-degrading bacteria is viable for mitigating metal inhibition of organic compound biodegradation in the remediation of mixed contaminated sites. Many microbial growth media used for toxicity testing contain high concentrations of metal-binding components such as phosphates that can reduce solution-phase metal concentrations thereby underestimate the real toxicity. In this study, we isolated two PAHs-degrading bacterial consortia from long-term mixed contaminated soils. We have developed a new mineral medium by optimising the concentrations of medium components to allow the bacterial growth and at the same time maintain high bioavailable metal (Cd(2+) as a model metal) in the medium. This medium has more than 60 % Cd as Cd(2+) at pH 6.5 as measured by an ion selective electrode and visual MINTEQ model. The Cd-tolerant patterns of the consortia were tested and minimum inhibitory concentration (MIC) derived. The consortium-5 had the highest MIC of 5 mg l(-1) Cd followed by consortium-9. Both cultures were able to completely metabolise 200 mg l(-1) phenanthrene in less than 4 days in the presence of 5 mg l(-1) Cd. The isolated metal-tolerant PAH-degrading bacterial cultures have great potential for bioremediation of mixed contaminated soils.

Recalcitrant Carbonaceous Material: A Source of Electron Donors for Anaerobic Microbial Metabolisms in the Subsurface?

NASA Astrophysics Data System (ADS)

Nixon, S. L.; Montgomery, W.; Sephton, M. A.; Cockell, C. S.

2014-12-01

More than 90% of organic material on Earth resides in sedimentary rocks in the form of kerogens; fossilized organic matter formed through selective preservation of high molecular weight biopolymers under anoxic conditions. Despite its prevalence in the subsurface, the extent to which this material supports microbial metabolisms is unknown. Whilst aerobic microorganisms are known to derive energy from kerogens within shales, utilization in anaerobic microbial metabolisms that proliferate in the terrestrial subsurface, such as microbial iron reduction, has yet to be demonstrated. Data are presented from microbial growth experiments in which kerogens and shales were supplied as the sole electron donor source for microbial iron reduction by an enrichment culture. Four well-characterized kerogens samples (representative of Types I-IV, classified by starting material), and two shale samples, were assessed. Organic analysis was carried out to investigate major compound classes present in each starting material. Parallel experiments were conducted to test inhibition of microbial iron reduction in the presence of each material when the culture was supplied with a full redox couple. The results demonstrate that iron-reducing microorganisms in this culture were unable to use kerogens and shales as a source of electron donors for energy acquisition, despite the presence of compound classes known to support this metabolism. Furthermore, the presence of these materials was found to inhibit microbial iron reduction to varying degrees, with some samples leading to complete inhibition. These results suggest that recalcitrant carbonaceous material in the terrestrial subsurface is not available for microbial iron reduction and similar metabolisms, such as sulphate-reduction. Further research is needed to investigate the inhibition exerted by these materials, and to assess whether these findings apply to other microbial consortia. These results may have significant implications for the role of anaerobic microbial metabolisms in the subsurface terrestrial carbon cycle. Kerogens are chemically similar to organic material in carbonaceous chondrites. As such, further study may provide insight into the potential availability of organic compounds for microbial metabolisms operating in the subsurface of Mars.

Characterization of Fecal Microbiota from a Salmonella Endemic Cattle Herd as Determined by Oligonucleotide Fingerprinting of RDNA Genes

USDA-ARS?s Scientific Manuscript database

The gastrointestinal (GI) tract microbiota is composed of complex communities. For all species examined thus far, culture and molecular analyses show that these communities are highly diverse and individuals harbor unique consortia. These microorganisms are influenced by the diet, host, and environm...

Host Genetic and Environmental Effects on Mouse Cecum Microbiota

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

Campbell, James H; Foster, Carmen M; Vishnivetskaya, Tatiana A

2012-01-01

The mammalian gut harbors complex and variable microbial communities, across both host phylogenetic space and conspecific individuals. A synergy of host genetic and environmental factors shape these communities and account for their variability, but their individual contributions and the selective pressures involved are still not well understood. We employed barcoded pyrosequencing of V1-2 and V4 regions of bacterial small subunit ribosomal RNA genes to characterize the effects of host genetics and environment on cecum assemblages in 10 genetically distinct, inbred mouse strains. Eight of these strains are the foundation of the Collaborative Cross (CC), a panel of mice derived frommore » a genetically diverse set of inbred founder strains, designed specifically for complex trait analysis. Diversity of gut microbiota was characterized by complementing phylogenetic and distance-based, sequence-clustering approaches. Significant correlations were found between the mouse strains and their gut microbiota, reflected by distinct bacterial communities. Cohabitation and litter had a reduced, although detectable effect, and the microbiota response to these factors varied by strain. We identified bacterial phylotypes that appear to be discriminative and strain-specific to each mouse line used. Cohabitation of different strains of mice revealed an interaction of host genetic and environmental factors in shaping gut bacterial consortia, in which bacterial communities became more similar but retained strain specificity. This study provides a baseline analysis of intestinal bacterial communities in the eight CC progenitor strains and will be linked to integrated host genotype, phenotype and microbiota research on the resulting CC panel.« less

Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics.

PubMed

Bokulich, Nicholas A; Collins, Thomas S; Masarweh, Chad; Allen, Greg; Heymann, Hildegarde; Ebeler, Susan E; Mills, David A

2016-06-14

Regionally distinct wine characteristics (terroir) are an important aspect of wine production and consumer appreciation. Microbial activity is an integral part of wine production, and grape and wine microbiota present regionally defined patterns associated with vineyard and climatic conditions, but the degree to which these microbial patterns associate with the chemical composition of wine is unclear. Through a longitudinal survey of over 200 commercial wine fermentations, we demonstrate that both grape microbiota and wine metabolite profiles distinguish viticultural area designations and individual vineyards within Napa and Sonoma Counties, California. Associations among wine microbiota and fermentation characteristics suggest new links between microbiota, fermentation performance, and wine properties. The bacterial and fungal consortia of wine fermentations, composed from vineyard and winery sources, correlate with the chemical composition of the finished wines and predict metabolite abundances in finished wines using machine learning models. The use of postharvest microbiota as an early predictor of wine chemical composition is unprecedented and potentially poses a new paradigm for quality control of agricultural products. These findings add further evidence that microbial activity is associated with wine terroir Wine production is a multi-billion-dollar global industry for which microbial control and wine chemical composition are crucial aspects of quality. Terroir is an important feature of consumer appreciation and wine culture, but the many factors that contribute to terroir are nebulous. We show that grape and wine microbiota exhibit regional patterns that correlate with wine chemical composition, suggesting that the grape microbiome may influence terroir In addition to enriching our understanding of how growing region and wine properties interact, this may provide further economic incentive for agricultural and enological practices that maintain regional microbial biodiversity. Copyright © 2016 Bokulich et al.

Governance of global health research consortia: Sharing sovereignty and resources within Future Health Systems.

PubMed

Pratt, Bridget; Hyder, Adnan A

2017-02-01

Global health research partnerships are increasingly taking the form of consortia that conduct programs of research in low and middle-income countries (LMICs). An ethical framework has been developed that describes how the governance of consortia comprised of institutions from high-income countries and LMICs should be structured to promote health equity. It encompasses initial guidance for sharing sovereignty in consortia decision-making and sharing consortia resources. This paper describes a first effort to examine whether and how consortia can uphold that guidance. Case study research was undertaken with the Future Health Systems consortium, performs research to improve health service delivery for the poor in Bangladesh, China, India, and Uganda. Data were thematically analysed and revealed that proposed ethical requirements for sharing sovereignty and sharing resources are largely upheld by Future Health Systems. Facilitating factors included having a decentralised governance model, LMIC partners with good research capacity, and firm budgets. Higher labour costs in the US and UK and the funder's policy of allocating funds to consortia on a reimbursement basis prevented full alignment with guidance on sharing resources. The lessons described in this paper can assist other consortia to more systematically link their governance policy and practice to the promotion of health equity. Copyright © 2016 Elsevier Ltd. All rights reserved.

Microbial Consortia Development and Microcosm and Column Experiments for Enhanced Bioremediation of Chlorinated Volatile Organic Compounds, West Branch Canal Creek Wetland Area, Aberdeen Proving Ground, Maryland

USGS Publications Warehouse

Lorah, Michelle M.; Majcher, Emily H.; Jones, Elizabeth J.; Voytek, Mary A.

2008-01-01

Chlorinated solvents, including 1,1,2,2-tetrachloroethane, tetrachloroethene, trichloroethene, carbon tetrachloride, and chloroform, are reaching land surface in localized areas of focused ground-water discharge (seeps) in a wetland and tidal creek in the West Branch Canal Creek area, Aberdeen Proving Ground, Maryland. In cooperation with the U.S. Army Garrison, Aberdeen Proving Ground, Maryland, the U.S. Geological Survey is developing enhanced bioremediation methods that simulate the natural anaerobic degradation that occurs without intervention in non-seep areas of the wetland. A combination of natural attenuation and enhanced bioremediation could provide a remedy for the discharging ground-water plumes that would minimize disturbance to the sensitive wetland ecosystem. Biostimulation (addition of organic substrate or nutrients) and bioaugmentation (addition of microbial consortium), applied either by direct injection at depth in the wetland sediments or by construction of a permeable reactive mat at the seep surface, were tested as possible methods to enhance anaerobic degradation in the seep areas. For the first phase of developing enhanced bioremediation methods for the contaminant mixtures in the seeps, laboratory studies were conducted to develop a microbial consortium to degrade 1,1,2,2-tetrachloroethane and its chlorinated daughter products under anaerobic conditions, and to test biostimulation and bioaugmentation of wetland sediment and reactive mat matrices in microcosms. The individual components required for the direct injection and reactive mat methods were then combined in column experiments to test them under groundwater- flow rates and contaminant concentrations observed in the field. Results showed that both direct injection and the reactive mat are promising remediation methods, although the success of direct injection likely would depend on adequately distributing and maintaining organic substrate throughout the wetland sediment in the seep area. For bioaugmentation, two mixed anaerobic cultures, named the 'West Branch Consortia' (WBC-1 and WBC-2), were developed by enrichment of wetland sediment collected from two contaminated sites in the study area where rapid and complete reductive dechlorination naturally occurs. WBC are capable of degrading 1,1,2,2-tetrachloroethane, 1,1,2-trichloroethane, 1,2-dichloroethane, tetrachloroethene, trichloroethene, cis- and trans-1,2-dichloroethene, and vinyl chloride to the non-chlorinated end-products ethene and ethane. In addition, the column experiments showed that the consortia could completely degrade carbon tetrachloride and chloroform, although they were not grown on these contaminants. No other cultures are known that can degrade the broad mixture of chlorinated alkanes, alkenes, and methanes as shown for WBC. WBC-2 (suspended in the culture media) is capable of complete dechlorination of 50 micromolar 1,1,2,2-tetrachloroethane to ethene in 1 to 2 days with little transient accumulation of chlorinated daughter products. Only about 5 percent of the clones sequenced from WBC-1 and WBC-2 were related to dechlorinating bacteria that have been studied previously in culture, indicating the presence of unknown dechlorinators. Dehalococcoides spp. comprised about 1 percent of WBC-1 and WBC-2, which is minor compared to the population size of about 30 percent in other dechlorinating consortia for chlorinated alkenes. Although both WBC-1 and WBC-2 showed efficient degradation in laboratory tests in this study, long-term cultivation of WBC-1, which was developed using hydrogen as the organic substrate, was determined to be infeasible. Thus, WBC-2, cultivated with lactate as the organic substrate, would be used in future tests. Nutrient (ammonia and phosphate mixture) addition to anaerobic microcosms constructed with wetland sediment and ground water collected from the study area showed some enhancement in the degradation rate of 1,1,2,2-tetrachloroethane, but degrada

Biogeochemical Typing of Paddy Field by a Data-Driven Approach Revealing Sub-Systems within a Complex Environment - A Pipeline to Filtrate, Organize and Frame Massive Dataset from Multi-Omics Analyses

PubMed Central

Ogawa, Diogo M. O.; Moriya, Shigeharu; Tsuboi, Yuuri; Date, Yasuhiro; Prieto-da-Silva, Álvaro R. B.; Rádis-Baptista, Gandhi; Yamane, Tetsuo; Kikuchi, Jun

2014-01-01

We propose the technique of biogeochemical typing (BGC typing) as a novel methodology to set forth the sub-systems of organismal communities associated to the correlated chemical profiles working within a larger complex environment. Given the intricate characteristic of both organismal and chemical consortia inherent to the nature, many environmental studies employ the holistic approach of multi-omics analyses undermining as much information as possible. Due to the massive amount of data produced applying multi-omics analyses, the results are hard to visualize and to process. The BGC typing analysis is a pipeline built using integrative statistical analysis that can treat such huge datasets filtering, organizing and framing the information based on the strength of the various mutual trends of the organismal and chemical fluctuations occurring simultaneously in the environment. To test our technique of BGC typing, we choose a rich environment abounding in chemical nutrients and organismal diversity: the surficial freshwater from Japanese paddy fields and surrounding waters. To identify the community consortia profile we employed metagenomics as high throughput sequencing (HTS) for the fragments amplified from Archaea rRNA, universal 16S rRNA and 18S rRNA; to assess the elemental content we employed ionomics by inductively coupled plasma optical emission spectroscopy (ICP-OES); and for the organic chemical profile, metabolomics employing both Fourier transformed infrared (FT-IR) spectroscopy and proton nuclear magnetic resonance (1H-NMR) all these analyses comprised our multi-omics dataset. The similar trends between the community consortia against the chemical profiles were connected through correlation. The result was then filtered, organized and framed according to correlation strengths and peculiarities. The output gave us four BGC types displaying uniqueness in community and chemical distribution, diversity and richness. We conclude therefore that the BGC typing is a successful technique for elucidating the sub-systems of organismal communities with associated chemical profiles in complex ecosystems. PMID:25330259

Biogeochemical typing of paddy field by a data-driven approach revealing sub-systems within a complex environment--a pipeline to filtrate, organize and frame massive dataset from multi-omics analyses.

PubMed

Ogawa, Diogo M O; Moriya, Shigeharu; Tsuboi, Yuuri; Date, Yasuhiro; Prieto-da-Silva, Álvaro R B; Rádis-Baptista, Gandhi; Yamane, Tetsuo; Kikuchi, Jun

2014-01-01

We propose the technique of biogeochemical typing (BGC typing) as a novel methodology to set forth the sub-systems of organismal communities associated to the correlated chemical profiles working within a larger complex environment. Given the intricate characteristic of both organismal and chemical consortia inherent to the nature, many environmental studies employ the holistic approach of multi-omics analyses undermining as much information as possible. Due to the massive amount of data produced applying multi-omics analyses, the results are hard to visualize and to process. The BGC typing analysis is a pipeline built using integrative statistical analysis that can treat such huge datasets filtering, organizing and framing the information based on the strength of the various mutual trends of the organismal and chemical fluctuations occurring simultaneously in the environment. To test our technique of BGC typing, we choose a rich environment abounding in chemical nutrients and organismal diversity: the surficial freshwater from Japanese paddy fields and surrounding waters. To identify the community consortia profile we employed metagenomics as high throughput sequencing (HTS) for the fragments amplified from Archaea rRNA, universal 16S rRNA and 18S rRNA; to assess the elemental content we employed ionomics by inductively coupled plasma optical emission spectroscopy (ICP-OES); and for the organic chemical profile, metabolomics employing both Fourier transformed infrared (FT-IR) spectroscopy and proton nuclear magnetic resonance (1H-NMR) all these analyses comprised our multi-omics dataset. The similar trends between the community consortia against the chemical profiles were connected through correlation. The result was then filtered, organized and framed according to correlation strengths and peculiarities. The output gave us four BGC types displaying uniqueness in community and chemical distribution, diversity and richness. We conclude therefore that the BGC typing is a successful technique for elucidating the sub-systems of organismal communities with associated chemical profiles in complex ecosystems.

Longitudinal analysis of microbiota in microalga Nannochloropsis salina cultures

DOE PAGES

Geng, Haifeng; Sale, Kenneth L.; Tran-Gyamfi, Mary Bao; ...

2016-03-08

Here, large-scale open microalgae cultivation has tremendous potential to make a significant contribution to replacing petroleum-based fuels with biofuels. Open algal cultures are unavoidably inhabited with a diversity of microbes that live on, influence, and shape the fate of these ecosystems. However, there is little understanding of the resilience and stability of the microbial communities in engineered semicontinuous algal systems. To evaluate the dynamics and resilience of the microbial communities in microalgae biofuel cultures, we conducted a longitudinal study on open systems to compare the temporal profiles of the microbiota from two multigenerational algal cohorts, which include one seeded withmore » the microbiota from an in-house culture and the other exogenously seeded with a natural-occurring consortia of bacterial species harvested from the Pacific Ocean. From these month-long, semicontinuous open microalga Nannochloropsis salina cultures, we sequenced a time-series of 46 samples, yielding 8804 operational taxonomic units derived from 9,160,076 high-quality partial 16S rRNA sequences. We provide quantitative evidence that clearly illustrates the development of microbial community is associated with microbiota ancestry. In addition, N. salina growth phases were linked with distinct changes in microbial phylotypes. Alteromonadeles dominated the community in the N. salina exponential phase whereas Alphaproteobacteria and Flavobacteriia were more prevalent in the stationary phase. We also demonstrate that the N. salina-associated microbial community in open cultures is diverse, resilient, and dynamic in response to environmental perturbations. This knowledge has general implications for developing and testing design principles of cultivated algal systems.« less

PRELIMINARY CHARACTERIZATION OF FOUR 2-CHLOROBENZOATE-DEGRADING ANAEROBIC BACTERIAL CONSORTIA

EPA Science Inventory

Dechlorination was the initial step of 2CB biodegradation in four 2-chlorobenzoate-degrading methanogenic consortia. Selected characteristics of orthoreductive dehalogenation were examined in consortia developed from the highest actively dechlorinating dilutions of the original 2...

Training Consortia: How They Work, How They Don't.

ERIC Educational Resources Information Center

Filipczak, Bob

1994-01-01

Looks at the pros and cons of training consortia. Suggests that they can be a cost-effective training strategy, especially for small companies. Describes three categories of consortia: private for-profit, private nonprofit, and public sector. (JOW)

A Latitudinal Metabolome of the Atlantic Ocean

NASA Astrophysics Data System (ADS)

Johnson, W.; Kido Soule, M. C.; Longnecker, K.; Kujawinski, E. B.

2016-02-01

Microbial consortia function via the exchange and transformation of small organic molecules or metabolites. These metabolites make up a pool of rapidly cycling organic matter in the ocean that is challenging to characterize due to its low concentrations. We seek to determine the distribution of these molecules and the factors that shape their abundance and flux. Through measurements of the abundance of a core set of metabolites, including nucleic acids, amino acids, sugars, vitamins, and signaling molecules, we gain a real-time snapshot of microbial activity. We used a targeted metabolomics technique to profile metabolite abundance in particulate and dissolved organic matter extracts collected from a 14,000 km transect running from 38˚S to 55˚N in the Western Atlantic Ocean. This extensive dataset is the first of its kind in the Atlantic Ocean and allows us to explore connections among metabolites as well as latitudinal trends in metabolite abundance. We found changes in the intracellular abundance of certain metabolites between low and high nutrient regions and a wide distribution of certain dissolved vitamins in the surface ocean. These measurements give us baseline data on the distribution of these metabolites and allow us to extend our understanding of microbial community activity in different regions of the ocean.

Powering microbes with electricity: direct electron transfer from electrodes to microbes.

PubMed

Lovley, Derek R

2011-02-01

The discovery of electrotrophs, microorganisms that can directly accept electrons from electrodes for the reduction of terminal electron acceptors, has spurred the investigation of a wide range of potential applications. To date, only a handful of pure cultures have been shown to be capable of electrotrophy, but this process has also been inferred in many studies with undefined consortia. Potential electron acceptors include: carbon dioxide, nitrate, metals, chlorinated compounds, organic acids, protons and oxygen. Direct electron transfer from electrodes to cells has many advantages over indirect electrical stimulation of microbial metabolism via electron shuttles or hydrogen production. Supplying electrons with electrodes for the bioremediation of chlorinated compounds, nitrate or toxic metals may be preferable to adding organic electron donors or hydrogen to the subsurface or bioreactors. The most transformative application of electrotrophy may be microbial electrosynthesis in which carbon dioxide and water are converted to multi-carbon organic compounds that are released extracellularly. Coupling photovoltaic technology with microbial electrosynthesis represents a novel photosynthesis strategy that avoids many of the drawbacks of biomass-based strategies for the production of transportation fuels and other organic chemicals. The mechanisms for direct electron transfer from electrodes to microorganisms warrant further investigation in order to optimize envisioned applications. © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.

Enrichment of denitrifying methane-oxidizing microorganisms using up-flow continuous reactors and batch cultures.

PubMed

Hatamoto, Masashi; Kimura, Masafumi; Sato, Takafumi; Koizumi, Masato; Takahashi, Masanobu; Kawakami, Shuji; Araki, Nobuo; Yamaguchi, Takashi

2014-01-01

Denitrifying anaerobic methane oxidizing (DAMO) microorganisms were enriched from paddy field soils using continuous-flow and batch cultures fed with nitrate or nitrite as a sole electron acceptor. After several months of cultivation, the continuous-flow cultures using nitrite showed remarkable simultaneous methane oxidation and nitrite reduction and DAMO bacteria belonging to phylum NC10 were enriched. A maximum volumetric nitrite consumption rate of 70.4±3.4 mg-N·L(-1)·day(-1) was achieved with very short hydraulic retention time of 2.1 hour. In the culture, about 68% of total microbial cells were bacteria and no archaeal cells were detected by fluorescence in situ hybridization. In the nitrate-fed continuous-flow cultures, 58% of total microbial cells were bacteria while archaeal cells accounted for 7% of total cell numbers. Phylogenetic analysis of pmoA gene sequence showed that enriched DAMO bacteria in the continuous-flow cultivation had over 98% sequence similarity to DAMO bacteria in the inoculum. In contrast, for batch culture, the enriched pmoA gene sequences had 89-91% sequence similarity to DAMO bacteria in the inoculum. These results indicate that electron acceptor and cultivation method strongly affect the microbial community structures of DAMO consortia.

Electricity generation using white and red wine lees in air cathode microbial fuel cells

NASA Astrophysics Data System (ADS)

Pepe Sciarria, Tommy; Merlino, Giuseppe; Scaglia, Barbara; D'Epifanio, Alessandra; Mecheri, Barbara; Borin, Sara; Licoccia, Silvia; Adani, Fabrizio

2015-01-01

Microbial fuel cell (MFC) is a useful biotechnology to produce electrical energy from different organic substrates. This work reports for the first time results of the application of single chamber MFCs to generate electrical energy from diluted white wine (WWL) and red wine (RWL) lees. Power obtained was of 8.2 W m-3 (262 mW m-2; 500 Ω) and of 3.1 W m-3 (111 mW m-2; 500Ω) using white and red wine lees, respectively. Biological processes lead to a reduction of chemical oxygen (TCOD) and biological oxygen demand (BOD5) of 27% and 83% for RWL and of 90% and 95% for WWL, respectively. These results depended on the degradability of organic compounds contained, as suggest by BOD5/TCOD of WWL (0.93) vs BOD5/TCOD of RWL (0.33), and to the high presence of polyphenols in RWL that inhibited the process. Coulombic efficiency (CE) of 15 ± 0%, for WWL, was in line with those reported in the literature for other substrates, i.e. CE of 14.9 ± 11.3%. Different substrates led to different microbial consortia, particularly at the anode. Bacterial species responsible for the generation of electricity, were physically connected to the electrode, where the direct electron transfer took place.

Prokaryotic diversity, composition structure, and phylogenetic analysis of microbial communities in leachate sediment ecosystems.

PubMed

Liu, Jingjing; Wu, Weixiang; Chen, Chongjun; Sun, Faqian; Chen, Yingxu

2011-09-01

In order to obtain insight into the prokaryotic diversity and community in leachate sediment, a culture-independent DNA-based molecular phylogenetic approach was performed with archaeal and bacterial 16S rRNA gene clone libraries derived from leachate sediment of an aged landfill. A total of 59 archaeal and 283 bacterial rDNA phylotypes were identified in 425 archaeal and 375 bacterial analyzed clones. All archaeal clones distributed within two archaeal phyla of the Euryarchaeota and Crenarchaeota, and well-defined methanogen lineages, especially Methanosaeta spp., are the most numerically dominant species of the archaeal community. Phylogenetic analysis of the bacterial library revealed a variety of pollutant-degrading and biotransforming microorganisms, including 18 distinct phyla. A substantial fraction of bacterial clones showed low levels of similarity with any previously documented sequences and thus might be taxonomically new. Chemical characteristics and phylogenetic inferences indicated that (1) ammonium-utilizing bacteria might form consortia to alleviate or avoid the negative influence of high ammonium concentration on other microorganisms, and (2) members of the Crenarchaeota found in the sediment might be involved in ammonium oxidation. This study is the first to report the composition of the microbial assemblages and phylogenetic characteristics of prokaryotic populations extant in leachate sediment. Additional work on microbial activity and contaminant biodegradation remains to be explored.

Suitability and setup of next-generation sequencing-based method for taxonomic characterization of aquatic microbial biofilm.

PubMed

Bakal, Tomas; Janata, Jiri; Sabova, Lenka; Grabic, Roman; Zlabek, Vladimir; Najmanova, Lucie

2018-06-16

A robust and widely applicable method for sampling of aquatic microbial biofilm and further sample processing is presented. The method is based on next-generation sequencing of V4-V5 variable regions of 16S rRNA gene and further statistical analysis of sequencing data, which could be useful not only to investigate taxonomic composition of biofilm bacterial consortia but also to assess aquatic ecosystem health. Five artificial materials commonly used for biofilm growth (glass, stainless steel, aluminum, polypropylene, polyethylene) were tested to determine the one giving most robust and reproducible results. The effect of used sampler material on total microbial composition was not statistically significant; however, the non-plastic materials (glass, metal) gave more stable outputs without irregularities among sample parallels. The bias of the method is assessed with respect to the employment of a non-quantitative step (PCR amplification) to obtain quantitative results (relative abundance of identified taxa). This aspect is often overlooked in ecological and medical studies. We document that sequencing of a mixture of three merged primary PCR reactions for each sample and further evaluation of median values from three technical replicates for each sample enables to overcome this bias and gives robust and repeatable results well distinguishing among sampling localities and seasons.

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.

Evaluation of Simultaneous Nutrient and COD Removal with Polyhydroxybutyrate (PHB) Accumulation Using Mixed Microbial Consortia under Anoxic Condition and Their Bioinformatics Analysis

PubMed Central

Jena, Jyotsnarani; Kumar, Ravindra; Dixit, Anshuman; Pandey, Sony; Das, Trupti

2015-01-01

Simultaneous nitrate-N, phosphate and COD removal was evaluated from synthetic waste water using mixed microbial consortia in an anoxic environment under various initial carbon load (ICL) in a batch scale reactor system. Within 6 hours of incubation, enriched DNPAOs (Denitrifying Polyphosphate Accumulating Microorganisms) were able to remove maximum COD (87%) at 2g/L of ICL whereas maximum nitrate-N (97%) and phosphate (87%) removal along with PHB accumulation (49 mg/L) was achieved at 8 g/L of ICL. Exhaustion of nitrate-N, beyond 6 hours of incubation, had a detrimental effect on COD and phosphate removal rate. Fresh supply of nitrate-N to the reaction medium, beyond 6 hours, helped revive the removal rates of both COD and phosphate. Therefore, it was apparent that in spite of a high carbon load, maximum COD and nutrient removal can be maintained, with adequate nitrate-N availability. Denitrifying condition in the medium was evident from an increasing pH trend. PHB accumulation by the mixed culture was directly proportional to ICL; however the time taken for accumulation at higher ICL was more. Unlike conventional EBPR, PHB depletion did not support phosphate accumulation in this case. The unique aspect of all the batch studies were PHB accumulation was observed along with phosphate uptake and nitrate reduction under anoxic conditions. Bioinformatics analysis followed by pyrosequencing of the mixed culture DNA from the seed sludge revealed the dominance of denitrifying population, such as Corynebacterium, Rhodocyclus and Paraccocus (Alphaproteobacteria and Betaproteobacteria). Rarefaction curve indicated complete bacterial population and corresponding number of OTUs through sequence analysis. Chao1 and Shannon index (H’) was used to study the diversity of sampling. “UCI95” and “LCI95” indicated 95% confidence level of upper and lower values of Chao1 for each distance. Values of Chao1 index supported the results of rarefaction curve. PMID:25689047

Evaluation of simultaneous nutrient and COD removal with polyhydroxybutyrate (PHB) accumulation using mixed microbial consortia under anoxic condition and their bioinformatics analysis.

PubMed

Jena, Jyotsnarani; Kumar, Ravindra; Dixit, Anshuman; Pandey, Sony; Das, Trupti

2015-01-01

Simultaneous nitrate-N, phosphate and COD removal was evaluated from synthetic waste water using mixed microbial consortia in an anoxic environment under various initial carbon load (ICL) in a batch scale reactor system. Within 6 hours of incubation, enriched DNPAOs (Denitrifying Polyphosphate Accumulating Microorganisms) were able to remove maximum COD (87%) at 2 g/L of ICL whereas maximum nitrate-N (97%) and phosphate (87%) removal along with PHB accumulation (49 mg/L) was achieved at 8 g/L of ICL. Exhaustion of nitrate-N, beyond 6 hours of incubation, had a detrimental effect on COD and phosphate removal rate. Fresh supply of nitrate-N to the reaction medium, beyond 6 hours, helped revive the removal rates of both COD and phosphate. Therefore, it was apparent that in spite of a high carbon load, maximum COD and nutrient removal can be maintained, with adequate nitrate-N availability. Denitrifying condition in the medium was evident from an increasing pH trend. PHB accumulation by the mixed culture was directly proportional to ICL; however the time taken for accumulation at higher ICL was more. Unlike conventional EBPR, PHB depletion did not support phosphate accumulation in this case. The unique aspect of all the batch studies were PHB accumulation was observed along with phosphate uptake and nitrate reduction under anoxic conditions. Bioinformatics analysis followed by pyrosequencing of the mixed culture DNA from the seed sludge revealed the dominance of denitrifying population, such as Corynebacterium, Rhodocyclus and Paraccocus (Alphaproteobacteria and Betaproteobacteria). Rarefaction curve indicated complete bacterial population and corresponding number of OTUs through sequence analysis. Chao1 and Shannon index (H') was used to study the diversity of sampling. "UCI95" and "LCI95" indicated 95% confidence level of upper and lower values of Chao1 for each distance. Values of Chao1 index supported the results of rarefaction curve.

Investigation on paper cup waste degradation by bacterial consortium and Eudrillus eugeinea through vermicomposting.

PubMed

Arumugam, Karthika; Renganathan, Seenivasagan; Babalola, Olubukola Oluranti; Muthunarayanan, Vasanthy

2018-04-01

Disposable Paper cups are a threat to the environment and are composed of 90% high strength paper with 5% thin coating of polyethylene. This polyethylene prevents the paper cup from undergoing degradation in the soil. Hence, in the present study two different approaches towards the management of paper cup waste through vermicomposting technology has been presented. The experimental setup includes 2 plastic reactors namely Vermicompost (VC) (Cow dung + Paper cup waste + Earthworm (Eudrillus eugeinea)) and Vermicompost with bacterial consortium (VCB) (Cow dung + Paper cup waste + Eudrillus eugeinea + Microbial consortia such as Bacillus anthracis, B. endophyticus, B. funiculus, B. thuringiensis, B. cereus, B. toyonensis, Virigibacillius chiquenigi, Acinetobacter baumanni and Lactobacillus pantheries). After treatment the physicochemical parameters were analysed. The results showed that the values of TOC (26.52 and 37.47%), TOM (36.01 and 33.13%) and C/N (15.02 and 11.92%) ratio are reduced in both VC and VCB whereas, the values of pH (8.01 and 7.56), EC (1.2-1.9 µs -1 and 1.4-1.9 µs -1 ), TP (46.1 and 51%), TMg (50.52 and 64.3%), TCa (50 and 64%), TNa (1.39 and 1.75%) and TK (1.75 and 1.86%) have increased. This study substantiates the addition of the microbial consortia augmenting the degradation in VCB reactor by reducing the period of process from 19 to 12 weeks. Further the characterisation of the vermicompost prepared from paper cup with FT-IR shows high degradation of carboxylic and aliphatic group; SEM analysis shows the disaggregation of cellulose and lignin; XRD shows the degradation of cellulose. All these analyses endorse the degradation of the paper cup waste faster with microbes (VCB). Thus, this present study high lights management of the paper cup waste in a relatively short period of time. Copyright © 2017 Elsevier Ltd. All rights reserved.

Research Guidelines in the Era of Large-scale Collaborations: An Analysis of Genome-wide Association Study Consortia

PubMed Central

Austin, Melissa A.; Hair, Marilyn S.; Fullerton, Stephanie M.

2012-01-01

Scientific research has shifted from studies conducted by single investigators to the creation of large consortia. Genetic epidemiologists, for example, now collaborate extensively for genome-wide association studies (GWAS). The effect has been a stream of confirmed disease-gene associations. However, effects on human subjects oversight, data-sharing, publication and authorship practices, research organization and productivity, and intellectual property remain to be examined. The aim of this analysis was to identify all research consortia that had published the results of a GWAS analysis since 2005, characterize them, determine which have publicly accessible guidelines for research practices, and summarize the policies in these guidelines. A review of the National Human Genome Research Institute’s Catalog of Published Genome-Wide Association Studies identified 55 GWAS consortia as of April 1, 2011. These consortia were comprised of individual investigators, research centers, studies, or other consortia and studied 48 different diseases or traits. Only 14 (25%) were found to have publicly accessible research guidelines on consortia websites. The available guidelines provide information on organization, governance, and research protocols; half address institutional review board approval. Details of publication, authorship, data-sharing, and intellectual property vary considerably. Wider access to consortia guidelines is needed to establish appropriate research standards with broad applicability to emerging forms of large-scale collaboration. PMID:22491085

Proper joint analysis of summary association statistics requires the adjustment of heterogeneity in SNP coverage pattern.

PubMed

Zhang, Han; Wheeler, William; Song, Lei; Yu, Kai

2017-07-07

As meta-analysis results published by consortia of genome-wide association studies (GWASs) become increasingly available, many association summary statistics-based multi-locus tests have been developed to jointly evaluate multiple single-nucleotide polymorphisms (SNPs) to reveal novel genetic architectures of various complex traits. The validity of these approaches relies on the accurate estimate of z-score correlations at considered SNPs, which in turn requires knowledge on the set of SNPs assessed by each study participating in the meta-analysis. However, this exact SNP coverage information is usually unavailable from the meta-analysis results published by GWAS consortia. In the absence of the coverage information, researchers typically estimate the z-score correlations by making oversimplified coverage assumptions. We show through real studies that such a practice can generate highly inflated type I errors, and we demonstrate the proper way to incorporate correct coverage information into multi-locus analyses. We advocate that consortia should make SNP coverage information available when posting their meta-analysis results, and that investigators who develop analytic tools for joint analyses based on summary data should pay attention to the variation in SNP coverage and adjust for it appropriately. Published by Oxford University Press 2017. This work is written by US Government employees and is in the public domain in the US.

Microbial life in cold, sulfur-rich environments: Investigations of an Arctic ecosystem and implications for life detection at Europa

NASA Astrophysics Data System (ADS)

Gleeson, Damhnait Fagan

2009-12-01

Exobiological investigations require a detailed understanding of life's interactions with its environment here on Earth before we can confidently recognize signs of these interactions at other worlds such as Europa. Using a cold, sulfur-based ecosystem at Borup Fiord pass in the Canadian High Arctic as a study site, I investigated how the supraglacial non-ice materials are represented across different scales in spectral data, how microbiology is influencing the mineralogy of the site, and whether the products of microbial sulfide oxidation preserve indications of their biogenic origin. A systematic scale-integrated approach was applied to query orbital (Hyperion), field, and laboratory spectra to identify sulfur-rich materials precipitated on a glacier. While sulfur, the main constituent of the deposits, is well represented in Hyperion data, minor constituents such as calcite and gypsum are partially or entirely masked. Absorption features of sulfates, where present, are shifted in wavelength due to the effects of mixing or temperature. Autonomous detection methods were successfully applied to monitor the generation and extent of the deposits, which show spectral similarities to Europa's non-ice materials. Geomicrobiological cultivation of sulfide oxidizing bacteria succeeded in demonstrating that the microbiological community present at the site has the potential to catalyze the generation of sulfur deposits. Sulfur generated in culture is present as biomineralized structures comprised of microbial filaments and sheaths along which sulfur globules are deposited. Consortia producing these structures are dominated by gamma-Proteobacteria closely related to Marinobacter, not previously known to oxidize sulfide. The sulfur structures produced by these consortia are not observed in abiotic controls and have the potential to serve as morphological biosignatures. Investigations into the biogenicity of field deposits reveal mineral assemblages with similar morphologies to those generated in culture. X-ray diffraction analyses show some evidence for rosickyite, a metastable form of biogenic sulfur. Mid-infrared laboratory spectroscopy also indicates the presence of organic functional groups diagnostic of proteins and fatty acids within the sulfur deposits. These combined investigations suggest that sulfur minerals extruded onto Europa's near surface, analogous to those of Borup Fiord pass, have the potential to contain identifiable biosignatures which low-temperature conditions could help stabilize and preserve.

What Role for Law, Human Rights, and Bioethics in an Age of Big Data, Consortia Science, and Consortia Ethics? The Importance of Trustworthiness.

PubMed

Dove, Edward S; Özdemir, Vural

2015-09-01

The global bioeconomy is generating new paradigm-shifting practices of knowledge co-production, such as collective innovation; large-scale, data-driven global consortia science (Big Science); and consortia ethics (Big Ethics). These bioeconomic and sociotechnical practices can be forces for progressive social change, but they can also raise predicaments at the interface of law, human rights, and bioethics. In this article, we examine one such double-edged practice: the growing, multivariate exploitation of Big Data in the health sector, particularly by the private sector. Commercial exploitation of health data for knowledge-based products is a key aspect of the bioeconomy and is also a topic of concern among publics around the world. It is exacerbated in the current age of globally interconnected consortia science and consortia ethics, which is characterized by accumulating epistemic proximity, diminished academic independence, "extreme centrism", and conflicted/competing interests among innovation actors. Extreme centrism is of particular importance as a new ideology emerging from consortia science and consortia ethics; this relates to invariably taking a middle-of-the-road populist stance, even in the event of human rights breaches, so as to sustain the populist support needed for consortia building and collective innovation. What role do law, human rights, and bioethics-separate and together-have to play in addressing these predicaments and opportunities in early 21st century science and society? One answer we propose is an intertwined ethico-legal normative construct, namely trustworthiness . By considering trustworthiness as a central pillar at the intersection of law, human rights, and bioethics, we enable others to trust us, which in turns allows different actors (both nonprofit and for-profit) to operate more justly in consortia science and ethics, as well as to access and responsibly use health data for public benefit.

What Role for Law, Human Rights, and Bioethics in an Age of Big Data, Consortia Science, and Consortia Ethics? The Importance of Trustworthiness

PubMed Central

Dove, Edward S.; Özdemir, Vural

2015-01-01

The global bioeconomy is generating new paradigm-shifting practices of knowledge co-production, such as collective innovation; large-scale, data-driven global consortia science (Big Science); and consortia ethics (Big Ethics). These bioeconomic and sociotechnical practices can be forces for progressive social change, but they can also raise predicaments at the interface of law, human rights, and bioethics. In this article, we examine one such double-edged practice: the growing, multivariate exploitation of Big Data in the health sector, particularly by the private sector. Commercial exploitation of health data for knowledge-based products is a key aspect of the bioeconomy and is also a topic of concern among publics around the world. It is exacerbated in the current age of globally interconnected consortia science and consortia ethics, which is characterized by accumulating epistemic proximity, diminished academic independence, “extreme centrism”, and conflicted/competing interests among innovation actors. Extreme centrism is of particular importance as a new ideology emerging from consortia science and consortia ethics; this relates to invariably taking a middle-of-the-road populist stance, even in the event of human rights breaches, so as to sustain the populist support needed for consortia building and collective innovation. What role do law, human rights, and bioethics—separate and together—have to play in addressing these predicaments and opportunities in early 21st century science and society? One answer we propose is an intertwined ethico-legal normative construct, namely trustworthiness. By considering trustworthiness as a central pillar at the intersection of law, human rights, and bioethics, we enable others to trust us, which in turns allows different actors (both nonprofit and for-profit) to operate more justly in consortia science and ethics, as well as to access and responsibly use health data for public benefit. PMID:26345196

Treatment of corn ethanol distillery wastewater using two-stage anaerobic digestion.

PubMed

Ráduly, B; Gyenge, L; Szilveszter, Sz; Kedves, A; Crognale, S

In this study the mesophilic two-stage anaerobic digestion (AD) of corn bioethanol distillery wastewater is investigated in laboratory-scale reactors. Two-stage AD technology separates the different sub-processes of the AD in two distinct reactors, enabling the use of optimal conditions for the different microbial consortia involved in the different process phases, and thus allowing for higher applicable organic loading rates (OLRs), shorter hydraulic retention times (HRTs) and better conversion rates of the organic matter, as well as higher methane content of the produced biogas. In our experiments the reactors have been operated in semi-continuous phase-separated mode. A specific methane production of 1,092 mL/(L·d) has been reached at an OLR of 6.5 g TCOD/(L·d) (TCOD: total chemical oxygen demand) and a total HRT of 21 days (5.7 days in the first-stage, and 15.3 days in the second-stage reactor). Nonetheless the methane concentration in the second-stage reactor was very high (78.9%); the two-stage AD outperformed the reference single-stage AD (conducted at the same reactor loading rate and retention time) by only a small margin in terms of volumetric methane production rate. This makes questionable whether the higher methane content of the biogas counterbalances the added complexity of the two-stage digestion.

Microbial ecology of sourdough fermentations: diverse or uniform?

PubMed

De Vuyst, L; Van Kerrebroeck, S; Harth, H; Huys, G; Daniel, H-M; Weckx, S

2014-02-01

Sourdough is a specific and stressful ecosystem inhabited by yeasts and lactic acid bacteria (LAB), mainly heterofermentative lactobacilli. On the basis of their inocula, three types of sourdough fermentation processes can be distinguished, namely backslopped ones, those initiated with starter cultures, and those initiated with a starter culture followed by backslopping. Typical sourdough LAB species are Lactobacillus fermentum, Lactobacillus paralimentarius, Lactobacillus plantarum, and Lactobacillus sanfranciscensis. Typical sourdough yeast species are Candida humilis, Kazachstania exigua, and Saccharomyces cerevisiae. Whereas region specificity is claimed in the case of artisan backslopped sourdoughs, no clear-cut relationship between a typical sourdough and its associated microbiota can be found, as this is dependent on the sampling, isolation, and identification procedures. Both simple and very complex consortia may occur. Moreover, a series of intrinsic and extrinsic factors may influence the composition of the sourdough microbiota. For instance, an influence of the flour (type, quality status, etc.) and the process parameters (temperature, pH, dough yield, backslopping practices, etc.) occurs. In this way, the presence of Lb. sanfranciscensis during sourdough fermentation depends on specific environmental and technological factors. Also, Triticum durum seems to select for obligately heterofermentative LAB species. Finally, there are indications that the sourdough LAB are of intestinal origin. Copyright © 2013 Elsevier Ltd. All rights reserved.

Clustering behavior in microbial communities from acute endodontic infections.

PubMed

Montagner, Francisco; Jacinto, Rogério C; Signoretti, Fernanda G C; Sanches, Paula F; Gomes, Brenda P F A

2012-02-01

Acute endodontic infections harbor heterogeneous microbial communities in both the root canal (RC) system and apical tissues. Data comparing the microbial structure and diversity in endodontic infections in related ecosystems, such as RC with necrotic pulp and acute apical abscess (AAA), are scarce in the literature. The aim of this study was to examine the presence of selected endodontic pathogens in paired samples from necrotic RC and AAA using polymerase chain reaction (PCR) followed by the construction of cluster profiles. Paired samples of RC and AAA exudates were collected from 20 subjects and analyzed by PCR for the presence of selected strict and facultative anaerobic strains. The frequency of species was compared between the RC and the AAA samples. A stringent neighboring clustering algorithm was applied to investigate the existence of similar high-order groups of samples. A dendrogram was constructed to show the arrangement of the sample groups produced by the hierarchical clustering. All samples harbored bacterial DNA. Porphyromonas endodontalis, Prevotella nigrescens, Filifactor alocis, and Tannerela forsythia were frequently detected in both RC and AAA samples. The selected anaerobic species were distributed in diverse small bacteria consortia. The samples of RC and AAA that presented at least one of the targeted microorganisms were grouped in small clusters. Anaerobic species were frequently detected in acute endodontic infections and heterogeneous microbial communities with low clustering behavior were observed in paired samples of RC and AAA. Copyright © 2012. Published by Elsevier Inc.

General practitioner commissioning consortia and budgetary risk: evidence from the modelling of 'fair share' practice budgets for mental health.

PubMed

Asthana, Sheena; Gibson, Alex; Hewson, Paul; Bailey, Trevor; Dibben, Chris

2011-04-01

To contribute to current policy debates regarding the devolution of commissioning responsibilities to locally-based consortia of general practices in England by assessing the potential magnitude and significance of budgetary risk for commissioning units of different sizes. Predictive distributions of practice-level mental health care resource needs (used by the Department of Health to set 'fair-share' practice budgets) are aggregated to a range of hypothetical, but spatially-contiguous, consortia serving populations of up to 400,000 patients. The resulting joint distributions describe the extent to which the legitimate mental health needs of consortia populations are likely to vary. Budgetary risk is calculated as the likelihood that a consortia's resource needs will, in any given year, exceed its allocation (taken as the mean of its predictive distribution) by more than 1%, 3%, 5% or 10%. The relationship between population size and budgetary risk is then explored. If between 500 and 600 consortia are created in England (serving 87,000 to 104,000 patients) then, in order to meet the legitimate mental health needs of their patients, each year around 15 to 26 consortia will overspend by at least 5%, and one or two by at least 10%. The budgetary risk faced by consortia serving smaller/larger populations can be read off the graphs provided. Unless steps are taken to mitigate budgetary risk, the devolution of decision-making and introduction of fixed budgets is likely to result in significant financial instability. It will be difficult to reconcile the policy objectives of devolved commissioning, best met through relatively small and fully accountable consortia, with the need for financial stability, which is best met by pooling risk across larger populations.

Higher Educational Consortia Organization: Functional Structures of Administration and Management.

ERIC Educational Resources Information Center

Lepchenske, George L.

The administrative and functional organization of higher education consortia are discussed. The need for cooperation between individual institutions has been established; one lone institution cannot encompass all knowledge generated. The rapid growth of consortia has generated extensive services, funding sources, developmental activities,…

Screening of a microbial consortium for selective degradation of lignin from tree trimmings.

PubMed

Fang, Xiuxiu; Li, Qiumin; Lin, Yunqin; Lin, Xinlei; Dai, Yiqi; Guo, Zexiang; Pan, Dezhao

2018-04-01

To acquire microbial consortia with effectively precedent degradation of lignin, samples obtained from rotten trunks, rotten stumps and soil near it were screened and isolated after generations of subculture. The dynamic change illustrated that their community structures were affected by pH and tended to be stable after 6 days' cultivation. The desired one, named DM-1, was gained through successive cultivation for over 5 generations, whose high selectivity in lignin degradation was observed within 16 days' cultivation (SV = 2.78). Meanwhile, a remarkable reduction in the fiber crystallinity of tree trimmings (10.35%) resulted from the bio-degradation of DM-1, displayed a greater exposure of cellulose by selective removal of lignin. The diversity analysis of DM-1 was investigated by PCR amplification and 16S rDNA sequencing, indicated that mesorhizobium, cellulosimicrobium, pandoraea, achromobacter and stenotrophomones were the predominant genera. Furthermore, fungi (3 strains), bacteria (4 strains) and actinomycetes (5 strains) constituted 12 strains in total were gained by plate isolation from DM-1. Copyright © 2018 Elsevier Ltd. All rights reserved.

Formulation of microbial cocktails for BTEX biodegradation.

PubMed

Nagarajan, Karthiga; Loh, Kai-Chee

2015-02-01

BTEX biodegradation by a mixed community of micro-organisms offers a promising approach in terms of cost-effectiveness and elimination of secondary pollution. Two bacterial strains, Pseudomonas putida F1 and Pseudomonas stutzeri OX1 were chosen to formulate synthetic consortia based on their ability to biodegrade the mono-aromatic compounds. Benzene and toluene supported the growth of both the strains; while ethyl benzene and o-xylene were only utilized as growth substrates by P. putida F1 and P. stutzeri OX1, respectively. In a mixed substrate system, P. putida F1 exhibited incomplete removal of o-xylene while P. stutzeri OX1 displayed cometabolic removal of ethyl benzene with dark coloration of the growth medium. The biodegradation potential of the two Pseudomonas species complemented each other and offered opportunities to explore their performance as a co-culture for enhanced BTEX biodegradation. Several microbial formulations were concocted and their BTEX biodegradation characteristics were evaluated. Mixed culture biodegradation ascertained the advantages of the co-culture over the individual Pseudomonas species. This study also emphasized the significance of inoculum density and species proportion while concocting preselected micro-organisms for enhanced BTEX biodegradation.

Methane gas generation from waste water extraction process of crude palm oil in experimental digesters

NASA Astrophysics Data System (ADS)

Dillon, A.; Penafiel, R.; Garzón, P. V.; Ochoa, V.

2015-12-01

Industrial processes to extract crude palm oil, generates large amounts of waste water. High concentrations of COD, ST, SV, NH4 + and low solubility of O2, make the treatment of these effluents starts with anaerobic processes. The anaerobic digestion process has several advantages over aerobic degradation: lower operating costs (not aeration), low sludge production, methane gas generation. The 4 stages of anaerobic digestion are: hydrolysis, acidogenic, acetogenesis and methanogenesis. Through the action of enzymes synthesized by microbial consortia are met. The products of each step to serve as reagents is conducted as follows. The organic load times and cell hydraulic retention, solids content, nutrient availability, pH and temperature are factors that influence directly in biodigesters. The objectives of this presentation is to; characterize the microbial inoculum and water (from palm oil wasted water) to be used in biodigestores, make specific methanogenic activity in bioassays, acclimatize the microorganisms to produce methane gas using basal mineral medium with acetate for the input power, and to determine the production of methane gas digesters high organic load.

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.

Consortia--A Viable Model and Medium for Distance Education in Developing Countries?

ERIC Educational Resources Information Center

Beaudoin, Michael F.

2009-01-01

Consortia are increasingly popular mechanisms by which educational institutions may achieve organisational goals that might be especially challenging to accomplish individually. Such collaborations are intended to offer courses and services through combined resources and expertise. Consortia designed to develop and deliver distance education…

Novel Hydrogen Production Systems Operative at Thermodynamic Extremes

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

Gunsalus, Robert

2012-11-30

We have employed a suite of molecular, bioinformatics, and biochemical tools to interrogate the thermodynamically limiting steps of H{sub 2} production from fatty acids in syntrophic communities. We also developed a new microbial model system that generates high H{sub 2} concentrations (over 17% of the gas phase) with high H{sub 2} yields of over 3 moles H{sub 2} per mole glucose. Lastly, a systems-based study of biohydrogen production in model anaerobic consortia was performed to begin identifying key regulated steps as a precursor to modeling co-metabolism. The results of these studies significantly expand our ability to predict and model systemsmore » for H{sub 2} production in novel anaerobes that are currently very poorly documented or understood.« less

Data sharing and intellectual property in a genomic epidemiology network: policies for large-scale research collaboration.

PubMed Central

Chokshi, Dave A.; Parker, Michael; Kwiatkowski, Dominic P.

2006-01-01

Genomic epidemiology is a field of research that seeks to improve the prevention and management of common diseases through an understanding of their molecular origins. It involves studying thousands of individuals, often from different populations, with exacting techniques. The scale and complexity of such research has required the formation of research consortia. Members of these consortia need to agree on policies for managing shared resources and handling genetic data. Here we consider data-sharing and intellectual property policies for an international research consortium working on the genomic epidemiology of malaria. We outline specific guidelines governing how samples and data are transferred among its members; how results are released into the public domain; when to seek protection for intellectual property; and how intellectual property should be managed. We outline some pragmatic solutions founded on the basic principles of promoting innovation and access. PMID:16710548

A Study of the Inter-Organizational Behavior in Consortia. Final Report.

ERIC Educational Resources Information Center

Silverman, Robert J.

In an attempt to formulate hypotheses and administrative guidelines for voluntary consortia in higher education, a heuristic framework was devised through which behavioral patterns of consortia member organizations and their representatives could be ascertained. The rationale, the framework, and the methodology of the study are first discussed.…

Sustainability for the Americas: Building the American Network of Sustainability Consortia

ERIC Educational Resources Information Center

Motloch, John; Pacheco, Pedro; Vann, John

2007-01-01

Purpose: To build awareness of an emergent global network of sustainability consortia, the network's Sustainability for the Americas (SFTA) regional cluster, its pilot US-Brazil Sustainability Consortium (USBSC), its subsequent North American Sustainability, Housing and Community Consortium (NASHCC), the process through which these consortia are…

Partner Power: A Study of Two Distance Education Consortia

ERIC Educational Resources Information Center

Pidduck, Anne Banks; Carey, Tom

2006-01-01

This research reports findings from a study which explored the process and criteria of partner selection--how and why partners are chosen--for two distance education consortia. The researchers reviewed recent literature on partnerships and partner selection. Two Canada-wide distance education consortia were identified as large-scale case studies…

Hanging Together To Avoid Hanging Separately: Opportunities for Academic Libraries and Consortia.

ERIC Educational Resources Information Center

Allen, Barbara McFadden; Hirshon, Arnold

1998-01-01

Discusses academic library consortia, examines types of consortia, and presents three case histories (OhioLINK, PALCI and CIC). Highlights include economic competition; changes in information access and delivery; growth of information technology; quality improvement; and future strategies, including pricing models for electronic information,…

Educational Cooperation: An Examination of Fourteen Consortia.

ERIC Educational Resources Information Center

Lepchenske, George L.

The development of consortia and cooperative educational services in higher education in response to financial pressures and social and governmental influences is examined. Consortia or cooperatives may be multi-channeled efforts, with each member struggling to advance its own self-interest at the cost of united goals and efforts, or thriving…

How big is too big or how many partners are needed to build a large project which still can be managed successfully?

NASA Astrophysics Data System (ADS)

Henkel, Daniela; Eisenhauer, Anton

2017-04-01

During the last decades, the number of large research projects has increased and therewith the requirement for multidisciplinary, multisectoral collaboration. Such complex and large-scale projects pose new competencies to form, manage, and use large, diverse teams as a competitive advantage. For complex projects the effort is magnified because multiple large international research consortia involving academic and non-academic partners, including big industries, NGOs, private and public bodies, all with cultural differences, individually discrepant expectations on teamwork and differences in the collaboration between national and multi-national administrations and research organisations, challenge the organisation and management of such multi-partner research consortia. How many partners are needed to establish and conduct collaboration with a multidisciplinary and multisectoral approach? How much personnel effort and what kinds of management techniques are required for such projects. This presentation identifies advantages and challenges of large research projects based on the experiences made in the context of an Innovative Training Network (ITN) project within Marie Skłodowska-Curie Actions of the European HORIZON 2020 program. Possible strategies are discussed to circumvent and avoid conflicts already at the beginning of the project.

Dynamic monitoring of horizontal gene transfer in soil

NASA Astrophysics Data System (ADS)

Cheng, H. Y.; Masiello, C. A.; Silberg, J. J.; Bennett, G. N.

2015-12-01

Soil microbial gene expression underlies microbial behaviors (phenotypes) central to many aspects of C, N, and H2O cycling. However, continuous monitoring of microbial gene expression in soils is challenging because genetically-encoded reporter proteins widely used in the lab are difficult to deploy in soil matrices: for example, green fluorescent protein cannot be easily visualized in soils, even in the lab. To address this problem we have developed a reporter protein that releases small volatile gases. Here, we applied this gas reporter in a proof-of-concept soil experiment, monitoring horizontal gene transfer, a microbial activity that alters microbial genotypes and phenotypes. Horizontal gene transfer is central to bacterial evolution and adaptation and is relevant to problems such as the spread of antibiotic resistance, increasing metal tolerance in superfund sites, and bioremediation capability of bacterial consortia. This process is likely to be impacted by a number of matrix properties not well-represented in the petri dish, such as microscale variations in water, nutrients, and O2, making petri-dish experiments a poor proxy for environmental processes. We built a conjugation system using synthetic biology to demonstrate the use of gas-reporting biosensors in safe, lab-based biogeochemistry experiments, and here we report the use of these sensors to monitor horizontal gene transfer in soils. Our system is based on the F-plasmid conjugation in Escherichia coli. We have found that the gas signal reports on the number of cells that acquire F-plasmids (transconjugants) in a loamy Alfisol collected from Kellogg Biological Station. We will report how a gas signal generated by transconjugants varies with the number of F-plasmid donor and acceptor cells seeded in a soil, soil moisture, and soil O2 levels.

Challenges for Complex Microbial Ecosystems: Combination of Experimental Approaches with Mathematical Modeling

PubMed Central

Haruta, Shin; Yoshida, Takehito; Aoi, Yoshiteru; Kaneko, Kunihiko; Futamata, Hiroyuki

2013-01-01

In the past couple of decades, molecular ecological techniques have been developed to elucidate microbial diversity and distribution in microbial ecosystems. Currently, modern techniques, represented by meta-omics and single cell observations, are revealing the incredible complexity of microbial ecosystems and the large degree of phenotypic variation. These studies propound that microbiological techniques are insufficient to untangle the complex microbial network. This minireview introduces the application of advanced mathematical approaches in combination with microbiological experiments to microbial ecological studies. These combinational approaches have successfully elucidated novel microbial behaviors that had not been recognized previously. Furthermore, the theoretical perspective also provides an understanding of the plasticity, robustness and stability of complex microbial ecosystems in nature. PMID:23995424

Diversity and Phylogenetic Structure of Two Complex Marine Microbial Communities

DTIC Science & Technology

2004-09-01

Science 190 and Engineering DOCTORAL DISSERTATION Diversity and Phylogenetic Structure of Two Complex Marine Microbial Communities by Vanja Klepac-Ceraj...Two Complex Marine Microbial Communities by Vanja Klepac-Ceraj Massachusetts Institute of Technology Cambridge, Massachusetts 02139 and Woods Hole...Phylogenetic Structure of Two Complex Marine Microbial Communities. Ph.D. Thesis. MIT/WHOI, 2004-11. Approved for publication; distribution unlimited

Preservation and detection of microstructural and taxonomic correlations in the carbon isotopic compositions of individual Precambrian microfossils

NASA Astrophysics Data System (ADS)

Williford, Kenneth H.; Ushikubo, Takayuki; Schopf, J. William; Lepot, Kevin; Kitajima, Kouki; Valley, John W.

2013-03-01

Here we present techniques for, and new data from, in situ carbon isotope (δ13C) analysis of Precambrian permineralized microscopic fossils with a reproducibility of 1-2‰ using secondary ion mass spectrometry (SIMS). Individual microfossils, selected for their excellent preservation, were analyzed in petrographic thin sections of stromatolitic cherts from the Proterozoic Gunflint (˜1880 Ma), Bitter Springs (˜830 Ma), Min'yar (˜740 Ma), and Chichkan (˜775 Ma) Formations. The range of δ13C values (-34.6‰ to -22.1‰ VPDB) among the 46 individuals analyzed falls within that expected for photoautotrophic carbon fixation by ribulose bisphosphate carboxylase (RuBisCO), consistent with morphology-based taxonomic assignments for these specimens. Microfossils classified as cyanobacteria from the Gunflint, Bitter Springs, and Min'yar Formations (for which published carbonate carbon isotope data can be used to estimate the δ13C of the original dissolved inorganic carbon substrate) exhibit a consistent ˜19‰ total fractionation (δ13C of dissolved inorganic carbon - δ13C of biomass) similar to that observed in living cyanobacteria, over a wide range of δ13Ccarb values (-2.9‰ to 3.4‰). In stromatolitic chert of the Min'yar Formation, morphologically diverse microfossils preserved in a ˜1 mm2 part of a microbial mat exhibit systematic isotopic differences among and within taxa that correlate with their morphologically inferred biological affinities and suggest that isotopic signatures of their original biosynthetic processes (e.g., lipid and peptidoglycan synthesis) are preserved. Isotopic offsets consistent with the different RuBisCO-based fractionations typical of cyanobacteria and photosynthetic eukaryotes are documented by the differing δ13C values of a colonial cyanobacterium (-22.6 ± 0.5‰) and a phytoplanktonic protistan acritarch (-28.9 ± 1.0‰) situated <1 cm apart in the stromatolitic Chichkan chert. These findings show for the first time the possibility of using in situ isotopic microanalysis of fossil microbial mats and ancient sediments in order to distinguish metabolic fingerprints within complex microbial ecosystems and consortia.

25 CFR 1001.9 - Selection criteria for tribes/consortia seeking advance planning grant funding.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 25 Indians 2 2013-04-01 2013-04-01 false Selection criteria for tribes/consortia seeking advance..., DEPARTMENT OF THE INTERIOR SELF-GOVERNANCE PROGRAM § 1001.9 Selection criteria for tribes/consortia seeking... before a tribe/consortium is admitted into the applicant pool? Any tribe/consortium that is not a self...

25 CFR 1000.103 - Do Tribes/Consortia need Secretarial approval to reallocate funds between programs that the Tribe...

Code of Federal Regulations, 2013 CFR

2013-04-01

... 25 Indians 2 2013-04-01 2013-04-01 false Do Tribes/Consortia need Secretarial approval to reallocate funds between programs that the Tribe/Consortium administers under the AFA? 1000.103 Section 1000....103 Do Tribes/Consortia need Secretarial approval to reallocate funds between programs that the Tribe...

25 CFR 1000.15 - How many additional Tribes/Consortia may participate in self-governance per year?

Code of Federal Regulations, 2010 CFR

2010-04-01

... 25 Indians 2 2010-04-01 2010-04-01 false How many additional Tribes/Consortia may participate in self-governance per year? 1000.15 Section 1000.15 Indians OFFICE OF THE ASSISTANT SECRETARY, INDIAN... Participation in Tribal Self-Governance Eligibility § 1000.15 How many additional Tribes/Consortia may...

The Decline of Competition: A Study of Cooperative Approaches to University Research Management. ASHE Annual Meeting Paper.

ERIC Educational Resources Information Center

Holland, Barbara A.

This paper analyzes the organizational strategies and dynamics of cooperation appropriate to research consortia. The experiences of nine existing research consortia are reviewed in an effort to propose guidelines for practice in the design of research consortia, and to expand understanding of the nature of interinstitutional cooperation. The nine…

Regional Consortia for E-Resources: A Case Study of Deals in the South China Region

ERIC Educational Resources Information Center

Chunrong, Luo; Jingfen, Wang; Zhinong, Zhou

2010-01-01

Purpose: The purpose of this paper is to analyse the current situation and the social and economic benefits from the consortia acquisitions of electronic resources by the China Academic Library and Information System (CALIS) South China Regional Centre and to recommend improvements for consortia acquisitions. Design/methodology/approach: Analyses…

Microbial Community Analysis of Anaerobic Reactors Treating Soft Drink Wastewater

PubMed Central

Narihiro, Takashi; Kim, Na-Kyung; Mei, Ran; Nobu, Masaru K.; Liu, Wen-Tso

2015-01-01

The anaerobic packed-bed (AP) and hybrid packed-bed (HP) reactors containing methanogenic microbial consortia were applied to treat synthetic soft drink wastewater, which contains polyethylene glycol (PEG) and fructose as the primary constituents. The AP and HP reactors achieved high COD removal efficiency (>95%) after 80 and 33 days of the operation, respectively, and operated stably over 2 years. 16S rRNA gene pyrotag analyses on a total of 25 biofilm samples generated 98,057 reads, which were clustered into 2,882 operational taxonomic units (OTUs). Both AP and HP communities were predominated by Bacteroidetes, Chloroflexi, Firmicutes, and candidate phylum KSB3 that may degrade organic compound in wastewater treatment processes. Other OTUs related to uncharacterized Geobacter and Spirochaetes clades and candidate phylum GN04 were also detected at high abundance; however, their relationship to wastewater treatment has remained unclear. In particular, KSB3, GN04, Bacteroidetes, and Chloroflexi are consistently associated with the organic loading rate (OLR) increase to 1.5 g COD/L-d. Interestingly, KSB3 and GN04 dramatically decrease in both reactors after further OLR increase to 2.0 g COD/L-d. These results indicate that OLR strongly influences microbial community composition. This suggests that specific uncultivated taxa may take central roles in COD removal from soft drink wastewater depending on OLR. PMID:25748027

Co-digestion, biostimulation and bioaugmentation to enhance methanation of brewer's spent grain.

PubMed

Goberna, Marta; Camacho, Maria del Mar; Lopez-Abadia, Juan Antonio; García, Carlos

2013-08-01

More than 300,000 tonnes of brewer's spent grain (BSG) is generated annually during beer production. This protein- and nutrient-rich by-product is mostly employed as an animal feedstuff. However, its marketability is compromised by its rapid deterioration owing to its high humidity and fermentable sugar content. Drying BSG can be achieved using the bio-energy generated from the anaerobic digestion of part of the BSG produced in the same brewery. We employed three types of strategies to enhance the biomethanation of BSG in mesophilic batch incubations. First, we co-digested BSG with peach flesh residues, juice residues, sewage sludge and pig slurry. Second, we supplemented BSG with chemical additives (carbon and energy sources) in order to biostimulate the methane-producing microbial communities. Finally, we used anaerobically acclimatised BSG to augment the initial microbial load in assays digesting BSG either alone or in co-digestion with sewage sludge. All co-substrates assayed were suitable to be fermented in combination with BSG, although methane production was highest for the mixtures with sewage sludge and pig slurry, with their high pH values and nutrient contents. Nine out of 14 combinations of stimulatory chemicals significantly enhanced BSG methanation compared with a non-supplemented control. Overall, bioaugmenting the anaerobic microbial consortia by using fermented BSG as an inoculum when co-digesting BSG with sewage sludge performed best in terms of methane yield.

Microbial Detoxification of Deoxynivalenol (DON), Assessed via a Lemna minor L. Bioassay, through Biotransformation to 3-epi-DON and 3-epi-DOM-1

PubMed Central

Vanhoutte, Ilse; De Mets, Laura; De Boevre, Marthe; Uka, Valdet; Di Mavungu, José Diana; De Saeger, Sarah; De Gelder, Leen; Audenaert, Kris

2017-01-01

Mycotoxins are toxic metabolites produced by fungi. To mitigate mycotoxins in food or feed, biotransformation is an emerging technology in which microorganisms degrade toxins into non-toxic metabolites. To monitor deoxynivalenol (DON) biotransformation, analytical tools such as ELISA and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) are typically used. However, these techniques do not give a decisive answer about the remaining toxicity of possible biotransformation products. Hence, a bioassay using Lemna minor L. was developed. A dose–response analysis revealed significant inhibition in the growth of L. minor exposed to DON concentrations of 0.25 mg/L and higher. Concentrations above 1 mg/L were lethal for the plant. This bioassay is far more sensitive than previously described systems. The bioassay was implemented to screen microbial enrichment cultures, originating from rumen fluid, soil, digestate and activated sludge, on their biotransformation and detoxification capability of DON. The enrichment cultures originating from soil and activated sludge were capable of detoxifying and degrading 5 and 50 mg/L DON. In addition, the metabolites 3-epi-DON and the epimer of de-epoxy-DON (3-epi-DOM-1) were found as biotransformation products of both consortia. Our work provides a new valuable tool to screen microbial cultures for their detoxification capacity. PMID:28208799

Microbial Detoxification of Deoxynivalenol (DON), Assessed via a Lemna minor L. Bioassay, through Biotransformation to 3-epi-DON and 3-epi-DOM-1.

PubMed

Vanhoutte, Ilse; De Mets, Laura; De Boevre, Marthe; Uka, Valdet; Di Mavungu, José Diana; De Saeger, Sarah; De Gelder, Leen; Audenaert, Kris

2017-02-13

Mycotoxins are toxic metabolites produced by fungi. To mitigate mycotoxins in food or feed, biotransformation is an emerging technology in which microorganisms degrade toxins into non-toxic metabolites. To monitor deoxynivalenol (DON) biotransformation, analytical tools such as ELISA and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) are typically used. However, these techniques do not give a decisive answer about the remaining toxicity of possible biotransformation products. Hence, a bioassay using Lemna minor L. was developed. A dose-response analysis revealed significant inhibition in the growth of L. minor exposed to DON concentrations of 0.25 mg/L and higher. Concentrations above 1 mg/L were lethal for the plant. This bioassay is far more sensitive than previously described systems. The bioassay was implemented to screen microbial enrichment cultures, originating from rumen fluid, soil, digestate and activated sludge, on their biotransformation and detoxification capability of DON. The enrichment cultures originating from soil and activated sludge were capable of detoxifying and degrading 5 and 50 mg/L DON. In addition, the metabolites 3-epi-DON and the epimer of de-epoxy-DON (3-epi-DOM-1) were found as biotransformation products of both consortia. Our work provides a new valuable tool to screen microbial cultures for their detoxification capacity.

Governance of Transnational Global Health Research Consortia and Health Equity.

PubMed

Pratt, Bridget; Hyder, Adnan A

2016-10-01

Global health research partnerships are increasingly taking the form of consortia of institutions from high-income countries and low- and middle-income countries that undertake programs of research. These partnerships differ from collaborations that carry out single projects in the multiplicity of their goals, scope of their activities, and nature of their management. Although such consortia typically aim to reduce health disparities between and within countries, what is required for them to do so has not been clearly defined. This article takes a conceptual approach to explore how the governance of transnational global health research consortia should be structured to advance health equity. To do so, it applies an account called shared health governance to derive procedural and substantive guidance. A checklist based on this guidance is proposed to assist research consortia determine where their governance practices strongly promote equity and where they may fall short.

Quantitative Monitoring of Microbial Species during Bioleaching of a Copper Concentrate.

PubMed

Hedrich, Sabrina; Guézennec, Anne-Gwenaëlle; Charron, Mickaël; Schippers, Axel; Joulian, Catherine

2016-01-01

Monitoring of the microbial community in bioleaching processes is essential in order to control process parameters and enhance the leaching efficiency. Suitable methods are, however, limited as they are usually not adapted to bioleaching samples and often no taxon-specific assays are available in the literature for these types of consortia. Therefore, our study focused on the development of novel quantitative real-time PCR (qPCR) assays for the quantification of Acidithiobacillus caldus, Leptospirillum ferriphilum, Sulfobacillus thermosulfidooxidans , and Sulfobacillus benefaciens and comparison of the results with data from other common molecular monitoring methods in order to evaluate their accuracy and specificity. Stirred tank bioreactors for the leaching of copper concentrate, housing a consortium of acidophilic, moderately thermophilic bacteria, relevant in several bioleaching operations, served as a model system. The microbial community analysis via qPCR allowed a precise monitoring of the evolution of total biomass as well as abundance of specific species. Data achieved by the standard fingerprinting methods, terminal restriction fragment length polymorphism (T-RFLP) and capillary electrophoresis single strand conformation polymorphism (CE-SSCP) on the same samples followed the same trend as qPCR data. The main added value of qPCR was, however, to provide quantitative data for each species whereas only relative abundance could be deduced from T-RFLP and CE-SSCP profiles. Additional value was obtained by applying two further quantitative methods which do not require nucleic acid extraction, total cell counting after SYBR Green staining and metal sulfide oxidation activity measurements via microcalorimetry. Overall, these complementary methods allow for an efficient quantitative microbial community monitoring in various bioleaching operations.

Quantitative Monitoring of Microbial Species during Bioleaching of a Copper Concentrate

PubMed Central

Hedrich, Sabrina; Guézennec, Anne-Gwenaëlle; Charron, Mickaël; Schippers, Axel; Joulian, Catherine

2016-01-01

Monitoring of the microbial community in bioleaching processes is essential in order to control process parameters and enhance the leaching efficiency. Suitable methods are, however, limited as they are usually not adapted to bioleaching samples and often no taxon-specific assays are available in the literature for these types of consortia. Therefore, our study focused on the development of novel quantitative real-time PCR (qPCR) assays for the quantification of Acidithiobacillus caldus, Leptospirillum ferriphilum, Sulfobacillus thermosulfidooxidans, and Sulfobacillus benefaciens and comparison of the results with data from other common molecular monitoring methods in order to evaluate their accuracy and specificity. Stirred tank bioreactors for the leaching of copper concentrate, housing a consortium of acidophilic, moderately thermophilic bacteria, relevant in several bioleaching operations, served as a model system. The microbial community analysis via qPCR allowed a precise monitoring of the evolution of total biomass as well as abundance of specific species. Data achieved by the standard fingerprinting methods, terminal restriction fragment length polymorphism (T-RFLP) and capillary electrophoresis single strand conformation polymorphism (CE-SSCP) on the same samples followed the same trend as qPCR data. The main added value of qPCR was, however, to provide quantitative data for each species whereas only relative abundance could be deduced from T-RFLP and CE-SSCP profiles. Additional value was obtained by applying two further quantitative methods which do not require nucleic acid extraction, total cell counting after SYBR Green staining and metal sulfide oxidation activity measurements via microcalorimetry. Overall, these complementary methods allow for an efficient quantitative microbial community monitoring in various bioleaching operations. PMID:28066365

Similar PAH Fate in Anaerobic Digesters Inoculated with Three Microbial Communities Accumulating Either Volatile Fatty Acids or Methane

PubMed Central

Braun, Florence; Hamelin, Jérôme; Bonnafous, Anaïs; Delgenès, Nadine; Steyer, Jean-Philippe; Patureau, Dominique

2015-01-01

Urban sludge produced on wastewater treatment plants are often contaminated by organic pollutants such as polycyclic aromatic hydrocarbons (PAH). Their removal under methanogenic conditions was already reported, but the factors influencing this removal remain unclear. Here, we determined the influence of microbial communities on PAH removal under controlled physico-chemical conditions. Twelve mesophilic anaerobic digesters were inoculated with three microbial communities extracted from ecosystems with contrasting pollution histories: a PAH contaminated soil, a PCB contaminated sediment and a low contaminated anaerobic sludge. These anaerobic digesters were operated during 100 days in continuous mode. A sterilised activated sludge, spiked with 13 PAH at concentrations usually encountered in full-scale wastewater treatment plants, was used as substrate. The dry matter and volatile solid degradation, the biogas production rate and composition, the volatile fatty acids (VFA) production and the PAH removals were monitored. Bacterial and archaeal communities were compared in abundance (qPCR), in community structure (SSCP fingerprinting) and in dominant microbial species (454-pyrosequencing). The bioreactors inoculated with the community extracted from low contaminated anaerobic sludge showed the greater methane production. The PAH removals ranged from 10 % to 30 %, respectively, for high and low molecular weight PAH, whatever the inoculums tested, and were highly correlated with the dry matter and volatile solid removals. The microbial community structure and diversity differed with the inoculum source; this difference was maintained after the 100 days of digestion. However, the PAH removal was not correlated to these diverse structures and diversities. We hence obtained three functional stable consortia with two contrasted metabolic activities, and three different pictures of microbial diversity, but similar PAH and matter removals. These results confirm that PAH removal depends on the molecule type and on the solid matter removal. But, as PAH elimination is similar whether the solid substrate is degraded into VFA or into methane, it seems that the fermentative communities are responsible for their elimination. PMID:25874750

Similar PAH fate in anaerobic digesters inoculated with three microbial communities accumulating either volatile fatty acids or methane.

PubMed

Braun, Florence; Hamelin, Jérôme; Bonnafous, Anaïs; Delgenès, Nadine; Steyer, Jean-Philippe; Patureau, Dominique

2015-01-01

Urban sludge produced on wastewater treatment plants are often contaminated by organic pollutants such as polycyclic aromatic hydrocarbons (PAH). Their removal under methanogenic conditions was already reported, but the factors influencing this removal remain unclear. Here, we determined the influence of microbial communities on PAH removal under controlled physico-chemical conditions. Twelve mesophilic anaerobic digesters were inoculated with three microbial communities extracted from ecosystems with contrasting pollution histories: a PAH contaminated soil, a PCB contaminated sediment and a low contaminated anaerobic sludge. These anaerobic digesters were operated during 100 days in continuous mode. A sterilised activated sludge, spiked with 13 PAH at concentrations usually encountered in full-scale wastewater treatment plants, was used as substrate. The dry matter and volatile solid degradation, the biogas production rate and composition, the volatile fatty acids (VFA) production and the PAH removals were monitored. Bacterial and archaeal communities were compared in abundance (qPCR), in community structure (SSCP fingerprinting) and in dominant microbial species (454-pyrosequencing). The bioreactors inoculated with the community extracted from low contaminated anaerobic sludge showed the greater methane production. The PAH removals ranged from 10% to 30%, respectively, for high and low molecular weight PAH, whatever the inoculums tested, and were highly correlated with the dry matter and volatile solid removals. The microbial community structure and diversity differed with the inoculum source; this difference was maintained after the 100 days of digestion. However, the PAH removal was not correlated to these diverse structures and diversities. We hence obtained three functional stable consortia with two contrasted metabolic activities, and three different pictures of microbial diversity, but similar PAH and matter removals. These results confirm that PAH removal depends on the molecule type and on the solid matter removal. But, as PAH elimination is similar whether the solid substrate is degraded into VFA or into methane, it seems that the fermentative communities are responsible for their elimination.

25 CFR 1000.88 - Do Tribes/Consortia need Secretarial approval to redesign BIA programs that the Tribe/Consortium...

Code of Federal Regulations, 2013 CFR

2013-04-01

... 25 Indians 2 2013-04-01 2013-04-01 false Do Tribes/Consortia need Secretarial approval to redesign BIA programs that the Tribe/Consortium administers under an AFA? 1000.88 Section 1000.88 Indians... in An Afa § 1000.88 Do Tribes/Consortia need Secretarial approval to redesign BIA programs that the...

Higher Education in Further Education Colleges: Indirectly Funded Partnerships: Codes of Practice for Franchise and Consortia Arrangements. Report.

ERIC Educational Resources Information Center

Higher Education Funding Council for England, Bristol.

This report provides codes of practice for two types of indirectly funded partnerships entered into by higher education institutions and further education sector colleges: franchises and consortia. The codes of practice set out guidance on the principles that should be reflected in the franchise and consortia agreements that underpin indirectly…

Microbial bebop: creating music from complex dynamics in microbial ecology.

PubMed

Larsen, Peter; Gilbert, Jack

2013-01-01

In order for society to make effective policy decisions on complex and far-reaching subjects, such as appropriate responses to global climate change, scientists must effectively communicate complex results to the non-scientifically specialized public. However, there are few ways however to transform highly complicated scientific data into formats that are engaging to the general community. Taking inspiration from patterns observed in nature and from some of the principles of jazz bebop improvisation, we have generated Microbial Bebop, a method by which microbial environmental data are transformed into music. Microbial Bebop uses meter, pitch, duration, and harmony to highlight the relationships between multiple data types in complex biological datasets. We use a comprehensive microbial ecology, time course dataset collected at the L4 marine monitoring station in the Western English Channel as an example of microbial ecological data that can be transformed into music. Four compositions were generated (www.bio.anl.gov/MicrobialBebop.htm.) from L4 Station data using Microbial Bebop. Each composition, though deriving from the same dataset, is created to highlight different relationships between environmental conditions and microbial community structure. The approach presented here can be applied to a wide variety of complex biological datasets.

Diel-scale temporal dynamics recorded for bacterial groups in Namib Desert soil

PubMed Central

Gunnigle, Eoin; Frossard, Aline; Ramond, Jean-Baptiste; Guerrero, Leandro; Seely, Mary; Cowan, Don A.

2017-01-01

Microbes in hot desert soil partake in core ecosystem processes e.g., biogeochemical cycling of carbon. Nevertheless, there is still a fundamental lack of insights regarding short-term (i.e., over a 24-hour [diel] cycle) microbial responses to highly fluctuating microenvironmental parameters like temperature and humidity. To address this, we employed T-RFLP fingerprinting and 454 pyrosequencing of 16S rRNA-derived cDNA to characterize potentially active bacteria in Namib Desert soil over multiple diel cycles. Strikingly, we found that significant shifts in active bacterial groups could occur over a single 24-hour period. For instance, members of the predominant Actinobacteria phyla exhibited a significant reduction in relative activity from morning to night, whereas many Proteobacterial groups displayed an opposite trend. Contrary to our leading hypothesis, environmental parameters could only account for 10.5% of the recorded total variation. Potential biotic associations shown through co-occurrence networks indicated that non-random inter- and intra-phyla associations were ‘time-of-day-dependent’ which may constitute a key feature of this system. Notably, many cyanobacterial groups were positioned outside and/or between highly interconnected bacterial associations (modules); possibly acting as inter-module ‘hubs’ orchestrating interactions between important functional consortia. Overall, these results provide empirical evidence that bacterial communities in hot desert soils exhibit complex and diel-dependent inter-community associations. PMID:28071697

Diel-scale temporal dynamics recorded for bacterial groups in Namib Desert soil

NASA Astrophysics Data System (ADS)

Gunnigle, Eoin; Frossard, Aline; Ramond, Jean-Baptiste; Guerrero, Leandro; Seely, Mary; Cowan, Don A.

2017-01-01

Microbes in hot desert soil partake in core ecosystem processes e.g., biogeochemical cycling of carbon. Nevertheless, there is still a fundamental lack of insights regarding short-term (i.e., over a 24-hour [diel] cycle) microbial responses to highly fluctuating microenvironmental parameters like temperature and humidity. To address this, we employed T-RFLP fingerprinting and 454 pyrosequencing of 16S rRNA-derived cDNA to characterize potentially active bacteria in Namib Desert soil over multiple diel cycles. Strikingly, we found that significant shifts in active bacterial groups could occur over a single 24-hour period. For instance, members of the predominant Actinobacteria phyla exhibited a significant reduction in relative activity from morning to night, whereas many Proteobacterial groups displayed an opposite trend. Contrary to our leading hypothesis, environmental parameters could only account for 10.5% of the recorded total variation. Potential biotic associations shown through co-occurrence networks indicated that non-random inter- and intra-phyla associations were ‘time-of-day-dependent’ which may constitute a key feature of this system. Notably, many cyanobacterial groups were positioned outside and/or between highly interconnected bacterial associations (modules); possibly acting as inter-module ‘hubs’ orchestrating interactions between important functional consortia. Overall, these results provide empirical evidence that bacterial communities in hot desert soils exhibit complex and diel-dependent inter-community associations.

Designed cell consortia as fragrance-programmable analog-to-digital converters.

PubMed

Müller, Marius; Ausländer, Simon; Spinnler, Andrea; Ausländer, David; Sikorski, Julian; Folcher, Marc; Fussenegger, Martin

2017-03-01

Synthetic biology advances the rational engineering of mammalian cells to achieve cell-based therapy goals. Synthetic gene networks have nearly reached the complexity of digital electronic circuits and enable single cells to perform programmable arithmetic calculations or to provide dynamic remote control of transgenes through electromagnetic waves. We designed a synthetic multilayered gaseous-fragrance-programmable analog-to-digital converter (ADC) allowing for remote control of digital gene expression with 2-bit AND-, OR- and NOR-gate logic in synchronized cell consortia. The ADC consists of multiple sampling-and-quantization modules sensing analog gaseous fragrance inputs; a gas-to-liquid transducer converting fragrance intensity into diffusible cell-to-cell signaling compounds; a digitization unit with a genetic amplifier circuit to improve the signal-to-noise ratio; and recombinase-based digital expression switches enabling 2-bit processing of logic gates. Synthetic ADCs that can remotely control cellular activities with digital precision may enable the development of novel biosensors and may provide bioelectronic interfaces synchronizing analog metabolic pathways with digital electronics.

Microbial communication leading to the activation of silent fungal secondary metabolite gene clusters

PubMed Central

Netzker, Tina; Fischer, Juliane; Weber, Jakob; Mattern, Derek J.; König, Claudia C.; Valiante, Vito; Schroeckh, Volker; Brakhage, Axel A.

2015-01-01

Microorganisms form diverse multispecies communities in various ecosystems. The high abundance of fungal and bacterial species in these consortia results in specific communication between the microorganisms. A key role in this communication is played by secondary metabolites (SMs), which are also called natural products. Recently, it was shown that interspecies “talk” between microorganisms represents a physiological trigger to activate silent gene clusters leading to the formation of novel SMs by the involved species. This review focuses on mixed microbial cultivation, mainly between bacteria and fungi, with a special emphasis on the induced formation of fungal SMs in co-cultures. In addition, the role of chromatin remodeling in the induction is examined, and methodical perspectives for the analysis of natural products are presented. As an example for an intermicrobial interaction elucidated at the molecular level, we discuss the specific interaction between the filamentous fungi Aspergillus nidulans and Aspergillus fumigatus with the soil bacterium Streptomyces rapamycinicus, which provides an excellent model system to enlighten molecular concepts behind regulatory mechanisms and will pave the way to a novel avenue of drug discovery through targeted activation of silent SM gene clusters through co-cultivations of microorganisms. PMID:25941517

Microbial communication leading to the activation of silent fungal secondary metabolite gene clusters.

PubMed

Netzker, Tina; Fischer, Juliane; Weber, Jakob; Mattern, Derek J; König, Claudia C; Valiante, Vito; Schroeckh, Volker; Brakhage, Axel A

2015-01-01

Microorganisms form diverse multispecies communities in various ecosystems. The high abundance of fungal and bacterial species in these consortia results in specific communication between the microorganisms. A key role in this communication is played by secondary metabolites (SMs), which are also called natural products. Recently, it was shown that interspecies "talk" between microorganisms represents a physiological trigger to activate silent gene clusters leading to the formation of novel SMs by the involved species. This review focuses on mixed microbial cultivation, mainly between bacteria and fungi, with a special emphasis on the induced formation of fungal SMs in co-cultures. In addition, the role of chromatin remodeling in the induction is examined, and methodical perspectives for the analysis of natural products are presented. As an example for an intermicrobial interaction elucidated at the molecular level, we discuss the specific interaction between the filamentous fungi Aspergillus nidulans and Aspergillus fumigatus with the soil bacterium Streptomyces rapamycinicus, which provides an excellent model system to enlighten molecular concepts behind regulatory mechanisms and will pave the way to a novel avenue of drug discovery through targeted activation of silent SM gene clusters through co-cultivations of microorganisms.

Marine phototrophic consortia transfer electrons to electrodes in response to reductive stress.

PubMed

Darus, Libertus; Ledezma, Pablo; Keller, Jürg; Freguia, Stefano

2016-03-01

This work studies how extracellular electron transfer (EET) from cyanobacteria-dominated marine microbial biofilms to solid electrodes is affected by the availability of inorganic carbon (Ci). The EET was recorded chronoamperometrically in the form of electrical current by a potentiostat in two identical photo-electrochemical cells using carbon electrodes poised at a potential of +0.6 V versus standard hydrogen electrode under 12/12 h illumination/dark cycles. The Ci was supplied by the addition of NaHCO3 to the medium and/or by sparging CO2 gas. At high Ci conditions, EET from the microbial biofilm to the electrodes was observed only during the dark phase, indicating the occurrence of a form of night-time respiration that can use insoluble electrodes as the terminal electron acceptor. At low or no Ci conditions, however, EET also occurred during illumination suggesting that, in the absence of their natural electron acceptor, some cyanobacteria are able to utilise solid electrodes as an electron sink. This may be a natural survival mechanism for cyanobacteria to maintain redox balance in environments with limiting CO2 and/or high light intensity.

Immobilization of Cr(VI) and Its Reduction to Cr(III) Phosphate by Granular Biofilms Comprising a Mixture of Microbes

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

Nancharaiah, Y.V.; Francis, A.; Dodge, C.

2010-04-01

We assessed the potential of mixed microbial consortia, in the form of granular biofilms, to reduce chromate and remove it from synthetic minimal medium. In batch experiments, acetate-fed granular biofilms incubated aerobically reduced 0.2 mM Cr(VI) from a minimal medium at 0.15 mM day-1 g-1, with reduction of 0.17 mM day-1 g-1 under anaerobic conditions. There was negligible removal of Cr(VI) (i) without granular biofilms, (ii) with lyophilized granular biofilms, and (iii) with granules in the absence of an electron donor. Analyses by X-ray absorption near edge spectroscopy (XANES) of the granular biofilms revealed the conversion of soluble Cr(VI) tomore » Cr(III). Extended X-ray absorption fine-structure (EXAFS) analysis of the Cr-laden granular biofilms demonstrated similarity to Cr(III) phosphate, indicating that Cr(III) was immobilized with phosphate on the biomass subsequent to microbial reduction. The sustained reduction of Cr(VI) by granular biofilms was confirmed in fed-batch experiments. Our study demonstrates the promise of granular-biofilm-based systems in treating Cr(VI)-containing effluents and wastewater.« less

Bio-rescue of marine environments: On the track of microbially-based metal/metalloid remediation.

PubMed

Marques, Catarina R

2016-09-15

The recent awareness of the huge relevance of marine resources and ecological services is driving regulatory demands for their protection from overwhelming contaminants, such as metals/metalloids. These contaminants enter and accumulate in different marine niches, hence deeply compromising their quality and integrity. Bioremediation has been flourishing to counteract metal/metalloid impacts, since it provides cost-effective and sustainable options by relying on ecology-based technologies. The potential of marine microbes for metal/metalloid bioremediation is the core of many studies, due to their high plasticity to overcome successive environmental hurdles. However, any thorough review on the advances of metal/metalloid bioremediation in marine environments was so far unveiled. This review is designed to (i) outline the characteristics and potential of marine microbes for metal/metalloid bioremediation, (ii) describe the underlying pathways of resistance and detoxification, as well as useful methodologies for their characterization, (iii) identify major bottlenecks on metal/metalloid bioremediation with marine microbes, (iv) present alternative strategies based on microbial consortia and engineered microbes for enhanced bioremediation, and (v) propose key research avenues to keep pace with a changing society, science and economy in a sustainable manner. Copyright © 2016 Elsevier B.V. All rights reserved.

Positive anodic poised potential regulates microbial fuel cell performance with the function of open and closed circuitry.

PubMed

Srikanth, S; Venkata Mohan, S; Sarma, P N

2010-07-01

Positive influence of poised potential on microbial fuel cell (MFC) performance was observed with increase in the applied potential up to 600 mV and decreased thereafter. Higher power output (79.33 mW/m(2)) was observed at 600 mV poised potential under open circuit operation (OC). Closed circuit operation (CC) showed almost negligible power output due to continuous electron discharge against an external load (100 Omega). However, CC operation resulted in the higher substrate (chemical oxygen demand (COD)) degradation [61.23% (control); 70.46% (OC; 600 mV); 74.15% (CC; 600 mV)] and total dissolved solids (TDS) removal [29.17% (control); 43.75% (OC; 600 mV); 72.92% (CC; 600 mV)] efficiencies compared to OC. Electron discharge and energy conversion efficiency was also observed to be higher with 600 mV poised potential. Poising potential showed additional redox couples (-0.29+/-0.05 mV) on cyclic voltammetry. Application of poised potential during startup phase will help to enrich electrochemically active consortia on anode resulting in improved performance of MFC. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Application of culture-dependent and culture-independent methods for the identification of Lactobacillus kefiranofaciens in microbial consortia present in kefir grains.

PubMed

Hamet, Maria Fernanda; Londero, Alejandra; Medrano, Micaela; Vercammen, Elisabeth; Van Hoorde, Koenraad; Garrote, Graciela L; Huys, Geert; Vandamme, Peter; Abraham, Analía G

2013-12-01

The biological and technological characteristics of kefiran as well as its importance in grain integrity led us to analyze the microbial kefir grain consortium with focus on Lactobacillus kefiranofaciens. The presence of L. kefiranofaciens in the nine kefir grains studied was demonstrated by denaturing gradient gel electrophoresis. By culture dependent methods applying a methodology focused on the search of this species, 22 isolates with typical morphology were obtained and identified applying a combination of SDS-PAGE of whole cell proteins, (GTG)5-PCR and sequence analysis of the housekeeping gene encoding the α-subunit of bacterial phenylalanyl-tRNA synthase (pheS). This polyphasic approach allowed the reliable identification of 11 L. kefiranofaciens, 5 Lactobacillus paracasei, 4 Lactobacillus kefiri and 2 Lactobacillus parakefiri isolates. Isolated L. kefiranofaciens strains produced polysaccharide in strain-dependent concentrations and EPS produced by them also differed in the degree of polymerization. The isolation and accurate identification of L. kefiranofaciens is relevant taking into account the important role of this microorganism in the grain ecosystem as well as its potential application as starter in food fermentations. Copyright © 2013 Elsevier Ltd. All rights reserved.

Isolation and characterization from solar salterns of North Algeria of a haloarchaeon producing a new halocin.

PubMed

Mazguene, Souhila; Rossi, Mosè; Gogliettino, Marta; Palmieri, Gianna; Cocca, Ennio; Mirino, Sara; Imadalou-Idres, Nacera; Benallaoua, Said

2018-03-01

Halophilic archaea, thriving in hypersaline environments, synthesize antimicrobial substances with an unknown role, called halocins. It has been suggested that halocin production gives transient competitive advantages to the producer strains and represents one of the environmental factors influencing the microbial community composition. Herein, we report on the antibacterial activity of a new haloarchaeon selected from solar salterns of the northern coast of Algeria. A total of 81 halophilic strains, isolated from the microbial consortia, were screened for the production of antimicrobial compounds by interspecies competition test and against a collection of commercial haloarchaea. On the basis of the partial 16S rRNA sequencing, the most efficient halocin producer was recognized as belonging to Haloferax (Hfx) sp., while the best indicator microorganism, showing high sensitivity toward halocin, was related to Haloarcula genus. The main morphological, physiological and biochemical properties of Hfx were investigated and a partial purification of the produced halocin was allowed to identify it as a surface membrane protein with a molecular mass between 30 and 40 kDa. Therefore, in this study, we isolated a new strain belonging to Haloferax genus and producing a promising antimicrobial compound useful for applications in health and food industries.

Comparative biodegradation of HDPE and LDPE using an indigenously developed microbial consortium.

PubMed

Satlewal, Alok; Soni, Ravindra; Zaidi, Mgh; Shouche, Yogesh; Goel, Reeta

2008-03-01

A variety of bacterial strains were isolated from waste disposal sites of Uttaranchal, India, and some from artificially developed soil beds containing maleic anhydride, glucose, and small pieces of polyethylene. Primary screening of isolates was done based on their ability to utilize high- and low-density polyethylenes (HDPE/LDPE) as a primary carbon source. Thereafter, a consortium was developed using potential strains. Furthermore, a biodegradation assay was carried out in 500-ml flasks containing minimal broth (250 ml) and HDPE/ LDPE at 5 mg/ml concentration. After incubation for two weeks, degraded samples were recovered through filtration and subsequent evaporation. Fourier transform infrared spectroscopy (FTIR) and simultaneous thermogravimetric-differential thermogravimetry-differential thermal analysis TG-DTG-DTA) were used to analyze these samples. Results showed that consortium-treated HDPE (considered to be more inert relative to LDPE) was degraded to a greater extent 22.41% weight loss) in comparison with LDPE (21.70% weight loss), whereas, in the case of untreated samples, weight loss was more for LDPE than HDPE (4.5% and 2.5%, respectively) at 400 degrees . Therefore, this study suggests that polyethylene could be degraded by utilizing microbial consortia in an eco-friendly manner.

Diversity of bacteria and glycosyl hydrolase family 48 genes in cellulolytic consortia enriched from thermophilic biocompost.

PubMed

Izquierdo, Javier A; Sizova, Maria V; Lynd, Lee R

2010-06-01

The enrichment from nature of novel microbial communities with high cellulolytic activity is useful in the identification of novel organisms and novel functions that enhance the fundamental understanding of microbial cellulose degradation. In this work we identify predominant organisms in three cellulolytic enrichment cultures with thermophilic compost as an inoculum. Community structure based on 16S rRNA gene clone libraries featured extensive representation of clostridia from cluster III, with minor representation of clostridial clusters I and XIV and a novel Lutispora species cluster. Our studies reveal different levels of 16S rRNA gene diversity, ranging from 3 to 18 operational taxonomic units (OTUs), as well as variability in community membership across the three enrichment cultures. By comparison, glycosyl hydrolase family 48 (GHF48) diversity analyses revealed a narrower breadth of novel clostridial genes associated with cultured and uncultured cellulose degraders. The novel GHF48 genes identified in this study were related to the novel clostridia Clostridium straminisolvens and Clostridium clariflavum, with one cluster sharing as little as 73% sequence similarity with the closest known relative. In all, 14 new GHF48 gene sequences were added to the known diversity of 35 genes from cultured species.

Biomineralization associated with microbial reduction of Fe3+ and oxidation of Fe2+ in solid minerals

USGS Publications Warehouse

Zhang, G.; Dong, H.; Jiang, H.; Kukkadapu, R.K.; Kim, J.; Eberl, D.; Xu, Z.

2009-01-01

Iron-reducing and oxidizing microorganisms gain energy through reduction or oxidation of iron, and by doing so play an important role in the geochemical cycling of iron. This study was undertaken to investigate mineral transformations associated with microbial reduction of Fe3+ and oxidation of Fe2+ in solid minerals. A fluid sample from the 2450 m depth of the Chinese Continental Scientific Drilling project was collected, and Fe3+-reducing and Fe2+-oxidizing microorganisms were enriched. The enrichment cultures displayed reduction of Fe3+ in nontronite and ferric citrate, and oxidation of Fe2+ in vivianite, siderite, and monosulfide (FeS). Additional experiments verified that the iron reduction and oxidation was biological. Oxidation of FeS resulted in the formation of goethite, lepidocrocite, and ferrihydrite as products. Although our molecular microbiological analyses detected Thermoan-aerobacter ethanolicus as a predominant organism in the enrichment culture, Fe3+ reduction and Fe2+ oxidation may be accomplished by a consortia of organisms. Our results have important environmental and ecological implications for iron redox cycling in solid minerals in natural environments, where iron mineral transformations may be related to the mobility and solubility of inorganic and organic contaminants.

Evaluation of support matrices for immobilization of anaerobic consortia for efficient carbon cycling in waste regeneration.

PubMed

Chauhan, Ashvini; Ogram, Andrew

2005-02-18

Efficient metabolism of fatty acids during anaerobic waste digestion requires development of consortia that include "fatty acid consuming H(2) producing bacteria" and methanogenic bacteria. The objective of this research was to optimize methanogenesis from fatty acids by evaluating a variety of support matrices for use in maintaining efficient syntrophic-methanogenic consortia. Tested matrices included clays (montmorillonite and bentonite), glass beads (106 and 425-600mum), microcarriers (cytopore, cytodex, cytoline, and cultispher; conventionally employed for cultivation of mammalian cell lines), BioSep beads (powdered activated carbon), and membranes (hydrophilic; nylon, polysulfone, and hydrophobic; teflon, polypropylene). Data obtained from headspace methane (CH(4)) analyses as an indicator of anaerobic carbon cycling efficiency indicated that material surface properties were important in maintenance and functioning of the anaerobic consortia. Cytoline yielded significantly higher CH(4) than other matrices as early as in the first week of incubation. 16S rRNA gene sequence analysis from crushed cytoline matrix showed the presence of Syntrophomonas spp. (butyrate oxidizing syntrophs) and Syntrophobacter spp. (propionate oxidizing syntrophs), with Methanosaeta spp. (acetate utilizing methanogen), and Methanospirillum spp. (hydrogen utilizing methanogen) cells. It is likely that the more hydrophobic surfaces provided a suitable surface for adherence of cells of syntrophic-methanogenic consortia. Cytoline also appeared to protect entrapped consortia from air, resulting in rapid methanogenesis after aerial exposure. Our study suggests that support matrices can be used in anaerobic digestors, pre-seeded with immobilized or entrapped consortia on support matrices, and may be of value as inoculant-adsorbents to rapidly initiate or recover proper system functioning following perturbation.

Contribution of Bicarbonate Assimilation to Carbon Pool Dynamics in the Deep Mediterranean Sea and Cultivation of Actively Nitrifying and CO2-Fixing Bathypelagic Prokaryotic Consortia.

PubMed

La Cono, Violetta; Ruggeri, Gioachino; Azzaro, Maurizio; Crisafi, Francesca; Decembrini, Franco; Denaro, Renata; La Spada, Gina; Maimone, Giovanna; Monticelli, Luis S; Smedile, Francesco; Giuliano, Laura; Yakimov, Michail M

2018-01-01

Covering two-thirds of our planet, the global deep ocean plays a central role in supporting life on Earth. Among other processes, this biggest ecosystem buffers the rise of atmospheric CO 2 . Despite carbon sequestration in the deep ocean has been known for a long time, microbial activity in the meso- and bathypelagic realm via the " assimilation of bicarbonate in the dark " (ABD) has only recently been described in more details. Based on recent findings, this process seems primarily the result of chemosynthetic and anaplerotic reactions driven by different groups of deep-sea prokaryoplankton. We quantified bicarbonate assimilation in relation to total prokaryotic abundance, prokaryotic heterotrophic production and respiration in the meso- and bathypelagic Mediterranean Sea. The measured ABD values, ranging from 133 to 370 μg C m -3 d -1 , were among the highest ones reported worldwide for similar depths, likely due to the elevated temperature of the deep Mediterranean Sea (13-14°C also at abyssal depths). Integrated over the dark water column (≥200 m depth), bicarbonate assimilation in the deep-sea ranged from 396 to 873 mg C m -2 d -1 . This quantity of produced de novo organic carbon amounts to about 85-424% of the phytoplankton primary production and covers up to 62% of deep-sea prokaryotic total carbon demand. Hence, the ABD process in the meso- and bathypelagic Mediterranean Sea might substantially contribute to the inorganic and organic pool and significantly sustain the deep-sea microbial food web. To elucidate the ABD key-players, we established three actively nitrifying and CO 2 -fixing prokaryotic enrichments. Consortia were characterized by the co-occurrence of chemolithoautotrophic Thaumarchaeota and chemoheterotrophic proteobacteria. One of the enrichments, originated from Ionian bathypelagic waters (3,000 m depth) and supplemented with low concentrations of ammonia, was dominated by the Thaumarchaeota "low-ammonia-concentration" deep-sea ecotype, an enigmatic and ecologically important group of organisms, uncultured until this study.

Contribution of Bicarbonate Assimilation to Carbon Pool Dynamics in the Deep Mediterranean Sea and Cultivation of Actively Nitrifying and CO2-Fixing Bathypelagic Prokaryotic Consortia

PubMed Central

La Cono, Violetta; Ruggeri, Gioachino; Azzaro, Maurizio; Crisafi, Francesca; Decembrini, Franco; Denaro, Renata; La Spada, Gina; Maimone, Giovanna; Monticelli, Luis S.; Smedile, Francesco; Giuliano, Laura; Yakimov, Michail M.

2018-01-01

Covering two-thirds of our planet, the global deep ocean plays a central role in supporting life on Earth. Among other processes, this biggest ecosystem buffers the rise of atmospheric CO2. Despite carbon sequestration in the deep ocean has been known for a long time, microbial activity in the meso- and bathypelagic realm via the “assimilation of bicarbonate in the dark” (ABD) has only recently been described in more details. Based on recent findings, this process seems primarily the result of chemosynthetic and anaplerotic reactions driven by different groups of deep-sea prokaryoplankton. We quantified bicarbonate assimilation in relation to total prokaryotic abundance, prokaryotic heterotrophic production and respiration in the meso- and bathypelagic Mediterranean Sea. The measured ABD values, ranging from 133 to 370 μg C m−3 d−1, were among the highest ones reported worldwide for similar depths, likely due to the elevated temperature of the deep Mediterranean Sea (13–14°C also at abyssal depths). Integrated over the dark water column (≥200 m depth), bicarbonate assimilation in the deep-sea ranged from 396 to 873 mg C m−2 d−1. This quantity of produced de novo organic carbon amounts to about 85–424% of the phytoplankton primary production and covers up to 62% of deep-sea prokaryotic total carbon demand. Hence, the ABD process in the meso- and bathypelagic Mediterranean Sea might substantially contribute to the inorganic and organic pool and significantly sustain the deep-sea microbial food web. To elucidate the ABD key-players, we established three actively nitrifying and CO2-fixing prokaryotic enrichments. Consortia were characterized by the co-occurrence of chemolithoautotrophic Thaumarchaeota and chemoheterotrophic proteobacteria. One of the enrichments, originated from Ionian bathypelagic waters (3,000 m depth) and supplemented with low concentrations of ammonia, was dominated by the Thaumarchaeota “low-ammonia-concentration” deep-sea ecotype, an enigmatic and ecologically important group of organisms, uncultured until this study. PMID:29403458

Improving the informed consent process in international collaborative rare disease research: effective consent for effective research

PubMed Central

Gainotti, Sabina; Turner, Cathy; Woods, Simon; Kole, Anna; McCormack, Pauline; Lochmüller, Hanns; Riess, Olaf; Straub, Volker; Posada, Manuel; Taruscio, Domenica; Mascalzoni, Deborah

2016-01-01

The increased international sharing of data in research consortia and the introduction of new technologies for sequencing challenge the informed consent (IC) process, adding complexities that require coordination between research centres worldwide. Rare disease consortia present special challenges since available data and samples may be very limited. Thus, it is especially relevant to ensure the best use of available resources but at the same time protect patients' right to integrity. To achieve this aim, there is an ethical duty to plan in advance the best possible consent procedure in order to address possible ethical and legal hurdles that could hamper research in the future. Therefore, it is especially important to identify key core elements (CEs) to be addressed in the IC documents for international collaborative research in two different situations: (1) new research collections (biobanks and registries) for which information documents can be created according to current guidelines and (2) established collections obtained without IC or with a previous consent that does not cover all CEs. We propose here a strategy to deal with consent in these situations. The principles have been applied and are in current practice within the RD-Connect consortia – a global research infrastructure funded by the European Commission Seventh Framework program but forward looking in terms of issues addressed. However, the principles established, the lessons learned and the implications for future research are of direct relevance to all internationally collaborative rare-disease projects. PMID:26860059

Municipal consortia for medicine procurement: impact on the stock-out and budget.

PubMed

Amaral, Silvâni Maria Sehnem de; Blatt, Carine Raquel

2011-08-01

The study evaluated the impact of the consortia on the budget and shortage of medicines for the basic pharmaceutical assistance component in Indaial municipality, Southern Brazil. The number of items with a stock out for at least one day decreased by 12% from 2008 to 2007 and 48% from 2009 to 2007; total costs decreased by 33%, when comparing procurement by consortia (2009) to municipal procurement (2007), and by 18% when compared to the average values of the 2009 Health Prices Database from the Ministry of Health. The procurement of medicines by the consortia decreased stock outs and represented an economy of scale, allowing for the procurement of a greater quantity of products with the same budget.

Use of Acetate, Propionate, and Butyrate for Reduction of Nitrate and Sulfate and Methanogenesis in Microcosms and Bioreactors Simulating an Oil Reservoir

PubMed Central

Shen, Yin; An, Dongshan; Voordouw, Gerrit

2017-01-01

ABSTRACT Acetate, propionate, and butyrate (volatile fatty acids [VFA]) occur in oil field waters and are frequently used for microbial growth of oil field consortia. We determined the kinetics of use of these VFA components (3 mM each) by an anaerobic oil field consortium in microcosms containing 2 mM sulfate and 0, 4, 6, 8, or 13 mM nitrate. Nitrate was reduced first, with a preference for acetate and propionate. Sulfate reduction then proceeded with propionate (but not butyrate) as the electron donor, whereas the fermentation of butyrate (but not propionate) was associated with methanogenesis. Microbial community analyses indicated that Paracoccus and Thauera (Paracoccus-Thauera), Desulfobulbus, and Syntrophomonas-Methanobacterium were the dominant taxa whose members catalyzed these three processes. Most-probable-number assays showed the presence of up to 107/ml of propionate-oxidizing sulfate-reducing bacteria (SRB) in waters from the Medicine Hat Glauconitic C field. Bioreactors with the same concentrations of sulfate and VFA responded similarly to increasing concentrations of injected nitrate as observed in the microcosms: sulfide formation was prevented by adding approximately 80% of the nitrate dose needed to completely oxidize VFA to CO2 in both. Thus, this work has demonstrated that simple time-dependent observations of the use of acetate, propionate, and butyrate for nitrate reduction, sulfate reduction, and methanogenesis in microcosms are a good proxy for these processes in bioreactors, monitoring of which is more complex. IMPORTANCE Oil field volatile fatty acids acetate, propionate, and butyrate were specifically used for nitrate reduction, sulfate reduction, and methanogenic fermentation. Time-dependent analyses of microcosms served as a good proxy for these processes in a bioreactor, mimicking a sulfide-producing (souring) oil reservoir: 80% of the nitrate dose required to oxidize volatile fatty acids to CO2 was needed to prevent souring in both. Our data also suggest that propionate is a good substrate to enumerate oil field SRB. PMID:28130297

Stochastic simulations of a synthetic bacteria-yeast ecosystem

PubMed Central

2012-01-01

Background The field of synthetic biology has greatly evolved and numerous functions can now be implemented by artificially engineered cells carrying the appropriate genetic information. However, in order for the cells to robustly perform complex or multiple tasks, co-operation between them may be necessary. Therefore, various synthetic biological systems whose functionality requires cell-cell communication are being designed. These systems, microbial consortia, are composed of engineered cells and exhibit a wide range of behaviors. These include yeast cells whose growth is dependent on one another, or bacteria that kill or rescue each other, synchronize, behave as predator-prey ecosystems or invade cancer cells. Results In this paper, we study a synthetic ecosystem comprising of bacteria and yeast that communicate with and benefit from each other using small diffusible molecules. We explore the behavior of this heterogeneous microbial consortium, composed of Saccharomyces cerevisiae and Escherichia coli cells, using stochastic modeling. The stochastic model captures the relevant intra-cellular and inter-cellular interactions taking place in and between the eukaryotic and prokaryotic cells. Integration of well-characterized molecular regulatory elements into these two microbes allows for communication through quorum sensing. A gene controlling growth in yeast is induced by bacteria via chemical signals and vice versa. Interesting dynamics that are common in natural ecosystems, such as obligatory and facultative mutualism, extinction, commensalism and predator-prey like dynamics are observed. We investigate and report on the conditions under which the two species can successfully communicate and rescue each other. Conclusions This study explores the various behaviors exhibited by the cohabitation of engineered yeast and bacterial cells. The way that the model is built allows for studying the dynamics of any system consisting of two species communicating with one another via chemical signals. Therefore, key information acquired by our model may potentially drive the experimental design of various synthetic heterogeneous ecosystems. PMID:22672814

Synthetic Klebsiella pneumoniae-Shewanella oneidensis Consortium Enables Glycerol-Fed High-Performance Microbial Fuel Cells.

PubMed

Li, Feng; Yin, Changji; Sun, Liming; Li, Yuanxiu; Guo, Xuewu; Song, Hao

2018-05-01

Microbial fuel cell (MFC) is an eco-friendly bio-electrochemical sys-tem that uses microorganism as biocatalyst to convert biomass into electricity. Glycerol, as a waste in the biodiesel refinery processes, is an appealing substrate for MFC. Nevertheless, glycerol cannot be utilized as carbon source by well-known exoelectrogens such as Shewanella oneidensis. Herein, to generate electricity by rapidly harnessing glycerol, the authors rationally constructed a Klebsiella pneumoniae-Shewanella oneidensis microbial consortium to efficiently harvest electricity from glyc-erol, in which K. pneumoniae converted glycerol into lactate, fed to S. oneidensis as carbon source and electron donor. To improve electricity output, the authors systematically engineered the consortium in terms of carbon flux distribution and efficiency of extracellular electron transfer (EET). To direct more carbon flux to lactate biosynthesis in K. pneumoniae, the authors eliminated the ethanol pathway by knocking out the alcohol dehydrogenase gene (adhE), and enhanced lactate biosynthesis by heterologously expressing a lactate dehydrogen-ase gene (ldhD) from Lactobacillus bulgaricus and a lactate transporter gene (lldP) from Escherichia coli. To facilitate EET between S. oneidensis and anode surfaces, a biosynthetic flavins pathway from Bacillus subtilis is introduced into S. oneidensis. The author further optimized the glycerol concentration, thus S. oneidensis could be continuously fed with lactate synthesized from K. pneumoniae at a constant rate. Our glycerol-fed MFC generated a maximum power density of 19.9 mW/m 2 , significantly higher than that of the wild-type consor-tium. This work suggested that engineering microbial consortia is an effi-cient strategy to expand the spectrum of usable carbon sources and promote electricity power production in MFCs. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Microbial mats in the Black Sea that anaerobically oxidise methane

NASA Astrophysics Data System (ADS)

Nauhaus, K.; Knittel, K.; Krüger, M.; Boetius, A.; Michaelis, W.; Widdel, F.

2003-04-01

Reef-forming microbial mats were recovered from methane seeps in anoxic waters of the northwestern Black Sea (BS) shelf. The microbial mats consist mainly of archaea (ANME-1 cluster) and sulfate-reducing bacteria (Desulfosarcina/Desulfococcus group). Laboratory incubations with homogenized subsamples of the mats revealed their ability for the anaerobic oxidation of methane (AOM). The phylogentic relationship of the sulfate reducing partner is the same as in the AOM consortia studied in sediment samples from a methane hydrate area (Hydrate Ridge (HR), Oregon, USA (1,2)). The archaeal partner however belongs to a different cluster than in the HR samples (ANME-2). Methane oxidation is coupled to sulfate reduction in a 1:1 stoichiometry. Elevated methane partial pressures (0.1 to 1.1 MPa) increased the sulfate reduction rates in the Black Sea samples only two-fold in contrast to 5-fold in HR samples. The optimal temperature for the BS samples is between 10 and 25^oC. In both samples AOM was not taking place if typical inhibitors for sulfate-reduction or methanogenesis were added, thus indicating a syntrophic relationship between the partner organisms. The intermediate that is exchanged between the methane oxidizing archaea and the sulfate-reducing bacterium is still unknown. Additions of the possible intermediates (Acetate, Formate, Hydrogen) did not result in higher sulfate reduction rates in the absence of methane. (1) Boetius, A. et al. (2000) A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature. 407: 623--626 (2) Nauhaus, K., Boetius, A., Krüger, M., Widdel, F. (2002) In vitro demonstration of anaerobic oxidation of methane coupled to sulphate reduction in sediment from a marine gas hydrate area. Environ. Microbiol. 4 (5): 296--305

Winter Insulation By Snow Accumulation in a Subarctic Treeline Ecosystem Increases Summer Carbon Cycling Rates

NASA Astrophysics Data System (ADS)

Parker, T.; Subke, J. A.; Wookey, P. A.

2014-12-01

The effect of snow accumulation on soil carbon and nutrient cycling is attracting substantial attention from researchers. We know that deeper snow accumulation caused by high stature vegetation increases winter microbial activity and therefore carbon and nitrogen flux rates. However, until now the effect of snow accumulation, by buffering winter soil temperature, on subsequent summer soil processes, has scarcely been considered. We carried out an experiment at an alpine treeline in subarctic Sweden in which soil monoliths, contained within PVC collars, were transplanted between forest (deep winter snow) and tundra heath (shallow winter snow). We measured soil CO2efflux over two growing seasons and quantified soil microbial biomass after the second winter. We showed that respiration rates of transplanted forest soil were significantly reduced compared with control collars (remaining in the forest) as a consequence of colder, but more variable, winter temperatures. We hypothesised that microbial biomass would be reduced in transplanted forests soils but found there was no difference compared to control. We therefore further hypothesised that the similarly sized microbial pool in the control is assembled differently to the transplant. We believe that the warmer winters in forests foster more active consortia of decomposer microbes as a result of different abiotic selection pressures. Using an ecosystem scale experimental approach, we have identified a mechanism that influences summer carbon cycling rates based solely on the amount of snow that accumulates the previous winter. We conclude that modification of snow depth as a consequence of changes in vegetation structure is an important mechanism influencing soil C stocks in ecosystems where snow persists for a major fraction of the year.

Towards Biogeochemical Modeling of Anaerobic Oxidation of Methane: Characterization of Microbial Communities in Methane-bearing North American Continental Margin Sediments

NASA Astrophysics Data System (ADS)

Graw, M. F.; Solomon, E. A.; Chrisler, W.; Krause, S.; Treude, T.; Ruppel, C. D.; Pohlman, J.; Colwell, F. S.

2015-12-01

Methane advecting through continental margin sediments may enter the water column and potentially contribute to ocean acidification and increase atmospheric methane concentrations. Anaerobic oxidation of methane (AOM), mediated by syntrophic consortia of anaerobic methanotrophic archaea and sulfate-reducing bacteria (ANME-SRB), consumes nearly all dissolved methane in methane-bearing sediments before it reaches the sediment-water interface. Despite the significant role ANME-SRB play in carbon cycling, our knowledge of these organisms and their surrounding microbial communities is limited. Our objective is to develop a metabolic model of ANME-SRB within methane-bearing sediments and to couple this to a geochemical reaction-transport model for these margins. As a first step towards this goal, we undertook fluorescent microscopic imaging, 16S rRNA gene deep-sequencing, and shotgun metagenomic sequencing of sediments from the US Pacific (Washington) and northern Atlantic margins where ANME-SRB are present. A successful Illumina MiSeq sequencing run yielded 106,257 bacterial and 857,834 archaeal 16S rRNA gene sequences from 12 communities from the Washington Margin using both universal prokaryotic and archaeal-specific primer sets. Fluorescent microscopy confirmed the presence of cells of the ANME-2c lineage in the sequenced communities. Microbial community characterization was coupled with measurements of sediment physical and geochemical properties and, for samples from the US Atlantic margin, 14C-based measurements of AOM rates and 35S-based measurements of sulfate reduction rates. These findings have the potential to increase understanding of ANME-SRB, their surrounding microbial communities, and their role in carbon cycling within continental margins. In addition, they pave the way for future efforts at developing a metabolic model of ANME-SRB and coupling it to geochemical models of the US Washington and Atlantic margins.

Fourier transform-infrared spectroscopic methods for microbial ecology: analysis of bacteria, bacteria-polymer mixtures and biofilms

NASA Technical Reports Server (NTRS)

Nichols, P. D.; Henson, J. M.; Guckert, J. B.; Nivens, D. E.; White, D. C.

1985-01-01

Fourier transform-infrared (FT-IR) spectroscopy has been used to rapidly and nondestructively analyze bacteria, bacteria-polymer mixtures, digester samples and microbial biofilms. Diffuse reflectance FT-IR (DRIFT) analysis of freeze-dried, powdered samples offered a means of obtaining structural information. The bacteria examined were divided into two groups. The first group was characterized by a dominant amide I band and the second group of organisms displayed an additional strong carbonyl stretch at approximately 1740 cm-1. The differences illustrated by the subtraction spectra obtained for microbes of the two groups suggest that FT-IR spectroscopy can be utilized to recognize differences in microbial community structure. Calculation of specific band ratios has enabled the composition of bacteria and extracellular or intracellular storage product polymer mixtures to be determined for bacteria-gum arabic (amide I/carbohydrate C-O approximately 1150 cm-1) and bacteria-poly-beta-hydroxybutyrate (amide I/carbonyl approximately 1740 cm-1). The key band ratios correlate with the compositions of the material and provide useful information for the application of FT-IR spectroscopy to environmental biofilm samples and for distinguishing bacteria grown under differing nutrient conditions. DRIFT spectra have been obtained for biofilms produced by Vibrio natriegens on stainless steel disks. Between 48 and 144 h, an increase in bands at approximately 1440 and 1090 cm-1 was seen in FT-IR spectra of the V. natriegens biofilm. DRIFT spectra of mixed culture effluents of anaerobic digesters show differences induced by shifts in input feedstocks. The use of flow-through attenuated total reflectance has permitted in situ real-time changes in biofilm formation to be monitored and provides a powerful tool for understanding the interactions within adherent microbial consortia.

Lithobiontic life: "Atacama rocks are well and alive".

PubMed

Gómez-Silva, Benito

2018-02-01

Our knowledge on the Microbiology of the Atacama Desert has increased steadily and substantially during the last two decades. This information now supports a paradigmatic change on the Atacama Desert from a sterile, uninhabitable territory to a hyperarid region colonized by a rich microbiota that includes extremophiles and extreme-tolerant microorganisms. Also, extensive reports are available on the prevalent physical and chemical environmental conditions, ecological niches and, the abundance, diversity and organization of the microbial life in the Atacama Desert. This territory is a highly desiccated environment due to the absence of regular rain events. Liquid water scarcity is the most serious environmental factor affecting the Atacama Desert microorganisms. The intense solar irradiation in this region contributes, in a synergistic fashion with desiccation, to limit the survival and growth of the microbial life. In order to overcome these two extreme conditions, successful microorganisms, organized as microbial consortia, take advantage of (a) the physical characteristics of lithic habitats, which provide sites for colonization on, within or below the rock substrate, the attenuation and filtration of the intense solar irradiation and, the collection of liquid water from incoming fog formations and by water vapour condensation and deliquescence on or within their surfaces, and (b) the biological adaptations of members of the microbial communities that allow them to synthesize hydrophilic macromolecules, antioxidants and UV-light absorbents. Lithic habitats have been considered specialized shelters where life forms can reach protection at environments subjected to extremes of desiccation and solar irradiation, here on Earth or elsewhere. This review is an overview of part of the scientific information collected on lithobionts from the Atacama Desert, their rock substrates and their strategies to cope with extremes of desiccation and intense photosynthetic active radiation and UV irradiations.

Microbial consortia controlling biogenic gas formation in the Qaidam Basin of western China

NASA Astrophysics Data System (ADS)

Shuai, Yanhua; Zhang, Shuichang; Grasby, Stephen E.; Hou, Weiguo; Chen, Zhuoheng; Huang, Ling; Kui, Mingqing; Xu, Yirui; Wang, Yang

2016-08-01

Knowledge of what controls the activity of subsurface microbial communities is critical for assessing and managing biogenic methane resources. In this study, 19 formation waters and five gas samples were collected at depths of 800 to 1900 m from Quaternary biogenic gas fields of the Qaidam Basin, China. The formation waters were brines with chloride (Cl) concentrations from 1200 to 2700 mM. Bacterial 16S rRNA gene copies ranged from 3.75 × 104 to 2.23 × 106 copies mL-1 of water, and those of archaea ranged from 2.44 × 103 to 4.66 × 107 copies mL-1 of water. Both bacterial and archaea 16 s rRNA gene copies were negatively correlated with Cl concentration. The microbial community structure differed significantly depending on Cl concentrations. At high Cl waters (>1800 mM), the microbial community showed a halophilic signature made up of several abundant taxonomic groups within Firmicules, γ-Proteobacteria, and methylotrophic Methanosarcinales. At low Cl, Firmicules and hydrogenotrophic methanogens were dominant members. The proportion of inferred hydrogenotrophic methanogens decreased from 89% to 14% of total archaeal reads with increasing Cl concentration; in contrast, methylotrophic species increased from 11% to 85%. Given that the proportion of hydrogenotrophic species was positively correlated with the archaeal gene abundances, we suggest that Cl concentrations primarily constrain the activity of archaea catalyzing H2 reduction of CO2. Our results show that dilution of formation waters is critical in the process of biogenic gas formation, suggesting that an engineered decrease in Cl concentrations may induce methanogenesis as a potential method to increase gas reserves in such areas in the future.

Bioremediation of PCB-contaminated shallow river sediments: The efficacy of biodegradation using individual bacterial strains and their consortia.

PubMed

Horváthová, Hana; Lászlová, Katarína; Dercová, Katarína

2018-02-01

Elimination of dangerous toxic and hydrophobic chlorinated aromatic compounds, mainly PCBs from the environment, is one of the most important aims of the environmental biotechnologies. In this work, biodegradation of an industrial mixture of PCBs (Delor 103, equivalent to Aroclor 1242) was performed using bacterial consortia composed of four bacterial strains isolated from the historically PCB-contaminated sediments and characterized as Achromobacter xylosoxidans, Stenotrophomonas maltophilia, Ochrobactrum anthropi and Rhodococcus ruber. The objective of this research was to determine the biodegradation ability of the individual strains and artificially prepared consortia composed of two or three bacterial strains mentioned above. Based on the growth parameters, six consortia were constructed and inoculated into the historically contaminated sediment samples collected in the efflux canal of Chemko Strážske plant - the former producer of the industrial mixtures of PCBs. The efficacy of the biotreatment, namely bioaugmentation, was evaluated by determination of ecotoxicity of treated and non-treated sediments. The most effective consortia were those containing the strain R. ruber. In the combination with A. xylosoxidans, the biodegradation of the sum of the indicator congeners was 85% and in the combination with S. maltophilia nearly 80%, with inocula applied in the ratio 1:1 in both cases. Consortium containing the strain R. ruber and S. maltophilia showed pronounced degradation of the highly chlorinated PCB congeners. Among the consortia composed of three bacterial strains, only that consisting of O. anthropi, R. ruber and A. xylosoxidans showed higher biodegradation (73%). All created consortia significally reduced the toxicity of the contaminated sediment. Copyright © 2017 Elsevier Ltd. All rights reserved.

Single-chamber microbial fuel cells as on-line shock-sensors for volatile fatty acids in anaerobic digesters.

PubMed

Schievano, Andrea; Colombo, Alessandra; Cossettini, Alessandra; Goglio, Andrea; D'Ardes, Vincenzo; Trasatti, Stefano; Cristiani, Pierangela

2018-01-01

In anaerobic digesters (AD), volatile fatty acids (VFAs) concentration is a critical operative parameter, which is usually manually monitored to prevent inhibition of microbial consortia. An on-line VFAs monitoring system as early-warning for increasing concentrations would be of great help for operators. Here, air-cathode membraneless microbial fuel cells (MFCs) were investigated as potential biosensors, whose electrical signal instantaneously moves from its steady value with the accumulation of VFAs in the anodic solution. MFCs were operated equipping four lab-scale ADs with carbon-based electrodes. Reactors were filled with the digestate from a full-scale AD and fed in batch with four kinds of feedstock (cheese whey, kitchen waste, citrus pulp and fishery waste). The MFC signal initially increased in parallel to VFAs production, then tended to a steady value for VFAs concentrations above 1000mg Ac L -1 . Peak concentrations of tVFAs (2500-4500mg Ac L -1 ) and MFCs potentials were negatively correlated (r=0.916, p<0.05), regardless of the type of substrate. Inhibition of the MFC system occurred when VFAs increased fast above 4000mg Ac L -1 . Polarization curves of electrodes stressed that electroactive bacteria on bioanodes were strongly subjected to inhibition. The inhibition of electroactivity on bioanode trended like typical shock-sensors, opening to direct application as early-warning monitoring system in full-scale ADs. Copyright © 2017 Elsevier Ltd. All rights reserved.

A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities

PubMed Central

Leung, Kaston; Zahn, Hans; Leaver, Timothy; Konwar, Kishori M.; Hanson, Niels W.; Pagé, Antoine P.; Lo, Chien-Chi; Chain, Patrick S.; Hallam, Steven J.; Hansen, Carl L.

2012-01-01

We present a programmable droplet-based microfluidic device that combines the reconfigurable flow-routing capabilities of integrated microvalve technology with the sample compartmentalization and dispersion-free transport that is inherent to droplets. The device allows for the execution of user-defined multistep reaction protocols in 95 individually addressable nanoliter-volume storage chambers by consecutively merging programmable sequences of picoliter-volume droplets containing reagents or cells. This functionality is enabled by “flow-controlled wetting,” a droplet docking and merging mechanism that exploits the physics of droplet flow through a channel to control the precise location of droplet wetting. The device also allows for automated cross-contamination-free recovery of reaction products from individual chambers into standard microfuge tubes for downstream analysis. The combined features of programmability, addressability, and selective recovery provide a general hardware platform that can be reprogrammed for multiple applications. We demonstrate this versatility by implementing multiple single-cell experiment types with this device: bacterial cell sorting and cultivation, taxonomic gene identification, and high-throughput single-cell whole genome amplification and sequencing using common laboratory strains. Finally, we apply the device to genome analysis of single cells and microbial consortia from diverse environmental samples including a marine enrichment culture, deep-sea sediments, and the human oral cavity. The resulting datasets capture genotypic properties of individual cells and illuminate known and potentially unique partnerships between microbial community members. PMID:22547789

Artificial electron acceptors decouple archaeal methane oxidation from sulfate reduction.

PubMed

Scheller, Silvan; Yu, Hang; Chadwick, Grayson L; McGlynn, Shawn E; Orphan, Victoria J

2016-02-12

The oxidation of methane with sulfate is an important microbial metabolism in the global carbon cycle. In marine methane seeps, this process is mediated by consortia of anaerobic methanotrophic archaea (ANME) that live in syntrophy with sulfate-reducing bacteria (SRB). The underlying interdependencies within this uncultured symbiotic partnership are poorly understood. We used a combination of rate measurements and single-cell stable isotope probing to demonstrate that ANME in deep-sea sediments can be catabolically and anabolically decoupled from their syntrophic SRB partners using soluble artificial oxidants. The ANME still sustain high rates of methane oxidation in the absence of sulfate as the terminal oxidant, lending support to the hypothesis that interspecies extracellular electron transfer is the syntrophic mechanism for the anaerobic oxidation of methane. Copyright © 2016, American Association for the Advancement of Science.

[Microbiocenosis of subgingival biofilm and intestinal content in chronic periodontal disease in patients with metabolic syndrome].

PubMed

Petrukhina, N B; Zorina, O A; Shikh, E V; Kartysheva, E V

The aim of the study was to assess correlations of subgingival biofilm and intestinal microbiota in patients with chronic periodontal disease (CPD) and metabolic syndrome (MS). The study included 80 patients divided in 2 groups: 40 healthy individuals with no signs of periodontal disease and 40 patients with CPD and MS. Oral and intestinal microbial consortia compositions were revealed using deep sequencing libraries of 16S rDNA. The study showed than the qualitative composition of the intestinal microbiome in patients with CPD differ significantly from the microbiome of controls. Real-time PCR of subgingival microflora in CPD patients revealed high content of P. gingivalis, T. forsythia and T. denticola, while in intestinal microbiome dominated representatives of Enterobacteriaceae and Eubacteriaceae families with signs of intestinal dysbiosis mostly associated with the decrease of protective species.

Biogeochemistry of a submerged groundwater seep ecosystem in Lake Huron near karst region of Alpena, MI

NASA Astrophysics Data System (ADS)

Kinsman-Costello, L. E.; Dick, G.; Sheik, C.; Burton, G. A.; Sheldon, N. D.

2015-12-01

Submerged groundwater seeps in Lake Huron establish ecosystems with distinctive geochemical conditions. In the Middle Island Sinkhole (MIS), a 23-m deep seep, groundwater seepage establishes low O2 (< 4 mg L-1), high sulfate (6 mM) conditions, in which a purple cyanobacteria-dominated mat thrives. The mat is capable of anoxygenic photosynthesis, oxygenic photosynthesis, and chemosynthesis. Within the top 3 cm of the mat-water interface, hydrogen sulfide concentrations increase to 1-7 mM. Little is known about the structure and function of microbes within organic-rich, high-sulfide sediments beneath the mat. Using pore water and sediment geochemical characterization along with microbial community analysis, we elucidated relationships between microbial community structure and ecosystem function along vertical gradients. In sediment pore waters, biologically reactive solutes (SO42-, NH4+, PO43-, and CH4) displayed steep vertical gradients, reflecting biological and geochemical functioning. In contrast, more conservative ions (Ca+2, Mg+2, Na+, and Cl-), did not change significantly with depth in MIS sediments, indicating groundwater influence in the sediment profile. MIS sediments contained more organic matter than typical Lake Huron sediments, and were generally higher in nutrients, metals, and sulfur (acid volatile sulfide). Using the Illumina MiSeq platform we detected 14,127 unique operational taxonomic units across sediment and surface mat samples. Microbial community composition in the MIS was distinctly different from non-groundwater affected areas at similar depth nearby in Lake Huron (ANOSIM, R= 0.74, p=0.002). MIS sediment communities were more diverse that MIS surface mat communities and changed with depth into sediments. MIS sediment community composition was related to several geochemical variables, including organic matter and multiple indicators of phosphorus availability. Elucidating the structure and function of microbial consortia in MIS, a highly unique and environmentally vulnerable ecosystem, provides a rare opportunity to understand relationships between microbial species and their environment and may provide insights into the evolution of life under ancient low-oxygen, high-sulfur conditions.

Fecal microbiome of growing pigs fed a cereal based diet including chicory (Cichorium intybus L.) or ribwort (Plantago lanceolata L.) forage.

PubMed

Dicksved, Johan; Jansson, Janet K; Lindberg, Jan Erik

2015-01-01

The purpose of this study was to investigate how inclusion of chicory forage or ribwort forage in a cereal-based diet influenced the fecal microbial community (microbiome) in newly weaned (35 days of age) piglets. The piglets were fed a cereal-based diet without (B) and with inclusion (80 and 160 g/kg air-dry forage) of vegetative shoots of chicory (C) and leaves of ribwort (R) forage in a 35-day growth trial. Fecal samples were collected at the start (D0), 17 (D17) and 35 (D35) days after weaning and profiles of the microbial consortia were generated using terminal restriction fragment length polymorphism (T-RFLP). 454-FLX pyrosequencing of 16S rRNA gene amplicons was used to analyze the microbial composition in a subset of the samples already analyzed with T-RFLP. The microbial clustering pattern was primarily dependent on age of the pigs, but diet effects could also be observed. Lactobacilli and enterobacteria were more abundant at D0, whereas the genera Streptococcus, Treponema, Clostridium, Clostridiaceae1 and Coprococcus were present in higher abundances at D35. Pigs fed ribwort had an increased abundance of sequences classified as Treponema and a reduction in lactobacilli. However, the abundance of Prevotellaceae increased with age in on both the chicory and the ribwort diet. Moreover, there were significant correlations between the abundance of Bacteroides and the digested amount of galactose, uronic acids and total non-starch polysaccharides, and between the abundance of Bacteroidales and the digested amount of xylose. This study demonstrated that both chicory and ribwort inclusion in the diet of newly weaned pigs influenced the composition of the fecal microbiota and that digestion of specific dietary components was correlated with species composition of the microbiota. Moreover, this study showed that the gut will be exposed to a dramatic shift in the microbial community structure several weeks after weaning.

Fecal microbiome of growing pigs fed a cereal based diet including chicory (Cichorium intybus L.) or ribwort (Plantago lanceolata L.) forage

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

Dicksved, Johan; Jansson, Janet K.; Lindberg, Jan Erik

BACKGROUND: The purpose of this study was to investigate how inclusion of chicory forage or ribwort forage in a cereal-based diet influenced the fecal microbial community (microbiome) in newly weaned (35 days of age) piglets. The piglets were fed a cereal-based diet without (B) and with inclusion (80 and 160 g/kg air-dry forage) of vegetative shoots of chicory (C) and leaves of ribwort (R) forage in a 35-day growth trial. Fecal samples were collected at the start (D0), 17 (D17) and 35 (D35) days after weaning and profiles of the microbial consortia were generated using terminal restriction fragment length polymorphismmore » (T-RFLP). 454-FLX pyrosequencing of 16S rRNA gene amplicons was used to analyze the microbial composition in a subset of the samples already analyzed with T-RFLP. RESULTS: The microbial clustering pattern was primarily dependent on age of the pigs, but diet effects could also be observed. Lactobacilli and enterobacteria were more abundant at D0, whereas the genera Streptococcus, Treponema, Clostridium, Clostridiaceae1 and Coprococcus were present in higher abundances at D35. Pigs fed ribwort had an increased abundance of sequences classified as Treponema and a reduction in lactobacilli. However, the abundance of Prevotellaceae increased with age in on both the chicory and the ribwort diet. Moreover, there were significant correlations between the abundance of Bacteroides and the digested amount of galactose, uronic acids and total non-starch polysaccharides, and between the abundance of Bacteroidales and the digested amount of xylose. CONCLUSION: This study demonstrated that both chicory and ribwort inclusion in the diet of newly weaned pigs influenced the composition of the fecal microbiota and that digestion of specific dietary components was correlated with species composition of the microbiota. Moreover, this study showed that the gut will be exposed to a dramatic shift in the microbial community structure several weeks after weaning.« less

Biofuel Cells Select for Microbial Consortia That Self-Mediate Electron Transfer

PubMed Central

Rabaey, Korneel; Boon, Nico; Siciliano, Steven D.; Verhaege, Marc; Verstraete, Willy

2004-01-01

Microbial fuel cells hold great promise as a sustainable biotechnological solution to future energy needs. Current efforts to improve the efficiency of such fuel cells are limited by the lack of knowledge about the microbial ecology of these systems. The purposes of this study were (i) to elucidate whether a bacterial community, either suspended or attached to an electrode, can evolve in a microbial fuel cell to bring about higher power output, and (ii) to identify species responsible for the electricity generation. Enrichment by repeated transfer of a bacterial consortium harvested from the anode compartment of a biofuel cell in which glucose was used increased the output from an initial level of 0.6 W m−2 of electrode surface to a maximal level of 4.31 W m−2 (664 mV, 30.9 mA) when plain graphite electrodes were used. This result was obtained with an average loading rate of 1 g of glucose liter−1 day−1 and corresponded to 81% efficiency for electron transfer from glucose to electricity. Cyclic voltammetry indicated that the enhanced microbial consortium had either membrane-bound or excreted redox components that were not initially detected in the community. Dominant species of the enhanced culture were identified by denaturing gradient gel electrophoresis and culturing. The community consisted mainly of facultative anaerobic bacteria, such as Alcaligenes faecalis and Enterococcus gallinarum, which are capable of hydrogen production. Pseudomonas aeruginosa and other Pseudomonas species were also isolated. For several isolates, electrochemical activity was mainly due to excreted redox mediators, and one of these mediators, pyocyanin produced by P. aeruginosa, could be characterized. Overall, the enrichment procedure, irrespective of whether only attached or suspended bacteria were examined, selected for organisms capable of mediating the electron transfer either by direct bacterial transfer or by excretion of redox components. PMID:15345423

National Network of Eisenhower Regional Consortia and Clearinghouse: Supporting the Improvement of Mathematics and Science in America's Schools. Evaluation Summary Report for 1995-2000 with In-Depth Evaluation of Training and Technical Assistance, Dissemination, and Collaboration and Networking Services.

ERIC Educational Resources Information Center

National Network of Eisenhower Regional Consortia and National Clearinghouse.

This report, addressed to sponsors and partners of the Eisenhower consortia and clearinghouse network as well as the staff of those organizations, contains the evaluation summary report of the National Network of Eisenhower Regional Consortia and Clearinghouse. It summarizes network outcomes over the 5-year period between 1995-2000. The report…

Synthetic microbial ecology and the dynamic interplay between microbial genotypes.

PubMed

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

2016-11-01

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

Systems Level Dissection of Anaerobic Methane Cycling: Quantitative Measurements of Single Cell Ecophysiology, Genetic Mechanisms, and Microbial Interactions

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

Orphan, Victoria; Tyson, Gene; Meile, Christof

The global biological CH4 cycle is largely controlled through coordinated and often intimate microbial interactions between archaea and bacteria, the majority of which are still unknown or have been only cursorily identified. Members of the methanotrophic archaea, aka ‘ANME’, are believed to play a major role in the cycling of methane in anoxic environments coupled to sulfate, nitrate, and possibly iron and manganese oxides, frequently forming diverse physical and metabolic partnerships with a range of bacteria. The thermodynamic challenges overcome by the ANME and their bacterial partners and corresponding slow rates of growth are common characteristics in anaerobic ecosystems, and,more » in stark contrast to most cultured microorganisms, this type of energy and resource limited microbial lifestyle is likely the norm in the environment. While we have gained an in-depth systems level understanding of fast-growing, energy-replete microorganisms, comparatively little is known about the dynamics of cell respiration, growth, protein turnover, gene expression, and energy storage in the slow-growing microbial majority. These fundamental properties, combined with the observed metabolic and symbiotic versatility of methanotrophic ANME, make these cooperative microbial systems a relevant (albeit challenging) system to study and for which to develop and optimize culture-independent methodologies, which enable a systems-level understanding of microbial interactions and metabolic networks. We used an integrative systems biology approach to study anaerobic sediment microcosms and methane-oxidizing bioreactors and expanded our understanding of the methanotrophic ANME archaea, their interactions with physically-associated bacteria, ecophysiological characteristics, and underlying genetic basis for cooperative microbial methane-oxidation linked with different terminal electron acceptors. Our approach is inherently multi-disciplinary and multi-scaled, combining transcriptional and proteomic analyses with high resolution microscopy techniques, and stable isotopic and chemical analyses that span community level ‘omics investigations (cm scale) to interspecies consortia (µm scale), to the individual cell and its subcellular components (nm scale). We have organized our methodological approach into three broad categories, RNA-based, Protein-targeted and Geochemical, each encompassing a range of scales, with many techniques and resulting datasets that are highly complementary with one another, and together, offer a unique systems-level perspective of methane-based microbial interactions.« less

Academic Library Consortia in Transition.

ERIC Educational Resources Information Center

Alberico, Ralph

2002-01-01

Using the example of the Virtual Library of Virginia, describes how library consortia are in a state of transformation as technology enables the development of virtual libraries while expanding opportunities for sharing printed works. (EV)

Copper enhances the activity and salt resistance of mixed methane-oxidizing communities.

PubMed

van der Ha, David; Hoefman, Sven; Boeckx, Pascal; Verstraete, Willy; Boon, Nico

2010-08-01

Effluents of anaerobic digesters are an underestimated source of greenhouse gases, as they are often saturated with methane. A post-treatment with methane-oxidizing bacterial consortia could mitigate diffuse emissions at such sites. Semi-continuously fed stirred reactors were used as model systems to characterize the influence of the key parameters on the activity of these mixed methanotrophic communities. The addition of 140 mg L(-1) NH (4) (+) -N had no significant influence on the activity nor did a temperature increase from 28 degrees C to 35 degrees C. On the other hand, addition of 0.64 mg L(-1) of copper(II) increased the methane removal rate by a factor of 1.5 to 1.7 since the activity of particulate methane monooxygenase was enhanced. The influence of different concentrations of NaCl was also tested, as effluents of anaerobic digesters often contain salt levels up to 10 g NaCl L(-1). At a concentration of 11 g NaCl L(-1), almost no methane-oxidizing activity was observed in the reactors without copper addition. Yet, reactors with copper addition exhibited a sustained activity in the presence of NaCl. A colorimetric test based on naphthalene oxidation showed that soluble methane monooxygenase was inhibited by copper, suggesting that the particulate methane monooxygenase was the active enzyme and thus more salt resistant. The results obtained demonstrate that the treatment of methane-saturated effluents, even those with increased ammonium (up to 140 mg L(-1) NH (4) (+) -N) and salt levels, can be mitigated by implementation of methane-oxidizing microbial consortia.

The System Effect: Scaling High-Impact Practices across Campuses

ERIC Educational Resources Information Center

Gagliardi, Jonathan S.; Martin, Rebecca R.; Wise, Kathleen; Blaich, Charles

2015-01-01

This chapter examines the role of systems and consortia in scaling and implementing undergraduate research through a study of the efforts of six systems and consortia working together with the Council on Undergraduate Research.

NLM's Medical Library Resource Improvement Grant for Consortia Development: a proposed outline to simplify the application process.

PubMed

Kabler, A W

1980-01-01

The National Library of Medicine's Resource Improvement Grant for Consortia is available to assist with developing hospital library consortia, and to support the development of basic healthy information collections. In an effort to simplify the grant application process, this paper presents suggestions for writing the narrative section of the first budget-period application, using the outline in NLM's Application Instructions for Consortium Applicants. Suggestions for writing the narratives of the second budget-period application and the collection development application are also included.

'Pop-Up' Governance: developing internal governance frameworks for consortia: the example of UK10K.

PubMed

Kaye, Jane; Muddyman, Dawn; Smee, Carol; Kennedy, Karen; Bell, Jessica

2015-01-01

Innovations in information technologies have facilitated the development of new styles of research networks and forms of governance. This is evident in genomics where increasingly, research is carried out by large, interdisciplinary consortia focussing on a specific research endeavour. The UK10K project is an example of a human genomics consortium funded to provide insights into the genomics of rare conditions, and establish a community resource from generated sequence data. To achieve its objectives according to the agreed timetable, the UK10K project established an internal governance system to expedite the research and to deal with the complex issues that arose. The project's governance structure exemplifies a new form of network governance called 'pop-up' governance. 'Pop-up' because: it was put together quickly, existed for a specific period, was designed for a specific purpose, and was dismantled easily on project completion. In this paper, we use UK10K to describe how 'pop-up' governance works on the ground and how relational, hierarchical and contractual governance mechanisms are used in this new form of network governance.

24 CFR 943.122 - How is a consortium organized?

Code of Federal Regulations, 2010 CFR

2010-04-01

... URBAN DEVELOPMENT PUBLIC HOUSING AGENCY CONSORTIA AND JOINT VENTURES Consortia § 943.122 How is a... participating PHAs, specifying a lead agency (see § 943.124), and submit a joint PHA Plan (§ 943.118). HUD...

The role of research in helping general practice commission efficient healthcare

PubMed Central

2011-01-01

The new commissioning consortia face a major challenge in improving the efficiency of the NHS. They are new organisations, and at the same time as establishing themselves they need to overcome significant obstacles to reforming services. Research evidence about the value of care can help consortia achieve efficiencies, but there are often delays between the provision of evidence and its routine use in policy and practice. The National Institute for Health Research (NIHR) has invested substantial funding in providing evidence for the NHS, and in this article we discuss how consortia can make sure they obtain and apply relevant evidence as quickly as possible, and also generate evidence on practical questions such as the impact of redesigned services. Partnership with NIHR research organizations, particularly the Collaborations for Leadership in Applied Research and Care (CLAHRCs), offer one approach to helping consortia commission efficient health care. PMID:25949644

Diet-Dependent Modular Dynamic Interactions of the Equine Cecal Microbiota

PubMed Central

Kristoffersen, Camilla; Jensen, Rasmus B.; Avershina, Ekaterina; Austbø, Dag; Tauson, Anne-Helene; Rudi, Knut

2016-01-01

Knowledge on dynamic interactions in microbiota is pivotal for understanding the role of bacteria in the gut. We herein present comprehensive dynamic models of the horse cecal microbiota, which include short-chained fatty acids, carbohydrate metabolic networks, and taxonomy. Dynamic models were derived from time-series data in a crossover experiment in which four cecum-cannulated horses were fed a starch-rich diet of hay supplemented with barley (starch intake 2 g kg−1 body weight per day) and a fiber-rich diet of only hay. Cecal contents were sampled via the cannula each h for 24 h for both diets. We observed marked differences in the microbial dynamic interaction patterns for Fibrobacter succinogenes, Lachnospiraceae, Streptococcus, Treponema, Anaerostipes, and Anaerovibrio between the two diet groups. Fluctuations and microbiota interactions were the most pronounced for the starch rich diet, with Streptococcus spp. and Anaerovibrio spp. showing the largest fluctuations. Shotgun metagenome sequencing revealed that diet differences may be explained by modular switches in metabolic cross-feeding between microbial consortia in which fermentation is linked to sugar alcohols and amino sugars for the starch-rich diet and monosaccharides for the fiber-rich diet. In conclusion, diet may not only affect the composition of the cecal microbiota, but also dynamic interactions and metabolic cross-feeding. PMID:27773914

Diet-Dependent Modular Dynamic Interactions of the Equine Cecal Microbiota.

PubMed

Kristoffersen, Camilla; Jensen, Rasmus B; Avershina, Ekaterina; Austbø, Dag; Tauson, Anne-Helene; Rudi, Knut

2016-12-23

Knowledge on dynamic interactions in microbiota is pivotal for understanding the role of bacteria in the gut. We herein present comprehensive dynamic models of the horse cecal microbiota, which include short-chained fatty acids, carbohydrate metabolic networks, and taxonomy. Dynamic models were derived from time-series data in a crossover experiment in which four cecum-cannulated horses were fed a starch-rich diet of hay supplemented with barley (starch intake 2 g kg -1 body weight per day) and a fiber-rich diet of only hay. Cecal contents were sampled via the cannula each h for 24 h for both diets. We observed marked differences in the microbial dynamic interaction patterns for Fibrobacter succinogenes, Lachnospiraceae, Streptococcus, Treponema, Anaerostipes, and Anaerovibrio between the two diet groups. Fluctuations and microbiota interactions were the most pronounced for the starch rich diet, with Streptococcus spp. and Anaerovibrio spp. showing the largest fluctuations. Shotgun metagenome sequencing revealed that diet differences may be explained by modular switches in metabolic cross-feeding between microbial consortia in which fermentation is linked to sugar alcohols and amino sugars for the starch-rich diet and monosaccharides for the fiber-rich diet. In conclusion, diet may not only affect the composition of the cecal microbiota, but also dynamic interactions and metabolic cross-feeding.

Vertically transmitted fecal IgA levels distinguish extra-chromosomal phenotypic variation

PubMed Central

Wallace, Meghan A.; D, Carey-Ann; Burnham; Virgin, Herbert W.; Stappenbeck, Thaddeus S.

2014-01-01

Summary The proliferation of genetically modified mouse models has exposed phenotypic variation between investigators and institutions that has been challenging to control1-5. In many cases, the microbiota is the presumed culprit of the variation. Current solutions to account for phenotypic variability include littermate and maternal controls or defined microbial consortia in gnotobiotic mice6,7. In conventionally raised mice, the microbiome is transmitted from the dam2,8,9. Here we show that microbially–driven dichotomous fecal IgA levels in WT mice within the same facility mimic the effects of chromosomal mutations. We observed in multiple facilities that vertically-transmissible bacteria in IgA-Low mice dominantly lowered fecal IgA levels in IgA-High mice after cohousing or fecal transplantation. In response to injury, IgA-Low mice showed increased damage that was transferable by fecal transplantation and driven by fecal IgA differences. We found that bacteria from IgA-Low mice degraded the secretory component (SC) of SIgA as well as IgA itself. These data indicate that phenotypic comparisons between mice must take into account the non-chromosomal hereditary variation between different breeders. We propose fecal IgA as one marker of microbial variability and conclude that cohousing and/or fecal transplantation enables analysis of progeny from different dams. PMID:25686606

Atrazine removal from aqueous solutions using submerged biological aerated filter.

PubMed

Baghapour, Mohammad Ali; Nasseri, Simin; Derakhshan, Zahra

2013-06-12

Atrazine is widely used in the agriculture as an herbicide. Due to its high mobility, Atrazine leaks into the groundwaters, surface waters, and drinking water wells. Many physical and chemical methods have been suggested for removing Atrazine from aquatic environments. However, these methods are very costly, have many performance problems, produce a lot of toxic intermediates which are very harmful and dangerous, and cannot completely mineralize Atrazine. In this study, biodegradation of Atrazine by microbial consortium was evaluated in the aquatic environment. In order to assess the Atrazine removal from the aquatic environment, submerged biological aerated filter (SBAF) was fed with synthetic wastewater based on sucrose and Atrazine at different hydraulic retention times (HRTs). The maximum efficiencies for Atrazine and Soluble Chemical Oxygen Demand (SCOD) removal were 97.9% and 98.9%, respectively. The study findings showed that Stover-Kincannon model had very good fitness (R2 > 99%) in loading Atrazine in the biofilter and by increasing the initial concentration of Atrazine, the removal efficiency increased. Aerobic mixed biofilm culture was observed to be suitable for the treatment of Atrazine from aquatic environment. There was no significant inhibition effect on mixed aerobic microbial consortia. Atrazine degradation depended on the strength of wastewater and the amount of Atrazine in the influent.

Atrazine removal from aqueous solutions using submerged biological aerated filter

PubMed Central

2013-01-01

Atrazine is widely used in the agriculture as an herbicide. Due to its high mobility, Atrazine leaks into the groundwaters, surface waters, and drinking water wells. Many physical and chemical methods have been suggested for removing Atrazine from aquatic environments. However, these methods are very costly, have many performance problems, produce a lot of toxic intermediates which are very harmful and dangerous, and cannot completely mineralize Atrazine. In this study, biodegradation of Atrazine by microbial consortium was evaluated in the aquatic environment. In order to assess the Atrazine removal from the aquatic environment, submerged biological aerated filter (SBAF) was fed with synthetic wastewater based on sucrose and Atrazine at different hydraulic retention times (HRTs). The maximum efficiencies for Atrazine and Soluble Chemical Oxygen Demand (SCOD) removal were 97.9% and 98.9%, respectively. The study findings showed that Stover-Kincannon model had very good fitness (R2 > 99%) in loading Atrazine in the biofilter and by increasing the initial concentration of Atrazine, the removal efficiency increased. Aerobic mixed biofilm culture was observed to be suitable for the treatment of Atrazine from aquatic environment. There was no significant inhibition effect on mixed aerobic microbial consortia. Atrazine degradation depended on the strength of wastewater and the amount of Atrazine in the influent. PMID:24499572

Authigenic carbonate precipitates from the NE Black Sea: a mineralogical, geochemical, and lipid biomarker study

NASA Astrophysics Data System (ADS)

Bahr, A.; Pape, T.; Bohrmann, G.; Mazzini, A.; Haeckel, M.; Reitz, A.; Ivanov, M.

2009-04-01

Carbonate precipitates recovered from 2,000 m water depth at the Dolgovskoy Mound (Shatsky Ridge, north eastern Black Sea) were studied using mineralogical, geochemical and lipid biomarker analyses. The carbonates differ in shape from simple pavements to cavernous structures with thick microbial mats attached to their lower side and within cavities. Low δ13C values measured on carbonates (-41 to -32‰ V-PDB) and extracted lipid biomarkers indicate that anaerobic oxidation of methane (AOM) played a crucial role in precipitating these carbonates. The internal structure of the carbonates is dominated by finely laminated coccolith ooze and homogeneous clay layers, both cemented by micritic high-magnesium calcite (HMC), and pure, botryoidal, yellowish low-magnesium calcite (LMC) grown in direct contact to microbial mats. δ18O measurements suggest that the authigenic HMC precipitated in equilibrium with the Black Sea bottom water while the yellowish LMC rims have been growing in slightly 18O-depleted interstitial water. Although precipitated under significantly different environmental conditions, especially with respect to methane availability, all analysed carbonate samples show lipid patterns that are typical for ANME-1 dominated AOM consortia, in the case of the HMC samples with significant contributions of allochthonous components of marine and terrestrial origin, reflecting the hemipelagic nature of the primary sediment.

How Specific Microbial Communities Benefit the Oil Industry: Dynamics of Alcanivorax spp. in Oil-Contaminated Intertidal Beach Sediments Undergoing Bioremediation

NASA Astrophysics Data System (ADS)

Singh, Arvind K.; Sherry, Angela; Gray, Neil D.; Jones, Martin D.; Röling, Wilfred F. M.; Head, Ian M.

The industrial revolution has led to significant increases in the consumption of petroleum hydrocarbons. Concomitant with this increase, hydrocarbon pollution has become a global problem resulting from emissions related to operational use, releases during production, pipeline failures and tanker spills. Importantly, in addition to these anthropogenic sources of hydrocarbon pollution, natural seeps alone account for about 50% of total petroleum hydrocarbon releases in the aquatic environment (National Research Council, 2003). The annual input from natural seeps would form a layer of hydrocarbons 20 molecules thick on the sea surface globally if it remained un-degraded (Prince, 2005). By contrast with natural seeps, many oil spills, e.g. Sea Empress (Milford Haven, UK), Prestige (Galicia, Spain), EXXON Valdez (Prince William Sound, Alaska, USA), released huge amounts of oil (thousands to hundreds of thousand tonnes; Table 24.1) in a locally confined area over a short period of time with a huge acute impact on the marine environment. These incidents have attracted the attention of both the general public and the scientific community due to their great impact on coastal ecosystems. Although many petroleum hydrocarbons are toxic, they are degraded by microbial consortia naturally present in marine ecosystems.

Pulsed (13)C2-Acetate Protein-SIP Unveils Epsilonproteobacteria as Dominant Acetate Utilizers in a Sulfate-Reducing Microbial Community Mineralizing Benzene.

PubMed

Starke, Robert; Keller, Andreas; Jehmlich, Nico; Vogt, Carsten; Richnow, Hans H; Kleinsteuber, Sabine; von Bergen, Martin; Seifert, Jana

2016-05-01

In a benzene-degrading and sulfate-reducing syntrophic consortium, a clostridium affiliated to the genus Pelotomaculum was previously described to ferment benzene while various sulfate-reducing Deltaproteobacteria and a member of the Epsilonproteobacteria were supposed to utilize acetate and hydrogen as key metabolites derived from benzene fermentation. However, the acetate utilization network within this community was not yet unveiled. In this study, we performed a pulsed (13)C2-acetate protein stable isotope probing (protein-SIP) approach continuously spiking low amounts of acetate (10 μM per day) in addition to the ongoing mineralization of unlabeled benzene. Metaproteomics revealed high abundances of Clostridiales followed by Syntrophobacterales, Desulfobacterales, Desulfuromonadales, Desulfovibrionales, Archaeoglobales, and Campylobacterales. Pulsed acetate protein-SIP results indicated that members of the Campylobacterales, the Syntrophobacterales, the Archaeoglobales, the Clostridiales, and the Desulfobacterales were linked to acetate utilization in descending abundance. The Campylobacterales revealed the fastest and highest (13)C incorporation. Previous experiments suggested that the activity of the Campylobacterales was not essential for anaerobic benzene degradation in the investigated community. However, these organisms were consistently detected in various hydrocarbon-degrading and sulfate-reducing consortia enriched from the same aquifer. Here, we demonstrate that this member of the Campylobacterales is the dominant acetate utilizer in the benzene-degrading microbial consortium.

Accounting for soil biotic effects on soil health and crop productivity in the design of crop rotations.

PubMed

Dias, Teresa; Dukes, Angela; Antunes, Pedro M

2015-02-01

There is an urgent need for novel agronomic improvements capable of boosting crop yields while alleviating environmental impacts. One such approach is the use of optimized crop rotations. However, a set of measurements that can serve as guiding principles for the design of crop rotations is lacking. Crop rotations take advantage of niche complementarity, enabling the optimization of nutrient use and the reduction of pests and specialist pathogen loads. However, despite the recognized importance of plant-soil microbial interactions and feedbacks for crop yield and soil health, this is ignored in the selection and management of crops for rotation systems. We review the literature and propose criteria for the design of crop rotations focusing on the roles of soil biota and feedback on crop productivity and soil health. We consider that identifying specific key organisms or consortia capable of influencing plant productivity is more important as a predictor of soil health and crop productivity than assessing the overall soil microbial diversity per se. As such, we propose that setting up soil feedback studies and applying genetic sequencing tools towards the development of soil biotic community databases has a strong potential to enable the establishment of improved soil health indicators for optimized crop rotations. © 2014 Society of Chemical Industry.

Development and composition of a mixed culture for bioremediation of chlorinated ethenes and ethanes

USGS Publications Warehouse

Jones, E.J.P.; Voytek, M.A.; Lorah, M.M.

2005-01-01

Microbial organisms capable of dechlorinating 1,1,2,2 tetrachloroethane (TeCA) and its chlorinated ethane and ethylene daughter products were enriched in surface sediments collected from the West Branch Canal Creek wetland area, leading to the formation of two mixed cultures using slightly different enrichment methods. Both WBC-1 and WBC-2 were capable of rapid and complete reductive dechlorination of TeCA and its daughter products (1,1,2-trichloroethane, 1,2-dichloroethane, trichloroethylene, 1,2-dichloroethylene, and vinyl chloride) to ethylene, and addition of either culture to wetland sediment and to engineered peat/compost mixtures resulted in significant enhancement of dechlorination. However, the WBC-2 culture supported better sustained activity and was more readily scaled up for application in bioaugmentation treatments, whereas dechlorination activity was gradually lost in WBC-1. The microbial composition of WBC-1 and WBC-2 were determined by cloning and sequencing 500 base pairs of the 16S rDNA gene and the methyl co-reductase. Methanogens identified in the consortia were members of the Order Methanomicrobiales, which includes acetoclastic methanogens. This is an abstract of a paper presented at the Proceedings of the 8th International In Situ and On-Site Bioremediation Symposium (Baltimore, MD 6/6-9/2005).

Response of Aquatic Bacterial Communities to Hydraulic Fracturing in Northwestern Pennsylvania: A Five-Year Study.

PubMed

Ulrich, Nikea; Kirchner, Veronica; Drucker, Rebecca; Wright, Justin R; McLimans, Christopher J; Hazen, Terry C; Campa, Maria F; Grant, Christopher J; Lamendella, Regina

2018-04-09

Horizontal drilling and hydraulic fracturing extraction procedures have become increasingly present in Pennsylvania where the Marcellus Shale play is largely located. The potential for long-term environmental impacts to nearby headwater stream ecosystems and aquatic bacterial assemblages is still incompletely understood. Here, we perform high-throughput sequencing of the 16 S rRNA gene to characterize the bacterial community structure of water, sediment, and other environmental samples (n = 189) from 31 headwater stream sites exhibiting different histories of fracking activity in northwestern Pennsylvania over five years (2012-2016). Stream pH was identified as a main driver of bacterial changes within the streams and fracking activity acted as an environmental selector for certain members at lower taxonomic levels within stream sediment. Methanotrophic and methanogenic bacteria (i.e. Methylocystaceae, Beijerinckiaceae, and Methanobacterium) were significantly enriched in sites exhibiting Marcellus shale activity (MSA+) compared to MSA- streams. This study highlighted potential sentinel taxa associated with nascent Marcellus shale activity and some of these taxa remained as stable biomarkers across this five-year study. Identifying the presence and functionality of specific microbial consortia within fracking-impacted streams will provide a clearer understanding of the natural microbial community's response to fracking and inform in situ remediation strategies.

Metagenomic Analyses Reveal That Energy Transfer Gene Abundances Can Predict the Syntrophic Potential of Environmental Microbial Communities.

PubMed

Oberding, Lisa; Gieg, Lisa M

2016-01-05

Hydrocarbon compounds can be biodegraded by anaerobic microorganisms to form methane through an energetically interdependent metabolic process known as syntrophy. The microorganisms that perform this process as well as the energy transfer mechanisms involved are difficult to study and thus are still poorly understood, especially on an environmental scale. Here, metagenomic data was analyzed for specific clusters of orthologous groups (COGs) related to key energy transfer genes thus far identified in syntrophic bacteria, and principal component analysis was used in order to determine whether potentially syntrophic environments could be distinguished using these syntroph related COGs as opposed to universally present COGs. We found that COGs related to hydrogenase and formate dehydrogenase genes were able to distinguish known syntrophic consortia and environments with the potential for syntrophy from non-syntrophic environments, indicating that these COGs could be used as a tool to identify syntrophic hydrocarbon biodegrading environments using metagenomic data.

Biohydrogen production from space crew's waste simulants using thermophilic consolidated bioprocessing.

PubMed

Wang, Jia; Bibra, Mohit; Venkateswaran, Kasthuri; Salem, David R; Rathinam, Navanietha Krishnaraj; Gadhamshetty, Venkataraman; Sani, Rajesh K

2018-05-01

Human waste simulants were for the first time converted into biohydrogen by a newly developed anaerobic microbial consortium via thermophilic consolidated bioprocessing. Four different BioH 2 -producing consortia (denoted as C1, C2, C3 and C4) were isolated, and developed using human waste simulants as substrate. The thermophilic consortium C3, which contained Thermoanaerobacterium, Caloribacterium, and Caldanaerobius species as the main constituents, showed the highest BioH 2 production (3.999 mmol/g) from human waste simulants under optimized conditions (pH 7.0 and 60 °C). The consortium C3 also produced significant amounts of BioH 2 (5.732 mmol/g and 2.186 mmol/g) using wastewater and activated sludge, respectively. The developed consortium in this study is a promising candidate for H 2 production in space applications as in situ resource utilization. Copyright © 2018 Elsevier Ltd. All rights reserved.