Microbial characterization of toluene-degrading denitrifying consortia obtained from terrestrial and marine ecosystems.

Science.gov (United States)

An, Y-J; Joo, Y-H; Hong, I-Y; Ryu, H-W; Cho, K-S

2004-10-01

The degradation characteristics of toluene coupled to nitrate reduction were investigated in enrichment culture and the microbial communities of toluene-degrading denitrifying consortia were characterized by denaturing gradient gel electrophoresis (DGGE) technique. Anaerobic nitrate-reducing bacteria were enriched from oil-contaminated soil samples collected from terrestrial (rice field) and marine (tidal flat) ecosystems. Enriched consortia degraded toluene in the presence of nitrate as a terminal electron acceptor. The degradation rate of toluene was affected by the initial substrate concentration and co-existence of other hydrocarbons. The types of toluene-degrading denitrifying consortia depended on the type of ecosystem. The clone RS-7 obtained from the enriched consortium of the rice field was most closely related to a toluene-degrading and denitrifying bacterium, Azoarcus denitrificians (A. tolulyticus sp. nov.). The clone TS-11 detected in the tidal flat enriched consortium was affiliated to Thauera sp. strain S2 (T. aminoaromatica sp. nov.) that was able to degrade toluene under denitrifying conditions. This indicates that environmental factors greatly influence microbial communities obtained from terrestrial (rice field) and marine (tidal flat) ecosystems.

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

Science.gov (United States)

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.

Soil-derived microbial consortia enriched with different plant biomass reveal distinct players acting in lignocellulose degradation

NARCIS (Netherlands)

de Lima Brossi, Maria Julia; Jiménez Avella, Diego; Cortes Tolalpa, Larisa; van Elsas, Jan

Here, we investigated how different plant biomass, and-for one substrate-pH, drive the composition of degrader microbial consortia. We bred such consortia from forest soil, incubated along nine aerobic sequential - batch enrichments with wheat straw (WS1, pH 7.2; WS2, pH 9.0), switchgrass (SG, pH

Effects of Spatial Localization on Microbial Consortia Growth.

Directory of Open Access Journals (Sweden)

Michael Venters

Full Text Available Microbial consortia are commonly observed in natural and synthetic systems, and these consortia frequently result in higher biomass production relative to monocultures. The focus here is on the impact of initial spatial localization and substrate diffusivity on the growth of a model microbial consortium consisting of a producer strain that consumes glucose and produces acetate and a scavenger strain that consumes the acetate. The mathematical model is based on an individual cell model where growth is described by Monod kinetics, and substrate transport is described by a continuum-based, non-equilibrium reaction-diffusion model where convective transport is negligible (e.g., in a biofilm. The first set of results focus on a single producer cell at the center of the domain and surrounded by an initial population of scavenger cells. The impact of the initial population density and substrate diffusivity is examined. A transition is observed from the highest initial density resulting in the greatest cell growth to cell growth being independent of initial density. A high initial density minimizes diffusive transport time and is typically expected to result in the highest growth, but this expected behavior is not predicted in environments with lower diffusivity or larger length scales. When the producer cells are placed on the bottom of the domain with the scavenger cells above in a layered biofilm arrangement, a similar critical transition is observed. For the highest diffusivity values examined, a thin, dense initial scavenger layer is optimal for cell growth. However, for smaller diffusivity values, a thicker, less dense initial scavenger layer provides maximal growth. The overall conclusion is that high density clustering of members of a food chain is optimal under most common transport conditions, but under some slow transport conditions, high density clustering may not be optimal for microbial growth.

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

Science.gov (United States)

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.

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

Energy Technology Data Exchange (ETDEWEB)

Bacosa, Hernando Pactao, E-mail: hernando.bacosa@utexas.edu [Graduate School of Environmental Studies, Tohoku University, Aoba 6-6-20, Aramaki, Aoba-ku, Sendai 980-8579 (Japan); Marine Science Institute, The University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX 78373 (United States); Inoue, Chihiro [Graduate School of Environmental Studies, Tohoku University, Aoba 6-6-20, Aramaki, Aoba-ku, Sendai 980-8579 (Japan)

2015-02-11

Highlights: • Most bacterial consortia from tsunami sediment degraded PAH mixture and pyrene. • The consortia were dominated by known and unknown PAHs-degrading bacteria. • Dokdonella clone is a potential new species and PAH degrader from tsunami sediment. • PAH-RHDα is better than nidA gene for estimating pyrene-degraders in the consortia. • First report on the PAH degradation and PAH-degrading bacteria from tsunami sediment. - Abstract: 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.

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

International Nuclear Information System (INIS)

Bacosa, Hernando Pactao; Inoue, Chihiro

2015-01-01

Highlights: • Most bacterial consortia from tsunami sediment degraded PAH mixture and pyrene. • The consortia were dominated by known and unknown PAHs-degrading bacteria. • Dokdonella clone is a potential new species and PAH degrader from tsunami sediment. • PAH-RHDα is better than nidA gene for estimating pyrene-degraders in the consortia. • First report on the PAH degradation and PAH-degrading bacteria from tsunami sediment. - Abstract: 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

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

Science.gov (United States)

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.

Degradation of organic pollutants by methane grown microbial consortia.

Science.gov (United States)

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).

Degradation of polycyclic aromatic hydrocarbons by microbial consortia enriched from three soils using two different culture media.

Science.gov (United States)

Wu, Manli; Chen, Liming; Tian, Yongqiang; Ding, Yi; Dick, Warren A

2013-07-01

A consortium composed of many different bacterial species is required to efficiently degrade polycyclic aromatic hydrocarbons (PAH) in oil-contaminated soil. We obtained six PAH-degrading microbial consortia from three oil-contaminated soils using two different isolation culture media. Denaturing gradient gel electrophoresis (DGGE) and sequence analyses of amplified 16s rRNA genes confirmed the bacterial community was greatly affected by both the culture medium and the soil from which the consortia were enriched. Three bacterial consortia enriched using malt yeast extract (MYE) medium showed higher degradation rates of PAHs than consortia enriched using Luria broth (LB) medium. Consortia obtained from a soil and then added back to that same soil was more effective in degrading PAHs than adding, to the same soil, consortia isolated from other, unrelated soils. This suggests that inoculum used for bioremediation should be from the same, or very similar nearby soils, as the soil that is actually being bioremediated. Copyright © 2013 Elsevier Ltd. All rights reserved.

Bioremediation of oil sludge contaminated soil using bulking agent mixture enriched consortia of microbial inoculants based by irradiated compost

International Nuclear Information System (INIS)

Tri Retno, D.L.; Mulyana, N.

2013-01-01

Bulking agent mixture enriched consortia of microbial inoculants based by irradiated compost was used on bioremediation of microcosm scale contaminated by hydrocarbon soil. Bioremediation composting was carried out for 42 days. Composting was done with a mixture of bulking agent (sawdust, residual sludge biogas and compost) by 30%, mud petroleum (oil sludge) by 20% and 50% of soil. Mixture of 80% soil and 20% oil sludge was used as a control. Irradiated compost was used as a carrier for consortia of microbial inoculants (F + B) which biodegradable hydrocarbons. Treatment variations include A1, A2, B1, B2, C1, C2, D1 and D2. Process parameters were observed to determine the optimal conditions include: temperature, pH, water content, TPC (Total Plate Count) and degradation of % TPH (Total Petroleum Hydrocarbon). Optimal conditions were achieved in the remediation of oil sludge contamination of 20% using the B2 treatment with the addition consortia of microbial inoculants based by irradiated compost of sawdust (bulking agentby 30% at concentrations of soil by 50% with TPH degradation optimal efficiency of 81.32%. The result of GC-MS analysis showed that bioremediation for 42 days by using a sawdust as a mixture of bulking agents which enriched consortia of microbial inoculants based by irradiated compost is biodegradeable, so initial hydrocarbons with the distribution of the carbon chain C-7 to C-54 into final hydrocarbons with the distribution of carbon chain C-6 to C-8. (author)

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

NARCIS (Netherlands)

Jiménez, Diego Javier; Brossi, Maria Julia de Lima; Schuckel, Julia; Kracun, Stjepan Kresimir; Willats, William George Tycho; van Elsas, Jan Dirk

2016-01-01

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),

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

Science.gov (United States)

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).

Thermophilic anaerobic oxidation of methane by marine microbial consortia.

Science.gov (United States)

Holler, Thomas; Widdel, Friedrich; Knittel, Katrin; Amann, Rudolf; Kellermann, Matthias Y; Hinrichs, Kai-Uwe; Teske, Andreas; Boetius, Antje; Wegener, Gunter

2011-12-01

The anaerobic oxidation of methane (AOM) with sulfate controls the emission of the greenhouse gas methane from the ocean floor. AOM is performed by microbial consortia of archaea (ANME) associated with partners related to sulfate-reducing bacteria. In vitro enrichments of AOM were so far only successful at temperatures ≤25 °C; however, energy gain for growth by AOM with sulfate is in principle also possible at higher temperatures. Sequences of 16S rRNA genes and core lipids characteristic for ANME as well as hints of in situ AOM activity were indeed reported for geothermally heated marine environments, yet no direct evidence for thermophilic growth of marine ANME consortia was obtained to date. To study possible thermophilic AOM, we investigated hydrothermally influenced sediment from the Guaymas Basin. In vitro incubations showed activity of sulfate-dependent methane oxidation between 5 and 70 °C with an apparent optimum between 45 and 60 °C. AOM was absent at temperatures ≥75 °C. Long-term enrichment of AOM was fastest at 50 °C, yielding a 13-fold increase of methane-dependent sulfate reduction within 250 days, equivalent to an apparent doubling time of 68 days. The enrichments were dominated by novel ANME-1 consortia, mostly associated with bacterial partners of the deltaproteobacterial HotSeep-1 cluster, a deeply branching phylogenetic group previously found in a butane-amended 60 °C-enrichment culture of Guaymas sediments. The closest relatives (Desulfurella spp.; Hippea maritima) are moderately thermophilic sulfur reducers. Results indicate that AOM and ANME archaea could be of biogeochemical relevance not only in cold to moderate but also in hot marine habitats.

Substrate Shift Reveals Roles for Members of Bacterial Consortia in Degradation of Plant Cell Wall Polymers

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Camila Carlos

2018-03-01

Full Text Available Deconstructing the intricate matrix of cellulose, hemicellulose, and lignin poses a major challenge in biofuel production. In diverse environments in nature, some microbial communities, are able to overcome plant biomass recalcitrance. Identifying key degraders of each component of plant cell wall can help improve biological degradation of plant feedstock. Here, we sequenced the metagenome of lignocellulose-adapted microbial consortia sub-cultured on xylan and alkali lignin media. We observed a drastic shift on community composition after sub-culturing, independently of the original consortia. Proteobacteria relative abundance increased after growth in alkali lignin medium, while Bacteroidetes abundance increased after growth in xylan medium. At the genus level, Pseudomonas was more abundant in the communities growing on alkali lignin, Sphingobacterium in the communities growing on xylan and Cellulomonas abundance was the highest in the original microbial consortia. We also observed functional convergence of microbial communities after incubation in alkali lignin, due to an enrichment of genes involved in benzoate degradation and catechol ortho-cleavage pathways. Our results represent an important step toward the elucidation of key members of microbial communities on lignocellulose degradation and may aide the design of novel lignocellulolytic microbial consortia that are able to efficiently degrade plant cell wall polymers.

Substrate Shift Reveals Roles for Members of Bacterial Consortia in Degradation of Plant Cell Wall Polymers.

Science.gov (United States)

Carlos, Camila; Fan, Huan; Currie, Cameron R

2018-01-01

Deconstructing the intricate matrix of cellulose, hemicellulose, and lignin poses a major challenge in biofuel production. In diverse environments in nature, some microbial communities, are able to overcome plant biomass recalcitrance. Identifying key degraders of each component of plant cell wall can help improve biological degradation of plant feedstock. Here, we sequenced the metagenome of lignocellulose-adapted microbial consortia sub-cultured on xylan and alkali lignin media. We observed a drastic shift on community composition after sub-culturing, independently of the original consortia. Proteobacteria relative abundance increased after growth in alkali lignin medium, while Bacteroidetes abundance increased after growth in xylan medium. At the genus level, Pseudomonas was more abundant in the communities growing on alkali lignin, Sphingobacterium in the communities growing on xylan and Cellulomonas abundance was the highest in the original microbial consortia. We also observed functional convergence of microbial communities after incubation in alkali lignin, due to an enrichment of genes involved in benzoate degradation and catechol ortho-cleavage pathways. Our results represent an important step toward the elucidation of key members of microbial communities on lignocellulose degradation and may aide the design of novel lignocellulolytic microbial consortia that are able to efficiently degrade plant cell wall polymers.

A Comparison of Modeling Approaches in Simulating Chlorinated Ethene Removal in a Constructed Wetland by a Microbial Consortia

National Research Council Canada - National Science Library

Campbell, Jason

2002-01-01

The purpose of this study is to compare different approaches to modeling the reductive dechlorination of chlorinated ethenes in the anaerobic region of an upward flow constructed wetland by microbial consortia...

Characterization of two diesel fuel degrading microbial consortia enriched from a non acclimated, complex source of microorganisms

Directory of Open Access Journals (Sweden)

Varese Giovanna C

2010-02-01

Full Text Available Abstract Background The bioremediation of soils impacted by diesel fuels is very often limited by the lack of indigenous microflora with the required broad substrate specificity. In such cases, the soil inoculation with cultures with the desired catabolic capabilities (bioaugmentation is an essential option. The use of consortia of microorganisms obtained from rich sources of microbes (e.g., sludges, composts, manure via enrichment (i.e., serial growth transfers on the polluting hydrocarbons would provide bioremediation enhancements more robust and reproducible than those achieved with specialized pure cultures or tailored combinations (co-cultures of them, together with none or minor risks of soil loading with unrelated or pathogenic allocthonous microorganisms. Results In this work, two microbial consortia, i.e., ENZ-G1 and ENZ-G2, were enriched from ENZYVEBA (a complex commercial source of microorganisms on Diesel (G1 and HiQ Diesel (G2, respectively, and characterized in terms of microbial composition and hydrocarbon biodegradation capability and specificity. ENZ-G1 and ENZ-G2 exhibited a comparable and remarkable biodegradation capability and specificity towards n-C10 to n-C24 linear paraffins by removing about 90% of 1 g l-1 of diesel fuel applied after 10 days of aerobic shaken flask batch culture incubation at 30°C. Cultivation dependent and independent approaches evidenced that both consortia consist of bacteria belonging to the genera Chryseobacterium, Acinetobacter, Psudomonas, Stenotrophomonas, Alcaligenes and Gordonia along with the fungus Trametes gibbosa. However, only the fungus was found to grow and remarkably biodegrade G1 and G2 hydrocarbons under the same conditions. The biodegradation activity and specificity and the microbial composition of ENZ-G1 and ENZ-G2 did not significantly change after cryopreservation and storage at -20°C for several months. Conclusions ENZ-G1 and ENZ-G2 are very similar highly enriched consortia

Characterization of two diesel fuel degrading microbial consortia enriched from a non acclimated, complex source of microorganisms.

Science.gov (United States)

Zanaroli, Giulio; Di Toro, Sara; Todaro, Daniela; Varese, Giovanna C; Bertolotto, Antonio; Fava, Fabio

2010-02-16

The bioremediation of soils impacted by diesel fuels is very often limited by the lack of indigenous microflora with the required broad substrate specificity. In such cases, the soil inoculation with cultures with the desired catabolic capabilities (bioaugmentation) is an essential option. The use of consortia of microorganisms obtained from rich sources of microbes (e.g., sludges, composts, manure) via enrichment (i.e., serial growth transfers) on the polluting hydrocarbons would provide bioremediation enhancements more robust and reproducible than those achieved with specialized pure cultures or tailored combinations (co-cultures) of them, together with none or minor risks of soil loading with unrelated or pathogenic allocthonous microorganisms. In this work, two microbial consortia, i.e., ENZ-G1 and ENZ-G2, were enriched from ENZYVEBA (a complex commercial source of microorganisms) on Diesel (G1) and HiQ Diesel (G2), respectively, and characterized in terms of microbial composition and hydrocarbon biodegradation capability and specificity. ENZ-G1 and ENZ-G2 exhibited a comparable and remarkable biodegradation capability and specificity towards n-C10 to n-C24 linear paraffins by removing about 90% of 1 g l-1 of diesel fuel applied after 10 days of aerobic shaken flask batch culture incubation at 30 degrees C. Cultivation dependent and independent approaches evidenced that both consortia consist of bacteria belonging to the genera Chryseobacterium, Acinetobacter, Psudomonas, Stenotrophomonas, Alcaligenes and Gordonia along with the fungus Trametes gibbosa. However, only the fungus was found to grow and remarkably biodegrade G1 and G2 hydrocarbons under the same conditions. The biodegradation activity and specificity and the microbial composition of ENZ-G1 and ENZ-G2 did not significantly change after cryopreservation and storage at -20 degrees C for several months. ENZ-G1 and ENZ-G2 are very similar highly enriched consortia of bacteria and a fungus capable of

Ferrihydrite-associated organic matter (OM stimulates reduction by Shewanella oneidensis MR-1 and a complex microbial consortia

Directory of Open Access Journals (Sweden)

R. E. Cooper

2017-11-01

acetate as an electron donor under Fe(III-reducing conditions. In summary, this study shows that increasing concentrations of OM in OM–mineral complexes determines microbial Fe(III reduction rates and shapes the microbial community structure involved in the reductive dissolution of ferrihydrite. Similarities observed between the complex Fe(III-reducing microbial consortia and the model Fe(III-reducer S. oneidensis MR-1 suggest electron-shuttling mechanisms dominate in OM-rich environments, including soils, sediments, and fens, where natural OM interacts with Fe(III oxides during mineral formation.

Ferrihydrite-associated organic matter (OM) stimulates reduction by Shewanella oneidensis MR-1 and a complex microbial consortia

Science.gov (United States)

Cooper, Rebecca Elizabeth; Eusterhues, Karin; Wegner, Carl-Eric; Totsche, Kai Uwe; Küsel, Kirsten

2017-11-01

donor under Fe(III)-reducing conditions. In summary, this study shows that increasing concentrations of OM in OM-mineral complexes determines microbial Fe(III) reduction rates and shapes the microbial community structure involved in the reductive dissolution of ferrihydrite. Similarities observed between the complex Fe(III)-reducing microbial consortia and the model Fe(III)-reducer S. oneidensis MR-1 suggest electron-shuttling mechanisms dominate in OM-rich environments, including soils, sediments, and fens, where natural OM interacts with Fe(III) oxides during mineral formation.

Microbial consortia in meat processing environments

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Characterization of anaerobic consortia coupled lignin depolymerization with biomethane generation.

Science.gov (United States)

Wu, Yi-Rui; He, Jianzhong

2013-07-01

Two sediment-free microbial consortia (LI3 and LP3) were established to depolymerize lignin under anaerobic conditions. During depolymerizing high molecular weight lignin to low molecular weight molecules, the two cultures produced biomethane up to 151.7 and 113.0 mL g(-1) total lignin. Furthermore, LI3 and LP3 could also utilize the biomass - oil palm empty fruit bunch fiber (OPEFB) to produce 190.6 and 195.6 mL methaneg(-1) total lignin in OPEFB, and at the same time improve the bioavailability of lignocellulosic matters for further enzymatic hydrolysis. The microbial community analysis by denature gradient gel electrophoresis (DGGE) and the high-density 16S rDNA gene microarray (PhyloChip) exhibited that Methanomethylovorans sp. (LI3) and Methanoculleus sp. (LP3) were the main methanogens present, and phylum Firmicutes and Bacteroidetes were mainly involved in the lignin depolymerization. The established microbial consortia with both lignin depolymerization and biomethane production provide profound application on the environmental friendly pretreatment of lignocellulosic materials. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

Directory of Open Access Journals (Sweden)

Ayaka Yamamuro

Full Text Available 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.

Composition and dynamics of biostimulated indigenous oil-degrading microbial consortia from the Irish, North and Mediterranean Seas: a mesocosm study.

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Gertler, Christoph; Näther, Daniela J; Cappello, Simone; Gerdts, Gunnar; Quilliam, Richard S; Yakimov, Michail M; Golyshin, Peter N

2012-09-01

Diversity of indigenous microbial consortia and natural occurrence of obligate hydrocarbon-degrading bacteria (OHCB) are of central importance for efficient bioremediation techniques. To investigate the microbial population dynamics and composition of oil-degrading consortia, we have established a series of identical oil-degrading mesocosms at three different locations, Bangor (Menai Straits, Irish Sea), Helgoland (North Sea) and Messina (Messina Straits, Mediterranean Sea). Changes in microbial community composition in response to oil spiking, nutrient amendment and filtration were assessed by ARISA and DGGE fingerprinting and 16Sr RNA gene library analysis. Bacterial and protozoan cell numbers were quantified by fluorescence microscopy. Very similar microbial population sizes and dynamics, together with key oil-degrading microorganisms, for example, Alcanivorax borkumensis, were observed at all three sites; however, the composition of microbial communities was largely site specific and included variability in relative abundance of OHCB. Reduction in protozoan grazing had little effect on prokaryotic cell numbers but did lead to a decrease in the percentage of A. borkumensis 16S rRNA genes detected in clone libraries. These results underline the complexity of marine oil-degrading microbial communities and cast further doubt on the feasibility of bioaugmentation practices for use in a broad range of geographical locations. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Detection of catabolic genes in indigenous microbial consortia isolated from a diesel-contaminated soil

International Nuclear Information System (INIS)

Milcic-Terzic, J.; Saval, S.; Lopez-Vidal, Y.; Vrvic, M.M.

2001-01-01

Bioremediation is often used for in situ remediation of petroleum-contaminated sites. The primary focus of this study was on understanding the indigenous microbial community which can survive in contaminated environment and is responsible for the degradation. Diesel, toluene and naphthalene-degrading microbial consortia were isolated from diesel-contaminated soil by growing on selective hydrocarbon substrates. The presence and frequency of the catabolic genes responsible for aromatic hydrocarbon biodegradation (xylE, ndoB) within the isolated consortia were screened using polymerase chain reaction PCR and DNA-DNA colony hybridization. The diesel DNA-extract possessed both the xylE catabolic gene for toluene, and the nah catabolic gene for polynuclear aromatic hydrocarbon degradation. The toluene DNA-extract possessed only the xylE catabolic gene, while the naphthalene DNA-extract only the ndoB gene. Restriction enzyme analysis with HaeIII indicated similar restriction patterns for the xylE gene fragment between toluene DNA-extract and a type strain, Pseudomonas putida ATCC 23973. A substantial proportion (74%) of the colonies from the diesel-consortium possessed the xylE gene, and the ndoB gene (78%), while a minority (29%) of the toluene-consortium harbored the xylE gene. 59% of the colonies from the naphthalene-consortium had the ndoB gene, and did not have the xylE gene. These results indicate that the microbial population has been naturally enriched in organisms carrying genes for aromatic hydrocarbon degradation and that significant aromatic biodegradative potential exists at the site. Characterization of the population genotype constitutes a molecular diagnosis which permits the determination of the catabolic potential of the site to degrade the contaminant present. (author)

Stimulation of Diesel Fuel Biodegradation by Indigenous Nitrogen Fixing Bacterial Consortia.

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Piehler; Swistak; Pinckney; Paerl

1999-07-01

> Abstract Successful stimulation of N2 fixation and petroleum hydrocarbon degradation in indigenous microbial consortia may decrease exogenous N requirements and reduce environmental impacts of bioremediation following petroleum pollution. This study explored the biodegradation of petroleum pollution by indigenous N2 fixing marine microbial consortia. Particulate organic carbon (POC) in the form of ground, sterile corn-slash (post-harvest leaves and stems) was added to diesel fuel amended coastal water samples to stimulate biodegradation of petroleum hydrocarbons by native microorganisms capable of supplying a portion of their own N. It was hypothesized that addition of POC to petroleum amended water samples from N-limited coastal waters would promote the growth of N2 fixing consortia and enhance biodegradation of petroleum. Manipulative experiments were conducted using samples from coastal waters (marinas and less polluted control site) to determine the effects of POC amendment on biodegradation of petroleum pollution by native microbial consortia. Structure and function of the microbial consortia were determined by measurement of N2 fixation (acetylene reduction), hydrocarbon biodegradation (14C hexadecane mineralization), bacterial biomass (AODC), number of hydrocarbon degrading bacteria (MPN), and bacterial productivity (3H-thymidine incorporation). Throughout this study there was a consistent enhancement of petroleum hydrocarbon degradation in response to the addition of POC. Stimulation of diesel fuel biodegradation following the addition of POC was likely attributable to increases in bacterial N2 fixation, diesel fuel bioavailability, bacterial biomass, and metabolic activity. Toxicity of the bulk phase water did not appear to be a factor affecting biodegradation of diesel fuel following POC addition. These results indicate that the addition of POC to diesel-fuel-polluted systems stimulated indigenous N2 fixing microbial consortia to degrade petroleum

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

Science.gov (United States)

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

Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass.

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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.

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

Science.gov (United States)

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.

Microbial consortia in mesocosm bioremediation trial using oil sorbents, slow-release fertilizer and bioaugmentation.

Science.gov (United States)

Gertler, Christoph; Gerdts, Gunnar; Timmis, Kenneth N; Golyshin, Peter N

2009-08-01

An experimental prototype oil boom including oil sorbents, slow-release fertilizers and biomass of the marine oil-degrading bacterium, Alcanivorax borkumensis, was applied for sorption and degradation of heavy fuel oil in a 500-L mesocosm experiment. Fingerprinting of DNA and small subunit rRNA samples for microbial activity conducted to study the changes in microbial communities of both the water body and on the oil sorbent surface showed the prevalence of A. borkumensis on the surface of the oil sorbent. Growth of this obligate oil-degrading bacterium on immobilized oil coincided with a 30-fold increase in total respiration. A number of DNA and RNA signatures of aromatic hydrocarbon-degrading bacteria were detected both in samples of water body and on oil sorbent. Ultimately, the heavy fuel oil in this mesocosm study was effectively removed from the water body. This is the first study to successfully investigate the fate of oil-degrading microbial consortia in an experimental prototype for a bioremediation strategy in offshore, coastal or ship-bound oil spill mitigation using a combination of mechanical and biotechnological techniques.

In Silico Identification of Microbial Partners to Form Consortia with Anaerobic Fungi

Directory of Open Access Journals (Sweden)

St. Elmo Wilken

2018-01-01

Full Text Available Lignocellulose is an abundant and renewable resource that holds great promise for sustainable bioprocessing. However, unpretreated lignocellulose is recalcitrant to direct utilization by most microbes. Current methods to overcome this barrier include expensive pretreatment steps to liberate cellulose and hemicellulose from lignin. Anaerobic gut fungi possess complex cellulolytic machinery specifically evolved to decompose crude lignocellulose, but they are not yet genetically tractable and have not been employed in industrial bioprocesses. Here, we aim to exploit the biomass-degrading abilities of anaerobic fungi by pairing them with another organism that can convert the fermentable sugars generated from hydrolysis into bioproducts. By combining experiments measuring the amount of excess fermentable sugars released by the fungal enzymes acting on crude lignocellulose, and a novel dynamic flux balance analysis algorithm, we screened potential consortia partners by qualitative suitability. Microbial growth simulations reveal that the fungus Anaeromyces robustus is most suited to pair with either the bacterium Clostridia ljungdahlii or the methanogen Methanosarcina barkeri—both organisms also found in the rumen microbiome. By capitalizing on simulations to screen six alternative organisms, valuable experimental time is saved towards identifying stable consortium members. This approach is also readily generalizable to larger systems and allows one to rationally select partner microbes for formation of stable consortia with non-model microbes like anaerobic fungi.

Polyhydroxyalkanoates (PHA) production from fermented crude glycerol: Study on the conversion of 1,3-propanediol to PHA in mixed microbial consortia

DEFF Research Database (Denmark)

Burniol Figols, Anna; Varrone, Cristiano; Daugaard, Anders Egede

2018-01-01

Crude glycerol, a by-product from the biodiesel industry, can be converted by mixed microbial consortia into 1,3-propanediol (1,3-PDO) and volatile fatty acids. In this study, further conversion of these main products into polyhydroxyalkanoates (PHA) was investigated with the focus on 1,3-PDO. Two...... different approaches for the enrichment of PHA accumulating microbial consortia using an aerobic dynamic feeding strategy were applied. With the first approach, where nitrogen was present during the whole cycle, no net production of PHA from 1,3-PDO was observed in the fermented effluent, not even...... the storage response. Nitrogen was still supplied during the famine phase. With the latter strategy, a net production of PHA from 1,3-PDO was observed at a yield of 0.24 Cmol PHA/Cmol 1,3-PDO. The overall yield from the fermented effluent was 0.42 Cmol PHA/Cmol substrate. Overall, the PHA yield from 1,3-PDO...

Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions.

Science.gov (United States)

Hubalek, Valerie; Buck, Moritz; Tan, BoonFei; Foght, Julia; Wendeberg, Annelie; Berry, David; Bertilsson, Stefan; Eiler, Alexander

2017-01-01

Syntrophy among Archaea and Bacteria facilitates the anaerobic degradation of organic compounds to CH 4 and CO 2 . Particularly during aliphatic and aromatic hydrocarbon mineralization, as in the case of crude oil reservoirs and petroleum-contaminated sediments, metabolic interactions between obligate mutualistic microbial partners are of central importance. Using micromanipulation combined with shotgun metagenomic approaches, we describe the genomes of complex consortia within short-chain alkane-degrading cultures operating under methanogenic conditions. Metabolic reconstruction revealed that only a small fraction of genes in the metagenome-assembled genomes encode the capacity for fermentation of alkanes facilitated by energy conservation linked to H 2 metabolism. Instead, the presence of inferred lifestyles based on scavenging anabolic products and intermediate fermentation products derived from detrital biomass was a common feature. Additionally, inferred auxotrophy for vitamins and amino acids suggests that the hydrocarbon-degrading microbial assemblages are structured and maintained by multiple interactions beyond the canonical H 2 -producing and syntrophic alkane degrader-methanogen partnership. Compared to previous work, our report points to a higher order of complexity in microbial consortia engaged in anaerobic hydrocarbon transformation. IMPORTANCE Microbial interactions between Archaea and Bacteria mediate many important chemical transformations in the biosphere from degrading abundant polymers to synthesis of toxic compounds. Two of the most pressing issues in microbial interactions are how consortia are established and how we can modulate these microbial communities to express desirable functions. Here, we propose that public goods (i.e., metabolites of high energy demand in biosynthesis) facilitate energy conservation for life under energy-limited conditions and determine the assembly and function of the consortia. Our report suggests that an

Electrochemical evaluation of Ti/TiO{sub 2}-polyaniline anodes for microbial fuel cells using hypersaline microbial consortia for synthetic-wastewater treatment

Energy Technology Data Exchange (ETDEWEB)

Benetton, X.D.; Navarro-Avila, S.G. [Univ. Autonoma de Yucatan, Yucatan (Mexico). Biotecnologia y Bioingenieria; Carrera-Figueiras, C. [Univ. Autonoma de Yucatan, Yucatan (Mexico). Quimica Fundamental y Aplicada

2010-07-01

This paper described the development of a titanium (Ti/TiO{sub 2}) polyaniline composite electrode. The electrode was designed for use with a microbial fuel cell (MFC) that generated electricity through the microbial biodegradation of organic compounds. A modified NBAF medium was used with a 20 mM acetate as an electron donor and 53 mM fumarate as an electron acceptor for a period of 96 hours at 37 degrees C. Strains were cultured under strict anaerobic conditions. Two microbial cultures were used: (1) pure cultures of Geobacter sulfur-reducens; and (2) an uncharacterized stable microbial consortia isolated from hypersaline swamp sediments. The anodes were made with an emeraldine form of PANI deposited over Ti/TiO{sub 2} electrodes. Electrochemical impedance spectroscopy (EIS) monitoring was used to determine the open circuit potential of the MFC. Negative real impedances were obtained and reproduced in all systems studied with the Ti/TiO{sub 2}-PANI anodes. The highest power density was obtained using the Geobacter sulfur-reducens culture. Further research is needed to study the mechanisms that contribute to the occurrence of negative real impedances. 23 refs., 1 tab., 5 figs.

Library Purchasing Consortia in the UK

Directory of Open Access Journals (Sweden)

David Ball

2001-07-01

Full Text Available The distribution of library purchasing consortia across the United Kingdom is uneven and sector-dependent. Only higher education libraries show a well developed regional infrastructure of purchasing consortia covering virtually all eligible libraries. While there are clear sectoral disparities amongst the library purchasing consortia surveyed, the size of consortium expenditure seems to determine whether procurement professionals are involved. Thus in those whose spend consistently exceeds European Commission guidelines’ thresholds, the involvement of purchasing professionals is much more likely, and also crucial to the successful navigation of such procedures.

Microbial consortia of gorgonian corals from the Aleutian islands.

Science.gov (United States)

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 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.

Ecological Insights into the Dynamics of Plant Biomass-Degrading Microbial Consortia.

Science.gov (United States)

Jiménez, Diego Javier; Dini-Andreote, Francisco; DeAngelis, Kristen M; Singer, Steven W; Salles, Joana Falcão; van Elsas, Jan Dirk

2017-10-01

Plant biomass (PB) is an important resource for biofuel production. However, the frequent lack of efficiency of PB saccharification is still an industrial bottleneck. The use of enzyme cocktails produced from PB-degrading microbial consortia (PB-dmc) is a promising approach to optimize this process. Nevertheless, the proper use and manipulation of PB-dmc depends on a sound understanding of the ecological processes and mechanisms that exist in these communities. This Opinion article provides an overview of arguments as to how spatiotemporal nutritional fluxes influence the successional dynamics and ecological interactions (synergism versus competition) between populations in PB-dmc. The themes of niche occupancy, 'sugar cheaters', minimal effective consortium, and the Black Queen Hypothesis are raised as key subjects that foster our appraisal of such systems. Here we provide a conceptual framework that describes the critical topics underpinning the ecological basis of PB-dmc, giving a solid foundation upon which further prospective experimentation can be developed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Community dynamics and glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass

Energy Technology Data Exchange (ETDEWEB)

Gladden, J.M.; Allgaier, M.; Miller, C.S.; Hazen, T.C.; VanderGheynst, J.S.; Hugenholtz, P.; Simmons, B.A.; Singer, S.W.

2011-05-01

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.

A formalized design process for bacterial consortia that perform logic computing.

Directory of Open Access Journals (Sweden)

Weiyue Ji

Full Text Available The concept of microbial consortia is of great attractiveness in synthetic biology. Despite of all its benefits, however, there are still problems remaining for large-scaled multicellular gene circuits, for example, how to reliably design and distribute the circuits in microbial consortia with limited number of well-behaved genetic modules and wiring quorum-sensing molecules. To manage such problem, here we propose a formalized design process: (i determine the basic logic units (AND, OR and NOT gates based on mathematical and biological considerations; (ii establish rules to search and distribute simplest logic design; (iii assemble assigned basic logic units in each logic operating cell; and (iv fine-tune the circuiting interface between logic operators. We in silico analyzed gene circuits with inputs ranging from two to four, comparing our method with the pre-existing ones. Results showed that this formalized design process is more feasible concerning numbers of cells required. Furthermore, as a proof of principle, an Escherichia coli consortium that performs XOR function, a typical complex computing operation, was designed. The construction and characterization of logic operators is independent of "wiring" and provides predictive information for fine-tuning. This formalized design process provides guidance for the design of microbial consortia that perform distributed biological computation.

Fungal–bacterial consortia increase diuron degradation in water-unsaturated systems

DEFF Research Database (Denmark)

Ellegaard-Jensen, Lea; Knudsen, Berith Elkær; Johansen, Anders

2014-01-01

organism. In addition, fungal hyphae may function as transport vectors for bacteria, thereby facilitating a more effective spreading of degrader organisms in the soil. A more rapid mineralization of the phenylurea herbicide diuron was found in sand with added microbial consortia consisting of both...... degrading bacteria and fungi. Facilitated transport of bacteria by fungal hyphae was demonstrated using a system where herbicide-spiked sand was separated from the consortium by a layer of sterile glass beads. Several fungal–bacterial consortia were investigated by combining different diuron...

Immunological detection of enzymes for sulfate reduction in anaerobic methane-oxidizing consortia.

Science.gov (United States)

Milucka, Jana; Widdel, Friedrich; Shima, Seigo

2013-05-01

Anaerobic oxidation of methane (AOM) coupled to sulfate reduction (SR) at marine gas seeps is performed by archaeal-bacterial consortia that have so far not been cultivated in axenic binary or pure cultures. Knowledge about possible biochemical reactions in AOM consortia is based on metagenomic retrieval of genes related to those in archaeal methanogenesis and bacterial sulfate reduction, and identification of a few catabolic enzymes in protein extracts. Whereas the possible enzyme for methane activation (a variant of methyl-coenzyme M reductase, Mcr) was shown to be harboured by the archaea, enzymes for sulfate activation and reduction have not been localized so far. We adopted a novel approach of fluorescent immunolabelling on semi-thin (0.3-0.5 μm) cryosections to localize two enzymes of the SR pathway, adenylyl : sulfate transferase (Sat; ATP sulfurylase) and dissimilatory sulfite reductase (Dsr) in microbial consortia from Black Sea methane seeps. Both Sat and Dsr were exclusively found in an abundant microbial morphotype (c. 50% of all cells), which was tentatively identified as Desulfosarcina/Desulfococcus-related bacteria. These results show that ANME-2 archaea in the Black Sea AOM consortia did not express bacterial enzymes of the canonical sulfate reduction pathway and thus, in contrast to previous suggestions, most likely cannot perform canonical sulfate reduction. Moreover, our results show that fluorescent immunolabelling on semi-thin cryosections which to our knowledge has been so far only applied on cell tissues, is a powerful tool for intracellular protein detection in natural microbial associations. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Bioremediation of chromium in tannery effluent by microbial consortia

African Journals Online (AJOL)

Chromium is the most toxic and common among the heavy metal pollutants of industrial effluents. In the present work the chromium remediation ability of Bacillus subtilis, Pseudomonas aeruginosa and Saccharomyces cerevisiae in consortia and in their immobilized forms was studied and their efficiencies were compared.

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

DEFF Research Database (Denmark)

Burniol Figols, Anna; Varrone, Cristiano; Le, Simone Balzer

2018-01-01

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 Cmol PHA/Cmol 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...

Modeling the mutualistic interactions between tubeworms and microbial consortia.

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Erik E Cordes

2005-03-01

Full Text Available The deep-sea vestimentiferan tubeworm Lamellibrachia luymesi forms large aggregations at hydrocarbon seeps in the Gulf of Mexico that may persist for over 250 y. Here, we present the results of a diagenetic model in which tubeworm aggregation persistence is achieved through augmentation of the supply of sulfate to hydrocarbon seep sediments. In the model, L. luymesi releases the sulfate generated by its internal, chemoautotrophic, sulfide-oxidizing symbionts through posterior root-like extensions of its body. The sulfate fuels sulfate reduction, commonly coupled to anaerobic methane oxidation and hydrocarbon degradation by bacterial-archaeal consortia. If sulfate is released by the tubeworms, sulfide generation mainly by hydrocarbon degradation is sufficient to support moderate-sized aggregations of L. luymesi for hundreds of years. The results of this model expand our concept of the potential benefits derived from complex interspecific relationships, in this case involving members of all three domains of life.

Use of biolog methodology for optimizing the degradation of hydrocarbons by bacterial consortia.

Science.gov (United States)

Ambrosoli, R; Bardi, L; Minati, J L; Belviso, S; Ricci, R; Marzona, M

2003-01-01

Biolog methodology was used for the preliminary screening of different cultural conditions in order to detect the best combination/s of factors influencing the metabolic performance of bacterial consortia active in the degradation of hydrocarbons. Two microbial consortia were tested for their activity on 2 hydrocarbons (nonadecane and eicosane) in presence of the following cultural coadjuvants: vegetal oil, beta-cyclodextrine, sodium acetate, mineral solution. Tests were conducted in Biolog MT plates, where only the redox indicator of microbial growth (tetrazolium violet) and no carbon sources are provided. The microwells were filled with various combinations of hydrocarbons, microbial inoculum and coadjuvants. Blanks were prepared with the same combinations but without hydrocarbons. The results obtained show the suitability of the methodology developed to identify the most active consortium and the conditions for its best degradation performance. The efficacy of Biolog methodology (Biolog Inc., USA) for the characterization of microbial communities on the basis of the metabolic profiles obtained on specific carbon sources in the microwells of Elisa-type plates, is widely acknowledged (Garland, 1997; Pietikäinen et al., 2000; Dauber and Wolters, 2000). Due to its aptitude to simultaneously evaluate multiple microbial responses and directly organize the results, it can be adapted to meet specific study purposes (Gamo and Shji, 1999). In the present research Biolog methodology was fitted for the preliminary screening of different cultural conditions, in order to detect the best combination/s of factors influencing the metabolic performance of bacterial consortia active in the degradation of aliphatic hydrocarbons, in view of their utilization for the bioremediation of polluted sites.

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

Science.gov (United States)

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.

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

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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.

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

Science.gov (United States)

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.

An overview of physico-chemical mechanisms of biogas production by microbial communities: a step towards sustainable waste management.

Science.gov (United States)

Goswami, Ramansu; Chattopadhyay, Pritam; Shome, Arunima; Banerjee, Sambhu Nath; Chakraborty, Amit Kumar; Mathew, Anil K; Chaudhury, Shibani

2016-06-01

Biogas is a combination of methane, CO 2 , nitrogen, H 2 S and traces of few other gases. Almost any organic waste can be biologically transformed into biogas and other energy-rich organic compounds through the process of anaerobic digestion (AD) and thus helping in sustainable waste management. Although microbes are involved in each step of AD, knowledge about those microbial consortia is limited due to the lack of phylogenetic and metabolic data of predominantly unculturable microorganisms. However, culture-independent methods like PCR-based ribotyping has been successfully employed to get information about the microbial consortia involved in AD. Microbes identified have been found to belong mainly to the bacterial phyla of Proteobacteria, Chloroflexi, Firmicutes and Bacteroidetes. Among the archaeal population, the majority have been found to be methanogens (mainly unculturable), the remaining being thermophilic microbes. Thus, the AD process as a whole could be controlled by regulating the microbial consortia involved in it. Optimization in the feedstock, pH, temperature and other physical parameters would be beneficial for the microbial growth and viability and thus helpful for biogas production in AD. Besides, the biogas production is also dependent upon the activity of several key genes, ion-specific transporters and enzymes, like genes coding for methyl-CoM reductase, formylmethanofuran transferase, formate dehydrogenase present in the microbes. Fishing for these high-efficiency genes will ultimately increase the biogas production and sustain the production plant.

Isolation, Screening and Development of Local Bacterial Consortia With Azo Dyes Decolourising Capability

Directory of Open Access Journals (Sweden)

Khadijah, O.

2009-01-01

Full Text Available A total of 1540 bacterial isolates were isolated and screened for their ability to degrade selected azo dyes. Of these, nine isolates were chosen for further studies based on their ability to degrade a wide spectrum of dyes efficiently and rapidly. Several microbial consortia were developed and tested for their effectiveness. Overall the consortia were able to degrade 70 - 100% colour within 72 hours compared to 60 – 97% colour removed by individual isolates. A microbial consortium labelled C15 showed good growth in agitation culture but the colour removal was best in static culture with 80 - 100% colour removed in less than 72 hours. Based on the 16S rRNA sequencing, two of the bacterial isolates in C15 belong to the Chryseobacterium genus while the other one belongs to Flavobacterium genus.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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

Phenotype fingerprinting suggests the involvement of single-genotype consortia in degradation of aromatic compounds by Rhodopseudomonas palustris.

Directory of Open Access Journals (Sweden)

Tatiana V Karpinets

Full Text Available Anaerobic degradation of complex organic compounds by microorganisms is crucial for development of innovative biotechnologies for bioethanol production and for efficient degradation of environmental pollutants. In natural environments, the degradation is usually accomplished by syntrophic consortia comprised of different bacterial species. This strategy allows consortium organisms to reduce efforts required for maintenance of the redox homeostasis at each syntrophic level. Cellular mechanisms that maintain the redox homeostasis during the degradation of aromatic compounds by one organism are not fully understood. Here we present a hypothesis that the metabolically versatile phototrophic bacterium Rhodopseudomonas palustris forms its own syntrophic consortia, when it grows anaerobically on p-coumarate or benzoate as a sole carbon source. We have revealed the consortia from large-scale measurements of mRNA and protein expressions under p-coumarate, benzoate and succinate degrading conditions using a novel computational approach referred as phenotype fingerprinting. In this approach, marker genes for known R. palustris phenotypes are employed to determine the relative expression levels of genes and proteins in aromatics versus non-aromatics degrading 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 conditions may lead to at least three R. palustris subpopulations utilizing p-coumarate, benzoate, and CO2 and H2. Benzoate degrading conditions may also produce 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 N2-fixing subpopulation in the benzoate degrading consortium has preferential activation of the

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

Energy Technology Data Exchange (ETDEWEB)

Burgos, A. [Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Edifici C, Campus de UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona (Spain); Departamento de Recursos Hidrobiológicos, Universidad de Nariño, Pasto (N) (Colombia); Maldonado, J. [Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Edifici C, Campus de UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona (Spain); De los Rios, A. [Museo Nacional de Ciencias Naturales(CSIC), Serrano 115 dpdo, 28006 Madrid (Spain); Solé, A. [Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Edifici C, Campus de UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona (Spain); Esteve, I., E-mail: isabel.esteve@uab.cat [Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Edifici C, Campus de UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona (Spain); Departamento de Recursos Hidrobiológicos, Universidad de Nariño, Pasto (N) (Colombia); Museo Nacional de Ciencias Naturales(CSIC), Serrano 115 dpdo, 28006 Madrid (Spain)

2013-09-15

Highlights: •We studied the tolerance-resistance of phototrophic microorganisms to copper and lead. •We determined the capacity of consortia of microorganisms to sequester copper and lead. •CLSM-λscan is a technique for evaluating in vivo effect of metals on microorganisms. •SEM-EDX and TEM-EDX determined the capacity of microorganisms to sequester metals. -- Abstract: 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

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

International Nuclear Information System (INIS)

Burgos, A.; Maldonado, J.; De los Rios, A.; Solé, A.; Esteve, I.

2013-01-01

Highlights: •We studied the tolerance-resistance of phototrophic microorganisms to copper and lead. •We determined the capacity of consortia of microorganisms to sequester copper and lead. •CLSM-λscan is a technique for evaluating in vivo effect of metals on microorganisms. •SEM-EDX and TEM-EDX determined the capacity of microorganisms to sequester metals. -- Abstract: 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

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

Science.gov (United States)

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.

The electric picnic: synergistic requirements for exoelectrogenic microbial communities

KAUST Repository

Kiely, Patrick D

2011-06-01

Characterization of the various microbial populations present in exoelectrogenic biofilms provides insight into the processes required to convert complex organic matter in wastewater streams into electrical current in bioelectrochemical systems (BESs). Analysis of the community profiles of exoelectrogenic microbial consortia in BESs fed different substrates gives a clearer picture of the different microbial populations present in these exoelectrogenic biofilms. Rapid utilization of fermentation end products by exoelectrogens (typically Geobacter species) relieves feedback inhibition for the fermentative consortia, allowing for rapid metabolism of organics. Identification of specific syntrophic processes and the communities characteristic of these anodic biofilms will be a valuable aid in improving the performance of BESs. © 2011 Elsevier Ltd.

Mining anaerobic digester consortia metagenomes for secreted carbohydrate active enzymes

DEFF Research Database (Denmark)

Wilkens, Casper; Busk, Peter Kamp; Pilgaard, Bo

thermophilic and mesophilic ADs a wide variety of carbohydrate active enzyme functions were discovered in the metagenomic sequencing of the microbial consortia. The most dominating type of glycoside hydrolases were β-glucosidases (up to 27%), α-amylases (up to 10%), α-glucosidases (up to 8%), α......, and food wastes (Alvarado et al., 2014). The processes and the roles of the microorganisms that are involved in biomass conversion and methane production in ADs are still not fully understood. We are investigating thermophilic and mesophilic ADs that use wastewater surplus sludge for methane production...... was done with the Peptide Pattern Recognition (PPR) program (Busk and Lange, 2013), which is a novel non-alignment based approach that can predict function of e.g. CAZymes. PPR identifies a set of short conserved sequences, which can be used as a finger print when mining genomes for novel enzymes. In both...

The electric picnic: synergistic requirements for exoelectrogenic microbial communities

KAUST Repository

Kiely, Patrick D; Regan, John M; Logan, Bruce E

2011-01-01

(BESs). Analysis of the community profiles of exoelectrogenic microbial consortia in BESs fed different substrates gives a clearer picture of the different microbial populations present in these exoelectrogenic biofilms. Rapid utilization of fermentation

Studies about behavior of microbial degradation of organic compounds

International Nuclear Information System (INIS)

Ohtsuka, Makiko

2003-02-01

Some of TRU waste include organic compounds, thus these organic compounds might be nutrients for microbial growth at disposal site. This disposal system might be exposed to high alkali condition by cement compounds as engineering barrier material. In the former experimental studies, it has been supposed that microbial exist under pH = 12 and the microbial activity acclimated to high alkali condition are able to degrade asphalt under anaerobic condition. Microbes are called extremophile that exist in cruel habitat as high alkali or reductive condition. We know less information about the activity of extremophile, though any recent studies reveal them. In this study, the first investigation is metabolic pathway as microbial activity, the second is microbial degradation of aromatic compounds in anaerobic condition, and the third is microbial activity under high alkali. Microbial metabolic pathway consist of two systems that fulfill their function each other. One system is to generate energy for microbial activities and the other is to convert substances for syntheses of organisms' structure materials. As these systems are based on redox reaction between substances, it is made chart of the microbial activity region using pH, Eh, and depth as parameter, There is much report that microbe is able to degrade aromatic compounds under aerobic or molecular O 2 utilizing condition. For degradation of aromatic compounds in anaerobic condition, supplying electron acceptor is required. Co-metabolism and microbial consortia has important role, too. Alcalophile has individual transporting system depending Na + and acidic compounds contained in cell wall. Generating energy is key for survival and growth under high alkali condition. Co-metabolism and microbial consortia are effective for microbial degradation of aromatic compounds under high alkali and reductive condition, and utilizable electron acceptor and degradable organic compounds are required for keeping microbial activity and

Vitamin and amino acid auxotrophy in anaerobic consortia operating under methanogenic condition

OpenAIRE

Eiler, Alexander; Bertilsson, Stefan; Berry, David; Wendeberg, Anneli; Foght, Julia; Tan, Boonfei; Buck, Moritz; Hubalek, Valeria

2017-01-01

Syntrophy among Archaea and Bacteria facilitates the anaerobic degradation of organic compounds to CH4 and CO2. Particularly during aliphatic and aromatic hydrocarbon mineralization, as in crude oil reservoirs and petroleum contaminated sediments, metabolic interactions between obligate mutualistic microbial partners are of central importance1. Using micromanipulation combined with shotgun metagenomic approaches, we disentangled the genomes of complex consortia inside a short chain alkane deg...

Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions

OpenAIRE

Valerie Hubalek; Moritz Buck; BoonFei Tan; Julia Foght; Annelie Wendeberg; David Berry; Stefan Bertilsson; Alexander Eiler; Karen G. Lloyd

2017-01-01

ABSTRACT Syntrophy among Archaea and Bacteria facilitates the anaerobic degradation of organic compounds to CH4 and CO2. Particularly during aliphatic and aromatic hydrocarbon mineralization, as in the case of crude oil reservoirs and petroleum-contaminated sediments, metabolic interactions between obligate mutualistic microbial partners are of central importance. Using micromanipulation combined with shotgun metagenomic approaches, we describe the genomes of complex consortia within short-ch...

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

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B. Orcutt

2008-11-01

Full Text Available 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.

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.

Science.gov (United States)

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.

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.

Directory of Open Access Journals (Sweden)

Simon P Rout

Full Text Available 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.

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

Science.gov (United States)

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.

Library Consortia in Germany

Directory of Open Access Journals (Sweden)

Werner Reinhardt

2001-07-01

Full Text Available Looking at the present situation in Germany consortia show a considerable variety of organizational forms. Only in the case of the Friedrich-Althoff-Consortium in Berlin-Brandenburg a corporate body with deed of partnership does exist. In other German states consortia have been formed which are represented by an individual library (e.g. Baden-Württemberg or by a central institution such as the Bayerische Staatsbibliothek in Bavaria or the Hochschulbibliothekszentrum NRW in North Rhine-Westphalia. Rarely contracts for nationwide consortia have been signed; resulting from an initiative of a professional society, the „Gesellschaft Deutscher Chemiker“, an agreement was reached allowing for the use of the Beilstein-Crossfire-database in participating universities all over Germany.

Investigations on abundance and activity of microbial sponge symbionts using quantitative real - time PCR

DEFF Research Database (Denmark)

Kumala, Lars; Hentschel, Ute; Bayer, Kristina

Marine sponges are hosts to dense and diverse microbial consortia that are likely to play a key role in the metabolic processes of the host sponge due to their enormous abundance. Common symbioses between nitrogen transforming microorganisms and sponges indicate complex nitrogen cycling within...... the host. Of particular interest is determining the community structure and function of microbial symbionts in order to gain deeper insight into host-symbiont interactions. We investigated the abundance and activity of microbial symbionts in two Mediterranean sponge species using quantitative real-time PCR....... An absolute quantification of functional genes and transcripts in archaeal and bacterial symbionts was conducted to determine their involvement in nitrification and denitrification, comparing the low microbial abundance (LMA) sponge Dysidea avara with the high microbial abundance (HMA) representative Aplysina...

Bar-coded pyrosequencing reveals the responses of PBDE-degrading microbial communities to electron donor amendments.

Directory of Open Access Journals (Sweden)

Meiying Xu

Full Text Available Polybrominated diphenyl ethers (PBDEs can be reductively degraded by microorganisms under anaerobic conditions. However, little is known about the effect of electron donors on microbial communities involved in PBDEs degradation. Here we employed 454 Titanium pyrosequencing to examine the phylogenetic diversity, composition, structure and dynamics of microbial communities from microcosms under the conditions of different electron donor amendments. The community structures in each of the five alternate electron donor enrichments were significantly shifted in comparison with those of the control microcosm. Commonly existing OTUs between the treatment and control consortia increased from 5 to 17 and more than 50% of OTUs increased around 13.7 to 186 times at least in one of the microcosms after 90-days enrichment. Although the microbial communities at different taxonomic levels were significantly changed by different environmental variable groups in redundancy analysis, significant correlations were observed between the microbial communities and PBDE congener profiles. The lesser-brominated PBDE congeners, tri-BDE congener (BDE-32 and hexa-BDE, were identified as the key factors shaping the microbial community structures at OTU level. Some rare populations, including the known dechlorinating bacterium, Dehalobacter, showed significant positive-correlation with the amounts of PBDE congeners in the consortia. The same results were also observed on some unclassified bacteria. These results suggest that PBDEs-degrading microbial communities can be successfully enriched, and their structures and compositions can be manipulated through adjusting the environmental parameters.

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

Energy Technology Data Exchange (ETDEWEB)

Orphan, Victoria Jeanne [California Inst. of Technology (CalTech), Pasadena, CA (United States). Division of Geological and Planetary Sciences

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 between 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

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

Science.gov (United States)

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.

Advanced Microscopy of Microbial Cells

DEFF Research Database (Denmark)

Haagensen, Janus Anders Juul; Regenberg, Birgitte; Sternberg, Claus

2011-01-01

microscopy, super-resolution optical microscopy (STED, SIM, PALM) as well as atomic force microscopy and Raman spectroscopy. Using examples of bistability in microbial populations as well as biofilm development and differentiation in bacterial and yeast consortia, we demonstrate the importance of microscopy...

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

Science.gov (United States)

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.

Community and Proteomic Analysis of Anaerobic Consortia Converting Tetramethylammonium to Methane

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Wei-Yu Chen

2017-01-01

Full Text Available Tetramethylammonium-degrading methanogenic consortia from a complete-mixing suspended sludge (CMSS and an upflow anaerobic sludge blanket (UASB reactors were studied using multiple PCR-based molecular techniques and shotgun proteomic approach. The prokaryotic 16S rRNA genes of the consortia were analyzed by quantitative PCR, high-throughput sequencing, and DGGE-cloning methods. The results showed that methanogenic archaea were highly predominant in both reactors but differed markedly according to community structure. Community and proteomic analysis revealed that Methanomethylovorans and Methanosarcina were the major players for the demethylation of methylated substrates and methane formation through the reduction pathway of methyl-S-CoM and possibly, acetyl-CoA synthase/decarbonylase-related pathways. Unlike high dominance of one Methanomethylovorans population in the CMSS reactor, diverse methylotrophic Methanosarcina species inhabited in syntrophy-like association with hydrogenotrophic Methanobacterium in the granular sludge of UASB reactor. The overall findings indicated the reactor-dependent community structures of quaternary amines degradation and provided microbial insight for the improved understanding of engineering application.

Community and Proteomic Analysis of Anaerobic Consortia Converting Tetramethylammonium to Methane

Science.gov (United States)

Chen, Wei-Yu; Kraková, Lucia; Pangallo, Domenico; Jeszeová, Lenka; Liu, Bing; Yasui, Hidenari

2017-01-01

Tetramethylammonium-degrading methanogenic consortia from a complete-mixing suspended sludge (CMSS) and an upflow anaerobic sludge blanket (UASB) reactors were studied using multiple PCR-based molecular techniques and shotgun proteomic approach. The prokaryotic 16S rRNA genes of the consortia were analyzed by quantitative PCR, high-throughput sequencing, and DGGE-cloning methods. The results showed that methanogenic archaea were highly predominant in both reactors but differed markedly according to community structure. Community and proteomic analysis revealed that Methanomethylovorans and Methanosarcina were the major players for the demethylation of methylated substrates and methane formation through the reduction pathway of methyl-S-CoM and possibly, acetyl-CoA synthase/decarbonylase-related pathways. Unlike high dominance of one Methanomethylovorans population in the CMSS reactor, diverse methylotrophic Methanosarcina species inhabited in syntrophy-like association with hydrogenotrophic Methanobacterium in the granular sludge of UASB reactor. The overall findings indicated the reactor-dependent community structures of quaternary amines degradation and provided microbial insight for the improved understanding of engineering application. PMID:29391857

Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River.

Science.gov (United States)

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

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

Science.gov (United States)

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.

Phylogenetic & Physiological Profiling of Microbial Communities of Contaminated Soils/Sediments: Identifying Microbial consortia...

Energy Technology Data Exchange (ETDEWEB)

Terence L. Marsh

2004-05-26

The goals of this study were: (1) survey the microbial community in soil samples from a site contaminated with heavy metals using new rapid molecular techniques that are culture-independent; (2) identify phylogenetic signatures of microbial populations that correlate with metal ion contamination; and (3) cultivate these diagnostic strains using traditional as well as novel cultivation techniques in order to identify organisms that may be of value in site evaluation/management or bioremediation.

Advanced Microscopy of Microbial Cells

DEFF Research Database (Denmark)

Haagensen, Janus Anders Juul; Regenberg, Birgitte; Sternberg, Claus

2011-01-01

Growing awareness of heterogeneity in cells of microbial populations has emphasized the importance of advanced microscopy for visualization and understanding of the molecular mechanisms underlying cell-to-cell variation. In this review, we highlight some of the recent advances in confocal...... microscopy, super-resolution optical microscopy (STED, SIM, PALM) as well as atomic force microscopy and Raman spectroscopy. Using examples of bistability in microbial populations as well as biofilm development and differentiation in bacterial and yeast consortia, we demonstrate the importance of microscopy...

Anaerobic decomposition of switchgrass by tropical soil-derived feedstock-adapted consortia.

Science.gov (United States)

DeAngelis, Kristen M; Fortney, Julian L; Borglin, Sharon; Silver, Whendee L; Simmons, Blake A; Hazen, Terry C

2012-01-01

Tropical forest soils decompose litter rapidly with frequent episodes of anoxic conditions, making it likely that bacteria using alternate terminal electron acceptors (TEAs) play a large role in decomposition. This makes these soils useful templates for improving biofuel production. To investigate how TEAs affect decomposition, we cultivated feedstock-adapted consortia (FACs) derived from two tropical forest soils collected from the ends of a rainfall gradient: organic matter-rich tropical cloud forest (CF) soils, which experience sustained low redox, and iron-rich tropical rain forest (RF) soils, which experience rapidly fluctuating redox. Communities were anaerobically passed through three transfers of 10 weeks each with switchgrass as a sole carbon (C) source; FACs were then amended with nitrate, sulfate, or iron oxide. C mineralization and cellulase activities were higher in CF-FACs than in RF-FACs. Pyrosequencing of the small-subunit rRNA revealed members of the Firmicutes, Bacteroidetes, and Alphaproteobacteria as dominant. RF- and CF-FAC communities were not different in microbial diversity or biomass. The RF-FACs, derived from fluctuating redox soils, were the most responsive to the addition of TEAs, while the CF-FACs were overall more efficient and productive, both on a per-gram switchgrass and a per-cell biomass basis. These results suggest that decomposing microbial communities in fluctuating redox environments are adapted to the presence of a diversity of TEAs and ready to take advantage of them. More importantly, these data highlight the role of local environmental conditions in shaping microbial community function that may be separate from phylogenetic structure. After multiple transfers, we established microbial consortia derived from two tropical forest soils with different native redox conditions. Communities derived from the rapidly fluctuating redox environment maintained a capacity to use added terminal electron acceptors (TEAs) after multiple

Molecular microbial ecology of lignocellulose mobilisation as a ...

African Journals Online (AJOL)

The community structure of complex microbial consortia which develop in lignocellulose packed passive treatment systems for acid mine drainage remediation were investigated. An understanding of interactions between these populations is important in determining mechanisms by which such systems operate.

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

Science.gov (United States)

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.

Academic Library Consortia in the United States: An Introduction

Directory of Open Access Journals (Sweden)

Sharon L. Bostick

2001-07-01

Full Text Available Library consortia in the United States arose from a need for sharing when resources or funding for those resources were scarce. This is as true today as it was over 100 years ago when the first American consortia were formed. Consortia continue to be a growing and important part of the library profession. This article will give an overview of academic library consortia, with special emphasis on the history and modern developments in the United States and provide a general introduction to the concept of library cooperation.

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

Science.gov (United States)

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

Biodegradation of oil spill by petroleum refineries using consortia of novel bacterial strains.

Science.gov (United States)

Singh, Bina; Bhattacharya, Amit; Channashettar, Veeranna A; Jeyaseelan, C Paul; Gupta, Sachin; Sarma, Priyangshu M; Mandal, Ajoy K; Lal, Banwari

2012-08-01

Feasibility study carried out at the site prior to the full scale study showed that the introduced bacterial consortium effectively adapted to the local environment of the soil at bioremediation site. The soil samples were collected from the contaminated fields after treatment with bacterial consortium at different time intervals and analyzed by gas chromatography after extraction with hexane and toluene. At time zero (just before initiation of bioremediation), the concentration of total petroleum hydrocarbons in the soil (25-cm horizon) of plot A, B, C and D was 30.90 %, 18.80 %, 25.90 % and 29.90 % respectively, after 360 days of treatment with microbial consortia was reduced to 0.97 %, 1.0 %, 1.0 %, and 1.1 % respectively. Whereas, only 5 % degradation was observed in the control plot after 365 days (microbial consortium not applied).

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

Science.gov (United States)

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.

Characterization of microbial consortia in a terephthalate-degrading anaerobic granular sludge system.

Science.gov (United States)

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.

Isolation of amoebic-bacterial consortia capable of degrading trichloroethylene

International Nuclear Information System (INIS)

Tyndall, R.L.; Ironside, K.; Little, C.D.; Katz, S.; Kennedy, J.

1990-01-01

Groundwater from a waste disposal site contaminated with chlorinated alkenes was examined for the presence of amoebic-bacterial consortia capable of degrading the suspected carcinogen, trichloroethylene (TCE). Consortia were readily isolated from all of four test wells. They contained free-living amoebae, and heterotrophic and methylotrophic bacteria. Electron microscopic examination showed bacteria localized throughout the amoebic cytoplasm and an abundance of hyphomicrobium, but not Type I methanotrophs. The presence of Type II methanotrophs was indirectly indicated by lipid analysis of one consortium. The consortia have been passaged for over two years on mineral salts media in a methane atmosphere, which would not be expected to maintain the heterotrophs or amoebae separately. The methanotrophic bacteria apparently provided a stable nutrient source, allowing the persistence of the various genera. By use of 14 C-radiotracer techniques, the degradation of TCE by the consortia was observed with 14 C eventuating predominantly in CO 2 and water-soluble products. In a more detailed examination of one consortia, the amoebae and heterotrohic components did not degrade TCE, while a mixed culture of heterotrophs and methanotrophs did degrade TCE, suggesting the latter component was the primary cause for the consortium's ability to degrade TCE. Amoebic-bacterial consortia may play a role in stabilizing and preserving methylotrophic bacteria in hostile environments

What Role for Law, Human Rights, and Bioethics in an Age of Big Data, Consortia Science, and Consortia Ethics? The Importance of Trustworthiness.

Science.gov (United States)

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

Science.gov (United States)

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

What Role for Law, Human Rights, and Bioethics in an Age of Big Data, Consortia Science, and Consortia Ethics? The Importance of Trustworthiness

Directory of Open Access Journals (Sweden)

Edward S. Dove

2015-08-01

Full Text Available 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.

Understanding the efficacy of influent waste water on microbial ...

African Journals Online (AJOL)

The assembling of microbial consortia in wastewater treatment facilities is a significance of environmental conditions. In the present research work, activated sludge from different wastewater treatment plants (WWTPs) were exploited at a molecular level to determine the influence of the complexity of the influent composition ...

Monitoring the fibrolytic potential of microbial ecosystems from domestic and wild ruminants browsing tanniferous forages

Directory of Open Access Journals (Sweden)

Nokwethemba Nqobile Philile Msimango

2016-03-01

Full Text Available Although the rumen microbiome has been reported to synthesize a rich source of symbiotic enzymes (exocellulase, endocellulase, hemicellulase and cellobiase, the digestion of tropical C4 grasses and browses by ruminants is still limited. Therefore, this study aimed to unveil potential fibrolytic microbial ecosystems from giraffe, kudu, impala and consortia (A1 [giraffe + kudu], A2 [giraffe + impala], A3 [kudu + impala], and A4 [giraffe + kudu + impala] browsing tanniferous plants, which can be used to improve forage utilization in domesticated goat. Crude protein enzyme extracts (CPZ from fresh faecal samples were precipitated by 60% ammonium sulphate and assayed for exocellulase, endocellulase and hemicellulase by incubating with crystalline cellulose, carboxymethyl cellulose and xylan at 38 °C with optimum pH of 5.5 to 6.5 for 1, 2, and 48 h, respectively. Enzyme specific activities were defined as μg of reducing sugar/mg CPZ. In vitro fermentation study was done by transferring 33 mL of fresh faecal inoculum into 67 mL of salivary buffer containing 1 g Acacia sieberiana and incubating for 72 h at 38 °C. Apparent degradability (APDeg, true degradability (TD, neutral detergent fibre degradability (NDFdeg, acid detergent fibre degradability (ADFdeg, microbial yield (MY, metabolizable energy (ME and total gas emitted (Gas were measured. Exocellulase activities were higher (P < 0.05 in all wild animals and consortia than those in goat except for A4. Minimal differences in hemicellulase activities (P < 0.05 were observed among goat and wild animals and consortia, while endocellulase activity was generally higher (P < 0.05 in goat than that in the rest of the systems. Apart from A3, TDeg, NDFdeg and ADFdeg were higher (P < 0.05 in all microbial ecosystems from wild animals and consortia than those in goat. Apparent degradability, MY and ME also varied (P < 0.05 among these systems. Giraffe, Kudu and A3 produced lower (P�

Training Consortia: How They Work, How They Don't.

Science.gov (United States)

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)

Bioaugmentation for Electricity Generation from Corn Stover Biomass Using Microbial Fuel Cells

KAUST Repository

Wang, Xin; Feng, Yujie; Wang, Heming; Qu, Youpeng; Yu, Yanling; Ren, Nanqi; Li, Nan; Wang, Elle; Lee, He; Logan, Bruce E.

2009-01-01

of microbial consortia specifically acclimated for biomass breakdown. A mixed culture that was developed to have a high saccharification rate with corn stover was added to singlechamber, air-cathode MFCs acclimated for power production using glucose. The MFC

The role of buying consortia among SMEs in the electricity market in Italy

International Nuclear Information System (INIS)

Alderighi, Marco

2007-01-01

We model the electricity market in Italy, focusing on the impact of buying consortia among SMEs on the behaviour of the large electricity producers and sellers. We show that consortia may in certain circumstances produce a pro-competitive result, i.e. they may induce a reduction of prices not only for consortia members but also for firms not in the consortia

Stay connected: Electrical conductivity of microbial aggregates.

Science.gov (United States)

Li, Cheng; Lesnik, Keaton Larson; Liu, Hong

2017-11-01

The discovery of direct extracellular electron transfer offers an alternative to the traditional understanding of diffusional electron exchange via small molecules. The establishment of electronic connections between electron donors and acceptors in microbial communities is critical to electron transfer via electrical currents. These connections are facilitated through conductivity associated with various microbial aggregates. However, examination of conductivity in microbial samples is still in its relative infancy and conceptual models in terms of conductive mechanisms are still being developed and debated. The present review summarizes the fundamental understanding of electrical conductivity in microbial aggregates (e.g. biofilms, granules, consortia, and multicellular filaments) highlighting recent findings and key discoveries. A greater understanding of electrical conductivity in microbial aggregates could facilitate the survey for additional microbial communities that rely on direct extracellular electron transfer for survival, inform rational design towards the aggregates-based production of bioenergy/bioproducts, and inspire the construction of new synthetic conductive polymers. Copyright © 2017 Elsevier Inc. All rights reserved.

Metabolic interactions between methanogenic consortia and anaerobic respiring bacteria

DEFF Research Database (Denmark)

Stams, A.J.; Oude Elferink, S.J.; Westermann, Peter

2003-01-01

Most types of anaerobic respiration are able to outcompete methanogenic consortia for common substrates if the respective electron acceptors are present in sufficient amounts. Furthermore, several products or intermediate compounds formed by anaerobic respiring bacteria are toxic to methanogenic...... consortia. Despite the potentially adverse effects, only few inorganic electron acceptors potentially utilizable for anaerobic respiration have been investigated with respect to negative interactions in anaerobic digesters. In this chapter we review competitive and inhibitory interactions between anaerobic...... respiring populations and methanogenic consortia in bioreactors. Due to the few studies in anaerobic digesters, many of our discussions are based upon studies of defined cultures or natural ecosystems...

Bacterial communities in full-scale wastewater treatment systems.

Science.gov (United States)

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.

Higher Educational Consortia Organization: Functional Structures of Administration and Management.

Science.gov (United States)

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,…

Governance of Transnational Global Health Research Consortia and Health Equity.

Science.gov (United States)

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.

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

Science.gov (United States)

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.

On-line electrochemical monitoring of microbially influenced corrosion

International Nuclear Information System (INIS)

Dowling, N.J.E.; Stansbury, E.E.; White, D.C.; Borenstein, S.W.; Danko, J.C.

1989-01-01

Newly emerging electrochemical measurement techniques can provide on-line, non-destructive monitoring of the average corrosion rate and indications of localized pitting corrosion together with insight into fundamental electrochemical mechanisms responsible for the corrosion process. This information is relevant to evaluating, monitoring, understanding and controlling microbially influenced corrosion (MIC). MIC of coupons exposed in sidestream devices on site or in laboratory-based experiments, where the corrosion response is accelerated by exposure to active consortia of microbes recovered from specific sites, can be utilized to evaluate mitigation strategies. The average corrosion rates can be determined by small amplitude cyclic voltametry (SACV), and AC impedance spectroscopy (EIS). EIS can also give insight into the mechanisms of the MIC and indications of localized corrosion. Pitting corrosion can be detected non-destructively with open circuit potential monitoring (OCP). OCP also responds to bacterial biofilm activities such as oxygen depletion and other electrochemical activities. Utilizing these methods, accelerated tests can be designed to direct the selection of materials, surface treatments of materials, and welding filler materials, as well as the optimization of chemical and mechanical countermeasures with the microbial consortia recovered and characterized from the specific sites of interest

Developing symbiotic consortia for lignocellulosic biofuel production

Energy Technology Data Exchange (ETDEWEB)

Zuroff, Trevor R.; Curtis, Wayne R. [Pennsylvania State Univ., University Park, PA (United States). Dept. of Chemical Engineering

2012-02-15

The search for petroleum alternatives has motivated intense research into biological breakdown of lignocellulose to produce liquid fuels such as ethanol. Degradation of lignocellulose for biofuel production is a difficult process which is limited by, among other factors, the recalcitrance of lignocellulose and biological toxicity of the products. Consolidated bioprocessing has been suggested as an efficient and economical method of producing low value products from lignocellulose; however, it is not clear whether this would be accomplished more efficiently with a single organism or community of organisms. This review highlights examples of mixtures of microbes in the context of conceptual models for developing symbiotic consortia for biofuel production from lignocellulose. Engineering a symbiosis within consortia is a putative means of improving both process efficiency and stability relative to monoculture. Because microbes often interact and exist attached to surfaces, quorum sensing and biofilm formation are also discussed in terms of consortia development and stability. An engineered, symbiotic culture of multiple organisms may be a means of assembling a novel combination of metabolic capabilities that can efficiently produce biofuel from lignocellulose. (orig.)

Partnering with Sandia National Laboratories through alliances or consortia

Energy Technology Data Exchange (ETDEWEB)

Winchell, B.M.

1994-12-01

To better facilitate working with industry, groups of industrial participants, and partners in alliances or consortia, Sandia National Laboratories presents information helpful to those outside groups as to the forms of arrangements that may be used to better facilitate partnering relationships between Sandia National Laboratories and consortia or alliances of outside parties. It is expected that these alliances and consortia will include both large and small for-profit industrial concerns, as well as not-for-profit entities such as universities, institutes, other research facilities, and other nonprofit institutions or consortia containing institutions. The intent of this report is to provide such outside groups with information that will facilitate rapid interactions with Sandia National Laboratories through some of these forms of business which will be discussed in this report. These are not the only approaches to facilitating business interactions with Sandia National Laboratories and it is not intended that this report be legal advice or required approaches to doing business with Sandia National Laboratories. The intent of this report is merely to suggest ways in which Sandia National Laboratories can work with outside parties in the most expeditious manner.

Partnering with Sandia National Laboratories through alliances or consortia

Energy Technology Data Exchange (ETDEWEB)

Winchell, B.M.

1994-04-01

To better facilitate working with industry, groups of industrial participants, and partners in alliances or consortia, Sandia National laboratories presents information helpful to those outside groups as to the forms of arrangements that may be used to better facilitate partnering relationships between Sandia National Laboratories and consortia or alliances of outside parties. It is expected that these alliances and consortia will include both large and small for-profit industrial concerns, as well as not-for-profit entities such as universities, institutes, other research facilities, and other nonprofit institutions or consortia containing institutions. The intent of this report is to provide such outside groups with information that will facilitate rapid interactions with Sandia National Laboratories through some of these forms of business which will be discussed in this report. These are not the only approaches to facilitating business interactions with Sandia National Laboratories and it is not intended that this report be legal advice or required approaches to doing business with Sandia National Laboratories. The intent of this report is merely to suggest ways in which Sandia National Laboratories can work with outside parties in the most expeditious manner.

RMS Titanic and the emergence of new concepts on consortial nature of microbial events.

Science.gov (United States)

Cullimore, D Roy; Pellegrino, Charles; Johnston, Lori

2002-01-01

The RMS Titanic sank in 1912 and created a historical event that still ripples through time. Stories were told and lessons learned but the science has only just begun. Today the fading remains of the ship resemble the hanging gardens of Babylon except that it is not plants that drape the walls but complex microbial growths called rusticles. These organisms have been found to be not a species, like plants and animals, but to be structures created by complex communities of bacterial species. Like the discovery of tube worms in the mid-oceanic vents, the nature of these rusticles presents another biological discovery of a fundamental nature. Essentially these microbial consortia on the RMS Titanic have generated structures of a mass that would rival whales and elephants while gradually extracting the iron from the steel. Rusticle-like consortia appear to play many roles within the environment, and it is perhaps the RMS Titanic that is showing that there is a new way to understand the form, function, and nature of microorganisms. This understanding would develop by considering the bacteria not as individual species functioning independently but as consortia of species functioning in community structures within a common habitat. This concept, if adopted, would change dramatically the manner in which a microbial ecologist and any scientist or engineer would view the occurrence of a slime, encrustation, biocolloid, rust flake, iron pan, salt deposit, and perhaps even some of the diseases that remain unexplained as a disease of unknown cause.

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

Science.gov (United States)

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

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

Science.gov (United States)

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.

New Strategies in Library Services Organization: Consortia University Libraries in Spain

Directory of Open Access Journals (Sweden)

Miguel Duarte Barrionuevo

2017-09-01

Full Text Available New political, economic, and technological developments, as well as the growth of information markets, in Spain have created a foundation for the creation of library consortia. The author describes the process by which different regions in Spain have organized university library consortia.

Governance of global health research consortia: Sharing sovereignty and resources within Future Health Systems.

Science.gov (United States)

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.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

A Study of the Inter-Organizational Behavior in Consortia. Final Report.

Science.gov (United States)

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.…

Response of core microbial consortia to hydrocarbon contaminations in coastal sediment habitats

Directory of Open Access Journals (Sweden)

Mathilde Jeanbille

2016-10-01

Full Text Available Traditionally, microbial surveys investigating the effect of chronic anthropogenic pressure such as polyaromatic hydrocarbons (PAHs contaminations consider just the alpha and beta diversity and ignore the interactions among the different taxa forming the microbial community. Here, we investigated the ecological relationships between the three domains of life (i.e. Bacteria, Archaea and Eukarya using 454 pyrosequencing data of the 16S rRNA and 18S rRNA genes from chronically impacted and pristine sediments, along the coasts of the Mediterranean Sea (Gulf of Lion, Vermillion coast, Corsica, Bizerte lagoon and Lebanon and the French Atlantic Ocean (Bay of Biscay and English Channel. Our approach provided a robust ecological framework for the partition of the taxa abundance distribution into 859 core OTUs and 6629 satellite OTUs. OTUs forming the core microbial community showed the highest sensitivity to changes in environmental and contaminant variations, with salinity, latitude, temperature, particle size distribution, total organic carbon (TOC and PAH concentrations as main drivers of community assembly. The core communities were dominated by Gammaproteobacteria and Deltaproteobacteria for Bacteria, by Thaumarchaeota, Bathyarchaeota and Thermoplasmata for Archaea and Metazoa and Dinoflagellata for Eukarya. In order to find associations among microorganisms, we generated a co-occurrence network in which PAHs were found to impact significantly the potential predator – prey relationship in one microbial consortium composed of ciliates and Actinobacteria. Comparison of network topological properties between contaminated and non-contaminated samples showed substantial differences in the structure of the network and indicated a higher vulnerability to environmental perturbations in the contaminated sediments.

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

Science.gov (United States)

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

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

Science.gov (United States)

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

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

Science.gov (United States)

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.

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

Science.gov (United States)

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

Hanging Together To Avoid Hanging Separately: Opportunities for Academic Libraries and Consortia.

Science.gov (United States)

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,…

Microbial biofilm study by synchrotron X-ray microscopy

International Nuclear Information System (INIS)

Pennafirme, S.; Lima, I.; Bitencourt, J.A.; Crapez, M.A.C.; Lopes, R.T.

2015-01-01

Microbial biofilm has already being used to remove metals and other pollutants from wastewater. In this sense, our proposal was to isolate and cultivate bacteria consortia from mangrove’s sediment resistant to Zn (II) and Cu (II) at 50 mg L −1 and to observe, through synchrotron X-ray fluorescence microscopy (microXRF), whether the biofilm sequestered the metal. The biofilm area analyzed was 1 mm 2 and a 2D map was generated (pixel size 20×20 μm 2 , counting time 5 s/point). The biofilm formation and retention followed the sequence Zn>Cu. Bacterial consortium zinc resistant formed dense biofilm and retained 63.83% of zinc, while the bacterial consortium copper resistant retained 3.21% of copper, with lower biofilm formation. Dehydrogenase activity of Zn resistant bacterial consortium was not negatively affect by 50 mg ml −1 zinc input, whereas copper resistant bacterial consortium showed a significant decrease on dehydrogenase activity (50 mg mL −1 of Cu input). In conclusion, biofilm may protect bacterial cells, acting as barrier against metal toxicity. The bacterial consortia Zn resistant, composed by Nitratireductor spp. and Pseudomonas spp formed dense biofilm and sequestered metal from water, decreasing the metal bioavailability. These bacterial consortia can be used in bioreactors and in bioremediation programs. - Highlights: • We studied bacterial bioremediation by microXRF. • Dense biofilm may act sequestering metal while protecting bacterial metabolism. • Nitratireductor spp. and Pseudomonas spp decreased seawater metal bioavailability. • Bacterial consortia from polluted areas may be used in bioremediation programs.

The removal of uranium from mining waste water using algal/microbial biomass

International Nuclear Information System (INIS)

Kalin, Margarete; Wheeler, W.N.; Meinrath, G.

2004-01-01

We describe a three step process for the removal of uranium (U) from dilute waste waters. Step one involves the sequestration of U on, in, and around aquatic plants such as algae. Cell wall ligands efficiently remove U(VI) from waste water. Growing algae continuously renew the cellular surface area. Step 2 is the removal of U-algal particulates from the water column to the sediments. Step 3 involves reducing U(VI) to U(IV) and transforming the ions into stable precipitates in the sediments. The algal cells provide organic carbon and other nutrients to heterotrophic microbial consortia to maintain the low E H , within which the U is transformed. Among the microorganisms, algae are of predominant interest for the ecological engineer because of their ability to sequester U and because some algae can live under many extreme environments, often in abundance. Algae grow in a wide spectrum of water qualities, from alkaline environments (Chara, Nitella) to acidic mine drainage waste waters (Mougeotia, Ulothrix). If they could be induced to grow in waste waters, they would provide a simple, long-term means to remove U and other radionuclides from U mining effluents. This paper reviews the literature on algal and microbial adsorption, reduction, and transformation of U in waste streams, wetlands, lakes and oceans

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

Directory of Open Access Journals (Sweden)

Eleftheria eAntoniou

2015-04-01

Full Text Available Biosurfactants (BS 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 biosurfactant 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 biosurfactant 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 (TLC and Fourier transform infrared spectroscopy (FT-IR. Results indicate that biosurfactant 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 implies that the BS producing microbes generate no more than the required amount of biosurfactants that enables biodegradation of the crude oil. Isolated pure strains were found to have higher specific production yields than the complex microbial marine community-consortia. The heavy oil fraction of crude oil 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.

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

Science.gov (United States)

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

The AHEC library program and consortia development in California.

Science.gov (United States)

Jensen, M A; Maddalena, B

1986-07-01

A brief history of the first Area Health Education Center (AHEC) Library Program in California is presented, with a description of methodology and results. The goals of this program were to develop and improve hospital library resources and services, to train hospital library personnel, and to promote resource sharing in a medically underserved area. The health sciences library consortium that evolved became a model for the ten other library consortia in the state. Based on AHEC's twelve years' experience with consortia, from 1973 to 1985, recommendations are made as to size, composition, leadership, outside funding, group participation, publicity, and linkages.

Cooperation in carbon source degradation shapes spatial self-organization of microbial consortia on hydrated surfaces.

Science.gov (United States)

Tecon, Robin; Or, Dani

2017-03-06

Mounting evidence suggests that natural microbial communities exhibit a high level of spatial organization at the micrometric scale that facilitate ecological interactions and support biogeochemical cycles. Microbial patterns are difficult to study definitively in natural environments due to complex biodiversity, observability and variable physicochemical factors. Here, we examine how trophic dependencies give rise to self-organized spatial patterns of a well-defined bacterial consortium grown on hydrated surfaces. The model consortium consisted of two Pseudomonas putida mutant strains that can fully degrade the aromatic hydrocarbon toluene. We demonstrated that obligate cooperation in toluene degradation (cooperative mutualism) favored convergence of 1:1 partner ratio and strong intermixing at the microscale (10-100 μm). In contrast, competition for benzoate, a compound degraded independently by both strains, led to distinct segregation patterns. Emergence of a persistent spatial pattern has been predicted for surface attached microbial activity in liquid films that mediate diffusive exchanges while permitting limited cell movement (colony expansion). This study of a simple microbial consortium offers mechanistic glimpses into the rules governing the assembly and functioning of complex sessile communities, and points to general principles of spatial organization with potential applications for natural and engineered microbial systems.

Consortia Focused on Photovoltaic R&D, Manufacturing, and Testing: A Review of Existing Models and Structures

Energy Technology Data Exchange (ETDEWEB)

Coggeshall, C.; Margolis, R. M.

2010-03-01

As the U.S. Department of Energy's (DOE's) Solar Energy Technologies Program prepares to initiate a new cost-shared research and development (R&D) effort on photovoltaic (PV) manufacturing, it is useful to review the experience to date with consortia focused on PV R&D, manufacturing, and testing. Information was gathered for this report by conducting interviews and accessing Web sites of 14 U.S. consortia and four European consortia, each with either a primary focus on or an emerging interest in PV technology R&D, manufacturing, or testing. Additional input was collected from several workshops held by the DOE and National Academy of Sciences (NAS) in 2009, which examined the practical steps -- including public-private partnerships and policy support -- necessary to enhance the United States' capacity to competitively manufacture photovoltaics. This report categorizes the 18 consortia into three groups: university-led consortia, industry-led consortia, and manufacturing and testing facilities consortia. The first section summarizes the organizations within the different categories, with a particular focus on the key benefits and challenges for each grouping. The second section provides a more detailed overview of each consortium, including the origins, goals, organization, membership, funding sources, and key contacts. This survey is a useful resource for stakeholders interested in PV manufacturing R&D, but should not imply endorsement of any of these groups.

Biomass and Neutral Lipid Production in Geothermal Microalgal Consortia

Science.gov (United States)

Bywaters, Kathryn F.; Fritsen, Christian H.

2015-01-01

Recently, technologies have been developed that offer the possibility of using algal biomass as feedstocks to energy producing systems – in addition to oil-derived fuels (Bird et al., 2011, 2012). Growing native mixed microalgal consortia for biomass in association with geothermal resources has the potential to mitigate negative impacts of seasonally low temperatures on biomass production systems as well as mitigate some of the challenges associated with growing unialgal strains. We assessed community composition, growth rates, biomass, and neutral lipid production of microalgal consortia obtained from geothermal hot springs in the Great Basin/Nevada area that were cultured under different thermal and light conditions. Biomass production rates ranged from 39.0 to 344.1 mg C L−1 day−1. The neutral lipid production in these consortia with and without shifts to lower temperatures and additions of bicarbonate (both environmental parameters that have been shown to enhance neutral lipid production) ranged from 0 to 38.74 mg free fatty acids (FFA) and triacylglycerols (TAG) L−1 day−1; the upper value was approximately 6% of the biomass produced. The higher lipid values were most likely due to the presence of Achnanthidium sp. Palmitic and stearic acids were the dominant free fatty acids. The S/U ratio (the saturated to unsaturated FA ratio) decreased for cultures shifted from their original temperature to 15°C. Biomass production was within the upper limits of those reported for individual strains, and production of neutral lipids was increased with secondary treatment. All results demonstrate a potential of culturing and manipulating resultant microalgal consortia for biomass-based energy production and perhaps even for biofuels. PMID:25763368

Biomass and Neutral Lipid Production in Geothermal Microalgal Consortia

Directory of Open Access Journals (Sweden)

Kathryn Faye Bywaters

2015-02-01

Full Text Available Recently, technologies have been developed that offer the possibility of using algal biomass as feedstocks to energy producing systems- in addition to oil-derived fuels (Bird et al., 2011;Bird et al., 2012. Growing native mixed microalgal consortia for biomass in association with geothermal resources has the potential to mitigate negative impacts of seasonally low temperatures on biomass production systems as well as mitigate some of the challenges associated with growing unialgal strains. We assessed community composition, growth rates, biomass and neutral lipid production of microalgal consortia obtained from geothermal hot springs in the Great Basin/Nevada area that were cultured under different thermal and light conditions. Biomass production rates ranged from 368 to 3246 mg C L-1 d-1. The neutral lipid production in these consortia with and without shifts to lower temperatures and additions of bicarbonate (both environmental parameters that have been shown to enhance neutral lipid production ranged from zero to 38.74 mg free fatty acids and triacylglycerols L-1 d-1, the upper value was approximately 6% of the biomass produced. The higher lipid values were most likely due to the presence of Achnanthidium sp. Palmitic and stearic acids were the dominant free fatty acids. The S/U ratio (the saturated to unsaturated FA ratio decreased for cultures shifted from their original temperature to 15°C. Biomass production was within the upper limits of those reported for individual strains, and production of neutral lipids was increased with secondary treatment – all results demonstrate a potential of culturing and manipulating resultant microalgal consortia for biomass-based energy production and perhaps even for biofuels.

Microbiome-wide association studies link dynamic microbial consortia to disease

Energy Technology Data Exchange (ETDEWEB)

Gilbert, Jack A.; Quinn, Robert A.; Debelius, Justine; Xu, Zhenjiang Z.; Morton, James; Garg, Neha; Jansson, Janet K.; Dorrestein, Pieter C.; Knight, Rob

2016-07-06

Rapid advances in DNA sequencing, metabolomics, proteomics and computation dramatically increase accessibility of microbiome studies and identify links between the microbiome and disease. Microbial time-series and multiple molecular perspectives enable Microbiome-Wide Association Studies (MWAS), analogous to Genome-Wide Association Studies (GWAS). Rapid research advances point towards actionable results, although approved clinical tests based on MWAS are still in the future. Appreciating the complexity of interactions between diet, chemistry, health and the microbiome, and determining the frequency of observations needed to capture and integrate this dynamic interface, is paramount for addressing the need for personalized and precision microbiome-based diagnostics and therapies.

Research Guidelines in the Era of Large-scale Collaborations: An Analysis of Genome-wide Association Study Consortia

Science.gov (United States)

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

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

Science.gov (United States)

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.

Microbial-immune cross-talk and regulation of the immune system.

Science.gov (United States)

Cahenzli, Julia; Balmer, Maria L; McCoy, Kathy D

2013-01-01

We are all born germ-free. Following birth we enter into a lifelong relationship with microbes residing on our body's surfaces. The lower intestine is home to the highest microbial density in our body, which is also the highest microbial density known on Earth (up to 10(12) /g of luminal contents). With our indigenous microbial cells outnumbering our human cells by an order of magnitude our body is more microbial than human. Numerous immune adaptations confine these microbes within the mucosa, enabling most of us to live in peaceful homeostasis with our intestinal symbionts. Intestinal epithelial cells not only form a physical barrier between the bacteria-laden lumen and the rest of the body but also function as multi-tasking immune cells that sense the prevailing microbial (apical) and immune (basolateral) milieus, instruct the underlying immune cells, and adapt functionally. In the constant effort to ensure intestinal homeostasis, the immune system becomes educated to respond appropriately and in turn immune status can shape the microbial consortia. Here we review how the dynamic immune-microbial dialogue underlies maturation and regulation of the immune system and discuss recent findings on the impact of diet on both microbial ecology and immune function. © 2012 The Authors. Immunology © 2012 Blackwell Publishing Ltd.

Microbial ecology of methanogenic crude oil biodegradation; from microbial consortia to heavy oil

Energy Technology Data Exchange (ETDEWEB)

Head, Ian M.; Maguire, Michael J.; Sherry, Angela; Grant, Russell; Gray, Neil D.; Aitken, Carolyn M.; Martin Jones, D.; Oldenburg, Thomas B.P.; Larter, Stephen R. [Petroleum Research Group, Geosciences, University of Calgary (Canada)

2011-07-01

This paper presents the microbial ecology of methanogenic crude oil biodegradation. Biodegraded petroleum reservoirs are one of the most dramatic indications of the deep biosphere. It is estimated that heavy oil and oil sands will account for a considerable amount of energy production in the future. Carbon, a major resource for deep subsurface microorganisms, and energy are contained in large quantities in petroleum reservoirs. The aerobic to anaerobic paradigm shift is explained. A key process for in-situ oil biodegradation in petroleum reservoirs is methanogenesis. New paradigms for in-reservoir crude oil biodegradation are discussed. Variations in anaerobic degradation of crude oil hydrocarbons are also discussed. A graph shows the different patterns of crude oil biodegradation under sulfate-reducing and methanogenic conditions. Alternative anaerobic alkane activation mechanisms are also shown. From the study, it can be concluded that methanogenic crude oil degradation is of global importance and led to the establishment of the world's enormous heavy oil deposits.

Key players and team play: anaerobic microbial communities in hydrocarbon-contaminated aquifers.

Science.gov (United States)

Kleinsteuber, Sabine; Schleinitz, Kathleen M; Vogt, Carsten

2012-05-01

Biodegradation of anthropogenic pollutants in shallow aquifers is an important microbial ecosystem service which is mainly brought about by indigenous anaerobic microorganisms. For the management of contaminated sites, risk assessment and control of natural attenuation, the assessment of in situ biodegradation and the underlying microbial processes is essential. The development of novel molecular methods, "omics" approaches, and high-throughput techniques has revealed new insight into complex microbial communities and their functions in anoxic environmental systems. This review summarizes recent advances in the application of molecular methods to study anaerobic microbial communities in contaminated terrestrial subsurface ecosystems. We focus on current approaches to analyze composition, dynamics, and functional diversity of subsurface communities, to link identity to activity and metabolic function, and to identify the ecophysiological role of not yet cultured microbes and syntrophic consortia. We discuss recent molecular surveys of contaminated sites from an ecological viewpoint regarding degrader ecotypes, abiotic factors shaping anaerobic communities, and biotic interactions underpinning the importance of microbial cooperation for microbial ecosystem services such as contaminant degradation.

78 FR 20665 - Pediatric Device Consortia Grant Program

Science.gov (United States)

2013-04-05

... development--concept formation, prototyping, preclinical, clinical, manufacturing, marketing, and commercialization. The consortia are expected to support a mix of projects at all stages of development, particularly the later stages of clinical, manufacturing, and marketing. [[Page 20666

Diversity and activity of benthic microbial communities at the North Alex mud volcano, Eastern Mediterranean

Science.gov (United States)

Makarow, Dorothee; Feseker, Tomas; Schmitz, Ruth; Treude, Tina

2010-05-01

North Alex mud volcano, located on the upper slope of the western Nile deep-sea fan, is characterized by an active seepage center transporting pore fluids, hydrocarbons and gases from deep subsurface sources to the sediment-water interface. Surface sediments feature steep temperature gradient of 8.5°C m-1. We sampled the top 40 cm of the sediments at different locations between the center and rim of the mud volcano to study the diversity, activity, and physiological characteristics of benthic microorganisms. The sediments revealed the activity of anaerobic oxidation of methane coupled to sulfate reduction with a mesophilic temperature optimum. Organisms involved in the process include consortia of methanotrophic archaea (ANME-2 group) and an unknown bacterial partner. Besides methanotrophic organisms the sediments harbored a variety of other bacterial and archaeal groups - including potentially thermophilic bacteria that could be involved in sulfur cycling. This poster presentation will provide an overview of microbial activities and community compositions of North Alex mud volcano sediments.

Culture-dependent and -independent approaches establish the complexity of a PAH-degrading microbial consortium

Energy Technology Data Exchange (ETDEWEB)

Vinas, M.; Sabate, J.; Solanas, A.M. [Barcelona Univ., Barcelona (Spain). Dept. of Microbiology; Guasp, C.; Lalucat, J. [Illes Balears Univ., Palma de Mallorca (Spain). Dept. of Biology

2005-11-15

Microbial consortia are used in the decontamination of polluted environmental sites. A microbial consortium obtained by batch enrichment culture is a closed system with controlled conditions in which micro-organisms with a potentially high growth rate are selected and become dominant. The aim of this study was to identify the members of consortium AM, in which earlier batch enrichment work had shown high biodegradation rates of the aromatic fraction of polycyclic aromatic hydrocarbon (PAH). The AM consortium was obtained by sequential enrichment in liquid culture with a PAH mixture of 3- and 4- ringed PAHs as the sole source of carbon and energy. The consortium was examined using a triple approach method based on various cultivation strategies, denaturing gradient electrophoresis (DGGE) and the screening of 16S and 18S rRNA gene clone libraries. Eleven different sequences by culture-dependent techniques and 7 by both DGGE and clone libraries were obtained, yielding 19 different microbial components. Proteobacteria were the dominant group, representing 83 per cent of the total, while the Cytophaga-Flexibactor-Bacteroides group (CFB) was 11 per cent, and Ascomycota fungi were 6 per cent. It was determined that {beta}-Proteobacteria were predominant in the DGGE and clone library methods, whereas they were a minority in culturable strains. The highest diversity and number of noncoincident sequences was achieved by the cultivation method that showed members of the {alpha},{beta}, and {gamma}-Proteobacteria, CFB bacterial group, and Ascomycota fungi. Only 6 of the 11 strains isolated showed PAH-degrading capability. The bacterial strain (AMS7) and the fungal strain (AMF1) achieved the greatest PAH depletion. Results indicated that polyphasic assessment is necessary for a proper understanding of the composition of a microbial consortium. It was concluded that microbial consortia are more complex than previously realized. 54 refs., 3 tabs., 3 figs.

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

Science.gov (United States)

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.

Cooperation in carbon source degradation shapes spatial self-organization of microbial consortia on hydrated surfaces

OpenAIRE

Tecon, Robin; Or, Dani

2017-01-01

Mounting evidence suggests that natural microbial communities exhibit a high level of spatial organization at the micrometric scale that facilitate ecological interactions and support biogeochemical cycles. Microbial patterns are difficult to study definitively in natural environments due to complex biodiversity, observability and variable physicochemical factors. Here, we examine how trophic dependencies give rise to self-organized spatial patterns of a well-defined bacterial consortium grow...

Biotechnology in petroleum recovery. The microbial EOR

Energy Technology Data Exchange (ETDEWEB)

Sen, Ramkrishna [Department of Biotechnology, Indian Institute of Technology (IIT), Kharagpur, West Bengal 721302 (India)

2008-12-15

Biotechnology has played a significant role in enhancing crude oil recovery from the depleted oil reservoirs to solve stagnant petroleum production, after a three-stage recovery process employing mechanical, physical and chemical methods. Biotechnologically enhanced oil recovery processes, known as microbial enhanced oil recovery (MEOR), involve stimulating indigenous reservoir microbes or injecting specially selected consortia of natural bacteria into the reservoir to produce specific metabolic events that lead to improved oil recovery. This also involves flooding with oil recovery agents produced ex situ by industrial or pilot scale fermentation. This paper essentially reviews the operating mechanisms and the progress made in enhanced oil recovery through the use of microbes and their metabolic products. Improvement in oil recovery by injecting solvents and gases or by energizing the reservoir microflora to produce them in situ for carbonate rock dissolution and reservoir re-pressurization has been enunciated. The role of biosurfactants in oil mobilization through emulsification and that of biopolymers for selective plugging of oil-depleted zones and for biofilm formation have been delineated. The spoil sport played by sulfate-reducing bacteria (SRB) in MEOR has also been briefly reviewed. The importance of mathematical models used in predicting the applicability of an MEOR strategy and the microbial growth and transport has been qualitatively discussed. The results of some laboratory studies and worldwide field trials applying ex situ and in situ MEOR technologies were compiled and interpreted. However, the potential of the MEOR technologies has not been fully realized due to poor yield of the useful microbial metabolic products, growth inhibition by accumulated toxic metabolites and longer time of incubation. A complete evaluation and assessment of MEOR from an engineering standpoint based on economics, applicability and performance is required to further

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

Science.gov (United States)

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 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.

Interspecies electron transfer in methanogenic propionate degrading consortia

NARCIS (Netherlands)

Bok, de F.A.M.; Plugge, C.M.; Stams, A.J.M.

2004-01-01

Propionate is a key intermediate in the conversion of complex organic matter under methanogenic conditions. Oxidation of this compound requires obligate syntrophic consortia of acetogenic proton- and bicarbonate reducing bacteria and methanogenic archaea. Although H-2 acts as an electron-carrier in

Polishing of municipal secondary effluent using native microalgae consortia.

Science.gov (United States)

Beltrán-Rocha, Julio César; Barceló-Quintal, Icela Dagmar; García-Martínez, Magdalena; Osornio-Berthet, Luis; Saavedra-Villarreal, Nidia; Villarreal-Chiu, Juan; López-Chuken, Ulrico Javier

2017-04-01

This work evaluates the use of native microalgae consortia for a dual role: polishing treatment of municipal wastewater effluents and microalgae biomass feedstock potential for biodiesel or biofertilizer production. An initial screening was undertaken to test N and P removal from secondary effluents and biomass production by 12 consortia. A subsequent treatment was performed by selected consortia (01 and 12) under three operational conditions: stirring (S), S + 12 h of daily aeration (S + A) and S + A enriched with CO 2 (S + AC). All treatments resulted in compliance with environmental regulations (e.g. Directive 91/271/EEC) and high removal efficiency of nutrients: 64-79% and 80-94% of total N and PO 4 3- -P respectively. During the experiments it was shown that pH alkalinization due to microalgae growth benefits the chemical removal of ammonia and phosphorus. Moreover, advantages of pH increase could be accomplished by intermittent CO 2 addition which in this research (treatment S + AC) promoted higher yield and lipid concentration. The resulting dry biomass analysis showed a low lipid content (0.5-4.3%) not ideal for biodiesel production. Moreover, the high rate of ash (29.3-53.0%) suggests that biomass could be readily recycled as a biofertilizer due to mineral supply and organic constituents formed by C, N and P (e.g. carbohydrate, protein, and lipids).

25 CFR 1001.8 - Selection criteria for tribes/consortia to receive a negotiation grant.

Science.gov (United States)

2010-04-01

... 25 Indians 2 2010-04-01 2010-04-01 false Selection criteria for tribes/consortia to receive a negotiation grant. 1001.8 Section 1001.8 Indians OFFICE OF THE ASSISTANT SECRETARY, INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR SELF-GOVERNANCE PROGRAM § 1001.8 Selection criteria for tribes/consortia to receive a negotiation grant. (a) Who may be...

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

Science.gov (United States)

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

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.

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

Directory of Open Access Journals (Sweden)

Evdokia Syranidou

Full Text Available 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.

The peer review process for awarding funds to international science research consortia: a qualitative developmental evaluation.

Science.gov (United States)

Gregorius, Stefanie; Dean, Laura; Cole, Donald C; Bates, Imelda

2017-01-01

Background:  Evaluating applications for multi-national, multi-disciplinary, dual-purpose research consortia is highly complex. There has been little research on the peer review process for evaluating grant applications and almost none on how applications for multi-national consortia are reviewed. Overseas development investments are increasingly being channelled into international science consortia to generate high-quality research while simultaneously strengthening multi-disciplinary research capacity. We need a better understanding of how such decisions are made and their effectiveness. Methods:  An award-making institution planned to fund 10 UK-Africa research consortia. Over two annual rounds, 34 out of 78 eligible applications were shortlisted and reviewed by at least five external reviewers before final selections were made by a face-to-face panel. We used an innovative approach involving structured, overt observations of award-making panel meetings and semi-structured interviews with panel members to explore how assessment criteria concerning research quality and capacity strengthening were applied during the peer review process. Data were coded and analysed using pre-designed matrices which incorporated categories relating to the assessment criteria. Results:  In general the process was rigorous and well-managed. However, lack of clarity about differential weighting of criteria and variations in the panel's understanding of research capacity strengthening resulted in some inconsistencies in use of the assessment criteria. Using the same panel for both rounds had advantages, in that during the second round consensus was achieved more quickly and the panel had increased focus on development aspects. Conclusion:  Grant assessment panels for such complex research applications need to have topic- and context-specific expertise. They must also understand research capacity issues and have a flexible but equitable and transparent approach. This study has

A multi-substrate approach for functional metagenomics-based screening for (hemi)cellulases in two wheat straw-degrading microbial consortia unveils novel thermoalkaliphilic enzymes.

Science.gov (United States)

Maruthamuthu, Mukil; Jiménez, Diego Javier; Stevens, Patricia; van Elsas, Jan Dirk

2016-01-28

Functional metagenomics is a promising strategy for the exploration of the biocatalytic potential of microbiomes in order to uncover novel enzymes for industrial processes (e.g. biorefining or bleaching pulp). Most current methodologies used to screen for enzymes involved in plant biomass degradation are based on the use of single substrates. Moreover, highly diverse environments are used as metagenomic sources. However, such methods suffer from low hit rates of positive clones and hence the discovery of novel enzymatic activities from metagenomes has been hampered. Here, we constructed fosmid libraries from two wheat straw-degrading microbial consortia, denoted RWS (bred on untreated wheat straw) and TWS (bred on heat-treated wheat straw). Approximately 22,000 clones from each library were screened for (hemi)cellulose-degrading enzymes using a multi-chromogenic substrate approach. The screens yielded 71 positive clones for both libraries, giving hit rates of 1:440 and 1:1,047 for RWS and TWS, respectively. Seven clones (NT2-2, T5-5, NT18-17, T4-1, 10BT, NT18-21 and T17-2) were selected for sequence analyses. Their inserts revealed the presence of 18 genes encoding enzymes belonging to twelve different glycosyl hydrolase families (GH2, GH3, GH13, GH17, GH20, GH27, GH32, GH39, GH53, GH58, GH65 and GH109). These encompassed several carbohydrate-active gene clusters traceable mainly to Klebsiella related species. Detailed functional analyses showed that clone NT2-2 (containing a beta-galactosidase of ~116 kDa) had highest enzymatic activity at 55 °C and pH 9.0. Additionally, clone T5-5 (containing a beta-xylosidase of ~86 kDa) showed > 90% of enzymatic activity at 55 °C and pH 10.0. This study employed a high-throughput method for rapid screening of fosmid metagenomic libraries for (hemi)cellulose-degrading enzymes. The approach, consisting of screens on multi-substrates coupled to further analyses, revealed high hit rates, as compared with recent other studies. Two

Oil-consuming microbial consortia floating in the Arabian Gulf

International Nuclear Information System (INIS)

Radwan, S.S.; Al-Hasan, R.H.; Ali, N.; Salamah, S.; Khanafer, M.

2005-01-01

Picocyanobacteria floating on the surface of the water body in the Arabian Gulf were found associated with heterotrophic bacteria. Haemocytometer counting of fresh 1 -cm surface water revealed 10 7 - 10 8 bacterial cells ml -1 , but only 10 2 - 10 3 cells ml -1 in 10-cm deep water samples. The heterotrophic bacteria comprised hydrocarbon utilizers that could grow on a mineral medium containing crude oil as sole carbon and energy source. Three-week liquid cultures of the picocyanobacteria Synechococcus, Synechocystis, Pleurocapsa and Dermocarpella were found by dilution plating to contain 10 6 - 10 13 oil-utilizing bacteria ml -1 . These were members of the genera Pseudomonas, Bacillus and Acinetobacter and nocardioforms. Growth and hydrocarbon consumption potential of individual types of oil-utilizing bacteria in culture were higher in the presence of the picocyanobacteria than in their absence. Evidence was presented that picocyanobacterial cells may accumulate hydrocarbons from the medium, and subsequently make those compounds available to the associated hydrocarbon-utilizing bacteria. It was concluded that this microbial consortium, which is apparently of cosmopolitan occurrence, could be active in controlling marine oil-pollution. (author)

Evaluation of simultaneous nutrient and COD removal with polyhydroxybutyrate (PHB) accumulation using mixed microbial consortia under anoxic condition and their bioinformatics analysis.

Science.gov (United States)

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.

Evaluation of simultaneous nutrient and COD removal with polyhydroxybutyrate (PHB accumulation using mixed microbial consortia under anoxic condition and their bioinformatics analysis.

Directory of Open Access Journals (Sweden)

Jyotsnarani Jena

Full Text Available 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.

Egypt’s Red Sea Coast: Phylogenetic analysis of cultured microbial consortia in industrialized sites

Directory of Open Access Journals (Sweden)

Ghada A. Mustafa

2014-08-01

Full Text Available The Red Sea has a unique geography and ecosystem and its shores are very rich in mangrove, macro-algae and coral reefs. Different sources of pollution are affecting the Red Sea shores and waters which impacts biological life including microbial life. We assessed the effects of industrialization, along the Egyptian Red Sea coast in eight coastal sites and two lakes, on microbial life. The bacterial community in sediment samples was analyzed using bacterial 16S rDNApyrosequencing of V6-V4 hypervariable regions. Taxonomical assignment of 131,402 significant reads to major bacterial taxa revealed five main bacterial phyla dominating the sampled Red Sea sites. This includes Proteobacteria (68%, Firmicutes (13%, Fusobacteria (12%, Bacteriodetes (6% and Spirochetes (0.03%. Further analysis revealed distinct bacterial consortium formed mainly of: 1 marine Vibrio’s- suggesting a Marine Vibrio phenomenon 2 potential human pathogens and 3 oil-degrading bacteria. We discuss a distinct microbial consortium in Solar Lake West near Taba/Eilat and Saline Lake in Ras Muhammad; revealing the highest abundance of human pathogens versus no pathogens, respectively. Our results draw attention to the affects of industrialization on the Red Sea, and suggest further analysis to overcome hazardous affects on the impacted sites.

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

Science.gov (United States)

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.

Evaluation of support matrices for immobilization of anaerobic consortia for efficient carbon cycling in waste regeneration.

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Risk reduction of international mining projects by means of investor consortia and diversification of external financing

International Nuclear Information System (INIS)

Kirchner, C.

1982-01-01

Investors and creditors of international mining projects bear specific risks which may be reduced by means of forming investor and financing consortia. Risk is defined for each actor separately. Project risk and investor risk respectively credit risk are useful categories in order to analyze risk reduction. In each case formation of consortia has a positive influence on the economic viability of the project, and thus reduces the project risk. Furthermore, formation of consortia leads to better compliance of the host country of the mining project with the project and financing agreements. Thus, investor and credit risk may be reduced. (orig.) [de

Exocellular electron transfer in anaerobic microbial communities.

Science.gov (United States)

Stams, Alfons J M; de Bok, Frank A M; Plugge, Caroline M; van Eekert, Miriam H A; Dolfing, Jan; Schraa, Gosse

2006-03-01

Exocellular electron transfer plays an important role in anaerobic microbial communities that degrade organic matter. Interspecies hydrogen transfer between microorganisms is the driving force for complete biodegradation in methanogenic environments. Many organic compounds are degraded by obligatory syntrophic consortia of proton-reducing acetogenic bacteria and hydrogen-consuming methanogenic archaea. Anaerobic microorganisms that use insoluble electron acceptors for growth, such as iron- and manganese-oxide as well as inert graphite electrodes in microbial fuel cells, also transfer electrons exocellularly. Soluble compounds, like humic substances, quinones, phenazines and riboflavin, can function as exocellular electron mediators enhancing this type of anaerobic respiration. However, direct electron transfer by cell-cell contact is important as well. This review addresses the mechanisms of exocellular electron transfer in anaerobic microbial communities. There are fundamental differences but also similarities between electron transfer to another microorganism or to an insoluble electron acceptor. The physical separation of the electron donor and electron acceptor metabolism allows energy conservation in compounds as methane and hydrogen or as electricity. Furthermore, this separation is essential in the donation or acceptance of electrons in some environmental technological processes, e.g. soil remediation, wastewater purification and corrosion.

Enzyme treatment to decrease solids and improve digestion of primary sewage sludge

CSIR Research Space (South Africa)

Roman, HJ

2006-05-01

Full Text Available In general, the trends of stable prevailing pH, low VFA concentrations and high TSS removal observed here indicate improved performance through the symbiotic relationship between acid producers and consumers. This involves close microbial consortia...

Interactions between plant and rhizosphere microbial communities in a metalliferous soil

International Nuclear Information System (INIS)

Epelde, Lur; Becerril, Jose M.; Barrutia, Oihana; Gonzalez-Oreja, Jose A.; Garbisu, Carlos

2010-01-01

In the present work, the relationships between plant consortia, consisting of 1-4 metallicolous pseudometallophytes with different metal-tolerance strategies (Thlaspi caerulescens: hyperaccumulator; Jasione montana: accumulator; Rumex acetosa: indicator; Festuca rubra: excluder), and their rhizosphere microbial communities were studied in a mine soil polluted with high levels of Cd, Pb and Zn. Physiological response and phytoremediation potential of the studied pseudometallophytes were also investigated. The studied metallicolous populations are tolerant to metal pollution and offer potential for the development of phytoextraction and phytostabilization technologies. T. caerulescens appears very tolerant to metal stress and most suitable for metal phytoextraction; the other three species enhance soil functionality. Soil microbial properties had a stronger effect on plant biomass rather than the other way around (35.2% versus 14.9%). An ecological understanding of how contaminants, ecosystem functions and biological communities interact in the long-term is needed for proper management of these fragile metalliferous ecosystems. - Rhizosphere microbial communities in highly polluted mine soils are determinant for the growth of pseudometallophytes.

Interactions between plant and rhizosphere microbial communities in a metalliferous soil

Energy Technology Data Exchange (ETDEWEB)

Epelde, Lur [NEIKER-Tecnalia, Department of Ecosystems, c/Berreaga 1, E-48160 Derio (Spain); Becerril, Jose M.; Barrutia, Oihana [Department of Plant Biology and Ecology, University of the Basque Country, UPV/EHU, P.O. Box 644, E-48080 Bilbao (Spain); Gonzalez-Oreja, Jose A. [NEIKER-Tecnalia, Department of Ecosystems, c/Berreaga 1, E-48160 Derio (Spain); Garbisu, Carlos, E-mail: cgarbisu@neiker.ne [NEIKER-Tecnalia, Department of Ecosystems, c/Berreaga 1, E-48160 Derio (Spain)

2010-05-15

In the present work, the relationships between plant consortia, consisting of 1-4 metallicolous pseudometallophytes with different metal-tolerance strategies (Thlaspi caerulescens: hyperaccumulator; Jasione montana: accumulator; Rumex acetosa: indicator; Festuca rubra: excluder), and their rhizosphere microbial communities were studied in a mine soil polluted with high levels of Cd, Pb and Zn. Physiological response and phytoremediation potential of the studied pseudometallophytes were also investigated. The studied metallicolous populations are tolerant to metal pollution and offer potential for the development of phytoextraction and phytostabilization technologies. T. caerulescens appears very tolerant to metal stress and most suitable for metal phytoextraction; the other three species enhance soil functionality. Soil microbial properties had a stronger effect on plant biomass rather than the other way around (35.2% versus 14.9%). An ecological understanding of how contaminants, ecosystem functions and biological communities interact in the long-term is needed for proper management of these fragile metalliferous ecosystems. - Rhizosphere microbial communities in highly polluted mine soils are determinant for the growth of pseudometallophytes.

Protocol for the microbial degradation of coumaphos from cattle dip

International Nuclear Information System (INIS)

Mulbry, W.; Karns, J.

1997-01-01

Insecticide wastes generated from livestock dipping operations are well suited for biodegradation processes since these wastes are concentrated, contained, and have no other significant toxic components. About 400,000 L of cattle dip wastes containing approximately 1500 mg/L of the organophosphate coumaphos are generated yearly along the Mexican border from a USDA program designed to control disease carrying cattle ticks. Use of unlined evaporation pits for the disposal of these wastes has resulted in highly contaminated soils underlying these sites. Previous work has shown that microbial consortia present in selected dip wastes can be induced to mineralize coumaphos. Our laboratory results show that these consortia are able to colonize plastic fibers in trickling biofilters and can be used in these filters to quickly metabolize coumaphos from dip wastes. A field scale biofilter capable of treating 15,000 litre batches of dip waste was used to reduce the coumaphos concentration in two successive 11,000 litre batch trials from 2000 mg/L to 10 mg/L in approximately 14 d. (author)

25 CFR 1000.15 - How many additional Tribes/Consortia may participate in self-governance per year?

Science.gov (United States)

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...

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

Science.gov (United States)

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.

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

Directory of Open Access Journals (Sweden)

Mallette Natasha

2009-12-01

Full Text Available Abstract 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

Library Consortia in Croatia

Directory of Open Access Journals (Sweden)

Maja Jokic

2001-07-01

Full Text Available The problem of the increasing number of information sources and their costs as well as more demanding users on the one side, and limited financial resources on the other, has not avoided Croatia. One of the attempts to deal with this state of affairs is associating libraries into consortia. A consortium could, through cooperative cataloguing, help optimise the processing of library material, it could help in solving the problem of rational ways of continuous education of staff and users and coordinate acquisition policy through common purchasing of information resources, from bibliographic databases to electronic journals under various licensing conditions. This last aspect of cooperation in a consortium will be dealt with in detail in the text that follows.

The licensing battlefield: consortia as new middlemen between publishers, agents and libraries: a view from the continent

NARCIS (Netherlands)

Verhagen, N.

2007-01-01

Consortia are everywhere nowadays. Every country and every region is now covered by at least one consortium. International co-operation is taking off as well, both formally and informally. Nevertheless there is a wide variation in the nature and size of consortia. One of the most distinguishing

Prokaryotic diversity, composition structure, and phylogenetic analysis of microbial communities in leachate sediment ecosystems.

Science.gov (United States)

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.

Characterization of microbial communities in pest colonized books by molecular biology tools

Directory of Open Access Journals (Sweden)

Franco Palla

2011-08-01

Full Text Available This work presents the identification of bacteria and fungi colonies in insect infesting books, by cultural-independent methodologies based on molecular biology techniques. Microbial genomic DNA extraction, in vitro amplification of specific target sequences by polymerase chain reactions (PCR, sequencing and sequence analysis were performed. These procedures minimized the samples amount, optimized the diagnostic studies on bacteria and fungi colonization and allowed the identification of many species also in complex microbial consortia. The molecular techniques for sure accomplish and integrate the microbiological standard methods (in vitro culture and morphological analyses (OM, SEM, CLSM, in order to understand the role of microorganisms in bio-deterioration of cultural assets. This monitoring is also indispensable to shed light on the risk for visitors and/or professionals to contract potential illnesses within indoor environments.

Cultivating microbial dark matter in benzene-degrading methanogenic consortia.

Science.gov (United States)

Luo, Fei; Devine, Cheryl E; Edwards, Elizabeth A

2016-09-01

The microbes responsible for anaerobic benzene biodegradation remain poorly characterized. In this study, we identified and quantified microbial populations in a series of 16 distinct methanogenic, benzene-degrading enrichment cultures using a combination of traditional 16S rRNA clone libraries (four cultures), pyrotag 16S rRNA amplicon sequencing (11 cultures), metagenome sequencing (1 culture) and quantitative polymerase chain reaction (qPCR; 12 cultures). An operational taxonomic unit (OTU) from the Deltaproteobacteria designated ORM2 that is only 84% to 86% similar to Syntrophus or Desulfobacterium spp. was consistently identified in all enrichment cultures, and typically comprised more than half of the bacterial sequences. In addition to ORM2, a sequence belonging to Parcubacteria (candidate division OD1) identified from the metagenome data was the only other OTU common to all the cultures surveyed. Culture transfers (1% and 0.1%) were made in the presence and absence of benzene, and the abundance of ORM2, OD1 and other OTUs was tracked over 415 days using qPCR. ORM2 sequence abundance increased only when benzene was present, while the abundance of OD1 and other OTUs increased even in the absence of benzene. Deltaproteobacterium ORM2 is unequivocally the benzene-metabolizing population. This study also hints at laboratory cultivation conditions for a member of the widely distributed yet uncultivated Parcubacteria (OD1). © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Azo dye reduction by mesophilic and thermophilic anaerobic consortia

NARCIS (Netherlands)

Santos, dos A.B.; Madrid, de M.P.; Stams, A.J.M.; Lier, van J.B.; Cervantes, F.J.

2005-01-01

The reduction of the azo dye model compounds Reactive Red 2 (RR2) and Reactive Orange 14 (RO14) by mesophilic (30 C) and thermophilic (55 C) anaerobic consortia was studied in batch assays. The contribution of fermentative and methanogenic microorganisms in both temperatures was evaluated in the

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

Science.gov (United States)

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.

Bioremediation of a polyaromatic hydrocarbon contaminated soil by native soil microbiota and bioaugmentation with isolated microbial consortia.

Science.gov (United States)

Silva, Isis Serrano; Santos, Eder da Costa dos; Menezes, Cristiano Ragagnin de; Faria, Andréia Fonseca de; Franciscon, Elisangela; Grossman, Matthew; Durrant, Lucia Regina

2009-10-01

Biodegradation of a mixture of PAHs was assessed in forest soil microcosms performed either without or with bioaugmentation using individual fungi and bacterial and a fungal consortia. Respiratory activity, metabolic intermediates and extent of PAH degradation were determined. In all microcosms the low molecular weight PAH's naphthalene, phenanthrene and anthracene, showed a rapid initial rate of removal. However, bioaugmentation did not significantly affect the biodegradation efficiency for these compounds. Significantly slower degradation rates were demonstrated for the high molecular weight PAH's pyrene, benz[a]anthracene and benz[a]pyrene. Bioaugmentation did not improve the rate or extent of PAH degradation, except in the case of Aspergillus sp. Respiratory activity was determined by CO(2) evolution and correlated roughly with the rate and timing of PAH removal. This indicated that the PAHs were being used as an energy source. The native microbiota responded rapidly to the addition of the PAHs and demonstrated the ability to degrade all of the PAHs added to the soil, indicating their ability to remediate PAH-contaminated soils.

Evolution of Yeast Consortia during the Fermentation of Kalamata Natural Black Olives upon Two Initial Acidification Treatments

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Stamatoula Bonatsou

2018-01-01

Full Text Available The objective of this study was to elucidate the yeast consortia structure and dynamics during Greek-style processing of Kalamata natural black olives in different brine solutions. Olives were subjected to spontaneous fermentation in 7% (w/v NaCl brine solution (control treatment or brine acidified with (a 0.5% (v/v vinegar, and (b 0.1% (v/v lactic acid at the onset of fermentation. Changes in microbial counts, pH, acidity, organic acids, sugars, and alcohols were analyzed for a period of 187 days. Yeast consortia diversity was evaluated at days 4, 34, 90, 140, and 187 of fermentation. A total of 260 isolates were characterized at sub-species level by rep-PCR genomic fingerprinting with the oligo-nucleotide primer (GTG5. The characterization of yeast isolates at species level was performed by sequencing of the D1/D2 domain of 26S rRNA gene. Results showed that yeasts dominated the process presenting a relatively broad range of biodiversity composed of 11 genera and 21 species. No lactic acid bacteria (LAB or Enterobacteriaceae could be enumerated after 20 and 10 days of fermentation, respectively. The dominant yeast species at the beginning were Aureobasidium pullulans for control and vinegar acidification treatments, and Candida naeodendra for lactic acid treatment. Between 34 and 140 days the dominant species were Candida boidinii, Candida molendinolei and Saccharomyces cerevisiae. In the end of fermentation the dominant species in all processes were C. boidinii and C. molendinolei, followed by Pichia manshurica and S. cerevisiae in lactic acid acidification treatment, P. manshurica in vinegar acidification treatment, and Pichia membranifaciens in control fermentation.

Hexavalent chromium reduction by bacterial consortia and pure strains from an alkaline industrial effluent.

Science.gov (United States)

Piñón-Castillo, H A; Brito, E M S; Goñi-Urriza, M; Guyoneaud, R; Duran, R; Nevarez-Moorillon, G V; Gutiérrez-Corona, J F; Caretta, C A; Reyna-López, G E

2010-12-01

To characterize the bacterial consortia and isolates selected for their role in hexavalent chromium removal by adsorption and reduction. Bacterial consortia from industrial wastes revealed significant Cr(VI) removal after 15 days when incubated in medium M9 at pH 6·5 and 8·0. The results suggested chromium reduction. The bacterial consortia diversity (T-RFLP based on 16S rRNA gene) indicated a highest number of operational taxonomic units in an alkaline carbonate medium mimicking in situ conditions. However, incubations under such conditions revealed low Cr(VI) removal. Genomic libraries were obtained for the consortia exhibiting optimal Cr(VI) removal (M9 medium at pH 6·5 and 8·0). They revealed the dominance of 16S rRNA gene sequences related to the genera Pseudomonas/Stenotrophomonas or Enterobacter/Halomonas, respectively. Isolates related to Pseudomonas fluorescens and Enterobacter aerogenes were efficient in Cr(VI) reduction and adsorption to the biomass. Cr(VI) reduction was better at neutral pH rather than under in situ conditions (alkaline pH with carbonate). Isolated strains exhibited significant capacity for Cr(VI) reduction and adsorption. Bacterial communities from chromium-contaminated industrial wastes as well as isolates were able to remove Cr(VI). The results suggest a good potential for bioremediation of industrial wastes when optimal conditions are applied. Journal of Applied Microbiology © 2010 The Society for Applied Microbiology. No claim to Mexican Government works.

Different cultivation methods to acclimatise ammonia-tolerant methanogenic consortia.

Science.gov (United States)

Tian, Hailin; Fotidis, Ioannis A; Mancini, Enrico; Angelidaki, Irini

2017-05-01

Bioaugmentation with ammonia tolerant-methanogenic consortia was proposed as a solution to overcome ammonia inhibition during anaerobic digestion process recently. However, appropriate technology to generate ammonia tolerant methanogenic consortia is still lacking. In this study, three basic reactors (i.e. batch, fed-batch and continuous stirred-tank reactors (CSTR)) operated at mesophilic (37°C) and thermophilic (55°C) conditions were assessed, based on methane production efficiency, incubation time, TAN/FAN (total ammonium nitrogen/free ammonia nitrogen) levels and maximum methanogenic activity. Overall, fed-batch cultivation was clearly the most efficient method compared to batch and CSTR. Specifically, by saving incubation time up to 150%, fed-batch reactors were acclimatised to nearly 2-fold higher FAN levels with a 37%-153% methanogenic activity improvement, compared to batch method. Meanwhile, CSTR reactors were inhibited at lower ammonia levels. Finally, specific methanogenic activity test showed that hydrogenotrophic methanogens were more active than aceticlastic methanogens in all FAN levels above 540mgNH 3 -NL -1 . Copyright © 2017 Elsevier Ltd. All rights reserved.

Higher Education in Further Education Colleges: Indirectly Funded Partnerships: Codes of Practice for Franchise and Consortia Arrangements. Report.

Science.gov (United States)

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…

76 FR 3145 - Pediatric Device Consortia Grant Program (P50)

Science.gov (United States)

2011-01-19

... providing grants to nonprofit consortia whose business model and approach to device development will either... younger at the time of diagnosis or treatment. DATES: Important dates are as follows: 1. The application..., rm. 2139, Rockville, MD 20852, 301- 827-7175. For more information on this funding opportunity...

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.

Science.gov (United States)

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.

Dissolution and degradation of crude oil droplets by different bacterial species and consortia by microcosm microfluidics

Science.gov (United States)

Jalali, Maryam; Sheng, Jian

2017-11-01

Bacteria are involved in cleanup and degradation of crude oil in polluted marine and soil environments. A number of bacterial species have been identified for consuming petroleum hydrocarbons with diverse metabolic capabilities. We conducted laboratory experiments to investigate bacterial consumption by monitoring the volume change to oil droplets as well as effects of oil droplet size on this process. To conduct our study, we developed a micro-bioassay containing an enclosed chamber with bottom substrate printed with stationary oil microdroplets and a digital holographic interferometer (DHI). The morphology of microdroplets was monitored in real time over 100 hours and instantaneous flow field was also measured by digital holographic microscope. The substrates with printed oil droplets were further evaluated with atomic force microscopy (AFM) at the end of each experiment. Three different bacteria species, Pseudomonas sp, Alcanivorax borkumensis, and Marinobacter hydrocarbonoclasticus, as well as six bacterial consortia were used in this study. The results show that droplets smaller than 20µm in diameter are not subject to bacterial degradation and the volume of droplet did not change beyond dissolution. Substantial species-specific behaviors have been observed in isolates. The experiments of consortia and various flow shears on biodegradation and dissolution are ongoing and will be reported.

Metabolic commensalism and competition in a two-species microbial consortium

DEFF Research Database (Denmark)

Christensen, Bjarke Bak; Haagensen, Janus Anders Juul; Heydorn, Arne

2002-01-01

We analyzed metabolic interactions and the importance of specific structural relationships in a benzyl alcohol-degrading microbial consortium comprising two species, Pseudomonas putida strain R1 and Acinetobacter strain C6, both of which are able to utilize benzyl alcohol as their sole carbon...... alcohol, which apparently gives Acinetobacter strain C6 a growth advantage, probably because it converts benzyl alcohol to benzoate with a higher yield per time unit than P. putida R1. In biofilms, however, the organisms establish structured, surface-attached consortia, in which heterogeneous ecological...... niches develop, and under these conditions competition for the primary carbon source is not the only determinant of biomass and population structure....

Control of Clostridium difficile infection by defined microbial communities

Science.gov (United States)

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

Syntrophic biodegradation of hydrocarbon contaminants.

Science.gov (United States)

Gieg, Lisa M; Fowler, S Jane; Berdugo-Clavijo, Carolina

2014-06-01

Anaerobic environments are crucial to global carbon cycling wherein the microbial metabolism of organic matter occurs under a variety of redox conditions. In many anaerobic ecosystems, syntrophy plays a key role wherein microbial species must cooperate, essentially as a single catalytic unit, to metabolize substrates in a mutually beneficial manner. Hydrocarbon-contaminated environments such as groundwater aquifers are typically anaerobic, and often methanogenic. Syntrophic processes are needed to biodegrade hydrocarbons to methane, and recent studies suggest that syntrophic hydrocarbon metabolism can also occur in the presence of electron acceptors. The elucidation of key features of syntrophic processes in defined co-cultures has benefited greatly from advances in 'omics' based tools. Such tools, along with approaches like stable isotope probing, are now being used to monitor carbon flow within an increasing number of hydrocarbon-degrading consortia to pinpoint the key microbial players involved in the degradative pathways. The metagenomic sequencing of hydrocarbon-utilizing consortia should help to further identify key syntrophic features and define microbial interactions in these complex communities. Copyright © 2013 Elsevier Ltd. All rights reserved.

MICROBIAL CELL-SURFACE HYDROPHOBICITY - THE INVOLVEMENT OF ELECTROSTATIC INTERACTIONS IN MICROBIAL ADHESION TO HYDROCARBONS (MATH)

NARCIS (Netherlands)

GEERTSEMADOORNBUSCH, GI; VANDERMEI, HC; BUSSCHER, HJ

Microbial adhesion to hydrocarbons (MATH) is the most commonly used method to determine microbial cell surface hydrophobicity. Since, however, the assay is based on adhesion, it is questionable whether the results reflect only the cell surface hydrophobicity or an interplay of hydrophobicity and

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

Science.gov (United States)

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

2017-07-15

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.

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

OpenAIRE

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

2015-01-01

Biosurfactants (BS) 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 biosurfactant producing strains or mixed consortia. The community structure of the best consortia based on the drop c...

Building Capacity For Innovation Through R&D Consortia in Health Projects: From Network Interaction to Systemic Transformation

Directory of Open Access Journals (Sweden)

Ria Hardiyati

2017-12-01

The research capacity in the area of vaccines has been long started from individual research conducted by researcher. It has been continued into organization research, and then developed into building innovation capacity through R&D consortia. However, in areas of stem cell there is still lack of evidence but it directly leaps to build innovation capacity through R&D consortia. Therefore further empirical evidence is needed to support the continuous trajectory.

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

Science.gov (United States)

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.

Bacterial communities in full-scale wastewater treatment systems

OpenAIRE

Cydzik-Kwiatkowska, Agnieszka; Zieli?ska, Magdalena

2016-01-01

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...

Screen-Printed Electrodes: New Tools for Developing Microbial Electrochemistry at Microscale Level

Directory of Open Access Journals (Sweden)

Marta Estevez-Canales

2015-11-01

Full Text Available Microbial electrochemical technologies (METs have a number of potential technological applications. In this work, we report the use of screen-printed electrodes (SPEs as a tool to analyze the microbial electroactivity by using Geobacter sulfurreducens as a model microorganism. We took advantage of the small volume required for the assays (75 μL and the disposable nature of the manufactured strips to explore short-term responses of microbial extracellular electron transfer to conductive materials under different scenarios. The system proved to be robust for identifying the bioelectrochemical response, while avoiding complex electrochemical setups, not available in standard biotechnology laboratories. We successfully validated the system for characterizing the response of Geobacter sulfurreducens in different physiological states (exponential phase, stationary phase, and steady state under continuous culture conditions revealing different electron transfer responses. Moreover, a combination of SPE and G. sulfurreducens resulted to be a promising biosensor for quantifying the levels of acetate, as well as for performing studies in real wastewater. In addition, the potential of the technology for identifying electroactive consortia was tested, as an example, with a mixed population with nitrate-reducing capacity. We therefore present SPEs as a novel low-cost platform for assessing microbial electrochemical activity at the microscale level.

Biodiesel production from microbial granules in sequencing batch reactor.

Science.gov (United States)

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.

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

KAUST Repository

Gertler, Christoph

2015-04-29

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. © 2015 Springer Science+Business Media New York

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

KAUST Repository

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

2015-01-01

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. © 2015 Springer Science+Business Media New York

Stimulation of bacterial DNA synthesis by algal exudates in attached algal-bacterial consortia

International Nuclear Information System (INIS)

Murray, R.E.; Cooksey, K.E.; Priscu, J.C.

1986-01-01

Algal-bacterial consortia attached to polystyrene surfaces were prepared in the laboratory by using the marine diatom Amphora coffeaeformis and the marine bacterium Vibrio proteolytica (the approved name of this bacterium is Vibrio proteolyticus. The organisms were attached to the surfaces at cell densities of approximately 5 x 10 4 cells cm -2 (diatoms) and 5 x 10 6 cells cm -2 (bacteria). The algal-bacterial consortia consistently exhibited higher rates of [ 3 H]thymidine incorporation than did biofilms composed solely of bacteria. The rates of [ 3 H]thymidine incorporation by the algal-bacterial consortia were fourfold greater than the rates of incorporation by monobacterial biofilms 16 h after biofilm formation and were 16-fold greater 70 h after biofilm formation. Extracellular material released from the attached Amphora cells supported rates of bacterial activity (0.8 x 10 -21 mol to 17.9 x 10 -21 mol of [ 3 H]thymidine incorporated cell -1 h -1 ) and growth (doubling time, 29.5 to 1.4 days) comparable to values reported for a wide variety of marine and freshwater ecosystems. In the presence of sessile diatom populations, DNA synthesis by attached V. proteolytica cells was light dependent and increased with increasing algal abundance. The metabolic activity of diatoms thus appears to be the rate-limiting process in biofilm development on illuminated surfaces under conditions of low bulk-water dissolved organic carbon

Comparative metagenomic analysis of PAH degradation in soil by a mixed microbial consortium.

Science.gov (United States)

Zafra, German; Taylor, Todd D; Absalón, Angel E; Cortés-Espinosa, Diana V

2016-11-15

In this study, we used a taxonomic and functional metagenomic approach to analyze some of the effects (e.g. displacement, permanence, disappearance) produced between native microbiota and a previously constructed Polycyclic Aromatic Hydrocarbon (PAH)-degrading microbial consortium during the bioremediation process of a soil polluted with PAHs. Bioaugmentation with a fungal-bacterial consortium and biostimulation of native microbiota using corn stover as texturizer produced appreciable changes in the microbial diversity of polluted soils, shifting native microbial communities in favor of degrading specific populations. Functional metagenomics showed changes in gene abundance suggesting a bias towards aromatic hydrocarbon and intermediary degradation pathways, which greatly favored PAH mineralization. In contrast, pathways favoring the formation of toxic intermediates such as cytochrome P450-mediated reactions were found to be significantly reduced in bioaugmented soils. PAH biodegradation in soil using the microbial consortium was faster and reached higher degradation values (84% after 30 d) as a result of an increased co-metabolic degradation when compared with other mixed microbial consortia. The main differences between inoculated and non-inoculated soils were observed in aromatic ring-hydroxylating dioxygenases, laccase, protocatechuate, salicylate and benzoate-degrading enzyme genes. Based on our results, we propose that several concurrent metabolic pathways are taking place in soils during PAH degradation. Copyright © 2016 Elsevier B.V. All rights reserved.

Microbial Degradation of a Recalcitrant Pesticide: Chlordecone.

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Chaussonnerie, Sébastien; Saaidi, Pierre-Loïc; Ugarte, Edgardo; Barbance, Agnès; Fossey, Aurélie; Barbe, Valérie; Gyapay, Gabor; Brüls, Thomas; Chevallier, Marion; Couturat, Loïc; Fouteau, Stéphanie; Muselet, Delphine; Pateau, Emilie; Cohen, Georges N; Fonknechten, Nuria; Weissenbach, Jean; Le Paslier, Denis

2016-01-01

Chlordecone (Kepone®) is a synthetic organochlorine insecticide (C 10 Cl 10 O) used worldwide mostly during the 1970 and 1980s. Its intensive application in the French West Indies to control the banana black weevil Cosmopolites sordidus led to a massive environmental pollution. Persistence of chlordecone in soils and water for numerous decades even centuries causes global public health and socio-economic concerns. In order to investigate the biodegradability of chlordecone, microbial enrichment cultures from soils contaminated by chlordecone or other organochlorines and from sludge of a wastewater treatment plant have been conducted. Different experimental procedures including original microcosms were carried out anaerobically over long periods of time. GC-MS monitoring resulted in the detection of chlorinated derivatives in several cultures, consistent with chlordecone biotransformation. More interestingly, disappearance of chlordecone (50 μg/mL) in two bacterial consortia was concomitant with the accumulation of a major metabolite of formula C 9 Cl 5 H 3 (named B1) as well as two minor metabolites C 10 Cl 9 HO (named A1) and C 9 Cl 4 H 4 (named B3). Finally, we report the isolation and the complete genomic sequences of two new Citrobacter isolates, closely related to Citrobacter amalonaticus , and that were capable of reproducing chlordecone transformation. Further characterization of these Citrobacter strains should yield deeper insights into the mechanisms involved in this transformation process.

NLM's Medical Library Resource Improvement Grant for Consortia Development: a proposed outline to simplify the application process.

Science.gov (United States)

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.

Microbial communities involved in methane production from hydrocarbons in oil sands tailings.

Science.gov (United States)

Siddique, Tariq; Penner, Tara; Klassen, Jonathan; Nesbø, Camilla; Foght, Julia M

2012-09-04

Microbial metabolism of residual hydrocarbons, primarily short-chain n-alkanes and certain monoaromatic hydrocarbons, in oil sands tailings ponds produces large volumes of CH(4) in situ. We characterized the microbial communities involved in methanogenic biodegradation of whole naphtha (a bitumen extraction solvent) and its short-chain n-alkane (C(6)-C(10)) and BTEX (benzene, toluene, ethylbenzene, and xylenes) components using primary enrichment cultures derived from oil sands tailings. Clone libraries of bacterial 16S rRNA genes amplified from these enrichments showed increased proportions of two orders of Bacteria: Clostridiales and Syntrophobacterales, with Desulfotomaculum and Syntrophus/Smithella as the closest named relatives, respectively. In parallel archaeal clone libraries, sequences affiliated with cultivated acetoclastic methanogens (Methanosaetaceae) were enriched in cultures amended with n-alkanes, whereas hydrogenotrophic methanogens (Methanomicrobiales) were enriched with BTEX. Naphtha-amended cultures harbored a blend of these two archaeal communities. The results imply syntrophic oxidation of hydrocarbons in oil sands tailings, with the activities of different carbon flow pathways to CH(4) being influenced by the primary hydrocarbon substrate. These results have implications for predicting greenhouse gas emissions from oil sands tailings repositories.

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

Science.gov (United States)

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.

Enhancing biodegradation of wastewater by microbial consortia with fractional factorial design

Energy Technology Data Exchange (ETDEWEB)

Chen Yuancai [State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, 510640, Guangdong (China); Lin Chejen, E-mail: Jerry.Lin@lamar.edu [Department of Civil Engineering, Lamar University, Beaumont, TX 77710-0024 (United States); School of Environmental Science and Engineering, South China University of Technology, Guangzhou, 510006, Guangdong (China); Jones, Gavin [Texas Research Institute for Environmental Studies, Sam Houston State University, Huntsville, TX 77341-2506 (United States); Fu Shiyu; Zhan Huaiyu [State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, 510640, Guangdong (China)

2009-11-15

Batch experiments were conducted on the degradation of synthetic and municipal wastewater by six different strains, i.e., Agrobacterium sp., Bacillus sp., Enterobacter cloacae, Gordonia, Pseudomonas stutzeri, Pseudomonas putida. By applying a fractional factorial design (FFD) of experiments, the influence of each strain and their interactions were quantified. An empirical model predicting the treatment efficiency was built based on the results of the FFD experiments with an R{sup 2} value of 99.39%. For single strain, Enterobacter cloacae, Gordonia and P. putida (p = 0.008, 0.009 and 0.023, respectively) showed significant enhancement on organic removal in the synthetic wastewater. Positive interaction from Enterobacter cloacae, Gordonia (p = 0.046) was found, indicating that syntrophic interaction existed, and their coexistence can improve total organic carbon (TOC) degradation. Verification experiments were performed to evaluate the effect of bioaugmentation by introducing three selected strains into an activated sludge reactor for treating municipal wastewater. The removal efficiency of TOC with the bioaugmentation was increased from 67-72% to 80-84% at an influent TOC concentration of 200 mg/L. The results derived from this study indicate that the FFD is a useful screening tool for optimizing the microbial community to enhance treatment efficiency.

Enhancing biodegradation of wastewater by microbial consortia with fractional factorial design

International Nuclear Information System (INIS)

Chen Yuancai; Lin Chejen; Jones, Gavin; Fu Shiyu; Zhan Huaiyu

2009-01-01

Batch experiments were conducted on the degradation of synthetic and municipal wastewater by six different strains, i.e., Agrobacterium sp., Bacillus sp., Enterobacter cloacae, Gordonia, Pseudomonas stutzeri, Pseudomonas putida. By applying a fractional factorial design (FFD) of experiments, the influence of each strain and their interactions were quantified. An empirical model predicting the treatment efficiency was built based on the results of the FFD experiments with an R 2 value of 99.39%. For single strain, Enterobacter cloacae, Gordonia and P. putida (p = 0.008, 0.009 and 0.023, respectively) showed significant enhancement on organic removal in the synthetic wastewater. Positive interaction from Enterobacter cloacae, Gordonia (p = 0.046) was found, indicating that syntrophic interaction existed, and their coexistence can improve total organic carbon (TOC) degradation. Verification experiments were performed to evaluate the effect of bioaugmentation by introducing three selected strains into an activated sludge reactor for treating municipal wastewater. The removal efficiency of TOC with the bioaugmentation was increased from 67-72% to 80-84% at an influent TOC concentration of 200 mg/L. The results derived from this study indicate that the FFD is a useful screening tool for optimizing the microbial community to enhance treatment efficiency.

Exploring Biogeochemistry and Microbial Diversity of Extant Microbialites in Mexico and Cuba

Science.gov (United States)

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

Digital Resource Sharing and Library Consortia in Italy

Directory of Open Access Journals (Sweden)

Tommaso Giordano

2017-09-01

Full Text Available Interlibrary cooperation in Italy is a fairly recent and not very widespread practice. Attention to the topic was aroused in the eighties with the Italian library network project. More recently, under the impetus toward technological innovation, there has been renewed (and more pragmatic interest in cooperation in all library sectors. Sharing electronic resources is the theme of greatest interest today in university libraries, where various initiatives are aimed at setting up consortia to purchase licenses and run digital products. A number of projects in hand are described, and emerging trends analyzed.

Trace Metal Requirements for Microbial Enzymes Involved in the Production and Consumption of Methane and Nitrous Oxide

Science.gov (United States)

Glass, Jennifer B.; Orphan, Victoria J.

2011-01-01

Fluxes of greenhouse gases to the atmosphere are heavily influenced by microbiological activity. Microbial enzymes involved in the production and consumption of greenhouse gases often contain metal cofactors. While extensive research has examined the influence of Fe bioavailability on microbial CO2 cycling, fewer studies have explored metal requirements for microbial production and consumption of the second- and third-most abundant greenhouse gases, methane (CH4), and nitrous oxide (N2O). Here we review the current state of biochemical, physiological, and environmental research on transition metal requirements for microbial CH4 and N2O cycling. Methanogenic archaea require large amounts of Fe, Ni, and Co (and some Mo/W and Zn). Low bioavailability of Fe, Ni, and Co limits methanogenesis in pure and mixed cultures and environmental studies. Anaerobic methane oxidation by anaerobic methanotrophic archaea (ANME) likely occurs via reverse methanogenesis since ANME possess most of the enzymes in the methanogenic pathway. Aerobic CH4 oxidation uses Cu or Fe for the first step depending on Cu availability, and additional Fe, Cu, and Mo for later steps. N2O production via classical anaerobic denitrification is primarily Fe-based, whereas aerobic pathways (nitrifier denitrification and archaeal ammonia oxidation) require Cu in addition to, or possibly in place of, Fe. Genes encoding the Cu-containing N2O reductase, the only known enzyme capable of microbial N2O conversion to N2, have only been found in classical denitrifiers. Accumulation of N2O due to low Cu has been observed in pure cultures and a lake ecosystem, but not in marine systems. Future research is needed on metalloenzymes involved in the production of N2O by enrichment cultures of ammonia oxidizing archaea, biological mechanisms for scavenging scarce metals, and possible links between metal bioavailability and greenhouse gas fluxes in anaerobic environments where metals may be limiting due to sulfide

The Bsc and the Health Management Consortia: A Case Study of its Applicability

Directory of Open Access Journals (Sweden)

Juliana Caroline Coutinho Coelho Guimarães

2012-12-01

Full Text Available The professional management development consistent with the demands of society is an undeniable reality in Public Health. The enactment of 11.107/2005 Law inserts an agenda for change in the reality of Health Consortia. Against this backdrop of change, uncertainty and social costs, we need to rethink management practices. The management supporting tools have been evolving rapidly since 1980, highlighting the Balanced Scorecard (BSC. The adoption of the BSC as a management supporting tool to consortia comes to meet the existing demand to improve professionalization in public administration. This article aims to analyze the applicability of a support management tool to a Health Consortia, based on BSC through a proposed pilot project in a consortium selected to do so. Thus, for the realization of this work, designed a Case Study in CISMEV - Consortium Health of Middle Velhas River, and developed a proposal for the construction of the BSC with nine distinct steps. Thus, it was possible to identify the key steps to be met for the adoption of new procedures and routines, as well as the challenges encountered in the development process of the BSC by public institutions. We also identified the possible gains from deploying this tool culminating in fulfilling the mission and building the organizational vision. It was felt that identifying motivators for choosing this tool, as well as their strengths and limitations are essential to the construction of this process with greater criticality.

Applicability of cryoconite consortia of microorganisms and glacier-dwelling animals in astrobiological studies

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Zawierucha Krzysztof

2017-06-01

Full Text Available For several years it has been of interest to astrobiologists to focus on Earth’s glaciers as a habitat that can be similar to glaciers on other moons and planets. Microorganisms on glaciers form consortia – cryoconite granules (cryoconites. They are granular/spherical mineral particles connected with archaea, cyanobacteria, heterotrophic bacteria, algae, fungi, and micro animals (mainly Tardigrada and Rotifera. Cryophilic organisms inhabiting glaciers have been studied in different aspects: from taxonomy, ecology and biogeography, to searching of biotechnological potentials and physiological strategies to survive in extreme glacial habitats. However, they have never been used in astrobiological experiments. The main aim of this paper is brief review of literature and supporting assumptions that cryoconite granules and microinvertebrates on glaciers, are promising models in astrobiology for looking for analogies and survival strategies in terms of icy planets and moons. So far, astrobiological research have been conducted on single strains of prokaryotes or microinvertebrates but never on a consortium of them. Due to the hypothetical similarity of glaciers on the Earth to those on other planets these cryoconites consortia of microorganisms and glacier microinvertebrates may be applied in astrobiological experiments instead of the limno-terrestrial ones used currently. Those consortia and animals have qualities to use them in such studies and they may be the key to understanding how organisms are able to survive, reproduce and remain active at low temperatures.

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

Science.gov (United States)

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

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

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Tuoyu Zhou

2017-09-01

Full Text Available 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.

Monitoring of the microbial communities involved in the soy sauce manufacturing process by PCR-denaturing gradient gel electrophoresis.

Science.gov (United States)

Tanaka, Yasushi; Watanabe, Jun; Mogi, Yoshinobu

2012-08-01

Soy sauce is a traditional seasoning produced through the fermentation of soybeans and wheat using microbes. In this study, the microbial communities involved in the soy sauce manufacturing process were analyzed by PCR-Denaturing Gradient Gel Electrophoresis (PCR-DGGE). The bacterial DGGE profile indicated that the bacterial microbes in the koji were Weissella cibaria (Weissella confusa, Weissella kimchii, Weissella salipiscis, Lactobacillus fermentum, Lactobacillus plantarum, Lactobacillus iners, or Streptococcus thermophilus), Staphylococcus gallinarum (or Staphylococcus xylosus), and Staphylococcus kloosii. In addition to these bacteria, Tetragenococcus halophilus was also detected in the mash during lactic acid fermentation. The fungal DGGE profile indicated that the fungal microbes in the koji were not only Aspergillus oryzae but also several yeasts. In the mash, Zygosaccharomyces rouxii appeared in the early fermentation stage, Candida etchellsii (or Candida nodaensis) and Candida versatilis were detected at the middle fermentation stage, and Candida etchellsii was detected at the mature fermentation stage. These results suggest that the microbial communities present during the soy sauce manufacturing process change drastically throughout its production. This is the first report to reveal the microbial communities involved in the soy sauce manufacturing process using a culture-independent method. Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.

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

Science.gov (United States)

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

Microbial communication leading to the activation of silent fungal secondary metabolite gene clusters

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Tina eNetzker

2015-04-01

Full Text Available 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.

The E-rate Program and Libraries and Library Consortia, 2000-2004: Trends and Issues

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Paul T. Jaeger

2005-06-01

Full Text Available The E-rate program has provided tremendous benefits to libraries, allowing many libraries and library systems to acquire technological equipment and services that would otherwise be too expensive, increasing the availability of public Internet access through libraries. This article analyzes the data related to the E-rate program and the discounts that it has provided to libraries and library systems between 2000 and 2004. By examining the E-rate data in a longitudinal manner, this article explores the trends in the application for and the provision of E-rate discounts to libraries and library consortia at national and state levels. The data suggest that, despite a number of controversies over the years, the program has provided a significant level of support for libraries and library consortia.

Curriculum Framework (CF) Implementation Conference. Report of the Regional Educational Laboratory Network Program and the National Network of Eisenhower Mathematics and Science Regional Consortia (Hilton Head Island, South Carolina, January 26-27, 1995).

Science.gov (United States)

Palmer, Jackie; Powell, Mary Jo

The Laboratory Network Program and the National Network of Eisenhower Mathematics and Science Regional Consortia, operating as the Curriculum Frameworks Task Force, jointly convened a group of educators involved in implementing state-level mathematics or science curriculum frameworks (CF). The Hilton Head (South Carolina) conference had a dual…

Fostering Innovation in the Manufacturing Sector through R&D Consortia

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McKittrick, M.

2017-12-01

In the U.S. Department of Energy, the Advanced Manufacturing Office (AMO) has the mission to catalyze research, development and adoption of energy-related advanced manufacturing technologies and practices to drive U.S. economic competitiveness and energy productivity. Within strategic areas of manufacturing, AMO brings together manufacturers, suppliers, institutes of higher education, national laboratories, and state and local governments in public-private R&D consortia to accelerate technology innovation. One such R&D Consortia is the Critical Materials Institute (CMI), established in 2013 and led by Ames Laboratory. CMI is a sustained, multidisciplinary effort to develop solutions across the materials lifecycle of materials essential to clean energy technologies and manufacturing, as well as reduce the impact of supply chain disruptions associated with these valuable resources. By bringing together scientists and engineers from diverse disciplines, CMI is addressing challenges in critical materials, including mineral processing, manufacture, substitution, efficient use, and end-of-life recycling; integrating scientific research, engineering innovation, manufacturing and process improvements; and developing a holistic solution to the materials challenges facing the nation. It includes expertise from four national laboratories, seven universities, and ten industry partners to minimize materials criticality as an impediment to the commercialization of clean energy technologies.

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

Science.gov (United States)

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

Studies on methanogenic consortia associated with mangrove sediments of Ennore.

Digital Repository Service at National Institute of Oceanography (India)

Ahila, N.K.; Kannapiran, E.; Ravindran, J.; Ramkumar, V.S.

page : www.jeb.co.in « E-mail : editor@jeb.co.in Journal of Environmental Biology, Vol. 35, 649-654, July 2014© Triveni Enterprises, Lucknow (India) Journal of Environmental Biology ISSN: 0254-8704 CODEN: JEBIDP Introduction Mangroves are complex...-National Institute of Oceanography, Biological Oceanography Division, Dona Paula, Goa – 403 004, India Abstract Key words In this study, methanogenic consortia were isolated and characterized from eight different sediment samples of mangrove ecosystem located...

Microbial Degradation of a Recalcitrant Pesticide: Chlordecone

Science.gov (United States)

Chaussonnerie, Sébastien; Saaidi, Pierre-Loïc; Ugarte, Edgardo; Barbance, Agnès; Fossey, Aurélie; Barbe, Valérie; Gyapay, Gabor; Brüls, Thomas; Chevallier, Marion; Couturat, Loïc; Fouteau, Stéphanie; Muselet, Delphine; Pateau, Emilie; Cohen, Georges N.; Fonknechten, Nuria; Weissenbach, Jean; Le Paslier, Denis

2016-01-01

Chlordecone (Kepone®) is a synthetic organochlorine insecticide (C10Cl10O) used worldwide mostly during the 1970 and 1980s. Its intensive application in the French West Indies to control the banana black weevil Cosmopolites sordidus led to a massive environmental pollution. Persistence of chlordecone in soils and water for numerous decades even centuries causes global public health and socio-economic concerns. In order to investigate the biodegradability of chlordecone, microbial enrichment cultures from soils contaminated by chlordecone or other organochlorines and from sludge of a wastewater treatment plant have been conducted. Different experimental procedures including original microcosms were carried out anaerobically over long periods of time. GC-MS monitoring resulted in the detection of chlorinated derivatives in several cultures, consistent with chlordecone biotransformation. More interestingly, disappearance of chlordecone (50 μg/mL) in two bacterial consortia was concomitant with the accumulation of a major metabolite of formula C9Cl5H3 (named B1) as well as two minor metabolites C10Cl9HO (named A1) and C9Cl4H4 (named B3). Finally, we report the isolation and the complete genomic sequences of two new Citrobacter isolates, closely related to Citrobacter amalonaticus, and that were capable of reproducing chlordecone transformation. Further characterization of these Citrobacter strains should yield deeper insights into the mechanisms involved in this transformation process. PMID:28066351

Microbial degradation of a recalcitrant pesticide: chlordecone.

Directory of Open Access Journals (Sweden)

Sébastien Chaussonnerie

2016-12-01

Full Text Available Chlordecone (Kepone® is a synthetic organochlorine insecticide (C10Cl10O used worldwide mostly during the 1970s and 1980s. Its intensive application in the French West Indies to control the banana black weevil Cosmopolites sordidus led to a massive environmental pollution. Persistence of chlordecone in soils and water for numerous decades even centuries causes global public health and socio-economic concerns. In order to investigate the biodegradability of chlordecone, microbial enrichment cultures from soils contaminated by chlordecone or other organochlorines and from sludge of a wastewater treatment plant have been conducted. Different experimental procedures including original microcosms were carried out anaerobically over long periods of time. GC-MS monitoring resulted in the detection of chlorinated derivatives in several cultures, consistent with chlordecone biotransformation. More interestingly, disappearance of chlordecone (50 µg/mL in two bacterial consortia was concomitant with the accumulation of a major metabolite of formula C9Cl5H3 (named B1 as well as two minor metabolites C10Cl9HO (named A1 and C9Cl4H4 (named B3. Finally, we report the isolation and the complete genomic sequences of two new Citrobacter isolates, closely related to Citrobacter amalonaticus, and that were capable of reproducing chlordecone transformation. Further characterization of these Citrobacter strains should yield deeper insights into the mechanisms involved in this transformation process.

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

Science.gov (United States)

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.

Successional patterns of key genes and processes involved in the microbial nitrogen cycle in a salt marsh chronosequence

NARCIS (Netherlands)

Salles, Joana Falcao; Cassia Pereira e Silva , de Michele; Dini-Andreote, Francisco; Dias, Armando C. F.; Guillaumaud, Nadine; Poly, Franck; van Elsas, Jan Dirk

Here, we investigated the patterns of microbial nitrogen cycling communities along a chronosequence of soil development in a salt marsh. The focus was on the abundance and structure of genes involved in N fixation (nifH), bacterial and archaeal ammonium oxidation (amoA; AOB and AOA), and the

A Comparison of Modeling Approaches in Simulating Chlorinated Ethene Removal in a Constructed Wetland by a Microbial Consortia

National Research Council Canada - National Science Library

Campbell, Jason

2002-01-01

... of the modeling approaches affect simulation results. Concepts like microbial growth in the form of a biofilm and spatially varying contaminant concentrations bring the validity of the CSTR assumption into question...

Biodegradation of sodium lauryl ether sulfate (SLES) by two different bacterial consortia.

Science.gov (United States)

Khleifat, Khaled M

2006-11-01

Two bacterial consortia capable of degrading SLES were isolated from a wastewater treatment plant. The two consortia consisted of three members, Acinetobacter calcoacetiacus and Klebsiella oxytoca in one co-culture (A-K) and Serratia odorifera in the second co-culture (S-A), which contains Acinetobacter calcoacetiacus as well. In all experiments, cells were grown on SLES (1000-7000 ppm) containing the M9 minimal medium as sole carbon source. The co-culture A-K demonstrated a higher growth rate (0.26 h(-1)) and significant greater viability than that of the co-culture S-A (0.21 h(-1)). Glucose, sucrose, maltose, mannitol, and succinic acid as carbon sources produced the same degradation rate (approximately 100 ppm/h) and enhanced the SLES degradation rate by 3-fold upon the control (without an added carbon source). In the case of the co-culture S-A, the situation was different; all the carbon sources being tested except maltose caused a repression in the degradation ability in a range between 25-100%. Maltose causes an enhancement by almost fivefold, compared with the positive control.

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

Science.gov (United States)

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.

Transcriptional Activities of the Microbial Consortium Living with the Marine Nitrogen-Fixing Cyanobacterium Trichodesmium Reveal Potential Roles in Community-Level Nitrogen Cycling.

Science.gov (United States)

Lee, Michael D; Webb, Eric A; Walworth, Nathan G; Fu, Fei-Xue; Held, Noelle A; Saito, Mak A; Hutchins, David A

2018-01-01

Trichodesmium is a globally distributed cyanobacterium whose nitrogen-fixing capability fuels primary production in warm oligotrophic oceans. Like many photoautotrophs, Trichodesmium serves as a host to various other microorganisms, yet little is known about how this associated community modulates fluxes of environmentally relevant chemical species into and out of the supraorganismal structure. Here, we utilized metatranscriptomics to examine gene expression activities of microbial communities associated with Trichodesmium erythraeum (strain IMS101) using laboratory-maintained enrichment cultures that have previously been shown to harbor microbial communities similar to those of natural populations. In enrichments maintained under two distinct CO 2 concentrations for ∼8 years, the community transcriptional profiles were found to be specific to the treatment, demonstrating a restructuring of overall gene expression had occurred. Some of this restructuring involved significant increases in community respiration-related transcripts under elevated CO 2 , potentially facilitating the corresponding measured increases in host nitrogen fixation rates. Particularly of note, in both treatments, community transcripts involved in the reduction of nitrate, nitrite, and nitrous oxide were detected, suggesting the associated organisms may play a role in colony-level nitrogen cycling. Lastly, a taxon-specific analysis revealed distinct ecological niches of consistently cooccurring major taxa that may enable, or even encourage, the stable cohabitation of a diverse community within Trichodesmium consortia. IMPORTANCE Trichodesmium is a genus of globally distributed, nitrogen-fixing marine cyanobacteria. As a source of new nitrogen in otherwise nitrogen-deficient systems, these organisms help fuel carbon fixation carried out by other more abundant photoautotrophs and thereby have significant roles in global nitrogen and carbon cycling. Members of the Trichodesmium genus tend to

Improvement of Biogas Production by Bioaugmentation

Directory of Open Access Journals (Sweden)

K. L. Kovács

2013-01-01

Full Text Available 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.

Improvement of Biogas Production by Bioaugmentation

Science.gov (United States)

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

Use of active consortia of constructed ternary bacterial cultures via mixture design for azo-dye decolorization enhancement

International Nuclear Information System (INIS)

Chen, B.-Y.; Wang, M.-Y.; Lu, W.-B.; Chang, J.-S.

2007-01-01

This first-attempt study used constructed bacterial consortia containing Escherichia coli DH5α (a weak decolorizer) and its UV-irradiated mutants (E. coli UVT1 and UV68; strong decolorizers) via equilateral triangle diagram and mixture experimental design to assess color removal during species evolution. The results showed that although strain DH5α was not an effective decolorizer, its presence might still played a significant role in affecting optimal color removal capabilities of mixed consortia (e.g., E. coli DH5α, UVT1 and UV68) for two model azo dyes; namely, reactive red 22 (RR22) and reactive black 5 (RB5). Contour analysis of ternary systems also clearly showed that decolorization of RR22 and RB5 by DH5α-containing active mixed consortia was more effective than mono-cultures of the stronger decolorizer alone (e.g., UVT1). The optimal composition of the mixed consortium (UV68, UVT1, DH5α) achieving the highest specific decolorization rate was (13%:58%:29%) and (0%:74%:26%) for decolorization of RR22 and RB5, respectively, with initial total cell density fixed at OD 600 = 3.5 ± 0.28

An enrichment of CRISPR and other defense-related features in marine sponge-associated microbial metagenomes

Directory of Open Access Journals (Sweden)

Hannes Horn

2016-11-01

Full Text Available 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 (CRISPR, restriction modification, DNA phosphorothioation and phage growth limitation systems were enriched in sponge metagenomes. These data suggest that defense is an important functional trait for an existence within sponges that requires mechanisms to defend against foreign DNA from microorganisms and viruses. 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.

Investigating the Microbial Degradation Potential in Oil Sands Fluid Fine Tailings Using Gamma Irradiation: A Metagenomic Perspective.

Science.gov (United States)

VanMensel, Danielle; Chaganti, Subba Rao; Boudens, Ryan; Reid, Thomas; Ciborowski, Jan; Weisener, Christopher

2017-08-01

Open-pit mining of the Athabasca oil sands has generated large volumes of waste termed fluid fine tailings (FFT), stored in tailings ponds. Accumulation of toxic organic substances in the tailings ponds is one of the biggest concerns. Gamma irradiation (GI) treatment could accelerate the biodegradation of toxic organic substances. Hence, this research investigates the response of the microbial consortia in GI-treated FFT materials with an emphasis on changes in diversity and organism-related stimuli. FFT materials from aged and fresh ponds were used in the study under aerobic and anaerobic conditions. Variations in the microbial diversity in GI-treated FFT materials were monitored for 52 weeks and significant stimuli (p tailings biogeochemistry and the impacts of GI treatment on microorganisms as an effect for targeting toxic organics. The outcomes of this study highlight the potential for this approach to accelerate stabilization and reclamation end points. Graphical Abstract.

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

Directory of Open Access Journals (Sweden)

Elizabeth Trembath-Reichert

2016-04-01

Full Text Available 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

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

Science.gov (United States)

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

76 FR 17391 - Applications for New Awards; United States-Brazil Higher Education Consortia Program

Science.gov (United States)

2011-03-29

... DEPARTMENT OF EDUCATION Applications for New Awards; United States-Brazil Higher Education...: United States (U.S.)- Brazil Higher Education Consortia Program Notice inviting applications for new... projects that include a plan to work with an institution of higher education (IHE) in another country in...

Isolation and characterization of novel hydrocarbon-degrading euryhaline consortia from crude oil and mangrove sediments.

Science.gov (United States)

Piedad Díaz, M; Grigson, S J; Peppiatt, C J; Burgess, J G

2000-11-01

Two novel and versatile bacterial consortia were developed for the biodegradation of hydrocarbons. They were isolated from crude oil from the Cormorant Field in the North Sea (MPD-7) and from sediment associated with mangrove roots (MPD-M). The bacterial consortia were able to degrade both aliphatic and aromatic hydrocarbons in crude oils very effectively in seawater (35 g/L NaCl) and synthetic media containing 0 to 100 g/L NaCl (1.7 M). Salinities over twice that of normal seawater decreased the biodegradation rates. However, even at the highest salinity biodegradation was significant. Ratios of nC17 to pristane and nC18 to phytane were significantly lowered across the range of salinity. The lowest values were at 0 and 20 g/L (0.34 M). Phytane was degraded in preference to pristane. The degradation of these compounds was constant over the salinity range, with evidence of a slight increase for consortium MPD-M with increasing salinity. In general, the consortium isolated from mangrove root sediments was more efficient in metabolizing North Sea crude oil than the consortium isolated from Cormorant crude oil. The 5 strains that comprise MPD-M have been tentatively identified as species of the genera Marinobacter, Bacillus, and Erwinia. This is the first report of hydrocarbon-degrading consortia isolated from crude oil and mangrove sediments that are capable of treating oily wastes over such a wide range of salinity.

Microbial degradation of waste hydrocarbons in oily sludge from some Romanian oil fields

International Nuclear Information System (INIS)

Lazar, I.; Dobrota, S.; Voicu, A.; Stefanescu, M.; Sandulescu, L.; Petrisor, I.G.

1999-01-01

During oil production and processing activities, significant quantities of oily sludge are produced. The sludge represents not only an environmental pollution source but also occupies big spaces in storage tanks. Romania, an experienced European oil-producing and processing country, is faced with environmental problems generated by oily sludge accumulations. Many such accumulations are to be submitted to bioremediation processes based on the hydrocarbon degradation activity of naturally occurring, selectively isolated bacteria. In this paper the results concerning a laboratory screening of several natural bacterial consortia and laboratory tests to establish the performance in degradation of hydrocarbons contained in oily sludges from Otesti oil field area, are presented. As a result of the laboratory screening, we selected six natural bacterial consortia (BCSl-I 1 to BCSl-I 6 ) with high ability in degradation of hydrocarbons from paraffinic and non-paraffinic asphaltic oils (between 25.53%-64.30% for non-paraffinic asphaltic oil and between 50.25%-72.97% for paraffinic oil). The laboratory tests proved that microbial degradation of hydrocarbons contained in oily sludge from Otesti oil field area varied from 16.75% to 95.85% in moving conditions (Erlenmeyers of 750 ml on rotary shaker at 200 rpm) and from 16.85% to 51.85% in static conditions (Petri dishes Oe 10 cm or vessels of 500 ml)

Indian Academic library consortia (IALC): A proposal for electronic resource sharing

OpenAIRE

Ghosh, Maitrayee

2002-01-01

Library & Information system networking in India have come into existence more than two decade ago. For so many years the term "Interlibrary loan or Exchange" has been in focus in the parlance of library management. This scenario has extended from its limited basis to become fully grown Consortia of various kinds. Since India is a developing country, we constantly work towards improving our infrastructure and technology to meet the demands of our scientists and researchers by taking the lead ...

Feasibility of bio-hydrogen production from sewage sludge using defined microbial consortium

Energy Technology Data Exchange (ETDEWEB)

Shireen Meher Kotay; Debabrata Das [Fermentation Technology Lab., Department of Biotechnology, Indian Institute of Technology Kharagpur, W.B., INDIA-721302 (India)

2006-07-01

Biological hydrogen production potential of a defined microbial consortium consisting of three facultative anaerobes, Enterobacter cloacae IIT-BT 08, Citrobacter freundii IIT-BT L139 and Bacillus coagulans IIT-BT S1 was studied. In this investigation their individual and combinatorial H{sub 2} production capabilities have been studied on defined media and pretreated sewage sludge. Defined medium, MYG (1% w/v Malt extract, 0.4% w/v yeast extract and 1% w/v glucose) with glucose as limiting substrate has been found to be most suitable for hydrogen production. Individually E. cloacae clearly gave higher yield (276 ml H{sub 2}/ g COD reduced) using defined medium than the other two strains. There was no considerable difference in maximal yield of hydrogen from individual and combinatorial (1:1:1 consortium) modes suggesting that E. cloacae dominated in the consortia on defined medium. Contradictorily, B. coagulans gave better bio-hydrogen yield (37.16 ml H{sub 2}/g COD consumed) than the other two strains when activated sewage sludge was used as substrate. The pretreatment of sludge included sterilization, (15% v/v) dilution and supplementation with 0.5%w/v glucose which was found to be essential to screen out the hydrogen consuming bacteria and ameliorate the hydrogenation. Considering (1:1:1) consortium as inoculum, interestingly yield of hydrogen was recorded to increase to 41.23 ml H{sub 2}/ g COD reduced inferring that in consortium, the substrate utilization was significantly higher. The hydrogen yield from pretreated sludge obtained in this study (35.54 ml H{sub 2} g sludge) has been found to be distinctively higher than the earlier reports (8.1 - 16.9 ml H{sub 2}/g sludge). However it was lower compared to the yield obtained from co-digestion of (83:17) food waste and sewage sludge (122 ml H{sub 2}/g carbohydrate COD). Employing formulated microbial consortia for bio-hydrogen production from sewage sludge was an attempt to augment the hydrogen yield from sludge

Feasibility of bio-hydrogen production from sewage sludge using defined microbial consortium

Energy Technology Data Exchange (ETDEWEB)

Shireen Meher Kotay; Debabrata Das [Fermentation Technology Lab., Department of Biotechnology, Indian Institute of Technology Kharagpur, W.B., INDIA-721302 (India)

2006-07-01

Biological hydrogen production potential of a defined microbial consortium consisting of three facultative anaerobes, Enterobacter cloacae IIT-BT 08, Citrobacter freundii IIT-BT L139 and Bacillus coagulans IIT-BT S1 was studied. In this investigation their individual and combinatorial H{sub 2} production capabilities have been studied on defined media and pretreated sewage sludge. Defined medium, MYG (1% w/v Malt extract, 0.4% w/v yeast extract and 1% w/v glucose) with glucose as limiting substrate has been found to be most suitable for hydrogen production. Individually E. cloacae clearly gave higher yield (276 ml H{sub 2}/ g COD reduced) using defined medium than the other two strains. There was no considerable difference in maximal yield of hydrogen from individual and combinatorial (1:1:1 consortium) modes suggesting that E. cloacae dominated in the consortia on defined medium. Contradictorily, B. coagulans gave better bio-hydrogen yield (37.16 ml H{sub 2}/ g COD consumed) than the other two strains when activated sewage sludge was used as substrate. The pretreatment of sludge included sterilization, (15% v/v) dilution and supplementation with 0.5% w/v glucose which was found to be essential to screen out the hydrogen consuming bacteria and ameliorate the hydrogenation. Considering (1:1:1) consortium as inoculum, interestingly yield of hydrogen was recorded to increase to 41.23 ml H{sub 2}/ g COD reduced inferring that in consortium, the substrate utilization was significantly higher. The hydrogen yield from pretreated sludge obtained in this study (35.54 ml H{sub 2}/ g sludge) has been found to be distinctively higher than the earlier reports (8.1 - 16.9 ml H{sub 2} / g sludge). However it was lower compared to the yield obtained from co-digestion of (83:17) food waste and sewage sludge (122 ml H{sub 2}/ g carbohydrate COD). Employing formulated microbial consortia for bio-hydrogen production from sewage sludge was an attempt to augment the hydrogen yield from

Feasibility of bio-hydrogen production from sewage sludge using defined microbial consortium

International Nuclear Information System (INIS)

Shireen Meher Kotay; Debabrata Das

2006-01-01

Biological hydrogen production potential of a defined microbial consortium consisting of three facultative anaerobes, Enterobacter cloacae IIT-BT 08, Citrobacter freundii IIT-BT L139 and Bacillus coagulans IIT-BT S1 was studied. In this investigation their individual and combinatorial H 2 production capabilities have been studied on defined media and pretreated sewage sludge. Defined medium, MYG (1% w/v Malt extract, 0.4% w/v yeast extract and 1% w/v glucose) with glucose as limiting substrate has been found to be most suitable for hydrogen production. Individually E. cloacae clearly gave higher yield (276 ml H 2 / g COD reduced) using defined medium than the other two strains. There was no considerable difference in maximal yield of hydrogen from individual and combinatorial (1:1:1 consortium) modes suggesting that E. cloacae dominated in the consortia on defined medium. Contradictorily, B. coagulans gave better bio-hydrogen yield (37.16 ml H 2 /g COD consumed) than the other two strains when activated sewage sludge was used as substrate. The pretreatment of sludge included sterilization, (15% v/v) dilution and supplementation with 0.5%w/v glucose which was found to be essential to screen out the hydrogen consuming bacteria and ameliorate the hydrogenation. Considering (1:1:1) consortium as inoculum, interestingly yield of hydrogen was recorded to increase to 41.23 ml H 2 / g COD reduced inferring that in consortium, the substrate utilization was significantly higher. The hydrogen yield from pretreated sludge obtained in this study (35.54 ml H 2 g sludge) has been found to be distinctively higher than the earlier reports (8.1 - 16.9 ml H 2 /g sludge). However it was lower compared to the yield obtained from co-digestion of (83:17) food waste and sewage sludge (122 ml H 2 /g carbohydrate COD). Employing formulated microbial consortia for bio-hydrogen production from sewage sludge was an attempt to augment the hydrogen yield from sludge. (authors)

Feasibility of bio-hydrogen production from sewage sludge using defined microbial consortium

International Nuclear Information System (INIS)

Shireen Meher Kotay; Debabrata Das

2006-01-01

Biological hydrogen production potential of a defined microbial consortium consisting of three facultative anaerobes, Enterobacter cloacae IIT-BT 08, Citrobacter freundii IIT-BT L139 and Bacillus coagulans IIT-BT S1 was studied. In this investigation their individual and combinatorial H 2 production capabilities have been studied on defined media and pretreated sewage sludge. Defined medium, MYG (1% w/v Malt extract, 0.4% w/v yeast extract and 1% w/v glucose) with glucose as limiting substrate has been found to be most suitable for hydrogen production. Individually E. cloacae clearly gave higher yield (276 ml H 2 / g COD reduced) using defined medium than the other two strains. There was no considerable difference in maximal yield of hydrogen from individual and combinatorial (1:1:1 consortium) modes suggesting that E. cloacae dominated in the consortia on defined medium. Contradictorily, B. coagulans gave better bio-hydrogen yield (37.16 ml H 2 / g COD consumed) than the other two strains when activated sewage sludge was used as substrate. The pretreatment of sludge included sterilization, (15% v/v) dilution and supplementation with 0.5% w/v glucose which was found to be essential to screen out the hydrogen consuming bacteria and ameliorate the hydrogenation. Considering (1:1:1) consortium as inoculum, interestingly yield of hydrogen was recorded to increase to 41.23 ml H 2 / g COD reduced inferring that in consortium, the substrate utilization was significantly higher. The hydrogen yield from pretreated sludge obtained in this study (35.54 ml H 2 / g sludge) has been found to be distinctively higher than the earlier reports (8.1 - 16.9 ml H 2 / g sludge). However it was lower compared to the yield obtained from co-digestion of (83:17) food waste and sewage sludge (122 ml H 2 / g carbohydrate COD). Employing formulated microbial consortia for bio-hydrogen production from sewage sludge was an attempt to augment the hydrogen yield from sludge. (authors)

Bioconversion of cellulose into electrical energy in microbial fuel cells

Science.gov (United States)

Rismani-Yazdi, Hamid

In microbial fuel cells (MFCs), bacteria generate electricity by mediating the oxidation of organic compounds and transferring the resulting electrons to an anode electrode. The first objective of this study was to test the possibility of generating electricity with rumen microorganisms as biocatalysts and cellulose as the electron donor in two-compartment MFCs. Maximum power density reached 55 mW/m2 (1.5 mA, 313 mV) with cellulose as the electron donor. Cellulose hydrolysis and electrode reduction were shown to support the production of current. The electrical current was sustained for over two months with periodic cellulose addition. Clarified rumen fluid and a soluble carbohydrate mixture, serving as the electron donors, could also sustain power output. The second objective was to analyze the composition of the bacterial communities enriched in the cellulose-fed MFCs. Denaturing gradient gel electrophoresis of PCR amplified 16S rRNA genes revealed that the microbial communities differed when different substrates were used in the MFCs. The anode-attached and the suspended consortia were shown to be different within the same MFC. Cloning and analysis of 16S rRNA gene sequences indicated that the most predominant bacteria in the anode-attached consortia were related to Clostridium spp., while Comamonas spp. was abundant in the suspended consortia. The external resistance affects the characteristic outputs of MFCs by controlling the flow of electrons from the anode to the cathode. The third objective of this study was to determine the effect of various external resistances on power output and coulombic efficiency of cellulose-fed MFCs. Four external resistances (20, 249, 480, and 1000 ohms) were tested with a systematic approach of operating parallel MFCs independently at constant circuit loads for three months. A maximum power density of 66 mWm-2 was achieved by MFCs with 20 ohms circuit load, while MFCs with 249, 480 and1000 ohms external resistances produced 57

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

Energy Technology Data Exchange (ETDEWEB)

Kristine L. Lowe; Bill W. Bogan; Wendy R. Sullivan; Kristine Mila H. Cruz; Brigid M. Lamb; John J. Kilbane II

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 bacterial 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.

Bioaugmentation for Electricity Generation from Corn Stover Biomass Using Microbial Fuel Cells

KAUST Repository

Wang, Xin

2009-08-01

Corn stover is usually treated by an energy-intensive or expensive process to extract sugars for bioenergy production. However, it is possible to directly generate electricity from corn stover in microbial fuel cells (MFCs) through the addition of microbial consortia specifically acclimated for biomass breakdown. A mixed culture that was developed to have a high saccharification rate with corn stover was added to singlechamber, air-cathode MFCs acclimated for power production using glucose. The MFC produced a maximum power of 331 mW/ m 2 with the bioaugmented mixed culture and corn stover, compared to 510 mW/m2 using glucose. Denaturing gradient gel electrophoresis (DGGE) showed the communities continued to evolve on both the anode and corn stover biomass over 60 days, with several bacteria identified including Rhodopseudomonas palustris. The use of residual solids from the steam exploded corn stover produced 8% more power (406 mW/m2) than the raw corn stover. These results show that it is possible to directly generate electricity from waste corn stover in MFCs through bioaugmentation using naturally occurring bacteria. © 2009 American Chemical Society.

Pre-genomic, genomic and post-genomic study of microbial communities involved in bioenergy.

Science.gov (United States)

Rittmann, Bruce E; Krajmalnik-Brown, Rosa; Halden, Rolf U

2008-08-01

Microorganisms can produce renewable energy in large quantities and without damaging the environment or disrupting food supply. The microbial communities must be robust and self-stabilizing, and their essential syntrophies must be managed. Pre-genomic, genomic and post-genomic tools can provide crucial information about the structure and function of these microbial communities. Applying these tools will help accelerate the rate at which microbial bioenergy processes move from intriguing science to real-world practice.

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

Science.gov (United States)

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.

Characterization of corrosive bacterial consortia isolated from petroleum-product-transporting pipelines

Energy Technology Data Exchange (ETDEWEB)

Rajasekar, Aruliah; Ting, Yen-Peng [National Univ. of Singapore (Singapore). Dept. of Chemical and Biomolecular Engineering; Anandkumar, Balakrishnan [Sourashtra Coll., Madurai (India). Dept. of Biotechnology; Maruthamuthu, Sundaram [Central Electrochemical Research Inst., Karaikudi (India). Biocorrosion Group; Rahman, Pattanathu K.S.M. [Teesside Univ., Tees Valley (United Kingdom). Chemical and Bioprocess Engineering Group

2010-01-15

Microbiologically influenced corrosion is a problem commonly encountered in facilities in the oil and gas industries. The present study describes bacterial enumeration and identification in diesel and naphtha pipelines located in the northwest and southwest region in India, using traditional cultivation technique and 16S rDNA gene sequencing. Phylogenetic analysis of 16S rRNA sequences of the isolates was carried out, and the samples obtained from the diesel and naphtha-transporting pipelines showed the occurrence of 11 bacterial species namely Serratia marcescens ACE2, Bacillus subtilis AR12, Bacillus cereus ACE4, Pseudomonas aeruginosa AI1, Klebsiella oxytoca ACP, Pseudomonas stutzeri AP2, Bacillus litoralis AN1, Bacillus sp., Bacillus pumilus AR2, Bacillus carboniphilus AR3, and Bacillus megaterium AR4. Sulfate-reducing bacteria were not detected in samples from both pipelines. The dominant bacterial species identified in the petroleum pipeline samples were B. cereus and S. marcescens in the diesel and naphtha pipelines, respectively. Therefore, several types of bacteria may be involved in biocorrosion arising from natural biofilms that develop in industrial facilities. In addition, localized (pitting) corrosion of the pipeline steel in the presence of the consortia was observed by scanning electron microscopy analysis. The potential role of each species in biofilm formation and steel corrosion is discussed. (orig.)

Benzoate-driven dehalogenation of chlorinated ethenes in microbial cultures from a contaminated aquifer

Energy Technology Data Exchange (ETDEWEB)

Bunge, M.; Kleikemper, J.; Miniaci, C.; Duc, L.; Muusse, M.G.; Zeyer, J. [Swiss Federal Institute of Technology (ETH), Zurich (Switzerland). Inst. of Biogeochemistry and Pollutant Dynamics, Soil Biology; Hause, G. [Halle-Wittenberg Univ., Halle (Germany). Biocenter

2007-10-15

Microbial dehalogenation of tetrachloroethene (PCE) and cis-dichloroethene (cis-DCE) was studied in cultures from a continuous stirred tank reactor initially inoculated with aquifer material from a PCE-contaminated site. Cultures amended with hydrogen and acetate readily dechlorinated PCE and cis-DCE; however, this transformation was incomplete and resulted in the accumulation of chlorinated intermediates and only small amounts of ethene within 60 days of incubation. Conversely, microbial PCE and cis-DCE dechlorination in cultures with benzoate and acetate resulted in the complete transformation to ethene within 30 days. Community fingerprinting by denaturing gradient gel electrophoresis (DGGE) revealed the predominance of phylotypes closely affiliated with Desulfitobacterium, Dehalococcoides, and Syntrophus species. The Dehalococcoides culture VZ, obtained from small whitish colonies in cis-DCE dechlorinating agarose cultures, revealed an irregular cell diameter between 200 and 500 nm, and a spherical or biconcave disk-shaped morphology. These organisms were identified as responsible for the dechlorination of cis-DCE to ethene in the PCE-dechlorinating consortia, operating together with the Desulfitobacterium as PCE-to-cis-DCE dehalogenating bacterium and with a Syntrophus species as potential hydrogen-producing partner in cultures with benzoate. (orig.)

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

Directory of Open Access Journals (Sweden)

Mathew L Frankel

Full Text Available 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.

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

Science.gov (United States)

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.

[Predominant strains of polycyclic aromatic hydrocarbon-degrading consortia from deep sea of the Middle Atlantic Ridge].

Science.gov (United States)

Cui, Zhisong; Shao, Zongze

2009-07-01

In order to identify the predominant strains of polycyclic aromatic hydrocarbon (PAH)-degrading consortia harboring in sea water and surface sediment collected from deep sea of the Middle Atlantic Ridge. We employed enrichment method and spread-plate method to isolate cultivable bacteria and PAHs degraders from deep sea samples. Phylogenetic analysis was conducted by 16S rRNA gene sequencing of the bacteria. Then we analyzed the dominant bacteria in the PAHs-degrading consortia by denaturing gradient gel electrophoresis (DGGE) combined with DNA sequencing. Altogether 16 cultivable bacteria were obtained, including one PAHs degrader Novosphingobium sp. 4D. Phylogenetic analysis showed that strains closely related to Alcanivorax dieselolei NO1A (5/16) and Tistrella mobilis TISTR 1108T (5/16) constituted two biggest groups among the cultivable bacteria. DGGE analysis showed that strain 4L (also 4M and 4N, Alcanivorax dieselolei NO1A, 99.21%), 4D (Novosphingobium pentaromativorans US6-1(T), 97.07%) and 4B (also 4E, 4H and 4K, Tistrella mobilis TISTR 1108T, > 99%) dominated the consortium MC2D. While in consortium MC3CO, the predominant strains were strain 5C (also 5H, Alcanivorax dieselolei NO1A, > 99%), uncultivable strain represented by band 5-8 (Novosphingobium aromaticivorans DSM 12444T, 99.41%), 5J (Tistrella mobilis TISTR 1108T, 99.52%) and 5F (also 5G, Thalassospira lucentensis DSM 14000T, degrading consortia in sea water and surface sediment of Middle Atlantic Ridge deep sea, with Novosphingobium spp. as their main PAHs degraders.

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

Science.gov (United States)

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.

Microbial Biotreatment of Actual Textile Wastewater in a Continuous Sequential Rice Husk Biofilter and the Microbial Community Involved

Science.gov (United States)

Lindh, Markus V.; Pinhassi, Jarone; Welander, Ulrika

2017-01-01

Textile dying processes often pollute wastewater with recalcitrant azo and anthraquinone dyes. Yet, there is little development of effective and affordable degradation systems for textile wastewater applicable in countries where water technologies remain poor. We determined biodegradation of actual textile wastewater in biofilters containing rice husks by spectrophotometry and liquid chromatography mass spectrometry. The indigenous microflora from the rice husks consistently performed >90% decolorization at a hydraulic retention time of 67 h. Analysis of microbial community composition of bacterial 16S rRNA genes and fungal internal transcribed spacer (ITS) gene fragments in the biofilters revealed a bacterial consortium known to carry azoreductase genes, such as Dysgonomonas, and Pseudomonas and the presence of fungal phylotypes such as Gibberella and Fusarium. Our findings emphasize that rice husk biofilters support a microbial community of both bacteria and fungi with key features for biodegradation of actual textile wastewater. These results suggest that microbial processes can substantially contribute to efficient and reliable degradation of actual textile wastewater. Thus, development of biodegradation systems holds promise for application of affordable wastewater treatment in polluted environments. PMID:28114377

Microbial Biotreatment of Actual Textile Wastewater in a Continuous Sequential Rice Husk Biofilter and the Microbial Community Involved.

Directory of Open Access Journals (Sweden)

Jörgen Forss

Full Text Available Textile dying processes often pollute wastewater with recalcitrant azo and anthraquinone dyes. Yet, there is little development of effective and affordable degradation systems for textile wastewater applicable in countries where water technologies remain poor. We determined biodegradation of actual textile wastewater in biofilters containing rice husks by spectrophotometry and liquid chromatography mass spectrometry. The indigenous microflora from the rice husks consistently performed >90% decolorization at a hydraulic retention time of 67 h. Analysis of microbial community composition of bacterial 16S rRNA genes and fungal internal transcribed spacer (ITS gene fragments in the biofilters revealed a bacterial consortium known to carry azoreductase genes, such as Dysgonomonas, and Pseudomonas and the presence of fungal phylotypes such as Gibberella and Fusarium. Our findings emphasize that rice husk biofilters support a microbial community of both bacteria and fungi with key features for biodegradation of actual textile wastewater. These results suggest that microbial processes can substantially contribute to efficient and reliable degradation of actual textile wastewater. Thus, development of biodegradation systems holds promise for application of affordable wastewater treatment in polluted environments.

Corn silage in dairy cow diets to reduce ruminal methanogenesis: effects on the rumen metabolically active microbial communities.

Science.gov (United States)

Lettat, A; Hassanat, F; Benchaar, C

2013-08-01

Methane produced by the methanogenic Archaea that inhabit the rumen is a potent greenhouse gas and represents an energy loss for the animal. Although several strategies have been proposed to mitigate enteric CH4 production, little is known about the effects of dietary changes on the microbial consortia involved in ruminal methanogenesis. Thus, the current study aimed to examine how the metabolically active microbes are affected when dairy cows were fed diets with increasing proportions of corn silage (CS). For this purpose, 9 ruminally cannulated lactating dairy cows were used in a replicated 3 × 3 Latin square design and fed a total mixed ration (60:40 forage:concentrate ratio on a dry matter basis) with the forage portion being either alfalfa silage (0% CS), corn silage (100% CS), or a 50:50 mixture (50% CS). Enteric CH4 production was determined using respiration chambers and total rumen content was sampled for the determination of fermentation characteristics and molecular biology analyses (cDNA-based length heterogeneity PCR, quantitative PCR). The cDNA-based length heterogeneity PCR targeting active microbes revealed similar bacterial communities in cows fed 0% CS and 50% CS diets, whereas important differences were observed between 0% CS and 100% CS diets, including a reduction in the bacterial richness and diversity in cows fed 100% CS diet. As revealed by quantitative PCR, feeding the 100% CS diet increased the number of total bacteria, Prevotella spp., Archaea, and methanogenic activity, though it reduced protozoal number. Meanwhile, increasing the CS proportion in the diet increased propionate concentration but decreased ruminal pH, CH4 production (L/kg of dry matter intake), and concentrations of acetate and butyrate. Based on these microbial and fermentation changes, and because CH4 production was reduced by feeding 100% CS diet, this study shows that the use of cDNA-based quantitative PCR to estimate archaeal growth and activity is not reliable

Microbial community analysis of anaerobic reactors treating soft drink wastewater.

Directory of Open Access Journals (Sweden)

Takashi Narihiro

Full Text Available 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.

25 CFR 1000.46 - Which Tribes/Consortia may be selected to receive a negotiation grant?

Science.gov (United States)

2010-04-01

... 25 Indians 2 2010-04-01 2010-04-01 false Which Tribes/Consortia may be selected to receive a negotiation grant? 1000.46 Section 1000.46 Indians OFFICE OF THE ASSISTANT SECRETARY, INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR ANNUAL FUNDING AGREEMENTS UNDER THE TRIBAL SELF-GOVERNMENT ACT AMENDMENTS TO THE INDIAN SELF-DETERMINATION AND EDUCATION ACT...

Insights into microbial communities involved in mercury methylation in the San Francisco Bay estuary

Science.gov (United States)

Machak, C.; Francis, C. A.

2013-12-01

San Francisco Bay (SFB) estuary is the largest estuary on the western coast of the United States, draining a watershed covering more than one third of the state of California. Mercury (Hg) contamination in SFB, as a result of gold and mercury mining in the Coast Range and Sierra Nevada region, has been observed for at least 150 years. Additional sources of Hg contamination to SFB come from active oil refineries, manufacturing, and wastewater treatment plants in the area. Concentrations of methylmercury in the sediment at the time of sample collection for the present study ranged from 0.011-3.88 μg/kg (dry weight). At some sites, the concentration exceeds wetland toxicity limits, posing a threat to the health of the ecosystem and potentially endangering humans that use the estuary for food and recreation. This study attempts to understand the factors that control the transformation of Hg to methylmercury by microorganisms in aquatic sediments, where the majority of Hg methylation is known to occur. Under anoxic conditions, some sulfate- and iron-reducing bacteria have the capacity to transform Hg into methylmercury. To better understand the microbial communities involved in Hg methylation, an extensive library of 16S rRNA sequences was generated (via Illumina sequencing) from sediment samples at 20 sites throughout the SFB estuary. In addition to genomic data, we have access to a massive database of geochemical measurements made by the SFB Regional Monitoring Program at the sampling locations. These measurements show that our sediment samples have varying methylmercury concentrations and span gradients in porewater sulfate and Fe(III), which are the two known alternative electron acceptors for mercury-methylating anaerobic bacteria. The sampling sites also span gradients in other geochemical factors known to influence microbial community composition (and potentially Hg mercury methylation), such as available organic carbon, pH, and salinity. We will present the

Microbial Degradation of Polycyclic Aromatic Hydrocarbons and Characterization of Bacteria

Science.gov (United States)

Tikilili, P. V.; Chirwa, E. M. N.

2010-01-01

Biodegradation of polycyclic aromatic hydrocarbons was studied. Naphthalene was used as a model compound to represent these compounds. Low initial concentrations of naphthalene in a range of 30-60 mg/L were completely degraded after incubation for 15 hrs by consortia from a landfill soil while consortia from minewater took more that 29 hrs to reach complete degradation.

FY 1999 report on the results of the project on the industrial science technology R and D. Development of utilization technology of biological resources such as bioconsortium system (Development of the bioconsortium system utilization/production technology); 1999 nendo sangyo gijutsu kenkyu kaihatsu jigyo. Fukugou seibutsukei tou seibutsu shigen riyo gijutsu kaihatsu (Fukugou seibutsukei riyo seisan gijutsu no kaihatsu) seika hokokusho

Energy Technology Data Exchange (ETDEWEB)

NONE

2000-03-01

For the purpose of developing the functional substance production technology, petroleum degrading/cleaning technology and high-grade utilization technology of the unused petroleum fraction, study was conducted of the culture control technology in substance production and substance decomposition by bioconsortia, and the FY 1999 results were reported. As to the functional material production technology, study was made of the separation/culture technology, functional substance production technology using bioconsortia (control substance searching method in the ocean microbial consortia system, isolation of control substance/structure determination/separation of production bacteria, elucidation of the inter-species communication substance function, heightening of function of the production microbial consortia), etc. Concerning the effective degrading/cleaning technology of petroleum compounds, study was made of the molecular genetic analysis technology, histochemical analysis technology, analysis technology of the solvent resistance mechanism, bioconsortia analysis system technology, global environmental purification technology such as the effective decomposition of environmental pollutants, etc. Relating to the high-grade utilization technology of the unused petroleum fraction, study was made of the chemical analysis of the photolysis crude oil, selection of the decomposition microbial consortia, etc. (NEDO)

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

Science.gov (United States)

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.

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

Energy Technology Data Exchange (ETDEWEB)

Segre, Daniel [Boston Univ., MA (United States); Marx, Christopher J. [Univ. of Idaho, Moscow, ID (United States); Northen, Trent [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

2018-01-03

The goal of our project was to implement a pipeline for the systematic, computationally-driven study and optimization of microbial interactions and their effect on lignocellulose degradation and biofuel production. We specifically sought to design and construct artificial microbial consortia that could collectively degrade lignocellulose from plant biomass, and produce precursors of energy-rich biofuels. This project fits into the bigger picture goal of helping identify a sustainable strategy for the production of energy-rich biofuels that would satisfy the existing energy constraints and demand of our society. Based on the observation that complex natural microbial communities tend to be metabolically efficient and ecologically robust, we pursued the study of a microbial system in which the desired engineering function is achieved through division of labor across multiple microbial species. Our approach was aimed at bypassing the complexity of natural communities by establishing a rational approach to design small synthetic microbial consortia. Towards this goal, we combined multiple approaches, including computer modeling of ecosystem-level microbial metabolism, mass spectrometry of metabolites, genetic engineering, and experimental evolution. The microbial production of biofuels from lignocellulose is a complex, multi-step process. Microbial consortia are an ideal approach to consolidated bioprocessing: a community of microorganisms performs a wide variety of functions more efficiently and is more resilient to environmental perturbations than a microbial monoculture. Each organism we chose for this project addresses a specific challenge: lignin degradation (Pseudomonas putida); (hemi)cellulose degradation (Cellulomonas fimi); lignin degradation product demethoxylation (Methylobacterium spp); generation of biofuel lipid precursors (Yarrowia lipolytica). These organisms are genetically tractable, aerobic, and have been used in biotechnological applications

Microbial interactions involving sulfur bacteria : implications for the ecology and evolution of bacterial communities

NARCIS (Netherlands)

Overmann, J; van Gemerden, H

2000-01-01

A major goal of microbial ecology is the identification and characterization of those microorganisms which govern transformations in natural ecosystems. This review summarizes our present knowledge of microbial interactions in the natural sulfur cycle. Central to the discussion is the recent

Ceramic Proppant Design for In-situ Microbially Enhanced Methane Recovery

Energy Technology Data Exchange (ETDEWEB)

Sparks, Taylor D. [Univ. of Utah, Salt Lake City, UT (United States); Mclennan, John [Univ. of Utah, Salt Lake City, UT (United States); Fuertez, John [Univ. of Utah, Salt Lake City, UT (United States); Han, Kyu-Bum [Univ. of Utah, Salt Lake City, UT (United States)

2017-12-29

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 and 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 CH₄ and CO₂ 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

25 CFR 1000.63 - Under what circumstances may planning and negotiation grants be awarded to Tribes/Consortia?

Science.gov (United States)

2010-04-01

... AMENDMENTS TO THE INDIAN SELF-DETERMINATION AND EDUCATION ACT Other Financial Assistance for Planning and... 25 Indians 2 2010-04-01 2010-04-01 false Under what circumstances may planning and negotiation... may planning and negotiation grants be awarded to Tribes/Consortia? At the discretion of the Director...

Adquisición de publicaciones electrónicas en consorcios de bibliotecas Acquisition of electronic journals in libraries consortia

Directory of Open Access Journals (Sweden)

Silvia Contardi

2004-12-01

Full Text Available El incremento en los precios de las suscripciones a publicaciones periódicas en los últimos años, motivó el hecho de que las bibliotecas universitarias intentaran solucionar este problema, uniéndose y formando consorcios de bibliotecas, dónde, además de cooperar, compartir y facilitar el acceso a la información, se logra disminuir los costos de adquisición de las revistas científicas internacionales, permitiendo así, continuar apoyando las actividades de educación e investigación. Se destacan las distintas condiciones relacionadas con la compra en consorcios: características, ventajas, desventajas, licencias y modelos de precios. Se evalúa además la experiencia de tres consorcios, en Australia, Grecia y Brasil, que se basaron en este sistema cooperativo para adquirir sus revistas electrónicas.Because of the dramatic increment in journal subscriptions prices during the last few years, Academic libraries solved this problem by joining and creating library consortia, where, besides cooperation, sharing and access information facilities, they managed to decrease the acquisition costs of international scientific journals, allowing to continue supporting education and research activities. activities. Details of different conditions related to consortia purchase are highlighted: characteristics, advantages, disadvantages, licences and pricing models. It also evaluates experience of consortia from Australia, Greece and Brazil, which are based on this cooperation system to acquire their e-journals.

Thermochemical Wastewater Valorization via Enhanced Microbial Toxicity Tolerance

Energy Technology Data Exchange (ETDEWEB)

Beckham, Gregg T [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Thelhawadigedara, Lahiru Niroshan Jayakody [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Johnson, Christopher W [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Pleitner, Brenna P [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Cleveland, Nicholas S [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Michener, William E [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Olstad-Thompson, Jessica L [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Vardon, Derek R [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Whitham, Jason M. [Oak Ridge National Laboratory; Giannone, Richard J. [Oak Ridge National Laboratory; Klingeman, Dawn M. [Oak Ridge National Laboratory; Brown, Robert C. [Iowa State University; Brown, Steven D. [Oak Ridge National Laboratory; LanzaTech, Inc.; Hettich, Robert L. [Oak Ridge National Laboratory; Guss, Adam M. [Oak Ridge National Laboratory

2018-04-17

Thermochemical (TC) biomass conversion processes such as pyrolysis and liquefaction generate considerable amounts of wastewater, which often contains highly toxic compounds that are incredibly challenging to convert via standard wastewater treatment approaches such as anaerobic digestion. These streams represent a cost for TC biorefineries, and a potential valorization opportunity, if effective conversion methods are developed. The primary challenge hindering microbial conversion of TC wastewater is toxicity. In this study, we employ a robust bacterium, Pseudomonas putida, with TC wastewater streams to demonstrate that aldehydes are the most inhibitory compounds in these streams. Proteomics, transcriptomics, and fluorescence-based immunoassays of P. putida grown in a representative wastewater stream indicate that stress results from protein damage, which we hypothesize is a primary toxicity mechanism. Constitutive overexpression of the chaperone genes, groEL, groES, and clpB, in a genome-reduced P. putida strain improves the tolerance towards multiple TC wastewater samples up to 200-fold. Moreover, the concentration ranges of TC wastewater are industrially relevant for further bioprocess development for all wastewater streams examined here, representing different TC process configurations. Furthermore, we demonstrate proof-of-concept polyhydroxyalkanoate production from the usable carbon in an exemplary TC wastewater stream. Overall, this study demonstrates that protein quality control machinery and repair mechanisms can enable substantial gains in microbial tolerance to highly toxic substrates, including heterogeneous waste streams. When coupled to other metabolic engineering advances such as expanded substrate utilization and enhanced product accumulation, this study generally enables new strategies for biological conversion of highly-toxic, organic-rich wastewater via engineered aerobic monocultures or designer consortia.

Quantitative monitoring of microbial species during bioleaching of a copper concentrate

Directory of Open Access Journals (Sweden)

Sabrina Hedrich

2016-12-01

Full Text Available 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.

Science.gov (United States)

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.

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

Science.gov (United States)

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

The strategic trade-offs for beneficial open innovation : the case of ''open source'' consortia in mobile OS development

NARCIS (Netherlands)

Querbes, A.

2011-01-01

The trivialization of smartphones has given rise to an architectural reconfiguration of the mobile operating system innovation process. We have also seen the recent emergence of three ?open source? consortia: the Symbian and LiMo Foundations, and the Open Handset Alliance. In this exploratory paper,

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

Science.gov (United States)

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

“Playing Well With Others”: New Opportunities for Library Consortia

Directory of Open Access Journals (Sweden)

James Wiser

2012-05-01

Full Text Available Libraries everywhere are facing a complex array of budget cuts, staff retirements, technological disruption, etc. Many libraries may feel that they do not possess the organizational strength they once enjoyed, and as a result, an increasing number are seeking out ways to collaborate with fellow institutions in order to serve their stakeholders more effectively. The library consortium landscape, however, is rather confusing, and an almost endless series of acronyms reflect the array of options for consortial participation. This article attempts to describe the various kinds of library consortia that currently serve libraries, and offers suggestions on how and when to leverage the collective power of a library consortium in order to maximize the efforts of any single library..

Electricity generation using white and red wine lees in air cathode microbial fuel cells

Science.gov (United States)

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.

Microbial interactions: ecology in a molecular perspective.

Science.gov (United States)

Braga, Raíssa Mesquita; Dourado, Manuella Nóbrega; Araújo, Welington Luiz

2016-12-01

The microorganism-microorganism or microorganism-host interactions are the key strategy to colonize and establish in a variety of different environments. These interactions involve all ecological aspects, including physiochemical changes, metabolite exchange, metabolite conversion, signaling, chemotaxis and genetic exchange resulting in genotype selection. In addition, the establishment in the environment depends on the species diversity, since high functional redundancy in the microbial community increases the competitive ability of the community, decreasing the possibility of an invader to establish in this environment. Therefore, these associations are the result of a co-evolution process that leads to the adaptation and specialization, allowing the occupation of different niches, by reducing biotic and abiotic stress or exchanging growth factors and signaling. Microbial interactions occur by the transference of molecular and genetic information, and many mechanisms can be involved in this exchange, such as secondary metabolites, siderophores, quorum sensing system, biofilm formation, and cellular transduction signaling, among others. The ultimate unit of interaction is the gene expression of each organism in response to an environmental (biotic or abiotic) stimulus, which is responsible for the production of molecules involved in these interactions. Therefore, in the present review, we focused on some molecular mechanisms involved in the microbial interaction, not only in microbial-host interaction, which has been exploited by other reviews, but also in the molecular strategy used by different microorganisms in the environment that can modulate the establishment and structuration of the microbial community. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Replacement of benthic communities in two Neoproterozoic-Cambrian subtropical-to-temperate rift basins, High Atlas and Anti-Atlas, Morocco

Science.gov (United States)

Clausen, Sébastien; Álvaro, J. Javier; Zamora, Samuel

2014-10-01

The ‘Cambrian explosion’ is often introduced as a major shift in benthic marine communities with a coeval decline of microbial consortia related to the diversification of metazoans and development of bioturbation (‘Agronomic Revolution’). Successive community replacements have been reported along with ecosystem diversification and increase in guild complexity from Neoproterozoic to Cambrian times. This process is recorded worldwide but with regional diachroneities, some of them directly controlled by the geodynamic conditions of sedimentary basins. The southern High Atlas and Anti-Atlas of Morocco record development of two rifts, Tonian (?) - early Cryogenian and latest Ediacarian-Cambrian in age, separated by the onset of the Pan-African Orogeny. This tectonically controlled, regional geodynamic change played a primary control on pattern and timing of benthic ecosystem replacements. Benthic communities include microbial consortia, archaeocyathan-thromboid reefal complexes, chancelloriid-echinoderm-sponge meadows, and deeper offshore echinoderm-dominated communities. Microbial consortia appeared in deeper parts of the Tonian (?) - early Cryogenian fluvio-deltaic progradational rift sequences, lacustrine environments of the Ediacaran Volcanic Atlasic Chain (Ouarzazate Supergroup) and the Ediacaran-Cambrian boundary interval, characterized by the peritidal-dominated Tifnout Member (Adoudou Formation). They persisted and were largely significant until Cambrian Age 3, as previous restricted marine conditions precluded the immigration of shelly metazoans in the relatively shallow epeiric parts of the Cambrian Atlas Rift. Successive Cambrian benthic communities were replaced as a result of distinct hydrodynamic and substrate conditions, which allow identification of biotic (e.g., antagonistic relationships between microbial consortia and echinoderms, and taphonomic feedback patterns in chancelloriid-echinoderm-sponge meadows) and abiotic (e.g., rifting

FY 1998 report on the results of the development of utilization technology of biological resources such as bioconsortia. Development of the bioconsortia system utilization/production technology; 1998 nendo fukugo seibutsukei nado seibutsu shigen riyo gijutsu kaihatsu seika hokokusho. Fukugo seibutsukei riyo seisan gijutsu no kaihatsu

Energy Technology Data Exchange (ETDEWEB)

NONE

1999-03-01

For the purpose of establishing the technology to use high grade functions of the bioconsortia system, the R and D were conducted, and the FY 1998 results were summed up. As to the study of functional material producing technology, screening of the 2400 strains owned by Marine Biotechnology Institute was conducted using reporter strain, and about 400 strains of homoserine lactone producing bacteria which are interbiological information convey substances were obtained. Concerning the effective decomposing/purifying technology of petroleum products, study of petroleum decomposition analysis technology was finished in the development of culture/control technology of petroleum decomposition microbial consortia constitutive bacteria. Relating to the analysis of the petroleum decomposition microbial consortia, changes in the bacteria population at the site of the heavy oil pollution accident on the Sea of Japan were investigated for the past one year by the PCR/DGGE method. It was found out that levels of the oil pollution in ocean could be assessed by measuring the concentration of Alcanivorax. As to the technology for highly utilizing unused petroleum fractions, conducted were the chemical analysis of photolytic crude oil, selection of the decomposition microbial consortia, etc. (NEDO)

Characterization of Microbial Fuel Cells at Microbially and Electrochemically Meaningful Time scales

KAUST Repository

Ren, Zhiyong; Yan, Hengjing; Wang, Wei; Mench, Matthew M.; Regan, John M.

2011-01-01

The variable biocatalyst density in a microbial fuel cell (MFC) anode biofilm is a unique feature of MFCs relative to other electrochemical systems, yet performance characterizations of MFCs typically involve analyses at electrochemically relevant

Enzymatic bioremediation of polyaromatic hydrocarbons by fungal consortia enriched from petroleum contaminated soil and oil seeds.

Science.gov (United States)

Balaji, V; Arulazhagan, P; Ebenezer, P

2014-05-01

The present study focuses on fungal strains capable of secreting extracellular enzymes by utilizing hydrocarbons present in the contaminated soil. Fungal strains were enriched from petroleum hydrocarbons contaminated soil samples collected from Chennai city, India. The potential fungi were isolated and screened for their enzyme secretion such as lipase, laccase, peroxidase and protease and also evaluated fungal enzyme mediated PAHs degradation. Total, 21 potential PAHs degrading fungi were isolated from PAHs contaminated soil, which belongs to 9 genera such as Aspergillus, Curvularia, Drechslera, Fusarium, Lasiodiplodia, Mucor Penicillium, Rhizopus, Trichoderma, and two oilseed-associated fungal genera such as Colletotrichum and Lasiodiplodia were used to test their efficacy in degradation of PAHs in polluted soil. Maximum lipase production was obtained with P. chrysogenum, M. racemosus and L. theobromae VBE1 under optimized cultural condition, which utilized PAHs in contaminated soil as sole carbon source. Fungal strains, P. chrysogenum, M. racemosus and L. theobromae VBE1, as consortia, used in the present study were capable of degrading branched alkane isoprenoids such as pristine (C17) and pyrene (C18) present in PAHs contaminated soil with high lipase production. The fungal consortia acts as potential candidate for bioremediation of PAHs contaminated environments.

Bioavailability of hydrocarbons to bacterial consortia during Triton X-100 mediated biodegradation in aqueous media.

Science.gov (United States)

Pęziak, Daria; Piotrowska, Aleksandra; Marecik, Roman; Lisiecki, Piotr; Woźniak, Marta; Szulc, Alicja; Ławniczak, Łukasz; Chrzanowski, Łukasz

2013-01-01

The aim of our study was to investigate the effect of Triton X-100 on the biodegradation efficiency of hexadecane and phenanthrene carried out by two bacterial consortia. It was established that the tested consortia were not able to directly uptake compounds closed in micelles. It was observed that in micellar systems the nonionic synthetic surfactant was preferentially degraded (the degradation efficiency of Triton X-100 after 21 days was 70% of the initial concentration - 500 mg/l), followed by a lesser decomposition of hydrocarbon released from the micelles (30% for hexadecane and 20% for phenanthrene). However, when hydrocarbons were used as the sole carbon source, 70% of hexadecane and 30% of phenanthrene were degraded. The degradation of the surfactant did not contribute to notable shifts in bacterial community dynamics, as determined by Real-Time PCR. The obtained results suggest that if surfactant-supplementation is to be used as an integral part of a bioremediation process, then possible bioavailability decrease due to entrapment of the contaminant into surfactant micelles should also be taken into consideration, as this phenomenon may have a negative impact on the biodegradation efficiency. Surfactant-induced mobilization of otherwise recalcitrant hydrocarbons may contribute to the spreading of contaminants in the environment and prevent their biodegradation.

Ammonium removal using algae-bacteria consortia: the effect of ammonium concentration, algae biomass, and light.

Science.gov (United States)

Jia, Huijun; Yuan, Qiuyan

2018-04-01

In this study, the effects of ammonium nitrogen concentration, algae biomass concentration, and light conditions (wavelength and intensity) on the ammonium removal efficiency of algae-bacteria consortia from wastewater were investigated. The results indicated that ammonium concentration and light intensity had a significant impact on nitrification. It was found that the highest ammonia concentration (430 mg N/L) in the influent resulted in the highest ammonia removal rate of 108 ± 3.6 mg N/L/days, which was two times higher than the influent with low ammonia concentration (40 mg N/L). At the lowest light intensity of 1000 Lux, algae biomass concentration, light wavelength, and light cycle did not show a significant effect on the performance of algal-bacterial consortium. Furthermore, the ammonia removal rate was approximately 83 ± 1.0 mg N/L/days, which was up to 40% faster than at the light intensity of 2500 Lux. It was concluded that the algae-bacteria consortia can effectively remove nitrogen from wastewater and the removal performance can be stabilized and enhanced using the low light intensity of 1000 Lux that is also a cost-effective strategy.

Recent Advances in the Study of Marine Microbial Biofilm: From the Involvement of Quorum Sensing in Its Production up to Biotechnological Application of the Polysaccharide Fractions

Directory of Open Access Journals (Sweden)

Paola Di Donato

2016-05-01

Full Text Available The present review will explore the most relevant findings on marine microbial biofilm, with particular attention towards its polysaccharide fraction, namely exopolysaccharide (EPS. EPSs of microbial origin are ubiquitous in nature, possess unique properties and can be isolated from the bacteria living in a variety of habitats, including fresh water or marine environments, extreme environments or different soil ecosystems. These biopolymers have many application in the field of biotechnology. Several studies showed that the biofilm formation is closely related to quorum sensing (QS systems, which is a mechanism relying on the production of small molecules defined as “autoinducers” that bacteria release in the surrounding environment where they accumulate. In this review, the involvement of microbial chemical communication, by QS mechanism, in the formation of marine biofilm will also be discussed.

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

Science.gov (United States)

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.

Exploring the Plant–Microbe Interface by Profiling the Surface-Associated Proteins of Barley Grains

DEFF Research Database (Denmark)

Sultan, Abida; Andersen, Birgit; Svensson, Birte

2016-01-01

Cereal grains are colonized by a microbial community that actively interacts with the plant via secretion of various enzymes, hormones, and metabolites. Microorganisms decompose plant tissues by a collection of depolymerizing enzymes, including β-1,4-xylanases, that are in turn inhibited by plant...... xylanase inhibitors. To gain insight into the importance of the microbial consortia and their interaction with barley grains, we used a combined gel-based (2-DE coupled to MALDI-TOF-TOF MS) and gel-free (LC–MS/MS) proteomics approach complemented with enzyme activity assays to profile the surface......-associated proteins and xylanolytic activities of two barley cultivars. The surface-associated proteome was dominated by plant proteins with roles in defense and stress-responses, while the relatively less abundant microbial (bacterial and fungal) proteins were involved in cell-wall and polysaccharide degradation...

Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery

Science.gov (United States)

Bernard, Guillaume; Pathmanathan, Jananan S; Lannes, Romain; Lopez, Philippe; Bapteste, Eric

2018-01-01

Abstract Microbes are the oldest and most widespread, phylogenetically and metabolically diverse life forms on Earth. However, they have been discovered only 334 years ago, and their diversity started to become seriously investigated even later. For these reasons, microbial studies that unveil novel microbial lineages and processes affecting or involving microbes deeply (and repeatedly) transform knowledge in biology. Considering the quantitative prevalence of taxonomically and functionally unassigned sequences in environmental genomics data sets, and that of uncultured microbes on the planet, we propose that unraveling the microbial dark matter should be identified as a central priority for biologists. Based on former empirical findings of microbial studies, we sketch a logic of discovery with the potential to further highlight the microbial unknowns. PMID:29420719

Consórcios Intermunicipais de Saúde: o caso do Paraná, Brasil Inter-municipal health consortia: the case of Paraná State, Brazil

Directory of Open Access Journals (Sweden)

Sônia Cristina Stefano Nicoletto

2005-02-01

Full Text Available Os Consórcios Intermunicipais de Saúde (CIS surgiram no âmbito do SUS no final da década de 80. Os gestores municipais aderiram a essa estratégia, visando potencializar as ações e serviços de saúde oferecidos à população. Esta pesquisa analisou o perfil dos CIS do Paraná, Brasil, focalizando a assistência médica especializada. Os dados são dos relatórios sobre os consórcios realizados pelo Conselho Estadual de Saúde e dos questionários enviados para os vinte CIS. Os parâmetros utilizados foram a Portaria nº 1.101 e dados publicados do perfil do sistema de saúde do Paraná em 2000. Dos 399 municípios paranaenses, 81,5% integram CIS. Os especialistas são cedidos pelos municípios (4,4%, Estado (13,6%, união (12,8%, ou contratados pelo próprio CIS (69,2%. A oferta de consultas especializadas não é suficiente ou sua distribuição é feita de forma inadequada. Há falha no mecanismo de referência e contra-referência. O CIS é um instrumento viável para ampliar e potencializar a capacidade dos municípios em ofertar consultas especializadas; porém, há necessidade de ser utilizado com critérios, planejamento e adequado sistema de referência e contra-referência.Inter-municipal health consortia emerged in Brazil's Unified National Health System (SUS policy in the late 1980s. Municipal health administrators adhered to this strategy with the aim of upgrading health services supplied to the population. This research analyzes the profile of such consortia in Paraná State, focusing on specialized medical care. Data were obtained from reports by the State Health Council and questionnaires sent to all 20 existing municipal health consortia. Governmental Decree no. 1,101 and data published in 2000 on the profile of the health system in Paraná were used as references. Of the 399 municipalities in Paraná State, 81.5% have joined municipal consortia. Specialists are allocated by municipalities (4.4%, the State government (13

Realizing Student, Faculty, and Institutional Outcomes at Scale: Institutionalizing Undergraduate Research, Scholarship, and Creative Activity within Systems and Consortia

Science.gov (United States)

Malachowski, Mitchell; Osborn, Jeffrey M.; Karukstis, Kerry K.; Ambos, Elizabeth L.

2015-01-01

This chapter reviews the evidence for the effectiveness of undergraduate research as a student, faculty, and institutional success pathway, and provides the context for the Council on Undergraduate Research's support for developing and enhancing undergraduate research in systems and consortia. The chapter also provides brief introductions to each…

25 CFR 1000.53 - Can Tribes/Consortia that receive advance planning grants also apply for a negotiation grant?

Science.gov (United States)

2010-04-01

... 25 Indians 2 2010-04-01 2010-04-01 false Can Tribes/Consortia that receive advance planning grants also apply for a negotiation grant? 1000.53 Section 1000.53 Indians OFFICE OF THE ASSISTANT SECRETARY, INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR ANNUAL FUNDING AGREEMENTS UNDER THE TRIBAL SELF-GOVERNMENT ACT AMENDMENTS TO THE INDIAN...

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

Science.gov (United States)

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.

Rapid establishment of phenol- and quinoline-degrading consortia driven by the scoured cake layer in an anaerobic baffled ceramic membrane bioreactor.

Science.gov (United States)

Wang, Wei; Wang, Shun; Ren, Xuesong; Hu, Zhenhu; Yuan, Shoujun

2017-11-01

Although toxic and refractory organics, such as phenol and quinoline, are decomposed by anaerobic bacteria, the establishment of specific degrading consortia is a relatively slow process. An anaerobic membrane bioreactor allows for complete biomass retention that can aid the establishment of phenol- and quinoline-degrading consortia. In this study, the anaerobic digestion of phenol (500 mg L -1 ) and quinoline (50 mg L -1 ) was investigated using an anaerobic baffled ceramic membrane bioreactor (ABCMBR). The results showed that, within 30 days, 99% of phenol, 98% of quinoline and 88% of chemical oxygen demand (COD) were removed. The substrate utilisation rates of the cake layer for phenol and quinoline, and specific methanogenic activity of the cake layer, were 7.58 mg phenol g -1  mixed liquor volatile suspended solids (MLVSS) day -1 , 8.23 mg quinoline g -1  MLVSS day -1 and 0.55 g COD CH4  g -1  MLVSS day -1 , respectively. The contribution of the cake layer to the removals of phenol and quinoline was extremely underestimated because the uncounted scoured cake layer was disregarded. Syntrophus was the key population for phenol and quinoline degradation, and it was more abundant in the cake layer than in the bulk sludge. The highly active scattered cake layer sped up the establishment of phenol- and quinoline-degrading consortia in the ABCMBR.

Configuration of biological wastewater treatment line and influent composition as the main factors driving bacterial community structure of activated sludge

OpenAIRE

Jaranowska, Paulina; Cydzik-Kwiatkowska, Agnieszka; Zieli?ska, Magdalena

2013-01-01

The structure of microbial consortia in wastewater treatment facilities is a resultant of environmental conditions created by the operational parameters of the purification process. In the research, activated sludge from nine Polish wastewater treatment plants (WWTPs) was investigated at a molecular level to determine the impact of the complexity of biological treatment line and the influent composition on the species structure and the diversity of bacterial consortia. The community fingerpri...

The Microbial DNA Index System (MiDIS): A tool for microbial pathogen source identification

Energy Technology Data Exchange (ETDEWEB)

Velsko, S. P. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2010-08-09

The microbial DNA Index System (MiDIS) is a concept for a microbial forensic database and investigative decision support system that can be used to help investigators identify the sources of microbial agents that have been used in a criminal or terrorist incident. The heart of the proposed system is a rigorous method for calculating source probabilities by using certain fundamental sampling distributions associated with the propagation and mutation of microbes on disease transmission networks. This formalism has a close relationship to mitochondrial and Y-chromosomal human DNA forensics, and the proposed decision support system is somewhat analogous to the CODIS and SWGDAM mtDNA databases. The MiDIS concept does not involve the use of opportunistic collections of microbial isolates and phylogenetic tree building as a basis for inference. A staged approach can be used to build MiDIS as an enduring capability, beginning with a pilot demonstration program that must meet user expectations for performance and validation before evolving into a continuing effort. Because MiDIS requires input from a a broad array of expertise including outbreak surveillance, field microbial isolate collection, microbial genome sequencing, disease transmission networks, and laboratory mutation rate studies, it will be necessary to assemble a national multi-laboratory team to develop such a system. The MiDIS effort would lend direction and focus to the national microbial genetics research program for microbial forensics, and would provide an appropriate forensic framework for interfacing to future national and international disease surveillance efforts.

Microbial diversity and their roles in the vinegar fermentation process.

Science.gov (United States)

Li, Sha; Li, Pan; Feng, Feng; Luo, Li-Xin

2015-06-01

Vinegar is one of the oldest acetic acid-diluted solution products in the world. It is produced from any fermentable sugary substrate by various fermentation methods. The final vinegar products possess unique functions, which are endowed with many kinds of compounds formed in the fermentation process. The quality of vinegar is determined by many factors, especially by the raw materials and microbial diversity involved in vinegar fermentation. Given that metabolic products from the fermenting strains are directly related to the quality of the final products of vinegar, the microbial diversity and features of the dominant strains involved in different fermentation stages should be analyzed to improve the strains and stabilize fermentation. Moreover, although numerous microbiological studies have been conducted to examine the process of vinegar fermentation, knowledge about microbial diversity and their roles involved in fermentation is still fragmentary and not systematic enough. Therefore, in this review, the dominant microorganism species involved in the stages of alcoholic fermentation and acetic acid fermentation of dissimilar vinegars were summarized. We also summarized various physicochemical properties and crucial compounds in disparate types of vinegar. Furthermore, the merits and drawbacks of vital fermentation methods were generalized. Finally, we described in detail the relationships among microbial diversity, raw materials, fermentation methods, physicochemical properties, compounds, functionality, and final quality of vinegar. The integration of this information can provide us a detailed map about the microbial diversity and function involved in vinegar fermentation.

Strategies and Methodologies for Developing Microbial Detoxification Systems to Mitigate Mycotoxins

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Yan Zhu

2017-04-01

Full Text Available 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.

Microbial processes in coastal pollution

International Nuclear Information System (INIS)

Capone, D.G.; Bauer, J.E.

1992-01-01

In this chapter, the authors describe the nature and range of some of the interactions that can occur between the microbiota and environmental contaminants in coastal areas. The implications of such interactions are also discussed. Pollutant types include inorganic nutrients, heavy metals, bulk organics, organic contaminants, pathogenic microorganisms and microbial pollutants. Both the effects of pollutants such as petroleum hydrocarbons on natural microbial populations and the mitigation of contaminant effects by complexation and biodegradation are considered. Finally, several areas of emerging concerns are presented that involve a confluence of biogeochemistry, microbial ecology and applied and public health microbiology. These concerns range in relevance from local/regional to oceanic/global scales. 308 ref

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

Science.gov (United States)

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

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

Science.gov (United States)

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.

Pyrosequencing reveals high-temperature cellulolytic microbial consortia in Great Boiling Spring after in situ lignocellulose enrichment.

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Joseph P Peacock

Full Text Available To characterize high-temperature cellulolytic microbial communities, two lignocellulosic substrates, ammonia fiber-explosion-treated corn stover and aspen shavings, were incubated at average temperatures of 77 and 85°C in the sediment and water column of Great Boiling Spring, Nevada. Comparison of 109,941 quality-filtered 16S rRNA gene pyrosequences (pyrotags from eight enrichments to 37,057 quality-filtered pyrotags from corresponding natural samples revealed distinct enriched communities dominated by phylotypes related to cellulolytic and hemicellulolytic Thermotoga and Dictyoglomus, cellulolytic and sugar-fermenting Desulfurococcales, and sugar-fermenting and hydrogenotrophic Archaeoglobales. Minor enriched populations included close relatives of hydrogenotrophic Thermodesulfobacteria, the candidate bacterial phylum OP9, and candidate archaeal groups C2 and DHVE3. Enrichment temperature was the major factor influencing community composition, with a negative correlation between temperature and richness, followed by lignocellulosic substrate composition. This study establishes the importance of these groups in the natural degradation of lignocellulose at high temperatures and suggests that a substantial portion of the diversity of thermophiles contributing to consortial cellulolysis may be contained within lineages that have representatives in pure culture.

Microbial xanthophylls.

Science.gov (United States)

Bhosale, Prakash; Bernstein, Paul S

2005-09-01

Xanthophylls are oxygenated carotenoids abundant in the human food supply. Lutein, zeaxanthin, and cryptoxanthin are major xanthophyll carotenoids in human plasma. The consumption of these xanthophylls is directly associated with reduction in the risk of cancers, cardiovascular disease, age-related macular degeneration, and cataract formation. Canthaxanthin and astaxanthin also have considerable importance in aquaculture for salmonid and crustacean pigmentation, and are of commercial interest for the pharmaceutical and food industries. Chemical synthesis is a major source for the heavy demand of xanthophylls in the consumer market; however, microbial producers also have potential as commercial sources. In this review, we discuss the biosynthesis, commercial utility, and major microbial sources of xanthophylls. We also present a critical review of current research and technologies involved in promoting microbes as potential commercial sources for mass production.

New concepts of microbial treatment processes for the nitrogen removal: effect of protein and amino acids degradation.

Science.gov (United States)

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.

Final Report Systems Level Analysis of the Function and Adaptive Responses of Methanogenic Consortia

Energy Technology Data Exchange (ETDEWEB)

Lovley, Derek R. [Univ. of Massachusetts, Amherst, MA (United States)

2015-03-09

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 in 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

Interconnection of Key Microbial Functional Genes for Enhanced Benzo[a]pyrene Biodegradation in Sediments by Microbial Electrochemistry.

Science.gov (United States)

Yan, Zaisheng; He, Yuhong; Cai, Haiyuan; Van Nostrand, Joy D; He, Zhili; Zhou, Jizhong; Krumholz, Lee R; Jiang, He-Long

2017-08-01

Sediment microbial fuel cells (SMFCs) can stimulate the degradation of polycyclic aromatic hydrocarbons in sediments, but the mechanism of this process is poorly understood at the microbial functional gene level. Here, the use of SMFC resulted in 92% benzo[a]pyrene (BaP) removal over 970 days relative to 54% in the controls. Sediment functions, microbial community structure, and network interactions were dramatically altered by the SMFC employment. Functional gene analysis showed that c-type cytochrome genes for electron transfer, aromatic degradation genes, and extracellular ligninolytic enzymes involved in lignin degradation were significantly enriched in bulk sediments during SMFC operation. Correspondingly, chemical analysis of the system showed that these genetic changes resulted in increases in the levels of easily oxidizable organic carbon and humic acids which may have resulted in increased BaP bioavailability and increased degradation rates. Tracking microbial functional genes and corresponding organic matter responses should aid mechanistic understanding of BaP enhanced biodegradation by microbial electrochemistry and development of sustainable bioremediation strategies.

Zinc bioaccumulation by microbial consortium isolated from nickel smelter sludge disposal site

Directory of Open Access Journals (Sweden)

Kvasnová Simona

2017-06-01

Full Text Available Heavy metal pollution is one of the most important environmental issues of today. Bioremediation by microorganisms is one of technologies extensively used for pollution treatment. In this study, we investigated the heavy metal resistance and zinc bioaccumulation by microbial consortium isolated from nickel sludge disposal site near Sereď (Slovakia. The composition of consortium was analyzed based on MALDI-TOF MS of cultivable bacteria and we have shown that the consortium was dominated by bacteria of genus Arthrobacter. While consortium showed very good growth in the zinc presence, it was able to remove only 15 % of zinc from liquid media. Selected members of consortia have shown lower growth rates in the zinc presence but selected isolates have shown much higher bioaccumulation abilities compared to whole consortium (up to 90 % of zinc removal for NH1 strain. Bioremediation is frequently accelerated through injection of native microbiota into a contaminated area. Based on data obtained in this study, we can conclude that careful selection of native microbiota could lead to the identification of bacteria with increased bioaccumulation abilities.

Strong linkage between active microbial communities and microbial carbon usage in a deglaciated terrain of the High Arctic

Science.gov (United States)

Kim, M.; Gyeong, H. R.; Lee, Y. K.

2017-12-01

Soil microorganisms play pivotal roles in ecosystem development and carbon cycling in newly exposed glacier forelands. However, little is known about carbon utilization pattern by metabolically active microbes over the course of ecosystem succession in these nutrient-poor environments. We investigated RNA-based microbial community dynamics and its relation to microbial carbon usage along the chronosequence of a High Arctic glacier foreland. Among microbial taxa surveyed (bacteria, archaea and fungi), bacteria are among the most metabolically active taxa with a dominance of Cyanobacteria and Actinobacteria. There was a strong association between microbial carbon usage and active Actinobacterial communities, suggesting that member of Actinobacteria are actively involved in organic carbon degradation in glacier forelands. Both bacterial community and microbial carbon usage are converged towards later stage of succession, indicating that the composition of soil organic carbon plays important roles in structuring bacterial decomposer communities during ecosystem development.

Anaerobic degradation of benzene by enriched consortia with humic acids as terminal electron acceptors

Energy Technology Data Exchange (ETDEWEB)

Cervantes, Francisco J., E-mail: fjcervantes@ipicyt.edu.mx [Division de Ciencias Ambientales, Instituto Potosino de Investigacion Cientifica y Tecnologica (IPICyT), Camino a la Presa San Jose 2055, Col. Lomas 4a. Seccion, San Luis Potosi, SLP, 78216 Mexico (Mexico); Mancilla, Ana Rosa; Toro, E. Emilia Rios-del [Division de Ciencias Ambientales, Instituto Potosino de Investigacion Cientifica y Tecnologica (IPICyT), Camino a la Presa San Jose 2055, Col. Lomas 4a. Seccion, San Luis Potosi, SLP, 78216 Mexico (Mexico); Alpuche-Solis, Angel G.; Montoya-Lorenzana, Lilia [Division de Biologia Molecular, Instituto Potosino de Investigacion Cientifica y Tecnologica (IPICyT), Camino a la Presa San Jose 2055, Col. Lomas 4a. Seccion, San Luis Potosi, SLP, 78216 Mexico (Mexico)

2011-11-15

Highlights: {yields} Enriched consortia were able to couple the anaerobic degradation of benzene to the reduction of humic acids. {yields} Electron-equivalents derived from anaerobic benzene oxidation were highly recovered as reduced humic acids. {yields} Several species from classes {beta}-, {delta}- and {gamma}-Proteobacteria were enriched during the anaerobic degradation of benzene. - Abstract: The anaerobic degradation of benzene coupled to the reduction of humic acids (HA) was demonstrated in two enriched consortia. Both inocula were able to oxidize benzene under strict anaerobic conditions when the humic model compound, anthraquinone-2,6-disulfonate (AQDS), was supplied as terminal electron acceptor. An enrichment culture originated from a contaminated soil was also able to oxidize benzene linked to the reduction of highly purified soil humic acids (HPSHA). In HPSHA-amended cultures, 9.3 {mu}M of benzene were degraded, which corresponds to 279 {+-} 27 micro-electron equivalents ({mu}Eq) L{sup -1}, linked to the reduction of 619 {+-} 81 {mu}Eq L{sup -1} of HPSHA. Neither anaerobic benzene oxidation nor reduction of HPSHA occurred in sterilized controls. Anaerobic benzene oxidation did not occur in soil incubations lacking HPSHA. Furthermore, negligible reduction of HPSHA occurred in the absence of benzene. The enrichment culture derived from this soil was dominated by two {gamma}-Proteobacteria phylotypes. A benzene-degrading AQDS-reducing enrichment originated from a sediment sample showed the prevalence of different species from classes {beta}-, {delta}- and {gamma}-Proteobacteria. The present study provides clear quantitative demonstration of anaerobic degradation of benzene coupled to the reduction of HA.

Anaerobic degradation of benzene by enriched consortia with humic acids as terminal electron acceptors

International Nuclear Information System (INIS)

Cervantes, Francisco J.; Mancilla, Ana Rosa; Toro, E. Emilia Rios-del; Alpuche-Solis, Angel G.; Montoya-Lorenzana, Lilia

2011-01-01

Highlights: → Enriched consortia were able to couple the anaerobic degradation of benzene to the reduction of humic acids. → Electron-equivalents derived from anaerobic benzene oxidation were highly recovered as reduced humic acids. → Several species from classes β-, δ- and γ-Proteobacteria were enriched during the anaerobic degradation of benzene. - Abstract: The anaerobic degradation of benzene coupled to the reduction of humic acids (HA) was demonstrated in two enriched consortia. Both inocula were able to oxidize benzene under strict anaerobic conditions when the humic model compound, anthraquinone-2,6-disulfonate (AQDS), was supplied as terminal electron acceptor. An enrichment culture originated from a contaminated soil was also able to oxidize benzene linked to the reduction of highly purified soil humic acids (HPSHA). In HPSHA-amended cultures, 9.3 μM of benzene were degraded, which corresponds to 279 ± 27 micro-electron equivalents (μEq) L -1 , linked to the reduction of 619 ± 81 μEq L -1 of HPSHA. Neither anaerobic benzene oxidation nor reduction of HPSHA occurred in sterilized controls. Anaerobic benzene oxidation did not occur in soil incubations lacking HPSHA. Furthermore, negligible reduction of HPSHA occurred in the absence of benzene. The enrichment culture derived from this soil was dominated by two γ-Proteobacteria phylotypes. A benzene-degrading AQDS-reducing enrichment originated from a sediment sample showed the prevalence of different species from classes β-, δ- and γ-Proteobacteria. The present study provides clear quantitative demonstration of anaerobic degradation of benzene coupled to the reduction of HA.

Air-dust-borne associations of phototrophic and hydrocarbon-utilizing microorganisms: promising consortia in volatile hydrocarbon bioremediation.

Science.gov (United States)

Al-Bader, Dhia; Eliyas, Mohamed; Rayan, Rihab; Radwan, Samir

2012-11-01

Aquatic and terrestrial associations of phototrophic and heterotrophic microorganisms active in hydrocarbon bioremediation have been described earlier. The question arises: do similar consortia also occur in the atmosphere? Dust samples at the height of 15 m were collected from Kuwait City air, and analyzed microbiologically for phototrophic and heterotrophic hydrocarbon-utilizing microorganisms, which were subsequently characterized according to their 16S rRNA gene sequences. The hydrocarbon utilization potential of the heterotrophs alone, and in association with the phototrophic partners, was measured quantitatively. The chlorophyte Gloeotila sp. and the two cyanobacteria Nostoc commune and Leptolyngbya thermalis were found associated with dust, and (for comparison) the cynobacteria Leptolyngbya sp. and Acaryochloris sp. were isolated from coastal water. All phototrophic cultures harbored oil vapor-utilizing bacteria in the magnitude of 10(5) g(-1). Each phototrophic culture had its unique oil-utilizing bacteria; however, the bacterial composition in Leptolyngbya cultures from air and water was similar. The hydrocarbon-utilizing bacteria were affiliated with Acinetobacter sp., Aeromonas caviae, Alcanivorax jadensis, Bacillus asahii, Bacillus pumilus, Marinobacter aquaeolei, Paenibacillus sp., and Stenotrophomonas maltophilia. The nonaxenic cultures, when used as inocula in batch cultures, attenuated crude oil in light and dark, and in the presence of antibiotics and absence of nitrogenous compounds. Aqueous and diethyl ether extracts from the phototrophic cultures enhanced the growth of the pertinent oil-utilizing bacteria in batch cultures, with oil vapor as a sole carbon source. It was concluded that the airborne microbial associations may be effective in bioremediating atmospheric hydrocarbon pollutants in situ. Like the aquatic and terrestrial habitats, the atmosphere contains dust-borne associations of phototrophic and heterotrophic hydrocarbon

Spectral Induced Polarization (SIP) monitoring during Microbial Enhanced Oil Recovery (MEOR)

Science.gov (United States)

Heenan, J. W.; Ntarlagiannis, D.; Slater, L. D.

2010-12-01

Jeffrey Heenan, Dimitrios Ntarlagiannis, Lee Slater Department of Earth and Environmental Sciences, Rutgers University, Newark NJ Microbial Enhanced Oil Recovery (MEOR) is an established, cost effective, method for enhancing tertiary oil recovery. Although not commonly used for shallow heavy oils, it could be a viable alternative since it can offer sustainable economic recovery and minimal environmental impact. A critical component of successful MEOR treatments is accurate, real time monitoring of the biodegradation processes resulting from the injection of microbial communities into the formation; results of recent biogeophysical research suggest that minimally-invasive geophysical methods could significantly contribute to such monitoring efforts. Here we present results of laboratory experiments, to assess the sensitivity of the spectral induced polarization method (SIP) to MEOR treatments. We used heavy oil, obtained from a shallow oilfield in SW Missouri, to saturate three sand columns. We then followed common industry procedures,and used a commercially available microbial consortia, to treat the oil columns. The active MEOR experiments were performed in duplicate while a control column maintained similar conditions, without promoting microbial activity and oil degradation. We monitored the SIP signatures, between 0.001 Hz and 1000 Hz, for a period of six months. To support the geophysical measurements we also monitored common geochemical parameters, including pH, Eh and fluid conductivity, and collected weekly fluid samples from the outflow and inflow for further analysis; fluid samples were analyzed to confirm that microbes actively degraded the heavy oils in the column while destructive analysis of the solid materials was performed upon termination of the experiment. Preliminary analysis of the results suggests that SIP is sensitive to MEOR processes. In both inoculated columns we recorded an increase in the low frequency polarization with time; measureable

Systems Level Dissection of Anaerobic Methane Cycling: Quantitative Measurements of Single Cell Ecophysiology, Genetic Mechanisms, and Microbial Interactions

Energy Technology Data Exchange (ETDEWEB)

Orphan, Victoria [California Inst. of Technology (CalTech), Pasadena, CA (United States); Tyson, Gene [University of Queensland, Brisbane Australia; Meile, Christof [University of Georgia, Athens, Georgia; McGlynn, Shawn [California Inst. of Technology (CalTech), Pasadena, CA (United States); Yu, Hang [California Inst. of Technology (CalTech), Pasadena, CA (United States); Chadwick, Grayson [California Inst. of Technology (CalTech), Pasadena, CA (United States); Marlow, Jeffrey [California Inst. of Technology (CalTech), Pasadena, CA (United States); Trembath-Reichert, Elizabeth [California Inst. of Technology (CalTech), Pasadena, CA (United States); Dekas, Anne [California Inst. of Technology (CalTech), Pasadena, CA (United States); Hettich, Robert [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Pan, Chongle [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Ellisman, Mark [University of California San Diego; Hatzenpichler, Roland [California Inst. of Technology (CalTech), Pasadena, CA (United States); Skennerton, Connor [California Inst. of Technology (CalTech), Pasadena, CA (United States); Scheller, Silvan [California Inst. of Technology (CalTech), Pasadena, CA (United States)

2017-12-25

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.

Consortia for Electronic Library Provision in Belgium

Directory of Open Access Journals (Sweden)

Julien Van Borm

2001-07-01

Full Text Available E-libraries just like the former paper-based libraries will become increasingly essential and indispensable tools in research and education. Library consortia seem to be the way to get e-libraries started all over the world. However, it is unclear yet whether this is going to be a longlasting workable model. The Belgian research libraries follow the international pattern and are rapidly becoming hybrid libraries especially in business, science, applied sciences and biomedicine (the STM disciplines. Still they have large paper bound collections on board and no library is willing to replace these in the near future by a purely electronic collection of journals. The fear of losing the content and thus the „raison d’être“ of the library and the concern for users not yet familiar with e-information sources are the cornerstone for a prudent, yet conservative policy. Increasingly e-information and e-journals are being taken on board. Paper and electronic go side by side in new hybrid libraries partly also due to the market policy set by the publishers in combining paper and electronic in an attempt to keep or improve the annual turnover reached during the past paper period. The transition from paper to electronic occurred in Belgium somewhat later than in other Western European countries. This confirms the position of Belgium often taking up an average position in Western Europe.

Road MAPs to engineer host microbiomes.

Science.gov (United States)

Oyserman, Ben O; Medema, Marnix H; Raaijmakers, Jos M

2017-12-02

Microbiomes contribute directly or indirectly to host health and fitness. Thus far, investigations into these emergent traits, referred to here as microbiome-associated phenotypes (MAPs), have been primarily qualitative and taxonomy-driven rather than quantitative and trait-based. We present the MAPs-first approach, a theoretical and experimental roadmap that involves quantitative profiling of MAPs across genetically variable hosts and subsequent identification of the underlying mechanisms. We outline strategies for developing 'modular microbiomes'-synthetic microbial consortia that are engineered in concert with the host genotype to confer different but mutually compatible MAPs to a single host or host population. By integrating host and microbial traits, these strategies will facilitate targeted engineering of microbiomes to the benefit of agriculture, human/animal health and biotechnology. Copyright © 2017. Published by Elsevier Ltd.

A novel membrane bioreactor inoculated with symbiotic sludge bacteria and algae: Performance and microbial community analysis.

Science.gov (United States)

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.

Fiscal 1997 research report on development of use technology of bio-resources such as complex biosystem (Development of use and production technologies of complex biosystems); 1997 nendo fukugo seibutsukei nado seibutsu shigen riyo gijutsu kaihatsu seika hokokusho (fukugo seibutsukei riyo seisan gijutsu no kaihatsu)

Energy Technology Data Exchange (ETDEWEB)

NONE

1998-03-01

This report summarizes the fiscal 1997 research results on production technology of functional materials, and the research study result for utilizing substance production and decomposition by complex biosystem for industries. For detecting technique of microorganisms in soil, staining by CFDA-AM was suitable, and allowed visualization of sulfate- reducing bacteria during culture. For research on functional analysis technology, study was made on atomic force microscope technology to detect microorganisms in environment and observe their fine structures. For research on detection, separation and cultivation technology of difficult-to-culture microorganisms, a molecular genetic analysis method of microbial communities and a determination method of their viability were selected. For functional substance production technology, study was made on technical utilization of bioflocculant produced by microbial consortia as environment-friendly oil removal reagent, and on gene transfer control in microbial consortia. For the research study for the project, survey was made on useful substances produced by complex biosystem. (NEDO)

Synthetic Klebsiella pneumoniae-Shewanella oneidensis Consortium Enables Glycerol-Fed High-Performance Microbial Fuel Cells.

Science.gov (United States)

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.

Bioremediation of 1,2-dichloroethane contaminated groundwater: Microcosm and microbial diversity studies

International Nuclear Information System (INIS)

Wang, S.Y.; Kuo, Y.C.; Huang, Y.Z.; Huang, C.W.; Kao, C.M.

2015-01-01

In this study, the effectiveness of bioremediating 1,2-dichloroethane (DCA)-contaminated groundwater under different oxidation–reduction processes was evaluated. Microcosms were constructed using indigenous bacteria and activated sludge as the inocula and cane molasses and a slow polycolloid-releasing substrate (SPRS) as the primary substrates. Complete DCA removal was obtained within 30 days under aerobic and reductive dechlorinating conditions. In anaerobic microcosms with sludge and substrate addition, chloroethane, vinyl chloride, and ethene were produced. The microbial communities and DCA-degrading bacteria in microcosms were characterized by 16S rRNA-based denatured-gradient-gel electrophoresis profiling and nucleotide sequence analyses. Real-time polymerase chain reaction was applied to evaluate the variations in Dehalococcoides spp. and Desulfitobacterium spp. Increase in Desulfitobacterium spp. indicates that the growth of Desulfitobacterium might be induced by DCA. Results indicate that DCA could be used as the primary substrate under aerobic conditions. The increased ethene concentrations imply that dihaloelimination was the dominate mechanism for DCA biodegradation. - Highlights: • DCA can be used as the primary substrate and degraded by the indigenous microbial consortia. • Reductive dechlorination of DCA can be enhanced by the supplement of substrates and sludge. • Dihaloelimination is the dominant mechanism for DCA dechlorination and ethene is the end product. • SPRS can serve as the primary substrate and creates anaerobic conditions for DCA dechlorination. • Reductive dechlorination is a feasible option for DCA-contaminated groundwater remediation. - DCA can serve as the primary substrate and degraded by indigenous bacteria aerobically. Dihaloelimination is the dominant mechanism and ethene is the end product via dechlorination

Similar PAH fate in anaerobic digesters inoculated with three microbial communities accumulating either volatile fatty acids or methane.

Science.gov (United States)

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

Similar PAH fate in anaerobic digesters inoculated with three microbial communities accumulating either volatile fatty acids or methane.

Directory of Open Access Journals (Sweden)

Florence Braun

Full Text Available 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

Microbially-reduced graphene scaffolds to facilitate extracellular electron transfer in microbial fuel cells.

Science.gov (United States)

Yuan, Yong; Zhou, Shungui; Zhao, Bo; Zhuang, Li; Wang, Yueqiang

2012-07-01

A one-pot method is exploited by adding graphene oxide (GO) and acetate into an microbial fuel cell (MFC) in which GO is microbially reduced, leading to in situ construction of a bacteria/graphene network in the anode. The obtained microbially reduced graphene (MRG) exhibits comparable conductivity and physical characteristics to the chemically reduced graphene. Electrochemical measurements reveal that the number of exoelectrogens involved in extracellular electron transfer (EET) to the solid electrode, increases due to the presence of graphene scaffolds, and the EET is facilitated in terms of electron transfer kinetics. As a result, the maximum power density of the MFC is enhanced by 32% (from 1440 to 1905 mW m(-2)) and the coulombic efficiency is improved by 80% (from 30 to 54%). The results demonstrate that the construction of the bacteria/graphene network is an effective alternative to improve the MFC performance. Copyright © 2012 Elsevier Ltd. All rights reserved.

Denitrification coupled with methane anoxic oxidation and microbial community involved identification

Directory of Open Access Journals (Sweden)

Renata Medici Frayne Cuba

2011-02-01

Full Text Available In this work, the biological denitrification associated with anoxic oxidation of methane and the microbial diversity involved were studied. Kinetic tests for nitrate (NO3- and nitrite (NO2- removal and methane uptake were carried out in 100 mL batch reactors incubated in a shaker (40 rpm at 30 ºC. Denitrificant/methanotrophic biomass was taken from a laboratory scale reactor fed with synthetic nitrified substrates (40 mgN L-1 of NO3- and subsequently NO2- and methane as carbon source. Results obtained from nitrate removal followed a first order reaction, presenting a kinetic apparent constant (kNO3 of 0.0577±0.0057d-1. Two notable points of the denitrification rate (0.12gNO3--N g-1 AVS d-1 and 0.07gNO3--N g-1 AVS d-1 were observed in the beginning and on the seventh day of operation. When nitrite was added as an electron acceptor, denitrification rates were improved, presenting an apparent kinetic constant (kNO2 of 0.0722±0.0044d-1, a maximum denitrification rate of 0.6gNO2--N g-1AVS d-1, and minimum denitrification rate of 0.1gNO2--N g-1AVS d-1 at the beginning and end of the test, respectively. Endogenous material supporting denitrification and methane concentration dissolved in the substrate was discarded from the control experiments in the absence of methane and seed, respectively. Methylomonas sp. was identified in the reactors fed with nitrate and nitrite as well as uncultured bacterium.

Two Pilot Plant Reactors Designed for the In Situ Bioremediation of Chlorobenzene-contaminated Ground Water: Hydrogeological and Chemical Characteristics and Bacterial Consortia

Energy Technology Data Exchange (ETDEWEB)

Vogt, Carsten, E-mail: vogt@umb.ufz.de; Alfreider, Albin [UFZ Centre for Environmental Research, Department of Environmental Microbiology (Germany); Lorbeer, Helmut [University of Technology Dresden, Institute of Waste Management and Contaminated Site Treatment (Germany); Ahlheim, Joerg; Feist, Bernd [UFZ Centre for Environmental Research, Department of Industrial and Mining Landscapes (Germany); Boehme, Olaf [GFE GmbH Halle (Germany); Weiss, Holger [UFZ Centre for Environmental Research, Department of Industrial and Mining Landscapes (Germany); Babel, Wolfgang; Wuensche, Lothar [UFZ Centre for Environmental Research, Department of Environmental Microbiology (Germany)

2002-05-15

The SAFIRA in situ pilot plant in Bitterfeld, Saxonia-Anhalt, Germany, currently serves as the test site for eight different in situ approaches to remediate anoxic chlorobenzene (CB)-contaminated ground water. Two reactors, both filled with original lignite-containing aquifer material, are designed for the microbiological in situ remediation of the ground water by the indigenous microbial consortia. In this study, the hydrogeological, chemical and microbiological conditions of the in flowing ground water and reactor filling material are presented,in order to establish the scientific basis for the start of the bioremediation process itself. The reactors were put into operation in June 1999. In the following, inflow CB concentrations in the ground water varied between 22 and 33 mg L{sup -1}; a chemical steady state for CB in both reactors was reached after 210 till 260 days operation time. The sediments were colonized by high numbers of aerobic, iron-reducing and denitrifying bacteria, as determined after 244 and 285 days of operation time. Furthermore, aerobic CB-degrading bacteria were detected in all reactor zones. Comparative sequence analysis of16S rDNA gene clone libraries suggest the dominance of Proteobacteria (Comamonadaceae, Alcaligenaceae, Gallionella group, Acidithiobacillus) and members of the class of low G+C gram-positive bacteria in the reactor sediments. In the inflowing ground water, sequences with phylogenetic affiliation to sulfate-reducing bacteria and sequences not affiliated with the known phyla of Bacteria, were found.

Two Pilot Plant Reactors Designed for the In Situ Bioremediation of Chlorobenzene-contaminated Ground Water: Hydrogeological and Chemical Characteristics and Bacterial Consortia

International Nuclear Information System (INIS)

Vogt, Carsten; Alfreider, Albin; Lorbeer, Helmut; Ahlheim, Joerg; Feist, Bernd; Boehme, Olaf; Weiss, Holger; Babel, Wolfgang; Wuensche, Lothar

2002-01-01

The SAFIRA in situ pilot plant in Bitterfeld, Saxonia-Anhalt, Germany, currently serves as the test site for eight different in situ approaches to remediate anoxic chlorobenzene (CB)-contaminated ground water. Two reactors, both filled with original lignite-containing aquifer material, are designed for the microbiological in situ remediation of the ground water by the indigenous microbial consortia. In this study, the hydrogeological, chemical and microbiological conditions of the in flowing ground water and reactor filling material are presented,in order to establish the scientific basis for the start of the bioremediation process itself. The reactors were put into operation in June 1999. In the following, inflow CB concentrations in the ground water varied between 22 and 33 mg L -1 ; a chemical steady state for CB in both reactors was reached after 210 till 260 days operation time. The sediments were colonized by high numbers of aerobic, iron-reducing and denitrifying bacteria, as determined after 244 and 285 days of operation time. Furthermore, aerobic CB-degrading bacteria were detected in all reactor zones. Comparative sequence analysis of16S rDNA gene clone libraries suggest the dominance of Proteobacteria (Comamonadaceae, Alcaligenaceae, Gallionella group, Acidithiobacillus) and members of the class of low G+C gram-positive bacteria in the reactor sediments. In the inflowing ground water, sequences with phylogenetic affiliation to sulfate-reducing bacteria and sequences not affiliated with the known phyla of Bacteria, were found

Implementation of Complex Biological Logic Circuits Using Spatially Distributed Multicellular Consortia

Science.gov (United States)

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

Mixed microalgae consortia growth under higher concentration of CO2 from unfiltered coal fired flue gas: Fatty acid profiling and biodiesel production.

Science.gov (United States)

Aslam, Ambreen; Thomas-Hall, Skye R; Manzoor, Maleeha; Jabeen, Faiza; Iqbal, Munawar; Uz Zaman, Qamar; Schenk, Peer M; Asif Tahir, M

2018-02-01

Biodiesel is produced by transesterification of fatty acid methyl esters (FAME) from oleaginous microalgae feedstock. Biodiesel fuel properties were studied and compared with biodiesel standards. Qualitative analysis of FAME was done while cultivating mixed microalgae consortia under three concentrations of coal fired flue gas (1%, 3.0% and 5.5% CO 2 ). Under 1% CO 2 concentration (flue gas), the FAME content was 280.3 μg/mL, whereas the lipid content was 14.03 μg/mL/D (day). Both FAMEs and lipid contents were low at other CO 2 concentrations (3.0 and 5.5%). However, mixed consortia in the presence of phosphate buffer and flue gas (PB + FG) showed higher saturated fatty acids (SFA) (36.28%) and unsaturated fatty acids (UFA) (63.72%) versus 5.5% CO 2 concentration, which might be responsible for oxidative stability of biodiesel. Subsequently, higher cetane number (52) and low iodine value (136.3 gI 2 /100 g) biodiesel produced from mixed consortia (PB + FG) under 5.5% CO 2 along with 50 mM phosphate buffer were found in accordance with European (EN 14214) standard. Results revealed that phosphate buffer significantly enhanced the biodiesel quality, but reduced the FAME yield. This study intended to develop an integrated approach for significant improvement in biodiesel quality under surplus phosphorus by utilizing waste flue gas (as CO 2 source) using microalgae. The CO 2 sequestration from industrial flue gas not only reduced greenhouse gases, but may also ensure the sustainable and eco-benign production of biodiesel. Copyright © 2018. Published by Elsevier B.V.

Harmonization of Glutamic Acid Decarboxylase and Islet Antigen-2 Autoantibody Assays for National Institute of Diabetes and Digestive and Kidney Diseases Consortia

OpenAIRE

Bonifacio, Ezio; Yu, Liping; Williams, Alastair K.; Eisenbarth, George S.; Bingley, Polly J.; Marcovina, Santica M.; Adler, Kerstin; Ziegler, Anette G.; Mueller, Patricia W.; Schatz, Desmond A.; Krischer, Jeffrey P.; Steffes, Michael W.; Akolkar, Beena

2010-01-01

Background/Rationale: Autoantibodies to islet antigen-2 (IA-2A) and glutamic acid decarboxylase (GADA) are markers for diagnosis, screening, and measuring outcomes in National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) consortia studies. A harmonization program was established to increase comparability of results within and among these studies.

Designed cell consortia as fragrance-programmable analog-to-digital converters.

Science.gov (United States)

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.

Comparative biodegradation of HDPE and LDPE using an indigenously developed microbial consortium.

Science.gov (United States)

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.

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.

Science.gov (United States)

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.

Microbial hydrocarbon degradation - bioremediation of oil spills

Energy Technology Data Exchange (ETDEWEB)

Atlas, R M [Louisville Univ., KY (United States). Dept. of Biology

1991-01-01

Bioremediation has become a major method employed in restoration of oil-polluted environments that makes use of natural microbial biodegradative activities. Bioremediation of petroleum pollutants overcomes the factors limiting rates of microbial hydrocarbon biodegradation. Often this involves using the enzymatic capabilities of the indigenous hydrocarbon-degrading microbial populations and modifying environmental factors, particularly concentrations of molecular oxygen, fixed forms of nitrogen and phosphate to achieve enhanced rates of hydrocarbon biodegradation. Biodegradation of oily sludges and bioremediation of oil-contaminated sites has been achieved by oxygen addition-e.g. by tilling soils in landfarming and by adding hydrogen peroxide or pumping oxygen into oiled aquifers along with addition of nitrogen- and phosphorous-containing fertilizers. The success of seeding oil spills with microbial preparations is ambiguous. Successful bioremediation of a major marine oil spill has been achieved based upon addition of nitrogen and phosphorus fertilizers. (author).

Improving nitrogen utilization efficiency of aquaponics by introducing algal-bacterial consortia.

Science.gov (United States)

Fang, Yingke; Hu, Zhen; Zou, Yina; Zhang, Jian; Zhu, Zhuoran; Zhang, Jianda; Nie, Lichao

2017-12-01

Aquaponics is a promising technology combining aquaculture with hydroponics. In this study, algal-bacterial consortia were introduced into aquaponics, i.e., algal-bacterial based aquaponics (AA), to improve the nitrogen utilization efficiency (NUE) of aquaponics. The results showed that the NUE of AA was 13.79% higher than that of media-based aquaponics (MA). In addition, higher NO 3 - removal by microalgae assimilation led to better water quality in AA, which made up for the deficiencies of poor aquaponic management of nitrate. As a result of lower NO 3 - concentrations and dramatically higher dissolved oxygen (DO) concentrations caused by microalgae photosynthesis in the photobioreactor, the N 2 O emission of AA was 89.89% lower than that of MA, although nosZ gene abundance in MA's hydroponic bed was approximately 30 times over that in AA. Considering the factors mentioned above, AA would improve the sustainability of aquaponics and have a good application foreground. Copyright © 2017 Elsevier Ltd. All rights reserved.

Who is healthy? Aspects to consider when including healthy volunteers in QST-based studies- a consensus statement by the EUROPAIN and NEUROPAIN consortia

DEFF Research Database (Denmark)

Gierthmühlen, Janne; Enax-Krumova, Elena K; Attal, Nadine

2015-01-01

studies, so that results are less likely to be false negative or false positive due to subject related factors.The EUROPAIN and NEUROPAIN consortia aimed to define factors influencing the variability in selection of healthy subjects in QST-based studies before the start of both projects and to give...

The impact of post-fire salvage logging on microbial nitrogen cyclers in Mediterranean forest soil.

Science.gov (United States)

Pereg, Lily; Mataix-Solera, Jorge; McMillan, Mary; García-Orenes, Fuensanta

2018-04-01

Forest fires are a regular occurrence in the Mediterranean basin. High severity fires and post-fire management can affect biological, chemical and physical properties of soil, including the composition and abundance of soil microbial communities. Salvage logging is a post-fire management strategy, which involves the removal of burnt wood from land after a fire. The main objective of this work was to evaluate the impact of post-fire salvage logging and microaggregation on soil microbial communities, specifically on the abundance of nitrogen cyclers and, thus, the potential of the soil for microbial nitrogen cycling. The abundance of nitrogen cyclers was assessed by quantification of microbial nitrogen cycling genes in soil DNA, including nifH (involved in nitrogen fixation), nirS/K and nosZ (involved in denitrification), amoA-B and amoA-Arch (involved in bacterial and archaeal nitrification, respectively). It was demonstrated that salvage logging reduced bacterial load post-fire when compared to tree retention control and resulted in significant changes to the abundance of functional bacteria involved in nitrogen cycling. Microbial gene pools involved in various stages of the nitrogen cycle were larger in control soil than in soil subjected to post-fire salvage logging and were significantly correlated with organic matter, available phosphorous, nitrogen and aggregate stability. The microaggregate fraction of the soil, which has been associated with greater organic carbon, was shown to be a hotspot for nitrogen cyclers particularly under salvage logging. The impact of post-fire management strategies on soil microbial communities needs to be considered in relation to maintaining ecosystem productivity, resilience and potential impact on climate change. Copyright © 2017 Elsevier B.V. All rights reserved.

Aerobic microbial dolomite at the nanometer scale : Implications for the geologic record

NARCIS (Netherlands)

Sánchez-Román, Mónica; Vasconcelos, Crisógono; Schmid, Thomas; Dittrich, Maria; McKenzie, Judith A.; Zenobi, Renato; Rivadeneyra, Maria A.

2008-01-01

Microbial experiments are the only proven approach to produce experimental dolomite under Earth's surface conditions. Although microbial metabolisms are known to induce dolomite precipitation by favoring dolomite growth kinetics, the involvement of microbes in the dolomite nucleation process is

Fourier transform-infrared spectroscopic methods for microbial ecology: analysis of bacteria, bacteria-polymer mixtures and biofilms

Science.gov (United States)

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.

Microbial Biofilm as a Smart Material

DEFF Research Database (Denmark)

Garde, Christian; Welch, Martin; Ferkinghoff-Borg, Jesper

2015-01-01

Microbial biofilm colonies will in many cases form a smart material capable of responding to external threats dependent on their size and internal state. The microbial community accordingly switches between passive, protective, or attack modes of action. In order to decide which strategy to employ......, it is essential for the biofilm community to be able to sense its own size. The sensor designed to perform this task is termed a quorum sensor, since it only permits collective behaviour once a sufficiently large assembly of microbes have been established. The generic quorum sensor construct involves two genes...

Structure and diversity of ground mesofauna inUlmus and Populus consortia in the industrial areas of mining and smelting complex of krivyi rig basin

Directory of Open Access Journals (Sweden)

V. V. Kachinskaya

2010-05-01

Full Text Available The structure and biological diversity of ground mesofauna on a consortium level of organisation of ecosystems are considered. Indicators of structural organisation and biodiversity of ground mesofauna were analised in Ulmus and Populus consortia in the conditions of industrial territories of mining and smelting complex of Krivyi Rig Basin. It is established that taxonomical structure of ground mesofauna is characterised by insignificant number and quantity of taxonomical groups. Prevalence of hortobionts and herpetobionts in morpho-ecological structure of the community testifies to their attachment to consortium’s determinants and influence of steppe climate on its structure. Dominance of phytophages and polyphages in trophic structure is caused by a combination of consortium determinants specificity and «a zone source» of the fauna formations. The structural organisation of ground mesofauna in consortia of Ulmus and Populus in the conditions of industrial sites is characterised by simplified taxonomical structure with low biodiversity at all levels.

Contribution of Bicarbonate Assimilation to Carbon Pool Dynamics in the Deep Mediterranean Sea and Cultivation of Actively Nitrifying and CO2-Fixing Bathypelagic Prokaryotic Consortia.

Science.gov (United States)

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

Contribution of Bicarbonate Assimilation to Carbon Pool Dynamics in the Deep Mediterranean Sea and Cultivation of Actively Nitrifying and CO2-Fixing Bathypelagic Prokaryotic Consortia

Science.gov (United States)

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

Catabolic and regulatory systems in Shewanella oneidensis MR-1 involved in electricity generation in microbial fuel cells

Directory of Open Access Journals (Sweden)

Atsushi eKouzuma

2015-06-01

Full Text Available Shewanella oneidensis MR-1 is a facultative anaerobe that respires using a variety of inorganic and organic compounds. MR-1 is also capable of utilizing extracellular solid materials, including anodes in microbial fuel cells (MFCs, as electron acceptors, thereby enabling electricity generation. As MFCs have the potential to generate electricity from biomass waste and wastewater, MR-1 has been extensively studied to identify the molecular systems that are involved in electricity generation in MFCs. These studies have demonstrated the importance of extracellular electron-transfer pathways that electrically connect the quinone pool in the cytoplasmic membrane to extracellular electron acceptors. Electricity generation is also dependent on intracellular catabolic pathways that oxidize electron donors, such as lactate, and regulatory systems that control the expression of genes encoding the components of catabolic and electron-transfer pathways. In addition, recent findings suggest that cell-surface polymers, e.g., exopolysaccharides, and secreted chemicals, which function as electron shuttles, are also involved in electricity generation. Despite these advances in our knowledge on the extracellular electron-transfer processes in MR-1, further efforts are necessary to fully understand the underlying intra- and extra-cellular molecular systems for electricity generation in MFCs. We suggest that investigating how MR-1 coordinates these systems to efficiently transfer electrons to electrodes and conserve electrochemical energy for cell proliferation is important for establishing the biological bases for MFCs.

Consortia Building: A Handshake and a Smile, Island Style

Directory of Open Access Journals (Sweden)

Patricia Cutright

2017-09-01

Full Text Available In the evaluation of consortia and what constitutes these entities the discussion runs the gamut. From small, loosely knit groups who are interested in cooperation for the sake of improving services to large membership driven organizations addressing multiple interests, all recognize the benefits of partnerships. The Federated States of Micronesia are located in the western Pacific Ocean and cover 3.2 million square miles. Throughout this scattering of small islands exists an enthusiastic library community of staff and users that have changed the outlook of libraries since 1991. Motivated by the collaboratvie ef orts of this group, a project has unfolded over the past year that will further enhance library services through staff training and education while utilizing innovative technology. In assessing the library needs of the region this group crafted the document "The Federated States of Micronesia Library Services Plan, 1999-2003," which coalesces the concepts, goals, and priorities put forward by a broad-based contingency of librarians. The compilation of the plan and its implementation demonstrate an understanding of the issues and exhibit the ingenuity, creativity, and willingness to solve problems on a grand scale addressing the needs of all libraries in this vast Pacific region.

Biological nitrate removal from synthetic wastewater using a fungal ...

African Journals Online (AJOL)

2007-04-02

-stage ... grass, instead of non-autoclaved grass containing natural microbial consortia, as sup- ... 25ºC within a 20 ℓ plastic bag, along with a 1 ℓ conical flask ... of cellulases and xylanases – the two major hydrolytic enzyme.

Microbial diversity of western Canadian subsurface coal beds and methanogenic coal enrichment cultures

Energy Technology Data Exchange (ETDEWEB)

Penner, Tara J.; Foght, Julia M. [Department of Biological Sciences, University of Alberta, Edmonton, Alberta (Canada); Budwill, Karen [Carbon and Energy Management, Alberta Innovates-Technology Futures, 250 Karl Clark Road, Edmonton, Alberta (Canada)

2010-05-01

Coalbed methane is an unconventional fuel source associated with certain coal seams. Biogenic methane can comprise a significant portion of the gas found in coal seams, yet the role of microbes in methanogenesis in situ is uncertain. The purpose of this study was to detect and identify major bacterial and archaeal species associated with coal sampled from sub-bituminous methane-producing coal beds in western Canada, and to examine the potential for methane biogenesis from coal. Enrichment cultures of coal samples were established to determine how nutrient amendment influenced the microbial community and methane production in the laboratory. 16S rRNA gene clone libraries were constructed using DNA extracted and amplified from uncultured coal samples and from methanogenic coal enrichment cultures. Libraries were screened using restriction fragment length polymorphism, and representative clones were sequenced. Most (> 50%) of the bacterial sequences amplified from uncultured coal samples were affiliated with Proteobacteria that exhibit nitrate reduction, nitrogen fixation and/or hydrogen utilization activities, including Pseudomonas, Thauera and Acidovorax spp., whereas enrichment cultures were dominated by Bacteroidetes, Clostridia and/or Lactobacillales. Archaeal 16S rRNA genes could not be amplified from uncultured coal, suggesting that methanogens are present in coal below the detection levels of our methods. However, enrichment cultures established with coal inocula produced significant volumes of methane and the archaeal clone libraries were dominated by sequences closely affiliated with Methanosarcina spp. Enrichment cultures incubated with coal plus organic nutrients produced more methane than either nutrient or coal supplements alone, implying that competent methanogenic consortia exist in coal beds but that nutrient limitations restrict their activity in situ. This report adds to the scant literature on coal bed microbiology and suggests how microbes may be

Microbial Detoxification of Deoxynivalenol (DON), Assessed via a Lemna minor L. Bioassay, through Biotransformation to 3-epi-DON and 3-epi-DOM-1.

Science.gov (United States)

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.

Microbial Detoxification of Deoxynivalenol (DON, Assessed via a Lemna minor L. Bioassay, through Biotransformation to 3-epi-DON and 3-epi-DOM-1

Directory of Open Access Journals (Sweden)

Ilse Vanhoutte

2017-02-01

Full Text Available 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.

Understanding the efficacy of influent waste water on microbial ...

African Journals Online (AJOL)

acer

composition on the species structure and the diversity of bacterial consortia. The community ... 2010; Kim et al., 2011; Ye et al., 2011; Zhang et al.,. 2011a; b), greatly ..... molecular fine scale analysis of natural ammonia-oxidizing populations.

Adaptation of Methanogenic Inocula to Anaerobic Digestion of Maize Silage

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Martyna Wojcieszak

2017-09-01

Full Text Available 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

Identification of key factors in Accelerated Low Water Corrosion through experimental simulation of tidal conditions: influence of stimulated indigenous microbiota

NARCIS (Netherlands)

Marty, F.; Gueuné, H.; Malard, E.; Sánchez-Amaya, J.M.; Sjögren, L.; Abbas, B.; Quillet, L.; van Loosdrecht, M.C.M.; Muyzer, G.

2014-01-01

Biotic and abiotic factors favoring Accelerated Low Water Corrosion (ALWC) on harbor steel structures remain unclear warranting their study under controlled experimental tidal conditions. Initial stimulation of marine microbial consortia by a pulse of organic matter resulted in localized corrosion

Passive treatment of wastewater and contaminated groundwater

Science.gov (United States)

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.

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

Science.gov (United States)

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

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

Science.gov (United States)

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.

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

Science.gov (United States)

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

2016-06-15

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

Physiological and metagenomic analyses of microbial mats involved in self-purification of mine waters contaminated with heavy metals

Directory of Open Access Journals (Sweden)

Lukasz Drewniak

2016-08-01

Full Text Available Two microbial mats found inside two old (gold and uranium mines in Zloty Stok and Kowary located in SW Poland seem to form a natural barrier that traps heavy metals leaking from dewatering systems. We performed complex physiological and metagenomic analyses to determine which microorganisms are the main driving agents responsible for self-purification of the mine waters and identify metabolic processes responsible for the observed features. SEM and energy dispersive X-ray microanalysis showed accumulation of heavy metals on the mat surface, whereas, sorption experiments showed that neither microbial mats were completely saturated with heavy metals present in the mine waters, indicating that they have a large potential to absorb significant quantities of metal. The metagenomic analysis revealed that Methylococcaceae and Methylophilaceae families were the most abundant in both communities, moreover, it strongly suggest that backbones of both mats were formed by filamentous bacteria, such as Leptothrix, Thiothrix, and Beggiatoa. The Kowary bacterial community was enriched with the Helicobacteraceae family, whereas the Zloty Stok community consist mainly of Sphingomonadaceae, Rhodobacteraceae, and Caulobacteraceae families. Functional (culture-based and metagenome (sequence-based analyses showed that bacteria involved in immobilization of heavy metals, rather than those engaged in mobilization, were the main driving force within the analyzed communities. In turn, a comparison of functional genes revealed that the biofilm formation and heavy metal resistance functions are more desirable in microorganisms engaged in water purification than the ability to utilize heavy metals in the respiratory process (oxidation-reduction. These findings provide insight on the activity of bacteria leading, from biofilm formation to self-purification, of mine waters contaminated with heavy metals

Effect of continuous oleate addition on microbial communities involved in anaerobic digestion process

DEFF Research Database (Denmark)

Baserba, Manel Garrido; Angelidaki, Irini; Karakashev, Dimitar Borisov

2012-01-01

bacterial consortium related to functional specialization of the species towards oleate degradation. For the archaeal domain, the sequences were affiliated within Euryarchaeota phylum with three major groups (Methanosarcina, Methanosaeta and Methanobacterium genera). Results obtained in this study deliver...... a comprehensive picture on oleate degrading microbial communities in high organic strength wastewater. The findings might be utilized for development of strategies for biogas production from lipid-riched wastes....

Discovery of enzymes for toluene synthesis from anoxic microbial communities

DEFF Research Database (Denmark)

Beller, Harry R.; Rodrigues, Andria V.; Zargar, Kamrun

2018-01-01

Microbial toluene biosynthesis was reported in anoxic lake sediments more than three decades ago, but the enzyme catalyzing this biochemically challenging reaction has never been identified. Here we report the toluene-producing enzyme PhdB, a glycyl radical enzyme of bacterial origin that catalyzes...... phenylacetate decarboxylation, and its cognate activating enzyme PhdA, a radical S-adenosylmethionine enzyme, discovered in two distinct anoxic microbial communities that produce toluene. The unconventional process of enzyme discovery from a complex microbial community (>300,000 genes), rather than from...... a microbial isolate, involved metagenomics- and metaproteomics-enabled biochemistry, as well as in vitro confirmation of activity with recombinant enzymes. This work expands the known catalytic range of glycyl radical enzymes (only seven reaction types had been characterized previously) and aromatic...

Ex situ bioremediation of oil-contaminated soil.

Science.gov (United States)

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.

An overview of field specific designs of microbial EOR

Energy Technology Data Exchange (ETDEWEB)

Robertson, E.P.; Bala, G.A.; Fox, S.L.; Jackson, J.D.; Thomas, C.P.

1995-12-01

The selection and design of a microbial enhanced oil recovery (MEOR) process for application in a specific field involves geological, reservoir, and biological characterization. Microbially mediated oil recovery mechanisms (biogenic gas, biopolymers, and biosurfactants) are defined by the types of microorganisms used. The engineering and biological character of a given reservoir must be understood to correctly select a microbial system to enhance oil recovery. The objective of this paper is to discuss the methods used to evaluate three fields with distinct characteristics and production problems for the applicability of MEOR technology. Reservoir characteristics and laboratory results indicated that MEOR would not be applicable in two of the three fields considered. The development of a microbial oil recovery process for the third field appeared promising. Development of a bacterial consortium capable of producing the desired metabolites was initiated and field isolates were characterized.

Comparative Fecal Metagenomics Unveils Unique Functional Capacity of the Swine Gut

Science.gov (United States)

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...

Microbial bioenergetics of coral-algal interactions

Directory of Open Access Journals (Sweden)

Ty N.F. Roach

2017-06-01

Full Text Available Human impacts are causing ecosystem phase shifts from coral- to algal-dominated reef systems on a global scale. As these ecosystems undergo transition, there is an increased incidence of coral-macroalgal interactions. Mounting evidence indicates that the outcome of these interaction events is, in part, governed by microbially mediated dynamics. The allocation of available energy through different trophic levels, including the microbial food web, determines the outcome of these interactions and ultimately shapes the benthic community structure. However, little is known about the underlying thermodynamic mechanisms involved in these trophic energy transfers. This study utilizes a novel combination of methods including calorimetry, flow cytometry, and optical oxygen measurements, to provide a bioenergetic analysis of coral-macroalgal interactions in a controlled aquarium setting. We demonstrate that the energetic demands of microbial communities at the coral-algal interaction interface are higher than in the communities associated with either of the macroorganisms alone. This was evident through higher microbial power output (energy use per unit time and lower oxygen concentrations at interaction zones compared to areas distal from the interface. Increases in microbial power output and lower oxygen concentrations were significantly correlated with the ratio of heterotrophic to autotrophic microbes but not the total microbial abundance. These results suggest that coral-algal interfaces harbor higher proportions of heterotrophic microbes that are optimizing maximal power output, as opposed to yield. This yield to power shift offers a possible thermodynamic mechanism underlying the transition from coral- to algal-dominated reef ecosystems currently being observed worldwide. As changes in the power output of an ecosystem are a significant indicator of the current state of the system, this analysis provides a novel and insightful means to quantify

Microbial pattern of pressure ulcer in pediatric patients

Science.gov (United States)

Paramita, D. A.; Khairina; Lubis, N. Z.

2018-03-01

Pressure ulcer (PU) is a localized trauma to the skin and or tissue beneath which lies in bony prominence due to pressure or pressure that combines with a sharp surface. Several studies have found that PU is a common problem in pediatrics population. Infection at the site of a PU is the most common complication in which the PU may host a resistant microorganism and may turn into a local infection that will be the source of bacteremia in hospitalized patients. To reveal which is the most common microbial species that underlie in pressure ulcer of pediatrics patients.A cross-sectional study was conducted in July-September 2017, involving 18 PU pediatric patients in Haji Adam Malik Hospital. To each subject, swab culture from the ulcer was madein microbial laboratory in Haji Adam Malik Hospital to determine the microbial pattern. This study found that the most common microbial pattern in pressure ulcers of pediatrics patient in Haji Adam Malik Hospital is Acinetobacter baumannii (22.2%).

Configuration of biological wastewater treatment line and influent composition as the main factors driving bacterial community structure of activated sludge.

Science.gov (United States)

Jaranowska, Paulina; Cydzik-Kwiatkowska, Agnieszka; Zielińska, Magdalena

2013-07-01

The structure of microbial consortia in wastewater treatment facilities is a resultant of environmental conditions created by the operational parameters of the purification process. In the research, activated sludge from nine Polish wastewater treatment plants (WWTPs) was investigated at a molecular level to determine the impact of the complexity of biological treatment line and the influent composition on the species structure and the diversity of bacterial consortia. The community fingerprints and technological data were subjected to the canonical correspondence and correlation analyses. The number of separated biological processes realized in the treatment line and the presence of industrial wastewater in the influent were the key factors determining the species structure of total and ammonia-oxidizing bacteria in biomass. The N2O-reducers community composition depended significantly on the design of the facility; the highest species richness of denitrifiers was noted in the WWTPs with separated denitrification tanks. The contribution of industrial streams to the inflow affected the diversity of total and denitrifying bacterial consortia and diminished the diversity of ammonia oxidizers. The obtained data are valuable for engineers since they revealed the main factors, including the design of wastewater treatment plant, influencing the microbial groups critical for the stability of purification processes.

Anaerobic microbial dehalogenation of organohalides-state of the art and remediation strategies.

Science.gov (United States)

Nijenhuis, Ivonne; Kuntze, Kevin

2016-04-01

Contamination and remediation of groundwater with halogenated organics and understanding of involved microbial reactions still poses a challenge. Over the last years, research in anaerobic microbial dehalogenation has advanced in many aspects providing information about the reaction, physiology of microorganisms as well as approaches to investigate the activity of microorganisms in situ. Recently published crystal structures of reductive dehalogenases (Rdh), heterologous expression systems and advanced analytical, proteomic and stable isotope approaches allow addressing the overall reaction and specific enzymes as well as co-factors involved during anaerobic microbial dehalogenation. In addition to Dehalococcoides spp., Dehalobacter and Dehalogenimonas strains have been recognized as important and versatile organohalide respirers. Together, these provide perspectives for integrated concepts allowing to improve and monitor in situ biodegradation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Gluconic Acid: Properties, Applications and Microbial Production

Directory of Open Access Journals (Sweden)

Sumitra Ramachandran

2006-01-01

Full Text Available Gluconic acid is a mild organic acid derived from glucose by a simple oxidation reaction. The reaction is facilitated by the enzyme glucose oxidase (fungi and glucose dehydrogenase (bacteria such as Gluconobacter. Microbial production of gluconic acid is the preferred method and it dates back to several decades. The most studied and widely used fermentation process involves the fungus Aspergillus niger. Gluconic acid and its derivatives, the principal being sodium gluconate, have wide applications in food and pharmaceutical industry. This article gives a review of microbial gluconic acid production, its properties and applications.

Perturbation of an arctic soil microbial community by metal nanoparticles

Energy Technology Data Exchange (ETDEWEB)

Kumar, Niraj [Department of Biology, Queen' s University, Kingston, Ontario K7L 3N6 (Canada); Shah, Vishal [Department of Biology, Dowling College, Oakdale, NY 11769 (United States); Walker, Virginia K., E-mail: walkervk@queensu.ca [Department of Biology, Queen' s University, Kingston, Ontario K7L 3N6 (Canada); Department of Biology, School of Environmental Studies and Department of Microbiology and Immunology, Queen' s University, Kingston, Ontario K7L 3N6 (Canada)

2011-06-15

Highlights: {yields} Silver, copper and silica nanoparticles had an impact on arctic soil {yields} A microbial community toxicity indicator was developed {yields} Community surveys using pyrosequencing confirmed a shift in bacterial biodiversity {yields} Troublingly, silver nanoparticles were highly toxic to a plant beneficial bacterium - Abstract: Technological advances allowing routine nanoparticle (NP) manufacture have enabled their use in electronic equipment, foods, clothing and medical devices. Although some NPs have antibacterial activity, little is known about their environmental impact and there is no information on the influence of NPs on soil in the possibly vulnerable ecosystems of polar regions. The potential toxicity of 0.066% silver, copper or silica NPs on a high latitude (>78{sup o}N) soil was determined using community level physiological profiles (CLPP), fatty acid methyl ester (FAME) assays and DNA analysis, including sequencing and denaturing gradient gel electrophoresis (DGGE). The results of these different investigations were amalgamated in order to develop a community toxicity indicator, which revealed that of the three NPs examined, silver NPs could be classified as highly toxic to these arctic consortia. Subsequent culture-based studies confirmed that one of the community-identified plant-associating bacteria, Bradyrhizobium canariense, appeared to have a marked sensitivity to silver NPs. Thus, NP contamination of arctic soils particularly by silver NPs is a concern and procedures for mitigation and remediation of such pollution should be a priority for investigation.

Perturbation of an arctic soil microbial community by metal nanoparticles

International Nuclear Information System (INIS)

Kumar, Niraj; Shah, Vishal; Walker, Virginia K.

2011-01-01

Highlights: → Silver, copper and silica nanoparticles had an impact on arctic soil → A microbial community toxicity indicator was developed → Community surveys using pyrosequencing confirmed a shift in bacterial biodiversity → Troublingly, silver nanoparticles were highly toxic to a plant beneficial bacterium - Abstract: Technological advances allowing routine nanoparticle (NP) manufacture have enabled their use in electronic equipment, foods, clothing and medical devices. Although some NPs have antibacterial activity, little is known about their environmental impact and there is no information on the influence of NPs on soil in the possibly vulnerable ecosystems of polar regions. The potential toxicity of 0.066% silver, copper or silica NPs on a high latitude (>78 o N) soil was determined using community level physiological profiles (CLPP), fatty acid methyl ester (FAME) assays and DNA analysis, including sequencing and denaturing gradient gel electrophoresis (DGGE). The results of these different investigations were amalgamated in order to develop a community toxicity indicator, which revealed that of the three NPs examined, silver NPs could be classified as highly toxic to these arctic consortia. Subsequent culture-based studies confirmed that one of the community-identified plant-associating bacteria, Bradyrhizobium canariense, appeared to have a marked sensitivity to silver NPs. Thus, NP contamination of arctic soils particularly by silver NPs is a concern and procedures for mitigation and remediation of such pollution should be a priority for investigation.

The microbial diversity, distribution, and ecology of permafrost in China: a review.

Science.gov (United States)

Hu, Weigang; Zhang, Qi; Tian, Tian; Cheng, Guodong; An, Lizhe; Feng, Huyuan

2015-07-01

Permafrost in China mainly located in high-altitude areas. It represents a unique and suitable ecological niche that can be colonized by abundant microbes. Permafrost microbial community varies across geographically separated locations in China, and some lineages are novel and possible endemic. Besides, Chinese permafrost is a reservoir of functional microbial groups involved in key biogeochemical cycling processes. In future, more work is necessary to determine if these phylogenetic groups detected by DNA-based methods are part of the viable microbial community, and their functional roles and how they potentially respond to climate change. This review summaries recent studies describing microbial biodiversity found in permafrost and associated environments in China, and provides a framework for better understanding the microbial ecology of permafrost.

BIOTIGER, A NATURAL MICROBIAL PRODUCT FOR ENHANCED HYDROCARBON RECOVERY FROM OIL SANDS.

Energy Technology Data Exchange (ETDEWEB)

Brigmon, R; Topher Berry, T; Whitney Jones, W; Charles Milliken, C

2008-05-27

BioTiger{trademark} is a unique microbial consortia that resulted from over 8 years of extensive microbiology screening and characterization of samples collected from a century-old Polish waste lagoon. BioTiger{trademark} shows rapid and complete degradation of aliphatic and aromatic hydrocarbons, produces novel surfactants, is tolerant of both chemical and metal toxicity and shows good activity at temperature and pH extremes. Although originally developed and used by the U.S. Department of Energy for bioremediation of oil-contaminated soils, recent efforts have proven that BioTiger{trademark} can also be used to increase hydrocarbon recovery from oil sands. This enhanced ex situ oil recovery process utilizes BioTiger{trademark} to optimize bitumen separation. A floatation test protocol with oil sands from Ft. McMurray, Canada was used for the BioTiger{trademark} evaluation. A comparison of hot water extraction/floatation test of the oil sands performed with BioTiger{trademark} demonstrated a 50% improvement in separation as measured by gravimetric analysis in 4 h and a five-fold increase at 25 hr. Since BioTiger{trademark} performs well at high temperatures and process engineering can enhance and sustain metabolic activity, it can be applied to enhance recovery of hydrocarbons from oil sands or other complex recalcitrant matrices.

Electricity production and microbial characterization of thermophilic microbial fuel cells.

Science.gov (United States)

Dai, Kun; Wen, Jun-Li; Zhang, Fang; Ma, Xi-Wen; Cui, Xiang-Yu; Zhang, Qi; Zhao, Ting-Jia; Zeng, Raymond J

2017-11-01

Thermophilic microbial fuel cell (TMFC) offers many benefits, but the investigations on the diversity of exoelectrogenic bacteria are scarce. In this study, a two-chamber TMFC was constructed using ethanol as an electron donor, and the microbial dynamics were analyzed by high-throughput sequencing and 16S rRNA clone-library sequencing. The open-circuit potential of TMFC was approximately 650mV, while the maximum voltage was around 550mV. The maximum power density was 437mW/m 2 , and the columbic efficiency in this work was 20.5±6.0%. The Firmicutes bacteria, related to the uncultured bacterium clone A55_D21_H_B_C01 with a similarity of 99%, accounted for 90.9% of all bacteria in the TMFC biofilm. This unknown bacterium has the potential to become a new thermophilic exoelectrogenic bacterium that is yet to be cultured. The development of TMFC-involved biotechnologies will be beneficial for the production of valuable chemicals and generation of energy in the future. Copyright © 2017 Elsevier Ltd. All rights reserved.

Influence of sire breed on the interplay among rumen microbial populations inhabiting the rumen liquid of the progeny in beef cattle.

Directory of Open Access Journals (Sweden)

Emma Hernandez-Sanabria

Full Text Available This study aimed to evaluate whether the host genetic background impact the ruminal microbial communities of the progeny of sires from three different breeds under different diets. Eighty five bacterial and twenty eight methanogen phylotypes from 49 individuals of diverging sire breed (Angus, ANG; Charolais, CHA; and Hybrid, HYB, fed high energy density (HE and low energy density (LE diets were determined and correlated with breed, rumen fermentation and phenotypic variables, using multivariate statistical approaches. When bacterial phylotypes were compared between diets, ANG offspring showed the lowest number of diet-associated phylotypes, whereas CHA and HYB progenies had seventeen and twenty-three diet-associated phylotypes, respectively. For the methanogen phylotypes, there were no sire breed-associated phylotypes; however, seven phylotypes were significantly different among breeds on either diet (P<0.05. Sire breed did not influence the metabolic variables measured when high energy diet was fed. A correlation matrix of all pairwise comparisons among frequencies of bacterial and methanogen phylotypes uncovered their relationships with sire breed. A cluster containing methanogen phylotypes M16 (Methanobrevibacter gottschalkii and M20 (Methanobrevibacter smithii, and bacterial phylotype B62 (Robinsoniella sp. in Angus offspring fed low energy diet reflected the metabolic interactions among microbial consortia. The clustering of the phylotype frequencies from the three breeds indicated that phylotypes detected in CHA and HYB progenies are more similar among them, compared to ANG animals. Our results revealed that the frequency of particular microbial phylotypes in the progeny of cattle may be influenced by the sire breed when different diets are fed and ultimately further impact host metabolic functions, such as feed efficiency.

Utilizing data consortia to monitor safety and effectiveness of biosimilars and their innovator products.

Science.gov (United States)

Baldziki, Mike; Brown, Jeff; Chan, Hungching; Cheetham, T Craig; Conn, Thomas; Daniel, Gregory W; Hendrickson, Mark; Hilbrich, Lutz; Johnson, Ayanna; Miller, Steven B; Moore, Tom; Motheral, Brenda; Priddy, Sarah A; Raebel, Marsha A; Randhawa, Gurvaneet; Surratt, Penny; Walraven, Cheryl; White, T Jeff; Bruns, Kevin; Carden, Mary Jo; Dragovich, Charlie; Eichelberger, Bernadette; Rosato, Edith; Sega, Todd

2015-01-01

The Biologics Price Competition and Innovation Act, introduced as part of the Affordable Care Act, directed the FDA to create an approval pathway for biologic products shown to be biosimilar or interchangeable with an FDA-approved innovator drug. These biosimilars will not be chemically identical to the reference agent. Investigational studies conducted with biosimilar agents will likely provide limited real-world evidence of their effectiveness and safety. How do we best monitor effectiveness and safety of biosimilar products once approved by the FDA and used more extensively by patients? To determine the feasibility of developing a distributed research network that will use health insurance plan and health delivery system data to detect biosimilar safety and effectiveness signals early and be able to answer important managed care pharmacy questions from both the government and managed care organizations. Twenty-one members of the AMCP Task Force on Biosimilar Collective Intelligence Systems met November 12, 2013, to discuss issues involved in designing this consortium and to explore next steps. The task force concluded that a managed care biosimilars research consortium would be of significant value. Task force members agreed that it is best to use a distributed research network structurally similar to existing DARTNet, HMO Research Network, and Mini-Sentinel consortia. However, for some surveillance projects that it undertakes, the task force recognizes it may need supplemental data from managed care and other sources (i.e., a "hybrid" structure model). The task force believes that AMCP is well positioned to lead the biosimilar-monitoring effort and that the next step to developing a biosimilar-innovator collective intelligence system is to convene an advisory council to address organizational governance.

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

Energy Technology Data Exchange (ETDEWEB)

DeAngelis, K.M.; Gladden, J.G.; Allgaier, M.; D' haeseleer, P.; Fortney, J.L.; Reddy, A.; Hugenholtz, P.; Singer, S.W.; Vander Gheynst, J.; Silver, W.L.; Simmons, B.; Hazen, T.C.

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. 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.

Preservation in microbial mats: mineralization by a talc-like phase of a fish embedded in a microbial sarcophagus

Science.gov (United States)

Iniesto, Miguel; Zeyen, Nina; López-Archilla, Ana; Bernard, Sylvain; Buscalioni, Ángela; Guerrero, M. Carmen; Benzerara, Karim

2015-09-01

Microbial mats have been repeatedly suggested to promote early fossilization of macroorganisms. Yet, experimental simulations of this process remain scarce. Here, we report results of 5 year-long experiments performed onfish carcasses to document the influence of microbial mats on mineral precipitation during early fossilization. Carcasses were initially placed on top of microbial mats. After two weeks, fishes became coated by the mats forming a compact sarcophagus, which modified the microenvironment close to the corpses. Our results showed that these conditions favoured the precipitation of a poorly crystalline silicate phase rich in magnesium. This talc-like mineral phase has been detected in three different locations within the carcasses placed in microbial mats for more than 4 years: 1) within inner tissues, colonized by several bacillary cells; 2) at the surface of bones of the upper face of the corpse buried in the mat; and 3) at the surface of several bones such as the dorsal fin which appeared to be gradually replaced by the Mg-silicate phase. This mineral phase has been previously shown to promote bacteria fossilization. Here we provide first experimental evidence that such Mg-rich phase can also be involved in exceptional preservation of animals.

An open source platform for multi-scale spatially distributed simulations of microbial ecosystems

Energy Technology Data Exchange (ETDEWEB)

Segre, Daniel [Boston Univ., MA (United States)

2014-08-14

The goal of this project was to develop a tool for facilitating simulation, validation and discovery of multiscale dynamical processes in microbial ecosystems. This led to the development of an open-source software platform for Computation Of Microbial Ecosystems in Time and Space (COMETS). COMETS performs spatially distributed time-dependent flux balance based simulations of microbial metabolism. Our plan involved building the software platform itself, calibrating and testing it through comparison with experimental data, and integrating simulations and experiments to address important open questions on the evolution and dynamics of cross-feeding interactions between microbial species.

The Robin, Erithacus Rubecula (Passeriformes, Turdidae, as a Component of Heterotrophic Consortia of Forest Cenoses, Northeast Ukraine. Part 2

Directory of Open Access Journals (Sweden)

Chaplygina A. B.

2016-12-01

Full Text Available The role of the robin as a determinant of heterotrophic consortia is considered. The robin is a consort of determinants of autotrophic consortia, which core is represented mostly by dominating species of deciduous trees (Quercus robur Linnaeus, 1753, Tilia cordata Miller, 1768, Acer platanoides Linnaeus, 1753, Acer campestre Linnaeus, 1753, and also by sedges (Carex sp. and grasses (Poaceae, connected with the determinants by fabric links. The robin also belongs to the concentr of the second and higher orders as a component of forest biogeocenoses and it is also the main determinant in species composition of the insects inhabiting bird nests. As a result of the taxonomic analysis of invertebrates in the robin nests, it has been found out that the most numerous class was Insecta (9 orders and 27 families, with the dominance of Coleoptera (30.7 %. The nidicolous fauna of the robin (38 species was dominated by zoophages along with parasites and hematophages such as Hippoboscidae (46.4 %. The percentage of phytophages and saprophages among the invertebrate nest inhabitants was somewhat less (21 % each, then followed necrophages (12 %. Zoophages and parasites also dominated according to the number of objects in the nests (42 %; n = 150, the less was the portion of phytophages (34 %, saprophages (18 %, and necrophages (6 %. The highest number of species and objects of zoophages was recorded for climax and mature biocenoses (oak forests in NNP “HL” and pine cenoses in NNP “H””.

BioTiger{sup TM} : a natural microbial product for enhanced hydrocarbon recovery from oil sands

Energy Technology Data Exchange (ETDEWEB)

Brigmon, R.L.; Berry, C.J.; Milliken, C.E.; Jones, W. [Savannah River National Laboratory, Aiken, SC (United States)

2008-07-01

This presentation discussed the feasibility of using BioTiger{sup TM} technology to increase hydrocarbon recovery from oil sands. This enhanced ex situ oil recovery processes was initially developed and used by the United States Department of Energy for bioremediation of soils contaminated with oil, but it may also be used to optimize bitumen separation. BioTiger was described as being a unique microbial consortia that has resulted from nearly a decade of extensive microbiology screening and characterization of samples collected from an old waste lagoon. The technology offers rapid and complete degradation of aliphatic and aromatic hydrocarbons and produces new surfactants. It is tolerant of both chemical and metal toxicity and has good activity at high temperatures at extreme pH levels. A flotation test protocol with oil sands from Fort McMurray, Alberta was used for the BioTiger evaluation. A comparison of hot water extraction/flotation test of the oil sands performed with BioTiger showed a 50 per cent improvement in separation as measured by gravimetric analysis. BioTiger is well suited for enhanced hydrocarbon recovery from oil sands because it performs well at high temperatures. 8 figs.

Microbial diversity in soil : Selection of microbial populations by plant and soil type and implications for disease suppressiveness

NARCIS (Netherlands)

Garbeva, P; van Veen, JA; van Elsas, JD

2004-01-01

An increasing interest has emerged with respect to the importance of microbial diversity in soil habitats. The extent of the diversity of microorganisms in soil is seen to be critical to the maintenance of soil health and quality, as a wide range of microorganisms is involved in important soil

Microbial nitrogen cycling in Arctic snowpacks

International Nuclear Information System (INIS)

Larose, Catherine; Vogel, Timothy M; Dommergue, Aurélien

2013-01-01

Arctic snowpacks are often considered as chemical reactors for a variety of chemicals deposited through wet and dry events, but are overlooked as potential sites for microbial metabolism of reactive nitrogen species. The fate of deposited species is critical since warming leads to the transfer of contaminants to snowmelt-fed ecosystems. Here, we examined the role of microorganisms and the potential pathways involved in nitrogen cycling in the snow. Next generation sequencing data were used to follow functional gene abundances and a 16S rRNA (ribosomal ribonucleic acid) gene microarray was used to follow shifts in microbial community structure during a two-month spring-time field study at a high Arctic site, Svalbard, Norway (79° N). We showed that despite the low temperatures and limited water supply, microbial communities inhabiting the snow cover demonstrated dynamic shifts in their functional potential to follow several different pathways of the nitrogen cycle. In addition, microbial specific phylogenetic probes tracked different nitrogen species over time. For example, probes for Roseomonas tracked nitrate concentrations closely and probes for Caulobacter tracked ammonium concentrations after a delay of one week. Nitrogen cycling was also shown to be a dominant process at the base of the snowpack. (letter)

Functional ecology of soil microbial communities along a glacier forefield in Tierra del Fuego (Chile).

Science.gov (United States)

Fernández-Martínez, Miguel A; Pointing, Stephen B; Pérez-Ortega, Sergio; Arróniz-Crespo, María; Green, T G Allan; Rozzi, Ricardo; Sancho, Leopoldo G; de Los Ríos, Asunción

2016-09-01

A previously established chronosequence from Pia Glacier forefield in Tierra del Fuego (Chile) containing soils of different ages (from bare soils to forest ones) is analyzed. We used this chronosequence as framework to postulate that microbial successional development would be accompanied by changes in functionality. To test this, the GeoChip functional microarray was used to identify diversity of genes involved in microbial carbon and nitrogen metabolism, as well as other genes related to microbial stress response and biotic interactions. Changes in putative functionality generally reflected succession-related taxonomic composition of soil microbiota. Major shifts in carbon fixation and catabolism were observed, as well as major changes in nitrogen metabolism. At initial microbial dominated succession stages, microorganisms could be mainly involved in pathways that help to increase nutrient availability, while more complex microbial transformations such as denitrification and methanogenesis, and later degradation of complex organic substrates, could be more prevalent at vegetated successional states. Shifts in virus populations broadly reflected changes in microbial diversity. Conversely, stress response pathways appeared relatively well conserved for communities along the entire chronosequence. We conclude that nutrient utilization is likely the major driver of microbial succession in these soils. [Int Microbiol 19(3):161-173 (2016)]. Copyright© by the Spanish Society for Microbiology and Institute for Catalan Studies.

Mechanism of acetaldehyde-induced deactivation of microbial lipases

Directory of Open Access Journals (Sweden)

Jaeger Karl E

2011-02-01

Full Text Available Abstract Background Microbial lipases represent the most important class of biocatalysts used for a wealth of applications in organic synthesis. An often applied reaction is the lipase-catalyzed transesterification of vinyl esters and alcohols resulting in the formation of acetaldehyde which is known to deactivate microbial lipases, presumably by structural changes caused by initial Schiff-base formation at solvent accessible lysine residues. Previous studies showed that several lipases were sensitive toward acetaldehyde deactivation whereas others were insensitive; however, a general explanation of the acetaldehyde-induced inactivation mechanism is missing. Results Based on five microbial lipases from Candida rugosa, Rhizopus oryzae, Pseudomonas fluorescens and Bacillus subtilis we demonstrate that the protonation state of lysine ε-amino groups is decisive for their sensitivity toward acetaldehyde. Analysis of the diverse modification products of Bacillus subtilis lipases in the presence of acetaldehyde revealed several stable products such as α,β-unsaturated polyenals, which result from base and/or amino acid catalyzed aldol condensation of acetaldehyde. Our studies indicate that these products induce the formation of stable Michael-adducts at solvent-accessible amino acids and thus lead to enzyme deactivation. Further, our results indicate Schiff-base formation with acetaldehyde to be involved in crosslinking of lipase molecules. Conclusions Differences in stability observed with various commercially available microbial lipases most probably result from different purification procedures carried out by the respective manufacturers. We observed that the pH of the buffer used prior to lyophilization of the enzyme sample is of utmost importance. The mechanism of acetaldehyde-induced deactivation of microbial lipases involves the generation of α,β-unsaturated polyenals from acetaldehyde which subsequently form stable Michael-adducts with the

Synthetic microbial ecology and the dynamic interplay between microbial genotypes.

Science.gov (United States)

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.

Relating microbial community structure to functioning in forest soil organic carbon transformation and turnover.

Science.gov (United States)

You, Yeming; Wang, Juan; Huang, Xueman; Tang, Zuoxin; Liu, Shirong; Sun, Osbert J

2014-03-01

Forest soils store vast amounts of terrestrial carbon, but we are still limited in mechanistic understanding on how soil organic carbon (SOC) stabilization or turnover is controlled by biotic and abiotic factors in forest ecosystems. We used phospholipid fatty acids (PLFAs) as biomarker to study soil microbial community structure and measured activities of five extracellular enzymes involved in the degradation of cellulose (i.e., β-1,4-glucosidase and cellobiohydrolase), chitin (i.e., β-1,4-N-acetylglucosaminidase), and lignin (i.e., phenol oxidase and peroxidase) as indicators of soil microbial functioning in carbon transformation or turnover across varying biotic and abiotic conditions in a typical temperate forest ecosystem in central China. Redundancy analysis (RDA) was performed to determine the interrelationship between individual PFLAs and biotic and abiotic site factors as well as the linkage between soil microbial structure and function. Path analysis was further conducted to examine the controls of site factors on soil microbial community structure and the regulatory pathway of changes in SOC relating to microbial community structure and function. We found that soil microbial community structure is strongly influenced by water, temperature, SOC, fine root mass, clay content, and C/N ratio in soils and that the relative abundance of Gram-negative bacteria, saprophytic fungi, and actinomycetes explained most of the variations in the specific activities of soil enzymes involved in SOC transformation or turnover. The abundance of soil bacterial communities is strongly linked with the extracellular enzymes involved in carbon transformation, whereas the abundance of saprophytic fungi is associated with activities of extracellular enzymes driving carbon oxidation. Findings in this study demonstrate the complex interactions and linkage among plant traits, microenvironment, and soil physiochemical properties in affecting SOC via microbial regulations.

An overview of field-specific designs of microbial EOR

Energy Technology Data Exchange (ETDEWEB)

Robertson, E.P.; Bala, G.A.; Fox, S.L.; Jackson, J.D.; Thomas, C.P. [Idaho National Engineering Lab., Idaho Falls, ID (United States)

1995-12-31

The selection and design of an MEOR process for application in a specific field involves geological, reservoir, and biological characterization. Microbially mediated oil recovery mechanisms (bigenic gas, biopolymers, and biosurfactants) are defined by the types of microorganisms used. The engineering and biological character of a given reservoir must be understood to correctly select a microbial system to enhance oil recovery. This paper discusses the methods used to evaluate three fields with distinct characteristics and production problems for the applicability of MEOR would not be applicable in two of the three fields considered. The development of a microbial oil recovery process for the third field appeared promising. Development of a bacterial consortium capable of producing the desired metabolites was initiated, and field isolates were characterized.

Subsurface associations of Acaryochloris-related picocyanobacteria with oil-utilizing bacteria in the Arabian Gulf water body: promising consortia in oil sediment bioremediation.

Science.gov (United States)

Al-Bader, Dhia; Eliyas, Mohamed; Rayan, Rihab; Radwan, Samir

2013-04-01

Two picocyanobacterial strains related to Acaryochloris were isolated from the Arabian Gulf, 3 m below the water surface, one from the north shore and the other from the south shore of Kuwait. Both strains were morphologically, ultrastructurally, and albeit to a less extend, phylogenetically similar to Acaryochloris. However, both isolates lacked chlorophyll d and produced instead chlorophyll a, as the major photosynthetic pigment. Both picocyanobacterial isolates were associated with oil-utilizing bacteria in the magnitude of 10(5) cells g(-1). According to their 16S rRNA gene sequences, bacteria associated with the isolate from the north were affiliated to Paenibacillus sp., Bacillus pumilus, and Marinobacter aquaeolei, but those associated with the isolate from the south were affiliated to Bacillus asahii and Alcanivorax jadensis. These bacterial differences were probably due to environmental variations. In batch cultures, the bacterial consortia in the nonaxenic biomass as well as the pure bacterial isolates effectively consumed crude oil and pure aliphatic and aromatic hydrocarbons, including very high-molecular-weight compounds. Water and diethylether extracts from the phototrophic biomass enhanced growth of individual bacterial isolates and their hydrocarbon-consumption potential in batch cultures. It was concluded that these consortia could be promising in bioremediation of hydrocarbon pollutants, especially heavy sediments in the marine ecosystem.

Microbial activity in bentonite buffers. Literature study

Energy Technology Data Exchange (ETDEWEB)

Ratto, M.; Itavaara, M.

2012-07-01

The proposed disposal concept for high-level radioactive wastes involves storing the wastes underground in copper-iron containers embedded in buffer material of compacted bentonite. Hydrogen sulphide production by sulphate-reducing prokaryotes is a potential mechanism that could cause corrosion of waste containers in repository conditions. The prevailing conditions in compacted bentonite buffer will be harsh. The swelling pressure is 7-8 MPa, the amount of free water is low and the average pore and pore throat diameters are small. This literature study aims to assess the potential of microbial activity in bentonite buffers. Literature on the environmental limits of microbial life in extreme conditions and the occurrence of sulphatereducing prokaryotes in extreme environments is reviewed briefly and the results of published studies characterizing microbes and microbial processes in repository conditions or in relevant subsurface environments are presented. The presence of bacteria, including SRBs, has been confirmed in deep groundwater and bentonite-based materials. Sulphate reducers have been detected in various high-pressure environments, and sulphate-reduction based on hydrogen as an energy source is considered a major microbial process in deep subsurface environments. In bentonite, microbial activity is strongly suppressed, mainly due to the low amount of free water and small pores, which limit the transport of microbes and nutrients. Spore-forming bacteria have been shown to survive in compacted bentonite as dormant spores, and they are able to resume a metabolically active state after decompaction. Thus, microbial sulphide production may increase in repository conditions if the dry density of the bentonite buffer is locally reduced. (orig.)

Molecular Characterization of Wetland Soil Bacterial Communities in Constructed Mesocosms

Science.gov (United States)

2008-03-01

projects, but little is known about the morphology and functionality of microbial consortia that perform bioremediation. In order to completely...affinity for Archaea and primer E533R has an affinity for both Archaea and Eukarya, these two universal primers are specific enough to 36 bacteria to

Research advances in dry anaerobic digestion process of solid ...

African Journals Online (AJOL)

The dry anaerobic digestion process is an innovative waste-recycling method to treat high-solidcontent bio-wastes. This can be done without dilution with water by microbial consortia in an oxygenfree environment to recover potential renewable energy and nutrient-rich fertilizer for sustainable solid waste management.

Potential for direct interspecies electron transfer in methanogenic wastewater digester aggregates

DEFF Research Database (Denmark)

Morita, Masahiko; Malvankar, Nikhil S; Franks, Ashley E

2011-01-01

Mechanisms for electron transfer within microbial aggregates derived from an upflow anaerobic sludge blanket reactor converting brewery waste to methane were investigated in order to better understand the function of methanogenic consortia. The aggregates were electrically conductive, with conduc...... for electron exchange in some methanogenic systems....

Hybridization-Based Detection of Helicobacter pylori at Human Body Temperature Using Advanced Locked Nucleic Acid (LNA) Probes

DEFF Research Database (Denmark)

Fontenete, Sílvia; Guimarães, Nuno; Leite, Marina

2013-01-01

The understanding of the human microbiome and its influence upon human life has long been a subject of study. Hence, methods that allow the direct detection and visualization of microorganisms and microbial consortia (e.g. biofilms) within the human body would be invaluable. In here, we assessed...

Characterizing microbial diversity and damage in mural paintings.

Science.gov (United States)

Rosado, Tânia; Mirão, José; Candeias, António; Caldeira, Ana Teresa

2015-02-01

Mural paintings are some of the oldest and most important cultural expressions of mankind and play an important role for the understanding of societies and civilizations. These cultural assets have high economic and cultural value and therefore their degradation has social and economic impact. The present work presents a novel microanalytical approach to understand the damages caused by microbial communities in mural paintings. This comprises the characterization and identification of microbial diversity and evaluation of damage promoted by their biological activity. Culture-dependent methods and DNA-based approaches like denaturing gradient gel electrophoresis (DGGE) and pyrosequencing are important tools in the isolation and identification of the microbial communities allowing characterization of the biota involved in the biodeterioration phenomena. Raman microspectrometry, infrared spectrometry, and variable pressure scanning electron microscopy coupled with energy-dispersive X-ray spectrometry are also useful tools for evaluation of the presence of microbial contamination and detection of the alteration products resulting from metabolic activity of the microorganisms. This study shows that the degradation status of mural paintings can be correlated to the presence of metabolically active microorganisms.

Geochip-based analysis of microbial communities in alpine meadow soils in the Qinghai-Tibetan plateau.

Science.gov (United States)

Zhang, Yuguang; Lu, Zhenmei; Liu, Shanshan; Yang, Yunfeng; He, Zhili; Ren, Zuohua; Zhou, Jizhong; Li, Diqiang

2013-03-29

GeoChip 3.0, a microbial functional gene array, containing ~28,000 oligonucleotide probes and targeting ~57,000 sequences from 292 functional gene families, provided a powerful tool for researching microbial community structure in natural environments. The alpine meadow is a dominant plant community in the Qinghai-Tibetan plateau, hence it is important to profile the unique geographical flora and assess the response of the microbial communities to environmental variables. In this study, Geochip 3.0 was employed to understand the microbial functional gene diversity and structure, and metabolic potential and the major environmental factors in shaping microbial communities structure of alpine meadow soil in Qinghai-Tibetan Plateau. A total of 6143 microbial functional genes involved in carbon degradation, carbon fixation, methane oxidation and production, nitrogen cycling, phosphorus utilization, sulphur cycling, organic remediation, metal resistance, energy process and other category were detected in six soil samples and high diversity was observed. Interestingly, most of the detected genes associated with carbon degradation were derived from cultivated organisms. To identify major environmental factors in shaping microbial communities, Mantel test and CCA Statistical analyses were performed. The results indicated that altitude, C/N, pH and soil organic carbon were significantly (P the microbial functional structure and a total of 80.97% of the variation was significantly explained by altitude, C/N and pH. The C/N contributed 38.2% to microbial functional gene variation, which is in accordance with the hierarchical clustering of overall microbial functional genes. High overall functional genes and phylogenetic diversity of the alpine meadow soil microbial communities existed in the Qinghai-Tibetan Plateau. Most of the genes involved in carbon degradation were derived from characterized microbial groups. Microbial composition and structures variation were

Microbial electricity generation enhances decabromodiphenyl ether (BDE-209 degradation.

Directory of Open Access Journals (Sweden)

Yonggang Yang

Full Text Available Due to environmental persistence and biotoxicity of polybrominated diphenyl ethers (PBDEs, it is urgent to develop potential technologies to remediate PBDEs. Introducing electrodes for microbial electricity generation to stimulate the anaerobic degradation of organic pollutants is highly promising for bioremediation. However, it is still not clear whether the degradation of PBDEs could be promoted by this strategy. In this study, we hypothesized that the degradation of PBDEs (e.g., BDE-209 would be enhanced under microbial electricity generation condition. The functional compositions and structures of microbial communities in closed-circuit microbial fuel cell (c-MFC and open-circuit microbial fuel cell (o-MFC systems for BDE-209 degradation were detected by a comprehensive functional gene array, GeoChip 4.0, and linked with PBDE degradations. The results indicated that distinctly different microbial community structures were formed between c-MFCs and o-MFCs, and that lower concentrations of BDE-209 and the resulting lower brominated PBDE products were detected in c-MFCs after 70-day performance. The diversity and abundance of a variety of functional genes in c-MFCs were significantly higher than those in o-MFCs. Most genes involved in chlorinated solvent reductive dechlorination, hydroxylation, methoxylation and aromatic hydrocarbon degradation were highly enriched in c-MFCs and significantly positively correlated with the removal of PBDEs. Various other microbial functional genes for carbon, nitrogen, phosphorus and sulfur cycling, as well as energy transformation process, were also significantly increased in c-MFCs. Together, these results suggest that PBDE degradation could be enhanced by introducing the electrodes for microbial electricity generation and by specifically stimulating microbial functional genes.

The old care paradigm is dead, long live the new sustainable care paradigm: how can GP commissioning consortia meet the demand challenges of 21st century healthcare?

Science.gov (United States)

Mackenzie, James

2011-07-01

There are many challenges facing the health system in the 21st century - the majority of which are related to managing demand for health services. To meet these challenges emerging GP commissioning consortia will need to take a new approach to commissioning health services - an approach that moves beyond the current acute-centred curative paradigm of care to a new sustainable paradigm of care that focuses on primary care, integrated services and upstream prevention to manage demand. A key part of this shift is the recognition that the health system does not operate in a vacuum and that strategic commissioning decisions must take account of wider determinants of health and well-being, and operate within the finite limits of the planet's natural resources. The sustainable development principle of balancing financial, social and environmental considerations is crucial in managing demand for health services and ensuring that the health system is resilient to risks of resource uncertainty and a changing climate. Building sustainability into the governance and contracting processes of GP commissioning consortia will help deliver efficiency savings, impact on system productivity, manage system risk and help manage demand through the health co-benefits of taking a whole systems approach to commissioning decisions. Commissioning services from providers committed to corporate social responsibility and sustainable business practices allows us to move beyond a health system that cures people reactively to one in which the health of individuals and populations is managed proactively through prevention and education. The opportunity to build sustainability principles into the culture of GP commissioning consortia upfront should be seized now to ensure the new model of commissioning endures and is fit for the future.

Biomineralization associated with microbial reduction of Fe3+ and oxidation of Fe2+ in solid minerals

Science.gov (United States)

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.

Structure of hydrocarbonoclastic nitrate-reducing bacterial communities in bioturbated coastal marine sediments.

Science.gov (United States)

Stauffert, Magalie; Cravo-Laureau, Cristiana; Duran, Robert

2014-09-01

The organisation of denitrifying microorganisms in oil-polluted bioturbated sediments was investigated in mesocosms under conditions as closer as possible to that observed in the environment. Molecular and culture-dependent approaches revealed that denitrifying Gammaproteobacteria were abundant in oil-polluted and bioturbated sediments suggesting that they may play a key role in hydrocarbon degradation in the environment. T-RFLP and gene libraries analyses targeting nirS gene showed that denitrifying microbial communities structure was slightly affected by either the addition of Hediste diversicolor or crude oil revealing the metabolic versatility of denitrifying microorganisms. From oil-polluted sediments, distinct denitrifying hydrocarbonoclastic bacterial consortia were obtained by enrichment cultures on high molecular weight polyaromatic hydrocarbons (PAHs) (dibenzothiophene, fluoranthene, pyrene and chrysene) under nitrate-reducing conditions. Interestingly, molecular characterisation of the consortia showed that the denitrifying communities obtained from oiled microcosms with addition of H. diversicolor were different to that observed without H. diversicolor addition, especially with fluoranthene and chrysene revealing the bacterial diversity involved in the degradation of these PAHs. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Microbial Nitrogen-Cycle Gene Abundance in Soil of Cropland Abandoned for Different Periods.

Science.gov (United States)

Huhe; Borjigin, Shinchilelt; Buhebaoyin; Wu, Yanpei; Li, Minquan; Cheng, Yunxiang

2016-01-01

In Inner Mongolia, steppe grasslands face desertification or degradation because of human overuse and abandonment after inappropriate agricultural management. The soils in these abandoned croplands exist in heterogeneous environments characterized by widely fluctuating microbial growth. Quantitative polymerase chain reaction analysis of microbial genes encoding proteins involved in the nitrogen cycle was used to study Azotobacter species, nitrifiers, and denitrifiers in the soils from steppe grasslands and croplands abandoned for 2, 6, and 26 years. Except for nitrifying archaea and nitrous oxide-reducing bacteria, the relative genotypic abundance of microbial communities involved in nitrogen metabolism differed by approximately 2- to 10-fold between abandoned cropland and steppe grassland soils. Although nitrogen-cycle gene abundances varied with abandonment time, the abundance patterns of nitrogen-cycle genes separated distinctly into abandoned cropland versus light-grazing steppe grassland, despite the lack of any cultivation for over a quarter-century. Plant biomass and plant diversity exerted a significant effect on the abundance of microbial communities that mediate the nitrogen cycle (P nitrogen cycle in recently abandoned croplands.

Microbial ecology of halo-alkaliphilic sulfur bacteria

NARCIS (Netherlands)

Foti, M.J.

2007-01-01

The research of this thesis focussed on the investigation of the microbial diversity in soda lakes, giving a special attention to the micro-organisms involved in the sulphur cycle. The present PhD was part of a bigger project aiming to develop a biological process for the removal of hydrogen

Efecto de la asociación alga-bacteria Bostrychia calliptera (Rhodomelaceae en el porcentaje de remoción de cromo en laboratorio The effect of chromium removal by Algae-bacteria Bostrychia calliptera (Rhodomelaceae consortia under laboratory conditions

Directory of Open Access Journals (Sweden)

Ana Lucía Rengifo-Gallego

2012-09-01

-bacteria (AB, ii algae with antibiotic (AA, iii algal surface sediment, Natural Bacterial Consortium (CBN, and iv the control without algae or bacteria. The experimental design followed a model of two factors (chromium concentration x combination types with repeated measures using one factor. The microbial population behavior and the chromium concentration percentage were monitored by using atomic absorption spectroscopy (AAS. According to the data, Algae-bacteria (AB treatment was the most efficient combination at 10mg/L (87%, whereas the bacterial consortia (CBN was the most efficient at 5mg/L (62.85%. The results showed significant differences of chromium uptake between algae-bacteria (AB and natural bacterial consortia (CBN, meaning the importance of those treatments in the chromium removal from coastal waters.

Bioremediation of chromium in tannery effluent by microbial consortia

African Journals Online (AJOL)

USER

2010-05-24

May 24, 2010 ... Chromium is the most toxic and common among the heavy metal pollutants of industrial effluents .... Chromium (Cleseari and Green, 1995) included the oxidation of .... like uranium in its cells might also match with its tendency.

Microbial ecology laboratory procedures manual NASA/MSFC

Science.gov (United States)

Huff, Timothy L.

1990-01-01

An essential part of the efficient operation of any microbiology laboratory involved in sample analysis is a standard procedures manual. The purpose of this manual is to provide concise and well defined instructions on routine technical procedures involving sample analysis and methods for monitoring and maintaining quality control within the laboratory. Of equal importance is the safe operation of the laboratory. This manual outlines detailed procedures to be followed in the microbial ecology laboratory to assure safety, analytical control, and validity of results.

Calibration and analysis of genome-based models for microbial ecology.

Science.gov (United States)

Louca, Stilianos; Doebeli, Michael

2015-10-16

Microbial ecosystem modeling is complicated by the large number of unknown parameters and the lack of appropriate calibration tools. Here we present a novel computational framework for modeling microbial ecosystems, which combines genome-based model construction with statistical analysis and calibration to experimental data. Using this framework, we examined the dynamics of a community of Escherichia coli strains that emerged in laboratory evolution experiments, during which an ancestral strain diversified into two coexisting ecotypes. We constructed a microbial community model comprising the ancestral and the evolved strains, which we calibrated using separate monoculture experiments. Simulations reproduced the successional dynamics in the evolution experiments, and pathway activation patterns observed in microarray transcript profiles. Our approach yielded detailed insights into the metabolic processes that drove bacterial diversification, involving acetate cross-feeding and competition for organic carbon and oxygen. Our framework provides a missing link towards a data-driven mechanistic microbial ecology.

Aerobic granular biomass: a novel biomaterial for efficient uranium removal

International Nuclear Information System (INIS)

Nancharaiah, Y.V.; Joshi, H.M.; Mohan, T.V.K.; Venugopalan, V.P.; Narasimhan, S.V.

2006-01-01

Aerobic microbial granules, self-immobilized microbial consortia cultured in aerobically operated bioreactors, primarily consist of mixed species of bacteria ensconced in an extracellular polymeric matrix of their own creation. Such aerobically grown microbial granules have attracted considerable research interest in environmental biotechnology. In recent times, it has been demonstrated that the granules could be used for efficient degradation of recalcitrant organic compounds and for the treatment of a growing number of wastes. The objective of this study was to investigate whether aerobic granules could be used as novel biomass material for biosorption of uranium from aqueous solutions

Microbial ecology-based engineering of Microbial Electrochemical Technologies.

Science.gov (United States)

Koch, Christin; Korth, Benjamin; Harnisch, Falk

2018-01-01

Microbial ecology is devoted to the understanding of dynamics, activity and interaction of microorganisms in natural and technical ecosystems. Bioelectrochemical systems represent important technical ecosystems, where microbial ecology is of highest importance for their function. However, whereas aspects of, for example, materials and reactor engineering are commonly perceived as highly relevant, the study and engineering of microbial ecology are significantly underrepresented in bioelectrochemical systems. This shortfall may be assigned to a deficit on knowledge and power of these methods as well as the prerequisites for their thorough application. This article discusses not only the importance of microbial ecology for microbial electrochemical technologies but also shows which information can be derived for a knowledge-driven engineering. Instead of providing a comprehensive list of techniques from which it is hard to judge the applicability and value of information for a respective one, this review illustrates the suitability of selected techniques on a case study. Thereby, best practice for different research questions is provided and a set of key questions for experimental design, data acquisition and analysis is suggested. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

"Innovation and Intellectual Property Policies in European Research Infrastructure Consortia - PART I: The Case of the European Spallation Source ERIC"

DEFF Research Database (Denmark)

Yu, Helen; Wested, Jakob; Minssen, Timo

2017-01-01

of the problems society is facing today. To facilitate the creation and operation of such RIs, the EU adopted legal frameworks for European Research Infrastructure Consortia (ERIC). On August 31, 2015, the European Spallation Source (ESS) was established as an ERIC. Under the ERIC Regulations and ESS Statutes......, the European Spallation Source ERIC is required to adopt various policy documents relating to the operation and management of the facility. These cover a wide variety of issues such as user access, public procurement, intellectual property rights (IPR), data management, and dissemination. One of the main goals...

Microbial syntrophy: interaction for the common good.

Science.gov (United States)

Morris, Brandon E L; Henneberger, Ruth; Huber, Harald; Moissl-Eichinger, Christine

2013-05-01

Classical definitions of syntrophy focus on a process, performed through metabolic interaction between dependent microbial partners, such as the degradation of complex organic compounds under anoxic conditions. However, examples from past and current scientific discoveries suggest that a new, simple but wider definition is necessary to cover all aspects of microbial syntrophy. We suggest the term 'obligately mutualistic metabolism', which still focuses on microbial metabolic cooperation but also includes an ecological aspect: the benefit for both partners. By the combined metabolic activity of microorganisms, endergonic reactions can become exergonic through the efficient removal of products and therefore enable a microbial community to survive with minimal energy resources. Here, we explain the principles of classical and non-classical syntrophy and illustrate the concepts with various examples. We present biochemical fundamentals that allow microorganism to survive under a range of environmental conditions and to drive important biogeochemical processes. Novel technologies have contributed to the understanding of syntrophic relationships in cultured and uncultured systems. Recent research highlights that obligately mutualistic metabolism is not limited to certain metabolic pathways nor to certain environments or microorganisms. This beneficial microbial interaction is not restricted to the transfer of reducing agents such as hydrogen or formate, but can also involve the exchange of organic, sulfurous- and nitrogenous compounds or the removal of toxic compounds. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Microbial bebop: creating music from complex dynamics in microbial ecology.

Science.gov (United States)

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.

Anaerobic bio-removal of uranium (VI) and chromium (VI): Comparison of microbial community structure

International Nuclear Information System (INIS)

Martins, Monica; Faleiro, Maria Leonor; Chaves, Sandra; Tenreiro, Rogerio; Santos, Erika; Costa, Maria Clara

2010-01-01

Several microbial communities, obtained from uranium contaminated and non-contaminated samples, were investigated for their ability to remove uranium (VI) and the cultures capable for this removal were further assessed on their efficiency for chromium (VI) removal. The highest efficiency for removal of both metals was observed on a consortium from a non-contaminated soil collected in Monchique thermal place, which was capable to remove 91% of 22 mg L -1 U(VI) and 99% of 13 mg L -1 Cr(VI). This study revealed that uranium (VI) removing communities have also ability to remove chromium (VI), but when uranium (VI) was replaced by chromium (VI) several differences in the structure of all bacterial communities were observed. TGGE and phylogenetic analysis of 16S rRNA gene showed that the uranium (VI) removing bacterial consortia are mainly composed by members of Rhodocyclaceae family and Clostridium genus. On the other hand, bacteria from Enterobacteriaceae family were detected in the community with ability for chromium (VI) removal. The existence of members of Enterobacteriaceae and Rhodocyclaceae families never reported as chromium or uranium removing bacteria, respectively, is also a relevant finding, encouraging the exploitation of microorganisms with new abilities that can be useful for bioremediation.

Anaerobic bio-removal of uranium (VI) and chromium (VI): Comparison of microbial community structure

Energy Technology Data Exchange (ETDEWEB)

Martins, Monica [Centro de Ciencias do Mar, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro (Portugal); Faleiro, Maria Leonor [IBB - Centro de Biomedicina Molecular e Estrutural, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro (Portugal); Chaves, Sandra; Tenreiro, Rogerio [Universidade de Lisboa, Faculdade de Ciencias, Centro de Biodiversidade, Genomica Integrativa e Funcional (BioFIG), Campus de FCUL, Campo Grande 1749-016 Lisboa (Portugal); Santos, Erika [Centro de Ciencias do Mar, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro (Portugal); Costa, Maria Clara, E-mail: mcorada@ualg.pt [Centro de Ciencias do Mar, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro (Portugal)

2010-04-15

Several microbial communities, obtained from uranium contaminated and non-contaminated samples, were investigated for their ability to remove uranium (VI) and the cultures capable for this removal were further assessed on their efficiency for chromium (VI) removal. The highest efficiency for removal of both metals was observed on a consortium from a non-contaminated soil collected in Monchique thermal place, which was capable to remove 91% of 22 mg L{sup -1} U(VI) and 99% of 13 mg L{sup -1} Cr(VI). This study revealed that uranium (VI) removing communities have also ability to remove chromium (VI), but when uranium (VI) was replaced by chromium (VI) several differences in the structure of all bacterial communities were observed. TGGE and phylogenetic analysis of 16S rRNA gene showed that the uranium (VI) removing bacterial consortia are mainly composed by members of Rhodocyclaceae family and Clostridium genus. On the other hand, bacteria from Enterobacteriaceae family were detected in the community with ability for chromium (VI) removal. The existence of members of Enterobacteriaceae and Rhodocyclaceae families never reported as chromium or uranium removing bacteria, respectively, is also a relevant finding, encouraging the exploitation of microorganisms with new abilities that can be useful for bioremediation.

Living microbial ecosystems within the active zone of catagenesis: Implications for feeding the deep biosphere

Science.gov (United States)

Horsfield, B.; Schenk, H. J.; Zink, K.; Ondrak, R.; Dieckmann, V.; Kallmeyer, J.; Mangelsdorf, K.; di Primio, R.; Wilkes, H.; Parkes, R. J.; Fry, J.; Cragg, B.

2006-06-01

Earth's largest reactive carbon pool, marine sedimentary organic matter, becomes increasingly recalcitrant during burial, making it almost inaccessible as a substrate for microorganisms, and thereby limiting metabolic activity in the deep biosphere. Because elevated temperature acting over geological time leads to the massive thermal breakdown of the organic matter into volatiles, including petroleum, the question arises whether microorganisms can directly utilize these maturation products as a substrate. While migrated thermogenic fluids are known to sustain microbial consortia in shallow sediments, an in situ coupling of abiotic generation and microbial utilization has not been demonstrated. Here we show, using a combination of basin modelling, kinetic modelling, geomicrobiology and biogeochemistry, that microorganisms inhabit the active generation zone in the Nankai Trough, offshore Japan. Three sites from ODP Leg 190 have been evaluated, namely 1173, 1174 and 1177, drilled in nearly undeformed Quaternary and Tertiary sedimentary sequences seaward of the Nankai Trough itself. Paleotemperatures were reconstructed based on subsidence profiles, compaction modelling, present-day heat flow, downhole temperature measurements and organic maturity parameters. Today's heat flow distribution can be considered mainly conductive, and is extremely high in places, reaching 180 mW/m 2. The kinetic parameters describing total hydrocarbon generation, determined by laboratory pyrolysis experiments, were utilized by the model in order to predict the timing of generation in time and space. The model predicts that the onset of present day generation lies between 300 and 500 m below sea floor (5100-5300 m below mean sea level), depending on well location. In the case of Site 1174, 5-10% conversion has taken place by a present day temperature of ca. 85 °C. Predictions were largely validated by on-site hydrocarbon gas measurements. Viable organisms in the same depth range have been

Microbial involvement in the formation of Cambrian sea-floor silica-iron oxide deposits, Australia

Science.gov (United States)

Duhig, Nathan C.; Davidson, Garry J.; Stolz, Joe

1992-06-01

The Cambrian-Ordovician Mount Windsor volcanic belt in northern Australia is host to stratiform lenses of massive ferruginous chert that are spatially associated with volcanogenic massive sulfide occurrences, in particular the Thalanga zinc-lead-copper-silver deposit. The rocks are composed principally of Fe2O3 and SiO2, with very low concentrations of alkalic elements, and lithogenous elements such as Al, Zr, and Ti; they are interpreted as nearly pure chemical sediments. Textural evidence is documented of the integral role of filamentous bacteria (and/or fungi) in depositing iron from hydrothermal fluids, and of the inorganic precipitation of silica-iron-oxyhydroxide gels that subsequently matured to subcrystalline and crystalline silica forms. At least three distinct iron-accumulating microbial forms are distinguished: networks of septate filaments, nonseptate filament networks, and extremely coarse branching filaments that do not reconnect. Values for δ34S in disseminated pyrite are up to 50‰ lighter than those of contemporaneous Cambrian seawater, suggesting postdepositional colonization of some ironstones by sulfur-reducing bacteria. The site not only preserves the textural interplay of biological and inorganic depositional processes in exhalites, but also extends the oldest known instance of microbial mediation in vent-proximal hydrothermal iron precipitation to at least 500 Ma.

Microbial Biofilm as a Smart Material

Directory of Open Access Journals (Sweden)

Christian Garde

2015-02-01

Full Text Available Microbial biofilm colonies will in many cases form a smart material capable of responding to external threats dependent on their size and internal state. The microbial community accordingly switches between passive, protective, or attack modes of action. In order to decide which strategy to employ, it is essential for the biofilm community to be able to sense its own size. The sensor designed to perform this task is termed a quorum sensor, since it only permits collective behaviour once a sufficiently large assembly of microbes have been established. The generic quorum sensor construct involves two genes, one coding for the production of a diffusible signal molecule and one coding for a regulator protein dedicated to sensing the signal molecules. A positive feedback in the signal molecule production sets a well-defined condition for switching into the collective mode. The activation of the regulator involves a slow dimerization, which allows low-pass filtering of the activation of the collective mode. Here, we review and combine the model components that form the basic quorum sensor in a number of Gram-negative bacteria, e.g., Pseudomonas aeruginosa.

Identification and functional properties of dominant lactic acid bacteria isolated from Kahudi, a traditional rapeseed fermented food product of Assam, India

Directory of Open Access Journals (Sweden)

Gunajit Goswami

2017-09-01

Full Text Available Kahudi or Pani tenga is a very unique fermented mustard product of Assam that is prepared by mixing coarsely ground mustard with extracts of acidic Garcinia pedunculata (Thekera or tamarind. Kahudi is produced through a spontaneous and uncontrolled solid state fermentation and very little scientific effort has been directed to understand its microflora and their functional properties. In this paper, we report the microbial flora and their dynamics during Kahudi fermentation with special emphasis on lactic acid bacteria (LAB. LAB were found to be dominant (8 log CFU/g over other microbial flora (4 log CFU/g during the fermentation process leading to Kahudi formation. The microbial load in Kahudi did not include any mycelial molds or pathogenic enteric bacteria. Combination of phenotypic parameters, biochemical tests, and 16S rDNA gene sequencing revealed the dominant group of LAB as Enterococcus durans, Lactobacillus plantarum, Lactobacillus fermentum, and Lactobacillus casei. The sugar fermentation and enzyme profile analysis revealed the ability of the microbial consortia to metabolize an array of indigestible sugars including D-mannose, mannitol, sorbitol, methyl-α-D-mannopyranoside, methyl-α-D-glucopyranoside, N-acetylglucosamine, amygdalin, and arbutin. Although the isolates showed good acid phosphatase activity they had weak extracellular phytase activity. This is the first report on the microbial dynamics and involvement of LAB during Kahudi fermentation.

Genomes in Turmoil: Frugality Drives Microbial Community Structure in Extremely Acidic Environments

Science.gov (United States)

Holmes, D. S.

2016-12-01

Extremely acidic environments (To gain insight into these issues, we have conducted deep bioinformatic analyses, including metabolic reconstruction of key assimilatory pathways, phylogenomics and network scrutiny of >160 genomes of acidophiles, including representatives from Archaea, Bacteria and Eukarya and at least ten metagenomes of acidic environments [Cardenas JP, et al. pp 179-197 in Acidophiles, eds R. Quatrini and D. B. Johnson, Caister Academic Press, UK (2016)]. Results yielded valuable insights into cellular processes, including carbon and nitrogen management and energy production, linking biogeochemical processes to organismal physiology. They also provided insight into the evolutionary forces that shape the genomic structure of members of acidophile communities. Niche partitioning can explain diversity patterns in rapidly changing acidic environments such as bioleaching heaps. However, in spatially and temporally homogeneous acidic environments genome flux appears to provide deeper insight into the composition and evolution of acidic consortia. Acidophiles have undergone genome streamlining by gene loss promoting mutual coexistence of species that exploit complementarity use of scarce resources consistent with the Black Queen hypothesis [Morris JJ et al. mBio 3: e00036-12 (2012)]. Acidophiles also have a large pool of accessory genes (the microbial super-genome) that can be accessed by horizontal gene transfer. This further promotes dependency relationships as drivers of community structure and the evolution of keystone species. Acknowledgements: Fondecyt 1130683; Basal CCTE PFB16

Value added phytoremediation of metal stressed soils using phosphate solubilizing microbial consortium.

Science.gov (United States)

Gupta, Pratishtha; Kumar, Vipin

2017-01-01

The presence of heavy metals in the soil is a matter of growing concern due to their toxic and non-biodegradable nature. Lack of effectiveness of various conventional methods due to economic and technical constraints resulted in the search for an eco-friendly and cost-effective biological techniques for heavy metal removal from the environment. Until now, phytoremediation has emerged as an innovative technique to address the problem. However, the efficiency of phytoremediation process is hindered under the high metal concentration conditions. Hence, phosphate solubilizing microbes (PSM) assisted phytoremediation technique is gaining more insight as it can reduce the contamination load even under elevated metal stressed conditions. These microbes convert heavy metals into soluble and bioavailable forms, which consequently facilitate phytoremediation. Several studies have reported that the use of microbial consortium for remediation is considered more effective as compared to single strain pure culture. Therefore, this review paper focuses on the current trends in research related to PSM mediated uptake of heavy metal by plants. The efficiency of PSM consortia in enhancing the phytoremediation process has also been reviewed. Moreover, the role of phosphatase enzymes in the mineralization of organic forms of phosphate in soil is further discussed. Biosurfactant mediated bioremediation of metal polluted soils is a matter of extensive research nowadays. Hence, the recent advancement of using biosurfactants in enhanced phytoremediation of metal stressed soils is also described.

Microbial functional genes enriched in the Xiangjiang River sediments with heavy metal contamination.

Science.gov (United States)

Jie, Shiqi; Li, Mingming; Gan, Min; Zhu, Jianyu; Yin, Huaqun; Liu, Xueduan

2016-08-08

Xiangjiang River (Hunan, China) has been contaminated with heavy metal for several decades by surrounding factories. However, little is known about the influence of a gradient of heavy metal contamination on the diversity, structure of microbial functional gene in sediment. To deeply understand the impact of heavy metal contamination on microbial community, a comprehensive functional gene array (GeoChip 5.0) has been used to study the functional genes structure, composition, diversity and metabolic potential of microbial community from three heavy metal polluted sites of Xiangjiang River. A total of 25595 functional genes involved in different biogeochemical processes have been detected in three sites, and different diversities and structures of microbial functional genes were observed. The analysis of gene overlapping, unique genes, and various diversity indices indicated a significant correlation between the level of heavy metal contamination and the functional diversity. Plentiful resistant genes related to various metal were detected, such as copper, arsenic, chromium and mercury. The results indicated a significantly higher abundance of genes involved in metal resistance including sulfate reduction genes (dsr) in studied site with most serious heavy metal contamination, such as cueo, mer, metc, merb, tehb and terc gene. With regard to the relationship between the environmental variables and microbial functional structure, S, Cu, Cd, Hg and Cr were the dominating factor shaping the microbial distribution pattern in three sites. This study suggests that high level of heavy metal contamination resulted in higher functional diversity and the abundance of metal resistant genes. These variation therefore significantly contribute to the resistance, resilience and stability of the microbial community subjected to the gradient of heavy metals contaminant in Xiangjiang River.

Laser engineering of microbial systems

Science.gov (United States)

Yusupov, V. I.; Gorlenko, M. V.; Cheptsov, V. S.; Minaev, N. V.; Churbanova, E. S.; Zhigarkov, V. S.; Chutko, E. A.; Evlashin, S. A.; Chichkov, B. N.; Bagratashvili, V. N.

2018-06-01

A technology of laser engineering of microbial systems (LEMS) based on the method of laser-induced transfer of heterogeneous mixtures containing microorganisms (laser bioprinting) is described. This technology involves laser printing of soil microparticles by focusing near-infrared laser pulses on a specially prepared gel/soil mixture spread onto a gold-coated glass plate. The optimal range of laser energies from the point of view of the formation of stable jets and droplets with minimal negative impact on living systems of giant accelerations, laser pulse irradiation, and Au nanoparticles was found. Microsamples of soil were printed on glucose-peptone-yeast agar plates to estimate the LEMS process influence on structural and morphological microbial diversity. The obtained results were compared with traditionally treated soil samples. It was shown that LEMS technology allows significantly increasing the biodiversity of printed organisms and is effective for isolating rare or unculturable microorganisms.

Hydrogen production by fermentative consortia

Energy Technology Data Exchange (ETDEWEB)

Valdez-Vazquez, Idania [Centro de Investigacion Cientifica y de Educacion Superior de Ensenada (CICESE), Department of Marine Biotechnology, Ensenada, B.C. Mexico (Mexico); Poggi-Varaldo, Hector M. [CINVESTAV-IPN, Department of Biotechnology and Bioengineering, PO Box 14-740, Mexico D.F. 07000 (Mexico)

2009-06-15

In this work, H{sub 2} production by anaerobic mixed cultures was reviewed. First, the different anaerobic microbial communities that have a direct relation with the generation or consumption of H{sub 2} are discussed. Then, the different methods used to inhibit the H{sub 2}-consuming bacteria are analyzed (mainly in the methanogenesis phase) such as biokinetic control (low pH and short hydraulic retention time), heat-shock treatment and chemical inhibitors along with their advantages/disadvantages for their application on an industrial scale. After that, biochemical pathways of carbohydrate degradation to H{sub 2}, organic acids and solvents are showed. Fourth, structure, diversity and dynamics of H{sub 2}-producers communities are detailed. Later, the hydrogenase structure and activity is related with H{sub 2} production. Also, the causes for H{sub 2} production inhibition are analyzed along with strategies to avoid it. Finally, immobilized-cells systems are presented as a way to enhance H{sub 2} production. (author)

Microbial bebop: creating music from complex dynamics in microbial ecology.

Directory of Open Access Journals (Sweden)

Peter Larsen

Full Text Available 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.

Radiation application for the utilization of microbial resources

International Nuclear Information System (INIS)

Lee, Young Keun; Kim, Jae Sung; Lee, Sang Jae

2007-07-01

Domestic microbes which had the antifungal, pesticide residue degradable, and heavy metal adsorbent activities were isolated individually. Mutants of their improved functions were induced by radiation. And finally microbial formulae of biocontroller were manufactured and respected to be industrialized promisingly. The effectiveness of the developed microbial formulae were confirmed in pepper, radish, and Chinese cabbage by field experiments for 5 kinds of fungal diseases. This technology is respected to be transferred to the agricultural companies. And a novel venture company could be established by the involved researchers using this technology. As a result, the productivity in environmentally-friendly farm could be improved gradually in the near future

Radiation application for the utilization of microbial resources

Energy Technology Data Exchange (ETDEWEB)

Lee, Young Keun; Kim, Jae Sung; Lee, Sang Jae [and others

2007-07-15

Domestic microbes which had the antifungal, pesticide residue degradable, and heavy metal adsorbent activities were isolated individually. Mutants of their improved functions were induced by radiation. And finally microbial formulae of biocontroller were manufactured and respected to be industrialized promisingly. The effectiveness of the developed microbial formulae were confirmed in pepper, radish, and Chinese cabbage by field experiments for 5 kinds of fungal diseases. This technology is respected to be transferred to the agricultural companies. And a novel venture company could be established by the involved researchers using this technology. As a result, the productivity in environmentally-friendly farm could be improved gradually in the near future.

Microbial biofilm growth on irradiated, spent nuclear fuel cladding

International Nuclear Information System (INIS)

Bruhn, D.F.; Frank, S.M.; Roberto, F.F.; Pinhero, P.J.; Johnson, S.G.

2009-01-01

A fundamental criticism regarding the potential for microbial influenced corrosion in spent nuclear fuel cladding or storage containers concerns whether the required microorganisms can, in fact, survive radiation fields inherent in these materials. This study was performed to unequivocally answer this critique by addressing the potential for biofilm formation, the precursor to microbial-influenced corrosion, in radiation fields representative of spent nuclear fuel storage environments. This study involved the formation of a microbial biofilm on irradiated spent nuclear fuel cladding within a hot cell environment. This was accomplished by introducing 22 species of bacteria, in nutrient-rich media, to test vessels containing irradiated cladding sections and that was then surrounded by radioactive source material. The overall dose rate exceeded 2 Gy/h gamma/beta radiation with the total dose received by some of the bacteria reaching 5 x 10 3 Gy. This study provides evidence for the formation of biofilms on spent-fuel materials, and the implication of microbial influenced corrosion in the storage and permanent deposition of spent nuclear fuel in repository environments

Microbial effects on radioactive wastes at SLB sites

International Nuclear Information System (INIS)

Colombo, P.

1982-01-01

The objectives of this study are to determine the significance of microbial degradation of organic wastes on radionuclide migration on shallow land burial for humid and arid sites, establish which mechanisms predominate and ascertain the conditions under which these mechanisms operate. Factors contolling gaseous eminations from low-level radioactive waste disposal sites are assessed. Importance of gaseous fluxes of methane, carbon dioxide and possibly hydrogen from the site stems from the inclusion of tritium and/or 14 C into the elemental composition of these compounds. In that the primary source of these gases is the biodegradation of organic components of the waste materials, primary emphasis of the study involved on examination of the biochemical pathways producing methane, carbon dioxide and hydrogen, and the environmental parameters controlling the activity of the microbial community involved. Although the methane and carbon dioxide production rate indicates the degradation rate of the organic substances in the waste, it does not predict the methane evolution rate from the trench site. Methane fluxes from the soil surface are equivalent to the net synthesis minus the quantity oxidized by the microbial community as the gas passes through the soil profile. Gas studies were performed at three commercial low-level radioactive waste disposal sites (West Valley, New York; Beatty, Nevada; Maxey Flats, Kentucky) during the period 1976 to 1978. The results of these studies are presented. 3 tables

Microbial ecology of bacterially mediated PCB biodegradation

International Nuclear Information System (INIS)

Pettigrew, C.A. Jr.

1989-01-01

The roles of plasmid mediated and consortia mediated polychlorinated biphenyl (PCB) biodegradation by bacterial populations isolated from PCB contaminated freshwater sediments were investigated. PCB degrading bacteria were isolated by DNA:DNA colony hybridization, batch enrichments, and chemostat enrichment. Analysis of substrate removal and metabolite production were done using chlorinated biphenyl spray plates, reverse phase high pressure liquid chromatography, Cl - detection, and 14 C-labeled substrate mineralization methods. A bacterial consortium, designated LPS10, involved in a concerted metabolic attack on chlorinated biphenyls, was shown to mineralize 4-chlorobiphenyl (4CB) and 4,4'-dichlorobiphenyl (4,4' CB). The LPS10 consortium was isolated by both batch and chemostat enrichment using 4CB and biphenyl (BP) as sole carbon source and was found to have tree bacterial isolates that predominated; these included: Pseudomonas, testosteroni LPS10A which mediated the breakdown of 4CB and 4,4' CB to the putative meta-cleavage product and subsequently to 4-chlorobenzoic acid (4CBA), an isolate tentatively identified as an Arthrobacter sp. LPS10B which mediated 4CBA degradation, and Pseudomonas putida by A LPS10C whose role in the consortium has not been determined

Agriculturally important microbial biofilms: Present status and future prospects.

Science.gov (United States)

Velmourougane, Kulandaivelu; Prasanna, Radha; Saxena, Anil Kumar

2017-07-01

Microbial biofilms are a fascinating subject, due to their significant roles in the environment, industry, and health. Advances in biochemical and molecular techniques have helped in enhancing our understanding of biofilm structure and development. In the past, research on biofilms primarily focussed on health and industrial sectors; however, lately, biofilms in agriculture are gaining attention due to their immense potential in crop production, protection, and improvement. Biofilms play an important role in colonization of surfaces - soil, roots, or shoots of plants and enable proliferation in the desired niche, besides enhancing soil fertility. Although reports are available on microbial biofilms in general; scanty information is published on biofilm formation by agriculturally important microorganisms (bacteria, fungi, bacterial-fungal) and their interactions in the ecosystem. Better understanding of agriculturally important bacterial-fungal communities and their interactions can have several implications on climate change, soil quality, plant nutrition, plant protection, bioremediation, etc. Understanding the factors and genes involved in biofilm formation will help to develop more effective strategies for sustainable and environment-friendly agriculture. The present review brings together fundamental aspects of biofilms, in relation to their formation, regulatory mechanisms, genes involved, and their application in different fields, with special emphasis on agriculturally important microbial biofilms. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Microbial Nitrogen-Cycle Gene Abundance in Soil of Cropland Abandoned for Different Periods.

Directory of Open Access Journals (Sweden)

Huhe

Full Text Available In Inner Mongolia, steppe grasslands face desertification or degradation because of human overuse and abandonment after inappropriate agricultural management. The soils in these abandoned croplands exist in heterogeneous environments characterized by widely fluctuating microbial growth. Quantitative polymerase chain reaction analysis of microbial genes encoding proteins involved in the nitrogen cycle was used to study Azotobacter species, nitrifiers, and denitrifiers in the soils from steppe grasslands and croplands abandoned for 2, 6, and 26 years. Except for nitrifying archaea and nitrous oxide-reducing bacteria, the relative genotypic abundance of microbial communities involved in nitrogen metabolism differed by approximately 2- to 10-fold between abandoned cropland and steppe grassland soils. Although nitrogen-cycle gene abundances varied with abandonment time, the abundance patterns of nitrogen-cycle genes separated distinctly into abandoned cropland versus light-grazing steppe grassland, despite the lack of any cultivation for over a quarter-century. Plant biomass and plant diversity exerted a significant effect on the abundance of microbial communities that mediate the nitrogen cycle (P < 0.002 and P < 0.03, respectively. The present study elucidates the ecology of bacteria that mediate the nitrogen cycle in recently abandoned croplands.

Key Concepts in Microbial Oceanography

Science.gov (United States)

Bruno, B. C.; Achilles, K.; Walker, G.; Weersing, K.; Team, A

2008-12-01

The Center for Microbial Oceanography: Research and Education (C-MORE) is a multi-institution Science and Technology Center, established by the National Science Foundation in 2006. C-MORE's research mission is to facilitate a more comprehensive understanding of the diverse assemblages of microorganisms in the sea, ranging from the genetic basis of marine microbial biogeochemistry including the metabolic regulation and environmental controls of gene expression, to the processes that underpin the fluxes of carbon, related bioelements, and energy in the marine environment. The C-MORE education and outreach program is focused on increasing scientific literacy in microbial oceanography among students, educators, and the general public. A first step toward this goal is defining the key concepts that constitute microbial oceanography. After lengthy discussions with scientists and educators, both within and outside C-MORE, we have arrived at six key concepts: 1) Marine microbes are very small and have been around for a long time; 2) Life on Earth could not exist without microbes; 3) Most marine microbes are beneficial; 4) Microbes are everywhere: they are extremely abundant and diverse; 5) Microbes significantly impact our global climate; and 6) There are new discoveries every day in the field of microbial oceanography. A C-MORE-produced brochure on these six key concepts will be distributed at the meeting. Advanced copies may be requested by email or downloaded from the C-MORE web site(http://cmore.soest.hawaii.edu/downloads/MO_key_concepts_hi-res.pdf). This brochure also includes information on career pathways in microbial oceanography, with the aim of broadening participation in the field. C-MORE is eager to work in partnership to incorporate these key concepts into other science literacy publications, particularly those involving ocean and climate literacy. We thank the following contributors and reviewers: P Chisholm, A Dolberry, and A Thompson (MIT); N Lawrence

Microbial Enzymatic Degradation of Biodegradable Plastics.

Science.gov (United States)

Roohi; Bano, Kulsoom; Kuddus, Mohammed; Zaheer, Mohammed R; Zia, Qamar; Khan, Mohammed F; Ashraf, Ghulam Md; Gupta, Anamika; Aliev, Gjumrakch

2017-01-01

The renewable feedstock derived biodegradable plastics are important in various industries such as packaging, agricultural, paper coating, garbage bags and biomedical implants. The increasing water and waste pollution due to the available decomposition methods of plastic degradation have led to the emergence of biodegradable plastics and biological degradation with microbial (bacteria and fungi) extracellular enzymes. The microbes utilize biodegradable polymers as the substrate under starvation and in unavailability of microbial nutrients. Microbial enzymatic degradation is suitable from bioremediation point of view as no waste accumulation occurs. It is important to understand the microbial interaction and mechanism involved in the enzymatic degradation of biodegradable plastics under the influence of several environmental factors such as applied pH, thermo-stability, substrate molecular weight and/or complexity. To study the surface erosion of polymer film is another approach for hydrolytic degradation characteristion. The degradation of biopolymer is associated with the production of low molecular weight monomer and generation of carbon dioxide, methane and water molecule. This review reported the degradation study of various existing biodegradable plastics along with the potent degrading microbes (bacteria and fungi). Patents available on plastic biodegradation with biotechnological significance is also summarized in this paper. This paper assesses that new disposal technique should be adopted for the degradation of polymers and further research is required for the economical production of biodegradable plastics along with their enzymatic degradation. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Two fundamentally different classes of microbial genes.

Science.gov (United States)

Wolf, Yuri I; Makarova, Kira S; Lobkovsky, Alexander E; Koonin, Eugene V

2016-11-07

The evolution of bacterial and archaeal genomes is highly dynamic and involves extensive horizontal gene transfer and gene loss 1-4 . Furthermore, many microbial species appear to have open pangenomes, where each newly sequenced genome contains more than 10% ORFans, that is, genes without detectable homologues in other species 5,6 . Here, we report a quantitative analysis of microbial genome evolution by fitting the parameters of a simple, steady-state evolutionary model to the comparative genomic data on the gene content and gene order similarity between archaeal genomes. The results reveal two sharply distinct classes of microbial genes, one of which is characterized by effectively instantaneous gene replacement, and the other consists of genes with finite, distributed replacement rates. These findings imply a conservative estimate of the size of the prokaryotic genomic universe, which appears to consist of at least a billion distinct genes. Furthermore, the same distribution of constraints is shown to govern the evolution of gene complement and gene order, without the need to invoke long-range conservation or the selfish operon concept 7 .

Relating Anaerobic Digestion Microbial Community and Process Function.

Science.gov (United States)

Venkiteshwaran, Kaushik; Bocher, Benjamin; Maki, James; Zitomer, Daniel

2015-01-01

Anaerobic digestion (AD) involves a consortium of microorganisms that convert substrates into biogas containing methane for renewable energy. The technology has suffered from the perception of being periodically unstable due to limited understanding of the relationship between microbial community structure and function. The emphasis of this review is to describe microbial communities in digesters and quantitative and qualitative relationships between community structure and digester function. Progress has been made in the past few decades to identify key microorganisms influencing AD. Yet, more work is required to realize robust, quantitative relationships between microbial community structure and functions such as methane production rate and resilience after perturbations. Other promising areas of research for improved AD may include methods to increase/control (1) hydrolysis rate, (2) direct interspecies electron transfer to methanogens, (3) community structure-function relationships of methanogens, (4) methanogenesis via acetate oxidation, and (5) bioaugmentation to study community-activity relationships or improve engineered bioprocesses.

Elevated temperature alters carbon cycling in a model microbial community

Science.gov (United States)

Mosier, A.; Li, Z.; Thomas, B. C.; Hettich, R. L.; Pan, C.; Banfield, J. F.

2013-12-01

Earth's climate is regulated by biogeochemical carbon exchanges between the land, oceans and atmosphere that are chiefly driven by microorganisms. Microbial communities are therefore indispensible to the study of carbon cycling and its impacts on the global climate system. In spite of the critical role of microbial communities in carbon cycling processes, microbial activity is currently minimally represented or altogether absent from most Earth System Models. Method development and hypothesis-driven experimentation on tractable model ecosystems of reduced complexity, as presented here, are essential for building molecularly resolved, benchmarked carbon-climate models. Here, we use chemoautotropic acid mine drainage biofilms as a model community to determine how elevated temperature, a key parameter of global climate change, regulates the flow of carbon through microbial-based ecosystems. This study represents the first community proteomics analysis using tandem mass tags (TMT), which enable accurate, precise, and reproducible quantification of proteins. We compare protein expression levels of biofilms growing over a narrow temperature range expected to occur with predicted climate changes. We show that elevated temperature leads to up-regulation of proteins involved in amino acid metabolism and protein modification, and down-regulation of proteins involved in growth and reproduction. Closely related bacterial genotypes differ in their response to temperature: Elevated temperature represses carbon fixation by two Leptospirillum genotypes, whereas carbon fixation is significantly up-regulated at higher temperature by a third closely related genotypic group. Leptospirillum group III bacteria are more susceptible to viral stress at elevated temperature, which may lead to greater carbon turnover in the microbial food web through the release of viral lysate. Overall, this proteogenomics approach revealed the effects of climate change on carbon cycling pathways and other

Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell

NARCIS (Netherlands)

Timmers, R.A.; Rothballer, M.; Strik, D.P.B.T.B.; Engel, M.; Schulz, M.; Hartmann, A.; Hamelers, H.V.M.; Buisman, C.J.N.

2012-01-01

The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into

Microbial cultures in open globe injuries in southern India.

Science.gov (United States)

Gupta, Arvind; Srinivasan, Renuka; Kaliaperumal, Subashini; Setia, Sajita

2007-07-01

To determine the risk factors leading to positive intraocular culture in patients with open globe injury. A prospective interventional study involving 110 eyes of 110 patients of more than 15 years of age, presenting with open globe injury, was undertaken. Emergency repair of the injured globe was done. Prolapsed intraocular tissue or aqueous humour was sent for microbial work up before repair. In endophthalmitis cases intravitreal antibiotics were given according to the antimicrobial sensitivity. Chi-square and logistic regression analysis were used to determine the risk factors. Fifty-six patients showed microbial contamination. Bacteria were cultured in 42 patients and fungi in 14 patients. Nineteen patients developed endophthalmitis, of which 18 patients showed microbial growth initially. In univariate analysis, initial visual acuity (8 mm, P 72 h, P 8 mm, P = 0.013) were associated with increased risk of positive microbial culture. Six patients had intraocular foreign body but were culture negative. Age, gender, site of injury and presence of cataract did not significantly affect the culture positivity. Microbial contamination is a risk factor for the development for endophthalmitis. Despite the high frequency of microbial contamination, it develops only in few cases. Systemic antibiotics, virulence of the organism and host factors play a role in the manifestation of endophthalmitis. Prophylaxis with intraocular antibiotics should be strongly considered in cases with poor vision at presentation, larger corneoscleral laceration, delayed surgical intervention and uveal tissue or vitreous prolapse.

The microbial mats of Pavilion Lake microbialites: examining the relationship between photosynthesis and carbonate precipitation

Science.gov (United States)

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

Theory of microbial genome evolution

Science.gov (United States)

Koonin, Eugene

Bacteria and archaea have small genomes tightly packed with protein-coding genes. This compactness is commonly perceived as evidence of adaptive genome streamlining caused by strong purifying selection in large microbial populations. In such populations, even the small cost incurred by nonfunctional DNA because of extra energy and time expenditure is thought to be sufficient for this extra genetic material to be eliminated by selection. However, contrary to the predictions of this model, there exists a consistent, positive correlation between the strength of selection at the protein sequence level, measured as the ratio of nonsynonymous to synonymous substitution rates, and microbial genome size. By fitting the genome size distributions in multiple groups of prokaryotes to predictions of mathematical models of population evolution, we show that only models in which acquisition of additional genes is, on average, slightly beneficial yield a good fit to genomic data. Thus, the number of genes in prokaryotic genomes seems to reflect the equilibrium between the benefit of additional genes that diminishes as the genome grows and deletion bias. New genes acquired by microbial genomes, on average, appear to be adaptive. Evolution of bacterial and archaeal genomes involves extensive horizontal gene transfer and gene loss. Many microbes have open pangenomes, where each newly sequenced genome contains more than 10% `ORFans', genes without detectable homologues in other species. A simple, steady-state evolutionary model reveals two sharply distinct classes of microbial genes, one of which (ORFans) is characterized by effectively instantaneous gene replacement, whereas the other consists of genes with finite, distributed replacement rates. These findings imply a conservative estimate of at least a billion distinct genes in the prokaryotic genomic universe.

The Canadian approach to microbial studies in nuclear waste management and disposal

International Nuclear Information System (INIS)

Stroes-Gascoyne, S.; Sargent, F.P.

1998-01-01

Many countries considering radioactive waste disposal have, or are considering programs to study and quantify microbial effects in terms of their particular disposal concept. Although there is an abundance of qualitative information, there is a need for quantitative data. Quantitative research should cover topics such as the kinetics of microbial activity in geological media, microbial effects on radionuclide migration in host rock (including effects of biofilms), tolerance to extreme conditions of radiation, heat and desiccation, microbially-influenced corrosion of waste containers and microbial gas production. The research should be performed in relevant disposal environments with the ultimate objective to quantify those effects that need to be included in models for predictive and safety assessment purposes. The Canadian approach to dealing with microbial effects involves a combination of pertinent, quantitative measurements from carefully designed laboratory studies and from large scale engineering experiments in AECL's Underground Research Laboratory (URL). The validity of these quantitative data is measured against observations from natural environments and analogues. An example is the viability of microbes in clay-based scaling materials. Laboratory studies have shown that the clay content of these barriers strongly affects microbial activity and movement. This is supported by natural environment and analogue observations that show clay deposits to contain very old tree segments and dense clay lenses in sediments to contain much smaller, less diverse and less active microbial populations than more porous sediments. This approach has allowed for focused, quantitative research on microbial effects in Canada. (author)

The role of the Consortia in the Italian wine production system and the impact of EU and national legislation

Directory of Open Access Journals (Sweden)

A Business Article by. Carlotta Gori

2014-06-01

Full Text Available The EU legislation has undergone a radical change in 2008, handling the Italian legislature the necessity to rethink on fundamental aspects of the national legislation. The changes were focused on the procedure of formation and revision of the designations of origin, opening up new and important perspectives for Consortia since, as inter-branch organizations, they can be acknowledged as representatives of the economic activities linked to the production and at least to one of the phases of processing or trade. The Consortium has become responsible for production specification, stock managing, new registration of the vines to a DO, supervision and protection.

Bioremediation potential of toxics by manipulation of deep terrestrial subsurface ecosystems

International Nuclear Information System (INIS)

Phelps, T.J.

1990-01-01

Mixed physiological types of bacteria in consortia recovered from subsurface contaminated sediments degrade mixed organic wastes containing carbon-rich (benzene, xylene, toluene) and halogenated hydrocarbon substrates (chlorobenzene, trichloroethylene, dichloroethylenes, vinyl chloride) in column bioreactors when provided with oxygen and methane and/or propane substrates. In expanded bed bioreactors degradation proceeds to 99% completion for several organic and chlorocarbon contaminants (60% for tetrachloroethylene) to carbon dioxide on repeated cycles in 21 days with little loss of volatiles in the control bioreactor except for a 70% loss of vinyl chloride in the control. Biodegradation is most efficient when the microbial consortia is maintained in a suboptimal nutritional state which can be monitored by ratios of endogenous storage lipid (poly beta-hydroxy alkanoic acid, PHA) to total phospholipid ester-linked fatty acids (PLFA). Under the best conditions the efficiency of biodegradation was 50-65 moles substrate (propane or propane + methane)/mole of TEC degraded. The microbial communities showed a rich diversity of microbes based on PLFA biomarkers. The effects of adding methane and/or propane in inducing specific subsets of the microbial community can readily be detected in the PLFA biomarker. Despite the presence of carbon rich substrates (benzene, toluene, xylene) in the mixed wastes, no evidence of plugging of interstitial spaces by exopolysaccharide was detected

Exometabolomic Analysis of Cross-Feeding Metabolites.

Science.gov (United States)

Lubbe, Andrea; Bowen, Benjamin P; Northen, Trent

2017-10-04

Microbial consortia have the potential to perform complex, industrially important tasks. The design of microbial consortia requires knowledge of the substrate preferences and metabolic outputs of each member, to allow understanding of potential interactions such as competition and beneficial metabolic exchange. Here, we used exometabolite profiling to follow the resource processing by a microbial co-culture of two biotechnologically relevant microbes, the bacterial cellulose degrader Cellulomonas fimi, and the oleaginous yeast Yarrowia lipolytica. We characterized the substrate preferences of the two strains on compounds typically found in lignocellulose hydrolysates. This allowed prediction that specific sugars resulting from hemicellulose polysaccharide degradation by C. fimi may serve as a cross-feeding metabolites to Y. lipolytica in co-culture. We also showed that products of ionic liquid-treated switchgrass lignocellulose degradation by C. fimi were channeled to Y. lipolytica in a co-culture. Additionally, we observed metabolites, such as shikimic acid accumulating in the co-culture supernatants, suggesting the potential for producing interesting co-products. Insights gained from characterizing the exometabolite profiles of individual and co-cultures of the two strains can help to refine this interaction, and guide strategies for making this an industrially viable co-culture to produce valuable products from lignocellulose material.

Microbial Rechargeable Battery

NARCIS (Netherlands)

Molenaar, Sam D.; Mol, Annemerel R.; Sleutels, Tom H.J.A.; Heijne, Ter Annemiek; Buisman, Cees J.N.

2016-01-01

Bioelectrochemical systems hold potential for both conversion of electricity into chemicals through microbial electrosynthesis (MES) and the provision of electrical power by oxidation of organics using microbial fuel cells (MFCs). This study provides a proof of concept for a microbial

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

Directory of Open Access Journals (Sweden)

Margaux eMesle

2015-06-01

Full Text Available 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 rocks, shales 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 of the carbon and energy source. Indeed, bitumen has a colloidal structure that may limit the accessibility to 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.

Characteristics of microbial community involved in early biofilms formation under the influence of wastewater treatment plant effluent.

Science.gov (United States)

Peng, Yuke; Li, Jie; Lu, Junling; Xiao, Lin; Yang, Liuyan

2018-04-01

Effluents from wastewater treatment plants (WWTPs) containing microorganisms and residual nutrients can influence the biofilm formation. Although the process and mechanism of bacterial biofilm formation have been well characterized, little is known about the characteristics and interaction of bacteria, archaea and eukaryotes in the early colonization, especially under the influence of WWTP effluent. The aim of this study was to characterize the important bacterial, archaeal and eukaryotic species in the early stage of biofilm formation downstream of the WWTP outlet. Water and biofilm samples were collected 24 and 48hr after the deposition of bio-cords in the stream. Illumina Miseq sequencing of the 16S and 18S rDNA showed that, among the three domains, the bacterial biofilm community had the largest alpha and beta diversity. The early bacterial colonizers appeared to be "biofilm-specific", with only a few dominant operational taxonomic units (OTUs) shared between the biofilm and the ambient water environment. Alpha-proteobacteria and Ciliophora tended to dominate the bacterial and eukaryotic communities, respectively, of the early biofilm already at 24hr, whereas archaea played only a minor role during the early stage of colonization. The network analysis showed that the three domains of microbial community connected highly during the early colonization and it might be a characteristic of the microbial communities in the biofilm formation process where co-occurrence relationships could drive coexistence and diversity maintenance within the microbial communities. Copyright © 2017. Published by Elsevier B.V.

Switchgrass ecotypes alter microbial contribution to deep-soil C

Science.gov (United States)

Roosendaal, Damaris; Stewart, Catherine E.; Denef, Karolien; Follett, Ronald F.; Pruessner, Elizabeth; Comas, Louise H.; Varvel, Gary E.; Saathoff, Aaron; Palmer, Nathan; Sarath, Gautam; Jin, Virginia L.; Schmer, Marty; Soundararajan, Madhavan

2016-05-01

Switchgrass (Panicum virgatum L.) is a C4, perennial grass that is being developed as a bioenergy crop for the United States. While aboveground biomass production is well documented for switchgrass ecotypes (lowland, upland), little is known about the impact of plant belowground productivity on microbial communities down deep in the soil profiles. Microbial dynamics in deeper soils are likely to exert considerable control on ecosystem services, including C and nutrient cycles, due to their involvement in such processes as soil formation and ecosystem biogeochemistry. Differences in root biomass and rooting characteristics of switchgrass ecotypes could lead to distinct differences in belowground microbial biomass and microbial community composition. We quantified root abundance and root architecture and the associated microbial abundance, composition, and rhizodeposit C uptake for two switchgrass ecotypes using stable-isotope probing of microbial phospholipid fatty acids (PLFAs) after 13CO2 pulse-chase labeling. Kanlow, a lowland ecotype with thicker roots, had greater plant biomass above- and belowground (g m-2), greater root mass density (mg cm-3), and lower specific root length (m g-1) compared to Summer, an upland ecotype with finer root architecture. The relative abundance of bacterial biomarkers dominated microbial PLFA profiles for soils under both Kanlow and Summer (55.4 and 53.5 %, respectively; P = 0.0367), with differences attributable to a greater relative abundance of Gram-negative bacteria in soils under Kanlow (18.1 %) compared to soils under Summer (16.3 %; P = 0.0455). The two ecotypes also had distinctly different microbial communities process rhizodeposit C: greater relative atom % 13C excess in Gram-negative bacteria (44.1 ± 2.3 %) under the thicker roots of Kanlow and greater relative atom % 13C excess in saprotrophic fungi under the thinner roots of Summer (48.5 ± 2.2 %). For bioenergy production systems, variation between switchgrass

Functional Gene Diversity and Metabolic Potential of the Microbial Community in an Estuary-Shelf Environment

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Yu Wang

2017-06-01

Full Text Available Microbes play crucial roles in various biogeochemical processes in the ocean, including carbon (C, nitrogen (N, and phosphorus (P cycling. Functional gene diversity and the structure of the microbial community determines its metabolic potential and therefore its ecological function in the marine ecosystem. However, little is known about the functional gene composition and metabolic potential of bacterioplankton in estuary areas. The East China Sea (ECS is a dynamic marginal ecosystem in the western Pacific Ocean that is mainly affected by input from the Changjiang River and the Kuroshio Current. Here, using a high-throughput functional gene microarray (GeoChip, we analyzed the functional gene diversity, composition, structure, and metabolic potential of microbial assemblages in different ECS water masses. Four water masses determined by temperature and salinity relationship showed different patterns of functional gene diversity and composition. Generally, functional gene diversity [Shannon–Weaner’s H and reciprocal of Simpson’s 1/(1-D] in the surface water masses was higher than that in the bottom water masses. The different presence and proportion of functional genes involved in C, N, and P cycling among the bacteria of the different water masses showed different metabolic preferences of the microbial populations in the ECS. Genes involved in starch metabolism (amyA and nplT showed higher proportion in microbial communities of the surface water masses than of the bottom water masses. In contrast, a higher proportion of genes involved in chitin degradation was observed in microorganisms of the bottom water masses. Moreover, we found a higher proportion of nitrogen fixation (nifH, transformation of hydroxylamine to nitrite (hao and ammonification (gdh genes in the microbial communities of the bottom water masses compared with those of the surface water masses. The spatial variation of microbial functional genes was significantly correlated

Microbial Murders Crime Scene Investigation: An Active Team-Based Learning Project that Enhances Student Enthusiasm and Comprehension of Clinical Microbial Pathogens.

Science.gov (United States)

Steel, J Jordan

2017-01-01

Microbial disease knowledge is a critical component of microbiology courses and is beneficial for many students' future careers. Microbiology courses traditionally cover core concepts through lectures and labs, but specific instruction on microbial diseases varies greatly depending on the instructor and course. A common project involves students researching and presenting a disease to the class. This method alone is not very effective, and course evaluations have consistently indicated that students felt they lacked adequate disease knowledge; therefore, a more hands-on and interactive disease project was developed called Microbial Murders. For this team-based project, a group of students chooses a pathogen, researches the disease, creates a "mugshot" of the pathogen, and develops a corresponding "crime scene," where a hypothetical patient has died from the microbe. Each group gives a presentation introducing the microbial pathogen, signs/symptoms, treatments, and overall characteristics. The students then visit each other's crime scenes to match the pathogen with the correct crime scene by critically thinking through the clues. This project has shown remarkable success. Surveys indicate that 73% of students thought the project helped them understand the material and 84% said it was worth their time. Student participation, excitement, understanding, and application of microbial disease knowledge have increased and are evident through an increase in course evaluations and in student assessment scores. This project is easy to implement and can be used in a wide variety of biology, microbiology, or health classes for any level (middle school through college).

Microbial biosensors

International Nuclear Information System (INIS)

Le Yu; Chen, Wilfred; Mulchandani, Ashok

2006-01-01

A microbial biosensor is an analytical device that couples microorganisms with a transducer to enable rapid, accurate and sensitive detection of target analytes in fields as diverse as medicine, environmental monitoring, defense, food processing and safety. The earlier microbial biosensors used the respiratory and metabolic functions of the microorganisms to detect a substance that is either a substrate or an inhibitor of these processes. Recently, genetically engineered microorganisms based on fusing of the lux, gfp or lacZ gene reporters to an inducible gene promoter have been widely applied to assay toxicity and bioavailability. This paper reviews the recent trends in the development and application of microbial biosensors. Current advances and prospective future direction in developing microbial biosensor have also been discussed

Childhood microbial keratitis

Directory of Open Access Journals (Sweden)

Abdullah G Al Otaibi

2012-01-01

Conclusion: Children with suspected microbial keratitis require comprehensive evaluation and management. Early recognition, identifying the predisposing factors and etiological microbial organisms, and instituting appropriate treatment measures have a crucial role in outcome. Ocular trauma was the leading cause of childhood microbial keratitis in our study.

Response of Functional Structure of Soil Microbial Community to Multi-level Nitrogen Additions on the Central Tibetan Plateau

Science.gov (United States)

Zhang, G.; Yuan, Y.

2015-12-01

The use of fossil fuels and fertilizers has increased the amount of biologically reactive nitrogen in the atmosphere over the past century. Tibet is the one of the most threatened regions by nitrogen deposition, thus understanding how its microbial communities function maybe of high importance to predicting microbial responses to nitrogen deposition. Here we describe a short-time nitrogen addition conducted in an alpine steppe ecosystem to investigate the response of functional structure of soil microbial community to multi-level nitrogen addition. Using a GeoChip 4.0, we showed that functional diversities and richness of functional genes were unchanged at low level of nitrogen fertilizer inputs (=40 kg N ha-1 yr-1). Detrended correspondence analysis indicated that the functional structure of microbial communities was markedly different across the nitrogen gradients. Most C degradation genes whose abundances significantly increased under elevated N fertilizer were those involved in the degradation of relatively labile C (starch, hemicellulose, cellulose), whereas the abundance of certain genes involved in the degradation of recalcitrant C (i.e. lignin) was largely decreased (such as manganese peroxidase, mnp). The results suggest that the elevated N fertilization rates might significantly accelerate the labile C degradation, but might not spur recalcitrant C degradation. The combined effect of gdh and ureC genes involved in N cycling appeared to shift the balance between ammonia and organic N toward organic N ammonification and hence increased the N mineralization potential. Moreover, Urease directly involved in urea mineralization significantly increased. Lastly, Canonical correspondence analysis showed that soil (TOC+NH4++NO3-+NO2-+pH) and plant (Aboveground plant productivity + Shannon Diversity) variables could explain 38.9% of the variation of soil microbial community composition. On the basis of above observations, we predict that increasing of nitrogen

Microbial and viral pathogens in colorectal cancer.

LENUS (Irish Health Repository)

Collins, Danielle

2011-05-01

The heterogenetic and sporadic nature of colorectal cancer has led to many epidemiological associations with causes of this disease. As our understanding of the underlying molecular processes in colorectal-cancer develops, the concept of microbial-epithelial interactions as an oncogenic trigger might provide a plausible hypothesis for the pathogenesis of colorectal cancer. By contrast with other cancers of the gastrointestinal tract (gastric carcinoma, mucosa-associated lymphoid-tissue lymphoma), a direct causal link between microbial infection (bacteria and viruses) and colorectal carcinoma has not been established. Studies support the involvement of these organisms in oncogenesis, however, in colorectal cancer, clinical data are lacking. Here, we discuss current evidence (both in vitro and clinical studies), and focus on a putative role for bacterial and viral pathogens as a cause of colorectal cancer.

Microbial and viral pathogens in colorectal cancer.

LENUS (Irish Health Repository)

Collins, Danielle

2012-02-01

The heterogenetic and sporadic nature of colorectal cancer has led to many epidemiological associations with causes of this disease. As our understanding of the underlying molecular processes in colorectal-cancer develops, the concept of microbial-epithelial interactions as an oncogenic trigger might provide a plausible hypothesis for the pathogenesis of colorectal cancer. By contrast with other cancers of the gastrointestinal tract (gastric carcinoma, mucosa-associated lymphoid-tissue lymphoma), a direct causal link between microbial infection (bacteria and viruses) and colorectal carcinoma has not been established. Studies support the involvement of these organisms in oncogenesis, however, in colorectal cancer, clinical data are lacking. Here, we discuss current evidence (both in vitro and clinical studies), and focus on a putative role for bacterial and viral pathogens as a cause of colorectal cancer.

Microorganism selection and performance in bioslurry reactors treating PAH-contaminated soil.

Science.gov (United States)

Cassidy, D P; Hudak, A J

2002-09-01

A continuous-flow reactor (CSTR) and a soil slurry-sequencing batch reactor (SS-SBR) were operated in 81 vessels for 200 days to treat a soil contaminated with polycyclic aromatic hydrocarbons (PAH). Filtered slurry samples were used to quantify bulk biosurfactant concentrations and PAH emulsification. Concentrations of Corynebacterium aquaticum, Flavobacterium mizutaii, Mycobacterium gastri, Pseudomonas aeruginosa, and Pseudomonas putida were determined using fatty acid methyl ester (FAME) analysis. The CSTR and SS-SBR selected microbial consortia with markedly different surfactant-producing and PAH-degrading abilities. Biosurfactant levels in the SS-SBR reached 4 times the critical micelle concentration (CMC) that resulted in considerable emulsification of PAH. In contrast, CSTR operation resulted in nomeasurable biosurfactant production. Total PAH removal efficiency was 93% in the SS-SBR, compared with only 66% in the CSTR, and stripping of PAH was 3 times less in the SS-SBR. Reversing the mode of operation on day 100 caused a complete reversal in microbial consortia and in reactor performance by day 140. These results show that bioslurry reactor operation can be manipulated to control overall reactor performance.

FY 1999 report on the results of the project on the industrial science technology R and D. Development of utilization technology of biological resources such as bioconsortium system (Development of the petroleum substituting fuel production technology using living organisms); 1999 nendo sangyo kagaku gijutsu kenkyu kaihatsu jigyo. Fukugou seibutsukei tou seibutsu shigen riyo gijutsu kaihatsu (Seibutsu riyo sekiyu daitai nenryo seizo gijutsu no kaihatsu) seika hokokusho

Energy Technology Data Exchange (ETDEWEB)

NONE

2000-03-01

For the purpose of establishing the high-grade utilization technology of unused seaweed/algae and production technology of useful substances using high-grade functions of bioconsortia, study was conducted, and the FY 1999 results were reported. In the analysis of the ocean environment adaptation mechanism, the R and D were made of a selection method of the marine microbial consortia using korormicin. In the study of the high-grade utilization technology of unused resources/substances such as marine-producing algae, several tens of the carrageenase producing microbial consortia were acquired from the surface of seaweed, and some carrageenase producing bacteria and non-producing bacteria were acquired by isolating as pure strains. In the study of the petroleum substituting useful resource production technology, developed was a monitoring system of the environmental stress using marine-product invertebrate/micro-algae symbiotic system. In the study of the high-grade utilization of large useful algae, elucidation of the related genes, fabrication of variants and analysis of genes were carried out for the bacterium BUP-7 which indicates activity of growth acceleration/shape formation of seaweed. (NEDO)

FY 1998 R and D of utilization of biological resources such as those in bioconsortia. Report on development results of techniques for utilization/production of organisms in bioconsortia; 1998 nendo fukugo seibutsukeinado seibutsu shigen riyo gijutsu kaihatsu seika hokokusho. Fukugo seibutsukei riyo seisan gijutsu no kaihatsu

Energy Technology Data Exchange (ETDEWEB)

NONE

1999-03-01

The objectives are set to analyze functions and interactions of organisms having specific functions, to develop the techniques for isolating and cultivating the constituent organisms, and thereby to develop the techniques for their industrial utilization, in order to develop the techniques for handling organisms in bioconsortia as the techniques to utilize their functions, e.g., production and decomposition of materials, and also to develop the techniques for culturing/controlling microorganisms in bioconsortia and for strengthening their functions. The FY 1998 themes are development of the functional material production technology, and comprehensive study for the project. More concretely, the former includes histochemical analytical technology (development of techniques for detecting microorganisms in soil, and of techniques for in-situ detection/isolation of specific microorganisms in bioconsortia and for analysis their functions), isolation and culture technology (development of detection, separation and cultivation technology of microorganisms that are not easily cultured), functional substance production technology (technical utilization of microbial consortia for production of environment-friendly oil/water separation polymers), and functional material production technology (development of methods for artificial gene exchange in microbial consortia). (NEDO)

The importance of anabolism in microbial control over soil carbon storage

Energy Technology Data Exchange (ETDEWEB)

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

2017-07-25

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

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

Science.gov (United States)

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.

Anaerobic microbial transformations of radioactive wastes in subsurface environments

International Nuclear Information System (INIS)

Francis, A.J.

1984-01-01

Radioactive wastes disposed of in subsurface environments contain a variety of radionuclides and organic compounds. Microorganisms play a major role in the transformation of organic and inorganic constituents of the waste and are partly responsible for the problems encountered at the waste disposal sites. These include microbial degradation of waste forms resulting in trench cover subsidence, migration of radionuclides, and production of radioactive gases such as 14 CO 2 , 14 CH 4 , HT, and CH 3 T. Microbial processes involved in solubilization, mobilization, and immobilization of toxic metals under aerobic and anaerobic conditions are reviewed. Complexing agents and several organic acids produced by microbial action affect mobilization of radionuclides and heavy metals from the wastes. Microorganisms play a significant role in the transformation and cycling of tritium in the environment by (i) oxidation of tritium and tritiated methane under aerobic conditions and (ii) production of tritium and tritiated methane from wastes containing tritiated water and organic compounds under anaerobic conditions. 23 references, 2 figures, 2 tables

Quality of Online Chat Reference Answers Differ between Local and Consortium Library Staff: Providing Consortium Staff with More Local Information Can Mitigate these Differences. A Review of: Meert, D.L., & Given, L.M. (2009. Measuring quality in chat reference consortia: A comparative analysis of responses to users’ queries.” College & Research Libraries, 70(1, 71‐84.

Directory of Open Access Journals (Sweden)

Laura Newton Miller

2010-03-01

Full Text Available Objective – To evaluate the quality of answers from a 24/7 online chat reference service by comparing the responses given by local and consortia library staff using in‐house reference standards, and by assessing whether or not the questions were answered in real time.Design – Comparative analysis of online chat reference transcripts.Setting – Large academic library in Alberta, Canada.Subjects – A total of online chat reference transcripts from the first year of consortium service were analyzed for this study. Of these, 252 were answered by local library staff and 226 from consortia (non‐local library staff.Methods – A stratified random sample of 1,402 transcripts were collected from the first year of consortium service (beginning of October to end of April. This method was then applied monthly, resulting in a sample size of 478 transcripts. In the first part of the study, responses were coded within the transcripts with a “yes” or “no” label to determine if they met the standards set by the local university library’s reference management. Reference transaction standards included questions regarding whether or not correct information or instructions were given and if not, whether the user was referred to an authoritative source for the correct information. The second part of the study coded transcripts with a “yes” or “no” designation as to whether the user received an answer from the staff member in “real time” and if not, was further analyzed to determine why the user did not receive a real‐time response. Each transcript was coded as reflecting one of four “question categories” that included library user information, request for instruction, request for academic information, and miscellaneous/non‐library questions.Main Results – When all question types were integrated, analysis revealed that local library staff met reference transaction standards 94% of the time. Consortia staff met these same

Microbial Regulation of Glucose Metabolism and Insulin Resistance

Directory of Open Access Journals (Sweden)

Silke Crommen

2017-12-01

Full Text Available Type 2 diabetes is a combined disease, resulting from a hyperglycemia and peripheral and hepatic insulin resistance. Recent data suggest that the gut microbiota is involved in diabetes development, altering metabolic processes including glucose and fatty acid metabolism. Thus, type 2 diabetes patients show a microbial dysbiosis, with reduced butyrate-producing bacteria and elevated potential pathogens compared to metabolically healthy individuals. Furthermore, probiotics are a known tool to modulate the microbiota, having a therapeutic potential. Current literature will be discussed to elucidate the complex interaction of gut microbiota, intestinal permeability and inflammation leading to peripheral and hepatic insulin resistance. Therefore, this review aims to generate a deeper understanding of the underlying mechanism of potential microbial strains, which can be used as probiotics.

Application of culture-dependent and culture-independent methods for the identification of Lactobacillus kefiranofaciens in microbial consortia present in kefir grains.

Science.gov (United States)

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.

Degradation of 1,1,2,2-tetrachloroethane and accumulation of vinyl chloride in wetland sediment microcosms and in situ porewater: biogeochemical controls and associations with microbial communities

Science.gov (United States)

Lorah, Michelle M.; Voytek, Mary A.

2004-05-01

(acetotrophs) appear to be involved in the biodegradation of VC. The relative abundance of Methanosarcinaceae, the only methanogen group with acetotrophic members, doubled in microcosms in which degradation of VC was observed. In addition, molecular analyses using primers specific for known dehalorespiring bacteria in the Dehalococcoides and Desulfuromonas groups showed the presence of these bacteria in microcosm slurry from the site that showed the highest VC production and degradation. Determination of biogeochemical controls and microbial consortia involved in TeCA degradation is leading to a better understanding of the heterogeneity in biodegradation rates and daughter product distribution in the wetland, improving capabilities for developing remediation and monitoring plans.

Study on microbial persistence in end-stage idiopathic dilated cardiomyopathy.

NARCIS (Netherlands)

Leeuw, N. de; Melchers, W.J.G.; Balk, A.H.M.M.; Jonge, N. de; Galama, J.M.D.

1999-01-01

Microbial persistence may be involved in the pathogenesis of idiopathic dilated cardiomyopathy (IDC). Therefore, we evaluated the role of various cardiopathogenic microorganisms in patients with end-stage IDC. In a previous study, we did not find evidence for the persistence of enterovirus RNA in