Mineralization and Detoxification of the Carcinogenic Azo Dye Congo Red and Real Textile Effluent by a Polyurethane Foam Immobilized Microbial Consortium in an Upflow Column Bioreactor.

PubMed

Lade, Harshad; Govindwar, Sanjay; Paul, Diby

2015-06-16

A microbial consortium that is able to grow in wheat bran (WB) medium and decolorize the carcinogenic azo dye Congo red (CR) was developed. The microbial consortium was immobilized on polyurethane foam (PUF). Batch studies with the PUF-immobilized microbial consortium showed complete removal of CR dye (100 mg·L-1) within 12 h at pH 7.5 and temperature 30 ± 0.2 °C under microaerophilic conditions. Additionally, 92% American Dye Manufactureing Institute (ADMI) removal for real textile effluent (RTE, 50%) was also observed within 20 h under the same conditions. An upflow column reactor containing PUF-immobilized microbial consortium achieved 99% CR dye (100 mg·L-1) and 92% ADMI removal of RTE (50%) at 35 and 20 mL·h-l flow rates, respectively. Consequent reduction in TOC (83 and 79%), COD (85 and 83%) and BOD (79 and 78%) of CR dye and RTE were also observed, which suggested mineralization. The decolorization process was traced to be enzymatic as treated samples showed significant induction of oxidoreductive enzymes. The proposed biodegradation pathway of the dye revealed the formation of lower molecular weight compounds. Toxicity studies with a plant bioassay and acute tests indicated that the PUF-immobilized microbial consortium favors detoxification of the dye and textile effluents.

Mineralization and Detoxification of the Carcinogenic Azo Dye Congo Red and Real Textile Effluent by a Polyurethane Foam Immobilized Microbial Consortium in an Upflow Column Bioreactor

PubMed Central

Lade, Harshad; Govindwar, Sanjay; Paul, Diby

2015-01-01

A microbial consortium that is able to grow in wheat bran (WB) medium and decolorize the carcinogenic azo dye Congo red (CR) was developed. The microbial consortium was immobilized on polyurethane foam (PUF). Batch studies with the PUF-immobilized microbial consortium showed complete removal of CR dye (100 mg·L−1) within 12 h at pH 7.5 and temperature 30 ± 0.2 °C under microaerophilic conditions. Additionally, 92% American Dye Manufactureing Institute (ADMI) removal for real textile effluent (RTE, 50%) was also observed within 20 h under the same conditions. An upflow column reactor containing PUF-immobilized microbial consortium achieved 99% CR dye (100 mg·L−1) and 92% ADMI removal of RTE (50%) at 35 and 20 mL·h−l flow rates, respectively. Consequent reduction in TOC (83 and 79%), COD (85 and 83%) and BOD (79 and 78%) of CR dye and RTE were also observed, which suggested mineralization. The decolorization process was traced to be enzymatic as treated samples showed significant induction of oxidoreductive enzymes. The proposed biodegradation pathway of the dye revealed the formation of lower molecular weight compounds. Toxicity studies with a plant bioassay and acute tests indicated that the PUF-immobilized microbial consortium favors detoxification of the dye and textile effluents. PMID:26086710

The ocean sampling day consortium.

PubMed

Kopf, Anna; Bicak, Mesude; Kottmann, Renzo; Schnetzer, Julia; Kostadinov, Ivaylo; Lehmann, Katja; Fernandez-Guerra, Antonio; Jeanthon, Christian; Rahav, Eyal; Ullrich, Matthias; Wichels, Antje; Gerdts, Gunnar; Polymenakou, Paraskevi; Kotoulas, Giorgos; Siam, Rania; Abdallah, Rehab Z; Sonnenschein, Eva C; Cariou, Thierry; O'Gara, Fergal; Jackson, Stephen; Orlic, Sandi; Steinke, Michael; Busch, Julia; Duarte, Bernardo; Caçador, Isabel; Canning-Clode, João; Bobrova, Oleksandra; Marteinsson, Viggo; Reynisson, Eyjolfur; Loureiro, Clara Magalhães; Luna, Gian Marco; Quero, Grazia Marina; Löscher, Carolin R; Kremp, Anke; DeLorenzo, Marie E; Øvreås, Lise; Tolman, Jennifer; LaRoche, Julie; Penna, Antonella; Frischer, Marc; Davis, Timothy; Katherine, Barker; Meyer, Christopher P; Ramos, Sandra; Magalhães, Catarina; Jude-Lemeilleur, Florence; Aguirre-Macedo, Ma Leopoldina; Wang, Shiao; Poulton, Nicole; Jones, Scott; Collin, Rachel; Fuhrman, Jed A; Conan, Pascal; Alonso, Cecilia; Stambler, Noga; Goodwin, Kelly; Yakimov, Michael M; Baltar, Federico; Bodrossy, Levente; Van De Kamp, Jodie; Frampton, Dion Mf; Ostrowski, Martin; Van Ruth, Paul; Malthouse, Paul; Claus, Simon; Deneudt, Klaas; Mortelmans, Jonas; Pitois, Sophie; Wallom, David; Salter, Ian; Costa, Rodrigo; Schroeder, Declan C; Kandil, Mahrous M; Amaral, Valentina; Biancalana, Florencia; Santana, Rafael; Pedrotti, Maria Luiza; Yoshida, Takashi; Ogata, Hiroyuki; Ingleton, Tim; Munnik, Kate; Rodriguez-Ezpeleta, Naiara; Berteaux-Lecellier, Veronique; Wecker, Patricia; Cancio, Ibon; Vaulot, Daniel; Bienhold, Christina; Ghazal, Hassan; Chaouni, Bouchra; Essayeh, Soumya; Ettamimi, Sara; Zaid, El Houcine; Boukhatem, Noureddine; Bouali, Abderrahim; Chahboune, Rajaa; Barrijal, Said; Timinouni, Mohammed; El Otmani, Fatima; Bennani, Mohamed; Mea, Marianna; Todorova, Nadezhda; Karamfilov, Ventzislav; Ten Hoopen, Petra; Cochrane, Guy; L'Haridon, Stephane; Bizsel, Kemal Can; Vezzi, Alessandro; Lauro, Federico M; Martin, Patrick; Jensen, Rachelle M; Hinks, Jamie; Gebbels, Susan; Rosselli, Riccardo; De Pascale, Fabio; Schiavon, Riccardo; Dos Santos, Antonina; Villar, Emilie; Pesant, Stéphane; Cataletto, Bruno; Malfatti, Francesca; Edirisinghe, Ranjith; Silveira, Jorge A Herrera; Barbier, Michele; Turk, Valentina; Tinta, Tinkara; Fuller, Wayne J; Salihoglu, Ilkay; Serakinci, Nedime; Ergoren, Mahmut Cerkez; Bresnan, Eileen; Iriberri, Juan; Nyhus, Paul Anders Fronth; Bente, Edvardsen; Karlsen, Hans Erik; Golyshin, Peter N; Gasol, Josep M; Moncheva, Snejana; Dzhembekova, Nina; Johnson, Zackary; Sinigalliano, Christopher David; Gidley, Maribeth Louise; Zingone, Adriana; Danovaro, Roberto; Tsiamis, George; Clark, Melody S; Costa, Ana Cristina; El Bour, Monia; Martins, Ana M; Collins, R Eric; Ducluzeau, Anne-Lise; Martinez, Jonathan; Costello, Mark J; Amaral-Zettler, Linda A; Gilbert, Jack A; Davies, Neil; Field, Dawn; Glöckner, Frank Oliver

2015-01-01

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.

Deeper insight into the structure of the anaerobic digestion microbial community; the biogas microbiome database is expanded with 157 new genomes.

PubMed

Treu, Laura; Kougias, Panagiotis G; Campanaro, Stefano; Bassani, Ilaria; Angelidaki, Irini

2016-09-01

This research aimed to better characterize the biogas microbiome by means of high throughput metagenomic sequencing and to elucidate the core microbial consortium existing in biogas reactors independently from the operational conditions. Assembly of shotgun reads followed by an established binning strategy resulted in the highest, up to now, extraction of microbial genomes involved in biogas producing systems. From the 236 extracted genome bins, it was remarkably found that the vast majority of them could only be characterized at high taxonomic levels. This result confirms that the biogas microbiome is comprised by a consortium of unknown species. A comparative analysis between the genome bins of the current study and those extracted from a previous metagenomic assembly demonstrated a similar phylogenetic distribution of the main taxa. Finally, this analysis led to the identification of a subset of common microbes that could be considered as the core essential group in biogas production. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Ocean Sampling Day Consortium

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

Kopf, Anna; Bicak, Mesude; Kottmann, Renzo

In this study, Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and theirmore » embedded functional traits.« less

The Ocean Sampling Day Consortium

DOE PAGES

Kopf, Anna; Bicak, Mesude; Kottmann, Renzo; ...

2015-06-19

In this study, Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and theirmore » embedded functional traits.« less

Biodegradation of diesel oil by a novel microbial consortium: comparison between co-inoculation with biosurfactant-producing strain and exogenously added biosurfactants.

PubMed

Mnif, Inès; Mnif, Sami; Sahnoun, Rihab; Maktouf, Sameh; Ayedi, Younes; Ellouze-Chaabouni, Semia; Ghribi, Dhouha

2015-10-01

Bioremediation, involving the use of microorganisms to detoxify or remove pollutants, is the most interesting strategy for hydrocarbon remediation. In this aim, four hydrocarbon-degrading bacteria were isolated from oil-contaminated soil in Tunisia. They were identified by the 16S rDNA sequence analysis, as Lysinibacillus bronitolerans RI18 (KF964487), Bacillus thuringiensis RI16 (KM111604), Bacillus weihenstephanensis RI12 (KM094930), and Acinetobacter radioresistens RI7 (KJ829530). Moreover, a lipopeptide biosurfactant produced by Bacillus subtilis SPB1, confirmed to increase diesel solubility, was tested to increase diesel biodegradation along with co-inoculation with two biosurfactant-producing strains. Culture studies revealed the enhancement of diesel biodegradation by the selected consortium with the addition of SPB1 lipopeptide and in the cases of co-inoculation by biosurfactant-producing strain. In fact, an improvement of about 38.42 and 49.65 % of diesel degradation was registered in the presence of 0.1 % lipopeptide biosurfactant and when culturing B. subtilis SPB1 strain with the isolated consortium, respectively. Furthermore, the best improvement, evaluated to about 55.4 %, was recorded when using the consortium cultured with B. subtilis SPB1 and A. radioresistens RI7 strains. Gas chromatography analyses were correlated with the gravimetric evaluation of the residual hydrocarbons. Results suggested the potential applicability of the selected consortium along with the ex situ- and in situ-added biosurfactant for the effective bioremediation of diesel-contaminated water and soil.

Performance assessment of a submerged membrane bioreactor using a novel microbial consortium.

PubMed

Chon, Kangmin; Lee, Kyungpyo; Kim, In-Soo; Jang, Am

2016-06-01

The performance of a submerged membrane bioreactor (MBR) with and without a novel microbial consortium (NMBR vs. CMBR) was compared to provide deeper insights into the effects of changes in water quality and dissolved organic matter (DOM) characteristics by a novel microbial consortium on the fouling characteristics of MBR processes. Despite similar operating conditions and identical DOM properties in the feed waters, NMBR exhibited a lower propensity to release polysaccharide-like compounds with low molecular weight by bacterial activities compared to CMBR. These compounds have a great fouling potential for MBR processes. Therefore, an increase in the transmembrane pressure (TMP) of NMBR (normalized TMP (TMP/TMP0): 1.14) was much slower and less significant than that observed in CMBR (TMP/TMP0: 2.61). These observations imply that the novel microbial consortium can efficiently mitigate membrane fouling by hydrophilic DOM in MBR processes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Electricity from methane by reversing methanogenesis

PubMed Central

McAnulty, Michael J.; G. Poosarla, Venkata; Kim, Kyoung-Yeol; Jasso-Chávez, Ricardo; Logan, Bruce E.; Wood, Thomas K.

2017-01-01

Given our vast methane reserves and the difficulty in transporting methane without substantial leaks, the conversion of methane directly into electricity would be beneficial. Microbial fuel cells harness electrical power from a wide variety of substrates through biological means; however, the greenhouse gas methane has not been used with much success previously as a substrate in microbial fuel cells to generate electrical current. Here we construct a synthetic consortium consisting of: (i) an engineered archaeal strain to produce methyl-coenzyme M reductase from unculturable anaerobic methanotrophs for capturing methane and secreting acetate; (ii) micro-organisms from methane-acclimated sludge (including Paracoccus denitrificans) to facilitate electron transfer by providing electron shuttles (confirmed by replacing the sludge with humic acids), and (iii) Geobacter sulfurreducens to produce electrons from acetate, to create a microbial fuel cell that converts methane directly into significant electrical current. Notably, this methane microbial fuel cell operates at high Coulombic efficiency. PMID:28513579

Electricity from methane by reversing methanogenesis

NASA Astrophysics Data System (ADS)

McAnulty, Michael J.; G. Poosarla, Venkata; Kim, Kyoung-Yeol; Jasso-Chávez, Ricardo; Logan, Bruce E.; Wood, Thomas K.

2017-05-01

Given our vast methane reserves and the difficulty in transporting methane without substantial leaks, the conversion of methane directly into electricity would be beneficial. Microbial fuel cells harness electrical power from a wide variety of substrates through biological means; however, the greenhouse gas methane has not been used with much success previously as a substrate in microbial fuel cells to generate electrical current. Here we construct a synthetic consortium consisting of: (i) an engineered archaeal strain to produce methyl-coenzyme M reductase from unculturable anaerobic methanotrophs for capturing methane and secreting acetate; (ii) micro-organisms from methane-acclimated sludge (including Paracoccus denitrificans) to facilitate electron transfer by providing electron shuttles (confirmed by replacing the sludge with humic acids), and (iii) Geobacter sulfurreducens to produce electrons from acetate, to create a microbial fuel cell that converts methane directly into significant electrical current. Notably, this methane microbial fuel cell operates at high Coulombic efficiency.

A Leptolyngbya-based microbial consortium for agro-industrial wastewaters treatment and biodiesel production.

PubMed

Tsolcha, Olga N; Tekerlekopoulou, Athanasia G; Akratos, Christos S; Antonopoulou, Georgia; Aggelis, George; Genitsaris, Savvas; Moustaka-Gouni, Maria; Vayenas, Dimitrios V

2018-04-22

A mixed cyanobacterial-mixotrophic algal population, dominated by the filamentous cyanobacterium Leptolyngbya sp. and the microalga Ochromonas (which contributed to the total photosynthetic population with rates of less than 5%), was studied under non-aseptic conditions for its efficiency to remove organic and inorganic compounds from different types of wastes/wastewaters while simultaneously producing lipids. Second cheese whey, poplar sawdust, and grass hydrolysates were used in lab-scale experiments, in photobioreactors that operated under aerobic conditions with different initial nutrient (C, N and P) concentrations. Nutrient removal rates, biomass productivity, and the maximum oil production rates were determined. The highest lipid production was achieved using the biologically treated dairy effluent (up to 14.8% oil in dry biomass corresponding to 124 mg L -1 ) which also led to high nutrient removal rates (up to 94%). Lipids synthesized by the microbial consortium contained high percentages of saturated and mono-unsaturated fatty acids (up to 75% in total lipids) for all the substrates tested, which implies that the produced biomass may be harnessed as a source of biodiesel.

Prebiotics Mediate Microbial Interactions in a Consortium of the Infant Gut Microbiome.

PubMed

Medina, Daniel A; Pinto, Francisco; Ovalle, Aline; Thomson, Pamela; Garrido, Daniel

2017-10-04

Composition of the gut microbiome is influenced by diet. Milk or formula oligosaccharides act as prebiotics, bioactives that promote the growth of beneficial gut microbes. The influence of prebiotics on microbial interactions is not well understood. Here we investigated the transformation of prebiotics by a consortium of four representative species of the infant gut microbiome, and how their interactions changed with dietary substrates. First, we optimized a culture medium resembling certain infant gut parameters. A consortium containing Bifidobacterium longum subsp. infantis , Bacteroides vulgatus , Escherichia coli and Lactobacillus acidophilus was grown on fructooligosaccharides (FOS) or 2'-fucosyllactose (2FL) in mono- or co-culture. While Bi. infantis and Ba. vulgatus dominated growth on 2FL, their combined growth was reduced. Besides, interaction coefficients indicated strong competition, especially on FOS. While FOS was rapidly consumed by the consortium, B. infantis was the only microbe displaying significant consumption of 2FL. Acid production by the consortium resembled the metabolism of microorganisms dominating growth in each substrate. Finally, the consortium was tested in a bioreactor, observing similar predominance but more pronounced acid production and substrate consumption. This study indicates that the chemical nature of prebiotics modulate microbial interactions in a consortium of infant gut species.

[Determination of sugars, organic acids and alcohols in microbial consortium fermentation broth from cellulose using high performance liquid chromatography].

PubMed

Jiang, Yan; Fan, Guifang; Du, Ran; Li, Peipei; Jiang, Li

2015-08-01

A high performance liquid chromatographic method was established for the determination of metabolites (sugars, organic acids and alcohols) in microbial consortium fermentation broth from cellulose. Sulfate was first added in the samples to precipitate calcium ions in microbial consortium culture medium and lower the pH of the solution to avoid the dissociation of organic acids, then the filtrates were effectively separated using high performance liquid chromatography. Cellobiose, glucose, ethanol, butanol, glycerol, acetic acid and butyric acid were quantitatively analyzed. The detection limits were in the range of 0.10-2.00 mg/L. The linear correlation coefficients were greater than 0.999 6 in the range of 0.020 to 1.000 g/L. The recoveries were in the range of 85.41%-115.60% with the relative standard deviations of 0.22% -4.62% (n = 6). This method is accurate for the quantitative analysis of the alcohols, organic acids and saccharides in microbial consortium fermentation broth from cellulose.

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

PubMed

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

2015-12-01

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

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

PubMed

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

2016-09-30

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

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

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Stable carbon isotope fractionation of chlorinated ethenes by a microbial consortium containing multiple dechlorinating genes.

PubMed

Liu, Na; Ding, Longzhen; Li, Haijun; Zhang, Pengpeng; Zheng, Jixing; Weng, Chih-Huang

2018-08-01

The study aimed to determine the possible contribution of specific growth conditions and community structures to variable carbon enrichment factors (Ɛ- carbon ) values for the degradation of chlorinated ethenes (CEs) by a bacterial consortium with multiple dechlorinating genes. Ɛ- carbon values for trichloroethylene, cis-1,2-dichloroethylene, and vinyl chloride were -7.24% ± 0.59%, -14.6% ± 1.71%, and -21.1% ± 1.14%, respectively, during their degradation by a microbial consortium containing multiple dechlorinating genes including tceA and vcrA. The Ɛ- carbon values of all CEs were not greatly affected by changes in growth conditions and community structures, which directly or indirectly affected reductive dechlorination of CEs by this consortium. Stability analysis provided evidence that the presence of multiple dechlorinating genes within a microbial consortium had little effect on carbon isotope fractionation, as long as the genes have definite, non-overlapping functions. Copyright © 2018 Elsevier Ltd. All rights reserved.

Biotechnological potential of microbial consortia and future perspectives.

PubMed

Bhatia, Shashi Kant; Bhatia, Ravi Kant; Choi, Yong-Keun; Kan, Eunsung; Kim, Yun-Gon; Yang, Yung-Hun

2018-05-15

Design of a microbial consortium is a newly emerging field that enables researchers to extend the frontiers of biotechnology from a pure culture to mixed cultures. A microbial consortium enables microbes to use a broad range of carbon sources. It provides microbes with robustness in response to environmental stress factors. Microbes in a consortium can perform complex functions that are impossible for a single organism. With advancement of technology, it is now possible to understand microbial interaction mechanism and construct consortia. Microbial consortia can be classified in terms of their construction, modes of interaction, and functions. Here we discuss different trends in the study of microbial functions and interactions, including single-cell genomics (SCG), microfluidics, fluorescent imaging, and membrane separation. Community profile studies using polymerase chain-reaction denaturing gradient gel electrophoresis (PCR-DGGE), amplified ribosomal DNA restriction analysis (ARDRA), and terminal restriction fragment-length polymorphism (T-RFLP) are also reviewed. We also provide a few examples of their possible applications in areas of biopolymers, bioenergy, biochemicals, and bioremediation.

A low-cost wheat bran medium for biodegradation of the benzidine-based carcinogenic dye Trypan Blue using a microbial consortium.

PubMed

Lade, Harshad; Kadam, Avinash; Paul, Diby; Govindwar, Sanjay

2015-03-25

Environmental release of benzidine-based dyes is a matter of health concern. Here, a microbial consortium was enriched from textile dye contaminated soils and investigated for biodegradation of the carcinogenic benzidine-based dye Trypan Blue using wheat bran (WB) as growth medium. The PCR-DGGE analysis of enriched microbial consortium revealed the presence of 15 different bacteria. Decolorization studies suggested that the microbial consortium has high metabolic activity towards Trypan Blue as complete removal of 50 mg∙L-1 dye was observed within 24 h at 30 ± 0.2 °C and pH 7. Significant reduction in TOC (64%) and COD (88%) of dye decolorized broths confirmed mineralization. Induction in azoreductase (500%), NADH-DCIP reductase (264%) and laccase (275%) proved enzymatic decolorization of dye. HPLC analysis of dye decolorized products showed the formation of six metabolites while the FTIR spectrum indicated removal of diazo bonds at 1612.30 and 1581.34 cm-1. The proposed dye degradation pathway based on GC-MS and enzyme analysis suggested the formation of two low molecular weight intermediates. Phytotoxicity and acute toxicity studies revealed the less toxic nature of the dye degradation products. These results provide experimental evidence for the utilization of agricultural waste as a novel low-cost growth medium for biodegradation of benzidine-based dyes, and suggested the potential of the microbial consortium in detoxification.

A Low-Cost Wheat Bran Medium for Biodegradation of the Benzidine-Based Carcinogenic Dye Trypan Blue Using a Microbial Consortium

PubMed Central

Lade, Harshad; Kadam, Avinash; Paul, Diby; Govindwar, Sanjay

2015-01-01

Environmental release of benzidine-based dyes is a matter of health concern. Here, a microbial consortium was enriched from textile dye contaminated soils and investigated for biodegradation of the carcinogenic benzidine-based dye Trypan Blue using wheat bran (WB) as growth medium. The PCR-DGGE analysis of enriched microbial consortium revealed the presence of 15 different bacteria. Decolorization studies suggested that the microbial consortium has high metabolic activity towards Trypan Blue as complete removal of 50 mg∙L−1 dye was observed within 24 h at 30 ± 0.2 °C and pH 7. Significant reduction in TOC (64%) and COD (88%) of dye decolorized broths confirmed mineralization. Induction in azoreductase (500%), NADH-DCIP reductase (264%) and laccase (275%) proved enzymatic decolorization of dye. HPLC analysis of dye decolorized products showed the formation of six metabolites while the FTIR spectrum indicated removal of diazo bonds at 1612.30 and 1581.34 cm−1. The proposed dye degradation pathway based on GC-MS and enzyme analysis suggested the formation of two low molecular weight intermediates. Phytotoxicity and acute toxicity studies revealed the less toxic nature of the dye degradation products. These results provide experimental evidence for the utilization of agricultural waste as a novel low-cost growth medium for biodegradation of benzidine-based dyes, and suggested the potential of the microbial consortium in detoxification. PMID:25815522

Biodegradation of food waste using microbial cultures producing thermostable α-amylase and cellulase under different pH and temperature.

PubMed

Awasthi, Mukesh Kumar; Wong, Jonathan W C; Kumar, Sunil; Awasthi, Sanjeev Kumar; Wang, Quan; Wang, Meijing; Ren, Xiuna; Zhao, Junchao; Chen, Hongyu; Zhang, Zengqiang

2018-01-01

The aim of this work was to study the biodegradation of food waste employing thermostable α-amylase and cellulase enzymes producing bacteria. Four potential isolates were identified which were capable of producing maximum amylase and cellulase and belong to the amylolytic strains, Brevibacillus borstelensis and Bacillus licheniformis; cellulolytic strains, Bacillus thuringiensis and Bacillus licheniformis, respectively. These strains were selected based on its higher cell density, enzymatic activities and stability at a wide range of pH and temperature compared to other strains. The results indicated that 1:1 ratio of pre and post consumed food wastes (FWs) were helpful to facilitate the degradation employing bacterial consortium. In addition, organic matter decomposition and chemical parameters of the end product quality also indicated that bacterial consortium was very effective for 1:1 ratio of FWs degradation as compared to the other treatments. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

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

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

2006-04-01

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

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

NASA Astrophysics Data System (ADS)

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

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

Quorum sensing molecules in activated sludge could trigger microalgae lipid synthesis.

PubMed

Zhang, Chaofan; Li, Qingcheng; Fu, Liang; Zhou, Dandan; Crittenden, John C

2018-05-18

Cultivating microalgae using wastewater is an economical strategy to produce biofuel; however, microbial contamination has to be controlled strictly. Microalgae lipid accumulation can be triggered by environmental pressures, and here, we studied whether microbial contamination is the pressure for microalgae. We hypothesized this pressure was forced via cell-to-cell communication with quorum sensing molecules (QSMs). In this work, we verified the impacts of QSMs produced by activated sludge (wastewater-born microbial consortiums) on both lipid content and biomass production of the microalgae Chlorophyta sp., since in combination, they determined lipid productivity. With QSMs stress, the lipid content of Chlorophyta sp. increased by ∼84%, while biomass production decreased only slightly. Consistently, enzymes on the fatty acid synthesis pathways were generally up-regulated, while they were slightly down-regulated for DNA replication. In summary, the total lipid production improved by 86%. These results revealed the positive effects of microbial contamination on microalgae biofuel production. Copyright © 2018 Elsevier Ltd. All rights reserved.

Anaerobic biodegradation of PAHs in mangrove sediment with amendment of NaHCO3.

PubMed

Li, Chun-Hua; Wong, Yuk-Shan; Wang, Hong-Yuan; Tam, Nora Fung-Yee

2015-04-01

Mangrove sediment is unique in chemical and biological properties. Many of them suffer polycyclic aromatic hydrocarbon (PAH) contamination. However, the study on PAH biological remediation for mangrove sediment is deficient. Enriched PAH-degrading microbial consortium and electron acceptor amendment are considered as two effective measures. Compared to other electron acceptors, the study on CO2, which is used by methanogens, is still seldom. This study investigated the effect of NaHCO3 amendment on the anaerobic biodegradation of four mixed PAHs, namely fluorene (Fl), phenanthrene (Phe), fluoranthene (Flua) and pyrene (Pyr), with or without enriched PAH-degrading microbial consortium in mangrove sediment slurry. The trends of various parameters, including PAH concentrations, microbial population size, electron-transport system activities, electron acceptor and anaerobic gas production were monitored. The results revealed that the inoculation of enriched PAH-degrading consortium had a significant effect with half lives shortened by 7-13 days for 3-ring PAHs and 11-24 days for 4-ring PAHs. While NaHCO3 amendment did not have a significant effect on the biodegradation of PAHs and other parameters, except that CO2 gas in the headspace of experimental flasks was increased. One of the possible reasons is that mangrove sediment contains high concentrations of other electron acceptors which are easier to be utilized by anaerobic bacteria, the other one is that the anaerobes in mangrove sediment can produce enough CO2 gas even without adding NaHCO3. Copyright © 2015. Published by Elsevier B.V.

An overview of field-specific designs of microbial EOR

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

Robertson, E.P.; Bala, G.A.; Fox, S.L.

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 processmore » for the third field appeared promising. Development of a bacterial consortium capable of producing the desired metabolites was initiated, and field isolates were characterized.« less

Stimulation of methane generation from nonproductive coal by addition of nutrients or a microbial consortium

USGS Publications Warehouse

Jones, Elizabeth J.P.; Voytek, Mary A.; Corum, Margo D.; Orem, William H.

2010-01-01

Biogenic formation of methane from coal is of great interest as an underexploited source of clean energy. The goal of some coal bed producers is to extend coal bed methane productivity and to utilize hydrocarbon wastes such as coal slurry to generate new methane. However, the process and factors controlling the process, and thus ways to stimulate it, are poorly understood. Subbituminous coal from a nonproductive well in south Texas was stimulated to produce methane in microcosms when the native population was supplemented with nutrients (biostimulation) or when nutrients and a consortium of bacteria and methanogens enriched from wetland sediment were added (bioaugmentation). The native population enriched by nutrient addition included Pseudomonas spp., Veillonellaceae, and Methanosarcina barkeri. The bioaugmented microcosm generated methane more rapidly and to a higher concentration than the biostimulated microcosm. Dissolved organics, including long-chain fatty acids, single-ring aromatics, and long-chain alkanes accumulated in the first 39 days of the bioaugmented microcosm and were then degraded, accompanied by generation of methane. The bioaugmented microcosm was dominated by Geobacter sp., and most of the methane generation was associated with growth of Methanosaeta concilii. The ability of the bioaugmentation culture to produce methane from coal intermediates was confirmed in incubations of culture with representative organic compounds. This study indicates that methane production could be stimulated at the nonproductive field site and that low microbial biomass may be limiting in situ methane generation. In addition, the microcosm study suggests that the pathway for generating methane from coal involves complex microbial partnerships.

Copper removal using a heavy-metal resistant microbial consortium in a fixed-bed reactor.

PubMed

Carpio, Isis E Mejias; Machado-Santelli, Glaucia; Sakata, Solange Kazumi; Ferreira Filho, Sidney Seckler; Rodrigues, Debora Frigi

2014-10-01

A heavy-metal resistant bacterial consortium was obtained from a contaminated river in São Paulo, Brazil and utilized for the design of a fixed-bed column for the removal of copper. Prior to the design of the fixed-bed bioreactor, the copper removal capacity by the live consortium and the effects of copper in the consortium biofilm formation were investigated. The Langmuir model indicated that the sorption capacity of the consortium for copper was 450.0 mg/g dry cells. The biosorption of copper into the microbial biomass was attributed to carboxyl and hydroxyl groups present in the microbial biomass. The effect of copper in planktonic cells to form biofilm under copper rich conditions was investigated with confocal microscopy. The results revealed that biofilm formed after 72 h exposure to copper presented a reduced thickness by 57% when compared to the control; however 84% of the total cells were still alive. The fixed-bed bioreactor was set up by growing the consortium biofilm on granular activated carbon (GAC) and analyzed for copper removal. The biofilm-GAC (BGAC) column retained 45% of the copper mass present in the influent, as opposed to 17% in the control column that contained GAC only. These findings suggest that native microbial communities in sites contaminated with heavy metals can be immobilized in fixed-bed bioreactors and used to treat metal contaminated water. Copyright © 2014 Elsevier Ltd. All rights reserved.

Effect of light on the production of bioelectricity and added-value microalgae biomass in a Photosynthetic Alga Microbial Fuel Cell.

PubMed

Gouveia, Luísa; Neves, Carole; Sebastião, Diogo; Nobre, Beatriz P; Matos, Cristina T

2014-02-01

This study demonstrates the simultaneous production of bioelectricity and added-value pigments in a Photosynthetic Alga Microbial Fuel Cell (PAMFC). A PAMFC was operated using Chlorella vulgaris in the cathode compartment and a bacterial consortium in the anode. The system was studied at two different light intensities and the maximum power produced was 62.7 mW/m(2) with a light intensity of 96 μE/(m(2)s). The results showed that increasing light intensity from 26 to 96 μE/(m(2)s) leads to an increase of about 6-folds in the power produced. Additionally, the pigments produced by the microalga were analysed and the results showed that the light intensity and PAMFC operation potentiated the carotenogenesis in the cathode compartment. The demonstrated possibility of producing added-value microalgae biomass in microbial fuel cell cathodes will increase the economic feasibility of these bioelectrochemical systems, allowing the development of energy efficient systems for wastewater treatment and carbon fixation. Copyright © 2013 Elsevier Ltd. All rights reserved.

Impact of anti-acidification microbial consortium on carbohydrate metabolism of key microbes during food waste composting.

PubMed

Song, Caihong; Li, Mingxiao; Qi, Hui; Zhang, Yali; Liu, Dongming; Xia, Xunfeng; Pan, Hongwei; Xi, Beidou

2018-07-01

This study investigated the effect of anti-acidification microbial consortium (AAMC), which act synergistically for rapid bioconversion of organic acids on carbohydrate metabolism of key microbes in the course of food waste (FW) composting by metaproteomics. AAMC was inoculated to the composting mass and compared with treatment with alkaline compounds and the control without any amendment. Inoculating AAMC could effectively accelerate carbohydrate degradation process and improve composting efficiency. Carbohydrate metabolic network profiles showed the inoculation with AAMC could increase significantly the types of enzymes catalysing the degradation of lignin, cellulose and hemicellulose. Furthermore, AAMC inoculum could increase not only diversities of microbes producing key enzymes in metabolism pathways of acetic and propionic acids, but also the amounts of these key enzymes. The increase of diversities of microbes could disperse the pressure from acidic adversity on microorganisms which were capable to degrade acetic and propionic acids. Copyright © 2018 Elsevier Ltd. All rights reserved.

Simultaneous biodegradation of three mononitrophenol isomers by a tailor-made microbial consortium immobilized in sequential batch reactors.

PubMed

Fu, H; Zhang, J-J; Xu, Y; Chao, H-J; Zhou, N-Y

2017-03-01

The ortho-nitrophenol (ONP)-utilizing Alcaligenes sp. strain NyZ215, meta-nitrophenol (MNP)-utilizing Cupriavidus necator JMP134 and para-nitrophenol (PNP)-utilizing Pseudomonas sp. strain WBC-3 were assembled as a consortium to degrade three nitrophenol isomers in sequential batch reactors. Pilot test was conducted in flasks to demonstrate that a mixture of three mononitrophenols at 0·5 mol l -1 each could be mineralized by this microbial consortium within 84 h. Interestingly, neither ONP nor MNP was degraded until PNP was almost consumed by strain WBC-3. By immobilizing this consortium into polyurethane cubes, all three mononitrophenols were continuously degraded in lab-scale sequential reactors for six batch cycles over 18 days. Total concentrations of ONP, MMP and PNP that were degraded were 2·8, 1·5 and 2·3 mol l -1 during this time course respectively. Quantitative real-time PCR analysis showed that each member in the microbial consortium was relatively stable during the entire degradation process. This study provides a novel approach to treat polluted water, particularly with a mixture of co-existing isomers. Nitroaromatic compounds are readily spread in the environment and pose great potential toxicity concerns. Here, we report the simultaneous degradation of three isomers of mononitrophenol in a single system by employing a consortium of three bacteria, both in flasks and lab-scale sequential batch reactors. The results demonstrate that simultaneous biodegradation of three mononitrophenol isomers can be achieved by a tailor-made microbial consortium immobilized in sequential batch reactors, providing a pilot study for a novel approach for the bioremediation of mixed pollutants, especially isomers present in wastewater. © 2016 The Society for Applied Microbiology.

Bioavailability of particle-associated Se to the bivalve Potamocorbula amurensis

USGS Publications Warehouse

Schlekat, C.E.; Dowdle, P.R.; Lee, B.-G.; Luoma, S.N.; Oremland, R.S.

2000-01-01

Elemental selenium, Se(0), is a prevalent chemical form in sediments, but little is known about its bioavailability. We evaluated the bioavailability of two forms of Se(0) by generating radioisotopic 75Se(0) through bacterial dissimilatory reduction of 75SeO32- by pure bacterial cultures (SES) and by an anaerobic sediment microbial consortium (SED). A third form was generated by reducing 75SeO32- with ascorbic acid (AA). Speciation determinations showed that AA and SES were >90% Se(0), but SED showed a mixture of Se(0), selenoanions, and a residual fraction. Pulse-chase techniques were used to measure assimilation efficiencies (AE) of these particulate Se forms by the bivalve Potamocorbula amurensis. Mean AE values were 3 ?? 2% for AA, 7 ?? 1% for SES, and 28 ?? 15% for SED, showing that the bioavailability of reduced, particle-associated Se is dependent upon its origin. To determine if oxidative microbial processes increased Se transfer, SES 75Se(0) was incubated with an aerobic sediment microbial consortium. After 113 d of incubation, 36% of SES Se(0) was oxidized to SeO32-. Assimilation of total particulate Se was unaffected however (mean AE = 5.5%). The mean AE from the diatom Phaeodactylum tricornutum was 58 ?? 8%, verifying the importance of Se associated with biogenic particles. Speciation and AE results from SED suggest that selenoanion reduction in wetlands and estuaries produces biologically available reduced selenium.Elemental selenium, Se(0), is a prevalent chemical form in sediments, but little is known about its bioavailability. We evaluated the bioavailability of two forms of Se(0) by generating radioisotopic 75Se(0) through bacterial dissimilatory reduction of 75SeO32- by pure bacterial cultures (SES) and by an anaerobic sediment microbial consortium (SED). A third form was generated by reducing 75SeO32 with ascorbic acid (AA). Speciation determinations showed that AA and SES were > 90% Se(0), but SED showed a mixture of Se(0), selenoanions, and a residual fraction. Pulse-chase techniques were used to measure assimilation efficiencies (AE) of these particulate Se forms by the bivalve Potamocorbula amurensis. Mean AE values were 3 ?? 2% for AA, 7 ?? 1% for SES, and 28 ?? 15% for SED, showing that the bioavailability of reduced, particle-associated Se is dependent upon its origin. To determine if oxidative microbial processes increased Se transfer, SES 75Se(0) was incubated with an aerobic sediment microbial consortium. After 113 d of incubation, 36% of SES Se(0) was oxidized to SeO32-. Assimilation of total particulate Se was unaffected however (mean AE = 5.5%). The mean AE from the diatom Phaeodactylum tricornutum was 58 ?? 8%, verifying the importance of Se associated with biogenic particles. Speciation and AE results from SED suggest that selenoanion reduction in wetlands and estuaries produces biologically available reduced selenium.

Bio-hydrogen production from tempeh and tofu processing wastes via fermentation process using microbial consortium: A mini-review

NASA Astrophysics Data System (ADS)

Rengga, Wara Dyah Pita; Wati, Diyah Saras; Siregar, Riska Yuliana; Wulandari, Ajeng Riswanti; Lestari, Adela Ayu; Chafidz, Achmad

2017-03-01

One of alternative energies that can replace fossil fuels is hydrogen. Hydrogen can be used to generate electricity and to power combustion engines for transportation. Bio-hydrogen produced from tempeh and tofu processing waste can be considered as a renewable energy. Bio-hydrogen produced from tempeh and tofu processing waste is beneficial because the waste of soybean straw and tofu processing waste is plentiful, cheap, renewable and biodegradable. Specification of tempeh and tofu processing waste were soybean straw and sludge of tofu processing. They contain carbohydrates (cellulose, hemicellulose, and lignin) and methane. This paper reviews the optimal condition to produce bio-hydrogen from tempeh and tofu processing waste. The production of bio-hydrogen used microbial consortium which were enriched from cracked cereals and mainly dominated by Clostridium butyricum and Clostridium roseum. The production process of bio-hydrogen from tempeh and tofu processing waste used acid pre-treatment with acid catalyzed hydrolysis to cleave the bond of hemicellulose and cellulose chains contained in biomass. The optimal production of bio-hydrogen has a yield of 6-6.8 mL/g at 35-60 °C, pH 5.5-7 in hydraulic retention time (HRT) less than 16 h. The production used a continuous system in an anaerobic digester. This condition can be used as a reference for the future research.

Influence of triethyl phosphate on phosphatase activity in shooting range soil: Isolation of a zinc-resistant bacterium with an acid phosphatase

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

Story, Sandra; Brigmon, Robin L.

Phosphatase-mediated hydrolysis of organic phosphate may be a viable means of stabilizing heavy metals via precipitation as a metal phosphate in bioremediation applications. We investigated the effect of triethyl phosphate (TEP) on soil microbial-phosphatase activity in a heavy-metal contaminated soil. Gaseous TEP has been used at subsurface sites for bioremediation of organic contaminants but not applied in heavy-metal contaminated areas. Little is known about how TEP affects microbial activity in soils and it is postulated that TEP can serve as a phosphate source in nutrient-poor groundwater and soil/sediments. Over a 3-week period, TEP amendment to microcosms containing heavy-metal contaminated soilmore » resulted in increased activity of soil acid-phosphatase and repression of alkaline phosphatase, indicating a stimulatory effect on the microbial population. A soil-free enrichment of microorganisms adapted to heavy-metal and acidic conditions was derived from the TEP-amended soil microcosms using TEP as the sole phosphate source and the selected microbial consortium maintained a high acid-phosphatase activity with repression of alkaline phosphatase. Addition of 5 mM zinc to soil-free microcosms had little effect on acid phosphatase but inhibited alkaline phosphatase. One bacterial member from the consortium, identified as Burkholderia cepacia sp., expressed an acid-phosphatase activity uninhibited by high concentrations of zinc and produced a soluble, indigo pigment under phosphate limitation. The pigment was produced in a phosphate-free medium and was not produced in the presence of TEP or phosphate ion, indicative of purple acid-phosphatase types that are pressed by bioavailable phosphate. Finally, these results demonstrate that TEP amendment was bioavailable and increased overall phosphatase activity in both soil and soil-free microcosms supporting the possibility of positive outcomes in bioremediation applications.« less

Influence of triethyl phosphate on phosphatase activity in shooting range soil: Isolation of a zinc-resistant bacterium with an acid phosphatase

DOE PAGES

Story, Sandra; Brigmon, Robin L.

2016-12-19

Phosphatase-mediated hydrolysis of organic phosphate may be a viable means of stabilizing heavy metals via precipitation as a metal phosphate in bioremediation applications. We investigated the effect of triethyl phosphate (TEP) on soil microbial-phosphatase activity in a heavy-metal contaminated soil. Gaseous TEP has been used at subsurface sites for bioremediation of organic contaminants but not applied in heavy-metal contaminated areas. Little is known about how TEP affects microbial activity in soils and it is postulated that TEP can serve as a phosphate source in nutrient-poor groundwater and soil/sediments. Over a 3-week period, TEP amendment to microcosms containing heavy-metal contaminated soilmore » resulted in increased activity of soil acid-phosphatase and repression of alkaline phosphatase, indicating a stimulatory effect on the microbial population. A soil-free enrichment of microorganisms adapted to heavy-metal and acidic conditions was derived from the TEP-amended soil microcosms using TEP as the sole phosphate source and the selected microbial consortium maintained a high acid-phosphatase activity with repression of alkaline phosphatase. Addition of 5 mM zinc to soil-free microcosms had little effect on acid phosphatase but inhibited alkaline phosphatase. One bacterial member from the consortium, identified as Burkholderia cepacia sp., expressed an acid-phosphatase activity uninhibited by high concentrations of zinc and produced a soluble, indigo pigment under phosphate limitation. The pigment was produced in a phosphate-free medium and was not produced in the presence of TEP or phosphate ion, indicative of purple acid-phosphatase types that are pressed by bioavailable phosphate. Finally, these results demonstrate that TEP amendment was bioavailable and increased overall phosphatase activity in both soil and soil-free microcosms supporting the possibility of positive outcomes in bioremediation applications.« less

Influence of triethyl phosphate on phosphatase activity in shooting range soil: Isolation of a zinc-resistant bacterium with an acid phosphatase.

PubMed

Story, Sandra; Brigmon, Robin L

2017-03-01

Phosphatase-mediated hydrolysis of organic phosphate may be a viable means of stabilizing heavy metals via precipitation as a metal phosphate in bioremediation applications. We investigated the effect of triethyl phosphate (TEP) on soil microbial-phosphatase activity in a heavy-metal contaminated soil. Gaseous TEP has been used at subsurface sites for bioremediation of organic contaminants but not applied in heavy-metal contaminated areas. Little is known about how TEP affects microbial activity in soils and it is postulated that TEP can serve as a phosphate source in nutrient-poor groundwater and soil/sediments. Over a 3-week period, TEP amendment to microcosms containing heavy-metal contaminated soil resulted in increased activity of soil acid-phosphatase and repression of alkaline phosphatase, indicating a stimulatory effect on the microbial population. A soil-free enrichment of microorganisms adapted to heavy-metal and acidic conditions was derived from the TEP-amended soil microcosms using TEP as the sole phosphate source and the selected microbial consortium maintained a high acid-phosphatase activity with repression of alkaline phosphatase. Addition of 5mM zinc to soil-free microcosms had little effect on acid phosphatase but inhibited alkaline phosphatase. One bacterial member from the consortium, identified as Burkholderia cepacia sp., expressed an acid-phosphatase activity uninhibited by high concentrations of zinc and produced a soluble, indigo pigment under phosphate limitation. The pigment was produced in a phosphate-free medium and was not produced in the presence of TEP or phosphate ion, indicative of purple acid-phosphatase types that are pressed by bioavailable phosphate. These results demonstrate that TEP amendment was bioavailable and increased overall phosphatase activity in both soil and soil-free microcosms supporting the possibility of positive outcomes in bioremediation applications. Copyright © 2016. Published by Elsevier Inc.

Biostimulation of metal-resistant microbial consortium to remove zinc from contaminated environments.

PubMed

Mejias Carpio, Isis E; Franco, Diego Castillo; Zanoli Sato, Maria Inês; Sakata, Solange; Pellizari, Vivian H; Seckler Ferreira Filho, Sidney; Frigi Rodrigues, Debora

2016-04-15

Understanding the diversity and metal removal ability of microorganisms associated to contaminated aquatic environments is essential to develop metal remediation technologies in engineered environments. This study investigates through 16S rRNA deep sequencing the composition of a biostimulated microbial consortium obtained from the polluted Tietê River in São Paulo, Brazil. The bacterial diversity of the biostimulated consortium obtained from the contaminated water and sediment was compared to the original sample. The results of the comparative sequencing analyses showed that the biostimulated consortium and the natural environment had γ-Proteobacteria, Firmicutes, and uncultured bacteria as the major classes of microorganisms. The consortium optimum zinc removal capacity, evaluated in batch experiments, was achieved at pH=5 with equilibrium contact time of 120min, and a higher Zn-biomass affinity (KF=1.81) than most pure cultures previously investigated. Analysis of the functional groups found in the consortium demonstrated that amine, carboxyl, hydroxyl, and phosphate groups present in the consortium cells were responsible for zinc uptake. Copyright © 2016 Elsevier B.V. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2017-11-01

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

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

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

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

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

Consolidated Bio-Processing of Cellulosic Biomass for Efficient Biofuel Production Using Yeast Consortium

NASA Astrophysics Data System (ADS)

Goyal, Garima

Fossil fuels have been the major source for liquid transportation fuels for ages. However, decline in oil reserves and environmental concerns have raised a lot of interest in alternative and renewable energy sources. One promising alternative is the conversion of plant biomass into ethanol. The primary biomass feed stocks currently being used for the ethanol industry have been food based biomass (corn and sugar cane). However, interest has recently shifted to replace these traditional feed-stocks with more abundant, non-food based cellulosic biomass such as agriculture wastes (corn stover) or crops (switch grass). The use of cellulosic biomass as feed stock for the production of ethanol via bio-chemical routes presents many technical challenges not faced with the use of corn or sugar-cane as feed-stock. Recently, a new process called consolidated Bio-processing (CBP) has been proposed. This process combines simultaneous saccharification of lignocellulose with fermentation of the resulting sugars into a single process step mediated by a single microorganism or microbial consortium. Although there is no natural microorganism that possesses all properties of lignocellulose utilization and ethanol production desired for CBP, some bacteria and fungi exhibit some of the essential traits. The yeast Saccharomyces cerevisiae is the most attractive host organism for the usage of this strategy due to its high ethanol productivity at close to theoretical yields (0.51g ethanol/g glucose consumed), high osmo- and ethanol- tolerance, natural robustness in industrial processes, and ease of genetic manipulation. Introduction of the cellulosome, found naturally in microorganisms, has shown new directions to deal with recalcitrant biomass. In this case enzymes work in synergy in order to hydrolyze biomass more effectively than in case of free enzymes. A microbial consortium has been successfully developed, which ensures the functional assembly of minicellulosome on the yeast surface composed of four yeast populations. These yeast populations include: one displaying scaffoldin on its surface and three populations secreting three different cellulases in the medium to hydrolyze the cellulose. The modular nature of the consortium system allows for the fine-tuning of each population by changing their initial inoculum ratio, thereby optimizing the cellulose hydrolysis and hence ethanol production. When comparing the optimized consortium with equal ratio consortium, the optimized one produced almost double the amount of ethanol (1.87 g/l) with a yield of 0.475 g ethanol/g cellulose. To further evaluate the feasibility of using consortium for CBP, it was grown at very low optical density (OD) under anaerobic conditions. Under stressful conditions like low OD and no oxygen, the consortium system was proficient in assembling the cellulosome on its surface and growing on the PAS-avicel as sole carbon source and concomitantly producing ethanol with a yield of 87% of the theoretical value. For the dynamic study of yeast consortium system, quantitative real time PCR was used to enumerate the individual yeast population in the mixed culture. At the end of the cultivation, ratios of each population in this consortium maintained similar number as the initial inoculums ratios, which further confirms the consortium system is suitable for the application of CBP.

Rapid mineralisation of the Organic Fraction of Municipal Solid Waste.

PubMed

Martínez-Valdez, F J; Martínez-Ramírez, C; Martínez-Montiel, L; Favela-Torres, E; Soto-Cruz, N O; Ramírez-Vives, F; Saucedo-Castañeda, G

2015-03-01

The effect of pH, C/N ratio, addition of a microbial consortium (MC) and temperature upon mineralisation of Organic Fraction of Municipal Solid Waste (OFMSW) was studied; mineralisation was measured through the CO2 production rate and total CO2 formation. Through this process up to 432.9mg of CO2g(-1) initial dry matter (IDM) after 2days of treatment was obtained. It was found that under a slightly acidic pH (5-6) and C/N of 30, the mineralisation process was accelerated. Moreover, temperature (27-50°C) had no effect on the total CO2 produced. The highest CO2 production rate (5.28d(-1)) was observed at 27°C, C/N ratio of 30 and 8% of microbial consortium; it is at least 3.52 times higher than that reported (1.5d(-1)). The highest release of reducing sugars was determined at 50°C, possibly due to an increase in hydrolytic enzymes. Results suggest the potential use of rapid mineralisation of OFMSW for further friendly environmental processes. Copyright © 2014 Elsevier Ltd. All rights reserved.

Influence of redox mediators and salinity level on the (bio)transformation of Direct Blue 71: kinetics aspects.

PubMed

Alvarez, Luis H; Meza-Escalante, Edna R; Gortáres-Moroyoqui, Pablo; Morales, Luz; Rosas, Krystal; García-Reyes, Bernardo; García-González, Alicone

2016-12-01

The rate-limiting step of azo dye decolorization was elucidated by exploring the microbial reduction of a model quinone and the chemical decolorization by previously reduced quinone at different salinity conditions (2-8%). Microbial experiments were performed in batch with a marine consortium. The decolorization of Direct Blue 71 (DB71) by the marine consortium at 2% salinity, mediated with anthraquinone-2,6-disulfonate (AQDS), showed the highest rate of decolorization as compared with those obtained with riboflavin, and two samples of humic acids. Moreover, the incubations at different salinity conditions (0-8%) performed with AQDS showed that the highest rate of decolorization of DB71 by the marine consortium occurred at 2% and 4% salinity. In addition, the highest microbial reduction rate of AQDS occurred in incubations at 0%, 2%, and 4% of salinity. The chemical reduction of DB71 by reduced AQDS occurred in two stages and proceeded faster at 4% and 6% salinity. The results indicate that the rate-limiting step during azo decolorization was the microbial reduction of AQDS. Copyright © 2016 Elsevier Ltd. All rights reserved.

Degradation of raw corn stover powder (RCSP) by an enriched microbial consortium and its community structure.

PubMed

Feng, Yujie; Yu, Yanling; Wang, Xin; Qu, Youpeng; Li, Dongmei; He, Weihua; Kim, Byung Hong

2011-01-01

A microbial consortium with a high cellulolytic activity was enriched to degrade raw corn stover powder (RCSP). This consortium degraded more than 51% of non-sterilized RCSP or 81% of non-sterilized filter paper within 8 days at 40°C under facultative anoxic conditions. Cellulosome-like structures were observed in scanning electron micrographs (SEM) of RCSP degradation residue. The high cellulolytic activity was maintained during 40 subcultures in a medium containing cellulosic substrate. Small ribosomal gene sequence analyses showed the consortium contains uncultured and cultured bacteria with or without cellulolytic activities. Among these bacteria, some are anaerobic others aerobic. Analyses of the culture filtrate showed a typical anoxic polysaccharide fermentation during the culturing process. Reducing sugar concentration increased at early stage followed by various fermentation products that were consumed at the late stage. Copyright © 2010 Elsevier Ltd. All rights reserved.

Microalgae-mediated simultaneous treatment of toxic thiocyanate and production of biodiesel.

PubMed

Ryu, Byung-Gon; Kim, Jungmin; Yoo, Gursong; Lim, Jun-Taek; Kim, Woong; Han, Jong-In; Yang, Ji-Won

2014-04-01

In this work, a method for simultaneously degrading the toxic pollutant, thiocyanate, and producing microalgal lipids using mixed microbial communities was developed. Aerobic activated sludge was used as the seed culture and thiocyanate was used as the sole nitrogen source. Two cultivation methods were sequentially employed: a lithoautotrophic mode and a photoautotrophic mode. Thiocyanate hydrolysis and a nitrification was found to occur under the first (lithoautotrophic) condition, while the oxidized forms of nitrogen were assimilated by the photoautotrophic consortium and lipids were produced under the second condition. The final culture exhibited good settling efficiency (∼ 70% settling over 10 min), which can benefit downstream processing. The highest CO2 fixation rate and lipid productivity were observed with 2.5% and 5% CO2, respectively. The proposed integrated algal-bacterial system appears to be a feasible and even beneficial option for thiocyanate treatment and production of microbial lipids. Copyright © 2014 Elsevier Ltd. All rights reserved.

Molecular characterization of a microbial consortium involved in methane oxidation coupled to denitrification under micro-aerobic conditions.

PubMed

Liu, Jingjing; Sun, Faqian; Wang, Liang; Ju, Xi; Wu, Weixiang; Chen, Yingxu

2014-01-01

Methane can be used as an alternative carbon source in biological denitrification because it is nontoxic, widely available and relatively inexpensive. A microbial consortium involved in methane oxidation coupled to denitrification (MOD) was enriched with nitrite and nitrate as electron acceptors under micro-aerobic conditions. The 16S rRNA gene combined with pmoA phylogeny of methanotrophs and nirK phylogeny of denitrifiers were analysed to reveal the dominant microbial populations and functional microorganisms. Real-time quantitative polymerase chain reaction results showed high numbers of methanotrophs and denitrifiers in the enriched consortium. The 16S rRNA gene clone library revealed that Methylococcaceae and Methylophilaceae were the dominant populations in the MOD ecosystem. Phylogenetic analyses of pmoA gene clone libraries indicated that all methanotrophs belonged to Methylococcaceae, a type I methanotroph employing the ribulose monophosphate pathway for methane oxidation. Methylotrophic denitrifiers of the Methylophilaceae that can utilize organic intermediates (i.e. formaldehyde, citrate and acetate) released from the methanotrophs played a vital role in aerobic denitrification. This study is the first report to confirm micro-aerobic denitrification and to make phylogenetic and functional assignments for some members of the microbial assemblages involved in MOD. © 2013 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Conversion of crude oil to methane by a microbial consortium enriched from oil reservoir production waters

PubMed Central

Berdugo-Clavijo, Carolina; Gieg, Lisa M.

2014-01-01

The methanogenic biodegradation of crude oil is an important process occurring in petroleum reservoirs and other oil-containing environments such as contaminated aquifers. In this process, syntrophic bacteria degrade hydrocarbon substrates to products such as acetate, and/or H2 and CO2 that are then used by methanogens to produce methane in a thermodynamically dependent manner. We enriched a methanogenic crude oil-degrading consortium from production waters sampled from a low temperature heavy oil reservoir. Alkylsuccinates indicative of fumarate addition to C5 and C6 n-alkanes were identified in the culture (above levels found in controls), corresponding to the detection of an alkyl succinate synthase encoding gene (assA/masA) in the culture. In addition, the enrichment culture was tested for its ability to produce methane from residual oil in a sandstone-packed column system simulating a mature field. Methane production rates of up to 5.8 μmol CH4/g of oil/day were measured in the column system. Amounts of produced methane were in relatively good agreement with hydrocarbon loss showing depletion of more than 50% of saturate and aromatic hydrocarbons. Microbial community analysis revealed that the enrichment culture was dominated by members of the genus Smithella, Methanosaeta, and Methanoculleus. However, a shift in microbial community occurred following incubation of the enrichment in the sandstone columns. Here, Methanobacterium sp. were most abundant, as were bacterial members of the genus Pseudomonas and other known biofilm forming organisms. Our findings show that microorganisms enriched from petroleum reservoir waters can bioconvert crude oil components to methane both planktonically and in sandstone-packed columns as test systems. Further, the results suggest that different organisms may contribute to oil biodegradation within different phases (e.g., planktonic vs. sessile) within a subsurface crude oil reservoir. PMID:24829563

Molecular characterization of a microbial consortium involved in methane oxidation coupled to denitrification under micro-aerobic conditions

PubMed Central

Liu, Jingjing; Sun, Faqian; Wang, Liang; Ju, Xi; Wu, Weixiang; Chen, Yingxu

2014-01-01

Methane can be used as an alternative carbon source in biological denitrification because it is nontoxic, widely available and relatively inexpensive. A microbial consortium involved in methane oxidation coupled to denitrification (MOD) was enriched with nitrite and nitrate as electron acceptors under micro-aerobic conditions. The 16S rRNA gene combined with pmoA phylogeny of methanotrophs and nirK phylogeny of denitrifiers were analysed to reveal the dominant microbial populations and functional microorganisms. Real-time quantitative polymerase chain reaction results showed high numbers of methanotrophs and denitrifiers in the enriched consortium. The 16S rRNA gene clone library revealed that Methylococcaceae and Methylophilaceae were the dominant populations in the MOD ecosystem. Phylogenetic analyses of pmoA gene clone libraries indicated that all methanotrophs belonged to Methylococcaceae, a type I methanotroph employing the ribulose monophosphate pathway for methane oxidation. Methylotrophic denitrifiers of the Methylophilaceae that can utilize organic intermediates (i.e. formaldehyde, citrate and acetate) released from the methanotrophs played a vital role in aerobic denitrification. This study is the first report to confirm micro-aerobic denitrification and to make phylogenetic and functional assignments for some members of the microbial assemblages involved in MOD. PMID:24245852

Evaluation of the microbial community in industrial rye sourdough upon continuous back-slopping propagation revealed Lactobacillus helveticus as the dominant species.

PubMed

Viiard, E; Mihhalevski, A; Rühka, T; Paalme, T; Sarand, I

2013-02-01

To assess the structure and stability of a dominant lactic acid bacteria (LAB) population during the propagation of rye sourdough in an industrial semi-fluid production over a period of 7 months. The sourdough was started from a 6-year-old freeze-dried sourdough originating from the same bakery. A unique microbial consortium consisting mainly of bacteria belonging to species Lactobacillus helveticus, Lactobacillus panis and Lactobacillus pontis was identified based on culture-dependent (Rep-PCR) and culture-independent [denaturing gradient gel electrophoresis (DGGE)] methods. Three of the isolated Lact. helveticus strains showed remarkable adaptation to the sourdough conditions. They differed from the type strain by the ability to ferment compounds specific to plant material, like salicin, cellobiose and sucrose, but did not ferment lactose. We showed remarkable stability of a LAB consortium in rye sourdough started from lyophilized sourdough and propagated in a large bakery for 7 months. Lactobacillus helveticus was detected as the dominant species in the consortium and was shown to be metabolically adapted to the sourdough environment. The use of an established and adapted microbial consortium as a starter is a good alternative to commercial starter strains. © 2012 The Society for Applied Microbiology.

Perennial Antarctic lake ice: an oasis for life in a polar desert

NASA Technical Reports Server (NTRS)

Priscu, J. C.; Fritsen, C. H.; Adams, E. E.; Giovannoni, S. J.; Paerl, H. W.; McKay, C. P.; Doran, P. T.; Gordon, D. A.; Lanoil, B. D.; Pinckney, J. L.

1998-01-01

The permanent ice covers of Antarctic lakes in the McMurdo Dry Valleys develop liquid water inclusions in response to solar heating of internal aeolian-derived sediments. The ice sediment particles serve as nutrient (inorganic and organic)-enriched microzones for the establishment of a physiologically and ecologically complex microbial consortium capable of contemporaneous photosynthesis, nitrogen fixation, and decomposition. The consortium is capable of physically and chemically establishing and modifying a relatively nutrient- and organic matter-enriched microbial "oasis" embedded in the lake ice cover.

Perennial Antarctic lake ice: an oasis for life in a polar desert.

PubMed

Priscu, J C; Fritsen, C H; Adams, E E; Giovannoni, S J; Paerl, H W; McKay, C P; Doran, P T; Gordon, D A; Lanoil, B D; Pinckney, J L

1998-06-26

The permanent ice covers of Antarctic lakes in the McMurdo Dry Valleys develop liquid water inclusions in response to solar heating of internal aeolian-derived sediments. The ice sediment particles serve as nutrient (inorganic and organic)-enriched microzones for the establishment of a physiologically and ecologically complex microbial consortium capable of contemporaneous photosynthesis, nitrogen fixation, and decomposition. The consortium is capable of physically and chemically establishing and modifying a relatively nutrient- and organic matter-enriched microbial "oasis" embedded in the lake ice cover.

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

PubMed Central

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

2015-01-01

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

Effects of adding bulking agent, inorganic nutrient and microbial inocula on biopile treatment for oil-field drilling waste.

PubMed

Ma, Jie; Yang, Yongqi; Dai, Xiaoli; Chen, Yetong; Deng, Hanmei; Zhou, Huijun; Guo, Shaohui; Yan, Guangxu

2016-05-01

Contamination from oil-field drilling waste is a worldwide environmental problem. This study investigated the performance of four bench-scale biopiles in treating drilling waste: 1) direct biopile (DW), 2) biopile plus oil-degrading microbial consortium (DW + M), 3) biopile plus microbial consortium and bulking agents (saw dust) (DW + M + BA), 4) biopile plus microbial consortium, bulking agents, and inorganic nutrients (Urea and K2HPO4) (DW + M + BA + N). Ninety days of biopiling removed 41.0%, 44.0%, 55.7% and 87.4% of total petroleum hydrocarbon (TPH) in the pile "DW", "DW + M", "DW + M + BA", and "DW + M + BA + N" respectively. Addition of inorganic nutrient and bulking agents resulted in a 56.9% and 26.6% increase in TPH removal efficiency respectively. In contrast, inoculation of hydrocarbon-degrading microorganisms only slightly enhanced the contaminant removal (increased 7.3%). The biopile with stronger contaminant removal also had higher pile temperature and lower pile pH (e.g., in "DW + M + BA + N"). GC-MS analysis shows that biopiling significantly reduced the total number of detected contaminants and changed the chemical composition. Overall, this study shows that biopiling is an effective remediation technology for drilling waste. Adding inorganic nutrients and bulking agents can significantly improve biopile performance while addition of microbial inocula had minimal positive impacts on contaminant removal. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

PubMed

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

2015-01-01

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

Development of a microbial process for the recovery of petroleum oil from depleted reservoirs at 91-96°C.

PubMed

Arora, Preeti; Ranade, Dilip R; Dhakephalkar, Prashant K

2014-08-01

A consortium of bacteria growing at 91°C and above (optimally at 96°C) was developed for the recovery of crude oil from declining/depleted oil reservoirs having temperature of more than 91°C. PCR-DGGE-Sequencing analysis of 16S rRNA gene fragments of NJS-4 consortium revealed the presence of four strains identified as members of the genus Clostridium. The metabolites produced by NJS-4 consortium included volatile fatty acids, organic acids, surfactants, exopolysaccarides and CO2, which reduced viscosity, emulsified crude oil and increased the pressure that facilitated displacement of emulsified oil towards the surface. NJS-4 enhanced oil recovery by 26.7% and 10.1% in sand pack trials and core flood studies respectively in optimized nutrient medium comprised of sucrose and sodium acetate as carbon/energy source and urea as nitrogen source (pH 7-9, 96°C, and 4% salinity). Nutrient medium for MEOR was constituted using commercial grade cheap nutrients to improve the economic viability of MEOR process. Copyright © 2014 Elsevier Ltd. All rights reserved.

Evaluation of Kefir as a New Anodic Biocatalyst Consortium for Microbial Fuel Cell.

PubMed

Silveira, Gustavo; Schneedorf, José Maurício

2018-02-21

Kefir, a combined consortium of bacteria and yeast encapsulated by a polymeric matrix of exopolysaccharides, was used as anodic biocatalyst in a two-chamber microbial fuel cell (MFC). Fermentation was followed during 72 h and polarization curves were obtained from linear sweep voltammetry. The effect of methylene blue as charge-transfer mediator in the kefir metabolism was evaluated. UV/Vis spectrophotometry and cyclic voltammetry were applied to evaluate the redox state of the mediator and to characterize the electrochemical activity, whereas current interruption was used for internal resistance determination. Aiming to establish a relationship between the microbial development inside the anodic chamber with the generated power in the MFC, total titratable acidity, pH, viscosity, carbohydrate assimilation, and microbial counting were assayed. The kefir-based MFC demonstrated a maximum power density of 54 mW m -2 after 24 h fermentation, revealing the potential use of kefir as a biocatalyst for microbial fuel cells.

Maximizing power generation from dark fermentation effluents in microbial fuel cell by selective enrichment of exoelectrogens and optimization of anodic operational parameters.

PubMed

Varanasi, Jhansi L; Sinha, Pallavi; Das, Debabrata

2017-05-01

To selectively enrich an electrogenic mixed consortium capable of utilizing dark fermentative effluents as substrates in microbial fuel cells and to further enhance the power outputs by optimization of influential anodic operational parameters. A maximum power density of 1.4 W/m 3 was obtained by an enriched mixed electrogenic consortium in microbial fuel cells using acetate as substrate. This was further increased to 5.43 W/m 3 by optimization of influential anodic parameters. By utilizing dark fermentative effluents as substrates, the maximum power densities ranged from 5.2 to 6.2 W/m 3 with an average COD removal efficiency of 75% and a columbic efficiency of 10.6%. A simple strategy is provided for selective enrichment of electrogenic bacteria that can be used in microbial fuel cells for generating power from various dark fermentative effluents.

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

PubMed Central

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

2008-01-01

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

Optimization of liquid fermentation of microbial consortium WSD-5 followed by saccharification and acidification of wheat straw.

PubMed

Wen, Boting; Yuan, Xufeng; Cao, Yanzhuan; Liu, Yan; Wang, Xiaofen; Cui, Zongjun

2012-08-01

The microbial consortium WSD-5 is composed of bacteria and fungi, and the cooperation and symbiosis of the contained microbes enhance the degradation ability of WSD-5. Experiment results showed that the highest cellulase and hemicellulase were obtained when ventilation volume was 4 L/min, stirring rate was 0 rpm, and substrate loading rate was 3%. After 6 days of cultivation, a 67.60% loss in wheat straw dry weight was observed. The crude enzyme secreted from WSD-5 after optimization was evaluated by experiments of saccharification and acidification. The maximum concentration of reducing sugars was 3254 mg/L after 48 h saccharification. The concentration of sCOD peaked on day 2 with a value of 4345 mg/L during acidification, and the biogas yield and methane yield were 22.3% and 32.3% higher than un-acidified samples. This study is the first attempt to explore both the saccharification and the acidification ability of crude enzymes secreted by microbial consortium. Copyright © 2012 Elsevier Ltd. All rights reserved.

High-throughput pyrosequencing used for the discovery of a novel cellulase from a thermophilic cellulose-degrading microbial consortium.

PubMed

Zhao, Chao; Chu, Yanan; Li, Yanhong; Yang, Chengfeng; Chen, Yuqing; Wang, Xumin; Liu, Bin

2017-01-01

To analyze the microbial diversity and gene content of a thermophilic cellulose-degrading consortium from hot springs in Xiamen, China using 454 pyrosequencing for discovering cellulolytic enzyme resources. A thermophilic cellulose-degrading consortium, XM70 that was isolated from a hot spring, used sugarcane bagasse as sole carbon and energy source. DNA sequencing of the XM70 sample resulted in 349,978 reads with an average read length of 380 bases, accounting for 133,896,867 bases of sequence information. The characterization of sequencing reads and assembled contigs revealed that most microbes were derived from four phyla: Geobacillus (Firmicutes), Thermus, Bacillus, and Anoxybacillus. Twenty-eight homologous genes belonging to 15 glycoside hydrolase families were detected, including several cellulase genes. A novel hot spring metagenome-derived thermophilic cellulase was expressed and characterized. The application value of thermostable sugarcane bagasse-degrading enzymes is shown for production of cellulosic biofuel. The practical power of using a short-read-based metagenomic approach for harvesting novel microbial genes is also demonstrated.

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

PubMed

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

2012-06-01

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

Characterization of Pustular Mats and Related Rivularia-Rich Laminations in Oncoids From the Laguna Negra Lake (Argentina).

PubMed

Mlewski, Estela C; Pisapia, Céline; Gomez, Fernando; Lecourt, Lena; Soto Rueda, Eliana; Benzerara, Karim; Ménez, Bénédicte; Borensztajn, Stephan; Jamme, Frédéric; Réfrégiers, Matthieu; Gérard, Emmanuelle

2018-01-01

Stromatolites are organo-sedimentary structures that represent some of the oldest records of the early biosphere on Earth. Cyanobacteria are considered as a main component of the microbial mats that are supposed to produce stromatolite-like structures. Understanding the role of cyanobacteria and associated microorganisms on the mineralization processes is critical to better understand what can be preserved in the laminated structure of stromatolites. Laguna Negra (Catamarca, Argentina), a high-altitude hypersaline lake where stromatolites are currently formed, is considered as an analog environment of early Earth. This study aimed at characterizing carbonate precipitation within microbial mats and associated oncoids in Laguna Negra. In particular, we focused on carbonated black pustular mats. By combining Confocal Laser Scanning Microscopy, Scanning Electron Microscopy, Laser Microdissection and Whole Genome Amplification, Cloning and Sanger sequencing, and Focused Ion Beam milling for Transmission Electron Microscopy, we showed that carbonate precipitation did not directly initiate on the sheaths of cyanobacterial Rivularia , which dominate in the mat. It occurred via organo-mineralization processes within a large EPS matrix excreted by the diverse microbial consortium associated with Rivularia where diatoms and anoxygenic phototrophic bacteria were particularly abundant. By structuring a large microbial consortium, Rivularia should then favor the formation of organic-rich laminations of carbonates that can be preserved in stromatolites. By using Fourier Transform Infrared spectroscopy and Synchrotron-based deep UV fluorescence imaging, we compared laminations rich in structures resembling Rivularia to putatively chemically-precipitated laminations in oncoids associated with the mats. We showed that they presented a different mineralogy jointly with a higher content in organic remnants, hence providing some criteria of biogenicity to be searched for in the fossil record.

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

PubMed

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

2018-08-15

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

Characterization of Pustular Mats and Related Rivularia-Rich Laminations in Oncoids From the Laguna Negra Lake (Argentina)

PubMed Central

Mlewski, Estela C.; Pisapia, Céline; Gomez, Fernando; Lecourt, Lena; Soto Rueda, Eliana; Benzerara, Karim; Ménez, Bénédicte; Borensztajn, Stephan; Jamme, Frédéric; Réfrégiers, Matthieu; Gérard, Emmanuelle

2018-01-01

Stromatolites are organo-sedimentary structures that represent some of the oldest records of the early biosphere on Earth. Cyanobacteria are considered as a main component of the microbial mats that are supposed to produce stromatolite-like structures. Understanding the role of cyanobacteria and associated microorganisms on the mineralization processes is critical to better understand what can be preserved in the laminated structure of stromatolites. Laguna Negra (Catamarca, Argentina), a high-altitude hypersaline lake where stromatolites are currently formed, is considered as an analog environment of early Earth. This study aimed at characterizing carbonate precipitation within microbial mats and associated oncoids in Laguna Negra. In particular, we focused on carbonated black pustular mats. By combining Confocal Laser Scanning Microscopy, Scanning Electron Microscopy, Laser Microdissection and Whole Genome Amplification, Cloning and Sanger sequencing, and Focused Ion Beam milling for Transmission Electron Microscopy, we showed that carbonate precipitation did not directly initiate on the sheaths of cyanobacterial Rivularia, which dominate in the mat. It occurred via organo-mineralization processes within a large EPS matrix excreted by the diverse microbial consortium associated with Rivularia where diatoms and anoxygenic phototrophic bacteria were particularly abundant. By structuring a large microbial consortium, Rivularia should then favor the formation of organic-rich laminations of carbonates that can be preserved in stromatolites. By using Fourier Transform Infrared spectroscopy and Synchrotron-based deep UV fluorescence imaging, we compared laminations rich in structures resembling Rivularia to putatively chemically-precipitated laminations in oncoids associated with the mats. We showed that they presented a different mineralogy jointly with a higher content in organic remnants, hence providing some criteria of biogenicity to be searched for in the fossil record. PMID:29872427

Characterization of cellulolytic microbial consortium enriched on Napier grass using metagenomic approaches.

PubMed

Kanokratana, Pattanop; Wongwilaiwalin, Sarunyou; Mhuantong, Wuttichai; Tangphatsornruang, Sithichoke; Eurwilaichitr, Lily; Champreda, Verawat

2018-04-01

Energy grass is a promising substrate for production of biogas by anaerobic digestion. However, the conversion efficiency is limited by the enzymatically recalcitrant nature of cellulosic wastes. In this study, an active, structurally stable mesophilic lignocellulolytic degrading microbial consortium (Np-LMC) was constructed from forest compost soil microbiota by successive subcultivation on Napier grass under facultative anoxic conditions. According to tagged 16S rRNA gene amplicon sequencing, increasing abundance of facultative Proteobacteria was found in the middle of batch cycle which was then subsequently replaced by the cellulose degraders Firmicutes and Bacteroidetes along with decreasing CMCase, xylanase, and β-glucanase activity profiles in the supernatant after 5 days of incubation. Anaerobic/facultative bacteria Dysgonomonas and Sedimentibacter and aerobic bacteria Comamonas were the major genera found in Np-LMC. The consortium was active on degradation of the native and delignified grass. Direct shotgun sequencing of the consortium metagenome revealed relatively high abundance of genes encoding for various lignocellulose degrading enzymes in 23 glycosyl hydrolase (GH) families compared to previously reported cellulolytic microbial communities in mammalian digestive tracts. Enzymes attacking cellulose and hemicellulose were dominated by GH2, 3, 5, 9, 10, 26, 28 and 43 in addition to a variety of carbohydrate esterases (CE) and auxiliary activities (AA), reflecting adaptation of the enzyme systems to the native herbaceous substrate. The consortium identified here represents the microcosm specifically bred on energy grass, with potential for enhancing degradation of fibrous substrates in bioenergy industry. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Nonylphenol biodegradation characterizations and bacterial composition analysis of an effective consortium NP-M2.

PubMed

Bai, Naling; Abuduaini, Rexiding; Wang, Sheng; Zhang, Meinan; Zhu, Xufen; Zhao, Yuhua

2017-01-01

Nonylphenol (NP), ubiquitously detected as the degradation product of nonionic surfactants nonylphenol polyethoxylates, has been reported as an endocrine disrupter. However, most pure microorganisms can degrade only limited species of NP with low degradation efficiencies. To establish a microbial consortium that can effectively degrade different forms of NP, in this study, we isolated a facultative microbial consortium NP-M2 and characterized the biodegradation of NP by it. NP-M2 could degrade 75.61% and 89.75% of 1000 mg/L NP within 48 h and 8 days, respectively; an efficiency higher than that of any other consortium or pure microorganism reported so far. The addition of yeast extract promoted the biodegradation more significantly than that of glucose. Moreover, surface-active compounds secreted into the extracellular environment were hypothesized to promote high-efficiency metabolism of NP. The detoxification of NP by this consortium was determined. The degradation pathway was hypothesized to be initiated by oxidization of the benzene ring, followed by step-wise side-chain biodegradation. The bacterial composition of NP-M2 was determined using 16S rDNA library, and the consortium was found to mainly comprise members of the Sphingomonas, Pseudomonas, Alicycliphilus, and Acidovorax genera, with the former two accounting for 86.86% of the consortium. The high degradation efficiency of NP-M2 indicated that it could be a promising candidate for NP bioremediation in situ. Copyright © 2016 Elsevier Ltd. All rights reserved.

Anaerobic digestion of the microalga Spirulina at extreme alkaline conditions: biogas production, metagenome, and metatranscriptome

PubMed Central

Nolla-Ardèvol, Vímac; Strous, Marc; Tegetmeyer, Halina E.

2015-01-01

A haloalkaline anaerobic microbial community obtained from soda lake sediments was used to inoculate anaerobic reactors for the production of methane rich biogas. The microalga Spirulina was successfully digested by the haloalkaline microbial consortium at alkaline conditions (pH 10, 2.0 M Na+). Continuous biogas production was observed and the obtained biogas was rich in methane, up to 96%. Alkaline medium acted as a CO2 scrubber which resulted in low amounts of CO2 and no traces of H2S in the produced biogas. A hydraulic retention time (HRT) of 15 days and 0.25 g Spirulina L−1 day−1 organic loading rate (OLR) were identified as the optimal operational parameters. Metagenomic and metatranscriptomic analysis showed that the hydrolysis of the supplied substrate was mainly carried out by Bacteroidetes of the “ML635J-40 aquatic group” while the hydrogenotrophic pathway was the main producer of methane in a methanogenic community dominated by Methanocalculus. PMID:26157422

Bioassay for estimating the biogenic methane-generating potential of coal samples

USGS Publications Warehouse

Jones, Elizabeth J.P.; Voytek, Mary A.; Warwick, Peter D.; Corum, Margo D.; Cohn, Alexander G.; Bunnell, Joseph E.; Clark, Arthur C.; Orem, William H.

2008-01-01

Generation of secondary biogenic methane in coal beds is likely controlled by a combination of factors such as the bioavailability of coal carbon, the presence of a microbial community to convert coal carbon to methane, and an environment supporting microbial growth and methanogenesis. A set of treatments and controls was developed to bioassay the bioavailability of coal for conversion to methane under defined laboratory conditions. Treatments included adding a well-characterized consortium of bacteria and methanogens (enriched from modern wetland sediments) and providing conditions to support endemic microbial activity. The contribution of desorbed methane in the bioassays was determined in treatments with bromoethane sulfonic acid, an inhibitor of microbial methanogenesis. The bioassay compared 16 subbituminous coal samples collected from beds in Texas (TX), Wyoming (WY), and Alaska (AK), and two bituminous coal samples from Pennsylvania (PA). New biogenic methane was observed in several samples of subbituminous coal with the microbial consortium added, but endemic activity was less commonly observed. The highest methane generation [80 µmol methane/g coal (56 scf/ton or 1.75 cm3/g)] was from a south TX coal sample that was collected from a non-gas-producing well. Subbituminous coals from the Powder River Basin, WY and North Slope Borough, AK contained more sorbed (original) methane than the TX coal sample and generated 0–23 µmol/g (up to 16 scf/ton or 0.5 cm3/g) new biogenic methane in the bioassay. Standard indicators of thermal maturity such as burial depth, nitrogen content, and calorific value did not explain differences in biogenic methane among subbituminous coal samples. No original methane was observed in two bituminous samples from PA, nor was any new methane generated in bioassays of these samples. The bioassay offers a new tool for assessing the potential of coal for biogenic methane generation, and provides a platform for studying the mechanisms involved in this economically important activity.

Biofuel Cells Select for Microbial Consortia That Self-Mediate Electron Transfer

PubMed Central

Rabaey, Korneel; Boon, Nico; Siciliano, Steven D.; Verhaege, Marc; Verstraete, Willy

2004-01-01

Microbial fuel cells hold great promise as a sustainable biotechnological solution to future energy needs. Current efforts to improve the efficiency of such fuel cells are limited by the lack of knowledge about the microbial ecology of these systems. The purposes of this study were (i) to elucidate whether a bacterial community, either suspended or attached to an electrode, can evolve in a microbial fuel cell to bring about higher power output, and (ii) to identify species responsible for the electricity generation. Enrichment by repeated transfer of a bacterial consortium harvested from the anode compartment of a biofuel cell in which glucose was used increased the output from an initial level of 0.6 W m−2 of electrode surface to a maximal level of 4.31 W m−2 (664 mV, 30.9 mA) when plain graphite electrodes were used. This result was obtained with an average loading rate of 1 g of glucose liter−1 day−1 and corresponded to 81% efficiency for electron transfer from glucose to electricity. Cyclic voltammetry indicated that the enhanced microbial consortium had either membrane-bound or excreted redox components that were not initially detected in the community. Dominant species of the enhanced culture were identified by denaturing gradient gel electrophoresis and culturing. The community consisted mainly of facultative anaerobic bacteria, such as Alcaligenes faecalis and Enterococcus gallinarum, which are capable of hydrogen production. Pseudomonas aeruginosa and other Pseudomonas species were also isolated. For several isolates, electrochemical activity was mainly due to excreted redox mediators, and one of these mediators, pyocyanin produced by P. aeruginosa, could be characterized. Overall, the enrichment procedure, irrespective of whether only attached or suspended bacteria were examined, selected for organisms capable of mediating the electron transfer either by direct bacterial transfer or by excretion of redox components. PMID:15345423

Biodegradation pattern of hydrocarbons from a fuel oil-type complex residue by an emulsifier-producing microbial consortium.

PubMed

Nievas, M L; Commendatore, M G; Esteves, J L; Bucalá, V

2008-06-15

The biodegradation of a hazardous waste (bilge waste), a fuel oil-type complex residue from normal ship operations, was studied in a batch bioreactor using a microbial consortium in seawater medium. Experiments with initial concentrations of 0.18 and 0.53% (v/v) of bilge waste were carried out. In order to study the biodegradation kinetics, the mass of n-alkanes, resolved hydrocarbons and unresolved complex mixture (UCM) hydrocarbons were assessed by gas chromatography (GC). Emulsification was detected in both experiments, possibly linked to the n-alkanes depletion, with differences in emulsification start times and extents according to the initial hydrocarbon concentration. Both facts influenced the hydrocarbon biodegradation kinetics. A sequential biodegradation of n-alkanes and UMC was found for the higher hydrocarbon content. Being the former growth associated, while UCM biodegradation was a non-growing process showing enzymatic-type biodegradation kinetics. For the lower hydrocarbon concentration, simultaneous biodegradation of n-alkanes and UMC were found before emulsification. Nevertheless, certain UCM biodegradation was observed after the medium emulsification. According to the observed kinetics, three main types of hydrocarbons (n-alkanes, biodegradable UCM and recalcitrant UCM) were found adequate to represent the multicomponent substrate (bilge waste) for future modelling of the biodegradation process.

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

PubMed

Li, Feng; Yin, Changji; Sun, Liming; Li, Yuanxiu; Guo, Xuewu; Song, Hao

2018-05-01

Microbial fuel cell (MFC) is an eco-friendly bio-electrochemical sys-tem that uses microorganism as biocatalyst to convert biomass into electricity. Glycerol, as a waste in the biodiesel refinery processes, is an appealing substrate for MFC. Nevertheless, glycerol cannot be utilized as carbon source by well-known exoelectrogens such as Shewanella oneidensis. Herein, to generate electricity by rapidly harnessing glycerol, the authors rationally constructed a Klebsiella pneumoniae-Shewanella oneidensis microbial consortium to efficiently harvest electricity from glyc-erol, in which K. pneumoniae converted glycerol into lactate, fed to S. oneidensis as carbon source and electron donor. To improve electricity output, the authors systematically engineered the consortium in terms of carbon flux distribution and efficiency of extracellular electron transfer (EET). To direct more carbon flux to lactate biosynthesis in K. pneumoniae, the authors eliminated the ethanol pathway by knocking out the alcohol dehydrogenase gene (adhE), and enhanced lactate biosynthesis by heterologously expressing a lactate dehydrogen-ase gene (ldhD) from Lactobacillus bulgaricus and a lactate transporter gene (lldP) from Escherichia coli. To facilitate EET between S. oneidensis and anode surfaces, a biosynthetic flavins pathway from Bacillus subtilis is introduced into S. oneidensis. The author further optimized the glycerol concentration, thus S. oneidensis could be continuously fed with lactate synthesized from K. pneumoniae at a constant rate. Our glycerol-fed MFC generated a maximum power density of 19.9 mW/m 2 , significantly higher than that of the wild-type consor-tium. This work suggested that engineering microbial consortia is an effi-cient strategy to expand the spectrum of usable carbon sources and promote electricity power production in MFCs. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bacterial community dynamic associated with autochthonous bioaugmentation for enhanced Cu phytoremediation of salt-marsh sediments.

PubMed

Almeida, C Marisa R; Oliveira, Tânia; Reis, Izabela; Gomes, Carlos R; Mucha, Ana P

2017-12-01

Autochthonous bioaugmentation for metal phytoremediation is still little explored, particularly its application to estuarine salt marshes, but results obtained so far are promising. Nevertheless, understanding the behaviour of the microbial communities in the process of bioaugmentation and their role in improving metal phytoremediation is very important to fully validate the application of this biological technology. This study aimed to characterize the bacterial community dynamic associated with the application of autochthonous bioaugmentation in an experimentation which showed that Phragmites australis rhizosphere microorganisms could increase this salt marsh plant potential to phytoremediate Cu contaminated sediments. Bacterial communities present in the autochthonous microbial consortium resistant to Cu added to the medium and in the sediment at the beginning and at the end of the experiment were characterized by ARISA. Complementarily, the consortium and the sediment used for its production were characterized by next generation sequencing using the pyrosequencing platform 454. The microbial consortium resistant to Cu obtained from non-vegetated sediment was dominated by the genus Lactococcus (46%), Raoultella (25%), Bacillus (12%) and Acinetobacter (11%), whereas the one obtained form rhizosediment was dominated by the genus Gluconacetobacter (77%), Bacillus (17%) and Dyella (3%). Results clearly showed that, after two months of experiment, Cu caused a shift in the bacterial community structure of sediments, an effect that was observed either with or without addition of the metal resistant microbial consortium. Therefore, bioaugmentation application improved the process of phytoremediation (metal translocation by the plant was increased) without inducing long term changes in the bacterial community structure of the sediments. So, phytoremediation combined with autochthonous bioaugmentation can be a suitable technology for the recovery of estuarine areas, contributing for an efficient risk management strategy of these coastal zones. Copyright © 2017. Published by Elsevier Ltd.

Interaction among multiple microorganisms and effects of nitrogen and carbon supplementations on lignin degradation.

PubMed

Lv, Yuancai; Chen, Yuancai; Sun, Shiying; Hu, Yongyou

2014-03-01

The mutual interactions among the consortium constructed by four indigenous bacteria and five inter-kingdom fusants and the effects of nitrogen and carbon supplementations on lignin degradation and laccase activity were investigated. Analyzed by Plackett-Burman and central composite design, the microbial consortium were optimized, Bacillus sp. (B) and PE-9 and Pseudomonas putida (Pp) and PE-9 had significant interactions on lignin degradation based on a 5% level of significance. The nitrogen and carbon supplementations played an important role in lignin degradation and laccase production. The ultimate lignin degradation efficiency of 96.0% and laccase activity of 268U/L were obtained with 0.5g/L of ammonium chloride and 2g/L of sucrose. Results suggested that a stable and effective microbial consortium in alkalescent conditions was successfully achieved through the introduction of fusants, which was significant for its industrial application. Copyright © 2013 Elsevier Ltd. All rights reserved.

Bioremediation and reclamation of soil contaminated with petroleum oil hydrocarbons by exogenously seeded bacterial consortium: a pilot-scale study.

PubMed

Mukherjee, Ashis K; Bordoloi, Naba K

2011-03-01

Spillage of petroleum hydrocarbons causes significant environmental pollution. Bioremediation is an effective process to remediate petroleum oil contaminant from the ecosystem. The aim of the present study was to reclaim a petroleum oil-contaminated soil which was unsuitable for the cultivation of crop plants by using petroleum oil hydrocarbon-degrading microbial consortium. Bacterial consortium consisting of Bacillus subtilis DM-04 and Pseudomonas aeruginosa M and NM strains were seeded to 20% (v/w) petroleum oil-contaminated soil, and bioremediation experiment was carried out for 180 days under laboratory condition. The kinetics of hydrocarbon degradation was analyzed using biochemical and gas chromatographic (GC) techniques. The ecotoxicity of the elutriates obtained from petroleum oil-contaminated soil before and post-treatment with microbial consortium was tested on germination and growth of Bengal gram (Cicer aretinum) and green gram (Phaseolus mungo) seeds. Bacterial consortium showed a significant reduction in total petroleum hydrocarbon level in contaminated soil (76% degradation) as compared to the control soil (3.6% degradation) 180 days post-inoculation. The GC analysis confirmed that bacterial consortium was more effective in degrading the alkane fraction compared to aromatic fraction of crude petroleum oil hydrocarbons in soil. The nitrogen, sulfur, and oxygen compounds fraction was least degraded. The reclaimed soil supported the germination and growth of crop plants (C. aretinum and P. mungo). In contrast, seeds could not be germinated in petroleum oil-contaminated soil. The present study reinforces the application of bacterial consortium rather than individual bacterium for the effective bioremediation and reclamation of soil contaminated with petroleum oil.

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

NONE

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

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

PubMed

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

2015-04-01

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

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

PubMed

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

2012-07-01

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

Improved TNT detoxification by starch addition in a nitrogen-fixing Methylophilus-dominant aerobic microbial consortium.

PubMed

Khan, Muhammad Imran; Lee, Jaejin; Yoo, Keunje; Kim, Seonghoon; Park, Joonhong

2015-12-30

In this study, a novel aerobic microbial consortium for the complete detoxification of 2,4,6-trinitrotoluene (TNT) was developed using starch as a slow-releasing carbon source under nitrogen-fixing conditions. Aerobic TNT biodegradation coupled with microbial growth was effectively stimulated by the co-addition of starch and TNT under nitrogen-fixing conditions. The addition of starch with TNT led to TNT mineralization via ring cleavage without accumulation of any toxic by-products, indicating improved TNT detoxification by the co-addition of starch and TNT. Pyrosequencing targeting the bacterial 16S rRNA gene suggested that Methylophilus and Pseudoxanthomonas population were significantly stimulated by the co-addition of starch and TNT and that the Methylophilus population became predominant in the consortium. Together with our previous study regarding starch-stimulated RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) degradation (Khan et al., J. Hazard. Mater. 287 (2015) 243-251), this work suggests that the co-addition of starch with a target explosive is an effective way to stimulate aerobic explosive degradation under nitrogen-fixing conditions for enhancing explosive detoxification. Copyright © 2015 Elsevier B.V. All rights reserved.

Humin as an electron donor for enhancement of multiple microbial reduction reactions with different redox potentials in a consortium.

PubMed

Zhang, Dongdong; Zhang, Chunfang; Xiao, Zhixing; Suzuki, Daisuke; Katayama, Arata

2015-02-01

A solid-phase humin, acting as an electron donor, was able to enhance multiple reductive biotransformations, including dechlorination of pentachlorophenol (PCP), dissimilatory reduction of amorphous Fe (III) oxide (FeOOH), and reduction of nitrate, in a consortium. Humin that was chemically reduced by NaBH4 served as an electron donor for these microbial reducing reactions, with electron donating capacities of 0.013 mmol e(-)/g for PCP dechlorination, 0.15 mmol e(-)/g for iron reduction, and 0.30 mmol e(-)/g for nitrate reduction. Two pairs of oxidation and reduction peaks within the humin were detected by cyclic voltammetry analysis. 16S rRNA gene sequencing-based microbial community analysis of the consortium incubated with different terminal electron acceptors, suggested that Dehalobacter sp., Bacteroides sp., and Sulfurospirillum sp. were involved in the PCP dechlorination, dissimilatory iron reduction, and nitrate reduction, respectively. These findings suggested that humin functioned as a versatile redox mediator, donating electrons for multiple respiration reactions with different redox potentials. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Characterization of a Microbial Consortium for the Bioremoval of Polycyclic Aromatic Hydrocarbons (PAHs) in Water

PubMed Central

Blanco-Enríquez, Esmeralda G.; Zavala-Díaz de la Serna, Francisco Javier; Peralta-Pérez, María del Rosario; Ballinas-Casarrubias, Lourdes; Salmerón, Iván; Rubio-Arias, Héctor; Rocha-Gutiérrez, Beatriz A.

2018-01-01

Pollution of freshwater ecosystems from polycyclic aromatic hydrocarbons (PAHs) is a global concern. The US Environmental Protection Agency (EPA) has included the PAHs pyrene, phenanthrene, and naphthalene among the 16 priority compounds of special concern for their toxicological effects. The aim of this study was to adapt and characterize a microbial consortium from ore waste with the potential to remove these three PAHs from water. This microbial consortium was exposed to the target PAHs at levels of 5, 10, 20, 50, and 100 mg L−1 for 14 days. PAH bioremoval was measured using the analytical technique of solid phase microextraction, followed by gas chromatography mass spectrometry (SPME-GC/MS). The results revealed that up to 90% of the target PAHs can be removed from water after 14 days at a concentration level of 100 mg L−1. The predominant group of microorganisms identified at the phylum taxonomic level were the Proteobacteria, while the Actinobacteria were the predominant subgroup. The removal of phenanthrene, naphthalene, and pyrene predominantly occurred in specimens of genera Stenotrophomonas, Williamsia, and Chitinophagaceae, respectively. This study demonstrates that the use of specific microorganisms is an alternative method of reducing PAH levels in water. PMID:29757264

An Economic Framework of Microbial Trade

PubMed Central

Mee, Michael T.

2015-01-01

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

Bioremoval of priority polycyclic aromatic hydrocarbons by a microbial community with high sorption ability.

PubMed

Sanches, Sandra; Martins, Mónica; Silva, Ana F; Galinha, Claudia F; Santos, Maria A; Pereira, Inês A C; Crespo, Maria Teresa Barreto

2017-02-01

The treatment of large volumes of wastewater during oil refining is presently a challenge. Bioremediation has been considered an eco-friendly approach for the removal of polycyclic aromatic hydrocarbons (PAHs), which are one of the most hazardous groups of organic micropollutants. However, it is crucial to identify native PAH-removing microorganisms for the development of an effective bioremediation process. This study reports the high potential of an anaerobic microbial consortium enriched from a petrochemical refinery wastewater to remove two priority PAHs-acenaphthene and phenanthrene. Seventy-seven percent of acenaphthene was removed within 17 h, whereas phenanthrene was no longer detected after 15 h. Bioremoval rates were extremely high (0.086 and 0.156 h -1 for acenaphthene and phenanthrene, respectively). The characterization of the microbial communities by next-generation sequencing and fluorescence in situ hybridization showed that the PAH-removing consortium was mainly composed by bacteria affiliated to Diaphorobacter and Paracoccus genera, independently of the PAH tested. Moreover, besides biodegradation, biosorption was a relevant mechanism involved in the removal of both PAHs, which is an important finding since biosorption is less expensive than biodegradation and can be carried out with dead biomass. Although biodegradation is the most commonly reported biological mechanism for PAH removal, this study demonstrated that biosorption by this microbial community may be extremely efficient for their removal. Given the outstanding ability of this microbial consortium to quickly remove the compounds addressed, it could be further applied for the bioremediation of PAHs in refinery wastewaters and other contaminated environments.

Genome-Centric Analysis of a Thermophilic and Cellulolytic Bacterial Consortium Derived from Composting

PubMed Central

Lemos, Leandro N.; Pereira, Roberta V.; Quaggio, Ronaldo B.; Martins, Layla F.; Moura, Livia M. S.; da Silva, Amanda R.; Antunes, Luciana P.; da Silva, Aline M.; Setubal, João C.

2017-01-01

Microbial consortia selected from complex lignocellulolytic microbial communities are promising alternatives to deconstruct plant waste, since synergistic action of different enzymes is required for full degradation of plant biomass in biorefining applications. Culture enrichment also facilitates the study of interactions among consortium members, and can be a good source of novel microbial species. Here, we used a sample from a plant waste composting operation in the São Paulo Zoo (Brazil) as inoculum to obtain a thermophilic aerobic consortium enriched through multiple passages at 60°C in carboxymethylcellulose as sole carbon source. The microbial community composition of this consortium was investigated by shotgun metagenomics and genome-centric analysis. Six near-complete (over 90%) genomes were reconstructed. Similarity and phylogenetic analyses show that four of these six genomes are novel, with the following hypothesized identifications: a new Thermobacillus species; the first Bacillus thermozeamaize genome (for which currently only 16S sequences are available) or else the first representative of a new family in the Bacillales order; the first representative of a new genus in the Paenibacillaceae family; and the first representative of a new deep-branching family in the Clostridia class. The reconstructed genomes from known species were identified as Geobacillus thermoglucosidasius and Caldibacillus debilis. The metabolic potential of these recovered genomes based on COG and CAZy analyses show that these genomes encode several glycoside hydrolases (GHs) as well as other genes related to lignocellulose breakdown. The new Thermobacillus species stands out for being the richest in diversity and abundance of GHs, possessing the greatest potential for biomass degradation among the six recovered genomes. We also investigated the presence and activity of the organisms corresponding to these genomes in the composting operation from which the consortium was built, using compost metagenome and metatranscriptome datasets generated in a previous study. We obtained strong evidence that five of the six recovered genomes are indeed present and active in that composting process. We have thus discovered three (perhaps four) new thermophillic bacterial species that add to the increasing repertoire of known lignocellulose degraders, whose biotechnological potential can now be investigated in further studies. PMID:28469608

Mechanism, Kinetics and Microbiology of Inhibition Caused by Long-Chain Fatty Acids in Anaerobic Digestion of Algal Biomass

DOE PAGES

Ma, Jingwei; Zhao, Quan-Bao; Laurens, Lieve L.; ...

2015-09-15

Oleaginous microalgae contain a high level of lipids, which can be extracted and converted to biofuel. The lipid-extracted residue can then be further utilized through anaerobic digestion to produce biogas. However, long-chain fatty acids (LCFAs) have been identified as the main inhibitory factor on microbial activity of anaerobic consortium. In this study, the mechanism of LCFA inhibition on anaerobic digestion of whole and lipid-extracted algal biomass was investigated with a range of calcium concentrations against various inoculum to substrate ratios as a means to alleviate the LCFA inhibition.

Mechanism, Kinetics and Microbiology of Inhibition Caused by Long-Chain Fatty Acids in Anaerobic Digestion of Algal Biomass

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

Ma, Jingwei; Zhao, Quan-Bao; Laurens, Lieve L.

Oleaginous microalgae contain a high level of lipids, which can be extracted and converted to biofuel. The lipid-extracted residue can then be further utilized through anaerobic digestion to produce biogas. However, long-chain fatty acids (LCFAs) have been identified as the main inhibitory factor on microbial activity of anaerobic consortium. In this study, the mechanism of LCFA inhibition on anaerobic digestion of whole and lipid-extracted algal biomass was investigated with a range of calcium concentrations against various inoculum to substrate ratios as a means to alleviate the LCFA inhibition.

Microbial fuel cells: Running on gas

NASA Astrophysics Data System (ADS)

Ren, Zhiyong Jason

2017-06-01

Methane is an abundant energy source that is used for power generation in thermal power plants via combustion, but direct conversion to electricity in fuel cells remains challenging. Now, a microbial fuel cell is demonstrated to efficiently convert methane directly to current by careful selection of a consortium of microorganisms.

Enhancement in current density and energy conversion efficiency of 3-dimensional MFC anodes using pre-enriched consortium and continuous supply of electron donors

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

Borole, Abhijeet P; Hamilton, Choo Yieng; Vishnivetskaya, Tatiana A

2011-01-01

Using a pre-enriched microbial consortium as the inoculum and continuous supply of carbon source, improvement in performance of a three-dimensional, flow-through MFC anode utilizing ferricyanide cathode was investigated. The power density increased from 170 W/m3 (1800 mW/m2) to 580 W/m3 (6130 mW/m2), when the carbon loading increased from 2.5 g/l-day to 50 g/l-day. The coulombic efficiency (CE) decreased from 90% to 23% with increasing carbon loading. The CEs are among the highest reported for glucose and lactate as the substrate with the maximum current density reaching 15.1 A/m2. This suggests establishment of a very high performance exoelectrogenic microbial consortium atmore » the anode. A maximum energy conversion efficiency of 54% was observed at a loading of 2.5 g/l-day. Biological characterization of the consortium showed presence of Burkholderiales and Rhodocyclales as the dominant members. Imaging of the biofilms revealed thinner biofilms compared to the inoculum MFC, but a 1.9-fold higher power density.« less

Characterization of a microbial consortium capable of rapid and simultaneous dechlorination of 1,1,2,2-tetrachloroethane and chlorinated ethane and ethene intermediates:

USGS Publications Warehouse

Jones, Elizabeth J.P.; Voytek, Mary A.; Lorah, Michelle M.; Kirshtein, Julie D.

2006-01-01

Mixed cultures capable of dechlorinating chlorinated ethanes and ethenes were enriched from contaminated wetland sediment at Aberdeen Proving Ground (APG) Maryland. The “West Branch Consortium” (WBC-2) was capable of degrading 1,1,2,2-tetrachloroethane (TeCA), trichloroethene (TCE), cis and trans 1,2-dichloroethene (DCE), 1,1,2-trichloroethane (TCA), 1,2-dichloroethane, and vinyl chloride to nonchlorinated end products ethene and ethane. WBC-2 dechlorinated TeCA, TCA, and cisDCE rapidly and simultaneously. A Clostridium sp. phylogenetically closely related to an uncultured member of a TCE-degrading consortium was numerically dominant in the WBC-2 clone library after 11 months of enrichment in culture. Clostridiales, including Acetobacteria, comprised 65% of the bacterial clones in WBC-2, with Bacteroides (14%), and epsilon Proteobacteria (14%) also numerically important. Methanogens identified in the consortium were members of the class Methanomicrobia, which includes acetoclastic methanogens. Dehalococcoidesdid not become dominant in the culture, although it was present at about 1% in the microbial population. The WBC-2 consortium provides opportunities for the in situbioremediation of sites contaminated with mixtures of chlorinated ethenes and ethanes.

Biodegradation of oil tank bottom sludge using microbial consortia.

PubMed

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

2007-06-01

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

Salinity effect on the metabolic pathway and microbial function in phenanthrene degradation by a halophilic consortium.

PubMed

Wang, Chongyang; Huang, Yong; Zhang, Zuotao; Wang, Hui

2018-04-25

With the close relationship between saline environments and industry, polycyclic aromatic hydrocarbons (PAHs) accumulate in saline/hypersaline environments. Therefore, PAHs degradation by halotolerant/halophilic bacteria has received increasing attention. In this study, the metabolic pathway of phenanthrene degradation by halophilic consortium CY-1 was first studied which showed a single upstream pathway initiated by dioxygenation at the C1 and C2 positions, and at several downstream pathways, including the catechol pathway, gentisic acid pathway and protocatechuic acid pathway. The effects of salinity on the community structure and expression of catabolic genes were further studied by a combination of high-throughput sequencing, catabolic gene clone library and real-time PCR. Pure cultures were also isolated from consortium CY-1 to investigate the contribution made by different microbes in the PAH-degrading process. Marinobacter is the dominant genus that contributed to the upstream degradation of phenanthrene especially in high salt content. Genus Halomonas made a great contribution in transforming intermediates in the subsequent degradation of catechol by using catechol 1,2-dioxygenase (C12O). Other microbes were predicted to be mediating bacteria that were able to utilize intermediates via different downstream pathways. Salinity was investigated to have negative effects on both microbial diversity and activity of consortium CY-1 and consortium CY-1 was found with a high degree of functional redundancy in saline environments.

Biodegradation of Methyl Tertiary Butyl Ether (MTBE) by a Microbial Consortium in a Continuous Up-Flow Packed-Bed Biofilm Reactor: Kinetic Study, Metabolite Identification and Toxicity Bioassays

PubMed Central

Alfonso-Gordillo, Guadalupe; Flores-Ortiz, César Mateo; Morales-Barrera, Liliana

2016-01-01

This study investigated the aerobic biodegradation of methyl tertiary-butyl ether (MTBE) by a microbial consortium in a continuous up-flow packed-bed biofilm reactor using tezontle stone particles as a supporting material for the biofilm. Although MTBE is toxic for microbial communities, the microbial consortium used here was able to resist MTBE loading rates up to 128.3 mg L-1 h-1, with removal efficiencies of MTBE and chemical oxygen demand (COD) higher than 90%. A linear relationship was observed between the MTBE loading rate and the MTBE removal rate, as well as between the COD loading rate and the COD removal rate, within the interval of MTBE loading rates from 11.98 to 183.71 mg L-1 h-1. The metabolic intermediate tertiary butyl alcohol (TBA) was not detected in the effluent during all reactor runs, and the intermediate 2-hydroxy butyric acid (2-HIBA) was only detected at MTBE loading rates higher than 128.3 mg L-1 h-1. The results of toxicity bioassays with organisms from two different trophic levels revealed that the toxicity of the influent was significantly reduced after treatment in the packed-bed reactor. The packed-bed reactor system used in this study was highly effective for the continuous biodegradation of MTBE and is therefore a promising alternative for detoxifying MTBE-laden wastewater and groundwater. PMID:27907122

Biodegradation of Methyl Tertiary Butyl Ether (MTBE) by a Microbial Consortium in a Continuous Up-Flow Packed-Bed Biofilm Reactor: Kinetic Study, Metabolite Identification and Toxicity Bioassays.

PubMed

Alfonso-Gordillo, Guadalupe; Flores-Ortiz, César Mateo; Morales-Barrera, Liliana; Cristiani-Urbina, Eliseo

2016-01-01

This study investigated the aerobic biodegradation of methyl tertiary-butyl ether (MTBE) by a microbial consortium in a continuous up-flow packed-bed biofilm reactor using tezontle stone particles as a supporting material for the biofilm. Although MTBE is toxic for microbial communities, the microbial consortium used here was able to resist MTBE loading rates up to 128.3 mg L-1 h-1, with removal efficiencies of MTBE and chemical oxygen demand (COD) higher than 90%. A linear relationship was observed between the MTBE loading rate and the MTBE removal rate, as well as between the COD loading rate and the COD removal rate, within the interval of MTBE loading rates from 11.98 to 183.71 mg L-1 h-1. The metabolic intermediate tertiary butyl alcohol (TBA) was not detected in the effluent during all reactor runs, and the intermediate 2-hydroxy butyric acid (2-HIBA) was only detected at MTBE loading rates higher than 128.3 mg L-1 h-1. The results of toxicity bioassays with organisms from two different trophic levels revealed that the toxicity of the influent was significantly reduced after treatment in the packed-bed reactor. The packed-bed reactor system used in this study was highly effective for the continuous biodegradation of MTBE and is therefore a promising alternative for detoxifying MTBE-laden wastewater and groundwater.

Adaptation of Methanogenic Inocula to Anaerobic Digestion of Maize Silage

PubMed Central

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

2017-01-01

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

Comparative biochemical methane potential of paragrass using an unacclimated and an acclimated microbial consortium.

PubMed

Nuchdang, Sasikarn; Khemkhao, Maneerat; Techkarnjanaruk, Somkiet; Phalakornkule, Chantaraporn

2015-05-01

The effect of inoculum sources on the anaerobic digestion of paragrass was investigated. Two types of sludge were used as the inoculums: an anaerobic sludge obtained from a domestic wastewater treatment plant (OS) and a sludge acclimated to fibrous substrates in raw palm oil mill effluent (AMC). Microbial activity assays showed that the AMC had hydrolytic and acetogenic activities two times greater than the activities of the OS. In addition, the production of methane from acetate by the AMC occurred without a lag phase, while it took 8 days for the OS to start producing methane from the same substrate. The biochemical methane potential after 80 days digestion was 316 ml STP/g VS(added) using the AMC, and 277 ml STP/g VS(added) using the OS. The methane potential of the paragrass was estimated to be 3337 Nm(3) CH4/ha a. Copyright © 2015 Elsevier Ltd. All rights reserved.

Microbial Consortium with High Cellulolytic Activity (MCHCA) for Enhanced Biogas Production

PubMed Central

Poszytek, Krzysztof; Ciezkowska, Martyna; Sklodowska, Aleksandra; Drewniak, Lukasz

2016-01-01

The use of lignocellulosic biomass as a substrate in agricultural biogas plants is very popular and yields good results. However, the efficiency of anaerobic digestion, and thus biogas production, is not always satisfactory due to the slow or incomplete degradation (hydrolysis) of plant matter. To enhance the solubilization of the lignocellulosic biomass various physical, chemical and biological pretreatment methods are used. The aim of this study was to select and characterize cellulose-degrading bacteria, and to construct a microbial consortium, dedicated for degradation of maize silage and enhancing biogas production from this substrate. Over 100 strains of cellulose-degrading bacteria were isolated from: sewage sludge, hydrolyzer from an agricultural biogas plant, cattle slurry and manure. After physiological characterization of the isolates, 16 strains (representatives of Bacillus, Providencia, and Ochrobactrum genera) were chosen for the construction of a Microbial Consortium with High Cellulolytic Activity, called MCHCA. The selected strains had a high endoglucanase activity (exceeding 0.21 IU/mL CMCase activity) and a wide range of tolerance to various physical and chemical conditions. Lab-scale simulation of biogas production using the selected strains for degradation of maize silage was carried out in a two-bioreactor system, similar to those used in agricultural biogas plants. The obtained results showed that the constructed MCHCA consortium is capable of efficient hydrolysis of maize silage, and increases biogas production by even 38%, depending on the inoculum used for methane fermentation. The results in this work indicate that the mesophilic MCHCA has a great potential for application on industrial scale in agricultural biogas plants. PMID:27014244

Reduction on the anaerobic biological activity inhibition caused by heavy metals and sulphates in effluents through chemical precipitation with soda and lime.

PubMed

Alves, L de Carvalho; Cammarota, M C; De França, F P

2006-12-01

The School of Chemistry Environmental Technology Laboratory generates 43.4 1 of effluent with low pH (0.7) and high contents of COD (1908 mgO2 l(-1)), phenol (132.1 mg l(-1)), sulfate (36700 mg l(-1)) and heavy metals (28.2 mg Hg l(-1); 82.1 mg Cr(total) l(-1); 30.8 mg Cu l(-1); 57.4 mg Fe(total) l(-1); 16.2 mg Al l(-1)) weekly. These data show that this effluent presents high toxicity for biological treatment, with a physical-chemical step being necessary before a biological step. Preliminary studies showed that the most toxic constituents of the effluent were sulfate, phenol and total chromium. In this work, a chemical precipitation step with sodium hydroxide or lime was evaluated for the toxicity reduction on anaerobic microbial consortium. These experiments were carried out with increasing concentrations of alkalis in the effluent in order to obtain pH initial values of 8-12. Similar results were obtained for COD (15-28%), turbidity (95-98%), phenol (13-24%) and total chromium (99.8-99.9%) removals in each condition studied with soda or lime. Sulfate was only removed by precipitation with lime, obtaining reductions from 84 to 88%. The toxicity on the anaerobic sludge was studied employing specific methanogenic activity (SMA) analysis of raw and treated effluent (after chemical precipitation step). The SMA experiments showed that chemical precipitation at pH 8 reduces the toxic effect of the effluent on anaerobic microbial consortium three times (with soda) and thirteen times (with lime). These results indicate that precipitation with lime is more efficient at toxicity removal, however the produced sludge volume is around two times higher than that produced with soda.

Biodegradation of phenanthrene in bioaugmented microcosm by consortium ASP developed from coastal sediment of Alang-Sosiya ship breaking yard.

PubMed

Patel, Vilas; Patel, Janki; Madamwar, Datta

2013-09-15

A phenanthrene-degrading bacterial consortium (ASP) was developed using sediment from the Alang-Sosiya shipbreaking yard at Gujarat, India. 16S rRNA gene-based molecular analyses revealed that the bacterial consortium consisted of six bacterial strains: Bacillus sp. ASP1, Pseudomonas sp. ASP2, Stenotrophomonas maltophilia strain ASP3, Staphylococcus sp. ASP4, Geobacillus sp. ASP5 and Alcaligenes sp. ASP6. The consortium was able to degrade 300 ppm of phenanthrene and 1000 ppm of naphthalene within 120 h and 48 h, respectively. Tween 80 showed a positive effect on phenanthrene degradation. The consortium was able to consume maximum phenanthrene at the rate of 46 mg/h/l and degrade phenanthrene in the presence of other petroleum hydrocarbons. A microcosm study was conducted to test the consortium's bioremediation potential. Phenanthrene degradation increased from 61% to 94% in sediment bioaugmented with the consortium. Simultaneously, bacterial counts and dehydrogenase activities also increased in the bioaugmented sediment. These results suggest that microbial consortium bioaugmentation may be a promising technology for bioremediation. Copyright © 2013 Elsevier Ltd. All rights reserved.

Bioremediation assessment of diesel-biodiesel-contaminated soil using an alternative bioaugmentation strategy.

PubMed

Colla, Tatiana Simonetto; Andreazza, Robson; Bücker, Francielle; de Souza, Marcela Moreira; Tramontini, Letícia; Prado, Gerônimo Rodrigues; Frazzon, Ana Paula Guedes; Camargo, Flávio Anastácio de Oliveira; Bento, Fátima Menezes

2014-02-01

This study investigated the effectiveness of successive bioaugmentation, conventional bioaugmentation, and biostimulation of biodegradation of B10 in soil. In addition, the structure of the soil microbial community was assessed by polymerase chain reaction-denaturing gradient gel electrophoresis. The consortium was inoculated on the initial and the 11th day of incubation for successive bioaugmentation and only on the initial day for bioaugmentation and conventional bioaugmentation. The experiment was conducted for 32 days. The microbial consortium was identified based on sequencing of 16S rRNA gene and consisted as Pseudomonas aeruginosa, Achromobacter xylosoxidans, and Ochrobactrum intermedium. Nutrient introduction (biostimulation) promoted a positive effect on microbial populations. The results indicate that the edaphic community structure and dynamics were different according to the treatments employed. CO2 evolution demonstrated no significant difference in soil microbial activity between biostimulation and bioaugmentation treatments. The total petroleum hydrocarbon (TPH) analysis indicated a biodegradation level of 35.7 and 32.2 % for the biostimulation and successive bioaugmentation treatments, respectively. Successive bioaugmentation displayed positive effects on biodegradation, with a substantial reduction in TPH levels.

F-16 Microbially Influenced Corrosion (MIC) Characterization & Prevention Study

DTIC Science & Technology

2011-05-12

Staphylococcus epidermidis Fungal Consortium Aspergillus fumigatus Fusarium oxysporum Penicillium oxalicum Rhodoturula sp. Trichoderma sp. Control...Growth, or Soil and Dirt Accumulation • Fungal Consortium – Aspergillus sp (FI-19) Aureobasidium pullulans (FI-16) – Fusarium oxysporum (FI-6) Fusarium...species (common environmental isolates) – Minimal impact to health & safety • Fungal species promote MIC of Al2024-T3 alloy • Intergranular attack with

Microbial growth under a high-pressure CO2 environment

NASA Astrophysics Data System (ADS)

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

2009-12-01

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

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

Doud, Devin F. R.; Angenent, Largus T.

Rhodopseudomonas palustris has emerged as a model microbe for the anaerobic metabolism of p-coumarate, which is an aromatic compound and a primary component of lignin. However, under an aerobic conditions, R.palustris must actively eliminate excess reducing equivalents through a number of known strategies (e.g., CO 2 fixation, H 2 evolution) to avoid lethal redox imbalance. Others had hypothesized that to ease the burden of this redox imbalance, a clonal population of R.palustris could functionally differentiate into a pseudo-consortium. Within this pseudo-consortium, one sub-population would perform the aromatic moiety degradation into acetate, while the other sub-population would oxidize acetate, resulting inmore » a single-genotype syntrophy through acetate sharing. Here, the objective was to test this hypothesis by utilizing microbial lelectrochemistry as a research tool with the extrac ellular-electron-transferring bacterium Geobacter sulfurreducens as a reporter strain replacing the hypothesized acetate-oxidizing sub-population. We used a 2×4 experimental design with pure cultures of R. palustris in serum bottles and co-cultures of R. palustris and G.sulfurreducens in bioelectrochemical systems.This experimental design included growth medium with and without bicarbonate to induce non-lethal and lethal redox imbalance conditions, respectively, in R. palustris. Finally, the design also included a mutant strain (NifA*) of R. palustris, which constitutively produces H 2, to serve both as a positive control for metabolite secretion (H 2) to G. sulfurreducens, and as a non-lethal redox control for without bicarbonate conditions. Our results demonstrate that acetate sharing between different sub-populations of R. palustris does not occur while degrading p-coumarate under either non-lethal or lethal redox imbalance conditions. Furthermore, this work highlights the strength of microbial electrochemistry as a tool for studying microbial syntrophy.« less

The metabolic pathway of metamifop degradation by consortium ME-1 and its bacterial community structure.

PubMed

Dong, Weiliang; Liu, Kuan; Wang, Fei; Xin, Fengxue; Zhang, Wenming; Zhang, Min; Wu, Hao; Ma, Jiangfeng; Jiang, Min

2017-06-01

Metamifop is universally used in agriculture as a post-emergence aryloxyphenoxy propionate herbicide (AOPP), however its microbial degradation mechanism remains unclear. Consortium ME-1 isolated from AOPP-contaminated soil can degrade metamifop completely after 6 days and utilize it as the carbon source for bacterial growth. Meanwhile, consortium ME-1 possessed the ability to degrade metamifop stably under a wide range of pH (6.0-10.0) or temperature (20-42 °C). HPLC-MS analysis shows that N-(2-fluorophenyl)-2-(4-hydroxyphenoxy)-N-methyl propionamide, 2-(4-hydroxyphenoxy)-propionic acid, 6-chloro-2-benzoxazolinone and N-methyl-2-fluoroaniline, were detected and identified as four intermediate metabolites. Based on the metabolites identified, a putative metabolic pathway of metamifop was proposed for the first time. In addition, the consortium ME-1 was also able to transform or degrade other AOPP such as fenoxaprop-p-ethyl, clodinafop-propargyl, quizalofop-p-ethyl and cyhalofop-butyl. Moreover, the community structure of ME-1 with lower microbial diversity compared with the initial soil sample was investigated by high throughput sequencing. β-Proteobacteria and Sphingobacteria were the largest class with sequence percentages of 46.6% and 27.55% at the class level. In addition, 50 genera were classified in consortium ME-1, of which Methylobacillus, Sphingobacterium, Bordetella and Flavobacterium were the dominant genera with sequence percentages of 25.79, 25.61, 14.68 and 9.55%, respectively.

Microbial hydroxylation of quinoline in contaminated groundwater: evidence for incorporation of the oxygen atom of water.

USGS Publications Warehouse

Pereira, W.E.; Rostad, C.E.; Leiker, T.J.; Updegraff, D.M.; Bennett, J.L.

1988-01-01

Studies conducted in an aquifer contaminated by creosote suggest that quinoline is converted to 2(1H)quinolinone by an indigenous consortium of microorganisms. Laboratory microbial experiments using H218O indicate that water is the source of the oxygen atom for this hydroxylation reaction under aerobic and anaerobic conditions.

Efficient bioconversion of organic wastes to high optical activity of l-lactic acid stimulated by cathode in mixed microbial consortium.

PubMed

Xue, Gang; Lai, Sizhou; Li, Xiang; Zhang, Wenjuan; You, Jiguang; Chen, Hong; Qian, Yajie; Gao, Pin; Liu, Zhenhong; Liu, Yanan

2017-12-12

Lactic acid is one of the emerging top biomass derived platform chemicals that can be fermented from organic wastes. This study evaluated the potential of Cathodic Electro-Fermentation (CEF) as a novel approach to enhance the yield of high optical activity (OA) of l-lactic acid from organic wastes using mixed microbial consortium. The fermentation process was stimulated through the cathode applied with -100 mV versus standard hydrogen electrode (SHE), which contributed to 4.73 times higher lactic acid productivity (0.6578 g L -1 h -1 ) compared to that in the open circuit control (0.1392 g L -1 h -1 ), and an improved OA of l-lactic acid was also observed (42.3% vs. 3.6% of the open circuit control). The study elucidated that the optimal voltage at -100 mV promoted the conversion of pyruvate to l-lactate by 77.9% compared to the Blank, which triggered the generation of l-lactic acid to occur rapidly even at low concentration of pyruvate. The significant variation of microbial community in family- and genus-level distributions were observed in CEF system. Furthermore, the open-circuit operation test demonstrated that the cathode providing in-situ electron supply was essential to achieve high efficient bioconversion of organic wastes to lactic acid. Our work highlights the feasibility of CEF to steer high value-added fermentation products deriving from organic wastes by the mixed microbial consortium. Copyright © 2017 Elsevier Ltd. All rights reserved.

Contributions of available substrates and activities of trophic microbial community to methanogenesis in vegetative and reproductive rice rhizospheric soil.

PubMed

Chawanakul, Sansanee; Chaiprasert, Pawinee; Towprayoon, Sirintornthep; Tanticharoen, Morakot

2009-01-01

Potential of methane production and trophic microbial activities at rhizospheric soil during rice cv. Supanbunri 1 cultivation were determined by laboratory anaerobic diluents vials. The methane production was higher from rhizospheric than non-rhizospheric soil, with the noticeable peaks during reproductive phase (RP) than vegetative phase (VP). Glucose, ethanol and acetate were the dominant available substrates found in rhizospheric soil during methane production at both phases. The predominance activities of trophic microbial consortium in methanogenesis, namely fermentative bacteria (FB), acetogenic bacteria (AGB), acetate utilizing bacteria (AB) and acetoclastic methanogens (AM) were also determined. At RP, these microbial groups were enhanced in the higher of methane production than VP. This correlates with our finding that methane production was greater at the rhizospheric soil with the noticeable peaks during RP (1,150 +/- 60 nmol g dw(-1) d(-1)) compared with VP (510 +/- 30 nmol g dw(-1) d(-1)). The high number of AM showed the abundant (1.1x10(4) cell g dw(-1)) with its high activity at RP, compared to the less activity with AM number at VP (9.8x10(2) cell g dw(-1)). Levels of AM are low in the total microbial population, being less than 1% of AB. These evidences revealed that the microbial consortium of these two phases were different.

Bioremediation of diuron contaminated soils by a novel degrading microbial consortium.

PubMed

Villaverde, J; Rubio-Bellido, M; Merchán, F; Morillo, E

2017-03-01

Diuron is a biologically active pollutant present in soil, water and sediments. It is persistent in soil, water and groundwater and slightly toxic to mammals and birds as well as moderately toxic to aquatic invertebrates. Its principal product of biodegradation, 3,4-dichloroaniline, exhibits a higher toxicity than diuron and is also persistent in the environment. On this basis, the objective of the study was to determine the potential capacity of a proposed novel diuron-degrading microbial consortium (DMC) for achieving not only diuron degradation, but its mineralisation both in solution as well as in soils with different properties. The consortium was tested in a soil solution where diuron was the only carbon source, and more than 98.8% of the diuron initially added was mineralised after only a few days. The consortium was composed of three diuron-degrading strains, Arthrobacter sulfonivorans, Variovorax soli and Advenella sp. JRO, the latter had been isolated in our laboratory from a highly contaminated industrial site. This work shows for the first time the potential capacity of a member of the genus Advenella to remediate pesticide-contaminated soils. However, neither of the three strains separately achieved mineralisation (ring- 14 C) of diuron in a mineral medium (MSM) with a trace nutrient solution (NS); combined in pairs, they mineralised 40% of diuron in solution, but the most relevant result was obtained in the presence of the three-member consortium, where complete diuron mineralisation was achieved after only a few days. In the presence of the investigated soils in suspension, the capacity of the consortium to mineralise diuron was evaluated, achieving mineralisation of a wide range of herbicides from 22.9 to 69.0%. Copyright © 2016 Elsevier Ltd. All rights reserved.

Removal of a mixture of pesticides by a Streptomyces consortium: Influence of different soil systems.

PubMed

Fuentes, María S; Raimondo, Enzo E; Amoroso, María J; Benimeli, Claudia S

2017-04-01

Although the use of organochlorine pesticides (OPs) is restricted or banned in most countries, they continue posing environmental and health concerns, so it is imperative to develop methods for removing them from the environment. This work is aimed to investigate the simultaneous removal of three OPs (lindane, chlordane and methoxychlor) from diverse types of systems by employing a native Streptomyces consortium. In liquid systems, a satisfactory microbial growth was observed accompanied by removal of lindane (40.4%), methoxychlor (99.5%) and chlordane (99.8%). In sterile soil microcosms, the consortium was able to grow without significant differences in the different textured soils (clay silty loam, sandy and loam), both contaminated or not contaminated with the OPs-mixture. The Streptomyces consortium was able to remove all the OPs in sterile soil microcosm (removal order: clay silty loam > loam > sandy). So, clay silty loam soil (CSLS) was selected for next assays. In non-sterile CSLS microcosms, chlordane removal was only about 5%, nonetheless, higher rates was observed for lindane (11%) and methoxychlor (20%). In CSLS slurries, the consortium exhibited similar growth levels, in the presence of or in the absence of the OPs-mixture. Not all pesticides were removed in the same way; the order of pesticide dissipation was: methoxychlor (26%)>lindane (12.5%)>chlordane (10%). The outlines of microbial growth and pesticides removal provide information about using actinobacteria consortium as strategies for bioremediation of OPs-mixture in diverse soil systems. Texture of soils and assay conditions (sterility, slurry formulation) were determining factors influencing the removal of each pesticide of the mixture. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

PubMed

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

2018-02-01

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

Characterization of bacterial consortium and its application in an ectopic fermentation system.

PubMed

Guo, Hui; Geng, Bing; Liu, Xue; Ye, Jing; Zhao, Yongkun; Zhu, Changxiong; Yuan, Hongli

2013-07-01

This study aimed to develop an ectopic fermentation system (EFS) to reduce the pollution of cow wastewater and to provide a basis for the production of biofertilizer with fermentation residues. Six thermophilic strains, three of which have efficient cellulose-degrading abilities and the other have good ammonia-N utilizing abilities, were chosen as the microbial inocula. The results showed that EFS inoculated with microbial consortium brought higher temperature and more wastewater was needed to ensure continuous fermentation. The pH values decreased in the early stage of fermentation, and then increased during the process. It caused increases in total Kjeldahl nitrogen, total phosphorous, and total potassium content. Decreases in organic matter content and C/N ratio were also observed. The high level of nutrients indicated the suitability of the paddings after fermentation for agronomic uses. It firstly attempted to combine cow wastewater treatment and bio-organic fertilizer production by EFS with mixed microbial culture. Copyright © 2013 Elsevier Ltd. All rights reserved.

Effects of nitrate injection on microbial enhanced oil recovery and oilfield reservoir souring.

PubMed

da Silva, Marcio Luis Busi; Soares, Hugo Moreira; Furigo, Agenor; Schmidell, Willibaldo; Corseuil, Henry Xavier

2014-11-01

Column experiments were utilized to investigate the effects of nitrate injection on sulfate-reducing bacteria (SRB) inhibition and microbial enhanced oil recovery (MEOR). An indigenous microbial consortium collected from the produced water of a Brazilian offshore field was used as inoculum. The presence of 150 mg/L volatile fatty acids (VFA´s) in the injection water contributed to a high biological electron acceptors demand and the establishment of anaerobic sulfate-reducing conditions. Continuous injection of nitrate (up to 25 mg/L) for 90 days did not inhibit souring. Contrariwise, in nitrogen-limiting conditions, the addition of nitrate stimulated the proliferation of δ-Proteobacteria (including SRB) and the associated sulfide concentration. Denitrification-specific nirK or nirS genes were not detected. A sharp decrease in water interfacial tension (from 20.8 to 14.5 mN/m) observed concomitantly with nitrate consumption and increased oil recovery (4.3 % v/v) demonstrated the benefits of nitrate injection on MEOR. Overall, the results support the notion that the addition of nitrate, at this particular oil reservoir, can benefit MEOR by stimulating the proliferation of fortuitous biosurfactant-producing bacteria. Higher nitrate concentrations exceeding the stoichiometric volatile fatty acid (VFA) biodegradation demands and/or the use of alternative biogenic souring control strategies may be necessary to warrant effective SRB inhibition down gradient from the injection wells.

Isolation of a sulfide-producing bacterial consortium from cooling-tower water: Evaluation of corrosive effects on galvanized steel.

PubMed

Ilhan-Sungur, Esra; Ozuolmez, Derya; Çotuk, Ayşın; Cansever, Nurhan; Muyzer, Gerard

2017-02-01

Sulfidogenic Clostridia and sulfate reducing bacteria (SRB) often cohabit in nature. The presence of these microorganisms can cause microbially influenced corrosion (MIC) of materials in different ways. To investigate this aspect, bacteria were isolated from cooling tower water and used in corrosion tests of galvanized steel. The identity of the isolates was determined by comparative sequence analysis of PCR-amplified 16S rDNA gene fragments, separated by denaturing gradient gel electrophoresis (DGGE). This analysis showed that, in spite of the isolation process, colonies were not pure and consisted of a mixture of bacteria affiliated with Desulfosporosinus meridiei and Clostridium sp. To evaluate the corrosive effect, galvanized steel coupons were incubated with a mixed culture for 4, 8, 24, 72, 96, 168, 360 and 744 h, along with a control set in sterile culture medium only. The corrosion rate was determined by weight loss, and biofilm formation and corroded surfaces were observed by scanning electron microscopy (SEM). Although the sulfide-producing bacterial consortium led to a slight increase in the corrosion of galvanized steel coupons, when compared to the previous studies it can be said that Clostridium sp. can reduce the corrosive effect of the Desulfosporosinus sp. strain. Copyright © 2016 Elsevier Ltd. All rights reserved.

Rapid Mineralization of Benzo[a]pyrene by a Microbial Consortium Growing on Diesel Fuel

PubMed Central

Kanaly, Robert A.; Bartha, Richard; Watanabe, Kazuya; Harayama, Shigeaki

2000-01-01

A microbial consortium which rapidly mineralized the environmentally persistent pollutant benzo[a]pyrene was recovered from soil. The consortium cometabolically converted [7-14C]benzo[a]pyrene to 14CO2 when it was grown on diesel fuel, and the extent of benzo[a]pyrene mineralization was dependent on both diesel fuel and benzo[a]pyrene concentrations. Addition of diesel fuel at concentrations ranging from 0.007 to 0.2% (wt/vol) stimulated the mineralization of 10 mg of benzo[a]pyrene per liter 33 to 65% during a 2-week incubation period. When the benzo[a]pyrene concentration was 10 to 100 mg liter−1 and the diesel fuel concentration was 0.1% (wt/vol), an inoculum containing 1 mg of cell protein per liter (small inoculum) resulted in mineralization of up to 17.2 mg of benzo[a]pyrene per liter in 16 days. This corresponded to 35% of the added radiolabel when the concentration of benzo[a]pyrene was 50 mg liter−1. A radiocarbon mass balance analysis recovered 25% of the added benzo[a]pyrene solubilized in the culture suspension prior to mineralization. Populations growing on diesel fuel most likely promoted emulsification of benzo[a]pyrene through the production of surface-active compounds. The consortium was also analyzed by PCR-denaturing gradient gel electrophoresis of 16S rRNA gene fragments, and 12 dominant bands, representing different sequence types, were detected during a 19-day incubation period. The onset of benzo[a]pyrene mineralization was compared to changes in the consortium community structure and was found to correlate with the emergence of at least four sequence types. DNA from 10 sequence types were successfully purified and sequenced, and that data revealed that eight of the consortium members were related to the class Proteobacteria but that the consortium also included members which were related to the genera Mycobacterium and Sphingobacterium. PMID:11010861

Application of culture-dependent and culture-independent methods for the identification of Lactobacillus kefiranofaciens in microbial consortia present in kefir grains.

PubMed

Hamet, Maria Fernanda; Londero, Alejandra; Medrano, Micaela; Vercammen, Elisabeth; Van Hoorde, Koenraad; Garrote, Graciela L; Huys, Geert; Vandamme, Peter; Abraham, Analía G

2013-12-01

The biological and technological characteristics of kefiran as well as its importance in grain integrity led us to analyze the microbial kefir grain consortium with focus on Lactobacillus kefiranofaciens. The presence of L. kefiranofaciens in the nine kefir grains studied was demonstrated by denaturing gradient gel electrophoresis. By culture dependent methods applying a methodology focused on the search of this species, 22 isolates with typical morphology were obtained and identified applying a combination of SDS-PAGE of whole cell proteins, (GTG)5-PCR and sequence analysis of the housekeeping gene encoding the α-subunit of bacterial phenylalanyl-tRNA synthase (pheS). This polyphasic approach allowed the reliable identification of 11 L. kefiranofaciens, 5 Lactobacillus paracasei, 4 Lactobacillus kefiri and 2 Lactobacillus parakefiri isolates. Isolated L. kefiranofaciens strains produced polysaccharide in strain-dependent concentrations and EPS produced by them also differed in the degree of polymerization. The isolation and accurate identification of L. kefiranofaciens is relevant taking into account the important role of this microorganism in the grain ecosystem as well as its potential application as starter in food fermentations. Copyright © 2013 Elsevier Ltd. All rights reserved.

Biodegradation of bilge water: Batch test under anaerobic and aerobic conditions and performance of three pilot aerobic Moving Bed Biofilm Reactors (MBBRs) at different filling fractions.

PubMed

Vyrides, Ioannis; Drakou, Efi-Maria; Ioannou, Stavros; Michael, Fotoula; Gatidou, Georgia; Stasinakis, Athanasios S

2018-07-01

The bilge water that is stored at the bottom of the ships is saline and greasy wastewater with a high Chemical Oxygen Demand (COD) fluctuations (2-12 g COD L -1 ). The aim of this study was to examine at a laboratory scale the biodegradation of bilge water using first anaerobic granular sludge followed by aerobic microbial consortium (consisted of 5 strains) and vice versa and then based on this to implement a pilot scale study. Batch results showed that granular sludge and aerobic consortium can remove up to 28% of COD in 13 days and 65% of COD removal in 4 days, respectively. The post treatment of anaerobic and aerobic effluent with aerobic consortium and granular sludge resulted in further 35% and 5% COD removal, respectively. The addition of glycine betaine or nitrates to the aerobic consortium did not enhance significantly its ability to remove COD from bilge water. The aerobic microbial consortium was inoculated in 3 pilot (200 L) Moving Bed Biofilm Reactors (MBBRs) under filling fractions of 10%, 20% and 40% and treated real bilge water for 165 days under 36 h HRT. The MBBR with a filling fraction of 40% resulted in the highest COD decrease (60%) compared to the operation of the MBBRs with a filling fraction of 10% and 20%. GC-MS analysis on 165 day pointed out the main organic compounds presence in the influent and in the MBBR (10% filling fraction) effluent. Copyright © 2018 Elsevier Ltd. All rights reserved.

Improvement of anaerobic digestion performance by continuous nitrogen removal with a membrane contactor treating a substrate rich in ammonia and sulfide.

PubMed

Lauterböck, B; Nikolausz, M; Lv, Z; Baumgartner, M; Liebhard, G; Fuchs, W

2014-04-01

The effect of reduced ammonia levels on anaerobic digestion was investigated. Two reactors were fed with slaughterhouse waste, one with a hollow fiber membrane contractor for ammonia removal and one without. Different organic loading rates (OLR) and free ammonia and sulfide concentrations were investigated. In the reactor with the membrane contactor, the NH4-N concentration was reduced threefold. At a moderate OLR (3.1 kg chemical oxygen demand - COD/m(3)/d), this reactor performed significantly better than the reference reactor. At high OLR (4.2 kg COD/m(3)/d), the reference reactor almost stopped producing methane (0.01 Nl/gCOD). The membrane reactor also showed a stable process with a methane yield of 0.23 Nl/g COD was achieved. Both reactors had predominantly a hydrogenotrophic microbial consortium, however in the membrane reactor the genus Methanosaeta (acetoclastic) was also detected. In general, all relevant parameters and the methanogenic consortium indicated improved anaerobic digestion of the reactor with the membrane. Copyright © 2014 Elsevier Ltd. All rights reserved.

Comparative mass spectrometry-based metabolomics strategies for the investigation of microbial secondary metabolites.

PubMed

Covington, Brett C; McLean, John A; Bachmann, Brian O

2017-01-04

Covering: 2000 to 2016The labor-intensive process of microbial natural product discovery is contingent upon identifying discrete secondary metabolites of interest within complex biological extracts, which contain inventories of all extractable small molecules produced by an organism or consortium. Historically, compound isolation prioritization has been driven by observed biological activity and/or relative metabolite abundance and followed by dereplication via accurate mass analysis. Decades of discovery using variants of these methods has generated the natural pharmacopeia but also contributes to recent high rediscovery rates. However, genomic sequencing reveals substantial untapped potential in previously mined organisms, and can provide useful prescience of potentially new secondary metabolites that ultimately enables isolation. Recently, advances in comparative metabolomics analyses have been coupled to secondary metabolic predictions to accelerate bioactivity and abundance-independent discovery work flows. In this review we will discuss the various analytical and computational techniques that enable MS-based metabolomic applications to natural product discovery and discuss the future prospects for comparative metabolomics in natural product discovery.

Isolation of a selected microbial consortium capable of degrading methyl parathion and p-nitrophenol from a contaminated soil site.

PubMed

Pino, Nancy J; Dominguez, Maria C; Penuela, Gustavo A

2011-01-01

A bacterial consortium with the ability to degrade methyl parathion and p-nitrophenol, using these compounds as the only carbon source, was obtained by selective enrichment in a medium with methyl parathion. Samples were taken from Moravia, Medellin; an area that is highly contaminated, owing to the fact that it was used as a garbage dump from 1974 to 1982. Acinetobacter sp, Pseudomonas putida, Bacillus sp, Pseudomonas aeruginosa Citrobacter freundii, Stenotrophomonas sp, Flavobacterium sp, Proteus vulgaris, Pseudomonas sp, Acinetobacter sp, Klebsiella sp and Proteus sp were the microorganisms identified within the consortium. In culture, the consortium was able to degrade 150 mg L⁻¹ of methyl-parathion and p-nitrophenol in 120 h, but after adding glucose or peptone to the culture, the time of degradation decreased to 24 h. In soil, the consortium was also able to degrade 150 mg L⁻¹ of methyl parathion in 120 h at different depths and also managed to decrease the toxicity.

Advanced nutrient removal from surface water by a consortium of attached microalgae and bacteria: A review.

PubMed

Liu, Junzhuo; Wu, Yonghong; Wu, Chenxi; Muylaert, Koenraad; Vyverman, Wim; Yu, Han-Qing; Muñoz, Raúl; Rittmann, Bruce

2017-10-01

Innovative and cost-effective technologies for advanced nutrient removal from surface water are urgently needed for improving water quality. Conventional biotechnologies, such as ecological floating beds, or constructed wetlands, are not effective in removing nutrients present at low-concentration. However, microalgae-bacteria consortium is promising for advanced nutrient removal from wastewater. Suspended algal-bacterial systems can easily wash out unless the hydraulic retention time is long, attached microalgae-bacteria consortium is more realistic. This critical review summarizes the fundamentals and status of attached microalgae-bacteria consortium for advanced nutrient removal from surface water. Key advantages are the various nutrient removal pathways, reduction of nutrients to very low concentration, and diversified photobioreactor configurations. Challenges include poor identification of functional species, poor control of the community composition, and long start-up times. Future research should focus on the selection and engineering of robust microbial species, mathematical modelling of the composition and functionality of the consortium, and novel photobioreactor configurations. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evaluation of microbial dynamics during post-consumption food waste composting.

PubMed

Awasthi, Sanjeev Kumar; Wong, Jonathan W C; Li, Jiao; Wang, Quan; Zhang, Zengqiang; Kumar, Sunil; Awasthi, Mukesh Kumar

2018-03-01

The objective of present study was to evaluate the efficacy of bacterial consortium to boost the microbial population and enzyme activities during post-consumption food waste (PCFWs) composting. Three treatments of PCFWs mixed with saw dust and 10% zeolite (dry weight basis) was design, where treatments T-2 and T-3 were applied with two distinctive bacterial consortium, respectively, while T-1 was served as control. The results showed that total aerobic proteolytic, amylolytic, cellulolytic, oil degrading and total aerobic bacteria populations were significantly higher in treatment T2 and T3 than T1. Consequently, the selected hydrolytic enzymes were also higher in T2 and T3 than T1, whose apparently gave the interesting information about rate of decomposition and end product stability. Furthermore, T2 and T3 showed significant correlations between the enzymatic activities and microbial population with other physico-chemical parameters. Based on germination assays and CO 2 -C evolution rate, T2 and T3 were considered phytotoxic free and highly stable final compost on day 56. Copyright © 2017 Elsevier Ltd. All rights reserved.

Understanding Kombucha Tea Fermentation: A Review.

PubMed

Villarreal-Soto, Silvia Alejandra; Beaufort, Sandra; Bouajila, Jalloul; Souchard, Jean-Pierre; Taillandier, Patricia

2018-03-01

Kombucha is a beverage of probable Manchurian origins obtained from fermented tea by a microbial consortium composed of several bacteria and yeasts. This mixed consortium forms a powerful symbiosis capable of inhibiting the growth of potentially contaminating bacteria. The fermentation process also leads to the formation of a polymeric cellulose pellicle due to the activity of certain strains of Acetobacter sp. The tea fermentation process by the microbial consortium was able to show an increase in certain biological activities which have been already studied; however, little information is available on the characterization of its active components and their evolution during fermentation. Studies have also reported that the use of infusions from other plants may be a promising alternative. Kombucha is a traditional fermented tea whose consumption has increased in the recent years due to its multiple functional properties such as anti-inflammatory potential and antioxidant activity. The microbiological composition of this beverage is quite complex and still more research is needed in order to fully understand its behavior. This study comprises the chemical and microbiological composition of the tea and the main factors that may affect its production. © 2018 Institute of Food Technologists®.

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

PubMed

Satlewal, Alok; Soni, Ravindra; Zaidi, Mgh; Shouche, Yogesh; Goel, Reeta

2008-03-01

A variety of bacterial strains were isolated from waste disposal sites of Uttaranchal, India, and some from artificially developed soil beds containing maleic anhydride, glucose, and small pieces of polyethylene. Primary screening of isolates was done based on their ability to utilize high- and low-density polyethylenes (HDPE/LDPE) as a primary carbon source. Thereafter, a consortium was developed using potential strains. Furthermore, a biodegradation assay was carried out in 500-ml flasks containing minimal broth (250 ml) and HDPE/ LDPE at 5 mg/ml concentration. After incubation for two weeks, degraded samples were recovered through filtration and subsequent evaporation. Fourier transform infrared spectroscopy (FTIR) and simultaneous thermogravimetric-differential thermogravimetry-differential thermal analysis TG-DTG-DTA) were used to analyze these samples. Results showed that consortium-treated HDPE (considered to be more inert relative to LDPE) was degraded to a greater extent 22.41% weight loss) in comparison with LDPE (21.70% weight loss), whereas, in the case of untreated samples, weight loss was more for LDPE than HDPE (4.5% and 2.5%, respectively) at 400 degrees . Therefore, this study suggests that polyethylene could be degraded by utilizing microbial consortia in an eco-friendly manner.

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

PubMed

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

2018-05-14

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

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

PubMed

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

2018-06-15

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

Substantially enhanced degradation of hexachlorocyclohexane isomers by a microbial consortium on acclimation.

PubMed

Elcey, C Daniel; Kunhi, A A Mohammad

2010-01-27

Widespread contamination of the environment, globally, has been caused by extensive and indiscriminate use of hexachlorocyclohexane (HCH) as an insecticide since the 1940s, threatening the biota including humans, and there is an urgent need to eliminate it, preferably through bioremediation technologies. A gamma-HCH-degrading microbial consortium was isolated by enrichment of a soil sample from a sugar cane field having a long history of technical grade HCH application. On acclimation the degrading ability improved substantially. The consortium, which took 10 days to degrade 25 microg mL(-1) of gamma-HCH, initially could mineralize even 300 microg mL(-1) of the substrate within 108 h on acclimation. With 300 microg mL(-1) substrate, the rate of degradation, as calculated for the early exponential phase, was 216 microg mL(-1) day(-1), the highest reported so far. An amount of 400 microg mL(-1) of gamma-HCH, however, was mineralized partially with only 78% Cl(-) release. No apparent accumulation of intermediary metabolites was observed up to 300 microg mL(-1) substrate, indicating a fast rate of mineralization. Aeration, mesophilic temperatures (20-35 degrees C), and near neutral pH (6.0-8.0) were favorable conditions for degradation. The presence of glucose at 1000 microg mL(-1) retarded the degradation, whereas cellulose and sawdust at 1600 microg mL(-1) and glucose at 100 microg mL(-1) did not show any marked effect. The consortium also mineralized alpha-, beta-, and delta-HCH efficiently. The consortium consisted of nine bacterial strains and a fungal strain, and individually they were able to degrade 10 microg mL(-1) of gamma-HCH. This mixed culture holds high potential for deployment in bioremediation of HCH-contaminated soils, waste dumpsites, and water bodies.

Single-genotype syntrophy by Rhodopseudomonas palustris is not a strategy to aid redox balance during anaerobic degradation of lignin monomers

DOE PAGES

Doud, Devin F. R.; Angenent, Largus T.

2016-07-14

Rhodopseudomonas palustris has emerged as a model microbe for the anaerobic metabolism of p-coumarate, which is an aromatic compound and a primary component of lignin. However, under an aerobic conditions, R.palustris must actively eliminate excess reducing equivalents through a number of known strategies (e.g., CO 2 fixation, H 2 evolution) to avoid lethal redox imbalance. Others had hypothesized that to ease the burden of this redox imbalance, a clonal population of R.palustris could functionally differentiate into a pseudo-consortium. Within this pseudo-consortium, one sub-population would perform the aromatic moiety degradation into acetate, while the other sub-population would oxidize acetate, resulting inmore » a single-genotype syntrophy through acetate sharing. Here, the objective was to test this hypothesis by utilizing microbial lelectrochemistry as a research tool with the extrac ellular-electron-transferring bacterium Geobacter sulfurreducens as a reporter strain replacing the hypothesized acetate-oxidizing sub-population. We used a 2×4 experimental design with pure cultures of R. palustris in serum bottles and co-cultures of R. palustris and G.sulfurreducens in bioelectrochemical systems.This experimental design included growth medium with and without bicarbonate to induce non-lethal and lethal redox imbalance conditions, respectively, in R. palustris. Finally, the design also included a mutant strain (NifA*) of R. palustris, which constitutively produces H 2, to serve both as a positive control for metabolite secretion (H 2) to G. sulfurreducens, and as a non-lethal redox control for without bicarbonate conditions. Our results demonstrate that acetate sharing between different sub-populations of R. palustris does not occur while degrading p-coumarate under either non-lethal or lethal redox imbalance conditions. Furthermore, this work highlights the strength of microbial electrochemistry as a tool for studying microbial syntrophy.« less

Acquisition of the yeast Kluyveromyces marxianus from unpasteurised milk by a kefir grain enhances kefir quality.

PubMed

Gethins, Loughlin; Rea, Mary C; Stanton, Catherine; Ross, R Paul; Kilcawley, Kieran; O'Sullivan, Maurice; Crotty, Suzanne; Morrissey, John P

2016-08-01

Kefir is a fermented milk beverage consumed for nutritional and health tonic benefits in many parts of the world. It is produced by the fermentation of milk with a consortium of bacteria and yeast embedded within a polysaccharide matrix. This consortium is not well defined and can vary substantially between kefir grains. There are little data on the microbial stability of kefir grains, nor on interactions between microbes in the grain and in the milk. To study this, a grain was split, with one half of each stored at -20°C and the other half passaged repeatedly in whole unpasteurised milk. Grains passaged in the unpasteurised milk recovered vigour and acquired the yeast Kluyveromyces marxainus from the milk which was confirmed to be the same strain by molecular typing. Furthermore, these passaged grains produced kefir that was distinguished chemically and organoleptically from the stored grains. Some changes in ultrastructure were also observed by scanning electron microscopy. The study showed that kefir grains can acquire yeast from their environment and the final product can be influenced by these newly acquired yeasts. Kluyveromyces marxianus is considered to be responsible for some of the most important characteristics of kefir so the finding that this yeast is part of the less stable microbiota is significant. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Hydrogen production by geobacter species and a mixed consortium in a microbial electrolysis cell.

PubMed

Call, Douglas F; Wagner, Rachel C; Logan, Bruce E

2009-12-01

A hydrogen utilizing exoelectrogenic bacterium (Geobacter sulfurreducens) was compared to both a nonhydrogen oxidizer (Geobacter metallireducens) and a mixed consortium in order to compare the hydrogen production rates and hydrogen recoveries of pure and mixed cultures in microbial electrolysis cells (MECs). At an applied voltage of 0.7 V, both G. sulfurreducens and the mixed culture generated similar current densities (ca. 160 A/m3), resulting in hydrogen production rates of ca. 1.9 m(3) H2/m3/day, whereas G. metallireducens exhibited lower current densities and production rates of 110 +/- 7 A/m3 and 1.3 +/- 0.1 m3 H2/m3/day, respectively. Before methane was detected in the mixed-culture MEC, the mixed consortium achieved the highest overall energy recovery (relative to both electricity and substrate energy inputs) of 82% +/- 8% compared to G. sulfurreducens (77% +/- 2%) and G. metallireducens (78% +/- 5%), due to the higher coulombic efficiency of the mixed consortium. At an applied voltage of 0.4 V, methane production increased in the mixed-culture MEC and, as a result, the hydrogen recovery decreased and the overall energy recovery dropped to 38% +/- 16% compared to 80% +/- 5% for G. sulfurreducens and 76% +/- 0% for G. metallireducens. Internal hydrogen recycling was confirmed since the mixed culture generated a stable current density of 31 +/- 0 A/m3 when fed hydrogen gas, whereas G. sulfurreducens exhibited a steady decrease in current production. Community analysis suggested that G. sulfurreducens was predominant in the mixed-culture MEC (72% of clones) despite its relative absence in the mixed-culture inoculum obtained from a microbial fuel cell reactor (2% of clones). These results demonstrate that Geobacter species are capable of obtaining similar hydrogen production rates and energy recoveries as mixed cultures in an MEC and that high coulombic efficiencies in mixed culture MECs can be attributed in part to the recycling of hydrogen into current.

Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen.

PubMed

Garg, Neha; Zeng, Yi; Edlund, Anna; Melnik, Alexey V; Sanchez, Laura M; Mohimani, Hosein; Gurevich, Alexey; Miao, Vivian; Schiffler, Stefan; Lim, Yan Wei; Luzzatto-Knaan, Tal; Cai, Shengxin; Rohwer, Forest; Pevzner, Pavel A; Cichewicz, Robert H; Alexandrov, Theodore; Dorrestein, Pieter C

2016-01-01

Microbes are commonly studied as individual species, but they exist as mixed assemblages in nature. At present, we know very little about the spatial organization of the molecules, including natural products that are produced within these microbial networks. Lichens represent a particularly specialized type of symbiotic microbial assemblage in which the component microorganisms exist together. These composite microbial assemblages are typically comprised of several types of microorganisms representing phylogenetically diverse life forms, including fungi, photosymbionts, bacteria, and other microbes. Here, we employed matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) imaging mass spectrometry to characterize the distributions of small molecules within a Peltigera lichen. In order to probe how small molecules are organized and localized within the microbial consortium, analytes were annotated and assigned to their respective producer microorganisms using mass spectrometry-based molecular networking and metagenome sequencing. The spatial analysis of the molecules not only reveals an ordered layering of molecules within the lichen but also supports the compartmentalization of unique functions attributed to various layers. These functions include chemical defense (e.g., antibiotics), light-harvesting functions associated with the cyanobacterial outer layer (e.g., chlorophyll), energy transfer (e.g., sugars) surrounding the sun-exposed cyanobacterial layer, and carbohydrates that may serve a structural or storage function and are observed with higher intensities in the non-sun-exposed areas (e.g., complex carbohydrates). IMPORTANCE Microbial communities have evolved over centuries to live symbiotically. The direct visualization of such communities at the chemical and functional level presents a challenge. Overcoming this challenge may allow one to visualize the spatial distributions of specific molecules involved in symbiosis and to define their functional roles in shaping the community structure. In this study, we examined the diversity of microbial genes and taxa and the presence of biosynthetic gene clusters by metagenomic sequencing and the compartmentalization of organic chemical components within a lichen using mass spectrometry. This approach allowed the identification of chemically distinct sections within this composite organism. Using our multipronged approach, various fungal natural products, not previously reported from lichens, were identified and two different fungal layers were visualized at the chemical level.

Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen

PubMed Central

Garg, Neha; Zeng, Yi; Edlund, Anna; Melnik, Alexey V.; Mohimani, Hosein; Gurevich, Alexey; Miao, Vivian; Schiffler, Stefan; Lim, Yan Wei; Luzzatto-Knaan, Tal; Cai, Shengxin; Rohwer, Forest; Pevzner, Pavel A.; Cichewicz, Robert H.; Alexandrov, Theodore

2016-01-01

ABSTRACT Microbes are commonly studied as individual species, but they exist as mixed assemblages in nature. At present, we know very little about the spatial organization of the molecules, including natural products that are produced within these microbial networks. Lichens represent a particularly specialized type of symbiotic microbial assemblage in which the component microorganisms exist together. These composite microbial assemblages are typically comprised of several types of microorganisms representing phylogenetically diverse life forms, including fungi, photosymbionts, bacteria, and other microbes. Here, we employed matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) imaging mass spectrometry to characterize the distributions of small molecules within a Peltigera lichen. In order to probe how small molecules are organized and localized within the microbial consortium, analytes were annotated and assigned to their respective producer microorganisms using mass spectrometry-based molecular networking and metagenome sequencing. The spatial analysis of the molecules not only reveals an ordered layering of molecules within the lichen but also supports the compartmentalization of unique functions attributed to various layers. These functions include chemical defense (e.g., antibiotics), light-harvesting functions associated with the cyanobacterial outer layer (e.g., chlorophyll), energy transfer (e.g., sugars) surrounding the sun-exposed cyanobacterial layer, and carbohydrates that may serve a structural or storage function and are observed with higher intensities in the non-sun-exposed areas (e.g., complex carbohydrates). IMPORTANCE Microbial communities have evolved over centuries to live symbiotically. The direct visualization of such communities at the chemical and functional level presents a challenge. Overcoming this challenge may allow one to visualize the spatial distributions of specific molecules involved in symbiosis and to define their functional roles in shaping the community structure. In this study, we examined the diversity of microbial genes and taxa and the presence of biosynthetic gene clusters by metagenomic sequencing and the compartmentalization of organic chemical components within a lichen using mass spectrometry. This approach allowed the identification of chemically distinct sections within this composite organism. Using our multipronged approach, various fungal natural products, not previously reported from lichens, were identified and two different fungal layers were visualized at the chemical level. PMID:28028548

Effects of substrate mineralogy on the biodegradability of fuel components

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

Apitz, S.E.; Meyers-Schulte, K.J.

1996-11-01

Experiments were carried out to determine the effects of mineralogy on the biodegradability of components of a whole fuel by a soil microbial consortium. Samples of quartz sand (Fischer Sea Sand) and illite clay (API 35) were spiked with marine diesel fuel, aged, slurried, and inoculated, and concentrations of fuel components were monitored over time. To help distinguish biotic from abiotic processes, identical samples were poisoned with mercuric chloride and were run in parallel. While there was a chromatographic and biomarker evidence of n-alkane biodegradation in the sand samples, illite samples showed no evidence of biogenic loss of aliphatic components.more » Polycyclic aromatic hydrocarbons, on the other hand, were lost equivalently on both minerals and in both cases were lost to a much greater extent than were total petroleum hydrocarbons (TPHs). These results suggest that under experimental conditions, illite inhibited the bioavailability of some TPH components to the soil microbial consortium.« less

Biodegradation of diesel/biodiesel blends by a consortium of hydrocarbon degraders: effect of the type of blend and the addition of biosurfactants.

PubMed

Owsianiak, Mikołaj; Chrzanowski, Łukasz; Szulc, Alicja; Staniewski, Jacek; Olszanowski, Andrzej; Olejnik-Schmidt, Agnieszka K; Heipieper, Hermann J

2009-02-01

Biodegradation experiments for diesel/biodiesel blends in liquid cultures by-petroleum degrading microbial consortium showed that for low amendments of biodiesel (10%) the overall biodegradation efficiency of the mixture after seven days was lower than for petroleum diesel fuel. Preferential usage of methyl esters in the broad biodiesel concentration range and diminished biodegradation of petroleum hydrocarbons for 10% biodiesel blend was confirmed. Rhamnolipids improved biodegradation efficiency only for blends with low content of biodiesel. Emulsion formation experiments showed that biodiesel amendments significantly affected dispersion of fuel mixtures in water. The presence of rhamnolipids biosurfactant affected stability of such emulsions and altered cell surface properties of tested consortium.

Bacterial community composition characterization of a lead-contaminated Microcoleus sp. consortium.

PubMed

Giloteaux, Ludovic; Solé, Antoni; Esteve, Isabel; Duran, Robert

2011-08-01

A Microcoleus sp. consortium, obtained from the Ebro delta microbial mat, was maintained under different conditions including uncontaminated, lead-contaminated, and acidic conditions. Terminal restriction fragment length polymorphism and 16S rRNA gene library analyses were performed in order to determine the effect of lead and culture conditions on the Microcoleus sp. consortium. The bacterial composition inside the consortium revealed low diversity and the presence of specific terminal-restriction fragments under lead conditions. 16S rRNA gene library analyses showed that members of the consortium were affiliated to the Alpha, Beta, and Gammaproteobacteria and Cyanobacteria. Sequences closely related to Achromobacter spp., Alcaligenes faecalis, and Thiobacillus species were exclusively found under lead conditions while sequences related to Geitlerinema sp., a cyanobacterium belonging to the Oscillatoriales, were not found in presence of lead. This result showed a strong lead selection of the bacterial members present in the Microcoleus sp. consortium. Several of the 16S rRNA sequences were affiliated to nitrogen-fixing microorganisms including members of the Rhizobiaceae and the Sphingomonadaceae. Additionally, confocal laser scanning microscopy and scanning and transmission electron microscopy showed that under lead-contaminated condition Microcoleus sp. cells were grouped and the number of electrodense intracytoplasmic inclusions was increased.

Biodegradability of fluoxetine, mefenamic acid, and metoprolol using different microbial consortiums.

PubMed

Velázquez, Yolanda Flores; Nacheva, Petia Mijaylova

2017-03-01

The biodegradation of fluoxetine, mefenamic acid, and metoprolol using ammonium-nitrite-oxidizing consortium, nitrite-oxidizing consortium, and heterotrophic biomass was evaluated in batch tests applying different retention times. The ammonium-nitrite-oxidizing consortium presented the highest biodegradation percentages for mefenamic acid and metoprolol, of 85 and 64% respectively. This consortium was also capable to biodegrade 79% of fluoxetine. The heterotrophic consortium showed the highest ability to biodegrade fluoxetine reaching 85%, and it also had a high potential for biodegrading mefenamic acid and metoprolol, of 66 and 58% respectively. The nitrite-oxidizing consortium presented the lowest biodegradation of the three pharmaceuticals, of less than 48%. The determination of the selected pharmaceuticals in the dissolved phase and in the biomass indicated that biodegradation was the major removal mechanism of the three compounds. Based on the obtained results, the biodegradation kinetics was adjusted to pseudo-first-order for the three pharmaceuticals. The values of k biol for fluoxetine, mefenamic acid, and metoprolol determined with the three consortiums indicated that ammonium-nitrite-oxidizing and heterotrophic biomass allow a partial biodegradation of the compounds, while no substantial biodegradation can be expected using nitrite-oxidizing consortium. Metoprolol was the less biodegradable compound. The sorption of fluoxetine and mefenamic acid onto biomass had a significant contribution for their removal (6-14%). The lowest sorption coefficients were obtained for metoprolol indicating that the sorption onto biomass is poor (3-4%), and the contribution of this process to the global removal can be neglected.

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

PubMed

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

2014-02-01

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

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

PubMed

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

2016-01-01

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

Mineral stimulation of subsurface microorganisms: release of limiting nutrients from silicates

USGS Publications Warehouse

Roger, Jennifer Roberts; Bennett, Philip C.

2004-01-01

Microorganisms play an important role in the weathering of silicate minerals in many subsurface environments, but an unanswered question is whether the mineral plays an important role in the microbial ecology. Silicate minerals often contain nutrients necessary for microbial growth, but whether the microbial community benefits from their release during weathering is unclear. In this study, we used field and laboratory approaches to investigate microbial interactions with minerals and glasses containing beneficial nutrients and metals. Field experiments from a petroleum-contaminated aquifer, where silicate weathering is substantially accelerated in the contaminated zone, revealed that phosphorus (P) and iron (Fe)-bearing silicate glasses were preferentially colonized and weathered, while glasses without these elements were typically barren of colonizing microorganisms, corroborating previous studies using feldspars. In laboratory studies, we investigated microbial weathering of silicates and the release of nutrients using a model ligand-promoted pathway. A metal-chelating organic ligand 3,4 dihydroxybenzoic acid (3,4 DHBA) was used as a source of chelated ferric iron, and a carbon source, to investigate mineral weathering rate and microbial metabolism.In the investigated aquifer, we hypothesize that microbes produce organic ligands to chelate metals, particularly Fe, for metabolic processes and also form stable complexes with Al and occasionally with Si. Further, the concentration of these ligands is apparently sufficient near an attached microorganism to destroy the silicate framework while releasing the nutrient of interest. In microcosms containing silicates and glasses with trace phosphate mineral inclusions, microbial biomass increased, indicating that the microbial community can use silicate-bound phosphate inclusions. The addition of a native microbial consortium to microcosms containing silicates or glasses with iron oxide inclusions correlated to accelerated weathering and release of Si into solution as well as the accelerated degradation of the model substrate 3,4 DHBA. We propose that silicate-bound P and Fe inclusions are bioavailable, and microorganisms may use organic ligands to dissolve the silicate matrix and access these otherwise limiting nutrients.

Modeling of competitive mutualistic relationships. Application to cellulose degradation by Streptomyces sp. strains.

PubMed

Thierie, Jacques; Penninckx, Michel J

2007-12-01

A "cascade" model depicts microbial degradation of a complex nutrient/substrate through a succession of intermediate compounds. Each stage is characterized by a particular species producing a typical degradation enzyme induced by its own degradation product. The final compound of the cascade consists of a single assimilable substrate used by all species. This results in a competition situation, whereas the contribution of all strains to the production of a complete set of efficient enzymes generates a mutualistic relationship. The model was shown to be appropriate to describe degradation of cellulose by a consortium of Streptomyces sp. strains. The simplicity and the model capacity for generalization are promising and could be used for various degradation processes both at laboratory and environmental scales.

EFFECT OF GROUND-WATER REMEDIATION ACTIVITIES ON INDIGENOUS MICROFLORA

EPA Science Inventory

The United States Environmental Protection Agency (EPA), working with the Interagency DNAPL Consortium, completed an independent evaluation of microbial responses to ground-water remediation technology demonstrations at Launch Pad 34 at Cape Canaveral Air Station in Brevard Count...

Column bioleaching of low-grade mining ore containing high level of smithsonite, talc, sphaerocobaltite and azurite.

PubMed

Ilyas, Sadia; Chi, Ruan; Bhatti, H N; Bhatti, I A; Ghauri, M A

2012-03-01

Present work describes the bioleaching potential of metals from low-grade mining ore containing smithsonite, sphaerocobaltite, azurite and talc as main gangue minerals with adapted consortium of Sulfobacillus thermosulfidooxidans strain-RDB and Thermoplasma acidophilum. Bioleaching potential improved markedly by added energy source, acid preleaching and adaptation of microbial consortium with mixed metal ions. During whole leaching period including acid preleaching stage of 960 h and bioleaching stage of 212 days about 76% Co, 70% Zn, 84% Cu, 72% Ni and 63% Fe leached out.

Viability of Azotobacter consortium in auxin production

NASA Astrophysics Data System (ADS)

Zulaika, Enny; Solikhah, Farihatus; Alami, Nur Hidayatul; Kuswytasari, Nengah Dwianita; Shovitri, Maya

2017-06-01

Azotobacter is a kind of rhizobacteria which is abundant in soil and having beneficial for plants due to its ability to produce auxin. Each isolated Azotobacter from Eco Urban Farming ITS were able to produce auxin individually. However, the isolated Azotobacter consortium was prefer to produce more auxin than the individual one. Synergism test were carried out in order to verify non-antagonism among Azotobacter isolates. Auxin production test was conducted by inoculating 100 ml of Azotobacter consortium starter in 400 ml nutrient broth by addition of 1.000 ppm of L-tryptophan while shaking 100 rpm in rotary shaker at room temperature for 8 weeks. Auxin concentration was measured spectrophotometrically according to the Salkowski method. The Azotobacter consortium showed living synergistically and able to produce 1,82 ppm auxin in 2 hours incubation time although the concentration was tend to decrease periodically.

Recovery of Elemental Tellurium Nanoparticles by the Reduction of Tellurium Oxyanions in a Methanogenic Microbial Consortium.

PubMed

Ramos-Ruiz, Adriana; Field, Jim A; Wilkening, Jean V; Sierra-Alvarez, Reyes

2016-02-02

This research focuses on the microbial recovery of elemental tellurium (Te(0)) from aqueous streams containing soluble tellurium oxyanions, tellurate (Te(VI)), and tellurite (Te(IV)). An anaerobic mixed microbial culture occurring in methanogenic granular sludge was able to biocatalyze the reduction of both Te oxyanions to produce Te(0) nanoparticles (NPs) in sulfur-free medium. Te(IV) reduction was seven times faster than that of Te(VI), such that Te(IV) did not accumulate to a great extent during Te(VI) reduction. Endogenous substrates in the granular sludge provided the electron equivalents required to reduce Te oxyanions; however, the reduction rates were modestly increased with an exogenous electron donor such as H2. The effect of four redox mediators (anthraquinone-2,6-disulfonate, hydroxocobalamin, riboflavin, and lawsone) was also tested. Riboflavin increased the rate of Te(IV) reduction eleven-fold and also enhanced the fraction Te recovered as extracellular Te(0) NPs from 21% to 64%. Lawsone increased the rate of Te(VI) reduction five-fold, and the fraction of Te recovered as extracellular material increased from 49% to 83%. The redox mediators and electron donors also impacted the morphologies and localization of Te(0) NPs, suggesting that NP production can be tailored for a particular application.

Recovery of Elemental Tellurium Nanoparticles by the Reduction of Tellurium Oxyanions in a Methanogenic Microbial Consortium

PubMed Central

Ramos-Ruiz, Adriana; Field, Jim A.; Wilkening, Jean V.; Sierra-Alvarez, Reyes

2016-01-01

This research focuses on the microbial recovery of elemental tellurium (Te0) from aqueous streams containing soluble tellurium oxyanions, tellurate (TeVI) and tellurite (TeIV). An anaerobic mixed microbial culture occurring in methanogenic granular sludge was able to biocatalyze the reduction of both Te oxyanions to produce Te0 nanoparticles (NPs) in sulfur-free medium. TeIV reduction was 7-fold faster than that of TeVI, such that TeIV did not accumulate to a great extent during TeVI reduction. Endogenous substrates in the granular sludge provided the electron equivalents required to reduce Te oxyanions; however, the reduction rates were modestly increased with an exogenous electron donor such as H2. The effect of four redox mediators (anthraquinone-2,6-disulfonate, hydroxocobalamin, riboflavin, and lawsone) was also tested. Riboflavin increased the rate of TeIV reduction by 11-fold and also enhanced the fraction Te recovered as extracellular Te0 NPs from 21% to 64%. Lawsone increased the rate of TeVI reduction by 5-fold and the fraction of Te recovered as extracellular material increased from 49% to 83%. The redox mediators and electron donors also impacted the morphologies and localization of Te0 NPs, suggesting that NP production can be tailored for a particular application. PMID:26735010

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

PubMed

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

2016-12-01

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

Degradation of paracetamol by pure bacterial cultures and their microbial consortium.

PubMed

Zhang, Lili; Hu, Jun; Zhu, Runye; Zhou, Qingwei; Chen, Jianmeng

2013-04-01

Three bacterial strains utilizing paracetamol as the sole carbon, nitrogen, and energy source were isolated from a paracetamol-degrading aerobic aggregate, and assigned to species of the genera Stenotrophomonas and Pseudomonas. The Stenotrophomonas species have not included any known paracetamol degraders until now. In batch cultures, the organisms f1, f2, and fg-2 could perform complete degradation of paracetamol at concentrations of 400, 2,500, and 2,000 mg/L or below, respectively. A combination of three microbial strains resulted in significantly improved degradation and mineralization of paracetamol. The co-culture was able to use paracetamol up to concentrations of 4,000 mg/L, and mineralized 87.1 % of the added paracetamol at the initial of 2,000 mg/L. Two key metabolites of the biodegradation pathway of paracetamol, 4-aminophenol, and hydroquinone were detected. Paracetamol was degraded predominantly via 4-aminophenol to hydroquinone with subsequent ring fission, suggesting new pathways for paracetamol-degrading bacteria. The degradation of paracetamol could thus be performed by the single isolates, but is stimulated by a synergistic interaction of the three-member consortium, suggesting a possible complementary interaction among the various isolates. The exact roles of each of the strains in the consortium need to be further elucidated.

Lignolytic-consortium omics analyses reveal novel genomes and pathways involved in lignin modification and valorization.

PubMed

Moraes, Eduardo C; Alvarez, Thabata M; Persinoti, Gabriela F; Tomazetto, Geizecler; Brenelli, Livia B; Paixão, Douglas A A; Ematsu, Gabriela C; Aricetti, Juliana A; Caldana, Camila; Dixon, Neil; Bugg, Timothy D H; Squina, Fabio M

2018-01-01

Lignin is a heterogeneous polymer representing a renewable source of aromatic and phenolic bio-derived products for the chemical industry. However, the inherent structural complexity and recalcitrance of lignin makes its conversion into valuable chemicals a challenge. Natural microbial communities produce biocatalysts derived from a large number of microorganisms, including those considered unculturable, which operate synergistically to perform a variety of bioconversion processes. Thus, metagenomic approaches are a powerful tool to reveal novel optimized metabolic pathways for lignin conversion and valorization. The lignin-degrading consortium (LigMet) was obtained from a sugarcane plantation soil sample. The LigMet taxonomical analyses (based on 16S rRNA) indicated prevalence of Proteobacteria , Actinobacteria and Firmicutes members, including the Alcaligenaceae and Micrococcaceae families, which were enriched in the LigMet compared to sugarcane soil. Analysis of global DNA sequencing revealed around 240,000 gene models, and 65 draft bacterial genomes were predicted. Along with depicting several peroxidases, dye-decolorizing peroxidases, laccases, carbohydrate esterases, and lignocellulosic auxiliary (redox) activities, the major pathways related to aromatic degradation were identified, including benzoate (or methylbenzoate) degradation to catechol (or methylcatechol), catechol ortho-cleavage, catechol meta-cleavage, and phthalate degradation. A novel Paenarthrobacter strain harboring eight gene clusters related to aromatic degradation was isolated from LigMet and was able to grow on lignin as major carbon source. Furthermore, a recombinant pathway for vanillin production was designed based on novel gene sequences coding for a feruloyl-CoA synthetase and an enoyl-CoA hydratase/aldolase retrieved from the metagenomic data set. The enrichment protocol described in the present study was successful for a microbial consortium establishment towards the lignin and aromatic metabolism, providing pathways and enzyme sets for synthetic biology engineering approaches. This work represents a pioneering study on lignin conversion and valorization strategies based on metagenomics, revealing several novel lignin conversion enzymes, aromatic-degrading bacterial genomes, and a novel bacterial strain of potential biotechnological interest. The validation of a biosynthetic route for vanillin synthesis confirmed the applicability of the targeted metagenome discovery approach for lignin valorization strategies.

The Impact of Saccharomyces cerevisiae on a Wine Yeast Consortium in Natural and Inoculated Fermentations

PubMed Central

Bagheri, Bahareh; Bauer, Florian F.; Setati, Mathabatha E.

2017-01-01

Natural, also referred to as spontaneous wine fermentations, are carried out by the native microbiota of the grape juice, without inoculation of selected, industrially produced yeast or bacterial strains. Such fermentations are commonly initiated by non-Saccharomyces yeast species that numerically dominate the must. Community composition and numerical dominance of species vary significantly between individual musts, but Saccharomyces cerevisiae will in most cases dominate the late stages of the fermentation and complete the process. Nevertheless, non-Saccharomyces species contribute significantly, positively or negatively, to the character and quality of the final product. The contribution is species and strain dependent and will depend on each species or strain’s absolute and relative contribution to total metabolically active biomass, and will therefore, be a function of its relative fitness within the microbial ecosystem. However, the population dynamics of multispecies fermentations are not well understood. Consequently, the oenological potential of the microbiome in any given grape must, can currently not be evaluated or predicted. To better characterize the rules that govern the complex wine microbial ecosystem, a model yeast consortium comprising eight species commonly encountered in South African grape musts and an ARISA based method to monitor their dynamics were developed and validated. The dynamics of these species were evaluated in synthetic must in the presence or absence of S. cerevisiae using direct viable counts and ARISA. The data show that S. cerevisiae specifically suppresses certain species while appearing to favor the persistence of other species. Growth dynamics in Chenin blanc grape must fermentation was monitored only through viable counts. The interactions observed in the synthetic must, were upheld in the natural must fermentations, suggesting the broad applicability of the observed ecosystem dynamics. Importantly, the presence of indigenous yeast populations did not appear to affect the broad interaction patterns between the consortium species. The data show that the wine ecosystem is characterized by both mutually supportive and inhibitory species. The current study presents a first step in the development of a model to predict the oenological potential of any given wine mycobiome. PMID:29085347

The Impact of Saccharomyces cerevisiae on a Wine Yeast Consortium in Natural and Inoculated Fermentations.

PubMed

Bagheri, Bahareh; Bauer, Florian F; Setati, Mathabatha E

2017-01-01

Natural, also referred to as spontaneous wine fermentations, are carried out by the native microbiota of the grape juice, without inoculation of selected, industrially produced yeast or bacterial strains. Such fermentations are commonly initiated by non- Saccharomyces yeast species that numerically dominate the must. Community composition and numerical dominance of species vary significantly between individual musts, but Saccharomyces cerevisiae will in most cases dominate the late stages of the fermentation and complete the process. Nevertheless, non- Saccharomyces species contribute significantly, positively or negatively, to the character and quality of the final product. The contribution is species and strain dependent and will depend on each species or strain's absolute and relative contribution to total metabolically active biomass, and will therefore, be a function of its relative fitness within the microbial ecosystem. However, the population dynamics of multispecies fermentations are not well understood. Consequently, the oenological potential of the microbiome in any given grape must, can currently not be evaluated or predicted. To better characterize the rules that govern the complex wine microbial ecosystem, a model yeast consortium comprising eight species commonly encountered in South African grape musts and an ARISA based method to monitor their dynamics were developed and validated. The dynamics of these species were evaluated in synthetic must in the presence or absence of S. cerevisiae using direct viable counts and ARISA. The data show that S. cerevisiae specifically suppresses certain species while appearing to favor the persistence of other species. Growth dynamics in Chenin blanc grape must fermentation was monitored only through viable counts. The interactions observed in the synthetic must, were upheld in the natural must fermentations, suggesting the broad applicability of the observed ecosystem dynamics. Importantly, the presence of indigenous yeast populations did not appear to affect the broad interaction patterns between the consortium species. The data show that the wine ecosystem is characterized by both mutually supportive and inhibitory species. The current study presents a first step in the development of a model to predict the oenological potential of any given wine mycobiome.

Metabolic retroconversion of trimethylamine N-oxide and the gut microbiota.

PubMed

Hoyles, Lesley; Jiménez-Pranteda, Maria L; Chilloux, Julien; Brial, Francois; Myridakis, Antonis; Aranias, Thomas; Magnan, Christophe; Gibson, Glenn R; Sanderson, Jeremy D; Nicholson, Jeremy K; Gauguier, Dominique; McCartney, Anne L; Dumas, Marc-Emmanuel

2018-04-20

The dietary methylamines choline, carnitine, and phosphatidylcholine are used by the gut microbiota to produce a range of metabolites, including trimethylamine (TMA). However, little is known about the use of trimethylamine N-oxide (TMAO) by this consortium of microbes. A feeding study using deuterated TMAO in C57BL6/J mice demonstrated microbial conversion of TMAO to TMA, with uptake of TMA into the bloodstream and its conversion to TMAO. Microbial activity necessary to convert TMAO to TMA was suppressed in antibiotic-treated mice, with deuterated TMAO being taken up directly into the bloodstream. In batch-culture fermentation systems inoculated with human faeces, growth of Enterobacteriaceae was stimulated in the presence of TMAO. Human-derived faecal and caecal bacteria (n = 66 isolates) were screened on solid and liquid media for their ability to use TMAO, with metabolites in spent media analysed by 1 H-NMR. As with the in vitro fermentation experiments, TMAO stimulated the growth of Enterobacteriaceae; these bacteria produced most TMA from TMAO. Caecal/small intestinal isolates of Escherichia coli produced more TMA from TMAO than their faecal counterparts. Lactic acid bacteria produced increased amounts of lactate when grown in the presence of TMAO but did not produce large amounts of TMA. Clostridia (sensu stricto), bifidobacteria, and coriobacteria were significantly correlated with TMA production in the mixed fermentation system but did not produce notable quantities of TMA from TMAO in pure culture. Reduction of TMAO by the gut microbiota (predominantly Enterobacteriaceae) to TMA followed by host uptake of TMA into the bloodstream from the intestine and its conversion back to TMAO by host hepatic enzymes is an example of metabolic retroconversion. TMAO influences microbial metabolism depending on isolation source and taxon of gut bacterium. Correlation of metabolomic and abundance data from mixed microbiota fermentation systems did not give a true picture of which members of the gut microbiota were responsible for converting TMAO to TMA; only by supplementing the study with pure culture work and additional metabolomics was it possible to increase our understanding of TMAO bioconversions by the human gut microbiota.

Phylogenetic characterization of a corrosive consortium isolated from a sour gas pipeline.

PubMed

Jan-Roblero, J; Romero, J M; Amaya, M; Le Borgne, S

2004-06-01

Biocorrosion is a common problem in oil and gas industry facilities. Characterization of the microbial populations responsible for biocorrosion and the interactions between different microorganisms with metallic surfaces is required in order to implement efficient monitoring and control strategies. Denaturing gradient gel electrophoresis (DGGE) analysis was used to separate PCR products and sequence analysis revealed the bacterial composition of a consortium obtained from a sour gas pipeline in the Gulf of Mexico. Only one species of sulfate-reducing bacteria (SRB) was detected in this consortium. The rest of the population consisted of enteric bacteria with different characteristics and metabolic capabilities potentially related to biocorrosion. Therefore, several types of bacteria may be involved in biocorrosion arising from natural biofilms that develop in industrial facilities. The low abundance of the detected SRB was evidenced by environmental scanning electron microscopy (ESEM). In addition, the localized corrosion of pipeline steel in the presence of the consortium was clearly observed by ESEM after removing the adhered bacteria.

Characterization of a microbial consortium capable of rapid and simultaneous dechlorination of 1,1,2,2-tetrachloroethane and chlorinated ethane and ethene intermediates

USGS Publications Warehouse

Jones, E.J.P.; Voytek, M.A.; Lorah, M.M.; Kirshtein, J.D.

2006-01-01

A study was carried out to develop a culture of microorganisms for bioaugmentation treatment of chlorinated-ethane contaminated groundwater at sites where dechlorination is incomplete or rates are too slow for effective remedation. Mixed cultures capable of dechlorinating chlorinated ethanes and ethenes were enriched from contaminated wetland sediment at Aberdeen Proving Ground (APG) Maryland. The West Branch Consortium (WBC-2) was capable of degrading 1,1,2,2-tetrachloroethane (TeCA), trichloroethylene (TCE), cis and trans 1,2-dichloroethylene (DCE), 1,1,2-trichloroethane (TCA), 1,2-dichloroethane, and vinyl chloride to nonchlorinated end products ethylene and ethane. WBC-2 dechlorinated TeCA, TCA, and cisDCE rapidly and simultaneously. Methanogens in the consortium were members of the class Methanomicrobia, which includes acetoclastic methanogens. The WBC-2 consortium provides opportunities for the in situ bioremediation of sites contaminated with mixtures of chlorinated ethylenes and ethanes.

Low temperature reduction of hexavalent chromium by a microbial enrichment consortium and a novel strain of Arthrobacter aurescens.

PubMed

Horton, Rene' N; Apel, William A; Thompson, Vicki S; Sheridan, Peter P

2006-01-25

Chromium is a transition metal most commonly found in the environment in its trivalent [Cr(III)] and hexavalent [Cr(VI)] forms. The EPA maximum total chromium contaminant level for drinking water is 0.1 mg/l (0.1 ppm). Many water sources, especially underground sources, are at low temperatures (less than or equal to 15 Centigrade) year round. It is important to evaluate the possibility of microbial remediation of Cr(VI) contamination using microorganisms adapted to these low temperatures (psychrophiles). Core samples obtained from a Cr(VI) contaminated aquifer at the Hanford facility in Washington were enriched in Vogel Bonner medium at 10 Centigrade with 0, 25, 50, 100, 200, 400 and 1000 mg/l Cr(VI). The extent of Cr(VI) reduction was evaluated using the diphenyl carbazide assay. Resistance to Cr(VI) up to and including 1000 mg/l Cr(VI) was observed in the consortium experiments. Reduction was slow or not observed at and above 100 mg/l Cr(VI) using the enrichment consortium. Average time to complete reduction of Cr(VI) in the 30 and 60 mg/l Cr(VI) cultures of the consortium was 8 and 17 days, respectively at 10 Centigrade. Lyophilized consortium cells did not demonstrate adsorption of Cr(VI) over a 24 hour period. Successful isolation of a Cr(VI) reducing organism (designated P4) from the consortium was confirmed by 16S rDNA amplification and sequencing. Average time to complete reduction of Cr(VI) at 10 Centigrade in the 25 and 50 mg/l Cr(VI) cultures of the isolate P4 was 3 and 5 days, respectively. The 16S rDNA sequence from isolate P4 identified this organism as a strain of Arthrobacter aurescens, a species that has not previously been shown to be capable of low temperature Cr(VI) reduction. A. aurescens, indigenous to the subsurface, has the potential to be a predominant metal reducer in enhanced, in situ subsurface bioremediation efforts involving Cr(VI) and possibly other heavy metals and radionuclides.

Low temperature reduction of hexavalent chromium by a microbial enrichment consortium and a novel strain of Arthrobacter aurescens

PubMed Central

Horton, Rene' N; Apel, William A; Thompson, Vicki S; Sheridan, Peter P

2006-01-01

Background Chromium is a transition metal most commonly found in the environment in its trivalent [Cr(III)] and hexavalent [Cr(VI)] forms. The EPA maximum total chromium contaminant level for drinking water is 0.1 mg/l (0.1 ppm). Many water sources, especially underground sources, are at low temperatures (less than or equal to 15 Centigrade) year round. It is important to evaluate the possibility of microbial remediation of Cr(VI) contamination using microorganisms adapted to these low temperatures (psychrophiles). Results Core samples obtained from a Cr(VI) contaminated aquifer at the Hanford facility in Washington were enriched in Vogel Bonner medium at 10 Centigrade with 0, 25, 50, 100, 200, 400 and 1000 mg/l Cr(VI). The extent of Cr(VI) reduction was evaluated using the diphenyl carbazide assay. Resistance to Cr(VI) up to and including 1000 mg/l Cr(VI) was observed in the consortium experiments. Reduction was slow or not observed at and above 100 mg/l Cr(VI) using the enrichment consortium. Average time to complete reduction of Cr(VI) in the 30 and 60 mg/l Cr(VI) cultures of the consortium was 8 and 17 days, respectively at 10 Centigrade. Lyophilized consortium cells did not demonstrate adsorption of Cr(VI) over a 24 hour period. Successful isolation of a Cr(VI) reducing organism (designated P4) from the consortium was confirmed by 16S rDNA amplification and sequencing. Average time to complete reduction of Cr(VI) at 10 Centigrade in the 25 and 50 mg/l Cr(VI) cultures of the isolate P4 was 3 and 5 days, respectively. The 16S rDNA sequence from isolate P4 identified this organism as a strain of Arthrobacter aurescens, a species that has not previously been shown to be capable of low temperature Cr(VI) reduction. Conclusion A. aurescens, indigenous to the subsurface, has the potential to be a predominant metal reducer in enhanced, in situ subsurface bioremediation efforts involving Cr(VI) and possibly other heavy metals and radionuclides. PMID:16436214

Microbial community in a precursory scenario of growing Tagetes patula in a lunar greenhouse

NASA Astrophysics Data System (ADS)

Kozyrovska, N. O.; Korniichuk, O. S.; Voznyuk, T. M.; Kovalchuk, M. V.; Lytvynenko, T. L.; Rogutskyy, I. S.; Mytrokhyn, O. V.; Estrella-Liopis, V. R.; Borodinova, T. I.; Mashkovska, S. P.; Foing, B. H.; Kordyum, V. A.

A confined prototype plant-microbial system is elaborated for demonstration of growing pioneer plants in a lunar greenhouse. A precursory scenario of growing Tagetes patula L. in a substrate anorthosite which is similar mineralogically and chemically to lunar silicate rocks includes the use of a microbial community. Microorganisms served for preventive substrate colonization to avoid infection by deleterious microorganisms as well as for bioleaching and delivering of nutritional elements from anorthosite to plants. A model consortium of a siliceous bacterium, biocontrol agents, and arbuscular mycorrhizal fungi provided an acceptable growth and blossoming of Tagetes patula L. under growth limiting factors in terrestrial conditions.

Microfluidics and microbial engineering.

PubMed

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

2016-02-07

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

The microbial ecology of wine grape berries.

PubMed

Barata, A; Malfeito-Ferreira, M; Loureiro, V

2012-02-15

Grapes have a complex microbial ecology including filamentous fungi, yeasts and bacteria with different physiological characteristics and effects upon wine production. Some species are only found in grapes, such as parasitic fungi and environmental bacteria, while others have the ability to survive and grow in wines, constituting the wine microbial consortium. This consortium covers yeast species, lactic acid bacteria and acetic acid bacteria. The proportion of these microorganisms depends on the grape ripening stage and on the availability of nutrients. Grape berries are susceptible to fungal parasites until véraison after which the microbiota of truly intact berries is similar to that of plant leaves, which is dominated by basidiomycetous yeasts (e.g. Cryptococcus spp., Rhodotorula spp. Sporobolomyces spp.) and the yeast-like fungus Aureobasidium pullulans. The cuticle of visually intact berries may bear microfissures and softens with ripening, increasing nutrient availability and explaining the possible dominance by the oxidative or weakly fermentative ascomycetous populations (e.g. Candida spp., Hanseniaspora spp., Metschnikowia spp., Pichia spp.) approaching harvest time. When grape skin is clearly damaged, the availability of high sugar concentrations on the berry surface favours the increase of ascomycetes with higher fermentative activity like Pichia spp. and Zygoascus hellenicus, including dangerous wine spoilage yeasts (e.g. Zygosaccharomyces spp., Torulaspora spp.), and of acetic acid bacteria (e.g. Gluconobacter spp., Acetobacter spp.). The sugar fermenting species Saccharomyces cerevisiae is rarely found on unblemished berries, being favoured by grape damage. Lactic acid bacteria are minor partners of grape microbiota and while being the typical agent of malolactic fermentation, Oenococcus oeni has been seldom isolated from grapes in the vineyard. Environmental ubiquitous bacteria of the genus Enterobacter spp., Enterococcus spp., Bacillus spp., Burkholderia spp., Serratia spp., Staphylococcus spp., among others, have been isolated from grapes but do not have the ability to grow in wines. Saprophytic moulds, like Botrytis cinerea, causing grey rot, or Aspergillus spp., possibly producing ochratoxin, are only active in the vineyard, although their metabolites may affect wine quality during grape processing. The impact of damaged grapes in yeast ecology has been underestimated mostly because of inaccurate grape sampling. Injured berries hidden in apparently sound bunches explain the recovery of a higher number of species when whole bunches are picked. Grape health status is the main factor affecting the microbial ecology of grapes, increasing both microbial numbers and species diversity. Therefore, the influence of abiotic (e.g. climate, rain, hail), biotic (e.g. insects, birds, phytopathogenic and saprophytic moulds) and viticultural (e.g. fungicides) factors is dependent on their primary damaging effect. Copyright © 2011 Elsevier B.V. All rights reserved.

Bacteria isolated from amoebae/bacteria consortium

DOEpatents

Tyndall, R.L.

1995-05-30

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

Bacteria isolated from amoebae/bacteria consortium

DOEpatents

Tyndall, Richard L.

1995-01-01

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

Hydrogen Production by Geobacter Species and a Mixed Consortium in a Microbial Electrolysis Cell▿

PubMed Central

Call, Douglas F.; Wagner, Rachel C.; Logan, Bruce E.

2009-01-01

A hydrogen utilizing exoelectrogenic bacterium (Geobacter sulfurreducens) was compared to both a nonhydrogen oxidizer (Geobacter metallireducens) and a mixed consortium in order to compare the hydrogen production rates and hydrogen recoveries of pure and mixed cultures in microbial electrolysis cells (MECs). At an applied voltage of 0.7 V, both G. sulfurreducens and the mixed culture generated similar current densities (ca. 160 A/m3), resulting in hydrogen production rates of ca. 1.9 m3 H2/m3/day, whereas G. metallireducens exhibited lower current densities and production rates of 110 ± 7 A/m3 and 1.3 ± 0.1 m3 H2/m3/day, respectively. Before methane was detected in the mixed-culture MEC, the mixed consortium achieved the highest overall energy recovery (relative to both electricity and substrate energy inputs) of 82% ± 8% compared to G. sulfurreducens (77% ± 2%) and G. metallireducens (78% ± 5%), due to the higher coulombic efficiency of the mixed consortium. At an applied voltage of 0.4 V, methane production increased in the mixed-culture MEC and, as a result, the hydrogen recovery decreased and the overall energy recovery dropped to 38% ± 16% compared to 80% ± 5% for G. sulfurreducens and 76% ± 0% for G. metallireducens. Internal hydrogen recycling was confirmed since the mixed culture generated a stable current density of 31 ± 0 A/m3 when fed hydrogen gas, whereas G. sulfurreducens exhibited a steady decrease in current production. Community analysis suggested that G. sulfurreducens was predominant in the mixed-culture MEC (72% of clones) despite its relative absence in the mixed-culture inoculum obtained from a microbial fuel cell reactor (2% of clones). These results demonstrate that Geobacter species are capable of obtaining similar hydrogen production rates and energy recoveries as mixed cultures in an MEC and that high coulombic efficiencies in mixed culture MECs can be attributed in part to the recycling of hydrogen into current. PMID:19820150

Synthetic Consortium of Escherichia coli for n-Butanol Production by Fermentation of the Glucose-Xylose Mixture.

PubMed

Saini, Mukesh; Lin, Li-Jen; Chiang, Chung-Jen; Chao, Yun-Peng

2017-11-22

The microbial production of n-butanol using glucose and xylose, the major components of plant biomass, can provide a sustainable and renewable fuel as crude oil replacement. However, Escherichia coli prefers glucose to xylose as programmed by carbohydrate catabolite repression (CCR). In this study, a synthetic consortium consisting of two strains was developed by transforming the CCR-insensitive strain into a glucose-selective strain and a xylose-selective strain. Furthermore, the dual culture was reshaped by distribution of the synthetic pathway of n-butanol into two strains. Consequently, the co-culture system enabled effective co-utilization of both sugars and production of 5.2 g/L n-butanol at 30 h. The result leads to the conversion yield and productivity accounting for 63% of the theoretical yield and 0.17 g L -1 h -1 , respectively. Overall, the technology platform as proposed is useful for production of other value-added chemicals, which require complicated pathways for their synthesis by microbial fermentation of a sugar mixture.

Inoculation with a psychrotrophic-thermophilic complex microbial agent accelerates onset and promotes maturity of dairy manure-rice straw composting under cold climate conditions.

PubMed

Gou, Changlong; Wang, Yuqiong; Zhang, Xiqing; Lou, Yujie; Gao, Yunhang

2017-11-01

The objective was to determine the effects of psychrotrophic-thermophilic complex microbial agent (PTCMA) comprised of a psychrotrophic bacterium consortium (PBC) and a thermophilic cellulolytic fungi consortium (TCFC), on composting in a cold climate. Mixtures of dairy manure and rice straw were inoculated with PTCMA, PBC, TCFC and sterile water (control) and composted at an initial ambient temperatures of -2 to 5°C. In compost piles inoculated with PBC or PTCMA, temperatures reached the thermophilic phase (>55°C) faster (8-11d) than piles inoculated with TCFC or control. Furthermore, compost inoculated with TCFC or PTCMA had greater decreases in total organic carbon and carbon-to-nitrogen ratios, as well as significant increases in total nitrogen, degradation of cellulose and lignin and germination index than PBC inoculation or Control compost. Consequently, inoculation with both (i.e. PTCMA) accelerated the onset and promoted maturity of composting under cold-climate conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

States and challenges for high-value biohythane production from waste biomass by dark fermentation technology.

PubMed

Liu, Zhidan; Zhang, Chong; Lu, Yuan; Wu, Xiao; Wang, Lang; Wang, Linjun; Han, Bing; Xing, Xin-Hui

2013-05-01

Hythane (H2+CH4) has attracted growing attention due to its versatile advantages as, for instance vehicle fuel. Biohythane consisting of biohydrogen and biomethane via two-stage fermentation is a potential high-value solution for the valorization of waste biomass resources and probably an alternative to the fossil based hythane. However, the significance and application potential of biohythane have not yet been fully recognized. This review focuses on the progress of biohydrogen and subsequent biomethane fermentation in terms of substrate, microbial consortium, reactor configuration, as well as the H2/CH4 ratio from the perspective of the feasibility of biohythane production in the past ten years. The current paper also covers how controls of the microbial consortium and bioprocess, system integration influence the biohythane productivity. Challenges and perspectives on biohythane technology will finally be addressed. This review provides a state-of-the-art technological insight into biohythane production by two-stage dark fermentation from biomass. Copyright © 2012 Elsevier Ltd. All rights reserved.

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

PubMed

Shanmugam, Bhuvanesh Kumar; Mahadevan, Surianarayanan

2015-11-01

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

Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia

PubMed Central

Ben Said, Sami; Or, Dani

2017-01-01

The metabolic diversity present in microbial communities enables cooperation toward accomplishing more complex tasks than possible by a single organism. Members of a consortium communicate by exchanging metabolites or signals that allow them to coordinate their activity through division of labor. In contrast with monocultures, evidence suggests that microbial consortia self-organize to form spatial patterns, such as observed in biofilms or in soil aggregates, that enable them to respond to gradient, to improve resource interception and to exchange metabolites more effectively. Current biotechnological applications of microorganisms remain rudimentary, often relying on genetically engineered monocultures (e.g., pharmaceuticals) or mixed-cultures of partially known composition (e.g., wastewater treatment), yet the vast potential of “microbial ecological power” observed in most natural environments, remains largely underused. In line with the Unified Microbiome Initiative (UMI) which aims to “discover and advance tools to understand and harness the capabilities of Earth's microbial ecosystems,” we propose in this concept paper to capitalize on ecological insights into the spatial and modular design of interlinked microbial consortia that would overcome limitations of natural systems and attempt to optimize the functionality of the members and the performance of the engineered consortium. The topology of the spatial connections linking the various members and the regulated fluxes of media between those modules, while representing a major engineering challenge, would allow the microbial species to interact. The modularity of such spatially linked microbial consortia (SLMC) could facilitate the design of scalable bioprocesses that can be incorporated as parts of a larger biochemical network. By reducing the need for a compatible growth environment for all species simultaneously, SLMC will dramatically expand the range of possible combinations of microorganisms and their potential applications. We briefly review existing tools to engineer such assemblies and optimize potential benefits resulting from the collective activity of their members. Prospective microbial consortia and proposed spatial configurations will be illustrated and preliminary calculations highlighting the advantages of SLMC over co-cultures will be presented, followed by a discussion of challenges and opportunities for moving forward with some designs. PMID:28670307

Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia.

PubMed

Ben Said, Sami; Or, Dani

2017-01-01

The metabolic diversity present in microbial communities enables cooperation toward accomplishing more complex tasks than possible by a single organism. Members of a consortium communicate by exchanging metabolites or signals that allow them to coordinate their activity through division of labor. In contrast with monocultures, evidence suggests that microbial consortia self-organize to form spatial patterns, such as observed in biofilms or in soil aggregates, that enable them to respond to gradient, to improve resource interception and to exchange metabolites more effectively. Current biotechnological applications of microorganisms remain rudimentary, often relying on genetically engineered monocultures (e.g., pharmaceuticals) or mixed-cultures of partially known composition (e.g., wastewater treatment), yet the vast potential of "microbial ecological power" observed in most natural environments, remains largely underused. In line with the Unified Microbiome Initiative (UMI) which aims to "discover and advance tools to understand and harness the capabilities of Earth's microbial ecosystems," we propose in this concept paper to capitalize on ecological insights into the spatial and modular design of interlinked microbial consortia that would overcome limitations of natural systems and attempt to optimize the functionality of the members and the performance of the engineered consortium. The topology of the spatial connections linking the various members and the regulated fluxes of media between those modules, while representing a major engineering challenge, would allow the microbial species to interact. The modularity of such spatially linked microbial consortia (SLMC) could facilitate the design of scalable bioprocesses that can be incorporated as parts of a larger biochemical network. By reducing the need for a compatible growth environment for all species simultaneously, SLMC will dramatically expand the range of possible combinations of microorganisms and their potential applications. We briefly review existing tools to engineer such assemblies and optimize potential benefits resulting from the collective activity of their members. Prospective microbial consortia and proposed spatial configurations will be illustrated and preliminary calculations highlighting the advantages of SLMC over co-cultures will be presented, followed by a discussion of challenges and opportunities for moving forward with some designs.

Diversity of the microbiota involved in wine and organic apple cider submerged vinegar production as revealed by DHPLC analysis and next-generation sequencing.

PubMed

Trček, Janja; Mahnič, Aleksander; Rupnik, Maja

2016-04-16

Unfiltered vinegar samples collected from three oxidation cycles of the submerged industrial production of each, red wine and organic apple cider vinegars, were sampled in a Slovene vinegar producing company. The samples were systematically collected from the beginning to the end of an oxidation cycle and used for culture-independent microbial analyses carried out by denaturing high pressure liquid chromatography (DHPLC) and Illumina MiSeq sequencing of 16S rRNA gene variable regions. Both approaches showed a very homogeneous bacterial structure during wine vinegar production but more heterogeneous during organic apple cider vinegar production. In all wine vinegar samples Komagataeibacter oboediens (formerly Gluconacetobacter oboediens) was a predominating species. In apple cider vinegar the acetic acid and lactic acid bacteria were two major groups of bacteria. The acetic acid bacterial consortium was composed of Acetobacter and Komagataeibacter with the Komagataeibacter genus outcompeting the Acetobacter in all apple cider vinegar samples at the end of oxidation cycle. Among the lactic acid bacterial consortium two dominating genera were identified, Lactobacillus and Oenococcus, with Oenococcus prevailing with increasing concentration of acetic acid in vinegars. Unexpectedly, a minor genus of the acetic acid bacterial consortium in organic apple cider vinegar was Gluconobacter, suggesting a possible development of the Gluconobacter population with a tolerance against ethanol and acetic acid. Among the accompanying bacteria of the wine vinegar, the genus Rhodococcus was detected, but it decreased substantially by the end of oxidation cycles. Copyright © 2016 Elsevier B.V. All rights reserved.

Microbial diversity in methane hydrate-bearing deep marine sediments core preserved in the original pressure.

NASA Astrophysics Data System (ADS)

Takahashi, Y.; Hata, T.; Nishida, H.

2017-12-01

In normal coring of deep marine sediments, the sampled cores are exposed to the pressure of the atmosphere, which results in dissociation of gas-hydrates and might change microbial diversity. In this study, we analyzed microbial composition in methane hydrate-bearing sediment core sampled and preserved by Hybrid-PCS (Pressure Coring System). We sliced core into three layers; (i) outside layer, which were most affected by drilling fluids, (ii) middle layer, and (iii) inner layer, which were expected to be most preserved as the original state. From each layer, we directly extracted DNA, and amplified V3-V4 region of 16S rRNA gene. We determined at least 5000 of nucleotide sequences of the partial 16S rDNA from each layer by Miseq (Illumina). In the all layers, facultative anaerobes, which can grow with or without oxygen because they can metabolize energy aerobically or anaerobically, were detected as majority. However, the genera which are often detected anaerobic environment is abundant in the inner layer compared to the outside layer, indicating that condition of drilling and preservation affect the microbial composition in the deep marine sediment core. This study was conducted as a part of the activity of the Research Consortium for Methane Hydrate Resources in Japan [MH21 consortium], and supported by JOGMEC (Japan Oil, Gas and Metals National Corporation). The sample was provided by AIST (National Institute of Advanced Industrial Science and Technology).

Microbial precipitation of dolomite in methanogenic groundwater

USGS Publications Warehouse

Roberts, Jennifer A.; Bennett, Philip C.; Gonzalez, Luis A.; Macpherson, G.L.; Milliken, Kitty L.

2004-01-01

We report low-temperature microbial precipitation of dolomite in dilute natural waters from both field and laboratory experiments. In a freshwater aquifer, microorganisms colonize basalt and nucleate nonstoichiometric dolomite on cell walls. In the laboratory, ordered dolomite formed at near-equilibrium conditions from groundwater with molar Mg:Ca ratios of <1; dolomite was absent in sterile experiments. Geochemical and microbiological data suggest that methanogens are the dominant metabolic guild in this system and are integral to dolomite precipitation. We hypothesize that the attached microbial consortium reacts with the basalt surface, releasing Mg and Ca into solution, which drives dolomite precipitation via nucleation on the cell wall. These findings provide insight into the long-standing dolomite problem and suggest a fundamental role for microbial processes in the formation of dolomite across a wide range of environmental conditions.

Microbial ecology of a crude oil contaminated aquifer

USGS Publications Warehouse

Bekins, B.A.; Cozzarelli, I.M.; Warren, E.; Godsy, E.M.

2002-01-01

Detailed microbial analyses of a glacial outwash aquifer contaminated by crude oil provide insights into the pattern of microbial succession from iron reducing to methanogenic in the anaerobic portion of the contaminant plume. We analysed sediments from this area for populations of aerobes, iron reducers, fermenters and methanogens, using the most probable number method. On the basis of the microbial data the anaerobic area can be divided into distinct physiological zones dominated by either iron-reducers or a consortium of fermenters and methanogens. Chemistry and permeability data show that methanogenic conditions develop first in areas of high hydrocarbon flux. Thus, we find methanogens both in high permeability horizons and also where separate-phase crude oil is present in either the saturated or unsaturated zone. Microbial numbers peak at the top of the separate-phase oil suggesting that growth is most rapid in locations with access to both hydrocarbons and nutrients infiltrating from the surface.

Microbial granulation for lactic acid production.

PubMed

Kim, Dong-Hoon; Lee, Mo-Kwon; Hwang, Yuhoon; Im, Wan-Taek; Yun, Yeo-Myeong; Park, Chul; Kim, Mi-Sun

2016-01-01

This work investigated the formation of microbial granules to boost the productivity of lactic acid (LA). The flocculated form of LA-producing microbial consortium, dominated by Lactobacillus sp. (91.5% of total sequence), was initially obtained in a continuous stirred-tank reactor (CSTR), which was fed with 2% glucose and operated at a hydraulic retention time (HRT) of 12 h and pH 5.0 ± 0.1 under a thermophilic condition (50°C). The mixed liquor in the CSTR was then transferred to an up-flow anaerobic sludge blanket reactor (UASB). The fermentation performance and granulation process were monitored with a gradual decrease of HRT from 8.0 to 0.17 h, corresponding to an increase in the substrate loading from 60 to 2,880 g glucose L(-1) d(-1) . As the operation continued, the accumulation of biomass in the UASB was clearly observed, which changed from flocculent to granular form with decrease in HRT. Up to the HRT decrease to 0.5 h, the LA concentration was maintained at 19-20 g L(-1) with over 90% of substrate removal efficiency. However, further decrease of HRT resulted in a decrease of LA concentration with increase in residual glucose. Nevertheless, the volumetric LA productivity continuously increased, reaching 67 g L-fermenter (-1) h(-1) at HRT 0.17 h. The size of LA-producing granules and hydrophobicity gradually increased with decrease in HRT, reaching 6.0 mm and 60%, respectively. These biogranules were also found to have high settling velocities and low porosities, ranging 2.69-4.73 cm s(-1) and 0.39-0.92, respectively. © 2015 Wiley Periodicals, Inc.

Zero-valent iron/biotic treatment system for perchlorate-contaminated water: lab-scale performance, modeling, and full-scale implications

EPA Science Inventory

The computer program AQUASIM was used to model biological treatment of perchlorate-contaminated water using zero-valent iron corrosion as the hydrogen gas source. The laboratory-scale column was seeded with an autohydrogenotrophic microbial consortium previously shown to degrade ...

Assessment of Variation in Microbial Community Amplicon Sequencing by the Microbiome Quality Control (MBQC) Project Consortium

EPA Science Inventory

Precision medicine has been made possible by the translation of ‘omics to the clinic, and human microbiome studies must likewise transition to applications in public health. This will require especially robust measurements and assimilation of data from multiple population-scale c...

Identification and characterization of an anaerobic ethanol-producing cellulolytic bacterial consortium from Great Basin hot springs with agricultural residues and energy crops.

PubMed

Zhao, Chao; Deng, Yunjin; Wang, Xingna; Li, Qiuzhe; Huang, Yifan; Liu, Bin

2014-09-01

In order to obtain the cellulolytic bacterial consortia, sediments from Great Basin hot springs (Nevada, USA) were sampled and enriched with cellulosic biomass as the sole carbon source. The bacterial composition of the resulting anaerobic ethanol-producing celluloytic bacterial consortium, named SV79, was analyzed. With methods of the full-length 16S rRNA librarybased analysis and denaturing gradient gel electrophoresis, 21 bacteria belonging to eight genera were detected from this consortium. Clones with closest relation to the genera Acetivibrio, Clostridium, Cellulosilyticum, Ruminococcus, and Sporomusa were predominant. The cellulase activities and ethanol productions of consortium SV79 using different agricultural residues (sugarcane bagasse and spent mushroom substrate) and energy crops (Spartina anglica, Miscanthus floridulus, and Pennisetum sinese Roxb) were studied. During cultivation, consortium SV79 produced the maximum filter paper activity (FPase, 9.41 U/ml), carboxymethylcellulase activity (CMCase, 6.35 U/ml), and xylanase activity (4.28 U/ml) with sugarcane bagasse, spent mushroom substrate, and S. anglica, respectively. The ethanol production using M. floridulus as substrate was up to 2.63 mM ethanol/g using gas chromatography analysis. It has high potential to be a new candidate for producing ethanol with cellulosic biomass under anoxic conditions in natural environments.

Process for whole cell saccharification of lignocelluloses to sugars using a dual bioreactor system

DOEpatents

Lu, Jue [Okemos, MI; Okeke, Benedict [Montgomery, AL

2012-03-27

The present invention describes a process for saccharification of lignocelluloses to sugars using whole microbial cells, which are enriched from cultures inoculated with paper mill waste water, wood processing waste and soil. A three-member bacterial consortium is selected as a potent microbial inocula and immobilized on inedible plant fibers for biomass saccharification. The present invention further relates the design of a dual bioreactor system, with various biocarriers for enzyme immobilization and repeated use. Sugars are continuously removed eliminating end-product inhibition and consumption by cell.

Development of biologically modified anodes for energy harvesting using microbial fuel cells

NASA Astrophysics Data System (ADS)

Sumner, James J.; Ganguli, Rahul; Chmelka, Brad

2012-06-01

Biological fuel cells hold promise as an alternative energy source to batteries for unattended ground sensor applications due to the fact that they can be extremely long lived. This lifetime can be extended over batteries by scavenging fuel from the deployed environment. Microbial fuel cells (MFC) are one class of such sources that produce usable energy from small organic compounds (i.e. sugars, alcohols, organic acids, and biopolymers) which can be easily containerized or scavenged from the environment. The use of microorganisms as the anodic catalysts is what makes these systems unique from other biofuel cell designs. One of the main drawbacks of engineering a sensor system powered by an MFC is that power densities and current flux are extremely low in currently reported systems. The power density is limited by the mass transfer of the fuel source to the catalyst, the metabolism of the microbial catalysts and the electron transfer from the organism to the anode. This presentation will focus on the development of a new style of microbially-modified anodes which will increase power density to a level where a practical power source can be engineered. This is being achieved by developing a three dimensional matrix as an artificial, conductive biofilm. These artificial biofilms will allow the capture of a consortium of microbes designed for efficient metabolism of the available fuel source. Also it will keep the microbes close to the electrode allowing ready access by fuel and providing a low resistance passage of the liberated electrons from fuel oxidation.

Phototrophic biofilm assembly in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions

PubMed Central

Cole, Jessica K.; Hutchison, Janine R.; Renslow, Ryan S.; Kim, Young-Mo; Chrisler, William B.; Engelmann, Heather E.; Dohnalkova, Alice C.; Hu, Dehong; Metz, Thomas O.; Fredrickson, Jim K.; Lindemann, Stephen R.

2014-01-01

Microbial autotroph-heterotroph interactions influence biogeochemical cycles on a global scale, but the diversity and complexity of natural systems and their intractability to in situ manipulation make it challenging to elucidate the principles governing these interactions. The study of assembling phototrophic biofilm communities provides a robust means to identify such interactions and evaluate their contributions to the recruitment and maintenance of phylogenetic and functional diversity over time. To examine primary succession in phototrophic communities, we isolated two unicyanobacterial consortia from the microbial mat in Hot Lake, Washington, characterizing the membership and metabolic function of each consortium. We then analyzed the spatial structures and quantified the community compositions of their assembling biofilms. The consortia retained the same suite of heterotrophic species, identified as abundant members of the mat and assigned to Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes. Autotroph growth rates dominated early in assembly, yielding to increasing heterotroph growth rates late in succession. The two consortia exhibited similar assembly patterns, with increasing relative abundances of members from Bacteroidetes and Alphaproteobacteria concurrent with decreasing relative abundances of those from Gammaproteobacteria. Despite these similarities at higher taxonomic levels, the relative abundances of individual heterotrophic species were substantially different in the developing consortial biofilms. This suggests that, although similar niches are created by the cyanobacterial metabolisms, the resulting webs of autotroph-heterotroph and heterotroph-heterotroph interactions are specific to each primary producer. The relative simplicity and tractability of the Hot Lake unicyanobacterial consortia make them useful model systems for deciphering interspecies interactions and assembly principles relevant to natural microbial communities. PMID:24778628

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

PubMed Central

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

2015-01-01

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

Apple Replant Disease: Role of microbial ecology in cause and control

USDA-ARS?s Scientific Manuscript database

1. Apple replant disease (ARD) has been reported from all major fruit-growing regions of the world, and is often caused by a consortium of biological agents. Development of non-fumigant alternatives for the control of this disease has been hindered by the absence of consensus concerning the etiology...

Within gut physiochemical variation does not correspond to distinct resident fungal and bacterial communities in the tree-killing xylophage, Anolophora glabripennis

USDA-ARS?s Scientific Manuscript database

Insect guts harbor diverse microbial assemblages that can be influenced by multiple factors, including gut physiology and interactions by the host with its environment. The Asian longhorned beetle (ALB; Anoplophora glabripennis) is an invasive tree–killing insect, which harbors a diverse consortium ...

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

PubMed

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

2014-01-01

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

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

PubMed

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

2011-01-01

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

Respirometric response and microbial succession of nitrifying sludge to m-cresol pulses in a sequencing batch reactor.

PubMed

Ordaz, Alberto; Sánchez, Mariana; Rivera, Rodrigo; Rojas, Rafael; Zepeda, Alejandro

2017-02-01

A nitrifying consortium was kinetically, stoichiometrically and molecularly characterized via the in situ pulse respirometric method and pyrosequencing analysis before and after the addition of m-cresol (25 mg C L -1 ) in a sequencing batch reactor (SBR). Five important kinetic and stoichiometric parameters were determined: the maximum oxygen uptake rate, the maximum nitrification rate, the oxidation yield, the biomass growth yield, and the substrate affinity constant. An inhibitory effect was observed in the nitrification process with a recovery of this by up to eight SBR cycles after m-cresol was added to the system. However, full recovery of the nitrification process was not observed, as the maximum oxygen uptake rate was 25% lower than that of the previous operation without m-cresol addition. Furthermore, the pyrosequencing analyses of the nitrifying consortium after the addition of only two pulses of 25 mg C L -1 m-cresol showed an important microbial community change represented by a decrease in the nitrifying populations and an increase in the populations degrading phenolic compounds.

Meeting report: GSC M5 roundtable at the 13th International Society for Microbial Ecology meeting in Seattle, WA, USA August 22-27, 2010

PubMed Central

Gilbert, Jack A.; Meyer, Folker; Knight, Rob; Field, Dawn; Kyrpides, Nikos; Yilmaz, Pelin; Wooley, John

2010-01-01

This report summarizes the proceedings of the Metagenomics, Metadata, Metaanalysis, Models and Metainfrastructure (M5) Roundtable at the 13th International Society for Microbial Ecology Meeting in Seattle, WA, USA August 22-27, 2010. The Genomic Standards Consortium (GSC) hosted this meeting as a community engagement exercise to describe the GSC to the microbial ecology community during this important international meeting. The roundtable included five talks given by members of the GSC, and was followed by audience participation in the form of a roundtable discussion. This report summarizes this event. Further information on the GSC and its range of activities can be found at http://www.gensc.org. PMID:21304725

Construction and screening of marine metagenomic libraries.

PubMed

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

2010-01-01

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

The role of bacterial consortium and organic amendment in Cu and Fe isotope fractionation in plants on a polluted mine site.

PubMed

Pérez Rodríguez, Nathalie; Langella, Francesca; Rodushkin, Ilia; Engström, Emma; Kothe, Erika; Alakangas, Lena; Öhlander, Björn

2014-01-01

Copper and iron isotope fractionation by plant uptake and translocation is a matter of current research. As a way to apply the use of Cu and Fe stable isotopes in the phytoremediation of contaminated sites, the effects of organic amendment and microbial addition in a mine-spoiled soil seeded with Helianthus annuus in pot experiments and field trials were studied. Results show that the addition of a microbial consortium of ten bacterial strains has an influence on Cu and Fe isotope fractionation by the uptake and translocation in pot experiments, with an increase in average of 0.99 ‰ for the δ(65)Cu values from soil to roots. In the field trial, the amendment with the addition of bacteria and mycorrhiza as single and double inoculation enriches the leaves in (65)Cu compared to the soil. As a result of the same trial, the δ(56)Fe values in the leaves are lower than those from the bulk soil, although some differences are seen according to the amendment used. Siderophores, possibly released by the bacterial consortium, can be responsible for this change in the Cu and Fe fractionation. The overall isotopic fractionation trend for Cu and Fe does not vary for pot and field experiments with or without bacteria. However, variations in specific metabolic pathways related to metal-organic complexation and weathering can modify particular isotopic signatures.

Stability of the rhizosphere and endophytic bacterial communities associated with Arabidopsis thaliana (L.) Heynh under impact of cosmic factors

NASA Astrophysics Data System (ADS)

Kordium, V. A.; Adamchuk-Chala, N. I.; Moshinec, H. V.

The orbital experiment will involve a growing of Arabidopsis plant seed to seed in the presence of a plant probiotic bacteria consortium introduced into the system The purpose of experiment is to characterize microbial community associated with Arabidopsis thaliana and determine how consortium of introduced bacteria along with the endemic plant-associated bacteria influences the plant development reproductive system and seed formation in spaceflight conditions The first study will be an examination of the survival of model bacteria in on the inoculated plant The second complex study is to examine the plant traits in particular the ultrastructure of root statocytes in order to determine whether the plant development proceeds normally under microgravity conditions on background of introduced bacteria and to assess the structural changes occurring in the cotyledons generative organs and seeds The third set of observations will concern studies of the structure of microbial community associated with Arabidopsis plants with traditional and molecular tools The fourth part of the work will be an examination of mobile genetic elements that can play a role in adaptation of bacteria to the spaceflight conditions however they may affect the stability of bacterial endo- and rhizosphere communities The final part of the proposal initiates the study of possible risk of the bacterial consortium use for a plant inoculation in spaceflight conditions An evaluation of this risk will be performed via examination of expression of the Klebsiella

Establishment of a Polychlorinated Biphenyl-Dechlorinating Microbial Consortium, Specific for Doubly Flanked Chlorines, in a Defined, Sediment-Free Medium

PubMed Central

Wu, Qingzhong; Sowers, Kevin R.; May, Harold D.

2000-01-01

Estuarine sediment from Charleston Harbor, South Carolina, was used as inoculum for the development of an anaerobic enrichment culture that specifically dechlorinates doubly flanked chlorines (i.e., chlorines bound to carbon that are flanked on both sides by other chlorine-carbon bonds) of polychlorinated biphenyls (PCBs). Dechlorination was restricted to the para chlorine in cultures enriched with 10 mM fumarate, 50 ppm (173 μM) 2,3,4,5-tetrachlorobiphenyl, and no sediment. Initially the rate of dechlorination decreased upon the removal of sediment from the medium. However, the dechlorinating activity was sustainable, and following sequential transfer in a defined, sediment-free estuarine medium, the activity increased to levels near that observed with sediment. The culture was nonmethanogenic, and molybdate, ampicillin, chloramphenicol, neomycin, and streptomycin inhibited dechlorination activity; bromoethanesulfonate and vancomycin did not. Addition of 17 PCB congeners indicated that the culture specifically removes double flanked chlorines, preferably in the para position, and does not attack ortho chlorines. This is the first microbial consortium shown to para or meta dechlorinate a PCB congener in a defined sediment-free medium. It is the second PCB-dechlorinating enrichment culture to be sustained in the absence of sediment, but its dechlorinating capabilities are entirely different from those of the other sediment-free PCB-dechlorinating culture, an ortho-dechlorinating consortium, and do not match any previously published Aroclor-dechlorinating patterns. PMID:10618202

Enriching Doctoral-Level Preparation Programs through a Nationwide Consortium Model: The National Leadership Consortium in Sensory Disabilities

ERIC Educational Resources Information Center

Kruemmling, Brooke; Hayes, Heather; Smith, Derrick W.

2017-01-01

The National Leadership Consortium in Sensory Disabilities (NLCSD) trained doctoral scholars at universities across the United States to increase the number and quality of professionals specializing in educating children with sensory disabilities. NLCSD produced 40 new doctorates and created a community of learners comprised of scholars, faculty,…

Biodegradation of 2,4,6-trichlorophenol in a packed-bed biofilm reactor equipped with an internal net draft tube riser for aeration and liquid circulation.

PubMed

Jesús, A Gómez-De; Romano-Baez, F J; Leyva-Amezcua, L; Juárez-Ramírez, C; Ruiz-Ordaz, N; Galíndez-Mayer, J

2009-01-30

For the aerobic biodegradation of the fungicide and defoliant 2,4,6-trichlorophenol (2,4,6-TCP), a bench-scale packed-bed bioreactor equipped with a net draft tube riser for liquid circulation and oxygenation (PB-ALR) was constructed. To obtain a high packed-bed volume relative to the whole bioreactor volume, a high A(D)/A(R) ratio was used. Reactor's downcomer was packed with a porous support of volcanic stone fragments. PB-ALR hydrodynamics and oxygen mass transfer behavior was evaluated and compared to the observed behavior of the unpacked reactor operating as an internal airlift reactor (ALR). Overall gas holdup values epsilon(G), and zonal oxygen mass transfer coefficients determined at various airflow rates in the PB-ALR, were higher than those obtained with the ALR. When comparing mixing time values obtained in both cases, a slight increment in mixing time was observed when reactor was operated as a PB-ALR. By using a mixed microbial community, the biofilm reactor was used to evaluate the aerobic biodegradation of 2,4,6-TCP. Three bacterial strains identified as Burkholderia sp., Burkholderia kururiensis and Stenotrophomonas sp. constituted the microbial consortium able to cometabolically degrade the 2,4,6-TCP, using phenol as primary substrate. This consortium removed 100% of phenol and near 99% of 2,4,6-TCP. Mineralization and dehalogenation of 2,4,6-TCP was evidenced by high COD removal efficiencies ( approximately 95%), and by the stoichiometric release of chloride ions from the halogenated compound ( approximately 80%). Finally, it was observed that the microbial consortium was also capable to metabolize 2,4,6-TCP without phenol as primary substrate, with high removal efficiencies (near 100% for 2,4,6-TCP, 92% for COD and 88% for chloride ions).

Electricity production and microbial biofilm characterization in cellulose-fed microbial fuel cells.

PubMed

Ren, Z; Steinberg, L M; Regan, J M

2008-01-01

Converting biodegradable materials into electricity, microbial fuel cells (MFCs) present a promising technology for renewable energy production in specific applications. Unlike typical soluble substrates that have been used as electron donors in MFC studies, cellulose is unique because it requires a microbial consortium that can metabolize both an insoluble electron donor (cellulose) and electron acceptor (electrode). In this study, electricity generation and the microbial ecology of cellulose-fed MFCs were analyzed using a defined co-culture of Clostridium cellulolyticum and Geobacter sulfurreducens. Fluorescent in situ hybridization and quantitative PCR showed that when particulate MN301 cellulose was used as sole substrate, most Clostridium cells were found adhered to cellulose particles in suspension, while most Geobacter cells were attached to the electrode. By comparison, both bacteria resided in suspension and biofilm samples when soluble carboxymethyl cellulose was used. This distinct function-related distribution of the bacteria suggests an opportunity to optimize reactor operation by settling cellulose and decanting supernatant to extend cellulose hydrolysis and improve cellulose-electricity conversion. (c) IWA Publishing 2008.

Relating Anaerobic Digestion Microbial Community and Process Function.

PubMed

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.

Aerobic granular sludge inoculated microbial fuel cells for enhanced epoxy reactive diluent wastewater treatment.

PubMed

Cheng, Kai; Hu, Jingping; Hou, Huijie; Liu, Bingchuan; Chen, Qin; Pan, Keliang; Pu, Wenhong; Yang, Jiakuan; Wu, Xu; Yang, Changzhu

2017-04-01

Microbial consortiums aggregated on the anode surface of microbial fuel cells (MFCs) are critical factors for electricity generation as well as biodegradation efficiencies of organic compounds. Here in this study, aerobic granular sludge (AGS) was assembled on the surface of the MFC anode to form an AGS-MFC system with superior performance on epoxy reactive diluent (ERD) wastewater treatment. AGS-MFCs successfully shortened the startup time from 13d to 7d compared to the ones inoculated with domestic wastewater. Enhanced toxicity tolerance as well as higher COD removal (77.8% vs. 63.6%) were achieved. The higher ERD wastewater treatment efficiency of AGS-MFC is possibly attributed to the diverse microbial population on MFC biofilm, as well as the synergic degradation of contaminants by both the MFC anode biofilm and AGS granules. Copyright © 2017 Elsevier Ltd. All rights reserved.

Long-term operation of microbial electrosynthesis cell reducing CO2 to multi-carbon chemicals with a mixed culture avoiding methanogenesis.

PubMed

Bajracharya, Suman; Yuliasni, Rustiana; Vanbroekhoven, Karolien; Buisman, Cees J N; Strik, David P B T B; Pant, Deepak

2017-02-01

In microbial electrosynthesis (MES), CO 2 can be reduced preferably to multi-carbon chemicals by a biocathode-based process which uses electrochemically active bacteria as catalysts. A mixed anaerobic consortium from biological origin typically produces methane from CO 2 reduction which circumvents production of multi-carbon compounds. This study aimed to develop a stable and robust CO 2 reducing biocathode from a mixed culture inoculum avoiding the methane generation. An effective approach was demonstrated based on (i) an enrichment procedure involving inoculum pre-treatment and several culture transfers in H 2 :CO 2 media, (ii) a transfer from heterotrophic to autotrophic growth and (iii) a sequential batch operation. Biomass growth and gradual acclimation to CO 2 electro-reduction accomplished a maximum acetate production rate of 400mgL catholyte -1 d -1 at -1V (vs. Ag/AgCl). Methane was never detected in more than 300days of operation. Accumulation of acetate up to 7-10gL -1 was repeatedly attained by supplying (80:20) CO 2 :N 2 mixture at -0.9 to -1V (vs. Ag/AgCl). In addition, ethanol and butyrate were also produced from CO 2 reduction. Thus, a robust CO 2 reducing biocathode can be developed from a mixed culture avoiding methane generation by adopting the specific culture enrichment and operation procedures without the direct addition of chemical inhibitor. Copyright © 2016 Elsevier B.V. All rights reserved.

New insights into the ecological interaction between grape berry microorganisms and Drosophila flies during the development of sour rot.

PubMed

Barata, André; Santos, Sara Correia; Malfeito-Ferreira, Manuel; Loureiro, Virgílio

2012-08-01

In this work, we studied the ecological interactions between grape berry microorganisms and Drosophila sp. flies involved in sour rot disease during grape ripening. After veráison the total microbial counts of grape berries affected by sour rot increased from about 2 log CFU/g of berries to more than 7 log CFU/g. Berry damage provoked a clear shift in yeast diversity from basidiomycetes to ascomycetous fermentative species. The latter were mostly Pichia terricola, Hanseniaspora uvarum, Candida zemplinina, and Zygoascus hellenicus. However, these species were not able to produce the metabolites characteristic of sour rot (gluconic and acetic acids) in inoculated berries. On the contrary, the acetic acid bacteria Gluconacetobacter saccharivorans produced high levels of these acids, mainly when berries were incubated in the presence of the insect Drosophila sp. Sour rot was not observed when grape bunches were physically separated from insects, even when berries were artificially injured. The wounds made in berry skin healed in the absence of insects, thus preventing the development of sour rot. Therefore, in the vineyard, the induction of sour rot depends on the contamination of wounded berries by a microbial consortium--yeasts and acetic acid bacteria--transported by drosophilid insects which disseminate sour rot among damaged berries. In the absence of these insects, plant defense mechanisms are effective and lead to skin healing, preventing disease spread. Thus, we showed that Drosophila sp. act as a vector for microorganisms associated with grape sour rot disease.

Rapid Generation and Testing of a Lassa Fever Vaccine Using VaxCelerate Platform

DTIC Science & Technology

2014-08-28

essentially the same way each time but is capable to producing effective vaccine responses to a range of pathogens, and to do this without the use of...this distributed vaccine development consortium to rapidly produce and test a novel vaccine of relevance to public health responses. In parallel...with this effort, the consortium produced and tested a modified version of its self-assembling vaccine protein that used a subunit of the full

Laboratory and field scale bioremediation of hexachlorocyclohexane (HCH) contaminated soils by means of bioaugmentation and biostimulation.

PubMed

Garg, Nidhi; Lata, Pushp; Jit, Simran; Sangwan, Naseer; Singh, Amit Kumar; Dwivedi, Vatsala; Niharika, Neha; Kaur, Jasvinder; Saxena, Anjali; Dua, Ankita; Nayyar, Namita; Kohli, Puneet; Geueke, Birgit; Kunz, Petra; Rentsch, Daniel; Holliger, Christof; Kohler, Hans-Peter E; Lal, Rup

2016-06-01

Hexachlorocyclohexane (HCH) contaminated soils were treated for a period of up to 64 days in situ (HCH dumpsite, Lucknow) and ex situ (University of Delhi) in line with three bioremediation approaches. The first approach, biostimulation, involved addition of ammonium phosphate and molasses, while the second approach, bioaugmentation, involved addition of a microbial consortium consisting of a group of HCH-degrading sphingomonads that were isolated from HCH contaminated sites. The third approach involved a combination of biostimulation and bioaugmentation. The efficiency of the consortium was investigated in laboratory scale experiments, in a pot scale study, and in a full-scale field trial. It turned out that the approach of combining biostimulation and bioaugmentation was most effective in achieving reduction in the levels of α- and β-HCH and that the application of a bacterial consortium as compared to the action of a single HCH-degrading bacterial strain was more successful. Although further degradation of β- and δ-tetrachlorocyclohexane-1,4-diol, the terminal metabolites of β- and δ-HCH, respectively, did not occur by the strains comprising the consortium, these metabolites turned out to be less toxic than the parental HCH isomers.

Key Factors Controlling the Applicability and Efficiency of Bioremediation of Chlorinated Ethenes In Situ

NASA Astrophysics Data System (ADS)

Zhang, M.; Yoshikawa, M.; Takeuchi, M.; Komai, T.

2012-12-01

Bioremediation has been considered as one of environmentally friendly and cost effective approaches for cleaning up the sites polluted by organic contaminants, such as chlorinated ethenes. Although bioremediation, in its widest sense, is not new, and many researches have been performed on bioremediation of different kinds of pollutants, an effective design and implication of in situ bioremediation still remains a challenging problem because of the complexity. Many factors may affect the applicability and efficiency of bioremediation of chlorinated ethenes in situ, which include the type and concentration of contaminants, biological, geological and hydro-geological conditions of the site, physical and chemical characteristics of groundwater and soils to be treated, as well as the constraints in engineering. In this presentation, an overview together with a detailed discussion on each factor will be provided. The influences of individual factors are discussed using the data obtained or cited from different sites and experiments, and thus under different environmental conditions. The results of this study illustrated that 1) the establishment of microbial consortium is of crucial importance for a complete degradation of chlorinated ethenes, 2) in situ control of favorable conditions for increasing microbial activities for bio-degradation through a designed pathway is the key to success, 3) the focus of a successful remediation system is to design an effective delivery process that is capable of producing adequate amendment mixing of contaminant-degrading bacteria, appropriate concentrations of electron acceptors, electron donors, and microbial nutrients in the subsurface treatment area.

Relationship between methanogenic archaea and subgingival microbial complexes in human periodontitis.

PubMed

Horz, H P; Robertz, N; Vianna, M E; Henne, K; Conrads, G

2015-10-01

We compared the amounts of methanogenic archaea with ten of the most important periodontal pathogens in 125 clinical samples. Correlation analysis suggests that the support of the periodontitis-associated bacterial consortium by methanogenic archaea may be driven through direct or indirect interactions with Prevotella intermedia. Copyright © 2015 Elsevier Ltd. All rights reserved.

Engineering a Synthetic Microbial Consortium for Comprehensive Conversion of Algae Biomass into Terpenes for Advanced Biofuels and Bioproducts

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

Wu, Weihua; Wu, Benjamin Chiau-Pin; Davis, Ryan Wesley

Recent strategies for algae-based biofuels have primarily focused on biodiesel production by exploiting high algal lipid yields under nutrient stress conditions. However, under conditions supporting robust algal biomass accumulation, carbohydrate and proteins typically comprise up to ~80% of the ash-free dry weight of algae biomass. Therefore, comprehensive utilization of algal biomass for production of multipurpose intermediate- to high-value bio-based products will promote scale-up of algae production and processing to commodity volumes. Terpenes are hydrocarbon and hydrocarbon-like (C:O>10:1) compounds with high energy density, and are therefore potentially promising candidates for the next generation of value added bio-based chemicals and “drop-in” replacementsmore » for petroleum-based fuels. In this study, we demonstrated the feasibility of bioconversion of proteins into sesquiterpene compounds as well as comprehensive bioconversion of algal carbohydrates and proteins into biofuels. To achieve this, the mevalonate pathway was reconstructed into an E. coli chassis with six different terpene synthases (TSs). Strains containing the various TSs produced a spectrum of sesquiterpene compounds in minimal medium containing amino acids as the sole carbon source. The sesquiterpene production was optimized through three different regulation strategies using chamigrene synthase as an example. The highest total terpene titer reached 166 mg/L, and was achieved by applying a strategy to minimize mevalonate accumulation in vivo. The highest yields of total terpene were produced under reduced IPTG induction levels (0.25 mM), reduced induction temperature (25°C), and elevated substrate concentration (20 g/L amino acid mixture). A synthetic bioconversion consortium consisting of two engineering E. coli strains (DH1-TS and YH40-TS) with reconstructed terpene biosynthetic pathways was designed for comprehensive single-pot conversion of algal carbohydrates and proteins to sesquiterpenes. The consortium yielded the highest total terpene yields (187 mg/L) at an inoculum ratio 2:1 of strain YH40-TS: DH1-TS, corresponding to 31 mg fuel/g algae biomass ash free dry weight. This study therefore demonstrates a feasible process for comprehensive algal biofuel production.« less

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

PubMed Central

2010-01-01

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

Zero-valent sulphur is a key intermediate in marine methane oxidation.

PubMed

Milucka, Jana; Ferdelman, Timothy G; Polerecky, Lubos; Franzke, Daniela; Wegener, Gunter; Schmid, Markus; Lieberwirth, Ingo; Wagner, Michael; Widdel, Friedrich; Kuypers, Marcel M M

2012-11-22

Emissions of methane, a potent greenhouse gas, from marine sediments are controlled by anaerobic oxidation of methane coupled primarily to sulphate reduction (AOM). Sulphate-coupled AOM is believed to be mediated by a consortium of methanotrophic archaea (ANME) and sulphate-reducing Deltaproteobacteria but the underlying mechanism has not yet been resolved. Here we show that zero-valent sulphur compounds (S(0)) are formed during AOM through a new pathway for dissimilatory sulphate reduction performed by the methanotrophic archaea. Hence, AOM might not be an obligate syntrophic process but may be carried out by the ANME alone. Furthermore, we show that the produced S(0)--in the form of disulphide--is disproportionated by the Deltaproteobacteria associated with the ANME. Our observations expand the diversity of known microbially mediated sulphur transformations and have significant implications for our understanding of the biogeochemical carbon and sulphur cycles.

Synergistic degradation of crude oil by indigenous bacterial consortium and exogenous fungus Scedosporium boydii.

PubMed

Yuan, Xiaoyu; Zhang, Xinying; Chen, Xueping; Kong, Dewen; Liu, Xiaoyan; Shen, Siyuan

2018-05-19

The purpose of this study was to investigate the potential of defined co-culture of indigenous bacterial consortium and exogenous fungus Scedosporium boydii for biodegradation of crude oil. After 7 days of incubation, residual oil, n-alkanes and aromatic fraction were analyzed. The degradation rate of crude oil was increased from 61.06% to 81.45% by the defined co-culture according to the 3:1 inoculation ratio of bacteria to fungi. The microbial activity was enhanced markedly and the formation of biofilms was accelerated after suitable inoculation of Scedosporium boydii. High throughput analysis showed that bacterial evenness and diversity were increased and the relative abundance of Paraburkholderia tropica was increased observably from 7.67% to 56.13% in the defined co-culture. These results indicated that synergistic degradation of crude oil in the bacteria-fungi consortium may be advantageous for bioremediation of petroleum-contaminated site. Copyright © 2018 Elsevier Ltd. All rights reserved.

Comparative Metagenomics of the Polymicrobial Black Band Disease of Corals

PubMed Central

Meyer, Julie L.; Paul, Valerie J.; Raymundo, Laurie J.; Teplitski, Max

2017-01-01

Black Band Disease (BBD), the destructive microbial consortium dominated by the cyanobacterium Roseofilum reptotaenium, affects corals worldwide. While the taxonomic composition of BBD consortia has been well-characterized, substantially less is known about its functional repertoire. We sequenced the metagenomes of Caribbean and Pacific black band mats and cultured Roseofilum and obtained five metagenome-assembled genomes (MAGs) of Roseofilum, nine of Proteobacteria, and 12 of Bacteroidetes. Genomic content analysis suggests that Roseofilum is a source of organic carbon and nitrogen, as well as natural products that may influence interactions between microbes. Proteobacteria and Bacteroidetes members of the disease consortium are suited to the degradation of amino acids, proteins, and carbohydrates. The accumulation of sulfide underneath the black band mat, in part due to a lack of sulfur oxidizers, contributes to the lethality of the disease. The presence of sulfide:quinone oxidoreductase genes in all five Roseofilum MAGs and in the MAGs of several heterotrophs demonstrates that resistance to sulfide is an important characteristic for members of the BBD consortium. PMID:28458657

Successive changes in community structure of an ethylbenzene-degrading sulfate-reducing consortium.

PubMed

Nakagawa, Tatsunori; Sato, Shinya; Yamamoto, Yoko; Fukui, Manabu

2002-06-01

The microbial community structure and successive changes in a mesophilic ethylbenzene-degrading sulfate-reducing consortium were for the first time clarified by the denaturing gradient gel electrophoresis (DGGE) analysis of the PCR amplified 16S rRNA gene fragments. At least ten bands on the DGGE gel were detected in the stationary phase. Phylogenetic analysis of the DGGE bands revealed that the consortium consisted of different eubacterial phyla including the delta subgroup of Proteobacteria, the order Sphingobacteriales, the order Spirochaetales, and the unknown bacterium. The most abundant band C was closely related to strain mXyS1, an m-xylene-degrading sulfate-reducing bacterium (SRB), and occurred as a sole band on DGGE gels in the logarithmic growth phase that 40% ethylbenzene was consumed accompanied by sulfide production. During further prolonged incubation, the dominancy of band C did not change. These results suggest that SRB corresponds to the most abundant band C and contributes mainly to the degradation of ethylbenzene coupled with sulfate reduction.

Electron donor preference of a reductive dechlorinating consortium

USGS Publications Warehouse

Lorah, M.M.; Majcher, E.; Jones, E.; Driedger, G.; Dworatzek, S.; Graves, D.

2005-01-01

A wetland sediment-derived microbial consortium was developed by the USGS and propagated in vitro to large quantities by SiREM Laboratory for use in bioaugmentation applications. The consortium had the capacity to completely dechlorinate 1,1,2,2-tetrachloroethene, tetrachloroethylene, trichloroethylene, 1,1,2-trichloroethane, cis- and trans-1,2-dichoroethylene, 1.1-dichloroethylene, 1,2-dichloroethane, vinyl chloride, carbon tetrachloride and chloroform. A suite of electron donors with characteristics useful for bioaugmentation applications was tested. The electron donors included lactate (the donor used during WBC-2 development), ethanol, chitin (Chitorem???), hydrogen releasing compound (HRC???), emulsified vegetable oil (Newman Zone???), and hydrogen gas. Ethanol, lactate, and chitin were particularly effective with respect to stimulating, supporting, and sustaining reductive dechlorination of the broad suite of chemicals that WBC-2 biodegraded. Chitorem??? was the most effective "slow release" electron donor tested. This is an abstract of a paper presented at the Proceedings of the 8th International In Situ and On-Site Bioremediation Symposium (Baltimore, MD 6/6-9/2005).

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

NASA Astrophysics Data System (ADS)

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

2016-02-01

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

Competitive substrate biodegradation during surfactant-enhanced remediation

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

Goudar, C.; Strevett, K.; Grego, J.

The impact of synthetic surfactants on the aqueous phase biodegradation of benzene, toluene, and p-xylene (BTpX) was studied using two anionic surfactants, sodium dodecyl sulfate (SDS) and sodium dodecyl benzene sulfonate (SDBS), and two nonionic surfactants, POE(20) sorbitan monooleate (T-maz-80) and octyl-phenolpoly(ethyleneoxy) ethanol (CA-620). Batch biodegradation experiments were performed to evaluate surfactant biodegradability using two different microbial cultures. Of the four surfactants used in this study, SDS and T-maz-80 were readily degraded by a microbial consortium obtained from an activated sludge treatment system, whereas only SDS was degraded by a microbial culture that was acclimated to BTpX. Biodegradation kinetic parametersmore » associated with SDS and T-maz-80 degradation by the activated sludge consortium were estimated using respirometric data in conjunction with a nonlinear parameter estimation technique as {mu}{sub max} = 0.93 h{sup {minus}1}, K{sub s}= 96.18 mg/L and {mu}{sub max} = 0.41 h{sup {minus}1}, K{sub s} = 31.92 mg/L, respectively. When both BTpX and surfactant were present in the reactor along with BTpX-acclimated microorganisms, two distinct biodegradation patterns were seen. SDS was preferentially utilized inhibiting hydrocarbon biodegradation, whereas, the other three surfactants had no impact on BTpX biodegradation. None of the four surfactants were toxic to the microbial cultures used in this study. Readily biodegradable surfactants are not very effective for subsurface remediation applications as they are rapidly consumed, and also because of their potential inhibitory effects on intrinsic hydrocarbon biodegradation. This greatly increases treatment costs as surfactant recovery and reuse are adversely affected.« less

Hydrogen sulfide oxidation by a microbial consortium in a recirculation reactor system: sulfur formation under oxygen limitation and removal of phenols.

PubMed

Alcantara, Sergio; Velasco, Antonio; Muñoz, Ana; Cid, Juan; Revah, Sergio; Razo-Flores, Elías

2004-02-01

Wastewater from petroleum refining may contain a number of undesirable contaminants including sulfides, phenolic compounds, and ammonia. The concentrations of these compounds must be reduced to acceptable levels before discharge. Sulfur formation and the effect of selected phenolic compounds on the sulfide oxidation were studied in autotrophic aerobic cultures. A recirculation reactor system was implemented to improve the elemental sulfur recovery. The relation between oxygen and sulfide was determined calculating the O2/S2- loading rates (Q(O2)/Q(S)2- = Rmt), which adequately defined the operation conditions to control the sulfide oxidation. Sulfur-producing steady states were achieved at Rmt ranging from 0.5 to 1.5. The maximum sulfur formation occurred at Rmt of 0.5 where 85% of the total sulfur added to the reactor as sulfide was transformed to elemental sulfur and 90% of it was recovered from the bottom of the reactor. Sulfide was completely oxidized to sulfate (Rmt of 2) in a stirred tank reactor, even when a mixture of phenolic compounds was present in the medium. Microcosm experiments showed that carbon dioxide production increased in the presence of the phenols, suggesting that these compounds were oxidized and that they may have been used as carbon and energy source by heterotrophic microorganisms present in the consortium.

Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir

PubMed Central

Walsh, Aaron M.; Crispie, Fiona; Kilcawley, Kieran; O’Sullivan, Orla; O’Sullivan, Maurice G.; Claesson, Marcus J.

2016-01-01

ABSTRACT Kefir is a putatively health-promoting dairy beverage that is produced when a kefir grain, consisting of a consortium of microorganisms, is added to milk to initiate a natural fermentation. Here, a detailed analysis was carried out to determine how the microbial population, gene content, and flavor of three kefirs from distinct geographic locations change over the course of 24-h fermentations. Metagenomic sequencing revealed that Lactobacillus kefiranofaciens was the dominant bacterial species in kefir during early stages of fermentations but that Leuconostoc mesenteroides became more prevalent in later stages. This pattern is consistent with an observation that genes involved in aromatic amino acid biosynthesis were absent from L. kefiranofaciens but were present in L. mesenteroides. Additionally, these shifts in the microbial community structure, and associated pathways, corresponded to changes in the levels of volatile compounds. Specifically, Acetobacter spp. correlated with acetic acid; Lactobacillus spp. correlated with carboxylic acids, esters and ketones; Leuconostoc spp. correlated with acetic acid and 2,3-butanedione; and Saccharomyces spp. correlated with esters. The correlation data suggest a causal relationship between microbial taxa and flavor that is supported by observations that addition of L. kefiranofaciens NCFB 2797 increased the levels of esters and ketones whereas addition of L. mesenteroides 213M0 increased the levels of acetic acid and 2,3-butanedione. Finally, we detected genes associated with probiotic functionalities in the kefir microbiome. Our results illustrate the dynamic nature of kefir fermentations and microbial succession patterns therein and can be applied to optimize the fermentation processes, flavors, and health-related attributes of this and other fermented foods. IMPORTANCE Traditional fermented foods represent relatively low-complexity microbial environments that can be used as model microbial communities to understand how microbes interact in natural environments. Our results illustrate the dynamic nature of kefir fermentations and microbial succession patterns therein. In the process, the link between individual species, and associated pathways, with flavor compounds is revealed and several genes that could be responsible for the purported gut health-associated benefits of consuming kefir are identified. Ultimately, in addition to providing an important fundamental insight into microbial interactions, this information can be applied to optimize the fermentation processes, flavors, and health-related attributes of this and other fermented foods. Author Video: An author video summary of this article is available. PMID:27822552

Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir.

PubMed

Walsh, Aaron M; Crispie, Fiona; Kilcawley, Kieran; O'Sullivan, Orla; O'Sullivan, Maurice G; Claesson, Marcus J; Cotter, Paul D

2016-01-01

Kefir is a putatively health-promoting dairy beverage that is produced when a kefir grain, consisting of a consortium of microorganisms, is added to milk to initiate a natural fermentation. Here, a detailed analysis was carried out to determine how the microbial population, gene content, and flavor of three kefirs from distinct geographic locations change over the course of 24-h fermentations. Metagenomic sequencing revealed that Lactobacillus kefiranofaciens was the dominant bacterial species in kefir during early stages of fermentations but that Leuconostoc mesenteroides became more prevalent in later stages. This pattern is consistent with an observation that genes involved in aromatic amino acid biosynthesis were absent from L. kefiranofaciens but were present in L. mesenteroides . Additionally, these shifts in the microbial community structure, and associated pathways, corresponded to changes in the levels of volatile compounds. Specifically, Acetobacter spp. correlated with acetic acid; Lactobacillus spp. correlated with carboxylic acids, esters and ketones; Leuconostoc spp. correlated with acetic acid and 2,3-butanedione; and Saccharomyces spp. correlated with esters. The correlation data suggest a causal relationship between microbial taxa and flavor that is supported by observations that addition of L. kefiranofaciens NCFB 2797 increased the levels of esters and ketones whereas addition of L. mesenteroides 213M0 increased the levels of acetic acid and 2,3-butanedione. Finally, we detected genes associated with probiotic functionalities in the kefir microbiome. Our results illustrate the dynamic nature of kefir fermentations and microbial succession patterns therein and can be applied to optimize the fermentation processes, flavors, and health-related attributes of this and other fermented foods. IMPORTANCE Traditional fermented foods represent relatively low-complexity microbial environments that can be used as model microbial communities to understand how microbes interact in natural environments. Our results illustrate the dynamic nature of kefir fermentations and microbial succession patterns therein. In the process, the link between individual species, and associated pathways, with flavor compounds is revealed and several genes that could be responsible for the purported gut health-associated benefits of consuming kefir are identified. Ultimately, in addition to providing an important fundamental insight into microbial interactions, this information can be applied to optimize the fermentation processes, flavors, and health-related attributes of this and other fermented foods.

Development of an Efficient Bacterial Consortium for the Potential Remediation of Hydrocarbons from Contaminated Sites

PubMed Central

Patowary, Kaustuvmani; Patowary, Rupshikha; Kalita, Mohan C.; Deka, Suresh

2016-01-01

The intrinsic biodegradability of hydrocarbons and the distribution of proficient degrading microorganisms in the environment are very crucial for the implementation of bioremediation practices. Among others, one of the most favorable methods that can enhance the effectiveness of bioremediation of hydrocarbon-contaminated environment is the application of biosurfactant producing microbes. In the present study, the biodegradation capacities of native bacterial consortia toward total petroleum hydrocarbons (TPH) with special emphasis to poly aromatic hydrocarbons were determined. The purpose of the study was to isolate TPH degrading bacterial strains from various petroleum contaminated soil of Assam, India and develop a robust bacterial consortium for bioremediation of crude oil of this native land. From a total of 23 bacterial isolates obtained from three different hydrocarbons contaminated samples five isolates, namely KS2, PG1, PG5, R1, and R2 were selected as efficient crude oil degraders with respect to their growth on crude oil enriched samples. Isolates KS2, PG1, and R2 are biosurfactant producers and PG5, R1 are non-producers. Fourteen different consortia were designed involving both biosurfactant producing and non-producing isolates. Consortium 10, which comprises two Bacillus strains namely, Bacillus pumilus KS2 and B. cereus R2 (identified by 16s rRNA sequencing) has shown the best result in the desired degradation of crude oil. The consortium showed degradation up to 84.15% of TPH after 5 weeks of incubation, as revealed from gravimetric analysis. FTIR (Fourier transform infrared) and GCMS (Gas chromatography-mass spectrometer) analyses were correlated with gravimetric data which reveals that the consortium has removed a wide range of petroleum hydrocarbons in comparison with abiotic control including different aliphatic and aromatic hydrocarbons. PMID:27471499

Optimization of biogenic methane production from coal

DOE PAGES

Fuertez, John; Nguyen, Van; McLennan, John D.; ...

2017-09-29

Given continuously increasing global energy needs, diversified efforts have been made to find and exploit new natural gas resources. These include coalbed methane (CBM), which represents an important global, unconventional source of natural gas. Efforts have been underway for some time to more effectively generate methane in-situ in coal plays by introduction of nutrients and/or microbial consortia. However, much is still to be learned about the limitations and environmental conditions that support microbial growth and are conducive to biogenic methane production from coal. Here we evaluated environmental conditions that led to increased methane production from subbituminous coal by introducing amore » foreign methanogenic consortium that included Methanobacterium sp. Furthermore, we used a central composite design (CCD) 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. An anticipated detrimental effect of NaCl concentration on methane production was observed for the consortium assessed. The range of feasible operational conditions comprised initial pH values between 4.2 and 6.8, temperatures between 23 °C and 37 °C, and NaCl concentrations between 3.7 mg/cm 3 and 9.0 mg/cm 3. Coal biogasification was optimal for this consortium at an initial pH value of 5.5, at 30 °C, and at a NaCl concentration 3.7 mg/cm 3 (i.e., 145,165 ppm, which is 25.6 sft 3/ton).« less

Optimization of biogenic methane production from coal

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

Fuertez, John; Nguyen, Van; McLennan, John D.

Given continuously increasing global energy needs, diversified efforts have been made to find and exploit new natural gas resources. These include coalbed methane (CBM), which represents an important global, unconventional source of natural gas. Efforts have been underway for some time to more effectively generate methane in-situ in coal plays by introduction of nutrients and/or microbial consortia. However, much is still to be learned about the limitations and environmental conditions that support microbial growth and are conducive to biogenic methane production from coal. Here we evaluated environmental conditions that led to increased methane production from subbituminous coal by introducing amore » foreign methanogenic consortium that included Methanobacterium sp. Furthermore, we used a central composite design (CCD) 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. An anticipated detrimental effect of NaCl concentration on methane production was observed for the consortium assessed. The range of feasible operational conditions comprised initial pH values between 4.2 and 6.8, temperatures between 23 °C and 37 °C, and NaCl concentrations between 3.7 mg/cm 3 and 9.0 mg/cm 3. Coal biogasification was optimal for this consortium at an initial pH value of 5.5, at 30 °C, and at a NaCl concentration 3.7 mg/cm 3 (i.e., 145,165 ppm, which is 25.6 sft 3/ton).« less

Bacterial diversity and reductive dehalogenase redundancy in a 1,2-dichloroethane-degrading bacterial consortium enriched from a contaminated aquifer

PubMed Central

2010-01-01

Background Bacteria possess a reservoir of metabolic functionalities ready to be exploited for multiple purposes. The use of microorganisms to clean up xenobiotics from polluted ecosystems (e.g. soil and water) represents an eco-sustainable and powerful alternative to traditional remediation processes. Recent developments in molecular-biology-based techniques have led to rapid and accurate strategies for monitoring and identification of bacteria and catabolic genes involved in the degradation of xenobiotics, key processes to follow up the activities in situ. Results We report the characterization of the response of an enriched bacterial community of a 1,2-dichloroethane (1,2-DCA) contaminated aquifer to the spiking with 5 mM lactate as electron donor in microcosm studies. After 15 days of incubation, the microbial community structure was analyzed. The bacterial 16S rRNA gene clone library showed that the most represented phylogenetic group within the consortium was affiliated with the phylum Firmicutes. Among them, known degraders of chlorinated compounds were identified. A reductive dehalogenase genes clone library showed that the community held four phylogenetically-distinct catalytic enzymes, all conserving signature residues previously shown to be linked to 1,2-DCA dehalogenation. Conclusions The overall data indicate that the enriched bacterial consortium shares the metabolic functionality between different members of the microbial community and is characterized by a high functional redundancy. These are fundamental features for the maintenance of the community's functionality, especially under stress conditions and suggest the feasibility of a bioremediation treatment with a potential prompt dehalogenation and a process stability over time. PMID:20170484

From Rare to Dominant: a Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation.

PubMed

Fuentes, Sebastián; Barra, Bárbara; Caporaso, J Gregory; Seeger, Michael

2016-02-01

Hydrocarbons are worldwide-distributed pollutants that disturb various ecosystems. The aim of this study was to characterize the short-lapse dynamics of soil microbial communities in response to hydrocarbon pollution and different bioremediation treatments. Replicate diesel-spiked soil microcosms were inoculated with either a defined bacterial consortium or a hydrocarbonoclastic bacterial enrichment and incubated for 12 weeks. The microbial community dynamics was followed weekly in microcosms using Illumina 16S rRNA gene sequencing. Both the bacterial consortium and enrichment enhanced hydrocarbon degradation in diesel-polluted soils. A pronounced and rapid bloom of a native gammaproteobacterium was observed in all diesel-polluted soils. A unique operational taxonomic unit (OTU) related to the Alkanindiges genus represented ∼ 0.1% of the sequences in the original community but surprisingly reached >60% after 6 weeks. Despite this Alkanindiges-related bloom, inoculated strains were maintained in the community and may explain the differences in hydrocarbon degradation. This study shows the detailed dynamics of a soil bacterial bloom in response to hydrocarbon pollution, resembling microbial blooms observed in marine environments. Rare community members presumably act as a reservoir of ecological functions in high-diversity environments, such as soils. This rare-to-dominant bacterial shift illustrates the potential role of a rare biosphere facing drastic environmental disturbances. Additionally, it supports the concept of "conditionally rare taxa," in which rareness is a temporary state conditioned by environmental constraints. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

From Rare to Dominant: a Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation

PubMed Central

Fuentes, Sebastián; Barra, Bárbara; Caporaso, J. Gregory

2015-01-01

Hydrocarbons are worldwide-distributed pollutants that disturb various ecosystems. The aim of this study was to characterize the short-lapse dynamics of soil microbial communities in response to hydrocarbon pollution and different bioremediation treatments. Replicate diesel-spiked soil microcosms were inoculated with either a defined bacterial consortium or a hydrocarbonoclastic bacterial enrichment and incubated for 12 weeks. The microbial community dynamics was followed weekly in microcosms using Illumina 16S rRNA gene sequencing. Both the bacterial consortium and enrichment enhanced hydrocarbon degradation in diesel-polluted soils. A pronounced and rapid bloom of a native gammaproteobacterium was observed in all diesel-polluted soils. A unique operational taxonomic unit (OTU) related to the Alkanindiges genus represented ∼0.1% of the sequences in the original community but surprisingly reached >60% after 6 weeks. Despite this Alkanindiges-related bloom, inoculated strains were maintained in the community and may explain the differences in hydrocarbon degradation. This study shows the detailed dynamics of a soil bacterial bloom in response to hydrocarbon pollution, resembling microbial blooms observed in marine environments. Rare community members presumably act as a reservoir of ecological functions in high-diversity environments, such as soils. This rare-to-dominant bacterial shift illustrates the potential role of a rare biosphere facing drastic environmental disturbances. Additionally, it supports the concept of “conditionally rare taxa,” in which rareness is a temporary state conditioned by environmental constraints. PMID:26590285

Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System

PubMed Central

Ho, Adrian; Angel, Roey; Veraart, Annelies J.; Daebeler, Anne; Jia, Zhongjun; Kim, Sang Yoon; Kerckhof, Frederiek-Maarten; Boon, Nico; Bodelier, Paul L. E.

2016-01-01

Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes. PMID:27602021

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

PubMed

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

2015-12-01

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

Feasibility of biohydrogen production from industrial wastes using defined microbial co-culture.

PubMed

Chen, Peng; Wang, Yuxia; Yan, Lei; Wang, Yiqing; Li, Suyue; Yan, Xiaojuan; Wang, Ningbo; Liang, Ning; Li, Hongyu

2015-05-06

The development of clean or novel alternative energy has become a global trend that will shape the future of energy. In the present study, 3 microbial strains with different oxygen requirements, including Clostridium acetobutylicum ATCC 824, Enterobacter cloacae ATCC 13047 and Kluyveromyces marxianus 15D, were used to construct a hydrogen production system that was composed of a mixed aerobic-facultative anaerobic-anaerobic consortium. The effects of metal ions, organic acids and carbohydrate substrates on this system were analyzed and compared using electrochemical and kinetic assays. It was then tested using small-scale experiments to evaluate its ability to convert starch in 5 L of organic wastewater into hydrogen. For the one-step biohydrogen production experiment, H1 medium (nutrient broth and potato dextrose broth) was mixed directly with GAM broth to generate H2 medium (H1 medium and GAM broth). Finally, Clostridium acetobutylicum ATCC 824, Enterobacter cloacae ATCC 13047 and Kluyveromyces marxianus 15D of three species microbial co-culture to produce hydrogen under anaerobic conditions. For the two-step biohydrogen production experiment, the H1 medium, after cultured the microbial strains Enterobacter cloacae ATCC 13047 and Kluyveromyces marxianus 15D, was centrifuged to remove the microbial cells and then mixed with GAM broth (H2 medium). Afterward, the bacterial strain Clostridium acetobutylicum ATCC 824 was inoculated into the H2 medium to produce hydrogen by anaerobic fermentation. The experimental results demonstrated that the optimum conditions for the small-scale fermentative hydrogen production system were at pH 7.0, 35°C, a mixed medium, including H1 medium and H2 medium with 0.50 mol/L ferrous chloride, 0.50 mol/L magnesium sulfate, 0.50 mol/L potassium chloride, 1% w/v citric acid, 5% w/v fructose and 5% w/v glucose. The overall hydrogen production efficiency in the shake flask fermentation group was 33.7 mL/h(-1).L(-1), and those the two-step and the one-step processes of the small-scale fermentative hydrogen production system were 41.2 mL/h(-1).L(-1) and 35.1 mL/h(-1).L(-1), respectively. Therefore, the results indicate that the hydrogen production efficiency of the two-step process is higher than that of the one-step process.

Optoelectronic Technology Consortium: Precompetitive Consortium for Optoelectronic Interconnect Technology

DTIC Science & Technology

1992-09-01

demonstrating the producibility of optoelectronic components for high-density/high-data-rate processors and accelerating the insertion of this technology...technology development stage, OETC will advance the development of optical components, produce links for a multiboard processor testbed demonstration, and...components that are affordable, initially at <$100 per line, and reliable, with a li~e BER᝺-15 and MTTF >10 6 hours. Under the OETC program, Honeywell will

Atrazine removal from aqueous solutions using submerged biological aerated filter.

PubMed

Baghapour, Mohammad Ali; Nasseri, Simin; Derakhshan, Zahra

2013-06-12

Atrazine is widely used in the agriculture as an herbicide. Due to its high mobility, Atrazine leaks into the groundwaters, surface waters, and drinking water wells. Many physical and chemical methods have been suggested for removing Atrazine from aquatic environments. However, these methods are very costly, have many performance problems, produce a lot of toxic intermediates which are very harmful and dangerous, and cannot completely mineralize Atrazine. In this study, biodegradation of Atrazine by microbial consortium was evaluated in the aquatic environment. In order to assess the Atrazine removal from the aquatic environment, submerged biological aerated filter (SBAF) was fed with synthetic wastewater based on sucrose and Atrazine at different hydraulic retention times (HRTs). The maximum efficiencies for Atrazine and Soluble Chemical Oxygen Demand (SCOD) removal were 97.9% and 98.9%, respectively. The study findings showed that Stover-Kincannon model had very good fitness (R2 > 99%) in loading Atrazine in the biofilter and by increasing the initial concentration of Atrazine, the removal efficiency increased. Aerobic mixed biofilm culture was observed to be suitable for the treatment of Atrazine from aquatic environment. There was no significant inhibition effect on mixed aerobic microbial consortia. Atrazine degradation depended on the strength of wastewater and the amount of Atrazine in the influent.

Atrazine removal from aqueous solutions using submerged biological aerated filter

PubMed Central

2013-01-01

Atrazine is widely used in the agriculture as an herbicide. Due to its high mobility, Atrazine leaks into the groundwaters, surface waters, and drinking water wells. Many physical and chemical methods have been suggested for removing Atrazine from aquatic environments. However, these methods are very costly, have many performance problems, produce a lot of toxic intermediates which are very harmful and dangerous, and cannot completely mineralize Atrazine. In this study, biodegradation of Atrazine by microbial consortium was evaluated in the aquatic environment. In order to assess the Atrazine removal from the aquatic environment, submerged biological aerated filter (SBAF) was fed with synthetic wastewater based on sucrose and Atrazine at different hydraulic retention times (HRTs). The maximum efficiencies for Atrazine and Soluble Chemical Oxygen Demand (SCOD) removal were 97.9% and 98.9%, respectively. The study findings showed that Stover-Kincannon model had very good fitness (R2 > 99%) in loading Atrazine in the biofilter and by increasing the initial concentration of Atrazine, the removal efficiency increased. Aerobic mixed biofilm culture was observed to be suitable for the treatment of Atrazine from aquatic environment. There was no significant inhibition effect on mixed aerobic microbial consortia. Atrazine degradation depended on the strength of wastewater and the amount of Atrazine in the influent. PMID:24499572

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

PubMed Central

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

Bacterial Community Analysis, New Exoelectrogen Isolation and Enhanced Performance of Microbial Electrochemical Systems Using Nano-Decorated Anodes

NASA Astrophysics Data System (ADS)

Xu, Shoutao

Microbial electrochemical systems (MESs) have attracted much research attention in recent years due to their promising applications in renewable energy generation, bioremediation, and wastewater treatment. In a MES, microorganisms interact with electrodes via electrons, catalyzing oxidation and reduction reactions at the anode and the cathode. The bacterial community of a high power mixed consortium MESs (maximum power density is 6.5W/m2) was analyzed by using denature gradient gel electrophoresis (DGGE) and 16S DNA clone library methods. The bacterial DGGE profiles were relatively complex (more than 10 bands) but only three brightly dominant bands in DGGE results. These results indicated there are three dominant bacterial species in mixed consortium MFCs. The 16S DNA clone library method results revealed that the predominant bacterial species in mixed culture is Geobacter sp (66%), Arcobacter sp and Citrobacter sp. These three bacterial species reached to 88% of total bacterial species. This result is consistent with the DGGE result which showed that three bright bands represented three dominant bacterial species. Exoelectrogenic bacterial strain SX-1 was isolated from a mediator-less microbial fuel cell by conventional plating techniques with ferric citrate as electron acceptor under anaerobic conditions. Phylogenetic analysis of the 16S rDNA sequence revealed that it was related to the members of Citrobacter genus with Citrobacter sp. sdy-48 being the most closely related species. The bacterial strain SX-1 produced electricity from citrate, acetate, glucose, sucrose, glycerol, and lactose in MFCs with the highest current density of 205 mA/m2 generated from citrate. Cyclic voltammetry analysis indicated that membrane associated proteins may play an important role in facilitating electron transfer from the bacteria to the electrode. This is the first study that demonstrates that Citrobacter species can transfer electrons to extracellular electron acceptors. Citrobacter strain SX-1 is capable of generating electricity from a wide range of substrates in MFCs. This finding increases the known diversity of power generating exoelectrogens and provids a new strain to explore the mechanisms of extracellular electron transfer from bacteria to electrode. The wide range of substrate utilization by SX-1 increases the application potential of MFCs in renewable energy generation and waste treatment. Anode properties are critical for the performance of microbial electrolysis cells (MECs). Inexpensive Fe nanoparticle modified graphite disks were used as anodes to preliminarily investigate the effects of nanoparticles on the performance of Shewanella oneidensis MR-1 in MECs. Results demonstrated that average current densities produced with Fe nanoparticle decorated anodes were up to 5.9-fold higher than plain graphite anodes. Whole genome microarray analysis of the gene expression showed that genes encoding biofilm formation were significantly up-regulated as a response to nanoparticle decorated anodes. Increased expression of genes related to nanowires, flavins and c-type cytochromes indicate that enhanced mechanisms of electron transfer to the anode may also have contributed to the observed increases in current density. The majority of the remaining differentially expressed genes were associated with electron transport and anaerobic metabolism demonstrating a systemic response to increased power loads. The carbon nanotube (CNT) is another form of nano materials. Carbon nanotube (CNT) modified graphite disks were used as anodes to investigate the effects of nanostructures on the performance S. oneidensis MR-1 in microbial electrolysis cells (MECs). The current densities produced with CNT decorated anodes were up to 5.6-fold higher than plain graphite anodes. Global transcriptome analysis showed that cytochrome c genes associated with extracellular electron transfer are up-expressed by CNT decorated anodes, which is the leading factor to contribute current increase in CNT decorated anode MECs. The up regulated genes encoded to flavin also contribute to current enhancement in CNT decorated anode MECs.

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

PubMed

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

2015-01-01

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

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

PubMed

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

2018-04-01

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

Draft genome sequence of a strictly anaerobic dichloromethane-degrading bacterium

DOE PAGES

Kleindienst, Sara; Higgins, Steven A.; Tsementzi, Despina; ...

2016-03-03

Here, an anaerobic, dichloromethane-degrading bacterium affiliated with novel Peptococcaceae was maintained in a microbial consortium. The organism originated from pristine freshwater sediment collected from Rio Mameyes in Luquillo, Puerto Rico, in October 2009 (latitude 18°21'43.9", longitude –65°46'8.4"). The draft genome sequence is 2.1 Mb and has a G+C content of 43.5%.

A Metagenomic Approach to Cyanobacterial Genomics

PubMed Central

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

2017-01-01

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

The microbial diversity of water kefir.

PubMed

Gulitz, Anna; Stadie, Jasmin; Wenning, Mareike; Ehrmann, Matthias A; Vogel, Rudi F

2011-12-15

The microbial diversity of water kefir, made from a mixture of water, dried figs, a slice of lemon and sucrose was studied. The microbial consortia residing in the granules of three water kefirs of different origins were analyzed. A collection of 453 bacterial isolates was obtained on different selective/differential media. Bacterial isolates were grouped with randomly amplified polymorphic DNA (RAPD)-PCR analyses. One representative of each RAPD genotype was identified by comparative 16S rDNA gene sequencing. The predominant genus in water kefirs I and II was Lactobacillus, which accounted for 82.1% in water kefir I and 72.1% in water kefir II of the bacterial isolates. The most abundant species in water kefirs I and II were Lactobacillus hordei and Lb. nagelii followed by considerably lower numbers of Lb. casei. Other lactic acid bacteria (LAB) were identified as Leuconostoc mesenteroides and Lc. citreum in all three water kefirs. The most abundant species in water kefir III was Lc. mesenteroides (28%) and Lc. citreum (24.3%). A total of 57 LAB belonging to the species of Lb. casei, Lb. hordei, Lb. nagelii, Lb. hilgardii and Lc. mesenteroides were able to produce exopolysacchrides from sucrose. Non LABs were identified as Acetobacter fabarum and Ac. orientalis. The Acetobacter species were more prevalent in consortium III. Cluster analyses of RAPD-PCR patterns revealed an interspecies diversity among the Lactobacillus and Acetobacter strains. Aditionally, Saccharomyces cerevisiae, Lachancea fermentati, Hanseniaospora valbyensis and Zygotorulaspora florentina were isolated and identified by comparison of partial 26S rDNA sequences and FTIR spectroscopy. Copyright © 2011. Published by Elsevier B.V.

Ability of sea-water bacterial consortium to produce electricity and denitrify water

NASA Astrophysics Data System (ADS)

Maruvada, Nagasamrat V. V.; Tommasi, Tonia; Kaza, Kesava Rao; Ruggeri, Bernardo

Sea is a store house for varied types of microbes with an ability to reduce and oxidize substances like iron, sulphur, carbon dioxide, etc. Most of these processes happen in the sea water environment, but can be applied for purification of wastewater. In the present paper, we discuss the use of a consortium of seawater bacteria in a fuel cell to produce electricity by oxidizing organic matter and reducing nitrates. We also discuss how the growth of the bacterial consortium can lead to an increased electricity production and decreased diffusional resistance in the cell. The analysis was done using electrochemical impedance spectroscopy (EIS), and linear sweep voltammetry (LSV). Here, we use bicarbonate buffered solution, which is the natural buffering agent found in sea. We show that the seawater bacterial consortium can be used in both the anode and cathode parts of the cell. The results confirm the adaptability of the seawater bacteria to different environments and can be used for various applications. Heritage, Erasmus Mundus Programme, European Commission.

Soil mesocosm studies on atrazine bioremediation.

PubMed

Sagarkar, Sneha; Nousiainen, Aura; Shaligram, Shraddha; Björklöf, Katarina; Lindström, Kristina; Jørgensen, Kirsten S; Kapley, Atya

2014-06-15

Accumulation of pesticides in the environment causes serious issues of contamination and toxicity. Bioremediation is an ecologically sound method to manage soil pollution, but the bottleneck here, is the successful scale-up of lab-scale experiments to field applications. This study demonstrates pilot-scale bioremediation in tropical soil using atrazine as model pollutant. Mimicking field conditions, three different bioremediation strategies for atrazine degradation were explored. 100 kg soil mesocosms were set-up, with or without atrazine application history. Natural attenuation and enhanced bioremediation were tested, where augmentation with an atrazine degrading consortium demonstrated best pollutant removal. 90% atrazine degradation was observed in six days in soil previously exposed to atrazine, while soil without history of atrazine use, needed 15 days to remove the same amount of amended atrazine. The bacterial consortium comprised of 3 novel bacterial strains with different genetic atrazine degrading potential. The progress of bioremediation was monitored by measuring the levels of atrazine and its intermediate, cyanuric acid. Genes from the atrazine degradation pathway, namely, atzA, atzB, atzD, trzN and trzD were quantified in all mesocosms for 60 days. The highest abundance of all target genes was observed on the 6th day of treatment. trzD was observed in the bioaugmented mesocosms only. The bacterial community profile in all mesocosms was monitored by LH-PCR over a period of two months. Results indicate that the communities changed rapidly after inoculation, but there was no drastic change in microbial community profile after 1 month. Results indicated that efficient bioremediation of atrazine using a microbial consortium could be successfully up-scaled to pilot scale. Copyright © 2014 Elsevier Ltd. All rights reserved.

Degradation of organic pollutants by methane grown microbial consortia.

PubMed

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

2005-10-01

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

Study of microbial diversity in plant-microbe interaction system with oil sludge contamination.

PubMed

Dhote, Monika; Kumar, Anil; Jajoo, Anjana; Juwarkar, Asha

2018-07-03

A 90 days greenhouse experiment was conducted for evaluation of soil microbial diversity in different treatments of rhizospheric and nonrhizospheric oil sludge contaminated soil. Various pot treatments (T1-T5) were as follows: 2% oil sludge contaminated soil was considered as control (T1); augmentation of control with preadapted microbial consortium was T2; addition of Vetiver zizanioide to control was T3; bioaugmentation of control along with V. zizanioide was T4; and bioaugmentation with V. zizanioide and bulking agent was T5. During the study, different microbial populations were determined in all treatments. Additionally, soil microbial diversity using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) of 16S rDNA was carried out. At the end of experimental period, significant increase in microbial number in bioaugmented rhizospheric treatments (T4 and T5) was observed as compared to non-rhizospheric and non-bioaugmented treatments (T2 and T3). The community and sequencing results revealed that combined treatment of plant and microbes resulted in improved microbial species and number. The dominant phyla belonged to γ proteobacteria, β proteobacteria, Chloroflexi, firmicutes, and uncultured bacteria. It is concluded that plant-microbe-soil system supports immense oil degrading microbial diversity and can be used as an effective indicator tool for remediation of oil sludge contaminated sites.

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

PubMed

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

2004-02-01

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

Microbial degradation of petroleum hydrocarbons.

PubMed

Varjani, Sunita J

2017-01-01

Petroleum hydrocarbon pollutants are recalcitrant compounds and are classified as priority pollutants. Cleaning up of these pollutants from environment is a real world problem. Bioremediation has become a major method employed in restoration of petroleum hydrocarbon polluted environments that makes use of natural microbial biodegradation activity. Petroleum hydrocarbons utilizing microorganisms are ubiquitously distributed in environment. They naturally biodegrade pollutants and thereby remove them from the environment. Removal of petroleum hydrocarbon pollutants from environment by applying oleophilic microorganisms (individual isolate/consortium of microorganisms) is ecofriendly and economic. Microbial biodegradation of petroleum hydrocarbon pollutants employs the enzyme catalytic activities of microorganisms to enhance the rate of pollutants degradation. This article provides an overview about bioremediation for petroleum hydrocarbon pollutants. It also includes explanation about hydrocarbon metabolism in microorganisms with a special focus on new insights obtained during past couple of years. Copyright © 2016 Elsevier Ltd. All rights reserved.

Omics-based interpretation of synergism in a soil-derived cellulose-degrading microbial community

PubMed Central

Zhou, Yizhuang; Pope, Phillip B.; Li, Shaochun; Wen, Bo; Tan, Fengji; Cheng, Shu; Chen, Jing; Yang, Jinlong; Liu, Feng; Lei, Xuejing; Su, Qingqing; Zhou, Chengran; Zhao, Jiao; Dong, Xiuzhu; Jin, Tao; Zhou, Xin; Yang, Shuang; Zhang, Gengyun; Yang, Huangming; Wang, Jian; Yang, Ruifu; Eijsink, Vincent G. H.; Wang, Jun

2014-01-01

Reaching a comprehensive understanding of how nature solves the problem of degrading recalcitrant biomass may eventually allow development of more efficient biorefining processes. Here we interpret genomic and proteomic information generated from a cellulolytic microbial consortium (termed F1RT) enriched from soil. Analyses of reconstructed bacterial draft genomes from all seven uncultured phylotypes in F1RT indicate that its constituent microbes cooperate in both cellulose-degrading and other important metabolic processes. Support for cellulolytic inter-species cooperation came from the discovery of F1RT microbes that encode and express complimentary enzymatic inventories that include both extracellular cellulosomes and secreted free-enzyme systems. Metabolic reconstruction of the seven F1RT phylotypes predicted a wider genomic rationale as to how this particular community functions as well as possible reasons as to why biomass conversion in nature relies on a structured and cooperative microbial community. PMID:24924356

Stress-Survival Gene Identification From an Acid Mine Drainage Algal Mat Community

NASA Astrophysics Data System (ADS)

Urbina-Navarrete, J.; Fujishima, K.; Paulino-Lima, I. G.; Rothschild-Mancinelli, B.; Rothschild, L. J.

2014-12-01

Microbial communities from acid mine drainage environments are exposed to multiple stressors to include low pH, high dissolved metal loads, seasonal freezing, and desiccation. The microbial and algal communities that inhabit these niche environments have evolved strategies that allow for their ecological success. Metagenomic analyses are useful in identifying species diversity, however they do not elucidate the mechanisms that allow for the resilience of a community under these extreme conditions. Many known or predicted genes encode for protein products that are unknown, or similarly, many proteins cannot be traced to their gene of origin. This investigation seeks to identify genes that are active in an algal consortium during stress from living in an acid mine drainage environment. Our approach involves using the entire community transcriptome for a functional screen in an Escherichia coli host. This approach directly targets the genes involved in survival, without need for characterizing the members of the consortium.The consortium was harvested and stressed with conditions similar to the native environment it was collected from. Exposure to low pH (< 3.2), high metal load, desiccation, and deep freeze resulted in the expression of stress-induced genes that were transcribed into messenger RNA (mRNA). These mRNA transcripts were harvested to build complementary DNA (cDNA) libraries in E. coli. The transformed E. coli were exposed to the same stressors as the original algal consortium to select for surviving cells. Successful cells incorporated the transcripts that encode survival mechanisms, thus allowing for selection and identification of the gene(s) involved. Initial selection screens for freeze and desiccation tolerance have yielded E. coli that are 1 order of magnitude more resistant to freezing (0.01% survival of control with no transcript, 0.2% survival of E. coli with transcript) and 3 orders of magnitude more resistant to desiccation (0.005% survival of control cells with no transcripts, 5% survival of cells with transcript).This work is transformative because genetic functions can be selected without having prior knowledge of the genes or of the organisms involved. Work continues to identify the genes responsible for tolerance to extreme conditions and the bio-mechanisms involved.

Draft Genome Sequence of Thermoanaerobacter sp. Strain A7A, Reconstructed from a Metagenome Obtained from a High-Temperature Hydrocarbon Reservoir in the Bass Strait, Australia

PubMed Central

Li, Dongmei; Greenfield, Paul; Rosewarne, Carly P.

2013-01-01

The draft genome sequence of Thermoanaerobacter sp. strain A7A was reconstructed from a metagenome of a microbial consortium obtained from the Tuna oil field in the Gippsland Basin, Australia. The organism is a strict anaerobe that is predicted to ferment a range of simple sugars and undertake sulfur reduction. PMID:24029756

Environmental microbiology as a mosaic of explored ecosystems and issues.

PubMed

Faure, Denis; Bonin, Patricia; Duran, Robert

2015-09-01

Microbes are phylogenetically (Archaea, Bacteria, Eukarya, and viruses) and functionally diverse. They colonize highly varied environments and rapidly respond to and evolve as a response to local and global environmental changes, including those induced by pollutants resulting from human activities. This review exemplifies the Microbial Ecology EC2CO consortium's efforts to explore the biology, ecology, diversity, and roles of microbes in aquatic and continental ecosystems.

Thermophilic microbial cellulose decomposition and methanogenesis pathways recharacterized by metatranscriptomic and metagenomic analysis

PubMed Central

Xia, Yu; Wang, Yubo; Fang, Herbert H. P.; Jin, Tao; Zhong, Huanzi; Zhang, Tong

2014-01-01

The metatranscriptomic recharacterization in the present study captured microbial enzymes at the unprecedented scale of 40,000 active genes belonged to 2,269 KEGG functions were identified. The novel information obtained herein revealed interesting patterns and provides an initial transcriptional insight into the thermophilic cellulose methanization process. Synergistic beta-sugar consumption by Thermotogales is crucial for cellulose hydrolysis in the thermophilic cellulose-degrading consortium because the primary cellulose degraders Clostridiales showed metabolic incompetence in subsequent beta-sugar pathways. Additionally, comparable transcription of putative Sus-like polysaccharide utilization loci (PULs) was observed in an unclassified order of Bacteroidetes suggesting the importance of PULs mechanism for polysaccharides breakdown in thermophilic systems. Despite the abundance of acetate as a fermentation product, the acetate-utilizing Methanosarcinales were less prevalent by 60% than the hydrogenotrophic Methanobacteriales. Whereas the aceticlastic methanogenesis pathway was markedly more active in terms of transcriptional activities in key genes, indicating that the less dominant Methanosarcinales are more active than their hydrogenotrophic counterparts in methane metabolism. These findings suggest that the minority of aceticlastic methanogens are not necessarily associated with repressed metabolism, in a pattern that was commonly observed in the cellulose-based methanization consortium, and thus challenge the causal likelihood proposed by previous studies. PMID:25330991

Pulsed (13)C2-Acetate Protein-SIP Unveils Epsilonproteobacteria as Dominant Acetate Utilizers in a Sulfate-Reducing Microbial Community Mineralizing Benzene.

PubMed

Starke, Robert; Keller, Andreas; Jehmlich, Nico; Vogt, Carsten; Richnow, Hans H; Kleinsteuber, Sabine; von Bergen, Martin; Seifert, Jana

2016-05-01

In a benzene-degrading and sulfate-reducing syntrophic consortium, a clostridium affiliated to the genus Pelotomaculum was previously described to ferment benzene while various sulfate-reducing Deltaproteobacteria and a member of the Epsilonproteobacteria were supposed to utilize acetate and hydrogen as key metabolites derived from benzene fermentation. However, the acetate utilization network within this community was not yet unveiled. In this study, we performed a pulsed (13)C2-acetate protein stable isotope probing (protein-SIP) approach continuously spiking low amounts of acetate (10 μM per day) in addition to the ongoing mineralization of unlabeled benzene. Metaproteomics revealed high abundances of Clostridiales followed by Syntrophobacterales, Desulfobacterales, Desulfuromonadales, Desulfovibrionales, Archaeoglobales, and Campylobacterales. Pulsed acetate protein-SIP results indicated that members of the Campylobacterales, the Syntrophobacterales, the Archaeoglobales, the Clostridiales, and the Desulfobacterales were linked to acetate utilization in descending abundance. The Campylobacterales revealed the fastest and highest (13)C incorporation. Previous experiments suggested that the activity of the Campylobacterales was not essential for anaerobic benzene degradation in the investigated community. However, these organisms were consistently detected in various hydrocarbon-degrading and sulfate-reducing consortia enriched from the same aquifer. Here, we demonstrate that this member of the Campylobacterales is the dominant acetate utilizer in the benzene-degrading microbial consortium.

Characterization of the biodegradation, bioremediation and detoxification capacity of a bacterial consortium able to degrade the fungicide thiabendazole.

PubMed

Perruchon, Chiara; Pantoleon, Anastasios; Veroutis, Dimitrios; Gallego-Blanco, Sara; Martin-Laurent, F; Liadaki, Kalliopi; Karpouzas, Dimitrios G

2017-12-01

Thiabendazole (TBZ) is a persistent fungicide used in the post-harvest treatment of fruits. Its application results in the production of contaminated effluents which should be treated before their environmental discharge. In the absence of efficient treatment methods in place, biological systems based on microbial inocula with specialized degrading capacities against TBZ could be a feasible treatment approach. Only recently the first bacterial consortium able to rapidly transform TBZ was isolated. This study aimed to characterize its biodegradation, bioremediation and detoxification potential. The capacity of the consortium to mineralize 14 C-benzyl-ring labelled TBZ was initially assessed. Subsequent tests evaluated its degradation capacity under various conditions (range of pH, temperatures and TBZ concentration levels) and relevant practical scenarios (simultaneous presence of other postharvest compounds) and its bioaugmentation potential in soils contaminated with increasing TBZ levels. Finally cytotoxicity assays explored its detoxification potential. The consortium effectively mineralized the benzoyl ring of the benzimidazole moiety of TBZ and degraded spillage level concentrations of the fungicide in aqueous cultures (750 mg L -1 ) and in soil (500 mg kg -1 ). It maintained its high degradation capacity in a wide range of pH (4.5-7.5) and temperatures (15-37 °C) and in the presence of other pesticides (ortho-phenylphenol and diphenylamine). Toxicity assays using the human liver cancer cell line HepG2 showed a progressive decrease in cytotoxicity, concomitantly with the biodegradation of TBZ, pointing to a detoxification process. Overall, the bacterial consortium showed high potential for future implementation in bioremediation and biodepuration applications.

Oil Production by a Consortium of Oleaginous Microorganisms grown on primary effluent wastewater

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

Hall, Jacqueline; Hetrick, Mary; French, Todd

Municipal wastewater could be a potential growth medium that has not been considered for cultivating oleaginous microorganisms. This study is designed to determine if a consortium of oleaginous microorganism can successfully compete for carbon and other nutrients with the indigenous microorganisms contained in primary effluent wastewater. RESULTS: The oleaginous consortium inoculated with indigenous microorganisms reached stationary phase within 24 h, reaching a maximum cell concentration of 0.58 g L -1. Water quality post-oleaginous consortium growth reached a maximum chemical oxygen demand (COD) reduction of approximately 81%, supporting the consumption of the glucose within 8 h. The oleaginous consortium increased themore » amount of oil produced per gram by 13% compared with indigenous microorganisms in raw wastewater. Quantitative polymerase chain reaction (qPCR) results show a substantial population increase in bacteria within the first 24 h when the consortium is inoculated into raw wastewater. This result, along with the fatty acid methyl esters (FAMEs) results, suggests that conditions tested were not sufficient for the oleaginous consortium to compete with the indigenous microorganisms.« less

Characterization of a bioflocculant produced by a consortium of Halomonas sp. Okoh and Micrococcus sp. Leo.

PubMed

Okaiyeto, Kunle; Nwodo, Uchechukwu U; Mabinya, Leonard V; Okoh, Anthony I

2013-10-16

The physicochemical and flocculating properties of a bioflocculant produced by a bacterial consortium composed of Halomonas sp. Okoh and Micrococcus sp. Leo were investigated. The purified bioflocculant was cation and pH dependent, and optimally flocculated kaolin clay suspension at a dosage of 0.1 mg/mL. The flocculating activity of the bioflocculant was stimulated in the presence of Ca2+, Mn2+, Al3+ and had a wide pH range of 2-10, with the highest flocculating activity of 86% at pH 8. The bioflocculant was thermostable and retained more than 70% of its flocculating activity after being heated at 80 °C for 30 min. Thermogravimetric analyses revealed a partial thermal decomposition of the biofloculant at 400 °C. The infrared spectrum showed the presence of hydroxyl, carboxyl and amino moieties as functional groups. The bioflocculant produced by the bacterial consortium appears to hold promising alternative to inorganic and synthetic organic flocculants that are widely used in wastewater treatment.

Characterization of a Bioflocculant Produced by a Consortium of Halomonas sp. Okoh and Micrococcus sp. Leo

PubMed Central

Okaiyeto, Kunle; Nwodo, Uchechukwu U.; Mabinya, Leonard V.; Okoh, Anthony I.

2013-01-01

The physicochemical and flocculating properties of a bioflocculant produced by a bacterial consortium composed of Halomonas sp. Okoh and Micrococcus sp. Leo were investigated. The purified bioflocculant was cation and pH dependent, and optimally flocculated kaolin clay suspension at a dosage of 0.1 mg/mL. The flocculating activity of the bioflocculant was stimulated in the presence of Ca2+, Mn2+, Al3+ and had a wide pH range of 2–10, with the highest flocculating activity of 86% at pH 8. The bioflocculant was thermostable and retained more than 70% of its flocculating activity after being heated at 80 °C for 30 min. Thermogravimetric analyses revealed a partial thermal decomposition of the biofloculant at 400 °C. The infrared spectrum showed the presence of hydroxyl, carboxyl and amino moieties as functional groups. The bioflocculant produced by the bacterial consortium appears to hold promising alternative to inorganic and synthetic organic flocculants that are widely used in wastewater treatment. PMID:24135818

Metagenomic Analysis of a Biphenyl-Degrading Soil Bacterial Consortium Reveals the Metabolic Roles of Specific Populations

PubMed Central

Garrido-Sanz, Daniel; Manzano, Javier; Martín, Marta; Redondo-Nieto, Miguel; Rivilla, Rafael

2018-01-01

Polychlorinated biphenyls (PCBs) are widespread persistent pollutants that cause several adverse health effects. Aerobic bioremediation of PCBs involves the activity of either one bacterial species or a microbial consortium. Using multiple species will enhance the range of PCB congeners co-metabolized since different PCB-degrading microorganisms exhibit different substrate specificity. We have isolated a bacterial consortium by successive enrichment culture using biphenyl (analog of PCBs) as the sole carbon and energy source. This consortium is able to grow on biphenyl, benzoate, and protocatechuate. Whole-community DNA extracted from the consortium was used to analyze biodiversity by Illumina sequencing of a 16S rRNA gene amplicon library and to determine the metagenome by whole-genome shotgun Illumina sequencing. Biodiversity analysis shows that the consortium consists of 24 operational taxonomic units (≥97% identity). The consortium is dominated by strains belonging to the genus Pseudomonas, but also contains betaproteobacteria and Rhodococcus strains. whole-genome shotgun (WGS) analysis resulted in contigs containing 78.3 Mbp of sequenced DNA, representing around 65% of the expected DNA in the consortium. Bioinformatic analysis of this metagenome has identified the genes encoding the enzymes implicated in three pathways for the conversion of biphenyl to benzoate and five pathways from benzoate to tricarboxylic acid (TCA) cycle intermediates, allowing us to model the whole biodegradation network. By genus assignment of coding sequences, we have also been able to determine that the three biphenyl to benzoate pathways are carried out by Rhodococcus strains. In turn, strains belonging to Pseudomonas and Bordetella are the main responsible of three of the benzoate to TCA pathways while the benzoate conversion into TCA cycle intermediates via benzoyl-CoA and the catechol meta-cleavage pathways are carried out by beta proteobacteria belonging to genera such as Achromobacter and Variovorax. We have isolated a Rhodococcus strain WAY2 from the consortium which contains the genes encoding the three biphenyl to benzoate pathways indicating that this strain is responsible for all the biphenyl to benzoate transformations. The presented results show that metagenomic analysis of consortia allows the identification of bacteria active in biodegradation processes and the assignment of specific reactions and pathways to specific bacterial groups. PMID:29497412

Aerobic De-Epoxydation of Trichothecene Mycotoxins by a Soil Bacterial Consortium Isolated Using In Situ Soil Enrichment.

PubMed

He, Wei-Jie; Yuan, Qing-Song; Zhang, You-Bing; Guo, Mao-Wei; Gong, An-Dong; Zhang, Jing-Bo; Wu, Ai-Bo; Huang, Tao; Qu, Bo; Li, He-Ping; Liao, Yu-Cai

2016-09-24

Globally, the trichothecene mycotoxins deoxynivalenol (DON) and nivalenol (NIV) are among the most widely distributed mycotoxins that contaminate small grain cereals. In this study, a bacterial consortium, PGC-3, with de-epoxydation activity was isolated from soil by an in situ soil enrichment method. Screening of 14 soil samples that were sprayed with DON revealed that 4 samples were able to biotransform DON into de-epoxydized DON (dE-DON). Among these, the PGC-3 consortium showed the highest and most stable activity to biotransform DON into dE-DON and NIV into dE-NIV. PGC-3 exhibited de-epoxydation activity at a wide range of pH (5-10) and temperatures (20-37 °C) values under aerobic conditions. Sequential subculturing with a continued exposure to DON substantially reduced the microbial population diversity of this consortium. Analyses of the 16S rDNA sequences indicated that PGC-3 comprised 10 bacterial genera. Among these, one species, Desulfitobacterium, showed a steady increase in relative abundance, from 0.03% to 1.55% (a 52-fold increase), as higher concentrations of DON were used in the subculture media, from 0 to 500 μg/mL. This study establishes the foundation to further develop bioactive agents that can detoxify trichothecene mycotoxins in cereals and enables for the characterization of detoxifying genes and their regulation.

Aerobic De-Epoxydation of Trichothecene Mycotoxins by a Soil Bacterial Consortium Isolated Using In Situ Soil Enrichment

PubMed Central

He, Wei-Jie; Yuan, Qing-Song; Zhang, You-Bing; Guo, Mao-Wei; Gong, An-Dong; Zhang, Jing-Bo; Wu, Ai-Bo; Huang, Tao; Qu, Bo; Li, He-Ping; Liao, Yu-Cai

2016-01-01

Globally, the trichothecene mycotoxins deoxynivalenol (DON) and nivalenol (NIV) are among the most widely distributed mycotoxins that contaminate small grain cereals. In this study, a bacterial consortium, PGC-3, with de-epoxydation activity was isolated from soil by an in situ soil enrichment method. Screening of 14 soil samples that were sprayed with DON revealed that 4 samples were able to biotransform DON into de-epoxydized DON (dE-DON). Among these, the PGC-3 consortium showed the highest and most stable activity to biotransform DON into dE-DON and NIV into dE-NIV. PGC-3 exhibited de-epoxydation activity at a wide range of pH (5–10) and temperatures (20–37 °C) values under aerobic conditions. Sequential subculturing with a continued exposure to DON substantially reduced the microbial population diversity of this consortium. Analyses of the 16S rDNA sequences indicated that PGC-3 comprised 10 bacterial genera. Among these, one species, Desulfitobacterium, showed a steady increase in relative abundance, from 0.03% to 1.55% (a 52-fold increase), as higher concentrations of DON were used in the subculture media, from 0 to 500 μg/mL. This study establishes the foundation to further develop bioactive agents that can detoxify trichothecene mycotoxins in cereals and enables for the characterization of detoxifying genes and their regulation. PMID:27669304

First evidence of mineralization of petroleum asphaltenes by a strain of Neosartorya fischeri

PubMed Central

Uribe‐Alvarez, Cristina; Ayala, Marcela; Perezgasga, Lucia; Naranjo, Leopoldo; Urbina, Héctor; Vazquez‐Duhalt, Rafael

2011-01-01

Summary A fungal strain isolated from a microbial consortium growing in a natural asphalt lake is able to grow in purified asphaltenes as the only source of carbon and energy. The asphaltenes were rigorously purified in order to avoid contamination from other petroleum fractions. In addition, most of petroporphyrins were removed. The 18S rRNA and β‐tubulin genomic sequences, as well as some morphologic characteristics, indicate that the isolate is Neosartorya fischeri. After 11 weeks of growth, the fungus is able to metabolize 15.5% of the asphaltenic carbon, including 13.2% transformed to CO2. In a medium containing asphaltenes as the sole source of carbon and energy, the fungal isolate produces extracellular laccase activity, which is not detected when the fungus grow in a rich medium. The results obtained in this work clearly demonstrate that there are microorganisms able to metabolize and mineralize asphaltenes, which is considered the most recalcitrant petroleum fraction. PMID:21624102

Screening For Alcohol-Producing Microbes

NASA Technical Reports Server (NTRS)

Schubert, Wayne W.

1988-01-01

Dye reaction rapidly identifies alcohol-producing microbial colonies. Method visually detects alcohol-producing micro-organisms, and distinguishes them from other microbial colonies that do not produce alcohol. Method useful for screening mixed microbial populations in environmental samples.

Microbially Enhanced Oil Recovery by Sequential Injection of Light Hydrocarbon and Nitrate in Low- And High-Pressure Bioreactors.

PubMed

Gassara, Fatma; Suri, Navreet; Stanislav, Paul; Voordouw, Gerrit

2015-10-20

Microbially enhanced oil recovery (MEOR) often involves injection of aqueous molasses and nitrate to stimulate resident or introduced bacteria. Use of light oil components like toluene, as electron donor for nitrate-reducing bacteria (NRB), offers advantages but at 1-2 mM toluene is limiting in many heavy oils. Because addition of toluene to the oil increased reduction of nitrate by NRB, we propose an MEOR technology, in which water amended with light hydrocarbon below the solubility limit (5.6 mM for toluene) is injected to improve the nitrate reduction capacity of the oil along the water flow path, followed by injection of nitrate, other nutrients (e.g., phosphate) and a consortium of NRB, if necessary. Hydrocarbon- and nitrate-mediated MEOR was tested in low- and high-pressure, water-wet sandpack bioreactors with 0.5 pore volumes of residual oil in place (ROIP). Compared to control bioreactors, those with 11-12 mM of toluene in the oil (gained by direct addition or by aqueous injection) and 80 mM of nitrate in the aqueous phase produced 16.5 ± 4.4% of additional ROIP (N = 10). Because toluene is a cheap commodity chemical, HN-MEOR has the potential to be a cost-effective method for additional oil production even in the current low oil price environment.

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

PubMed

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

2011-02-28

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

Anaerobic treatment of palm oil mill effluent in batch reactor with digested biodiesel waste as starter and natural zeolite for microbial immobilization

NASA Astrophysics Data System (ADS)

Setyowati, Paulina Adina Hari; Halim, Lenny; Mellyanawaty, Melly; Sudibyo, Hanifrahmawan; Budhijanto, Wiratni

2017-05-01

Palm oil mill effluent (POME) is the wastewater discharged from sludge separation, sterilization, and clarification process of palm oil industries. Each ton of palm oil produces about half ton of high organic load wastewater. Up to now, POME treatment is done in lagoon, leaving major problems in land requirement and greenhouse gasses release. The increasing of palm oil production provokes the urgency of appropriate technology application in treating POME to prevent the greenhouse gasses emission while exploit POME as renewable energy source. The purposes of this study were firstly to test the effectiveness of using the digested biodiesel waste as the inoculum and secondly to evaluate the effectiveness of natural zeolite addition in minimizing the inhibitory effect in digesting POME. It was expected that the oil-degrading bacteria in the inoculum would shorten the adaptation period in digesting POME. Furthermore, the consortium formation of anaerobic bacteria accelerated by natural zeolite powder addition would increase the microbial resistance to the inhibitors contained in the POME. The batch digesters, containing 0 (control); 17; 38; and 63 g natural zeolite/g sCOD substrate were observed for 43 days. The result showed that zeolite addition did not give significant effect on sCOD reduction (97.3-98.6% of initial sCOD). Moreover, addition of immobilization media up to 17 g natural zeolite/g stimulated the acidification and biogas production up to 10% higher than control. The purity of methane produced with various amount of immobilization media did not differ for each variation, i.e. 50-54% v/v methane. The increasing amount of natural zeolite up to 63 g/g sCOD did not significantly enhance biogas product rate nor methane content.

Biofilm comprising phototrophic, diazotrophic, and hydrocarbon-utilizing bacteria: a promising consortium in the bioremediation of aquatic hydrocarbon pollutants.

PubMed

Al-Bader, Dhia; Kansour, Mayada K; Rayan, Rehab; Radwan, Samir S

2013-05-01

Biofilms harboring simultaneously anoxygenic and oxygenic phototrophic bacteria, diazotrophic bacteria, and hydrocarbon-utilizing bacteria were established on glass slides suspended in pristine and oily seawater. Via denaturing gradient gel electrophoresis analysis on PCR-amplified rRNA gene sequence fragments from the extracted DNA from biofilms, followed by band amplification, biofilm composition was determined. The biofilms contained anoxygenic phototrophs belonging to alphaproteobacteria; pico- and filamentous cyanobacteria (oxygenic phototrophs); two species of the diazotroph Azospirillum; and two hydrocarbon-utilizing gammaproteobacterial genera, Cycloclasticus and Oleibacter. The coexistence of all these microbial taxa with different physiologies in the biofilm makes the whole community nutritionally self-sufficient and adequately aerated, a condition quite suitable for the microbial biodegradation of aquatic pollutant hydrocarbons.

Changes in bacterial community of anthracene bioremediation in municipal solid waste composting soil*

PubMed Central

Zhang, Shu-ying; Wang, Qing-feng; Wan, Rui; Xie, Shu-guang

2011-01-01

Polycyclic aromatic hydrocarbons (PAHs) are common contaminants in a municipal solid waste (MSW) composting site. Knowledge of changes in microbial structure is useful to identify particular PAH degraders. However, the microbial community in the MSW composting soil and its change associated with prolonged exposure to PAHs and subsequent biodegradation remain largely unknown. In this study, anthracene was selected as a model compound. The bacterial community structure was investigated using terminal restriction fragment length polymorphism (TRFLP) and 16S rRNA gene clone library analysis. The two bimolecular tools revealed a large shift of bacterial community structure after anthracene amendment and subsequent biodegradation. Genera Methylophilus, Mesorhizobium, and Terrimonas had potential links to anthracene biodegradation, suggesting a consortium playing an active role. PMID:21887852

Microbial Fuel Cell Transformation of Recalcitrant Organic Compounds in Support of Biosensor Research

DTIC Science & Technology

2014-03-27

simulant similar in structure to sarin (Obee and Satyapal, 1998). Literature on the biodegradation of DMMP is limited. In 2005, the DMMP Consortium...undergoes fermentation to acetate and hydrogen. Other 9 substrates, such as such sugars, may ferment to ethanol first. Current production occurs from...the ARB utilization of the fermentation product acetate, but electrons are lost in the form of hydrogen to methanogenesis. Therefore, the current

The role of acetogens in microbially influenced corrosion of steel

PubMed Central

Mand, Jaspreet; Park, Hyung Soo; Jack, Thomas R.; Voordouw, Gerrit

2014-01-01

Microbially influenced corrosion (MIC) of iron (Fe0) by sulfate-reducing bacteria (SRB) has been studied extensively. Through a mechanism, that is still poorly understood, electrons or hydrogen (H2) molecules are removed from the metal surface and used as electron donor for sulfate reduction. The resulting ferrous ions precipitate in part with the sulfide produced, forming characteristic black iron sulfide. Hydrogenotrophic methanogens can also contribute to MIC. Incubation of pipeline water samples, containing bicarbonate and some sulfate, in serum bottles with steel coupons and a headspace of 10% (vol/vol) CO2 and 90% N2, indicated formation of acetate and methane. Incubation of these samples in serum bottles, containing medium with coupons and bicarbonate but no sulfate, also indicated that formation of acetate preceded the formation of methane. Microbial community analyses of these enrichments indicated the presence of Acetobacterium, as well as of hydrogenotrophic and acetotrophic methanogens. The formation of acetate by homoacetogens, such as Acetobacterium woodii from H2 (or Fe0) and CO2, is potentially important, because acetate is a required carbon source for many SRB growing with H2 and sulfate. A consortium of the SRB Desulfovibrio vulgaris Hildenborough and A. woodii was able to grow in defined medium with H2, CO2, and sulfate, because A. woodii provides the acetate, needed by D. vulgaris under these conditions. Likewise, general corrosion rates of metal coupons incubated with D. vulgaris in the presence of acetate or in the presence of A. woodii were higher than in the absence of acetate or A. woodii, respectively. An extended MIC model capturing these results is presented. PMID:24917861

Impacts of sewer deposits on the urban river sediment after rainy season and bioremediation of polluted sediment.

PubMed

Chang, Suyun; Tang, Yinqi; Dong, Lixin; Zhan, Qiang; Xu, Wei

2018-05-01

Impacts of deposits discharged from a municipal pipe on urban river sediment were investigated in the Hucang River in Tianjin, China. At the outlet of the pump station, the average concentrations of total nitrogen (TN), total phosphorus (TP), and total organic carbon (TOC) in the sediment increased sharply from 2390, 799, and 14,600 mg/kg to 6500, 3700, and 153,000 mg/kg, respectively, and remained stable at high level after the rainy season. A portion of pollutants would migrate along the river, and the concentration was usually in a negative relationship with the distance. The average Shannon-Wiener value on the upstream section was higher than those on the downstream sections. This revealed that the deposits discharged decreased the bacterial diversity in the sediment, and high concentrations of pollutants may markedly change the bacterial community structure in the sediment. To reduce the pollution of the urban river after rainy season, four kinds of microbial consortiums A (Zhangda), B (Aiersi), C (Qinghe), and D (Inpipe) were applied to bioremediate the polluted sediment in lab scale. Bioaugmentation with microbial consortium A showed good performance on the bioremediation of the polluted sediment. The average removal efficiency of TN, TP, and organic matter reached 35.5, 43.7, and 39.1%, respectively, after 22 days of treatment. Moreover, the bacterial evenness and diversity in the sediment markedly increased, indicating that the microbial environment was more favourable after bioaugmentation and sustainable development would be guaranteed. This study improves our understanding of the impacts of deposits discharged from a stormwater drain system on urban river sediment, and explores the effectiveness of bioaugmentation for the bioremediation of polluted sediment, which will provide the basis of sewer deposit pollution control.

Characterization of a Highly Enriched Microbial Consortium Reductively Dechlorinating 2,3-Dichlorophenol and 2,4,6-Trichlorophenol and the Corresponding cprA Genes from River Sediment.

PubMed

El-Sayed, Wael S

2016-08-26

Anaerobic reductive dechlorination of 2,3-dichlorophenol (2,3DCP) and 2,4,6-trichlorophenol (2,4,6TCP) was investigated in microcosms from River Nile sediment. A stable sediment-free anaerobic microbial consortium reductively dechlorinating 2,3DCP and 2,4,6TCP was established. Defined sediment-free cultures showing stable dechlorination were restricted to ortho chlorine when enriched with hydrogen as the electron donor, acetate as the carbon source, and either 2,3-DCP or 2,4,6-TCP as electron acceptors. When acetate, formate, or pyruvate were used as electron donors, dechlorination activity was lost. Only lactate can replace dihydrogen as an electron donor. However, the dechlorination potential was decreased after successive transfers. To reveal chlororespiring species, the microbial community structure of chlorophenol-reductive dechlorinating enrichment cultures was analyzed by PCR-denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments. Eight dominant bacteria were detected in the dechlorinating microcosms including members of the genera Citrobacter, Geobacter, Pseudomonas, Desulfitobacterium, Desulfovibrio and Clostridium. Highly enriched dechlorinating cultures were dominated by four bacterial species belonging to the genera Pseudomonas, Desulfitobacterium, and Clostridium. Desulfitobacterium represented the major fraction in DGGE profiles indicating its importance in dechlorination activity, which was further confirmed by its absence resulting in complete loss of dechlorination. Reductive dechlorination was confirmed by the stoichiometric dechlorination of 2,3DCP and 2,4,6TCP to metabolites with less chloride groups and by the detection of chlorophenol RD cprA gene fragments in dechlorinating cultures. PCR amplified cprA gene fragments were cloned and sequenced and found to cluster with the cprA/pceA type genes of Dehalobacter restrictus.

Enhanced degradation of isoproturon in an agricultural soil by a Sphingomonas sp. strain and a microbial consortium.

PubMed

Li, Renyi; Dörfler, Ulrike; Munch, Jean Charles; Schroll, Reiner

2017-02-01

Isoproturon (IPU) degradation in an agricultural soil inoculated with an isolated IPU-degrader strain (Sphingomonas sp. strain AK1, IS) or a microbial consortium (MC) harboring this strain, with or without carrier material, were investigated in soil microcosm experiments during 46 days. Effect of the carrier material and inoculation size on IPU-degradation efficacy of the inoculants were studied. Mineralization, extractable residues and non-extractable residues of 14 C-labeled IPU were analyzed. The low IPU mineralization in untreated soil (7.0%) was enhanced to different extents by inoculation of IS (17.4%-46.0%) or MC (58.9%-67.5%). Concentrations of IPU residues in soils amended with MC (0.002-0.095 μg g dry soil -1 ) were significantly lower than in soils amended with IS (0.02-0.67 μg g dry soil -1 ) and approximately 10 times lower than in the uninoculated soil (0.06-0.80 μg g dry soil -1 ). Less extractable residues and non-extractable residues were detected in soil with higher IPU mineralization. Inoculation size (as indicated by the volume of liquid cultures or by the number of carrier particles) determined the IPU-removal efficacy of IS in soil, but this effect was less pronounced for MC. The low sorption of IPU to soil and the decreasing IPU-mineralizing rates suggested incapability of IS to establish the IPU-mineralizing function in the soil. The thorough removal of IPU and persistent IPU-mineralizing activity of soil inoculated with MC indicated a high persistence of IPU-metabolic trait. Our results showed that microbial consortia might be more efficient than single degrader strains to enhance clean-up of organic chemicals in soil. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

PubMed

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

2017-08-01

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

Effect of inoculation with white-rot fungi and fungal consortium on the composting efficiency of municipal solid waste.

PubMed

Voběrková, Stanislava; Vaverková, Magdalena D; Burešová, Alena; Adamcová, Dana; Vršanská, Martina; Kynický, Jindřich; Brtnický, Martin; Adam, Vojtěch

2017-03-01

An investigation was carried out on the effect of inoculation methods on the compost of an organic fraction of municipal solid waste. Three types of white-rot fungi (Phanerochaete chrysosporium, Trametes versicolor and Fomes fomentarius), and a consortium of these fungi, were used. The study assessed their influence on microbial enzymatic activities and the quality of the finished compost. It was found that the addition of white-rot fungi to municipal solid waste (after 37days of composting) could be a useful strategy for enhancing the properties of the final compost product. In comparison with the control sample (compost without inoculation), it accelerates degradation of solid waste as indicated by changes in C/N, electrical conductivity and pH. However, the effectiveness of waste degradation and compost maturation depends on the type of microorganism used for inoculation. The presence of inoculants, such as Trametes versicolor and Fomes fomentarius, led to a higher degrading ratio and a better degree of maturity. This resulted in an increase of enzymatic activities (especially dehydrogenase and protease) and a germination index in comparison with inoculation using Phanerochaete chrysosporium or a consortium of fungi. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evaluating robustness of a diesel-degrading bacterial consortium isolated from contaminated soil.

PubMed

Sydow, Mateusz; Owsianiak, Mikołaj; Szczepaniak, Zuzanna; Framski, Grzegorz; Smets, Barth F; Ławniczak, Łukasz; Lisiecki, Piotr; Szulc, Alicja; Cyplik, Paweł; Chrzanowski, Łukasz

2016-12-25

It is not known whether diesel-degrading bacterial communities are structurally and functionally robust when exposed to different hydrocarbon types. Here, we exposed a diesel-degrading consortium to model either alkanes, cycloalkanes or aromatic hydrocarbons as carbon sources to study its structural resistance. The structural resistance was low, with changes in relative abundances of up to four orders of magnitude, depending on hydrocarbon type and bacterial taxon. This low resistance is explained by the presence of hydrocarbon-degrading specialists in the consortium and differences in growth kinetics on individual hydrocarbons. However, despite this low resistance, structural and functional resilience were high, as verified by re-exposing the hydrocarbon-perturbed consortium to diesel fuel. The high resilience is either due to the short exposure time, insufficient for permanent changes in consortium structure and function, or the ability of some consortium members to be maintained during exposure on degradation intermediates produced by other members. Thus, the consortium is expected to cope with short-term exposures to narrow carbon feeds, while maintaining its structural and functional integrity, which remains an advantage over biodegradation approaches using single species cultures. Copyright © 2016 Elsevier B.V. All rights reserved.

Review of the cultivation program within the National Alliance for Advanced Biofuels and Bioproducts

DOE PAGES

Lammers, Peter J.; Huesemann, Michael; Boeing, Wiebke; ...

2016-12-12

The cultivation efforts within the National Alliance for Advanced Biofuels and Bioproducts (NAABB) were developed to provide four major goals for the consortium, which included biomass production for downstream experimentation, development of new assessment tools for cultivation, development of new cultivation reactor technologies, and development of methods for robust cultivation. The NAABB consortium testbeds produced over 1500 kg of biomass for downstream processing. The biomass production included a number of model production strains, but also took into production some of the more promising strains found through the prospecting efforts of the consortium. Cultivation efforts at large scale are intensive andmore » costly, therefore the consortium developed tools and models to assess the productivity of strains under various environmental conditions, at lab scale, and validated these against scaled outdoor production systems. Two new pond-based bioreactor designs were tested for their ability to minimize energy consumption while maintaining, and even exceeding, the productivity of algae cultivation compared to traditional systems. Also, molecular markers were developed for quality control and to facilitate detection of bacterial communities associated with cultivated algal species, including the Chlorella spp. pathogen, Vampirovibrio chlorellavorus, which was identified in at least two test site locations in Arizona and New Mexico. Finally, the consortium worked on understanding methods to utilize compromised municipal wastewater streams for cultivation. In conclusion, this review provides an overview of the cultivation methods and tools developed by the NAABB consortium to produce algae biomass, in robust low energy systems, for biofuel production.« less

Exploring the Bacterial Microbiota of Colombian Fermented Maize Dough "Masa Agria" (Maiz Añejo).

PubMed

Chaves-Lopez, Clemencia; Serio, Annalisa; Delgado-Ospina, Johannes; Rossi, Chiara; Grande-Tovar, Carlos D; Paparella, Antonello

2016-01-01

Masa Agria is a naturally fermented maize dough produced in Colombia, very common in the traditional gastronomy. In this study we used culture-dependent and RNA-based pyrosequencing to investigate the bacterial community structure of Masa Agria samples produced in the south west of Colombia. The mean value of cell density was 7.6 log CFU/g of presumptive lactic acid bacteria, 5.4 log cfu/g for presumptive acetic bacteria and 5.6 og CFU/g for yeasts. The abundance of these microorganisms is also responsible for the low pH (3.1-3.7) registered. Although the 16S rRNA pyrosequencing revealed that the analyzed samples were different in bacteria richness and diversity, the genera Lactobacillus, Weissella, and Acetobacter were predominant. In particular, the most common species were Lactobacillus plantarum and Acetobacter fabarum, followed by L. fermentum, L. vaccinostercus, and Pediococcus argentinicus. Several microorganisms of environmental origin, such as Dechloromonas and most of all Sphingobium spp., revealed in each sample, were detected, and also bacteria related to maize, such as Phytoplasma. In conclusion, our results elucidated for the first time the structures of the bacterial communities of Masa Agria samples obtained from different producers, identifying the specific dominant species and revealing a complete picture of the bacterial consortium in this specific niche. The selective pressure of tropical environments may favor microbial biodiversity characterized by a useful technological potential.

A novel production process for optically pure L-lactic acid from kitchen refuse using a bacterial consortium at high temperatures.

PubMed

Tashiro, Yukihiro; Matsumoto, Hiroko; Miyamoto, Hirokuni; Okugawa, Yuki; Pramod, Poudel; Miyamoto, Hisashi; Sakai, Kenji

2013-10-01

We investigated L-lactic acid production in static batch fermentation of kitchen refuse using a bacterial consortium from marine-animal-resource (MAR) composts at temperatures ranging from 30 to 65 °C. At relatively low temperatures butyric acid accumulated, whereas at higher temperatures L-lactic acid was produced. In particular, fermentation at 50 °C produced 34.5 g L(-1) L-lactic acid with 90% lactic acid selectivity and 100% optical purity. Denaturing gradient gel electrophoresis indicated that dominant bacteria present in the original MAR composts diminished rapidly and Bacillus coagulans strains became the dominant contributors to L-lactic acid production at 45, 50 and 55 °C. This is the first report of the achievement of 100% optical purity of L-lactic acid using a bacterial consortium. Copyright © 2013 Elsevier Ltd. All rights reserved.

MICROBIAL FERMENTATION OF ABUNDANT BIOPOLYMERS: CELLULOSE AND CHITIN

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

Leschine, Susan

Our research has dealt with seven major areas of investigation: i) characterization of cellulolytic members of microbial consortia, with special attention recently given to Clostridium phytofermentans, a bacterium that decomposes cellulose and produces uncommonly large amounts of ethanol, ii) investigations of the chitinase system of Cellulomonas uda; including the purification and characterization of ChiA, the major component of this enzyme system, iii) molecular cloning, sequence and structural analysis of the gene that encodes ChiA in C. uda, iv) biofilm formation by C. uda on nutritive surfaces, v) investigations of the effects of humic substances on cellulose degradation by anaerobic cellulolyticmore » microbes, vi) studies of nitrogen metabolism in cellulolytic anaerobes, and vii) understanding the molecular architecture of the multicomplex cellulase-xylanase system of Clostridium papyrosolvens. Also, progress toward completing the research of more recent projects is briefly summarized. Major accomplishments include: 1. Characterization of Clostridium phytofermentans, a cellulose-fermenting, ethanol-producing bacterium from forest soil. The characterization of a new cellulolytic species isolated from a cellulose-decomposing microbial consortium from forest soil was completed. This bacterium is remarkable for the high concentrations of ethanol produced during cellulose fermentation, typically more than twice the concentration produced by other species of cellulolytic clostridia. 2. Examination of the use of chitin as a source of carbon and nitrogen by cellulolytic microbes. We discovered that many cellulolytic anaerobes and facultative aerobes are able to use chitin as a source of both carbon and nitrogen. This major discovery expands our understanding of the biology of cellulose-fermenting bacteria and may lead to new applications for these microbes. 3. Comparative studies of the cellulase and chitinase systems of Cellulomonas uda. Results of these studies indicate that the chitinase and cellulase systems of this bacterium are distinct in terms of the proteins involved and the regulation of their production. 4. Characterization of the chitinase system of C. uda. A 70,000-Mr endochitinase, designated ChiA, was purified from C. uda culture supernatant fluids and characterized. 5. Analysis of chiA, which codes for the major enzymatic component of the chitinase system of C. uda. The gene encoding the endochitinase ChiA in C. uda was cloned, its complete nucleotide sequence was determined and its implications were investigated. 6. Formation of biofilms by C. uda on cellulose and chitin. Microscopic observations indicated that, under conditions of nitrogen limitation, C. uda cells grew as a biofilm attached tightly to the surface of cellulose or chitin. 7. Development of tools for a genetic approach to studies of cellulose fermentation by cellulolytic clostridia. We have explored the potential of various techniques, and obtained evidence indicating that Tn916 mutagenesis may be particularly effective in this regard. As part of this research, we identified the presence of a plasmid in one strain, which was cloned, sequenced, and analyzed for its utility in the development of vectors for genetic studies. 8. Effects of humic substances on cellulose degradation by anaerobic cellulolytic microbes. We determined that humic substances play an important role in the anaerobic cellulose decomposition and in the physiology of cellulose-fermenting soil bacteria. 9. Nitrogenases of cellulolytic clostridia. We described a nitrogenase gene from a cellulolytic clostridium and presented evidence, based on sequence analyses and conserved gene order, for lateral gene transfer between this bacterium and a methanogenic archaeon. 10. Characterization of Clostridium hungatei, a new N2-fixing cellulolytic species isolated from a methanogenic consortium from soil. 11. Understanding the molecular architecture of the multicomplex cellulase-xylanase system of Clostridium papyrosolvens. We discovered that C. papyrosolvens produces a multiprotein, multicomplex cellulase-xylanase enzyme system that hydrolyzes crystalline cellulose, and we have described this system in detail.« less

Symbiosis insights through metagenomic analysis of a microbial consortium.

PubMed

Woyke, Tanja; Teeling, Hanno; Ivanova, Natalia N; Huntemann, Marcel; Richter, Michael; Gloeckner, Frank Oliver; Boffelli, Dario; Anderson, Iain J; Barry, Kerrie W; Shapiro, Harris J; Szeto, Ernest; Kyrpides, Nikos C; Mussmann, Marc; Amann, Rudolf; Bergin, Claudia; Ruehland, Caroline; Rubin, Edward M; Dubilier, Nicole

2006-10-26

Symbioses between bacteria and eukaryotes are ubiquitous, yet our understanding of the interactions driving these associations is hampered by our inability to cultivate most host-associated microbes. Here we use a metagenomic approach to describe four co-occurring symbionts from the marine oligochaete Olavius algarvensis, a worm lacking a mouth, gut and nephridia. Shotgun sequencing and metabolic pathway reconstruction revealed that the symbionts are sulphur-oxidizing and sulphate-reducing bacteria, all of which are capable of carbon fixation, thus providing the host with multiple sources of nutrition. Molecular evidence for the uptake and recycling of worm waste products by the symbionts suggests how the worm could eliminate its excretory system, an adaptation unique among annelid worms. We propose a model that describes how the versatile metabolism within this symbiotic consortium provides the host with an optimal energy supply as it shuttles between the upper oxic and lower anoxic coastal sediments that it inhabits.

Functional consortium for denitrifying sulfide removal process.

PubMed

Chen, Chuan; Ren, Nanqi; Wang, Aijie; Liu, Lihong; Lee, Duu-Jong

2010-03-01

Denitrifying sulfide removal (DSR) process simultaneously converts sulfide, nitrate, and chemical oxygen demand from industrial wastewaters to elemental sulfur, nitrogen gas, and carbon dioxide, respectively. This investigation utilizes a dilution-to-extinction approach at 10(-2) to 10(-6) dilutions to elucidate the correlation between the composition of the microbial community and the DSR performance. In the original suspension and in 10(-2) dilution, the strains Stenotrophomonas sp., Thauera sp., and Azoarcus sp. are the heterotrophic denitrifiers and the strains Paracoccus sp. and Pseudomonas sp. are the sulfide-oxidizing denitrifers. The 10(-4) dilution is identified as the functional consortium for the present DSR system, which comprises two functional strains, Stenotrophomonas sp. strain Paracoccus sp. At 10(-6) dilution, all DSR performance was lost. The functions of the constituent cells in the DSR granules were discussed based on data obtained using the dilution-to-extinction approach.

Carrier mounted bacterial consortium facilitates oil remediation in the marine environment.

PubMed

Simons, Keryn L; Sheppard, Petra J; Adetutu, Eric M; Kadali, Krishna; Juhasz, Albert L; Manefield, Mike; Sarma, Priyangshu M; Lal, Banwari; Ball, Andrew S

2013-04-01

Marine oil pollution can result in the persistent presence of weathered oil. Currently, removal of weathered oil is reliant on chemical dispersants and physical removal, causing further disruption. In contrast few studies have examined the potential of an environmentally sustainable method using a hydrocarbon degrading microbial community attached to a carrier. Here, we used a tank mesocosm system (50 l) to follow the degradation of weathered oil (10 g l(-1)) using a bacterial consortium mobilised onto different carrier materials (alginate or shell grit). GCMS analysis demonstrated that the extent of hydrocarbon degradation was dependent upon the carrier material. Augmentation of shell grit with nutrients and exogenous hydrocarbon degraders resulted in 75±14% removal of >C32 hydrocarbons after 12 weeks compared to 20±14% for the alginate carrier. This study demonstrated the effectiveness of a biostimulated and bioaugmented carrier material to degrade marine weathered oil. Copyright © 2013 Elsevier Ltd. All rights reserved.

Application of a bacterial extracellular polymeric substance in heavy metal adsorption in a co-contaminated aqueous system

PubMed Central

de Oliveira Martins, Paula Salles; de Almeida, Narcisa Furtado; Leite, Selma Gomes Ferreira

2008-01-01

The application of a bacterial extracellular polymeric substance (EPS) in the bioremediation of heavy metals (Cd, Zn and Cu) by a microbial consortium in a hydrocarbon co-contaminated aqueous system was studied. At the low concentrations used in this work (1.00 ppm of each metal), it was not observed an inhibitory effect on the cellular growing. In the other hand, the application of the EPS lead to a lower concentration of the free heavy metals in solution, once a great part of them is adsorbed in the polymeric matrix (87.12% of Cd; 19.82% of Zn; and 37.64% of Cu), when compared to what is adsorbed or internalized by biomass (5.35% of Cd; 47.35% of Zn; and 24.93% of Cu). It was noted an increase of 24% in the consumption of ethylbenzene, among the gasoline components that were quantified, in the small interval of time evaluated (30 hours). Our results suggest that, if the experiments were conducted in a larger interval of time, it would possibly be noted a higher effect in the degradation of gasoline compounds. Still, considering the low concentrations that were evaluated, it is possible that a real system could be bioremediated by natural attenuation process, demonstrated by the low effect of those levels of contaminants and co-contaminants over the naturally present microbial consortium. PMID:24031307

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

PubMed

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.

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

NASA Technical Reports Server (NTRS)

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

2002-01-01

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

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

PubMed Central

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

2002-01-01

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

Metagenomic insight of nitrogen metabolism in a tannery wastewater treatment plant bioaugmented with the microbial consortium BM-S-1.

PubMed

Sul, Woo-Jun; Kim, In-Soo; Ekpeghere, Kalu I; Song, Bongkeun; Kim, Bong-Soo; Kim, Hong-Gi; Kim, Jong-Tae; Koh, Sung-Cheol

2016-11-09

Nitrogen (N) removal in a tannery wastewater treatment plant was significantly enhanced by the bioaugmentation of the novel consortium BM-S-1. In order to identify dominant taxa responsible for N metabolisms in the different stages of the treatment process, Illumina MiSeq Sequencer was used to conduct metagenome sequencing of the microbial communities in the different stages of treatment system, including influent (I), buffering (B), primary aeration (PA), secondary aeration (SA) and sludge digestion (SD). Based on MG-RAST analysis, the dominant phyla were Proteobacteria, Bacteroidetes and Firmicutes in B, PA, SA and SD, whereas Firmicutes was the most dominant in I before augmentation. The augmentation increased the abundance of the denitrification genes found in the genera such as Ralstonia (nirS, norB and nosZ), Pseudomonas (narG, nirS and norB) and Escherichia (narG) in B and PA. In addition, Bacteroides, Geobacter, Porphyromonasand Wolinella carrying nrfA gene encoding dissimilatory nitrate reduction to ammonium were abundantly present in B and PA. This was corroborated with the higher total N removal in these two stages. Thus, metagenomic analysis was able to identify the dominant taxa responsible for dissimilatory N metabolisms in the tannery wastewater treatment system undergoing bioaugmentation. This metagenomic insight into the nitrogen metabolism will contribute to a successful monitoring and operation of the eco-friendly tannery wastewater treatment system.

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

PubMed

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

2015-11-01

The electrochemical activity of two seawater microbial consortia were investigated in three-electrode bioelectrochemical cells. Two seawater inocula - from the Sunshine Coast (SC) and Gold Coast (GC) shores of Australia - were enriched at +0.6 V vs. SHE using 12/12 h day/night cycles. After re-inoculation, the SC consortium developed a fully-reversible cathodic/anodic current, with a max. of -62 mA m(-2) during the day and +110 mA m(-2) at night, while the GC exhibited negligible daytime output but +98 mA m(-2) at night. Community analysis revealed that both enrichments were dominated by cyanobacteria, indicating their potential as biocatalysts for indirect light conversion to electricity. Moreover, the presence of γ-proteobacterium Congregibacter in SC biofilm was likely related to the cathodic reductive current, indicating its effectiveness at catalysing cathodic oxygen reduction at a surprisingly high potential. For the first time a correlation between a dual microbial community and fully reversible current is reported. Copyright © 2015 Elsevier Ltd. All rights reserved.

Impact of silver nanoparticles on benthic prokaryotes in heavy metal-contaminated estuarine sediments in a tropical environment.

PubMed

Antizar-Ladislao, B; Bhattacharya, B D; Ray Chaudhuri, S; Sarkar, S K

2015-10-15

Little knowledge is available about the potential impact of commercial silver nanoparticles (Ag-NPs) on estuarine microbial communities. The Hugli river estuary, India, is susceptible to heavy metals pollution through boat traffic, and there is the potential for Ag-NP exposure via effluent discharged from ongoing municipal and industrial activities located in close proximity. This study investigated the effects of commercial Ag-NPs on native microbial communities in estuarine sediments collected from five stations, using terminal restriction fragment length polymorphism (T-RFLP) technique. An increase in the number of bacteria in consortium in sediments was observed following exposure to Ag-NPs. In general microbial communities may be resistant in estuarine systems to the antimicrobial effects of commercial Ag-NPs, but key microorganisms, such as Pelobacter propionicus, disappeared following exposure to Ag-NPs. In conclusion, the T-RFLP analysis indicated that Ag-NPs have the potential to shape estuarine sediment bacterial community structure. Copyright © 2015 Elsevier Ltd. All rights reserved.

Identification of the potential of microbial combinations obtained from spent mushroom cultivation substrates for use in textile effluent decolorization.

PubMed

Singh, Rajender; Ahlawat, O P; Rajor, Anita

2012-12-01

The study presents variation in microbial population of Agaricus bisporus, Pleurotus sajor-caju and Volvariella volvacea spent substrates (SMS) along with ligninolytic enzymes activity and textile effluent decolorization potential of microorganisms isolated from these. The effect of temperature, pH, carbon sources and immobilizing agents on effluent decolorization using different combinations of these microorganisms has also been studied. SMS of P. sajor-caju harbored highest population and diversity of bacteria and fungi compared to other SMSs. Schizophyllum commune and Pezizomycotina sp. from P. sajor-caju SMS, exhibited highest activities of laccase (11.8 and 8.32U mL(-1)) and lignin peroxidase (339 and 318 UL(-1)), while Pseudomonas fluorescens of Manganese peroxidase. Highest decolorization was in presence of glucose and sucrose at 30°C, and microbial consortium comprised of the immobilized forms of S. commune and Pezizomycotina sp. on wheat straw and broth cultures of P. fluorescens, Bacillus licheniformis and Bacillus pumilus. Copyright © 2012 Elsevier Ltd. All rights reserved.

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

PubMed

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

2017-03-01

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

Microbial safety of fresh produce

USDA-ARS?s Scientific Manuscript database

The book entitled “Microbial Safety of Fresh Produce” with 23 chapters is divided into following six sections: Microbial contamination of fresh produce, Pre-harvest strategies, post-harvest interventions, Produce safety during processing and handling, Public, legal, and economic Perspectives, and Re...

The biogeochemical fate of nickel during microbial ISA degradation; implications for nuclear waste disposal.

PubMed

Kuippers, Gina; Boothman, Christopher; Bagshaw, Heath; Ward, Michael; Beard, Rebecca; Bryan, Nicholas; Lloyd, Jonathan R

2018-06-08

Intermediate level radioactive waste (ILW) generally contains a heterogeneous range of organic and inorganic materials, of which some are encapsulated in cement. Of particular concern are cellulosic waste items, which will chemically degrade under the conditions predicted during waste disposal, forming significant quantities of isosaccharinic acid (ISA), a strongly chelating ligand. ISA therefore has the potential to increase the mobility of a wide range of radionuclides via complex formation, including Ni-63 and Ni-59. Although ISA is known to be metabolized by anaerobic microorganisms, the biodegradation of metal-ISA complexes remains unexplored. This study investigates the fate of a Ni-ISA complex in Fe(III)-reducing enrichment cultures at neutral pH, representative of a microbial community in the subsurface. After initial sorption of Ni onto Fe(III)oxyhydroxides, microbial ISA biodegradation resulted in >90% removal of the remaining Ni from solution when present at 0.1 mM, whereas higher concentrations of Ni proved toxic. The microbial consortium associated with ISA degradation was dominated by close relatives to Clostridia and Geobacter species. Nickel was preferentially immobilized with trace amounts of biogenic amorphous iron sulfides. This study highlights the potential for microbial activity to help remove chelating agents and radionuclides from the groundwater in the subsurface geosphere surrounding a geodisposal facility.

Microbial Diversity Analysis of Fermented Mung Beans (Lu-Doh-Huang) by Using Pyrosequencing and Culture Methods

PubMed Central

Chao, Shiou-Huei; Huang, Hui-Yu; Chang, Chuan-Hsiung; Yang, Chih-Hsien; Cheng, Wei-Shen; Kang, Ya-Huei; Watanabe, Koichi; Tsai, Ying-Chieh

2013-01-01

In Taiwanese alternative medicine Lu-doh-huang (also called Pracparatum mungo), mung beans are mixed with various herbal medicines and undergo a 4-stage process of anaerobic fermentation. Here we used high-throughput sequencing of the 16S rRNA gene to profile the bacterial community structure of Lu-doh-huang samples. Pyrosequencing of samples obtained at 7 points during fermentation revealed 9 phyla, 264 genera, and 586 species of bacteria. While mung beans were inside bamboo sections (stages 1 and 2 of the fermentation process), family Lactobacillaceae and genus Lactobacillus emerged in highest abundance; Lactobacillus plantarum was broadly distributed among these samples. During stage 3, the bacterial distribution shifted to family Porphyromonadaceae, and Butyricimonas virosa became the predominant microbial component. Thereafter, bacterial counts decreased dramatically, and organisms were too few to be detected during stage 4. In addition, the microbial compositions of the liquids used for soaking bamboo sections were dramatically different: Exiguobacterium mexicanum predominated in the fermented soybean solution whereas B. virosa was predominant in running spring water. Furthermore, our results from pyrosequencing paralleled those we obtained by using the traditional culture method, which targets lactic acid bacteria. In conclusion, the microbial communities during Lu-doh-huang fermentation were markedly diverse, and pyrosequencing revealed a complete picture of the microbial consortium. PMID:23700436

Ecological Effect of Arginine on Oral Microbiota.

PubMed

Zheng, Xin; He, Jinzhi; Wang, Lin; Zhou, Shuangshuang; Peng, Xian; Huang, Shi; Zheng, Liwei; Cheng, Lei; Hao, Yuqing; Li, Jiyao; Xu, Jian; Xu, Xin; Zhou, Xuedong

2017-08-03

Dental caries is closely associated with the microbial dybiosis between acidogenic/aciduric pathogens and alkali-generating commensal bacteria colonized in the oral cavity. Our recent studies have shown that arginine may represent a promising anti-caries agent by modulating microbial composition in an in vitro consortium. However, the effect of arginine on the oral microbiota has yet to be comprehensively delineated in either clinical cohort or in vitro biofilm models that better represent the microbial diversity of oral cavity. Here, by employing a clinical cohort and a saliva-derived biofilm model, we demonstrated that arginine treatment could favorably modulate the oral microbiota of caries-active individuals. Specifically, treatment with arginine-containing dentifrice normalized the oral microbiota of caries-active individuals similar to that of caries-free controls in terms of microbial structure, abundance of typical species, enzymatic activities of glycolysis and alkali-generation related enzymes and their corresponding transcripts. Moreover, we found that combinatory use of arginine with fluoride could better enrich alkali-generating Streptococcus sanguinis and suppress acidogenic/aciduric Streptococcus mutans, and thus significantly retard the demineralizing capability of saliva-derived oral biofilm. Hence, we propose that fluoride and arginine have a potential synergistic effect in maintaining an eco-friendly oral microbial equilibrium in favor of better caries management.

NASA Systems Engineering Research Consortium: Defining the Path to Elegance in Systems

NASA Technical Reports Server (NTRS)

Watson, Michael D.; Farrington, Phillip A.

2016-01-01

The NASA Systems Engineering Research Consortium was formed at the end of 2010 to study the approaches to producing elegant systems on a consistent basis. This has been a transformative study looking at the engineering and organizational basis of systems engineering. The consortium has engaged in a variety of research topics to determine the path to elegant systems. In the second year of the consortium, a systems engineering framework emerged which structured the approach to systems engineering and guided our research. This led in the third year to set of systems engineering postulates that the consortium is continuing to refine. The consortium has conducted several research projects that have contributed significantly to the understanding of systems engineering. The consortium has surveyed the application of the NASA 17 systems engineering processes, explored the physics and statistics of systems integration, and considered organizational aspects of systems engineering discipline integration. The systems integration methods have included system exergy analysis, Akaike Information Criteria (AIC), State Variable Analysis, Multidisciplinary Coupling Analysis (MCA), Multidisciplinary Design Optimization (MDO), System Cost Modelling, System Robustness, and Value Modelling. Organizational studies have included the variability of processes in change evaluations, margin management within the organization, information theory of board structures, social categorization of unintended consequences, and initial looks at applying cognitive science to systems engineering. Consortium members have also studied the bidirectional influence of policy and law with systems engineering.

NASA Systems Engineering Research Consortium: Defining the Path to Elegance in Systems

NASA Technical Reports Server (NTRS)

Watson, Michael D.; Farrington, Phillip A.

2016-01-01

The NASA Systems Engineering Research Consortium was formed at the end of 2010 to study the approaches to producing elegant systems on a consistent basis. This has been a transformative study looking at the engineering and organizational basis of systems engineering. The consortium has engaged in a variety of research topics to determine the path to elegant systems. In the second year of the consortium, a systems engineering framework emerged which structured the approach to systems engineering and guided our research. This led in the third year to set of systems engineering postulates that the consortium is continuing to refine. The consortium has conducted several research projects that have contributed significantly to the understanding of systems engineering. The consortium has surveyed the application of the NASA 17 systems engineering processes, explored the physics and statistics of systems integration, and considered organizational aspects of systems engineering discipline integration. The systems integration methods have included system energy analysis, Akaike Information Criteria (AIC), State Variable Analysis, Multidisciplinary Coupling Analysis (MCA), Multidisciplinary Design Optimization (MDO), System Cost Modeling, System Robustness, and Value Modeling. Organizational studies have included the variability of processes in change evaluations, margin management within the organization, information theory of board structures, social categorization of unintended consequences, and initial looks at applying cognitive science to systems engineering. Consortium members have also studied the bidirectional influence of policy and law with systems engineering.

Evaluation of thermophilic fungal consortium for organic municipal solid waste composting.

PubMed

Awasthi, Mukesh Kumar; Pandey, Akhilesh Kumar; Khan, Jamaluddin; Bundela, Pushpendra Singh; Wong, Jonathan W C; Selvam, Ammaiyappan

2014-09-01

Influence of fungal consortium and different turning frequency on composting of organic fraction of municipal solid waste (OFMSW) was investigated to produce compost with higher agronomic value. Four piles of OFMSW were prepared: three piles were inoculated with fungal consortium containing 5l each spore suspensions of Trichoderma viride, Aspergillus niger and Aspergillus flavus and with a turning frequency of weekly (Pile 1), twice a week (Pile 2) and daily (Pile 3), while Pile 4 with weekly turning and without fungal inoculation served as control. The fungal consortium with weekly (Pile 1) turning frequency significantly affected temperature, pH, TOC, TKN, C/N ratio and germination index. High degradation of organic matter and early maturity was observed in Pile 1. Results indicate that fungal consortium with weekly turning frequency of open windrows were more cost-effective in comparison with other technologies for efficient composting and yield safe end products. Copyright © 2014 Elsevier Ltd. All rights reserved.

Impact of oil spills on coral reefs can be reduced by bioremediation using probiotic microbiota

PubMed Central

Fragoso ados Santos, Henrique; Duarte, Gustavo Adolpho Santos; Rachid, Caio TavoraCoelho da Costa; Chaloub, Ricardo Moreira; Calderon, Emiliano Nicolas; Marangoni, Laura Fernandes de Barros; Bianchini, Adalto; Nudi, Adriana Haddad; do Carmo, Flávia Lima; van Elsas, Jan Dirk; Rosado, Alexandre Soares; Castro, Clovis Barreira e; Peixoto, Raquel Silva

2015-01-01

Several anthropogenic factors, including contamination by oil spills, constitute a threat to coral reef health. Current methodologies to remediate polluted marine environments are based on the use of chemical dispersants; however, these can be toxic to the coral holobiont. In this study, a probiotic bacterial consortium was produced from the coral Mussismilia harttii and was trained to degrade water-soluble oil fractions (WSFs). Additionally, we assessed the effect of WSFs on the health of M. harttii in tanks and evaluated the bacterial consortium as a bioremediation agent. The consortium was responsible for the highly efficient degradation of petroleum hydrocarbons, and it minimised the effects of WSFs on coral health, as indicated by raised photosynthetic efficiencies. Moreover, the impact of WSFs on the coral microbiome was diminished by the introduced bacterial consortium. Following introduction, the bacterial consortium thus had a dual function, i.e promoting oil WSF degradation and improving coral health with its probiotic features. PMID:26658023

Impact of oil spills on coral reefs can be reduced by bioremediation using probiotic microbiota.

PubMed

Fragoso Ados Santos, Henrique; Duarte, Gustavo Adolpho Santos; Rachid, Caio TavoraCoelho da Costa; Chaloub, Ricardo Moreira; Calderon, Emiliano Nicolas; Marangoni, Laura Fernandes de Barros; Bianchini, Adalto; Nudi, Adriana Haddad; do Carmo, Flávia Lima; van Elsas, Jan Dirk; Rosado, Alexandre Soares; Castro, Clovis Barreira E; Peixoto, Raquel Silva

2015-12-14

Several anthropogenic factors, including contamination by oil spills, constitute a threat to coral reef health. Current methodologies to remediate polluted marine environments are based on the use of chemical dispersants; however, these can be toxic to the coral holobiont. In this study, a probiotic bacterial consortium was produced from the coral Mussismilia harttii and was trained to degrade water-soluble oil fractions (WSFs). Additionally, we assessed the effect of WSFs on the health of M. harttii in tanks and evaluated the bacterial consortium as a bioremediation agent. The consortium was responsible for the highly efficient degradation of petroleum hydrocarbons, and it minimised the effects of WSFs on coral health, as indicated by raised photosynthetic efficiencies. Moreover, the impact of WSFs on the coral microbiome was diminished by the introduced bacterial consortium. Following introduction, the bacterial consortium thus had a dual function, i.e promoting oil WSF degradation and improving coral health with its probiotic features.

Support of Gulf of Mexico Hydrate Research Consortium: Activities to Support Establishment of a Sea Floor Monitoring Station Project

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

Carol Lutken

The Gulf of Mexico Hydrates Research Consortium (GOM-HRC) was established in 1999 to assemble leaders in gas hydrates research. The Consortium is administered by the Center for Marine Resources and Environmental Technology, CMRET, at the University of Mississippi. The primary objective of the group is to design and emplace a remote monitoring station or sea floor observatory (MS/SFO) on the sea floor in the northern Gulf of Mexico by the year 2007, in an area where gas hydrates are known to be present at, or just below, the sea floor. This mission, although unavoidably delayed by hurricanes and other disturbances,more » necessitates assembling a station that will monitor physical and chemical parameters of the marine environment, including sea water and sea-floor sediments, on a more-or-less continuous basis over an extended period of time. In 2005, biological monitoring, as a means of assessing environmental health, was added to the mission of the MS/SFO. Establishment of the Consortium has succeeded in fulfilling the critical need to coordinate activities, avoid redundancies and communicate effectively among researchers in the arena of gas hydrates research. Complementary expertise, both scientific and technical, has been assembled to promote innovative research methods and construct necessary instrumentation. The observatory has now achieved a microbial dimension in addition to the geophysical, geological, and geochemical components it had already included. Initial components of the observatory, a probe that collects pore-fluid samples and another that records sea floor temperatures, were deployed in Mississippi Canyon 118 in May of 2005. Follow-up deployments, planned for fall 2005, had to be postponed due to the catastrophic effects of Hurricane Katrina (and later, Rita) on the Gulf Coast. Station/observatory completion, anticipated for 2007, will likely be delayed by at least one year. The CMRET has conducted several research cruises during this reporting period: one in April, one in June, one in September. April's effort was dedicated to surveying the mound at MC118 with the Surface-Source-Deep-Receiver (SSDR) seismic surveying system. This survey was completed in June and water column and bottom samples were collected via box coring. A microbial filtering system developed by Consortium participants at the University of Georgia was also deployed, run for {approx}12 hours and retrieved. The September cruise, designed to deploy, test, and in some cases recover, geochemical and microbial instruments and experiments took place aboard Harbor Branch's Seward Johnson and employed the Johnson SeaLink manned submersible. The seafloor monitoring station/observatory is funded approximately equally by three federal Agencies: Minerals Management Services (MMS) of the Department of the Interior (DOI), National Energy Technology Laboratory (NETL) of the Department of Energy (DOE), and the National Institute for Undersea Science and Technology (NIUST), an agency of the National Oceanographic and Atmospheric Administration (NOAA). Subcontractors with FY03 funding fulfilled their technical reporting requirements in a previously submitted report (41628R10). Only unresolved matching funds issues remain and will be addressed in the report of the University of Mississippi's Office of Research and Sponsored Programs. In addition, Barrodale Computing Services Ltd. (BCS) completed their work; their final report is the bulk of the semiannual report that precedes (abstract truncated)« less

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

PubMed

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

2015-05-19

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

Maple sap predominant microbial contaminants are correlated with the physicochemical and sensorial properties of maple syrup.

PubMed

Filteau, Marie; Lagacé, Luc; Lapointe, Gisèle; Roy, Denis

2012-03-01

Maple sap processing and microbial contamination are significant aspects that affect maple syrup quality. In this study, two sample sets from 2005 and 2008 were used to assess the maple syrup quality variation and its relationship to microbial populations, with respect to processing, production site and harvesting period. The abundance of maple sap predominant bacteria (Pseudomonas fluorescens group and two subgroups, Rahnella spp., Janthinobacterium spp., Leuconostoc mesenteroides) and yeast (Mrakia spp., Mrakiella spp.,Guehomyces pullulans) was assessed by quantitative PCR. Maple syrup properties were analyzed by physicochemical and sensorial methods. Results indicate that P. fluorescens, Mrakia spp., Mrakiella spp. G. pullulans and Rahnella spp. are stable contaminants of maple sap, as they were found for every production site throughout the flow period. Multiple factor analysis reports a link between the relative abundance of P. fluorescens group and Mrakia spp. in maple sap with maple and vanilla odor as well as flavor of maple syrup. This evidence supports the contribution of these microorganisms or a consortium of predominant microbial contaminants to the characteristic properties of maple syrup. Copyright © 2011 Elsevier B.V. All rights reserved.

Conceptualizing a Genomics Software Institute (GSI)

PubMed Central

Gilbert, Jack A.; Catlett, Charlie; Desai, Narayan; Knight, Rob; White, Owen; Robbins, Robert; Sankaran, Rajesh; Sansone, Susanna-Assunta; Field, Dawn; Meyer, Folker

2012-01-01

Microbial ecology has been enhanced greatly by the ongoing ‘omics revolution, bringing half the world's biomass and most of its biodiversity into analytical view for the first time; indeed, it feels almost like the invention of the microscope and the discovery of the new world at the same time. With major microbial ecology research efforts accumulating prodigious quantities of sequence, protein, and metabolite data, we are now poised to address environmental microbial research at macro scales, and to begin to characterize and understand the dimensions of microbial biodiversity on the planet. What is currently impeding progress is the need for a framework within which the research community can develop, exchange and discuss predictive ecosystem models that describe the biodiversity and functional interactions. Such a framework must encompass data and metadata transparency and interoperation; data and results validation, curation, and search; application programming interfaces for modeling and analysis tools; and human and technical processes and services necessary to ensure broad adoption. Here we discuss the need for focused community interaction to augment and deepen established community efforts, beginning with the Genomic Standards Consortium (GSC), to create a science-driven strategic plan for a Genomic Software Institute (GSI). PMID:22675605

The microbial community of a biofilm contact reactor for the treatment of winery wastewater.

PubMed

de Beer, D M; Botes, M; Cloete, T E

2018-02-01

To utilize a three-tiered approach to provide insight into the microbial community structure, the spatial distribution and the metabolic capabilities of organisms of a biofilm in the two towers of a high-rate biological contact reactor treating winery wastewater. Next-generation sequencing indicated that bacteria primarily responsible for the removal of carbohydrates, sugars and alcohol were more abundant in tower 1 than tower 2 while nitrifying and denitrifying bacteria were more abundant in tower 2. Yeast populations differed in each tower. Fluorescent in situ hybridization coupled with confocal microscopy showed distribution of organisms confirming an oxygen gradient across the biofilm depth. The Biolog system (ECO plates) specified the different carbon-metabolizing profiles of the two biofilms. The three-tiered approach confirmed that the addition of a second subunit to the bioreactor, expanded the treatment capacity by augmenting the microbial and metabolic diversity of the system, improving the treatment scope of the system. A three-tiered biofilm analysis provided data required to optimize the design of a bioreactor to provide favourable conditions for the development of a microbial consortium, which has optimal waste removal properties for the treatment requirements at hand. © 2017 The Society for Applied Microbiology.

Effect of multiwalled carbon nanotubes on UASB microbial consortium.

PubMed

Yadav, Tushar; Mungray, Alka A; Mungray, Arvind K

2016-03-01

The continuous rise in production and applications of carbon nanotubes (CNTs) has grown a concern about their fate and toxicity in the environment. After use, these nanomaterials pass through sewage and accumulate in wastewater treatment plants. Since, such plants rely on biological degradation of wastes; their activity may decrease due to the presence of CNTs. This study investigated the effect of multiwalled carbon nanotubes (MWCNTs) on upflow anaerobic sludge blanket (UASB) microbial activity. The toxic effect on microbial viability, extracellular polymeric substances (EPS), volatile fatty acids (VFA), and biogas generation was determined. The reduction in a colony-forming unit (CFU) was 29 and 58 % in 1 and 100 mg/L test samples, respectively, as compared to control. The volatile fatty acids and biogas production was also found reduced. The scanning electron microscopy (SEM) and fluorescent microscopy images confirmed that the MWCNT mediated microbial cell damage. This damage caused the increase in EPS carbohydrate, protein, and DNA concentration. Fourier transform infrared (FTIR) spectroscopy results supported the alterations in sludge EPS due to MWCNT. Our observations offer a new insight to understand the nanotoxic effect of MWCNTs on UASB microflora in a complex environment system.

CPTAC Launches Proteomics Data Portal | Office of Cancer Clinical Proteomics Research

Cancer.gov

The National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) announces the launch of the CPTAC Data Portal. The Data Portal hosts all the data that is currently being produced by the consortium with additional historic data from CPTAC 1. The total amount of hosted data exceeds over 500 GB of RAW data in over 800 files.

Compost bacteria and fungi that influence growth and development of Agaricus bisporus and other commercial mushrooms.

PubMed

Kertesz, Michael A; Thai, Meghann

2018-02-01

Mushrooms are an important food crop for many millions of people worldwide. The most important edible mushroom is the button mushroom (Agaricus bisporus), an excellent example of sustainable food production which is cultivated on a selective compost produced from recycled agricultural waste products. A diverse population of bacteria and fungi are involved throughout the production of Agaricus. A range of successional taxa convert the wheat straw into compost in the thermophilic composting process. These initially break down readily accessible compounds and release ammonia, and then assimilate cellulose and hemicellulose into compost microbial biomass that forms the primary source of nutrition for the Agaricus mycelium. This key process in composting is performed by a microbial consortium consisting of the thermophilic fungus Mycothermus thermophilus (Scytalidium thermophilum) and a range of thermophilic proteobacteria and actinobacteria, many of which have only recently been identified. Certain bacterial taxa have been shown to promote elongation of the Agaricus hyphae, and bacterial activity is required to induce production of the mushroom fruiting bodies during cropping. Attempts to isolate mushroom growth-promoting bacteria for commercial mushroom production have not yet been successful. Compost bacteria and fungi also cause economically important losses in the cropping process, causing a range of destructive diseases of mushroom hyphae and fruiting bodies. Recent advances in our understanding of the key bacteria and fungi in mushroom compost provide the potential to improve productivity of mushroom compost and to reduce the impact of crop disease.

Revealing the Bacterial Butyrate Synthesis Pathways by Analyzing (Meta)genomic Data

PubMed Central

Vital, Marius; Howe, Adina Chuang

2014-01-01

ABSTRACT Butyrate-producing bacteria have recently gained attention, since they are important for a healthy colon and when altered contribute to emerging diseases, such as ulcerative colitis and type II diabetes. This guild is polyphyletic and cannot be accurately detected by 16S rRNA gene sequencing. Consequently, approaches targeting the terminal genes of the main butyrate-producing pathway have been developed. However, since additional pathways exist and alternative, newly recognized enzymes catalyzing the terminal reaction have been described, previous investigations are often incomplete. We undertook a broad analysis of butyrate-producing pathways and individual genes by screening 3,184 sequenced bacterial genomes from the Integrated Microbial Genome database. Genomes of 225 bacteria with a potential to produce butyrate were identified, including many previously unknown candidates. The majority of candidates belong to distinct families within the Firmicutes, but members of nine other phyla, especially from Actinobacteria, Bacteroidetes, Fusobacteria, Proteobacteria, Spirochaetes, and Thermotogae, were also identified as potential butyrate producers. The established gene catalogue (3,055 entries) was used to screen for butyrate synthesis pathways in 15 metagenomes derived from stool samples of healthy individuals provided by the HMP (Human Microbiome Project) consortium. A high percentage of total genomes exhibited a butyrate-producing pathway (mean, 19.1%; range, 3.2% to 39.4%), where the acetyl-coenzyme A (CoA) pathway was the most prevalent (mean, 79.7% of all pathways), followed by the lysine pathway (mean, 11.2%). Diversity analysis for the acetyl-CoA pathway showed that the same few firmicute groups associated with several Lachnospiraceae and Ruminococcaceae were dominating in most individuals, whereas the other pathways were associated primarily with Bacteroidetes. PMID:24757212

Chemometric formulation of bacterial consortium-AVS for improved decolorization of resonance-stabilized and heteropolyaromatic dyes.

PubMed

Kumar, Madhava Anil; Kumar, Vaidyanathan Vinoth; Premkumar, Manickam Periyaraman; Baskaralingam, Palanichamy; Thiruvengadaravi, Kadathur Varathachary; Dhanasekaran, Anuradha; Sivanesan, Subramanian

2012-11-01

A bacterial consortium-AVS, consisting of Pseudomonas desmolyticum NCIM 2112, Kocuria rosea MTCC 1532 and Micrococcus glutamicus NCIM 2168 was formulated chemometrically, using the mixture design matrix based on the design of experiments methodology. The formulated consortium-AVS decolorized acid blue 15 and methylene blue with a higher average decolorization rate, which is more rapid than that of the pure cultures. The UV-vis spectrophotometric, Fourier transform infra red spectrophotometric and high performance liquid chromatographic analysis confirm that the decolorization was due to biodegradation by oxido-reductive enzymes, produced by the consortium-AVS. The toxicological assessment of plant growth parameters and the chlorophyll pigment concentrations of Phaseolus mungo and Triticum aestivum seedlings revealed the reduced toxic nature of the biodegraded products. Copyright © 2012 Elsevier Ltd. All rights reserved.

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

PubMed

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

2001-07-01

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

Microbiological and kinetic aspects of a biofilter for the removal of toluene from waste gases

PubMed

Acuna; Perez; Auria; Revah

1999-04-20

Microbiological and kinetic aspects of a biofilter inoculated with a consortium of five bacteria and two yeast adapted to remove toluene vapors were investigated. Initially the toluene sorption isotherm on peat and the effect of different environmental conditions on the toluene consumption rates of this consortium were measured. The fast start-up of the biofilter and the decay in the elimination capacity (EC) were reproduced using microcosm assays with toluene successive additions. Nutrient limitation and a large degree of heterogeneity were also detected. EC values, extrapolated from microcosms, were higher than biofilter EC when it was operating close to 100% efficiency but tended to relate better as the biofilter EC diminished. In studies on the microbial evolution in the biofilter, an increase in the cell count and variation in the ecology of the consortium were noted. Bacterial counts up to 10 x 10(11) cfu/gdry peat were found in 88 days, which corresponds to about a 10(4) increase from inoculum. Observations with SEM showed a nonuniform biofilm development on the support and the presence of an extracellular material. The results obtained in this work demonstrated that activity measurement in microcosms concomitant to the biofilter operation could be an important tool for understanding, predicting and improving the biofiltration performance. Copyright 1999 John Wiley & Sons, Inc.

Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass

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

D'haeseleer, Patrik; Gladden, John M.; Allgaier, Martin

2013-07-19

Thermophilic bacteria are a potential source of enzymes for the deconstruction of lignocellulosic biomass. However, the complement of proteins used to deconstruct biomass and the specific roles of different microbial groups in thermophilic biomass deconstruction are not well-explored. Here we report on the metagenomic and proteogenomic analyses of a compost-derived bacterial consortium adapted to switchgrass at elevated temperature with high levels of glycoside hydrolase activities. Near-complete genomes were reconstructed for the most abundant populations, which included composite genomes for populations closely related to sequenced strains of Thermus thermophilus and Rhodothermus marinus, and for novel populations that are related to thermophilicmore » Paenibacilli and an uncultivated subdivision of the littlestudied Gemmatimonadetes phylum. Partial genomes were also reconstructed for a number of lower abundance thermophilic Chloroflexi populations. Identification of genes for lignocellulose processing and metabolic reconstructions suggested Rhodothermus, Paenibacillus and Gemmatimonadetes as key groups for deconstructing biomass, and Thermus as a group that may primarily metabolize low molecular weight compounds. Mass spectrometry-based proteomic analysis of the consortium was used to identify .3000 proteins in fractionated samples from the cultures, and confirmed the importance of Paenibacillus and Gemmatimonadetes to biomass deconstruction. These studies also indicate that there are unexplored proteins with important roles in bacterial lignocellulose deconstruction.« less

Bioaugmentation of rapid sand filters by microbiome priming with a nitrifying consortium will optimize production of drinking water from groundwater.

PubMed

Albers, Christian Nyrop; Ellegaard-Jensen, Lea; Hansen, Lars Hestbjerg; Sørensen, Sebastian R

2018-02-01

Ammonium oxidation to nitrite and then to nitrate (nitrification) is a key process in many waterworks treating groundwater to make it potable. In rapid sand filters, nitrifying microbial communities may evolve naturally from groundwater bacteria entering the filters. However, in new filters this may take several months, and in some cases the nitrification process is never sufficiently rapid to be efficient or is only performed partially, with nitrite as an undesired end product. The present study reports the first successful priming of nitrification in a rapid sand filter treating groundwater. It is shown that nitrifying communities could be enriched by microbiomes from well-functioning rapid sand filters in waterworks and that the enriched nitrifying consortium could be used to inoculate fresh filters, significantly shortening the time taken for the nitrification process to start. The key nitrifiers in the enrichment were different from those in the well-functioning filter, but similar to those that initiated the nitrification process in fresh filters without inoculation. Whether or not the nitrification was primed with the enriched nitrifying consortium, the bacteria performing the nitrification process during start-up appeared to be slowly outcompeted by Nitrospira, the dominant nitrifying bacterium in well-functioning rapid sand filters. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

Acuna, M.E.; Perez, F.; Revah, S.

Microbiological and kinetic aspects of a biofilter inoculated with a consortium of five bacteria and two yeast adapted to remove toluene vapors were investigated. Initially the toluene sorption isotherm on peat and the effect of different environmental conditions on the toluene consumption rates of this consortium were measured. The fast start-up of the biofilter and the decay in the elimination capacity (EC) were reproduced using microcosm assays with toluene successive additions. Nutrient limitation and a large degree of heterogeneity were also detected. EC values, extrapolated from microcosms, were higher than biofilter EC when it was operating close to 100% efficiencymore » but tended to relate better as the biofilter EC diminished. In studies on the microbial evolution in the biofilter, an increase in the cell count and variation in the ecology of the consortium were noted. Bacterial counts up to 10 {times} 10{sup 11} cfu/g{sub dry peat} were found in 88 days, which corresponds to about a 10{sup 4} increase from inoculum. Observations with SEM showed a nonuniform biofilm development on the support and the presence of an extracellular material. The results obtained in this work demonstrated that activity measurement in microcosms concomitant to the biofilter operation could be an important tool for understanding, predicting and improving the biofiltration performance.« less

Biochemical and Molecular Phylogenetic Study of Agriculturally Useful Association of a Nitrogen-Fixing Cyanobacterium and Nodule Sinorhizobium with Medicago sativa L.

PubMed Central

Karaushu, E. V.; Kravzova, T. R.; Vorobey, N. A.; Kiriziy, D. A.; Olkhovich, O. P.; Taran, N. Yu.; Kots, S. Ya.; Omarova, E.

2015-01-01

Seed inoculation with bacterial consortium was found to increase legume yield, providing a higher growth than the standard nitrogen treatment methods. Alfalfa plants were inoculated by mono- and binary compositions of nitrogen-fixing microorganisms. Their physiological and biochemical properties were estimated. Inoculation by microbial consortium of Sinorhizobium meliloti T17 together with a new cyanobacterial isolate Nostoc PTV was more efficient than the single-rhizobium strain inoculation. This treatment provides an intensification of the processes of biological nitrogen fixation by rhizobia bacteria in the root nodules and an intensification of plant photosynthesis. Inoculation by bacterial consortium stimulates growth of plant mass and rhizogenesis and leads to increased productivity of alfalfa and to improving the amino acid composition of plant leaves. The full nucleotide sequence of the rRNA gene cluster and partial sequence of the dinitrogenase reductase (nifH) gene of Nostoc PTV were deposited to GenBank (JQ259185.1, JQ259186.1). Comparison of these gene sequences of Nostoc PTV with all sequences present at the GenBank shows that this cyanobacterial strain does not have 100% identity with any organisms investigated previously. Phylogenetic analysis showed that this cyanobacterium clustered with high credibility values with Nostoc muscorum. PMID:26114100

Biochemical and Molecular Phylogenetic Study of Agriculturally Useful Association of a Nitrogen-Fixing Cyanobacterium and Nodule Sinorhizobium with Medicago sativa L.

PubMed

Karaushu, E V; Lazebnaya, I V; Kravzova, T R; Vorobey, N A; Lazebny, O E; Kiriziy, D A; Olkhovich, O P; Taran, N Yu; Kots, S Ya; Popova, A A; Omarova, E; Koksharova, O A

2015-01-01

Seed inoculation with bacterial consortium was found to increase legume yield, providing a higher growth than the standard nitrogen treatment methods. Alfalfa plants were inoculated by mono- and binary compositions of nitrogen-fixing microorganisms. Their physiological and biochemical properties were estimated. Inoculation by microbial consortium of Sinorhizobium meliloti T17 together with a new cyanobacterial isolate Nostoc PTV was more efficient than the single-rhizobium strain inoculation. This treatment provides an intensification of the processes of biological nitrogen fixation by rhizobia bacteria in the root nodules and an intensification of plant photosynthesis. Inoculation by bacterial consortium stimulates growth of plant mass and rhizogenesis and leads to increased productivity of alfalfa and to improving the amino acid composition of plant leaves. The full nucleotide sequence of the rRNA gene cluster and partial sequence of the dinitrogenase reductase (nifH) gene of Nostoc PTV were deposited to GenBank (JQ259185.1, JQ259186.1). Comparison of these gene sequences of Nostoc PTV with all sequences present at the GenBank shows that this cyanobacterial strain does not have 100% identity with any organisms investigated previously. Phylogenetic analysis showed that this cyanobacterium clustered with high credibility values with Nostoc muscorum.

Can nitrification bring us to Mars? The role of microbial interactions on nitrogen recovery in life support systems

NASA Astrophysics Data System (ADS)

Christiaens, Marlies E. R.; Lasseur, Christophe; Clauwaert, Peter; Boon, Nico; Ilgrande, Chiara; Vlaeminck, Siegfried

2016-07-01

Human habitation in space requires artificial environment recirculating fundamental elements to enable the highest degree of autonomy . The European Space Agency, supported by a large consortoium of European organisationsdevelop the Micro-Ecological Life Support System (MELiSSA) to transform the mission wastes waste (a.o. organic fibers, CO2, and urine) into water, oxygen, and food (Lasseur et al., 2010). Among these wastes, astronauts' urine has a high potential to provide nitrogen as a fertilizer for food production. As higher plant growth in space is typically proposed to be performed in hydroponics, liquid fertilizer containing nitrates is preferred. An Additional Unit for Water Treatment is developed for urine nitrification by means of a synthetic microbial community. The key players in this consortium are ureolytic bacteria to hydrolyse the main nitrogen source in urine, urea, to ammonium and carbon dioxide as well as oxidation of organic compounds present in urine, ammonium oxidizing bacteria (AOB) to convert ammonium to nitrite (nitritation), and the nitrate oxidizing bacteria (NOB) to produce nitrate (nitratation). Pure AOB strains Nitrosomonas ureae Nm10 and Nitrosomonas europaea ATCC 19718, pure NOB strains Nitrobacter winogradskyi Nb-255 and Nitrobacter vulgaris Z, and interactions within synthetic consortia of one AOB and one NOB or all together were tested. As the initial salinity of fresh urine can be as high as 30 mS/cm, the functionality of selected pure strains and synthetic consortia was evaluated by means of the nitritation and nitratation activity at varying NaCl salinities (5, 10, and 30 mS/cm). The nitritation activity of pure AOB strains was compared with the synthetic consortia. Both N. ureae and Ns. europaea benefit from the presence of Nb. winogradskyi as the ammonium oxidation rates of 1.7 ± 0.7 and 6.4 ± 0.6 mg N/L.d at 5 mS/cm, respectively, doubled. These results are in line with the findings of Perez et al (2015) observing a lower transcription of stress-response genes in Ns. europaea when grown in co-culture with Nb. winogradskyi. Only N. ureae had a similar response when combined with Nb. vulgaris. The synthetic consortium combining all AOB and NOB could not improve the activity rate of a pure culture of Ns. europaea. Increasing salinity did not affect these trends except for the synthetic consortium combining all AOB and NOB at 30 mS/cm as activity only reached 3.7 ± 0.6 mg N/L.d. In case of the nitratation activity, the presence of an AOB was not beneficial. For pure cultures of Nb. winogradskyi and Nb. vulgaris the activity rates 57.6 ± 3.6 and 10.9 ± 0.9 mg N/L.d at 5 mS/cm did not change or decreased resulting in NO2- accumulation, respectively. The consortium combining all AOB and NOB reached 40.8 ± 0.5 mg N/L.d at 5 mS/cm. Similar trends were valid for increasing salt concentrations. However, Nb. winogradskyi seemed to be salt sensitive at 30 mS/cm as the nitratation activity both in pure and coculture decreased about 70% or 50% if combined with Ns. ureae compared to 5 mS/cm. The combination of all AOB and NOB at 30 mS/cm reached the highest activity rate of 30.7 ± 0.8 mg N/L.d. Overall, a coculture of Ns. europaea and Nb. winogradskyi gave highest activity rates except for higher salinity nitratation. A synthetic consortium with all strains could cope better with the latter however with a drastic decrease in NH4+ oxidation compared to the coculture. For space application of urine nitrification, both communities should be further tested.

Bioconversion of waste office paper to hydrogen using pretreated rumen fluid inoculum.

PubMed

Botta, Lívia Silva; Ratti, Regiane Priscila; Sakamoto, Isabel Kimiko; Ramos, Lucas Rodrigues; Silva, Edson Luiz; Varesche, Maria Bernadete Amâncio

2016-12-01

In this study, a microbial consortium from an acid-treated rumen fluid was used to improve the yields of H 2 production from paper residues in batch reactors. The anaerobic batch reactors, which contained paper and cellulose, were operated under three conditions: (1) 0.5 g paper/L, (2) 2 g paper/L, and (3) 4 g paper/L. Cellulase was added to promote the hydrolysis of paper to soluble sugars. The H 2 yields were 5.51, 4.65, and 3.96 mmol H 2 /g COD, respectively, with substrate degradation ranging from 56 to 65.4 %. Butyric acid was the primary soluble metabolite in the three reactors, but pronounced solventogenesis was detected in the reactors incubated with increased paper concentrations (2.0 and 4.0 g/L). A substantial prevalence of Clostridium acetobutylicum (99 % similarity) was observed in the acid-treated rumen fluid, which has been recognized as an efficient H 2 -producing strain in addition to ethanol and n-butanol which were also detected in the reactors.

Evaluation of Lighting Systems, Carbon Sources, and Bacteria Cultures on Photofermentative Hydrogen Production.

PubMed

Hu, Chengcheng; Choy, Sing-Ying; Giannis, Apostolos

2018-05-01

Fluorescent and incandescent lighting systems were applied for batch photofermentative hydrogen production by four purple non-sulfur photosynthetic bacteria (PNSB). The hydrogen production efficiency of Rhodopseudomonas palustris, Rhodobacter sphaeroides, Rhodobacter capsulatus, and Rhodospirillum rubrum was evaluated using different carbon sources (acetate, butyrate, lactate, and malate). Incandescent light was found to be more effective for bacteria cell growth and hydrogen production. It was observed that PNSB followed substrate selection criteria for hydrogen production. Only R. palustris was able to produce hydrogen using most carbon sources. Cell density was almost constant, but cell growth rate and hydrogen production were significantly varied under the different lighting systems. The kinetics study suggested that initial substrate concentration had a positive correlation with lag phase duration. Among the PNSB, R. palustris grew faster and had higher hydrogen yields of 1.58, 4.92, and 2.57 mol H 2 /mol using acetate, butyrate, and lactate, respectively. In the integrative approach with dark fermentation effluents rich in organic acids, R. palustris should be enriched in the phototrophic microbial consortium of the continuous hydrogen production system.

Biohydrogen and methane production via a two-step process using an acid pretreated native microalgae consortium.

PubMed

Carrillo-Reyes, Julian; Buitrón, Germán

2016-12-01

A native microalgae consortium treated under thermal-acidic hydrolysis was used to produce hydrogen and methane in a two-step sequential process. Different acid concentrations were tested, generating hydrogen and methane yields of up to 45mLH 2 gVS -1 and 432mLCH 4 gVS -1 , respectively. The hydrogen production step solubilized the particulate COD (chemical oxygen demand) up to 30%, creating considerable amounts of volatile fatty acids (up to 10gCODL -1 ). It was observed that lower acid concentration presented higher hydrogen and methane production potential. The results revealed that thermal acid hydrolysis of a native microalgae consortium is a simple but effective strategy for producing hydrogen and methane in the sequential process. In addition to COD removal (50-70%), this method resulted in an energy recovery of up to 15.9kJ per g of volatile solids of microalgae biomass, one of the highest reported. Copyright © 2016 Elsevier Ltd. All rights reserved.

Microbial toxicity and biodegradability of perfluorooctane sulfonate (PFOS) and shorter chain perfluoroalkyl and polyfluoroalkyl substances (PFASs).

PubMed

Ochoa-Herrera, Valeria; Field, Jim A; Luna-Velasco, Antonia; Sierra-Alvarez, Reyes

2016-09-14

Perfluorooctane sulfonate (PFOS) and related perfluoroalkyl and polyfluoroalkyl substances (PFASs) are emerging contaminants that have been widely applied in consumer and industrial applications for decades. However, PFOS has raised public concern due to its high bioaccumulative character, environmental persistence, and toxicity. Shorter PFASs such as perfluorobutane sulfonate (PFBS) and polyfluoroalkyl compounds have been proposed as alternatives to PFOS but it is unclear whether these fluorinated substances pose a risk for public health and the environment. The objective of this research was to investigate the microbial toxicity and the susceptibility to microbial degradation of PFOS and several related fluorinated compounds, i.e., short-chain perfluoroalkyl and polyfluoroalkyl sulfonic and carboxylic acids. None of the compounds tested were toxic to the methanogenic activity of anaerobic wastewater sludge even at very high concentrations (up to 500 mg L -1 ). All PFASs evaluated were highly resistant to microbial degradation. PFOS was not reductively dehalogenated by the anaerobic microbial consortium even after very long periods of incubation (3.4 years). Similarly, the tested short chain perfluoroalkyl substances (i.e., PFBS and trifluoroacetic acid) and a polyfluoroalkyl PFOS analogue, 6 : 2 fluorotelomer sulfonic acid (FTSA) were also resistant to anaerobic biodegradation. Likewise, no conclusive evidence of microbial degradation was observed under aerobic conditions for any of the short-chain perfluoroalkyl and polyfluoroalkyl carboxylic acids tested after 32 weeks of incubation. Collectively, these results indicate that PFOS and its alternatives such as short chain perfluoroalkyl sulfonates and carboxylates and their polyfluorinated homologues are highly resistant to microbial degradation.

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

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

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

1999-06-01

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

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

PubMed

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

2016-03-01

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

Rhizosphere engineering: Enhancing sustainable plant ecosystem productivity

DOE PAGES

Ahkami, Amir H.; White, III, Richard Allen; Handakumbura, Pubudu P.; ...

2017-04-21

Here, the rhizosphere is arguably the most complex microbial habitat on earth, comprising an integrated network of plant roots, soil and a diverse microbial consortium of bacteria, archaea, viruses, and microeukaryotes. Understanding, predicting and controlling the structure and function of the rhizosphere will allow us to harness plant-microbe interactions and other rhizosphere activities as a means to increase or restore plant ecosystem productivity, improve plant responses to a wide range of environmental perturbations, and mitigate effects of climate change by designing ecosystems for long-term soil carbon storage. Here, we review critical knowledge gaps in rhizosphere science, and how mechanistic understandingmore » of rhizosphere interactions can be leveraged in rhizosphere engineering efforts with the goal of maintaining sustainable plant ecosystem services for food and bioenergy production in an ever changing global climate.« less

Rhizosphere engineering: Enhancing sustainable plant ecosystem productivity

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

Ahkami, Amir H.; White, III, Richard Allen; Handakumbura, Pubudu P.

Here, the rhizosphere is arguably the most complex microbial habitat on earth, comprising an integrated network of plant roots, soil and a diverse microbial consortium of bacteria, archaea, viruses, and microeukaryotes. Understanding, predicting and controlling the structure and function of the rhizosphere will allow us to harness plant-microbe interactions and other rhizosphere activities as a means to increase or restore plant ecosystem productivity, improve plant responses to a wide range of environmental perturbations, and mitigate effects of climate change by designing ecosystems for long-term soil carbon storage. Here, we review critical knowledge gaps in rhizosphere science, and how mechanistic understandingmore » of rhizosphere interactions can be leveraged in rhizosphere engineering efforts with the goal of maintaining sustainable plant ecosystem services for food and bioenergy production in an ever changing global climate.« less

The Functional Potential of Microbial Communities in Hydraulic Fracturing Source Water and Produced Water from Natural Gas Extraction Characterized by Metagenomic Sequencing

PubMed Central

Mohan, Arvind Murali; Bibby, Kyle J.; Lipus, Daniel; Hammack, Richard W.; Gregory, Kelvin B.

2014-01-01

Microbial activity in produced water from hydraulic fracturing operations can lead to undesired environmental impacts and increase gas production costs. However, the metabolic profile of these microbial communities is not well understood. Here, for the first time, we present results from a shotgun metagenome of microbial communities in both hydraulic fracturing source water and wastewater produced by hydraulic fracturing. Taxonomic analyses showed an increase in anaerobic/facultative anaerobic classes related to Clostridia, Gammaproteobacteria, Bacteroidia and Epsilonproteobacteria in produced water as compared to predominantly aerobic Alphaproteobacteria in the fracturing source water. The metabolic profile revealed a relative increase in genes responsible for carbohydrate metabolism, respiration, sporulation and dormancy, iron acquisition and metabolism, stress response and sulfur metabolism in the produced water samples. These results suggest that microbial communities in produced water have an increased genetic ability to handle stress, which has significant implications for produced water management, such as disinfection. PMID:25338024

The functional potential of microbial communities in hydraulic fracturing source water and produced water from natural gas extraction characterized by metagenomic sequencing

DOE PAGES

Mohan, Arvind Murali; Bibby, Kyle J.; Lipus, Daniel; ...

2014-10-22

Microbial activity in produced water from hydraulic fracturing operations can lead to undesired environmental impacts and increase gas production costs. However, the metabolic profile of these microbial communities is not well understood. Here, for the first time, we present results from a shotgun metagenome of microbial communities in both hydraulic fracturing source water and wastewater produced by hydraulic fracturing. Taxonomic analyses showed an increase in anaerobic/facultative anaerobic classes related to Clostridia, Gammaproteobacteria, Bacteroidia and Epsilonproteobacteria in produced water as compared to predominantly aerobic Alphaproteobacteria in the fracturing source water. Thus, the metabolic profile revealed a relative increase in genes responsiblemore » for carbohydrate metabolism, respiration, sporulation and dormancy, iron acquisition and metabolism, stress response and sulfur metabolism in the produced water samples. These results suggest that microbial communities in produced water have an increased genetic ability to handle stress, which has significant implications for produced water management, such as disinfection.« less

The functional potential of microbial communities in hydraulic fracturing source water and produced water from natural gas extraction characterized by metagenomic sequencing.

PubMed

Mohan, Arvind Murali; Bibby, Kyle J; Lipus, Daniel; Hammack, Richard W; Gregory, Kelvin B

2014-01-01

Microbial activity in produced water from hydraulic fracturing operations can lead to undesired environmental impacts and increase gas production costs. However, the metabolic profile of these microbial communities is not well understood. Here, for the first time, we present results from a shotgun metagenome of microbial communities in both hydraulic fracturing source water and wastewater produced by hydraulic fracturing. Taxonomic analyses showed an increase in anaerobic/facultative anaerobic classes related to Clostridia, Gammaproteobacteria, Bacteroidia and Epsilonproteobacteria in produced water as compared to predominantly aerobic Alphaproteobacteria in the fracturing source water. The metabolic profile revealed a relative increase in genes responsible for carbohydrate metabolism, respiration, sporulation and dormancy, iron acquisition and metabolism, stress response and sulfur metabolism in the produced water samples. These results suggest that microbial communities in produced water have an increased genetic ability to handle stress, which has significant implications for produced water management, such as disinfection.

The 2011 PHARMINE report on pharmacy and pharmacy education in the European Union

PubMed Central

Atkinson, Jeffrey; Rombaut, Bart

The PHARMINE consortium consists of 50 universities from European Union member states or other European countries that are members of the European Association of Faculties of Pharmacy (EAFP). EU partner associations representing community (PGEU), hospital (EAHP) and industrial pharmacy (EIPG), together with the European Pharmacy Students’ Association (EPSA) are also part of the consortium. The consortium surveyed pharmacies and pharmacists in different settings: community, hospital, industry and other sectors. The consortium also looked at how European Union higher education institutions and courses are organised. The PHARMINE survey of pharmacy and pharmacy education in Europe produced country profiles with extensive information for EU member states and several other European countries. These data are available at: http://www.pharmine.org/losse_paginas/Country_Profiles/. This 2011 PHARMINE report presents the project and data, and some preliminary analysis on the basic question of how pharmacy education is adapted to pharmacy practice in the EU. PMID:24198854

Characterization of a compost biofiltration system degrading dichloromethane

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

Ergas, S.J.; Kinney, K.; Fuller, M.E.

1994-11-05

The effects of acclimatization of microbial populations, compound concentration, and media pH on the biodegradation of low concentration dichloromethane emissions in biofiltration systems was evaluated. Greater than 98% removal efficiency was achieved for dichloromethane at superficial velocities from 1 to 15 m[sup 3]/m[sup 2][center dot]min and inlet concentrations of 3 and 50 ppm[sub v]. Although acclimatization of microbial populations to toluene occurred within 2 weeks of operation start-up, initial dichloromethane acclimatization took place over a period of 10 weeks. This period was shortened to 10 days when a laboratory grown consortium of dichloromethane degrading organisms, isolated from a previously acclimatizedmore » column, was introduced into fresh biofilter media. The mixed culture consisted of 12 members, which together were able to degrade dichloromethane at concentrations up to 500 mg/L. Only one member of the consortium was able to degrade dichloromethane in pure culture, and the presence of the other members did not affect the rate of biodegradation in solution culture. Although high removal efficiencies for dichloromethane were sustained for more than 4 months in a biofilter column receiving an inlet gas stream with 3 ppm[sub v] of dichloromethane, acidification of the column and resulting decline in performance occurred when a 50-ppm[sub v] inlet concentration was used. A biofilm model incorporating first order biodegradation kinetics provided a good fit to observed concentration profiles, and may prove to be a useful tool for designing biofiltration systems for low concentration VOC emissions.« less

Exploring the Bacterial Microbiota of Colombian Fermented Maize Dough “Masa Agria” (Maiz Añejo)

PubMed Central

Chaves-Lopez, Clemencia; Serio, Annalisa; Delgado-Ospina, Johannes; Rossi, Chiara; Grande-Tovar, Carlos D.; Paparella, Antonello

2016-01-01

Masa Agria is a naturally fermented maize dough produced in Colombia, very common in the traditional gastronomy. In this study we used culture-dependent and RNA-based pyrosequencing to investigate the bacterial community structure of Masa Agria samples produced in the south west of Colombia. The mean value of cell density was 7.6 log CFU/g of presumptive lactic acid bacteria, 5.4 log cfu/g for presumptive acetic bacteria and 5.6 og CFU/g for yeasts. The abundance of these microorganisms is also responsible for the low pH (3.1–3.7) registered. Although the 16S rRNA pyrosequencing revealed that the analyzed samples were different in bacteria richness and diversity, the genera Lactobacillus, Weissella, and Acetobacter were predominant. In particular, the most common species were Lactobacillus plantarum and Acetobacter fabarum, followed by L. fermentum, L. vaccinostercus, and Pediococcus argentinicus. Several microorganisms of environmental origin, such as Dechloromonas and most of all Sphingobium spp., revealed in each sample, were detected, and also bacteria related to maize, such as Phytoplasma. In conclusion, our results elucidated for the first time the structures of the bacterial communities of Masa Agria samples obtained from different producers, identifying the specific dominant species and revealing a complete picture of the bacterial consortium in this specific niche. The selective pressure of tropical environments may favor microbial biodiversity characterized by a useful technological potential. PMID:27524979

Freshwater Recirculating Aquaculture System Operations Drive Biofilter Bacterial Community Shifts around a Stable Nitrifying Consortium of Ammonia-Oxidizing Archaea and Comammox Nitrospira

PubMed Central

Bartelme, Ryan P.; McLellan, Sandra L.; Newton, Ryan J.

2017-01-01

Recirculating aquaculture systems (RAS) are unique engineered ecosystems that minimize environmental perturbation by reducing nutrient pollution discharge. RAS typically employ a biofilter to control ammonia levels produced as a byproduct of fish protein catabolism. Nitrosomonas (ammonia-oxidizing), Nitrospira, and Nitrobacter (nitrite-oxidizing) species are thought to be the primary nitrifiers present in RAS biofilters. We explored this assertion by characterizing the biofilter bacterial and archaeal community of a commercial scale freshwater RAS that has been in operation for >15 years. We found the biofilter community harbored a diverse array of bacterial taxa (>1000 genus-level taxon assignments) dominated by Chitinophagaceae (~12%) and Acidobacteria (~9%). The bacterial community exhibited significant composition shifts with changes in biofilter depth and in conjunction with operational changes across a fish rearing cycle. Archaea also were abundant, and were comprised solely of a low diversity assemblage of Thaumarchaeota (>95%), thought to be ammonia-oxidizing archaea (AOA) from the presence of AOA ammonia monooxygenase genes. Nitrosomonas were present at all depths and time points. However, their abundance was >3 orders of magnitude less than AOA and exhibited significant depth-time variability not observed for AOA. Phylogenetic analysis of the nitrite oxidoreductase beta subunit (nxrB) gene indicated two distinct Nitrospira populations were present, while Nitrobacter were not detected. Subsequent identification of Nitrospira ammonia monooxygenase alpha subunit genes in conjunction with the phylogenetic placement and quantification of the nxrB genotypes suggests complete ammonia-oxidizing (comammox) and nitrite-oxidizing Nitrospira populations co-exist with relatively equivalent and stable abundances in this system. It appears RAS biofilters harbor complex microbial communities whose composition can be affected directly by typical system operations while supporting multiple ammonia oxidation lifestyles within the nitrifying consortium. PMID:28194147

Assessment of the horizontal transfer of functional genes as a suitable approach for evaluation of the bioremediation potential of petroleum-contaminated sites: a mini-review.

PubMed

Shahi, Aiyoub; Ince, Bahar; Aydin, Sevcan; Ince, Orhan

2017-06-01

Petroleum sludge contains recalcitrant residuals. These compounds because of being toxic to humans and other organism are of the major concerns. Therefore, petroleum sludge should be safely disposed. Physicochemical methods which are used by this sector are mostly expensive and need complex devices. Bioremediation methods because of being eco-friendly and cost-effective overcome most of the limitations of physicochemical treatments. Microbial strains capable to degrade petroleum hydrocarbons are practically present in all soils and sediments and their population density increases in contact with contaminants. Bacterial strains cannot degrade alone all kinds of petroleum hydrocarbons, rather microbial consortium should collaborate with each other for degradation of petroleum hydrocarbon mixtures. Horizontal transfer of functional genes between bacteria plays an important role in increasing the metabolic potential of the microbial community. Therefore, selecting a suitable degrading gene and tracking its horizontal transfer would be a useful approach to evaluate the bioremediation process and to assess the bioremediation potential of contaminated sites.

Effect of composites based nickel foam anode in microbial fuel cell using Acetobacter aceti and Gluconobacter roseus as a biocatalysts.

PubMed

Karthikeyan, Rengasamy; Krishnaraj, Navanietha; Selvam, Ammaiyappan; Wong, Jonathan Woon-Chung; Lee, Patrick K H; Leung, Michael K H; Berchmans, Sheela

2016-10-01

This study explores the use of materials such as chitosan (chit), polyaniline (PANI) and titanium carbide (TC) as anode materials for microbial fuel cells. Nickel foam (NF) was used as the base anode substrate. Four different types of anodes (NF, NF/PANI, NF/PANI/TC, NF/PANI/TC/Chit) are thus prepared and used in batch type microbial fuel cells operated with a mixed consortium of Acetobacter aceti and Gluconobacter roseus as the biocatalysts and bad wine as a feedstock. A maximum power density of 18.8Wm(-3) (≈2.3 times higher than NF) was obtained in the case of the anode modified with a composite of PANI/TC/Chit. The MFCs running under a constant external resistance of (50Ω) yielded 14.7% coulombic efficiency with a maximum chemical oxygen demand (COD) removal of 87-93%. The overall results suggest that the catalytic materials embedded in the chitosan matrix show the best performance and have potentials for further development. Copyright © 2016 Elsevier Ltd. All rights reserved.

[Acclimatization and characteristics of microbial community in sulphate-dependent anaerobic methane oxidation].

PubMed

Xi, Jing-Ru; Liu, Su-Qin; Li, Lin; Liu, Jun-Xin

2014-12-01

The greenhouse effect of methane is 26 times worse than that of carbon dioxide, and wastewater containing high concentrations of sulfate is harmful to water, soil and plants. Therefore, anaerobic oxidation of methane driven by sulfate is one of the effective ways for methane reduction. In this paper, with sulfate as the electron accepter, a microbial consortium capable of oxidating methane under anaerobic condition was cultured. The diversity and characteristics of bacterial and archaeal community were investigated by PCR-DGGE, and phylogenetic analysis of the dominant microorganisms was also carried out. The DGGE fingerprints showed that microbial community structure changed distinctly, and the abundance of methane-oxidizing archea and sulfate-reducing bacteria increased in the acclimatization system added sulfate. After acclimatization, the bacterial diversity increased, while archaea diversity decreased slightly. The representative bands in the DGGE profiles were excised and sequenced. Results indicated that the dominant species in the acclimatization system were Spirochaetes, Desulfuromonadales, Methanosarcinales, Methanosaeta. Methane converted into carbon dioxide while sulfate transformed into hydrogen sulfide and sulfur in the process of anaerobic methane oxidation accompanied by sulphate reduction.

Biodegradation of complex hydrocarbons in spent engine oil by novel bacterial consortium isolated from deep sea sediment.

PubMed

Ganesh Kumar, A; Vijayakumar, Lakshmi; Joshi, Gajendra; Magesh Peter, D; Dharani, G; Kirubagaran, R

2014-10-01

Complex hydrocarbon and aromatic compounds degrading marine bacterial strains were isolated from deep sea sediment after enrichment on spent engine (SE) oil. Phenotypic characterization and phylogenetic analysis of 16S rRNA gene sequences showed the isolates were related to members of the Pseudoalteromonas sp., Ruegeria sp., Exiguobacterium sp. and Acinetobacter sp. Biodegradation using 1% (v/v) SE oil with individual and mixed strains showed the efficacy of SE oil utilization within a short retention time. The addition of non-ionic surfactant 0.05% (v/v) Tween 80 as emulsifying agent enhanced the solubility of hydrocarbons and renders them more accessible for biodegradation. The degradation of several compounds and the metabolites formed during the microbial oxidation process were confirmed by Fourier transform infrared spectroscopy and Gas chromatography-mass spectrometry analyses. The potential of this consortium to biodegrade SE oil with and without emulsifying agent provides possible application in bioremediation of oil contaminated marine environment. Copyright © 2014 Elsevier Ltd. All rights reserved.

Discovery of a trans-Dichloroethene-Respiring Dehalogenimonas Species in the 1,1,2,2-Tetrachloroethane-Dechlorinating WBC-2 Consortium

PubMed Central

Manchester, Marie J.; Hug, Laura A.; Zarek, Matt; Zila, Anna

2012-01-01

The WBC-2 consortium is an organohalide-respiring anaerobic microbial enrichment culture capable of dechlorinating 1,1,2,2-tetrachloroethane (TeCA) to ethene. In the WBC-2 culture, TeCA is first transformed to trans-dichloroethene (tDCE) by dichloroelimination; tDCE is subsequently transformed to vinyl chloride (VC) and then to ethene by hydrogenolysis. Analysis of 16S rRNA gene clone libraries from culture DNA revealed sequences from three putative dechlorinating organisms belonging to Dehalococcoides, Dehalobacter, and Dehalogenimonas genera. Quantitative PCR primers were designed for each of these sequences, and their abundance was quantified in enrichment cultures over time. These data revealed that complete dechlorination of TeCA to ethene involves all three organisms. Dehalobacter spp. grew during the dihaloelimination of TeCA to tDCE, while Dehalococcoides and Dehalogenimonas spp. grew during hydrogenolysis of tDCE to ethene. This is the first time a genus other than Dehalococcoides has been implicated in dechlorination of tDCE to VC. PMID:22635995

In situ biodegradation of naphthenic acids in oil sands tailings pond water using indigenous algae-bacteria consortium.

PubMed

Mahdavi, Hamed; Prasad, Vinay; Liu, Yang; Ulrich, Ania C

2015-01-01

In this study, the biodegradation of total acid-extractable organics (TAOs), commonly called naphthenic acids (NAs), was investigated. An indigenous microbial culture containing algae and bacteria was taken from the surface of a tailings pond and incubated over the course of 120days. The influence of light, oxygen and the presence of indigenous algae and bacteria, and a diatom (Navicula pelliculosa) on the TAO removal rate were elucidated. The highest biodegradation rate was observed with bacteria growth only (without light exposure) with a half-life (t(1/2)) of 203days. The algae-bacteria consortium enhanced the detoxification process, however, bacterial biomass played the main role in toxicity reduction. Principal component analysis (PCA) conducted on FT-IR spectra, identified functional groups and bonds (representing potential markers for biotransformation of TAOs) as follows: hydroxyl, carboxyl and amide groups along with CH, arylH, arylOH and NH bonds. Copyright © 2015 Elsevier Ltd. All rights reserved.

Improved fermentation performance in an expanded ectopic fermentation system inoculated with thermophilic bacteria.

PubMed

Guo, Hui; Zhu, Changxiong; Geng, Bing; Liu, Xue; Ye, Jing; Tian, Yunlong; Peng, Xiawei

2015-12-01

Previous research showed that ectopic fermentation system (EFS) inoculated with thermophilic bacteria is an excellent alternative for cow wastewater treatment. In this study, the effects of thermophilic bacterial consortium on the efficiency and quality of the fermentation process in EFS were evaluated by measuring physicochemical and environmental factors and the changes in organic matter composition. In parallel, the microbial communities correlated with fermentation performance were identified. Inoculation of EFS with thermophilic bacterial consortium led to higher temperatures, increased wastewater requirements for continuous fermentation, and improved quality of the litters in terms of physicochemical factors, security test, functional group analysis, and bacterial community composition. The relationship between the transformation of organic component and the dominant bacteria species indicated that environmental factors contributed to strain growth, which subsequently promoted the fermentation process. The results highlight the great potential of EFS model for wide application in cow wastewater treatment and re-utilization as bio-fertilizer. Copyright © 2015 Elsevier Ltd. All rights reserved.

Slurry-phase biodegradation of weathered oily sludge waste.

PubMed

Machín-Ramírez, C; Okoh, A I; Morales, D; Mayolo-Deloisa, K; Quintero, R; Trejo-Hernández, M R

2008-01-01

We assessed the biodegradation of a typical oily sludge waste (PB401) in Mexico using several regimes of indigenous microbial consortium and relevant bioremediation strategies in slurry-phase system. Abiotic loss of total petroleum hydrocarbons (TPH) in the PB401 was insignificant, and degradation rates under the various treatment conditions ranged between 666.9 and 2168.7 mg kg(-1) day(-1) over a 15 days reaction period, while viable cell count peaked at between log(10)5.7 and log(10)7.4 cfu g(-1). Biostimulation with a commercial fertilizer resulted in 24% biodegradation of the TPH in the oily waste and a corresponding peak cell density of log(10)7.4 cfu g(-1). Addition of non-indigenous adapted consortium did not appear to enhance the removal of TPH from the oily waste. It would appear that the complexities of the components of the alkylaromatic fraction of the waste limited biodegradation rate even in a slurry system.

Consolidated bioprocessing of lignocellulosic biomass to lactic acid by a synthetic fungal-bacterial consortium.

PubMed

Shahab, Robert L; Luterbacher, Jeremy S; Brethauer, Simone; Studer, Michael H

2018-05-01

Consolidated bioprocessing (CBP) of lignocellulosic feedstocks to platform chemicals requires complex metabolic processes, which are commonly executed by single genetically engineered microorganisms. Alternatively, synthetic consortia can be employed to compartmentalize the required metabolic functions among different specialized microorganisms as demonstrated in this work for the direct production of lactic acid from lignocellulosic biomass. We composed an artificial cross-kingdom consortium and co-cultivated the aerobic fungus Trichoderma reesei for the secretion of cellulolytic enzymes with facultative anaerobic lactic acid bacteria. We engineered ecological niches to enable the formation of a spatially structured biofilm. Up to 34.7 gL -1 lactic acid could be produced from 5% (w/w) microcrystalline cellulose. Challenges in converting pretreated lignocellulosic biomass include the presence of inhibitors, the formation of acetic acid and carbon catabolite repression. In the CBP consortium hexoses and pentoses were simultaneously consumed and metabolic cross-feeding enabled the in situ degradation of acetic acid. As a result, superior product purities were achieved and 19.8 gL -1 (85.2% of the theoretical maximum) of lactic acid could be produced from non-detoxified steam-pretreated beech wood. These results demonstrate the potential of consortium-based CBP technologies for the production of high value chemicals from pretreated lignocellulosic biomass in a single step. © 2018 Wiley Periodicals, Inc.

A framework for human microbiome research

PubMed Central

Methé, Barbara A.; Nelson, Karen E.; Pop, Mihai; Creasy, Heather H.; Giglio, Michelle G.; Huttenhower, Curtis; Gevers, Dirk; Petrosino, Joseph F.; Abubucker, Sahar; Badger, Jonathan H.; Chinwalla, Asif T.; Earl, Ashlee M.; FitzGerald, Michael G.; Fulton, Robert S.; Hallsworth-Pepin, Kymberlie; Lobos, Elizabeth A.; Madupu, Ramana; Magrini, Vincent; Martin, John C.; Mitreva, Makedonka; Muzny, Donna M.; Sodergren, Erica J.; Versalovic, James; Wollam, Aye M.; Worley, Kim C.; Wortman, Jennifer R.; Young, Sarah K.; Zeng, Qiandong; Aagaard, Kjersti M.; Abolude, Olukemi O.; Allen-Vercoe, Emma; Alm, Eric J.; Alvarado, Lucia; Andersen, Gary L.; Anderson, Scott; Appelbaum, Elizabeth; Arachchi, Harindra M.; Armitage, Gary; Arze, Cesar A.; Ayvaz, Tulin; Baker, Carl C.; Begg, Lisa; Belachew, Tsegahiwot; Bhonagiri, Veena; Bihan, Monika; Blaser, Martin J.; Bloom, Toby; Vivien Bonazzi, J.; Brooks, Paul; Buck, Gregory A.; Buhay, Christian J.; Busam, Dana A.; Campbell, Joseph L.; Canon, Shane R.; Cantarel, Brandi L.; Chain, Patrick S.; Chen, I-Min A.; Chen, Lei; Chhibba, Shaila; Chu, Ken; Ciulla, Dawn M.; Clemente, Jose C.; Clifton, Sandra W.; Conlan, Sean; Crabtree, Jonathan; Cutting, Mary A.; Davidovics, Noam J.; Davis, Catherine C.; DeSantis, Todd Z.; Deal, Carolyn; Delehaunty, Kimberley D.; Dewhirst, Floyd E.; Deych, Elena; Ding, Yan; Dooling, David J.; Dugan, Shannon P.; Dunne, Wm. Michael; Durkin, A. Scott; Edgar, Robert C.; Erlich, Rachel L.; Farmer, Candace N.; Farrell, Ruth M.; Faust, Karoline; Feldgarden, Michael; Felix, Victor M.; Fisher, Sheila; Fodor, Anthony A.; Forney, Larry; Foster, Leslie; Di Francesco, Valentina; Friedman, Jonathan; Friedrich, Dennis C.; Fronick, Catrina C.; Fulton, Lucinda L.; Gao, Hongyu; Garcia, Nathalia; Giannoukos, Georgia; Giblin, Christina; Giovanni, Maria Y.; Goldberg, Jonathan M.; Goll, Johannes; Gonzalez, Antonio; Griggs, Allison; Gujja, Sharvari; Haas, Brian J.; Hamilton, Holli A.; Harris, Emily L.; Hepburn, Theresa A.; Herter, Brandi; Hoffmann, Diane E.; Holder, Michael E.; Howarth, Clinton; Huang, Katherine H.; Huse, Susan M.; Izard, Jacques; Jansson, Janet K.; Jiang, Huaiyang; Jordan, Catherine; Joshi, Vandita; Katancik, James A.; Keitel, Wendy A.; Kelley, Scott T.; Kells, Cristyn; Kinder-Haake, Susan; King, Nicholas B.; Knight, Rob; Knights, Dan; Kong, Heidi H.; Koren, Omry; Koren, Sergey; Kota, Karthik C.; Kovar, Christie L.; Kyrpides, Nikos C.; La Rosa, Patricio S.; Lee, Sandra L.; Lemon, Katherine P.; Lennon, Niall; Lewis, Cecil M.; Lewis, Lora; Ley, Ruth E.; Li, Kelvin; Liolios, Konstantinos; Liu, Bo; Liu, Yue; Lo, Chien-Chi; Lozupone, Catherine A.; Lunsford, R. Dwayne; Madden, Tessa; Mahurkar, Anup A.; Mannon, Peter J.; Mardis, Elaine R.; Markowitz, Victor M.; Mavrommatis, Konstantinos; McCorrison, Jamison M.; McDonald, Daniel; McEwen, Jean; McGuire, Amy L.; McInnes, Pamela; Mehta, Teena; Mihindukulasuriya, Kathie A.; Miller, Jason R.; Minx, Patrick J.; Newsham, Irene; Nusbaum, Chad; O’Laughlin, Michelle; Orvis, Joshua; Pagani, Ioanna; Palaniappan, Krishna; Patel, Shital M.; Pearson, Matthew; Peterson, Jane; Podar, Mircea; Pohl, Craig; Pollard, Katherine S.; Priest, Margaret E.; Proctor, Lita M.; Qin, Xiang; Raes, Jeroen; Ravel, Jacques; Reid, Jeffrey G.; Rho, Mina; Rhodes, Rosamond; Riehle, Kevin P.; Rivera, Maria C.; Rodriguez-Mueller, Beltran; Rogers, Yu-Hui; Ross, Matthew C.; Russ, Carsten; Sanka, Ravi K.; Pamela Sankar, J.; Sathirapongsasuti, Fah; Schloss, Jeffery A.; Schloss, Patrick D.; Schmidt, Thomas M.; Scholz, Matthew; Schriml, Lynn; Schubert, Alyxandria M.; Segata, Nicola; Segre, Julia A.; Shannon, William D.; Sharp, Richard R.; Sharpton, Thomas J.; Shenoy, Narmada; Sheth, Nihar U.; Simone, Gina A.; Singh, Indresh; Smillie, Chris S.; Sobel, Jack D.; Sommer, Daniel D.; Spicer, Paul; Sutton, Granger G.; Sykes, Sean M.; Tabbaa, Diana G.; Thiagarajan, Mathangi; Tomlinson, Chad M.; Torralba, Manolito; Treangen, Todd J.; Truty, Rebecca M.; Vishnivetskaya, Tatiana A.; Walker, Jason; Wang, Lu; Wang, Zhengyuan; Ward, Doyle V.; Warren, Wesley; Watson, Mark A.; Wellington, Christopher; Wetterstrand, Kris A.; White, James R.; Wilczek-Boney, Katarzyna; Wu, Yuan Qing; Wylie, Kristine M.; Wylie, Todd; Yandava, Chandri; Ye, Liang; Ye, Yuzhen; Yooseph, Shibu; Youmans, Bonnie P.; Zhang, Lan; Zhou, Yanjiao; Zhu, Yiming; Zoloth, Laurie; Zucker, Jeremy D.; Birren, Bruce W.; Gibbs, Richard A.; Highlander, Sarah K.; Weinstock, George M.; Wilson, Richard K.; White, Owen

2012-01-01

A variety of microbial communities and their genes (microbiome) exist throughout the human body, playing fundamental roles in human health and disease. The NIH funded Human Microbiome Project (HMP) Consortium has established a population-scale framework which catalyzed significant development of metagenomic protocols resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 to 18 body sites up to three times, which to date, have generated 5,177 microbial taxonomic profiles from 16S rRNA genes and over 3.5 Tb of metagenomic sequence. In parallel, approximately 800 human-associated reference genomes have been sequenced. Collectively, these data represent the largest resource to date describing the abundance and variety of the human microbiome, while providing a platform for current and future studies. PMID:22699610

Kinetics of carbendazim degradation in a horizontal tubular biofilm reactor.

PubMed

Alvarado-Gutiérrez, María Luisa; Ruiz-Ordaz, Nora; Galíndez-Mayer, Juvencio; Santoyo-Tepole, Fortunata; Curiel-Quesada, Everardo; García-Mena, Jaime; Ahuatzi-Chacón, Deifilia

2017-04-01

The fungicide carbendazim is an ecotoxic agent affecting aquatic biota. Due to its suspected hormone-disrupting effects, it is considered a "priority hazard substance" by the Water Framework Directive of the European Commission, and its degradation is of major concern. In this work, a horizontal tubular biofilm reactor (HTBR) operating in plug-flow regime was used to study the kinetics of carbendazim removal by an acclimated microbial consortium. The reactor was operated in steady state continuous culture at eight different carbendazim loading rates. The concentrations of the fungicide were determined at several distances of the HTBR. At the loading rates tested, the highest instantaneous removal rates were observed in the first section of the tubular biofilm reactor. No evidence of inhibition of the catabolic activity of the microbial community was found. Strains of the genera Flectobacillus, Klebsiella, Stenotrophomonas, and Flavobacterium were identified in the biofilm; the last three degrade carbendazim in axenic culture.

Microbial mats: an ecological niche for fungi

PubMed Central

Cantrell, Sharon A.; Duval-Pérez, Lisabeth

2013-01-01

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

Electricity generation from carbon monoxide in a single chamber microbial fuel cell.

PubMed

Mehta, P; Hussain, A; Tartakovsky, B; Neburchilov, V; Raghavan, V; Wang, H; Guiot, S R

2010-05-05

Electricity production from carbon monoxide (CO) is demonstrated in a single chamber microbial fuel cell (MFC) with a CoTMPP-based air cathode. The MFC was inoculated with anaerobic sludge and continuously sparged with CO as a sole carbon source. Volumetric power output was maximized at a CO flow rate of 4.8LLR(-1)d(-1) reaching 6.4mWLR(-1). Several soluble and gaseous degradation products including hydrogen, methane, and acetate were detected, resulting in a relatively low apparent Coulombic efficiency of 8.7%. Tests also demonstrated electricity production from hydrogen and acetate with the highest and fastest increase in voltage exhibited after acetate injection. It is hypothesized that electricity generation in a CO-fed MFC is accomplished by a consortium of carboxydotrophic and carbon monoxide - tolerant anodophilic microorganisms. Crown Copyright © 2010. Published by Elsevier Inc. All rights reserved.

A framework for human microbiome research.

PubMed

2012-06-13

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies.

Selection of an actinobacteria mixed culture for chlordane remediation. Pesticide effects on microbial morphology and bioemulsifier production.

PubMed

Fuentes, María S; Colin, Verónica L; Amoroso, María J; Benimeli, Claudia S

2016-02-01

Chlordane bioremediation using actinobacteria mixed culture is an attractive clean-up technique. Their ability to produce bioemulsifiers could increase the bioavailability of this pesticide. In order to select a defined actinobacteria mixed culture for chlordane remediation, compatibility assays were performed among six Streptomyces strains. The strains did not show growth inhibition, and they were assayed for chlordane removal, either as pure or as mixed cultures. In pure cultures, all of the strains showed specific dechlorination activity (1.42-24.20 EU mg(-1)) and chlordane removal abilities (91.3-95.5%). The specific dechlorination activity was mainly improved with cultures of three or four microorganisms. The mixed culture consisting of Streptomyces sp. A2-A5-A13 was selected. Their ability to produce bioemulsifiers in the presence of glucose or chlordane was tested, but no significant differences were observed (p > 0.05). However, the stability of the emulsions formed was linked to the carbon source used. Only in chlordane presence the emulsions retained 100% of their initial height. Finally, the selected consortium showed a high degree of sporulation in the pesticide presence. This is the first study on the effects that chlordane exerts on microbe morphology and emulsifier production for a defined mixed culture of Streptomyces with ability to remediate the pesticide. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Application of Endophytic Pseudomonas fluorescens and a Bacterial Consortium to Brassica napus Can Increase Plant Height and Biomass under Greenhouse and Field Conditions

PubMed Central

Lally, Richard D.; Galbally, Paul; Moreira, António S.; Spink, John; Ryan, David; Germaine, Kieran J.; Dowling, David N.

2017-01-01

Plant associated bacteria with plant growth promotion (PGP) properties have been proposed for use as environmentally friendly biofertilizers for sustainable agriculture; however, analysis of their efficacy in the field is often limited. In this study, greenhouse and field trials were carried out using individual endophytic Pseudomonas fluorescens strains, the well characterized rhizospheric P. fluorescens F113 and an endophytic microbial consortium of 10 different strains. These bacteria had been previously characterized with respect to their PGP properties in vitro and had been shown to harbor a range of traits associated with PGP including siderophore production, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, and inorganic phosphate solubilization. In greenhouse experiments individual strains tagged with gfp and Kmr were applied to Brassica napus as a seed coat and were shown to effectively colonize the rhizosphere and root of B. napus and in addition they demonstrated a significant increase in plant biomass compared with the non-inoculated control. In the field experiment, the bacteria (individual and consortium) were spray inoculated to winter oilseed rape B. napus var. Compass which was grown under standard North Western European agronomic conditions. Analysis of the data provides evidence that the application of the live bacterial biofertilizers can enhance aspects of crop development in B. napus at field scale. The field data demonstrated statistically significant increases in crop height, stem/leaf, and pod biomass, particularly, in the case of the consortium inoculated treatment. However, although seed and oil yield were increased in the field in response to inoculation, these data were not statistically significant under the experimental conditions tested. Future field trials will investigate the effectiveness of the inoculants under different agronomic conditions. PMID:29312422

Microbial Standards of Commercially Available Produce

NASA Technical Reports Server (NTRS)

Scotten, Jessica

2017-01-01

Limits and guidelines are set on microbial counts in produce to protect the consumer. Different agencies make specifications, which constitute when a product becomes unsafe for human consumption. Producers design their procedures to comply with the limits, but they are responsible creating their own internal standards. The limits and guidelines are summarized here to be applied to assess the microbial safety of the NASA Veggie Program.

Innovative MIOR Process Utilizing Indigenous Reservoir Constituents

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

D. O. Hitzman; A. K. Stepp; D. M. Dennis

This research program is directed at improving the knowledge of reservoir ecology and developing practical microbial solutions for improving oil production. The goal is to identify indigenous microbial populations which can produce beneficial metabolic products and develop a methodology to stimulate those select microbes with nutrient amendments to increase oil recovery. This microbial technology has the capability of producing multiple oil-releasing agents. Experimental laboratory work is underway. Microbial cultures have been isolated from produced water samples. Comparative laboratory studies demonstrating in situ production of microbial products as oil recovery agents were conducted in sand packs with natural field waters withmore » cultures and conditions representative of oil reservoirs. Field pilot studies are underway.« less

Comparison of six methods for the recovery of PCR-compatible microbial DNA from an agricultural biogas plant.

PubMed

Stagnati, L; Soffritti, G; Lanubile, A; Busconi, M

2017-05-01

Six different commercial methods were compared to evaluate their efficiency in recovering high quantity/quality PCR compatible microbial DNA from an agricultural biogas plant. Within the last two decades, biogas plants have been developed to produce energy from organic wastes and from devoted biomass. The complex biotransformations are performed by a diverse consortium of microorganisms that is an important reserve of genes and enzymatic activities with a huge range of applications in various commercial fields. In this respect, the ability to isolate DNA from a complex matrix is of high importance. Important parameters of the recovered DNA are good yield, purity, and quality. The methods examined showed considerable differences about quantity and quality of the recovered DNA and, usually, it was observed that a higher amount was accompanied by more degradation. DNA purity was determined by its PCR amplificability. Only two methods were able to provide DNA pure enough to be directly amplified. For the rest of the methods, a few intermediate steps such as dilution and/or the addition of polyvinylpyrrolidone were necessary to remove the inhibitors present and to amplify the DNA. Real-time PCR analysis evidenced that, as expected, prokaryotic DNA was much more abundant than eukaryotic DNA, but some methods were more suited to recovering prokaryotic or eukaryotic DNA. The digestion analysis of ribosomal DNA amplicons confirmed the influence of the methods on the final output, allowing the recovery of only a fraction of the present species as determined by sequencing a small prokaryotic and eukaryotic ribosomal library.

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

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

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

1999-06-01

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

Diversity, composition, and geographical distribution of microbial communities in California salt marsh sediments

USGS Publications Warehouse

Cordova-Kreylos, A. L.; Cao, Y.; Green, P.G.; Hwang, H.-M.; Kuivila, K.M.; LaMontagne, M.G.; Van De Werfhorst, L. C.; Holden, P.A.; Scow, K.M.

2006-01-01

The Pacific Estuarine Ecosystem Indicators Research Consortium seeks to develop bioindicators of toxicant-induced stress and bioavailability for wetland biota. Within this framework, the effects of environmental and pollutant variables on microbial communities were studied at different spatial scales over a 2-year period. Six salt marshes along the California coastline were characterized using phospholipid fatty acid (PLFA) analysis and terminal restriction fragment length polymorphism (TRFLP) analysis. Additionally, 27 metals, six currently used pesticides, total polychlorinated biphenyls and polycyclic aromatic hydrocarbons, chlordanes, nonachlors, dichlorodiphenyldichloroethane, and dichlorodiphenyldichloroethylene were analyzed. Sampling was performed over large (between salt marshes), medium (stations within a marsh), and small (different channel depths) spatial scales. Regression and ordination analysis suggested that the spatial variation in microbial communities exceeded the variation attributable to pollutants. PLFA analysis and TRFLP canonical correspondence analysis (CCA) explained 74 and 43% of the variation, respectively, and both methods attributed 34% of the variation to tidal cycles, marsh, year, and latitude. After accounting for spatial variation using partial CCA, we found that metals had a greater effect on microbial community composition than organic pollutants had. Organic carbon and nitrogen contents were positively correlated with PLFA biomass, whereas total metal concentrations were positively correlated with biomass and diversity. Higher concentrations of heavy metals were negatively correlated with branched PLFAs and positively correlated with methyl- and cyclo-substituted PLFAs. The strong relationships observed between pollutant concentrations and some of the microbial indicators indicated the potential for using microbial community analyses in assessments of the ecosystem health of salt marshes. Copyright ?? 2006, American Society for Microbiology. All Rights Reserved.

Diversity, Composition, and Geographical Distribution of Microbial Communities in California Salt Marsh Sediments

PubMed Central

Córdova-Kreylos, Ana Lucía; Cao, Yiping; Green, Peter G.; Hwang, Hyun-Min; Kuivila, Kathryn M.; LaMontagne, Michael G.; Van De Werfhorst, Laurie C.; Holden, Patricia A.; Scow, Kate M.

2006-01-01

The Pacific Estuarine Ecosystem Indicators Research Consortium seeks to develop bioindicators of toxicant-induced stress and bioavailability for wetland biota. Within this framework, the effects of environmental and pollutant variables on microbial communities were studied at different spatial scales over a 2-year period. Six salt marshes along the California coastline were characterized using phospholipid fatty acid (PLFA) analysis and terminal restriction fragment length polymorphism (TRFLP) analysis. Additionally, 27 metals, six currently used pesticides, total polychlorinated biphenyls and polycyclic aromatic hydrocarbons, chlordanes, nonachlors, dichlorodiphenyldichloroethane, and dichlorodiphenyldichloroethylene were analyzed. Sampling was performed over large (between salt marshes), medium (stations within a marsh), and small (different channel depths) spatial scales. Regression and ordination analysis suggested that the spatial variation in microbial communities exceeded the variation attributable to pollutants. PLFA analysis and TRFLP canonical correspondence analysis (CCA) explained 74 and 43% of the variation, respectively, and both methods attributed 34% of the variation to tidal cycles, marsh, year, and latitude. After accounting for spatial variation using partial CCA, we found that metals had a greater effect on microbial community composition than organic pollutants had. Organic carbon and nitrogen contents were positively correlated with PLFA biomass, whereas total metal concentrations were positively correlated with biomass and diversity. Higher concentrations of heavy metals were negatively correlated with branched PLFAs and positively correlated with methyl- and cyclo-substituted PLFAs. The strong relationships observed between pollutant concentrations and some of the microbial indicators indicated the potential for using microbial community analyses in assessments of the ecosystem health of salt marshes. PMID:16672478

Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor

PubMed Central

Imachi, Hiroyuki; Aoi, Ken; Tasumi, Eiji; Saito, Yumi; Yamanaka, Yuko; Saito, Yayoi; Yamaguchi, Takashi; Tomaru, Hitoshi; Takeuchi, Rika; Morono, Yuki; Inagaki, Fumio; Takai, Ken

2011-01-01

Microbial methanogenesis in subseafloor sediments is a key process in the carbon cycle on the Earth. However, the cultivation-dependent evidences have been poorly demonstrated. Here we report the cultivation of a methanogenic microbial consortium from subseafloor sediments using a continuous-flow-type bioreactor with polyurethane sponges as microbial habitats, called down-flow hanging sponge (DHS) reactor. We anaerobically incubated methane-rich core sediments collected from off Shimokita Peninsula, Japan, for 826 days in the reactor at 10 °C. Synthetic seawater supplemented with glucose, yeast extract, acetate and propionate as potential energy sources was provided into the reactor. After 289 days of operation, microbiological methane production became evident. Fluorescence in situ hybridization analysis revealed the presence of metabolically active microbial cells with various morphologies in the reactor. DNA- and RNA-based phylogenetic analyses targeting 16S rRNA indicated the successful growth of phylogenetically diverse microbial components during cultivation in the reactor. Most of the phylotypes in the reactor, once it made methane, were more closely related to culture sequences than to the subsurface environmental sequence. Potentially methanogenic phylotypes related to the genera Methanobacterium, Methanococcoides and Methanosarcina were predominantly detected concomitantly with methane production, while uncultured archaeal phylotypes were also detected. Using the methanogenic community enrichment as subsequent inocula, traditional batch-type cultivations led to the successful isolation of several anaerobic microbes including those methanogens. Our results substantiate that the DHS bioreactor is a useful system for the enrichment of numerous fastidious microbes from subseafloor sediments and will enable the physiological and ecological characterization of pure cultures of previously uncultivated subseafloor microbial life. PMID:21654849

Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor.

PubMed

Imachi, Hiroyuki; Aoi, Ken; Tasumi, Eiji; Saito, Yumi; Yamanaka, Yuko; Saito, Yayoi; Yamaguchi, Takashi; Tomaru, Hitoshi; Takeuchi, Rika; Morono, Yuki; Inagaki, Fumio; Takai, Ken

2011-12-01

Microbial methanogenesis in subseafloor sediments is a key process in the carbon cycle on the Earth. However, the cultivation-dependent evidences have been poorly demonstrated. Here we report the cultivation of a methanogenic microbial consortium from subseafloor sediments using a continuous-flow-type bioreactor with polyurethane sponges as microbial habitats, called down-flow hanging sponge (DHS) reactor. We anaerobically incubated methane-rich core sediments collected from off Shimokita Peninsula, Japan, for 826 days in the reactor at 10 °C. Synthetic seawater supplemented with glucose, yeast extract, acetate and propionate as potential energy sources was provided into the reactor. After 289 days of operation, microbiological methane production became evident. Fluorescence in situ hybridization analysis revealed the presence of metabolically active microbial cells with various morphologies in the reactor. DNA- and RNA-based phylogenetic analyses targeting 16S rRNA indicated the successful growth of phylogenetically diverse microbial components during cultivation in the reactor. Most of the phylotypes in the reactor, once it made methane, were more closely related to culture sequences than to the subsurface environmental sequence. Potentially methanogenic phylotypes related to the genera Methanobacterium, Methanococcoides and Methanosarcina were predominantly detected concomitantly with methane production, while uncultured archaeal phylotypes were also detected. Using the methanogenic community enrichment as subsequent inocula, traditional batch-type cultivations led to the successful isolation of several anaerobic microbes including those methanogens. Our results substantiate that the DHS bioreactor is a useful system for the enrichment of numerous fastidious microbes from subseafloor sediments and will enable the physiological and ecological characterization of pure cultures of previously uncultivated subseafloor microbial life.

Consortium inoculum of five thermo-tolerant phosphate solubilizing Actinomycetes for multipurpose biofertilizer preparation

PubMed Central

Nandimath, Arusha P.; Karad, Dilip D.; Gupta, Shantikumar G.; Kharat, Arun S.

2017-01-01

Background and Objectives: Alkaline pH of the soil facilitates the conversion of phosphate present in phosphate fertilizer applied in the field to insoluble phosphate which is not available to plants. Problem of soluble phosphate deficiency arises, primarily due to needless use of phosphate fertilizer. We sought to biofertilizer with the thermo-tolerant phosphate solubilizing actinomycetes consortium that could convert insoluble phosphate to soluble phosphate at wider temperature range. Materials and Methods: In the present investigation consortium of five thermo-tolerant phosphate solubilizing actinomycetes was applied for preparation of inoculum to produce multipurpose bio-fertilizer. Phosphates solubilizing thermo-tolerant 32 actinomycetes strains were processed for identification with the use of PIBWIN software and were screened for phosphate solubilizing activity. Results: Amongst these five actinomycetes were selected on the basis of their ability to produce cellulase, chitinase, pectinase, protease, lipase, amylase and phosphate solubilizing enzymes. Ability to produce these enzymes at 28°C and 50°C were examined. Biofertilizer was prepared by using agricultural waste as a raw material. While preparation of bio-fertilizer the pH decreased from 7.5 to 4.3 and temperature increased up to 74°C maximum at the end of 4th week and in subsequent week it started to decline gradually till it reached around 50°C, which was found to be stable up to eighth week. This thermo-tolerant actinomycetes consortium released soluble phosphate of up to 46.7 μg ml−1. Conclusion: As the mesophilic organisms die out at high temperature of composting hence thormo-tolerant actinomycetes would be the better substitute for preparation of phosphate solubilizing bio-fertilizer with added potential to degrade complex macromolecules in composting. PMID:29296275

Consortium inoculum of five thermo-tolerant phosphate solubilizing Actinomycetes for multipurpose biofertilizer preparation.

PubMed

Nandimath, Arusha P; Karad, Dilip D; Gupta, Shantikumar G; Kharat, Arun S

2017-10-01

Alkaline pH of the soil facilitates the conversion of phosphate present in phosphate fertilizer applied in the field to insoluble phosphate which is not available to plants. Problem of soluble phosphate deficiency arises, primarily due to needless use of phosphate fertilizer. We sought to biofertilizer with the thermo-tolerant phosphate solubilizing actinomycetes consortium that could convert insoluble phosphate to soluble phosphate at wider temperature range. In the present investigation consortium of five thermo-tolerant phosphate solubilizing actinomycetes was applied for preparation of inoculum to produce multipurpose bio-fertilizer. Phosphates solubilizing thermo-tolerant 32 actinomycetes strains were processed for identification with the use of PIBWIN software and were screened for phosphate solubilizing activity. Amongst these five actinomycetes were selected on the basis of their ability to produce cellulase, chitinase, pectinase, protease, lipase, amylase and phosphate solubilizing enzymes. Ability to produce these enzymes at 28°C and 50°C were examined. Biofertilizer was prepared by using agricultural waste as a raw material. While preparation of bio-fertilizer the pH decreased from 7.5 to 4.3 and temperature increased up to 74°C maximum at the end of 4 th week and in subsequent week it started to decline gradually till it reached around 50°C, which was found to be stable up to eighth week. This thermo-tolerant actinomycetes consortium released soluble phosphate of up to 46.7 μg ml -1 . As the mesophilic organisms die out at high temperature of composting hence thormo-tolerant actinomycetes would be the better substitute for preparation of phosphate solubilizing bio-fertilizer with added potential to degrade complex macromolecules in composting.

Multiple Syntrophic Interactions in a Terephthalate-Degrading Methanogenic Consortium

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

Lykidis, Athanasios; Chen, Chia-Lung; Tringe, Susannah G.

2010-08-05

Terephthalate (TA) is one of the top 50 chemicals produced worldwide. Its production results in a TA-containing wastewater that is treated by anaerobic processes through a poorly understood methanogenic syntrophy. Using metagenomics, we characterized the methanogenic consortium tinside a hyper-mesophilic (i.e., between mesophilic and thermophilic), TA-degrading bioreactor. We identified genes belonging to dominant Pelotomaculum species presumably involved in TA degradation through decarboxylation, dearomatization, and modified ?-oxidation to H{sub 2}/CO{sub 2} and acetate. These intermediates are converted to CH{sub 4}/CO{sub 2} by three novel hyper-mesophilic methanogens. Additional secondary syntrophic interactions were predicted in Thermotogae, Syntrophus and candidate phyla OP5 and WWE1more » populations. The OP5 encodes genes capable of anaerobic autotrophic butyrate production and Thermotogae, Syntrophus and WWE1 have the genetic potential to oxidize butyrate to COsub 2}/H{sub 2} and acetate. These observations suggest that the TA-degrading consortium consists of additional syntrophic interactions beyond the standard H{sub 2}-producing syntroph ? methanogen partnership that may serve to improve community stability.« less

Biodegradation of diesel fuel by a microbial consortium in the presence of 1-alkoxymethyl-2-methyl-5-hydroxypyridinium chloride homologues.

PubMed

Chrzanowski, Lukasz; Stasiewicz, Monika; Owsianiak, Mikołaj; Szulc, Alicja; Piotrowska-Cyplik, Agnieszka; Olejnik-Schmidt, Agnieszka K; Wyrwas, Bogdan

2009-09-01

Fast development of ionic liquids as gaining more and more attention valuable chemicals will undoubtedly lead to environmental pollution. New formulations and application of ionic liquids may result in contamination in the presence of hydrophobic compounds, such as petroleum mixtures. We hypothesize that in the presence of diesel fuel low-water-soluble ionic liquids may become more toxic to hydrocarbon-degrading microorganisms. In this study the influence of 1-alkoxymethyl-2-methyl-5-hydroxypyridinium chloride homologues (side-chain length from C(3) to C(18)) on biodegradation of diesel fuel by a bacterial consortium was investigated. Whereas test performed for the consortium cultivated on disodium succinate showed that toxicity of the investigated ionic liquids decreased with increase in side-chain length, only higher homologues (C(8)-C(18)) caused a decrease in diesel fuel biodegradation. As a result of exposure to toxic compounds also modification in cell surface hydrophobicity was observed (MATH). Disulphine blue active substances method was employed to determine partitioning index of ionic liquids between water and diesel fuel phase, which varied from 1.1 to 51% for C(3) and C(18) homologues, respectively. We conclude that in the presence of hydrocarbons acting as a solvent, the increased bioavailability of hydrophobic homologues is responsible for the decrease in biodegradation efficiency of diesel fuel.

Improvement of simultaneous Cr(VI) and phenol removal by an immobilised bacterial consortium and characterisation of biodegradation products.

PubMed

Ontañon, Ornella M; González, Paola S; Barros, Germán G; Agostini, Elizabeth

2017-07-25

Microbial bioremediation emerged some decades ago as an eco-friendly technology to restore polluted sites. Traditionally, the search for microorganisms suitable for bioremediation has been based on the selection of isolated strains able to remove a specific type of pollutant. However, this strategy has now become obsolete, since co-pollution is a global reality. Thus, current studies attempt to find bacterial cultures capable of coping with a mixture of organic and inorganic compounds. In this sense, the bacterial consortium SFC 500-1 has demonstrated efficiency for Cr(VI) and phenol removal, both of which are found in many industrial wastewaters. In the present study, the ability of SFC 500-1 for simultaneous removal was improved through its entrapment in a Ca-alginate matrix. This strategy led to an increased removal of Cr(VI), which was partially reduced to Cr(III). Immobilised cells were able to tolerate and degrade phenol up to 1,500mg/l at high rates, forming catechol and cis,cis-muconate as oxidation intermediates. Successful removal potential through 5 cycles of reuse, as well as after long-term storage, was another important advantage of the immobilised consortium. These characteristics make SFC 500-1 an interesting system for potential application in the biotreatment of co-polluted effluents. Copyright © 2017. Published by Elsevier B.V.

Contamination of Fresh Produce by Microbial Indicators on Farms and in Packing Facilities: Elucidation of Environmental Routes

PubMed Central

Bartz, Faith E.; Lickness, Jacquelyn Sunshine; Heredia, Norma; Fabiszewski de Aceituno, Anna; Newman, Kira L.; Hodge, Domonique Watson; Jaykus, Lee-Ann; García, Santos

2017-01-01

ABSTRACT To improve food safety on farms, it is critical to quantify the impact of environmental microbial contamination sources on fresh produce. However, studies are hampered by difficulties achieving study designs with powered sample sizes to elucidate relationships between environmental and produce contamination. Our goal was to quantify, in the agricultural production environment, the relationship between microbial contamination on hands, soil, and water and contamination on fresh produce. In 11 farms and packing facilities in northern Mexico, we applied a matched study design: composite samples (n = 636, equivalent to 11,046 units) of produce rinses were matched to water, soil, and worker hand rinses during two growing seasons. Microbial indicators (coliforms, Escherichia coli, Enterococcus spp., and somatic coliphage) were quantified from composite samples. Statistical measures of association and correlations were calculated through Spearman's correlation, linear regression, and logistic regression models. The concentrations of all microbial indicators were positively correlated between produce and hands (ρ range, 0.41 to 0.75; P < 0.01). When E. coli was present on hands, the handled produce was nine times more likely to contain E. coli (P < 0.05). Similarly, when coliphage was present on hands, the handled produce was eight times more likely to contain coliphage (P < 0.05). There were relatively low concentrations of indicators in soil and water samples, and a few sporadic significant associations were observed between contamination of soil and water and contamination of produce. This methodology provides a foundation for future field studies, and results highlight the need for interventions surrounding farmworker hygiene and sanitation to reduce microbial contamination of farmworkers' hands. IMPORTANCE This study of the relationships between microbes on produce and in the farm environment can be used to support the design of targeted interventions to prevent or reduce microbial contamination of fresh produce with associated reductions in foodborne illness. PMID:28363965

Contamination of Fresh Produce by Microbial Indicators on Farms and in Packing Facilities: Elucidation of Environmental Routes.

PubMed

Bartz, Faith E; Lickness, Jacquelyn Sunshine; Heredia, Norma; Fabiszewski de Aceituno, Anna; Newman, Kira L; Hodge, Domonique Watson; Jaykus, Lee-Ann; García, Santos; Leon, Juan S

2017-06-01

To improve food safety on farms, it is critical to quantify the impact of environmental microbial contamination sources on fresh produce. However, studies are hampered by difficulties achieving study designs with powered sample sizes to elucidate relationships between environmental and produce contamination. Our goal was to quantify, in the agricultural production environment, the relationship between microbial contamination on hands, soil, and water and contamination on fresh produce. In 11 farms and packing facilities in northern Mexico, we applied a matched study design: composite samples ( n = 636, equivalent to 11,046 units) of produce rinses were matched to water, soil, and worker hand rinses during two growing seasons. Microbial indicators (coliforms, Escherichia coli , Enterococcus spp., and somatic coliphage) were quantified from composite samples. Statistical measures of association and correlations were calculated through Spearman's correlation, linear regression, and logistic regression models. The concentrations of all microbial indicators were positively correlated between produce and hands (ρ range, 0.41 to 0.75; P < 0.01). When E. coli was present on hands, the handled produce was nine times more likely to contain E. coli ( P < 0.05). Similarly, when coliphage was present on hands, the handled produce was eight times more likely to contain coliphage ( P < 0.05). There were relatively low concentrations of indicators in soil and water samples, and a few sporadic significant associations were observed between contamination of soil and water and contamination of produce. This methodology provides a foundation for future field studies, and results highlight the need for interventions surrounding farmworker hygiene and sanitation to reduce microbial contamination of farmworkers' hands. IMPORTANCE This study of the relationships between microbes on produce and in the farm environment can be used to support the design of targeted interventions to prevent or reduce microbial contamination of fresh produce with associated reductions in foodborne illness. Copyright © 2017 American Society for Microbiology.

The Development of the Milwaukee Consortium for Hmong Health: Capacity Building Through Direct Community Engagement.

PubMed

Sparks, Shannon M; Vang, Pang C

2015-01-01

Hmong women experience increased incidence and mortality rates for cervical cancer, yet their cancer risk is often masked by their inclusion within the comparatively low-risk Asian American and Pacific Islander (AAPI) category. Key to this disparity is late stage at diagnosis, a consequence of low rates of screening. This article describes the establishment and community engagement efforts of the Milwaukee Consortium for Hmong Health, established in 2008 to build capacity to investigate and address barriers to screening and cancer care. The Consortium facilitated a series of three community dialogues to explore with community members effective ways to overcome barriers to accessing screening and cancer care. The community dialogues produced a series of six recommendations for action, detailed herein, supported and prioritized by the community. We posit that the integral involvement of the Hmong community from the outset promoted buy-in of ensuing Consortium education and outreach efforts, and helped to ensure fit with community perspectives, needs, and priorities.

Microbial electrosynthetic cells

DOEpatents

May, Harold D.; Marshall, Christopher W.; Labelle, Edward V.

2018-01-30

Methods are provided for microbial electrosynthesis of H.sub.2 and organic compounds such as methane and acetate. Method of producing mature electrosynthetic microbial populations by continuous culture is also provided. Microbial populations produced in accordance with the embodiments as shown to efficiently synthesize H.sub.2, methane and acetate in the presence of CO.sub.2 and a voltage potential. The production of biodegradable and renewable plastics from electricity and carbon dioxide is also disclosed.

Epigenome data release: a participant-centered approach to privacy protection.

PubMed

Dyke, Stephanie O M; Cheung, Warren A; Joly, Yann; Ammerpohl, Ole; Lutsik, Pavlo; Rothstein, Mark A; Caron, Maxime; Busche, Stephan; Bourque, Guillaume; Rönnblom, Lars; Flicek, Paul; Beck, Stephan; Hirst, Martin; Stunnenberg, Henk; Siebert, Reiner; Walter, Jörn; Pastinen, Tomi

2015-07-17

Large-scale epigenome mapping by the NIH Roadmap Epigenomics Project, the ENCODE Consortium and the International Human Epigenome Consortium (IHEC) produces genome-wide DNA methylation data at one base-pair resolution. We examine how such data can be made open-access while balancing appropriate interpretation and genomic privacy. We propose guidelines for data release that both reduce ambiguity in the interpretation of open-access data and limit immediate access to genetic variation data that are made available through controlled access.

Biomethanation under psychrophilic conditions.

PubMed

Dhaked, Ram Kumar; Singh, Padma; Singh, Lokendra

2010-12-01

The biomethanation of organic matter represents a long-standing, well-established technology. Although at mesophilic and thermophilic temperatures the process is well understood, current knowledge on psychrophilic biomethanation is somewhat scarce. Methanogenesis is particularly sensitive to temperature, which not only affects the activity and structure of the microbial community, but also results in a change in the degradation pathway of organic matter. There is evidence of psychrophilic methanogenesis in natural environments, and a number of methanogenic archaea have been isolated with optimum growth temperatures of 15-25 °C. At psychrophilic temperatures, large amounts of heat are needed to operate reactors, thus resulting in a marginal or negative overall energy yield. Biomethanation at ambient temperature can alleviate this requirement, but for stable biogas production, a microbial consortium adapted to low temperatures or a psychrophilic consortium is required. Single-step or two-step high rate anaerobic reactors [expanded granular sludge bed (EGSB) and up flow anaerobic sludge bed (UASB)] have been used for the treatment of low strength wastewater. Simplified versions of these reactors, such as anaerobic sequencing batch reactors (ASBR) and anaerobic migrating blanket reactor (AMBR) have also been developed with the aim of reducing volume and cost. This technology has been further simplified and extended for the disposal of night soil in high altitude, low temperature areas of the Himalayas, where the hilly terrain, non-availability of conventional energy, harsh climate and space constraints limit the application of complicated reactors. Biomethanation at psychrophilic temperatures and the contribution made to night-soil degradation in the Himalayas are reviewed in this article. Copyright © 2010 Elsevier Ltd. All rights reserved.

Degradation of acetaminophen by Delftia tsuruhatensis and Pseudomonas aeruginosa in a membrane bioreactor.

PubMed

De Gusseme, Bart; Vanhaecke, Lynn; Verstraete, Willy; Boon, Nico

2011-02-01

The incidence and fate of pharmaceuticals in the water cycle impose a growing concern for the future reuse of treated water. Because of the recurrent global use of drugs such as Acetaminophen (APAP), an analgesic and antipyretic drug, they are often detected in wastewater treatment plant (WWTP) effluents, receiving surface waters and drinking water resources. In this study, the removal of APAP has been demonstrated in a membrane bioreactor (MBR) fed with APAP as the sole carbon source. After 16 days of operation, at a hydraulic retention time (HRT) of 5 days, more than 99.9% removal was obtained when supplying a synthetic WWTP effluent with 100 μg APAP L(-1). Batch experiments indicated no sorption of APAP to the biomass, no influence of the WWTP effluent matrix, and the capability of the microbial consortium to remove APAP at environmentally relevant concentrations (8.3 μg APAP L(-1)). Incubation with allylthiourea, an ammonia monooxygenase inhibitor, demonstrated that the APAP removal was mainly associated with heterotrophic bacteria and not with the ammonia-oxidizing bacteria. Two APAP degrading strains were isolated from the MBR biomass and identified as Delftia tsuruhatensis and Pseudomonas aeruginosa. During incubation of the isolates, hydroquinone - a potentially toxic transformation product - was temporarily formed but further degraded and/or metabolized. These results suggest that the specific enrichment of a microbial consortium in an MBR operated at a high sludge age might be a promising strategy for post-treatment of WWTP effluents containing pharmaceuticals. © 2010 Elsevier Ltd. All rights reserved.

Microbial Physiology of the Conversion of Residual Oil to Methane: A Protein Prospective

NASA Astrophysics Data System (ADS)

Morris, Brandon E. L.; Bastida-Lopez, Felipe; von Bergen, Martin; Richnow, Hans-Hermann; Suflita, Joseph M.

2010-05-01

Traditional petroleum recovery techniques are unable to extract the majority of oil in most petroliferous deposits. The recovery of even a fraction of residual hydrocarbon in conventional reserves could represent a substantive energy supply. To this end, the microbial conversion of residual oil to methane has gained increasing relevance in recent years [1,2]. Worldwide demand for methane is expected to increase through 2030 [3], as it is a cleaner-burning alternative to traditional fuels [4]. To investigate the microbial physiology of hydrocarbon-decomposition and ultimate methanogenesis, we initiated a two-pronged approach. First, a model alkane-degrading sulfate-reducing bacterium, Desulfoglaeba alkanexedens, was used to interrogate the predominant metabolic pathway(s) differentially expressed during growth on either n-decane or butyrate. A total of 81 proteins were differentially expressed during bacterial growth on butyrate, while 100 proteins were unique to the alkane-grown condition. Proteins related to alkylsuccinate synthase, or the homologous 1-methyl alkylsuccinate synthase, were identified only in the presence of the hydrocarbon. Secondly, we used a newly developed stable isotope probing technique [5] targeted towards proteins to monitor the flux of carbon through a residual oil-degrading bacterial consortium enriched from a gas-condensate contaminated aquifer [1]. Combined carbon and hydrogen stable isotope fractionation identified acetoclastic methanogenesis as the dominant process in this system. Such findings agree with the previous clone library characterization of the consortium. Furthermore, hydrocarbon activation was determined to be the rate-limiting process during the net conversion of residual oil to methane. References 1. Gieg, L.M., K.E. Duncan, and J.M. Suflita, Bioenegy production via microbial conversion of residual oil to natural gas. Appl Environ Micro, 2008. 74(10): p. 3022-3029. 2. Jones, D.M., et al., Crude-oil biodegradation via methanogenesis in subsurface petroleum reserviors. Nature, 2008. 451: p. 176-180. 3. US-DOE, E.I.A., International Energy Outlook 2009. 2009, United States Department of Energy: Washington D.C. 4. DeLuchi, M.A., Emissions of greenhouse gases from the use of transportation fuels and electricity, US-DoE, Editor. 1991, Center for Transportation Research, Argonne National Laboratory: Chicago, Illinois. 5. Jehmlich, N., et al., Protein-based stable isotope probing (Protein-SIP) reveals active species within anoxic mixed cultures. ISME, 2008. 2: p. 1122-1133.

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

PubMed Central

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

2016-01-01

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

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

PubMed

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

2016-01-01

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

Core flooding tests to investigate the effects of IFT reduction and wettability alteration on oil recovery during MEOR process in an Iranian oil reservoir.

PubMed

Rabiei, Arash; Sharifinik, Milad; Niazi, Ali; Hashemi, Abdolnabi; Ayatollahi, Shahab

2013-07-01

Microbial enhanced oil recovery (MEOR) refers to the process of using bacterial activities for more oil recovery from oil reservoirs mainly by interfacial tension reduction and wettability alteration mechanisms. Investigating the impact of these two mechanisms on enhanced oil recovery during MEOR process is the main objective of this work. Different analytical methods such as oil spreading and surface activity measurements were utilized to screen the biosurfactant-producing bacteria isolated from the brine of a specific oil reservoir located in the southwest of Iran. The isolates identified by 16S rDNA and biochemical analysis as Enterobacter cloacae (Persian Type Culture Collection (PTCC) 1798) and Enterobacter hormaechei (PTCC 1799) produce 1.53 g/l of biosurfactant. The produced biosurfactant caused substantial surface tension reduction of the growth medium and interfacial tension reduction between oil and brine to 31 and 3.2 mN/m from the original value of 72 and 29 mN/m, respectively. A novel set of core flooding tests, including in situ and ex situ scenarios, was designed to explore the potential of the isolated consortium as an agent for MEOR process. Besides, the individual effects of wettability alteration and IFT reduction on oil recovery efficiency by this process were investigated. The results show that the wettability alteration of the reservoir rock toward neutrally wet condition in the course of the adsorption of bacteria cells and biofilm formation are the dominant mechanisms on the improvement of oil recovery efficiency.

Enhanced solvent production by metabolic engineering of a twin-clostridial consortium.

PubMed

Wen, Zhiqiang; Minton, Nigel P; Zhang, Ying; Li, Qi; Liu, Jinle; Jiang, Yu; Yang, Sheng

2017-01-01

The efficient fermentative production of solvents (acetone, n-butanol, and ethanol) from a lignocellulosic feedstock using a single process microorganism has yet to be demonstrated. Herein, we developed a consolidated bioprocessing (CBP) based on a twin-clostridial consortium composed of Clostridium cellulovorans and Clostridium beijerinckii capable of producing cellulosic butanol from alkali-extracted, deshelled corn cobs (AECC). To accomplish this a genetic system was developed for C. cellulovorans and used to knock out the genes encoding acetate kinase (Clocel_1892) and lactate dehydrogenase (Clocel_1533), and to overexpress the gene encoding butyrate kinase (Clocel_3674), thereby pulling carbon flux towards butyrate production. In parallel, to enhance ethanol production, the expression of a putative hydrogenase gene (Clocel_2243) was down-regulated using CRISPR interference (CRISPRi). Simultaneously, genes involved in organic acids reassimilation (ctfAB, cbei_3833/3834) and pentose utilization (xylR, cbei_2385 and xylT, cbei_0109) were engineered in C. beijerinckii to enhance solvent production. The engineered twin-clostridia consortium was shown to decompose 83.2g/L of AECC and produce 22.1g/L of solvents (4.25g/L acetone, 11.5g/L butanol and 6.37g/L ethanol). This titer of acetone-butanol-ethanol (ABE) approximates to that achieved from a starchy feedstock. The developed twin-clostridial consortium serves as a promising platform for ABE fermentation from lignocellulose by CBP. Copyright © 2016 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Predicting Species-Resolved Macronutrient Acquisition during Succession in a Model Phototrophic Biofilm Using an Integrated ‘Omics Approach

PubMed Central

Lindemann, Stephen R.; Mobberley, Jennifer M.; Cole, Jessica K.; Markillie, L. M.; Taylor, Ronald C.; Huang, Eric; Chrisler, William B.; Wiley, H. S.; Lipton, Mary S.; Nelson, William C.; Fredrickson, James K.; Romine, Margaret F.

2017-01-01

The principles governing acquisition and interspecies exchange of nutrients in microbial communities and how those exchanges impact community productivity are poorly understood. Here, we examine energy and macronutrient acquisition in unicyanobacterial consortia for which species-resolved genome information exists for all members, allowing us to use multi-omic approaches to predict species’ abilities to acquire resources and examine expression of resource-acquisition genes during succession. Metabolic reconstruction indicated that a majority of heterotrophic community members lacked the genes required to directly acquire the inorganic nutrients provided in culture medium, suggesting high metabolic interdependency. The sole primary producer in consortium UCC-O, cyanobacterium Phormidium sp. OSCR, displayed declining expression of energy harvest, carbon fixation, and nitrate and sulfate reduction proteins but sharply increasing phosphate transporter expression over 28 days. Most heterotrophic members likewise exhibited signs of phosphorus starvation during succession. Though similar in their responses to phosphorus limitation, heterotrophs displayed species-specific expression of nitrogen acquisition genes. These results suggest niche partitioning around nitrogen sources may structure the community when organisms directly compete for limited phosphate. Such niche complementarity around nitrogen sources may increase community diversity and productivity in phosphate-limited phototrophic communities. PMID:28659875

Applying functional metagenomics to search for novel lignocellulosic enzymes in a microbial consortium derived from a thermophilic composting phase of sugarcane bagasse and cow manure.

PubMed

Colombo, Lívia Tavares; de Oliveira, Marcelo Nagem Valério; Carneiro, Deisy Guimarães; de Souza, Robson Assis; Alvim, Mariana Caroline Tocantins; Dos Santos, Josenilda Carlos; da Silva, Cynthia Canêdo; Vidigal, Pedro Marcus Pereira; da Silveira, Wendel Batista; Passos, Flávia Maria Lopes

2016-09-01

Environments where lignocellulosic biomass is naturally decomposed are sources for discovery of new hydrolytic enzymes that can reduce the high cost of enzymatic cocktails for second-generation ethanol production. Metagenomic analysis was applied to discover genes coding carbohydrate-depleting enzymes from a microbial laboratory subculture using a mix of sugarcane bagasse and cow manure in the thermophilic composting phase. From a fosmid library, 182 clones had the ability to hydrolyse carbohydrate. Sequencing of 30 fosmids resulted in 12 contigs encoding 34 putative carbohydrate-active enzymes belonging to 17 glycosyl hydrolase (GH) families. One third of the putative proteins belong to the GH3 family, which includes β-glucosidase enzymes known to be important in the cellulose-deconstruction process but present with low activity in commercial enzyme preparations. Phylogenetic analysis of the amino acid sequences of seven selected proteins, including three β-glucosidases, showed low relatedness with protein sequences deposited in databases. These findings highlight microbial consortia obtained from a mixture of decomposing biomass residues, such as sugar cane bagasse and cow manure, as a rich resource of novel enzymes potentially useful in biotechnology for saccharification of lignocellulosic substrate.

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

PubMed

Wu, J H; Liu, W T; Tseng, I C; Cheng, S S

2001-02-01

The microbial composition and spatial distribution in a terephthalate-degrading anaerobic granular sludge system were characterized using molecular techniques. 16S rDNA clone library and sequence analysis revealed that 78.5% of 106 bacterial clones belonged to the delta subclass of the class Proteobacteria; the remaining clones were assigned to the green non-sulfur bacteria (7.5%), Synergistes (0.9%) and unidentified divisions (13.1%). Most of the bacterial clones in the delta-Proteobacteria formed a novel group containing no known bacterial isolates. For the domain Archaea, 81.7% and 18.3% of 72 archaeal clones were affiliated with Methanosaeta and Methanospirillum, respectively. Spatial localization of microbial populations inside granules was determined by transmission electron microscopy and fluorescent in situ hybridization with oligonucleotide probes targeting the novel delta-proteobacterial group, the acetoclastic Methanosaeta, and the hydrogenotrophic Methanospirillum and members of Methanobacteriaceae. The novel group included at least two different populations with identical rod-shape morphology, which made up more than 87% of the total bacterial cells, and were closely associated with methanogenic populations to form a nonlayered granular structure. This novel group was presumed to be the primary bacterial population involved in the terephthalate degradation in the methanogenic granular consortium.

Mineral Ecology: Surface Specific Colonization and Geochemical Drivers of Biofilm Accumulation, Composition, and Phylogeny

PubMed Central

Jones, Aaron A.; Bennett, Philip C.

2017-01-01

This study tests the hypothesis that surface composition influences microbial community structure and growth of biofilms. We used laboratory biofilm reactors (inoculated with a diverse subsurface community) to explore the phylogenetic and taxonomic variability in microbial communities as a function of surface type (carbonate, silicate, aluminosilicate), media pH, and carbon and phosphate availability. Using high-throughput pyrosequencing, we found that surface type significantly controlled ~70–90% of the variance in phylogenetic diversity regardless of environmental pressures. Consistent patterns also emerged in the taxonomy of specific guilds (sulfur-oxidizers/reducers, Gram-positives, acidophiles) due to variations in media chemistry. Media phosphate availability was a key property associated with variation in phylogeny and taxonomy of whole reactors and was negatively correlated with biofilm accumulation and α-diversity (species richness and evenness). However, mineral-bound phosphate limitations were correlated with less biofilm. Carbon added to the media was correlated with a significant increase in biofilm accumulation and overall α-diversity. Additionally, planktonic communities were phylogenetically distant from those in biofilms. All treatments harbored structurally (taxonomically and phylogenetically) distinct microbial communities. Selective advantages within each treatment encouraged growth and revealed the presence of hundreds of additional operational taxonomix units (OTU), representing distinct consortiums of microorganisms. Ultimately, these results provide evidence that mineral/rock composition significantly influences microbial community structure, diversity, membership, phylogenetic variability, and biofilm growth in subsurface communities. PMID:28400754

Enrichment of anaerobic syngas-converting bacteria from thermophilic bioreactor sludge.

PubMed

Alves, Joana I; Stams, Alfons J M; Plugge, Caroline M; Alves, M Madalena; Sousa, Diana Z

2013-12-01

Thermophilic (55 °C) anaerobic microbial communities were enriched with a synthetic syngas mixture (composed of CO, H2 , and CO2 ) or with CO alone. Cultures T-Syn and T-CO were incubated and successively transferred with syngas (16 transfers) or CO (9 transfers), respectively, with increasing CO partial pressures from 0.09 to 0.88 bar. Culture T-Syn, after 4 successive transfers with syngas, was also incubated with CO and subsequently transferred (9 transfers) with solely this substrate - cultures T-Syn-CO. Incubation with syngas and CO caused a rapid decrease in the microbial diversity of the anaerobic consortium. T-Syn and T-Syn-CO showed identical microbial composition and were dominated by Desulfotomaculum and Caloribacterium species. Incubation initiated with CO resulted in the enrichment of bacteria from the genera Thermincola and Thermoanaerobacter. Methane was detected in the first two to three transfers of T-Syn, but production ceased afterward. Acetate was the main product formed by T-Syn and T-Syn-CO. Enriched T-CO cultures showed a two-phase conversion, in which H2 was formed first and then converted to acetate. This research provides insight into how thermophilic anaerobic communities develop using syngas/CO as sole energy and carbon source can be steered for specific end products and subsequent microbial synthesis of chemicals. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Inhibition and enhancement of microbial surface colonization: the role of silicate composition

USGS Publications Warehouse

Roberts, Jennifer A.

2004-01-01

Classical treatment of cell attachment by models of filtration or coulombic attraction assumes that attachment of cells to mineral surfaces would be controlled by factors such as response to predation, collision efficiency, or coulombic attraction between the charged groups at the mineral and cell surfaces. In the study reported here, the passive model of attachment was investigated using a native microbial consortium and a variety of Al- and Fe-bearing silicates and oxides to determine if other controls, such as mineral composition, also influence the interaction between cells and surfaces. Results from in situ colonization studies in an anaerobic groundwater at pH 6.8 combined with most probable number analyses (MPN) of surface-adherent cells demonstrate that electrostatic effects dominate microbial colonization on positively charged oxide surfaces regardless of mineral composition. In contrast, on negatively charged silicate minerals and glasses, the solid phase composition is a factor in determining the extent of microbial colonization, as well as the diversity of the attached community. In particular, silicates containing more than 1.2% Al exhibit less biomass than Al-poor silicates and MPN suggests a shift in community diversity, possibly indicating Al toxicity on these surfaces. When Fe is present in the silicate, however, this trend is reversed and abundant colonization of the surface is observed. Here, microorganisms preferentially colonize those silicate surfaces that offer beneficial nutrients and avoid those that contain potentially toxic elements.

Groundwater mixing at fracture intersections triggers massive iron-rich microbial mats

NASA Astrophysics Data System (ADS)

Bochet, O.; Le Borgne, T.; Bethencourt, L.; Aquilina, L.; Dufresne, A.; Pédrot, M.; Farasin, J.; Abbott, B. W.; Labasque, T.; Chatton, E.; Lavenant, N.; Petton, C.

2017-12-01

While most freshwater on Earth resides and flows in groundwater systems, these deep subsurface environments are often assumed to have little biogeochemical activity compared to surface environments. Here we report a massive microbial mat of iron-oxidizing bacteria, flourishing 60 meters below the surface, far below the mixing zone where most microbial activity is believed to occur. The abundance of microtubular structures in the mat hinted at the prevalence of of Leptothrix ochracea, but metagenomic analysis revealed a diverse consortium of iron-oxidizing bacteria dominated by unknown members of the Gallionellaceae family. This deep biogeochemical hot spot formed at the intersection of bedrock fractures, which maintain redox gradients by mixing water with different residence times and chemical compositions. Using measured fracture properties and hydrological conditions we developed a quantitative model to simulate the reactive zone where such deep hot spots could occur. While seasonal fluctuations are generally thought to decrease with depth, we found that meter-scale changes in water table level moved the depth of the reactive zone hundreds of meters because the microaerophilic threshold for ironoxidizers is highly sensitive to changes in mixing rates at fracture intersections. These results demonstrate that dynamic microbial communities can be sustained deep below the surface in bedrock fractures. Given the ubiquity of fractures at multiple scales in Earth's subsurface, such deep hot spots may strongly influence global biogeochemical cycles.

Biodegradation of rhamnolipids in liquid cultures: effect of biosurfactant dissipation on diesel fuel/B20 blend biodegradation efficiency and bacterial community composition.

PubMed

Chrzanowski, Łukasz; Dziadas, Mariusz; Ławniczak, Łukasz; Cyplik, Paweł; Białas, Wojciech; Szulc, Alicja; Lisiecki, Piotr; Jeleń, Henryk

2012-05-01

Bacterial utilization of rhamnolipids during biosurfactant-supplemented biodegradation of diesel and B20 (20% biodiesel and 80% diesel v/v) fuels was evaluated under conditions with full aeration or with nitrate and nitrite as electron acceptors. Rhamnolipid-induced changes in community dynamics were assessed by employing real-time PCR and the ddCt method for relative quantification. The experiments with rhamnolipids at 150 mg/l, approx. double critical micelle concentration (CMC) and diesel oil confirmed that rhamnolipids were readily degraded by a soil-isolated consortium of hydrocarbon degraders in all samples, under both aerobic and nitrate-reducing conditions. The presence of rhamnolipids increased the dissipation rates for B20 constituents under aerobic conditions, but did not influence the biodegradation rate of pure diesel. No effect was observed under nitrate-reducing conditions. The biodegradation of rhamnolipids did not favor the growth of any specific consortium member, which proved that the employed biosurfactant did not interfere with the microbial equilibrium during diesel/biodiesel biodegradation. Copyright © 2012 Elsevier Ltd. All rights reserved.

Data set on the bioprecipitation of sulfate and trivalent arsenic by acidophilic non-traditional sulfur reducing bacteria.

PubMed

de Matos, Letícia Paiva; Costa, Patrícia Freitas; Moreira, Mariana; Gomes, Paula Cristine Silva; de Queiroz Silva, Silvana; Gurgel, Leandro Vinícius Alves; Teixeira, Mônica Cristina

2018-04-01

Data presented here are related to the original paper "Simultaneous removal of sulfate and arsenic using immobilized non-traditional sulfate reducing bacteria (SRB) mixed culture and alternative low-cost carbon sources" published by same authors (Matos et al., 2018) [1]. The data set here presented aims to facilitate this paper comprehension by giving readers some additional information. Data set includes a brief description of experimental conditions and the results obtained during both batch and semi-continuous reactors experiments. Data confirmed arsenic and sulfate were simultaneously removed under acidic pH by using a biological treatment based on the activity of a non-traditional sulfur reducing bacteria consortium. This microbial consortium was able to utilize glycerol, powdered chicken feathers as carbon donors, and proved to be resistant to arsenite up to 8.0 mg L - 1 . Data related to sulfate and arsenic removal efficiencies, residual arsenite and sulfate contents, pH and Eh measurements obtained under different experimental conditions were depicted in graphical format. Refers to https://doi.org/10.1016/j.cej.2017.11.035.

Characteristics of electron transport chain and affecting factors for thiosulfate-driven perchlorate reduction.

PubMed

Zhang, Chao; Guo, Jianbo; Lian, Jing; Lu, Caicai; Ngo, Huu Hao; Guo, Wenshan; Song, Yuanyuan; Guo, Yankai

2017-10-01

The mechanism for perchlorate reduction was investigated using thiosulfate-driven (T-driven) perchlorate reduction bacteria. The influences of various environmental conditions on perchlorate reduction, including pH, temperature and electron acceptors were examined. The maximum perchlorate removal rate was observed at pH 7.5 and 40 °C. Perchlorate reduction was delayed due to the coexistence of perchlorate-chlorate and perchlorate-nitrate. The mechanism of the T-driven perchlorate reduction electron transport chain (ETC) was also investigated by utilizing different inhibitors. The results were as follows: firstly, the NADH dehydrogenase was not involved in the ETC; secondly, the FAD dehydrogenase and quinone loop participated in the ETC; and thirdly, cytochrome oxidase was the main pathway in the ETC. Meanwhile, microbial consortium structure analysis indicated that Sulfurovum which can oxidize sulfur compounds coupled to the reduction of nitrate or perchlorate was the primary bacterium in the T-driven and sulfur-driven consortium. This study generates a better understanding of the mechanism of T-driven perchlorate reduction. Copyright © 2017 Elsevier Ltd. All rights reserved.

Influence of coral and algal exudates on microbially mediated reef metabolism.

PubMed

Haas, Andreas F; Nelson, Craig E; Rohwer, Forest; Wegley-Kelly, Linda; Quistad, Steven D; Carlson, Craig A; Leichter, James J; Hatay, Mark; Smith, Jennifer E

2013-01-01

Benthic primary producers in tropical reef ecosystems can alter biogeochemical cycling and microbial processes in the surrounding seawater. In order to quantify these influences, we measured rates of photosynthesis, respiration, and dissolved organic carbon (DOC) exudate release by the dominant benthic primary producers (calcifying and non-calcifying macroalgae, turf-algae and corals) on reefs of Mo'orea French Polynesia. Subsequently, we examined planktonic and benthic microbial community response to these dissolved exudates by measuring bacterial growth rates and oxygen and DOC fluxes in dark and daylight incubation experiments. All benthic primary producers exuded significant quantities of DOC (roughly 10% of their daily fixed carbon) into the surrounding water over a diurnal cycle. The microbial community responses were dependent upon the source of the exudates and whether the inoculum of microbes included planktonic or planktonic plus benthic communities. The planktonic and benthic microbial communities in the unamended control treatments exhibited opposing influences on DO concentration where respiration dominated in treatments comprised solely of plankton and autotrophy dominated in treatments with benthic plus plankon microbial communities. Coral exudates (and associated inorganic nutrients) caused a shift towards a net autotrophic microbial metabolism by increasing the net production of oxygen by the benthic and decreasing the net consumption of oxygen by the planktonic microbial community. In contrast, the addition of algal exudates decreased the net primary production by the benthic communities and increased the net consumption of oxygen by the planktonic microbial community thereby resulting in a shift towards net heterotrophic community metabolism. When scaled up to the reef habitat, exudate-induced effects on microbial respiration did not outweigh the high oxygen production rates of benthic algae, such that reef areas dominated with benthic primary producers were always estimated to be net autotrophic. However, estimates of microbial consumption of DOC at the reef scale surpassed the DOC exudation rates suggesting net consumption of DOC at the reef-scale. In situ mesocosm experiments using custom-made benthic chambers placed over different types of benthic communities exhibited identical trends to those found in incubation experiments. Here we provide the first comprehensive dataset examining direct primary producer-induced, and indirect microbially mediated alterations of elemental cycling in both benthic and planktonic reef environments over diurnal cycles. Our results highlight the variability of the influence of different benthic primary producers on microbial metabolism in reef ecosystems and the potential implications for energy transfer to higher trophic levels during shifts from coral to algal dominance on reefs.

Biogeography of a human oral microbiome at the micron scale

PubMed Central

Mark Welch, Jessica L.; Rossetti, Blair J.; Rieken, Christopher W.; Dewhirst, Floyd E.; Borisy, Gary G.

2016-01-01

The spatial organization of complex natural microbiomes is critical to understanding the interactions of the individual taxa that comprise a community. Although the revolution in DNA sequencing has provided an abundance of genomic-level information, the biogeography of microbiomes is almost entirely uncharted at the micron scale. Using spectral imaging fluorescence in situ hybridization as guided by metagenomic sequence analysis, we have discovered a distinctive, multigenus consortium in the microbiome of supragingival dental plaque. The consortium consists of a radially arranged, nine-taxon structure organized around cells of filamentous corynebacteria. The consortium ranges in size from a few tens to a few hundreds of microns in radius and is spatially differentiated. Within the structure, individual taxa are localized at the micron scale in ways suggestive of their functional niche in the consortium. For example, anaerobic taxa tend to be in the interior, whereas facultative or obligate aerobes tend to be at the periphery of the consortium. Consumers and producers of certain metabolites, such as lactate, tend to be near each other. Based on our observations and the literature, we propose a model for plaque microbiome development and maintenance consistent with known metabolic, adherence, and environmental considerations. The consortium illustrates how complex structural organization can emerge from the micron-scale interactions of its constituent organisms. The understanding that plaque community organization is an emergent phenomenon offers a perspective that is general in nature and applicable to other microbiomes. PMID:26811460

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

PubMed

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

2018-06-01

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

Photochemical alteration of organic carbon draining permafrost soils shifts microbial metabolic pathways and stimulates respiration.

PubMed

Ward, Collin P; Nalven, Sarah G; Crump, Byron C; Kling, George W; Cory, Rose M

2017-10-03

In sunlit waters, photochemical alteration of dissolved organic carbon (DOC) impacts the microbial respiration of DOC to CO 2 . This coupled photochemical and biological degradation of DOC is especially critical for carbon budgets in the Arctic, where thawing permafrost soils increase opportunities for DOC oxidation to CO 2 in surface waters, thereby reinforcing global warming. Here we show how and why sunlight exposure impacts microbial respiration of DOC draining permafrost soils. Sunlight significantly increases or decreases microbial respiration of DOC depending on whether photo-alteration produces or removes molecules that native microbial communities used prior to light exposure. Using high-resolution chemical and microbial approaches, we show that rates of DOC processing by microbes are likely governed by a combination of the abundance and lability of DOC exported from land to water and produced by photochemical processes, and the capacity and timescale that microbial communities have to adapt to metabolize photo-altered DOC.The role of dissolved organic carbon (DOC) photo-alteration in the microbial respiration of DOC to CO 2 is unclear. Here, the authors show that the impact of this mechanism depends on whether photo-alteration of DOC produces or removes molecules used by native microbial communities prior to light exposure.

An Annotated Bibliography of Studies and Reports Produced by the Advanced Decision Architectures Consortium of the Collaborative Technology Alliance from 2001 to 2010

DTIC Science & Technology

2010-12-01

Bradshaw, J. M. (2008). How to Do with Owl What People Say You Can’t. In Proceedings of 2008 IEEE Conference on Policy, Palisades, NY. Bradshaw, J...Architectures Consortium of the Collaborative Technology Alliance from 2001 to 2010 91 Bradshaw, J. M. (2008). How to Do with Owl What People Say You...would not want separate modules, say , for problem detection skills and sensemaking skills.• The same scenarios should be training sensemaking and

Bioremediation of oil-based drill cuttings by a halophilic consortium isolated from oil-contaminated saline soil.

PubMed

Rezaei Somee, Maryam; Shavandi, Mahmoud; Dastgheib, Seyed Mohammad Mehdi; Amoozegar, Mohammad Ali

2018-05-01

Oil-based drill cuttings are hazardous wastes containing complex hydrocarbons, heavy metals, and brine. Their remediation is a crucial step before release to the environment. In this work, we enriched a halophilic consortium, from oil-polluted saline soil, which is capable of degrading diesel as the main pollutant of oil-based drill cuttings. The degradation ability of the consortium was evaluated in microcosms using two different diluting agents (fine sand and biologically active soil). During the bioremediation process, the bacterial community dynamics of the microcosms was surveyed using PCR amplification of a fragment of 16S rRNA gene followed by denaturing gradient gel electrophoresis (DGGE). The diesel degradation rates were monitored by total petroleum hydrocarbon (TPH) measurement and the total count of heterotrophic and diesel-degrading bacteria. After 3 months, the microcosm containing fine sand and drill cuttings with the ratio of 1:1 (initial TPH of 36,000 mg/kg) showed the highest TPH removal (40%) and its dominant bacterial isolates belonged to the genera Dietzia, Arthrobacter , and Halomonas . DGGE results also confirmed the role of these genera in drill cuttings remediation. DGGE analysis of the bacterial diversity showed that Propionibacterium, Salinimicrobium, Marinobacter , and Dietzia are dominant in active soil microcosm; whereas Bacillus, Salinibacillus , and Marinobacter are abundant in sand microcosm. Our results suggest that the bioaugmentation strategy would be more successful if the diluting agent does not contain a complex microbial community.

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

PubMed

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

2012-01-01

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

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

PubMed Central

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

2012-01-01

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

Physiological characterization of a broad spectrum reductively dechlorinating consortium

USGS Publications Warehouse

Lorah, M.M.; Majcher, E.; Jones, E.; Driedger, G.; Dworatzek, S.; Graves, D.

2005-01-01

A wetland sediment-derived microbial consortium (WBC-2) was developed by the US Geological Survey and propagated in vitro to large quantities by SiREM Laboratory for potential use in bioaugmentation applications. On the basis of bench-scale tests, the consortium could completely dechlorinate 1,1,2,2-tetrachloroethylene, tetrachloroethylene, trichloroethylene, 1,1,2-trichloroethane, cis- and trans-1,2-dichoroethylene, 1,1-dichloroethylene, 1,2-dichloroethane, and vinyl chloride in culture medium. Batch microcosms were carried out under anaerobic conditions in culture medium with neutral pH and with pH adjusted from acidic (pH 4, 5, and 6) to alkaline (pH 8 and 9). To evaluate oxygen sensitivity of WBC-2, an aliquot was removed from an anaerobic culture vessel and poured into smaller containers on the bench top where a series of oxygen exposures were applied to the culture by bubbling ambient air through the culture at a rate of ??? 100 mL/min. Chlorinated methanes tended to inhibit activity of a wide range of microorganisms. Although toxicity effects from CT addition were observed with WBC-2 in liquid culture at 3 mg/L concentration, WBC-2 in the columns could maintain degradation of CT and chloroform (CF) and of the chlorinated ethanes and ethylenes at CT and CF concentrations of 10 and 20 mg/L, respectively. This is an abstract of a paper presented at the Proceedings of the 8th International In Situ and On-Site Bioremediation Symposium (Baltimore, MD 6/6-9/2005).

Biomass and bioenergy production potential of microalgae consortium in open and closed bioreactors using untreated carpet industry effluent as growth medium.

PubMed

Chinnasamy, Senthil; Bhatnagar, Ashish; Claxton, Ronald; Das, K C

2010-09-01

Improved wastewater management with beneficial utilization will result in enhanced sustainability and enormous cost savings in industries. Algae cultivation systems viz. raceway ponds, vertical tank reactors (VTR) and polybags were evaluated for mass production of algal consortium using carpet industry (CI) untreated wastewater. Overall areal biomass productivity of polybags (21.1 g m(-2)d(-1)) was the best followed by VTR (8.1 g m(-2)d(-1)) and raceways (5.9 g m(-2)d(-1)). An estimated biomass productivity of 51 and 77 tons ha(-1)year(-1) can be achieved using 20 and 30 L capacity polybags, respectively with triple row arrangement. Biomass obtained from algal consortium was rich in proteins (approximately 53.8%) and low in carbohydrates (approximately 15.7%) and lipids (approximately 5.3%). Consortium cultivated in polybags has the potential to produce 12,128 m(3) of biomethane ha(-1)year(-1). To be economically viable, the capital expenditure for polybag reactors needs to be reduced to $10 m(-2) for bioenergy/biofuel production. (c) 2010 Elsevier Ltd. All rights reserved.

Inner-City Energy and Environmental Education Consortium: Student`s Standing Committee workshop. Appendix 13.8

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

Not Available

1992-10-23

This report is the fourth working document produced by the Inner-City Energy and Environmental Education Consortium under a Department of Energy planning grant to the Weston Institute. It was prepared in a Student`s Standing Committee workshop held at the Johns Hopkins School of Continuing Studies Downtown Center, 1 Charles Plaza in Baltimore, Maryland. Twenty two participants representing Consortium institutions attended the workshop. Weston Institute provided staff support for the conduct of the workshop and prepared this report. Workshop participants addressed the question What will be the most effective methods to excite and empower students to enter and to succeed inmore » energy and environmental careers? The results of the workshop are presented in the order of importance attached to each proposed method, or grouping of methods, by the participants.« less

Innovative MIOR Process Utilizing Indigenous Reservoir Constituents

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

Hitzman, D.O.; Stepp, A.K.; Dennis, D.M.

This research program was directed at improving the knowledge of reservoir ecology and developing practical microbial solutions for improving oil production. The goal was to identify indigenous microbial populations which can produce beneficial metabolic products and develop a methodology to stimulate those select microbes with inorganic nutrient amendments to increase oil recovery. This microbial technology has the capability of producing multiple oil-releasing agents.

Innovative MIOR Process Utilizing Indigenous Reservoir Constituents

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

Hitzman, D.O.; stepp, A.K.; Dennis, D.M.

This research program was directed at improving the knowledge of reservoir ecology and developing practical microbial solutions for improving oil production. The goal was to identify indigenous microbial populations which can produce beneficial metabolic products and develop a methodology to stimulate those select microbes with nutrient amendments to increase oil recovery. This microbial technology has the capability of producing multiple oil-releasing agents.

Microbial factories for recombinant pharmaceuticals

PubMed Central

Ferrer-Miralles, Neus; Domingo-Espín, Joan; Corchero, José Luis; Vázquez, Esther; Villaverde, Antonio

2009-01-01

Most of the hosts used to produce the 151 recombinant pharmaceuticals so far approved for human use by the Food and Drug Administration (FDA) and/or by the European Medicines Agency (EMEA) are microbial cells, either bacteria or yeast. This fact indicates that despite the diverse bottlenecks and obstacles that microbial systems pose to the efficient production of functional mammalian proteins, namely lack or unconventional post-translational modifications, proteolytic instability, poor solubility and activation of cell stress responses, among others, they represent convenient and powerful tools for recombinant protein production. The entering into the market of a progressively increasing number of protein drugs produced in non-microbial systems has not impaired the development of products obtained in microbial cells, proving the robustness of the microbial set of cellular systems (so far Escherichia coli and Saccharomyces cerevisae) developed for protein drug production. We summarize here the nature, properties and applications of all those pharmaceuticals and the relevant features of the current and potential producing hosts, in a comparative way. PMID:19317892

Microbial consortium role in processing liquid waste of vegetables in Keputran Market Surabaya as organic liquid fertilizer ferti-plus

NASA Astrophysics Data System (ADS)

Rizqi, Fauziah; Supriyanto, Agus; Lestari, Intan; Lita Indri D., L.; Elmi Irmayanti, A.; Rahmaniyah, Fadilatur

2016-03-01

Many activities in this market is directly proportional to increase production of vegetables waste, especially surabaya. Therefore, in this study aims to utilize liquid waste of vegetables into liquid organic fertilizer by mixing microbial consorsium. The microbial consorsium consist of Azotobacter chrococcum, Azospirillum brasilense, Rhizobium leguminosarum, Bacillus subtilis, Bacillus megaterium, Pseudomonas putida, and Pseudomonas fluorescens. Ttreatment of microbial concentrations (5%, 10%, 15%) and the length of the incubation period (7 days, 14 days, 21 days) used in this research. The parameters used are: C/N ratio, levels of CNP, and BOD value. This study uses a standard organic fertilizer value according SNI19-7030-2004, The results show the value of C/N ratio comply with the ISO standards. C levels showed an increase during the incubation period but not compare with standards. N levels that compare with standards are microbial treatment in all group concentration except control group with an incubation period of 21 days is > 7. P levels compare with the existing standards in the group of microbe concentration of 10% and 15% during the incubation period. The value of the initial BOD liquid waste of vegetable is 790.25 mg / L, this value indicates that the waste should not go into the water body. Accordingly, the results of this study can not be used as a liquid organic fertilizer, but potentially if it is used as a natural career or build natural soil. The Building natural soil is defined as the natural ingredients that can be used to improve soil properties.

Predominance and metabolic potential of Halanaerobium spp. in produced water from hydraulically fractured Marcellus Shale wells

DOE PAGES

Lipus, Daniel; Vikram, Amit; Ross, Daniel; ...

2017-02-03

Here, microbial activity in the produced water from hydraulically fractured oil and gas wells may potentially interfere with hydrocarbon production and cause damage to the well and surface infrastructure via corrosion, sulfide release, and fouling. In this study, we surveyed the microbial abundance and community structure of produced water sampled from 42 Marcellus Shale wells in southwestern Pennsylvania (well age ranged from 150 to 1,846 days) to better understand the microbial diversity of produced water. We sequenced the V4 region of the 16S rRNA gene to assess taxonomy and utilized quantitative PCR (qPCR) to evaluate the microbial abundance across allmore » 42 produced water samples. Bacteria of the order Halanaerobiales were found to be the most abundant organisms in the majority of the produced water samples, emphasizing their previously suggested role in hydraulic fracturing-related microbial activity. Statistical analyses identified correlations between well age and biocide formulation and the microbial community, in particular, the relative abundance of Halanaerobiales. We further investigated the role of members of the order Halanaerobiales in produced water by reconstructing and annotating a Halanaerobium draft genome (named MDAL1), using shotgun metagenomic sequencing and metagenomic binning. The recovered draft genome was found to be closely related to the species H. congolense, an oil field isolate, and Halanaerobium sp. strain T82-1, also recovered from hydraulic fracturing produced water. Reconstruction of metabolic pathways revealed Halanaerobium sp. strain MDAL1 to have the potential for acid production, thiosulfate reduction, and biofilm formation, suggesting it to have the ability to contribute to corrosion, souring, and biofouling events in the hydraulic fracturing infrastructure.« less

Predominance and metabolic potential of Halanaerobium spp. in produced water from hydraulically fractured Marcellus Shale wells

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

Lipus, Daniel; Vikram, Amit; Ross, Daniel

Here, microbial activity in the produced water from hydraulically fractured oil and gas wells may potentially interfere with hydrocarbon production and cause damage to the well and surface infrastructure via corrosion, sulfide release, and fouling. In this study, we surveyed the microbial abundance and community structure of produced water sampled from 42 Marcellus Shale wells in southwestern Pennsylvania (well age ranged from 150 to 1,846 days) to better understand the microbial diversity of produced water. We sequenced the V4 region of the 16S rRNA gene to assess taxonomy and utilized quantitative PCR (qPCR) to evaluate the microbial abundance across allmore » 42 produced water samples. Bacteria of the order Halanaerobiales were found to be the most abundant organisms in the majority of the produced water samples, emphasizing their previously suggested role in hydraulic fracturing-related microbial activity. Statistical analyses identified correlations between well age and biocide formulation and the microbial community, in particular, the relative abundance of Halanaerobiales. We further investigated the role of members of the order Halanaerobiales in produced water by reconstructing and annotating a Halanaerobium draft genome (named MDAL1), using shotgun metagenomic sequencing and metagenomic binning. The recovered draft genome was found to be closely related to the species H. congolense, an oil field isolate, and Halanaerobium sp. strain T82-1, also recovered from hydraulic fracturing produced water. Reconstruction of metabolic pathways revealed Halanaerobium sp. strain MDAL1 to have the potential for acid production, thiosulfate reduction, and biofilm formation, suggesting it to have the ability to contribute to corrosion, souring, and biofouling events in the hydraulic fracturing infrastructure.« less

Gut microbial profile analysis by MiSeq sequencing of pancreatic carcinoma patients in China

PubMed Central

Xie, Haiyang; Li, Ang; Lu, Haifeng; Xu, Shaoyan; Zhou, Lin; Zhang, Hua; Cui, Guangying; Chen, Xinhua; Liu, Yuanxing; Wu, Liming; Qin, Nan; Sun, Ranran; Wang, Wei; Li, Lanjuan; Wang, Weilin; Zheng, Shusen

2017-01-01

Pancreatic carcinoma (PC) is a lethal cancer. Gut microbiota is associated with some risk factors of PC, e.g. obesity and types II diabetes. However, the specific gut microbial profile in clinical PC in China has never been reported. This prospective study collected 85 PC and 57 matched healthy controls (HC) to analyze microbial characteristics by MiSeq sequencing. The results showed that gut microbial diversity was decreased in PC with an unique microbial profile, which partly attributed to its decrease of alpha diversity. Microbial alterations in PC featured by the increase of certain pathogens and lipopolysaccharides-producing bacteria, and the decrease of probiotics and butyrate-producing bacteria. Microbial community in obstruction cases was separated from the un-obstructed cases. Streptococcus was associated with the bile. Furthermore, 23 microbial functions e.g. Leucine and LPS biosynthesis were enriched, while 13 functions were reduced in PC. Importantly, based on 40 genera associated with PC, microbial markers achieves a high classification power with AUC of 0.842. In conclusion, gut microbial profile was unique in PC, providing a microbial marker for non-invasive PC diagnosis. PMID:29221120

Preliminary investigations of the rhizosphere nature of hydroponically grown lettuces

NASA Astrophysics Data System (ADS)

Antunes, Inês; Paille, Christel; Lasseur, Christophe

Due to capabilities of current launchers, future manned exploration beyond the Earth orbit will imply long journeys and extended stays on planet surfaces. For this reason, it is of a great importance to develop a Regenerative Life Support System that enables the crew to be, to a very large extent, metabolic consumables self-sufficient. In this context, the European Space Agency, associated with a scientific and engineering con-sortium, initiated in 1989 the Micro-Ecological Life Support System Alternative (MELiSSA) project. This concept, inspired on a terrestrial ecosystem (i.e. a lake), comprises five intercon-nected compartments inhabited by micro-organisms and higher-plants aiming to produce food, fresh water, and oxygen from organic waste, carbon dioxide, and minerals. Given the important role of the higher-plant compartment for the consumption of carbon dioxide and the production of oxygen, potable water, and food, it was decided to study the microbial communities present in the root zone of the plants (i.e. the rhizosphere), and their synergistic and antagonistic influences in the plant growth. This understanding is important for later investigations concerning the technology involved in the higher plant compartment, since the final goal is to integrate this compartment inside the MELiSSA loop and to guarantee a healthy and controlled environment for the plants to grow under reduced-gravity conditions. To perform a preliminary assessment of the microbial populations of the root zone, lettuces were grown in a hydroponic system and their growth was characterized in terms of nutrient uptake, plant diameter, and plant wet and dry weights. In parallel, the microbial population, bacteria and fungi, present in the hydroponic medium and also inside and outside the roots were analyzed in terms of quantity and nature. The goal of this presentation is to give a preliminary review in the plant root zone of the micro-organisms communities and as well their proportions. The collected information will then be correlated to each phase of the growth of the lettuces and to the results for the corresponding growth parameters. This will enable characterization of the microbial communities in the rhizosphere and the understanding of how these populations influence each phase of the plant growth. Conclusions are proposed for further investigations.

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

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

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

2000-04-01

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

Potential microbial risk factors related to soil amendments and irrigation water of potato crops.

PubMed

Selma, M V; Allende, A; López-Gálvez, F; Elizaquível, P; Aznar, R; Gil, M I

2007-12-01

This study assesses the potential microbial risk factors related to the use of soil amendments and irrigation water on potato crops, cultivated in one traditional and two intensive farms during two harvest seasons. The natural microbiota and potentially pathogenic micro-organisms were evaluated in the soil amendment, irrigation water, soil and produce. Uncomposted amendments and residual and creek water samples showed the highest microbial counts. The microbial load of potatoes harvested in spring was similar among the tested farms despite the diverse microbial levels of Listeria spp. and faecal coliforms in the potential risk sources. However, differences in total coliform load of potato were found between farms cultivated in the autumn. Immunochromatographic rapid tests and the BAM's reference method (Bacteriological Analytical Manual; AOAC International) were used to detect Escherichia coli O157:H7 from the potential risk sources and produce. Confirmation of the positive results by polymerase chain reaction procedures showed that the immunochromatographic assay was not reliable as it led to false-positive results. The potentially pathogenic micro-organisms of soil amendment, irrigation water and soil samples changed with the harvest seasons and the use of different agricultural practices. However, the microbial load of the produce was not always influenced by these risk sources. Improvements in environmental sample preparation are needed to avoid interferences in the use of immunochromatographic rapid tests. The potential microbial risk sources of fresh produce should be regularly controlled using reliable detection methods to guarantee their microbial safety.

Analyses of n-alkanes degrading community dynamics of a high-temperature methanogenic consortium enriched from production water of a petroleum reservoir by a combination of molecular techniques.

PubMed

Zhou, Lei; Li, Kai-Ping; Mbadinga, Serge Maurice; Yang, Shi-Zhong; Gu, Ji-Dong; Mu, Bo-Zhong

2012-08-01

Despite the knowledge on anaerobic degradation of hydrocarbons and signature metabolites in the oil reservoirs, little is known about the functioning microbes and the related biochemical pathways involved, especially about the methanogenic communities. In the present study, a methanogenic consortium enriched from high-temperature oil reservoir production water and incubated at 55 °C with a mixture of long chain n-alkanes (C(15)-C(20)) as the sole carbon and energy sources was characterized. Biodegradation of n-alkanes was observed as methane production in the alkanes-amended methanogenic enrichment reached 141.47 μmol above the controls after 749 days of incubation, corresponding to 17 % of the theoretical total. GC-MS analysis confirmed the presence of putative downstream metabolites probably from the anaerobic biodegradation of n-alkanes and indicating an incomplete conversion of the n-alkanes to methane. Enrichment cultures taken at different incubation times were subjected to microbial community analysis. Both 16S rRNA gene clone libraries and DGGE profiles showed that alkanes-degrading community was dynamic during incubation. The dominant bacterial species in the enrichment cultures were affiliated with Firmicutes members clustering with thermophilic syntrophic bacteria of the genera Moorella sp. and Gelria sp. Other represented within the bacterial community were members of the Leptospiraceae, Thermodesulfobiaceae, Thermotogaceae, Chloroflexi, Bacteroidetes and Candidate Division OP1. The archaeal community was predominantly represented by members of the phyla Crenarchaeota and Euryarchaeota. Corresponding sequences within the Euryarchaeota were associated with methanogens clustering with orders Methanomicrobiales, Methanosarcinales and Methanobacteriales. On the other hand, PCR amplification for detection of functional genes encoding the alkylsuccinate synthase α-subunit (assA) was positive in the enrichment cultures. Moreover, the appearance of a new assA gene sequence identified in day 749 supported the establishment of a functioning microbial species in the enrichment. Our results indicate that n-alkanes are converted to methane slowly by a microbial community enriched from oilfield production water and fumarate addition is most likely the initial activation step of n-alkanes degradation under thermophilic methanogenic conditions.

76 FR 8707 - Syngenta Seeds, Inc.; Determination of Nonregulated Status for Corn Genetically Engineered To...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-15

... for Corn Genetically Engineered To Produce an Enzyme That Facilitates Ethanol Production AGENCY... event 3272, which has been genetically engineered to produce a microbial enzyme that facilitates ethanol... transformation event 3272, which has been genetically engineered to produce a microbial enzyme that facilitates...

Preliminary biogeochemical assessment of EPICA LGM and Holocene ice samples

NASA Astrophysics Data System (ADS)

Bulat, S.; Alekhina, I.; Marie, D.; Wagenbach, D.; Raynaud, D.; Petit, J. R.

2009-04-01

We are investigating the biological content (biomass and microbial diversity of Aeolian origin) of EPICA ice core within the frame of EPICA Microbiology consortium*. Two ice core sections were selected from EPICA Dome C and Droning Maud Land, both from LGM and Holocene. Preliminary measurements of DOC (dissolved organic content) and microbial cell concentrations have been performed. Both analyses showed the very low biomass and ultra low DOC content. Trace DNA analyses are in a progress. The ice sections were decontaminated in LGGE cold and clean room facilities benefiting the protocol developed for Vostok ice core studies. The melt water was then shared between two party laboratories for a complementary approach in studying microbial content. Prior to biology the melt water was tested for chemical contaminant ions and organic acids, DOC and dust contents. The biological methods included all the spectra of appropriate molecular techniques (gDNA extraction, PCR, clone libraries and sequencing). As preliminary results, both LGM (well identified by dust fallout) and Holocene ice samples (EDC99 and EDML) proved to be extremely clear (i.e. pristine) in terms of biomass (less then 4 cells per ml) and DOC contents (less then 5 ppbC). There was no obvious difference between LGM and Holocene in cell counts, while LGM showed a bit high organic carbon content. The latter in terms of biology means ultra-oligotrophic conditions (i.e., no possibility for heterotrophic life style). In fact no metabolizing microbial cells or propagating populations are expected at these depths at temperature -38oC and lower (limiting life temperature threshold is -20°C). Nevertheless some life seeds brought in Antarctica with precipitation could be well preserved because the age is rather young (21 kyr and less). Trying to identify these aliens and document their distribution during last climate cycle the meltwater was concentrated about 1000 times down. The genomic DNA was extracted and very weak signals were possible to generate which are now under cloning. The signals were hard to reproduce because of rather low volume of samples. More ice volume is needed to get the biosignal stronger and reproducible. Meantime we are adjusting PCR and in addition testing DNA repair-enzyme cocktail in case of DNA damage. As a preliminary conclusion we would like to highlight the following. Both Holocene and LGM ice samples (EDC99 and EDML) are very clean in terms of Ultra low biomass and Ultra low DOC content. The most basal ice of EDC and EDML ice cores could help in assessing microbial biomass and diversity if present under the glacier at the ice-bedrock boundary. * The present-day consortium includes S. Bulat, I. Alekhina, P. Normand, D. Prieur, J-R. Petit and D. Raynaud (France) and E. Willerslev and J.P. Steffensen (Denmark)

Inhibiting mild steel corrosion from sulfate-reducing bacteria using antimicrobial-producing biofilms in Three-Mile-Island process water.

PubMed

Zuo, R; Ornek, D; Syrett, B C; Green, R M; Hsu, C-H; Mansfeld, F B; Wood, T K

2004-04-01

Biofilms were used to produce gramicidin S (a cyclic decapeptide) to inhibit corrosion-causing, sulfate-reducing bacteria (SRB). In laboratory studies these biofilms protected mild steel 1010 continuously from corrosion in the aggressive, cooling service water of the AmerGen Three-Mile-Island (TMI) nuclear plant, which was augmented with reference SRB. The growth of both reference SRB (Gram-positive Desulfosporosinus orientis and Gram-negative Desulfovibrio vulgaris) was shown to be inhibited by supernatants of the gramicidin-S-producing bacteria as well as by purified gramicidin S. Electrochemical impedance spectroscopy and mass loss measurements showed that the protective biofilms decreased the corrosion rate of mild steel by 2- to 10-fold when challenged with the natural SRB of the TMI process water supplemented with D. orientis or D. vulgaris. The relative corrosion inhibition efficiency was 50-90% in continuous reactors, compared to a biofilm control which did not produce the antimicrobial gramicidin S. Scanning electron microscope and reactor images also revealed that SRB attack was thwarted by protective biofilms that secrete gramicidin S. A consortium of beneficial bacteria (GGPST consortium, producing gramicidin S and other antimicrobials) also protected the mild steel.

Biodegradation of free cyanide and subsequent utilisation of biodegradation by-products by Bacillus consortia: optimisation using response surface methodology.

PubMed

Mekuto, Lukhanyo; Ntwampe, Seteno Karabo Obed; Jackson, Vanessa Angela

2015-07-01

A mesophilic alkali-tolerant bacterial consortium belonging to the Bacillus genus was evaluated for its ability to biodegrade high free cyanide (CN(-)) concentration (up to 500 mg CN(-)/L), subsequent to the oxidation of the formed ammonium and nitrates in a continuous bioreactor system solely supplemented with whey waste. Furthermore, an optimisation study for successful cyanide biodegradation by this consortium was evaluated in batch bioreactors (BBs) using response surface methodology (RSM). The input variables, that is, pH, temperature and whey-waste concentration, were optimised using a numerical optimisation technique where the optimum conditions were found to be as follows: pH 9.88, temperature 33.60 °C and whey-waste concentration of 14.27 g/L, under which 206.53 mg CN(-)/L in 96 h can be biodegraded by the microbial species from an initial cyanide concentration of 500 mg CN(-)/L. Furthermore, using the optimised data, cyanide biodegradation in a continuous mode was evaluated in a dual-stage packed-bed bioreactor (PBB) connected in series to a pneumatic bioreactor system (PBS) used for simultaneous nitrification, including aerobic denitrification. The whey-supported Bacillus sp. culture was not inhibited by the free cyanide concentration of up to 500 mg CN(-)/L, with an overall degradation efficiency of ≥ 99 % with subsequent nitrification and aerobic denitrification of the formed ammonium and nitrates over a period of 80 days. This is the first study to report free cyanide biodegradation at concentrations of up to 500 mg CN(-)/L in a continuous system using whey waste as a microbial feedstock. The results showed that the process has the potential for the bioremediation of cyanide-containing wastewaters.

Ideonella sakaiensis sp. nov., isolated from a microbial consortium that degrades poly(ethylene terephthalate).

PubMed

Tanasupawat, Somboon; Takehana, Toshihiko; Yoshida, Shosuke; Hiraga, Kazumi; Oda, Kohei

2016-08-01

A Gram-stain-negative, aerobic, non-spore-forming, rod-shaped bacterium, designed strain 201-F6T, was isolated from a microbial consortium that degrades poly(ethylene terephthalate) (PET) collected in Sakai city, Japan, and was characterized on the basis of a polyphasic taxonomic study. The cells were motile with a polar flagellum. The strain contained cytochrome oxidase and catalase. It grew within the pH range 5.5-9.0 (optimally at pH 7-7.5) and at 15-42 ºC (optimally at 30-37 ºC). The major isoprenoid quinone was ubiquinone with eight isoprene units (Q-8). C16 : 0, C17 : 0 cyclo, C18 :1ω7c and C12 : 0 2-OH were the predominant cellular fatty acids. The major polar lipids were phosphatidylethanolamine, lyso-phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The G+C content of genomic DNA was 70.4 mol%. Phylogenetic analysis using the 16S rRNA gene sequences showed that strain 201-F6T was affiliated to the genus Ideonella, and was closely related to Ideonella dechloratans LMG 28178T (97.7 %) and Ideonella azotifigens JCM 15503T (96.6 %). Strain 201-F6T could be clearly distinguished from the related species of the genus Ideonella by its physiological and biochemical characteristics as well as by its phylogenetic position and DNA-DNA relatedness. Therefore, the strain represents a novel species of the genus Ideonella, for which the name Ideonella sakaiensis sp. nov. (type strain 201-F6T=NBRC 110686T=TISTR 2288T) is proposed.

Harnessing biodiesel-producing microbes: from genetic engineering of lipase to metabolic engineering of fatty acid biosynthetic pathway.

PubMed

Yan, Jinyong; Yan, Yunjun; Madzak, Catherine; Han, Bingnan

2017-02-01

Microbial production routes, notably whole-cell lipase-mediated biotransformation and fatty-acids-derived biosynthesis, offer new opportunities for synthesizing biodiesel. They compare favorably to immobilized lipase and chemically catalyzed processes. Genetically modified whole-cell lipase-mediated in vitro route, together with in vivo and ex vivo microbial biosynthesis routes, constitutes emerging and rapidly developing research areas for effective production of biodiesel. This review presents recent advances in customizing microorganisms for producing biodiesel, via genetic engineering of lipases and metabolic engineering (including system regulation) of fatty-acids-derived pathways. Microbial hosts used include Escherichia coli, Saccharomyces cerevisiae, Pichia pastoris and Aspergillus oryzae. These microbial cells can be genetically modified to produce lipases under different forms: intracellularly expressed, secreted or surface-displayed. They can be metabolically redesigned and systematically regulated to obtain balanced biodiesel-producing cells, as highlighted in this study. Such genetically or metabolically modified microbial cells can support not only in vitro biotransformation of various common oil feedstocks to biodiesel, but also de novo biosynthesis of biodiesel from glucose, glycerol or even cellulosic biomass. We believe that the genetically tractable oleaginous yeast Yarrowia lipolytica could be developed to an effective biodiesel-producing microbial cell factory. For this purpose, we propose several engineered pathways, based on lipase and wax ester synthase, in this promising oleaginous host.

[Thermoacidophilic micirobial community oxidizing the gold-bearing flotation concentrate of a pyrite-arsenopyrite ore].

PubMed

Paniushkina, A E; Tsaplina, I A; Grigor'eva, N V; Kondrat'eva, T F

2014-01-01

An aboriginal community of thermophilic acidophilic chemolithotrophic microorganisms (ACM) was isolated from a sample of pyrite gold-bearing flotation concentrateat 45-47 degrees C and pH 1.8-2.0. Compared to an experimental thermoacidophilic microbial consortium formed in the course of cultivation in parallel bioreactors, it had lower rates of iron leaching and oxidation, while its rate of sulfur oxidation was higher. A new thermophilic acidophilic microbial community was obtained by mutual enrichment with the micioorganisms from thie experimental and aboriginal communities during oxidation of sulfide ore flotation concentrate at 47 degrees C. The dominant bacteria of this new ACM community were Acidithiobacillus caldus strains (the most active sulfur oxidizers) and Sulfobacillus thermotolerans strains (active oxidizers of both iron and sulfur), while iron-oxidizing archaea of the family Ferroplasmaceae and heterotrophic bacteria Alicyclobacillus tolerans were the minor components. The new ACM community showed promise for leaching/oxidation of sulfides from flotation concentrates at high pulp density (S:L = 1:4).

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

PubMed Central

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

2014-01-01

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

Cyanobacteria cause black staining of the National Museum of the American Indian Building, Washington, DC, USA.

PubMed

Cappitelli, Francesca; Salvadori, Ornella; Albanese, Domenico; Villa, Federica; Sorlini, Claudia

2012-01-01

Microbial deterioration of stone is a widely recognised problem affecting monuments and buildings all over the world. In this paper, dark-coloured staining, putatively attributed to microorganisms, on areas of the National Museum of the American Indian Building, Washington, DC, USA, were studied. Observations by optical and electron microscopy of surfaces and cross sections of limestone indicated that biofilms, which penetrated up to a maximum depth of about 1 mm, were mainly composed of cyanobacteria, with the predominance of Gloeocapsa and Lyngbya. Denaturing gradient gel electrophoresis analysis revealed that the microbial community also included eukaryotic algae (Trebouxiophyceae) and fungi (Ascomycota), along with a consortium of bacteria. Energy-dispersive X-ray spectroscopy analysis showed the same elemental composition in stained and unstained areas of the samples, indicating that the discolouration was not due to abiotic chemical changes within the stone. The dark pigmentation of the stone was correlated with the high content of scytonemin, which was found in all samples.

Predominance and Metabolic Potential of Halanaerobium spp. in Produced Water from Hydraulically Fractured Marcellus Shale Wells.

PubMed

Lipus, Daniel; Vikram, Amit; Ross, Daniel; Bain, Daniel; Gulliver, Djuna; Hammack, Richard; Bibby, Kyle

2017-04-15

Microbial activity in the produced water from hydraulically fractured oil and gas wells may potentially interfere with hydrocarbon production and cause damage to the well and surface infrastructure via corrosion, sulfide release, and fouling. In this study, we surveyed the microbial abundance and community structure of produced water sampled from 42 Marcellus Shale wells in southwestern Pennsylvania (well age ranged from 150 to 1,846 days) to better understand the microbial diversity of produced water. We sequenced the V4 region of the 16S rRNA gene to assess taxonomy and utilized quantitative PCR (qPCR) to evaluate the microbial abundance across all 42 produced water samples. Bacteria of the order Halanaerobiales were found to be the most abundant organisms in the majority of the produced water samples, emphasizing their previously suggested role in hydraulic fracturing-related microbial activity. Statistical analyses identified correlations between well age and biocide formulation and the microbial community, in particular, the relative abundance of Halanaerobiales We further investigated the role of members of the order Halanaerobiales in produced water by reconstructing and annotating a Halanaerobium draft genome (named MDAL1), using shotgun metagenomic sequencing and metagenomic binning. The recovered draft genome was found to be closely related to the species H. congolense , an oil field isolate, and Halanaerobium sp. strain T82-1, also recovered from hydraulic fracturing produced water. Reconstruction of metabolic pathways revealed Halanaerobium sp. strain MDAL1 to have the potential for acid production, thiosulfate reduction, and biofilm formation, suggesting it to have the ability to contribute to corrosion, souring, and biofouling events in the hydraulic fracturing infrastructure. IMPORTANCE There are an estimated 15,000 unconventional gas wells in the Marcellus Shale region, each generating up to 8,000 liters of hypersaline produced water per day throughout its lifetime (K. Gregory, R. Vidic, and D. Dzombak, Elements 7:181-186, 2011, https://doi.org/10.2113/gselements.7.3.181; J. Arthur, B. Bohm, and M. Layne, Gulf Coast Assoc Geol Soc Trans 59:49-59, 2009; https://www.marcellusgas.org/index.php). Microbial activity in produced waters could lead to issues with corrosion, fouling, and souring, potentially interfering with hydraulic fracturing operations. Previous studies have found microorganisms contributing to corrosion, fouling, and souring to be abundant across produced water samples from hydraulically fractured wells; however, these findings were based on a limited number of samples and well sites. In this study, we investigated the microbial community structure in produced water samples from 42 unconventional Marcellus Shale wells, confirming the dominance of the genus Halanaerobium in produced water and its metabolic potential for acid and sulfide production and biofilm formation. Copyright © 2017 American Society for Microbiology.

Predominance and Metabolic Potential of Halanaerobium spp. in Produced Water from Hydraulically Fractured Marcellus Shale Wells

PubMed Central

Lipus, Daniel; Vikram, Amit; Ross, Daniel; Bain, Daniel; Gulliver, Djuna; Hammack, Richard

2017-01-01

ABSTRACT Microbial activity in the produced water from hydraulically fractured oil and gas wells may potentially interfere with hydrocarbon production and cause damage to the well and surface infrastructure via corrosion, sulfide release, and fouling. In this study, we surveyed the microbial abundance and community structure of produced water sampled from 42 Marcellus Shale wells in southwestern Pennsylvania (well age ranged from 150 to 1,846 days) to better understand the microbial diversity of produced water. We sequenced the V4 region of the 16S rRNA gene to assess taxonomy and utilized quantitative PCR (qPCR) to evaluate the microbial abundance across all 42 produced water samples. Bacteria of the order Halanaerobiales were found to be the most abundant organisms in the majority of the produced water samples, emphasizing their previously suggested role in hydraulic fracturing-related microbial activity. Statistical analyses identified correlations between well age and biocide formulation and the microbial community, in particular, the relative abundance of Halanaerobiales. We further investigated the role of members of the order Halanaerobiales in produced water by reconstructing and annotating a Halanaerobium draft genome (named MDAL1), using shotgun metagenomic sequencing and metagenomic binning. The recovered draft genome was found to be closely related to the species H. congolense, an oil field isolate, and Halanaerobium sp. strain T82-1, also recovered from hydraulic fracturing produced water. Reconstruction of metabolic pathways revealed Halanaerobium sp. strain MDAL1 to have the potential for acid production, thiosulfate reduction, and biofilm formation, suggesting it to have the ability to contribute to corrosion, souring, and biofouling events in the hydraulic fracturing infrastructure. IMPORTANCE There are an estimated 15,000 unconventional gas wells in the Marcellus Shale region, each generating up to 8,000 liters of hypersaline produced water per day throughout its lifetime (K. Gregory, R. Vidic, and D. Dzombak, Elements 7:181–186, 2011, https://doi.org/10.2113/gselements.7.3.181; J. Arthur, B. Bohm, and M. Layne, Gulf Coast Assoc Geol Soc Trans 59:49–59, 2009; https://www.marcellusgas.org/index.php). Microbial activity in produced waters could lead to issues with corrosion, fouling, and souring, potentially interfering with hydraulic fracturing operations. Previous studies have found microorganisms contributing to corrosion, fouling, and souring to be abundant across produced water samples from hydraulically fractured wells; however, these findings were based on a limited number of samples and well sites. In this study, we investigated the microbial community structure in produced water samples from 42 unconventional Marcellus Shale wells, confirming the dominance of the genus Halanaerobium in produced water and its metabolic potential for acid and sulfide production and biofilm formation. PMID:28159795

Conserved Responses in a War of Small Molecules between a Plant-Pathogenic Bacterium and Fungi.

PubMed

Spraker, Joseph E; Wiemann, Philipp; Baccile, Joshua A; Venkatesh, Nandhitha; Schumacher, Julia; Schroeder, Frank C; Sanchez, Laura M; Keller, Nancy P

2018-05-22

Small-molecule signaling is one major mode of communication within the polymicrobial consortium of soil and rhizosphere. While microbial secondary metabolite (SM) production and responses of individual species have been studied extensively, little is known about potentially conserved roles of SM signals in multilayered symbiotic or antagonistic relationships. Here, we characterize the SM-mediated interaction between the plant-pathogenic bacterium Ralstonia solanacearum and the two plant-pathogenic fungi Fusarium fujikuroi and Botrytis cinerea We show that cellular differentiation and SM biosynthesis in F. fujikuroi are induced by the bacterially produced lipopeptide ralsolamycin (synonym ralstonin A). In particular, fungal bikaverin production is induced and preferentially accumulates in fungal survival spores (chlamydospores) only when exposed to supernatants of ralsolamycin-producing strains of R. solanacearum Although inactivation of bikaverin biosynthesis moderately increases chlamydospore invasion by R. solanacearum , we show that other metabolites such as beauvericin are also induced by ralsolamycin and contribute to suppression of R. solanacearum growth in vitro Based on our findings that bikaverin antagonizes R. solanacearum and that ralsolamycin induces bikaverin biosynthesis in F. fujikuroi , we asked whether other bikaverin-producing fungi show similar responses to ralsolamycin. Examining a strain of B. cinerea that horizontally acquired the bikaverin gene cluster from Fusarium , we found that ralsolamycin induced bikaverin biosynthesis in this fungus. Our results suggest that conservation of microbial SM responses across distantly related fungi may arise from horizontal transfer of protective gene clusters that are activated by conserved regulatory cues, e.g., a bacterial lipopeptide, providing consistent fitness advantages in dynamic polymicrobial networks. IMPORTANCE Bacteria and fungi are ubiquitous neighbors in many environments, including the rhizosphere. Many of these organisms are notorious as economically devastating plant pathogens, but little is known about how they communicate chemically with each other. Here, we uncover a conserved antagonistic communication between the widespread bacterial wilt pathogen Ralstonia solanacearum and plant-pathogenic fungi from disparate genera, Fusarium and Botrytis Exposure of Fusarium fujikuroi to the bacterial lipopeptide ralsolamycin resulted in production of the antibacterial metabolite bikaverin specifically in fungal tissues invaded by Ralstonia Remarkably, ralsolamycin induction of bikaverin was conserved in a Botrytis cinerea isolate carrying a horizontally transferred bikaverin gene cluster. These results indicate that horizontally transferred gene clusters may carry regulatory prompts that contribute to conserved fitness functions in polymicrobial environments. Copyright © 2018 Spraker et al.

Completion of the 2011 National Land Cover Database for the conterminous United States – Representing a decade of land cover change information

USGS Publications Warehouse

Homer, Collin G.; Dewitz, Jon; Yang, Limin; Jin, Suming; Danielson, Patrick; Xian, George Z.; Coulston, John; Herold, Nathaniel; Wickham, James; Megown, Kevin

2015-01-01

The National Land Cover Database (NLCD) provides nationwide data on land cover and land cover change at the native 30-m spatial resolution of the Landsat Thematic Mapper (TM). The database is designed to provide five-year cyclical updating of United States land cover and associated changes. The recent release of NLCD 2011 products now represents a decade of consistently produced land cover and impervious surface for the Nation across three periods: 2001, 2006, and 2011 (Homer et al., 2007; Fry et al., 2011). Tree canopy cover has also been produced for 2011 (Coluston et al., 2012; Coluston et al., 2013). With the release of NLCD 2011, the database provides the ability to move beyond simple change detection to monitoring and trend assessments. NLCD 2011 represents the latest evolution of NLCD products, continuing its focus on consistency, production, efficiency, and product accuracy. NLCD products are designed for widespread application in biology, climate, education, land management, hydrology, environmental planning, risk and disease analysis, telecommunications and visualization, and are available for no cost at http://www.mrlc.gov. NLCD is produced by a Federal agency consortium called the Multi-Resolution Land Characteristics Consortium (MRLC) (Wickham et al., 2014). In the consortium arrangement, the U.S. Geological Survey (USGS) leads NLCD land cover and imperviousness production for the bulk of the Nation; the National Oceanic and Atmospheric Administration (NOAA) completes NLCD land cover for the conterminous U.S. (CONUS) coastal zones; and the U.S. Forest Service (USFS) designs and produces the NLCD tree canopy cover product. Other MRLC partners collaborate through resource or data contribution to ensure NLCD products meet their respective program needs (Wickham et al., 2014).

Microbial response to single-cell protein production and brewery wastewater treatment

PubMed Central

Lee, Jackson Z; Logan, Andrew; Terry, Seth; Spear, John R

2015-01-01

As global fisheries decline, microbial single-cell protein (SCP) produced from brewery process water has been highlighted as a potential source of protein for sustainable animal feed. However, biotechnological investigation of SCP is difficult because of the natural variation and complexity of microbial ecology in wastewater bioreactors. In this study, we investigate microbial response across a full-scale brewery wastewater treatment plant and a parallel pilot bioreactor modified to produce an SCP product. A pyrosequencing survey of the brewery treatment plant showed that each unit process selected for a unique microbial community. Notably, flow equalization basins were dominated by Prevotella, methanogenesis effluent had the highest levels of diversity, and clarifier wet-well samples were sources of sequences for the candidate bacterial phyla of TM7 and BD1-5. Next, the microbial response of a pilot bioreactor producing SCP was tracked over 1 year, showing that two different production trials produced two different communities originating from the same starting influent. However, SCP production resulted generally in enrichment of several clades of rhizospheric diazotrophs of Alphaproteobacteria and Betaproteobacteria in the bioreactor and even more so in the final product. These diazotrophs are potentially useful as the basis of a SCP product for commercial feed production. PMID:24837420

Development of a Chlorine Dosing Strategy for Fresh Produce Washing Process to Maintain Microbial Food Safety and Minimize Residual Chlorine.

PubMed

Chen, Xi; Hung, Yen-Con

2018-06-01

The residual free chlorine level in fresh produce wash solution is closely correlated to the chemical and microbial safety of produce. Excess amount of free chlorine can quickly react with organic matters to form hazardous disinfection by-products (DBPs) above EPA-permitted levels, whereas deficiency of residual chlorine in produce wash solution may result in incompletely removing pathogens on produce. The purpose of this study was to develop a chlorine dosing strategy to optimize the chlorine dosage during produce washing process without impacting the microbial safety of fresh produce. Prediction equations were developed to estimate free chlorine needed to reach targeted residual chlorine at various sanitizer pH and organic loads, and then validated using fresh-cut iceberg lettuce and whole strawberries in an automated produce washer. Validation results showed that equations successfully predicted the initial chlorine concentration needed to achieve residual chlorine at 10, 30, 60, and 90 mg/L for both lettuce and strawberry washing processes, with the root mean squared error at 4.45 mg/L. The Escherichia coli O157:H7 reductions only slightly increased on iceberg lettuce and strawberries with residual chlorine increasing from 10 to 90 mg/L, indicating that lowering residual chlorine to 10 mg/L would not compromise the antimicrobial efficacy of chlorine-based sanitizer. Based on the prediction equations and E. coli O157:H7 reduction results, a chlorine dosing strategy was developed to help the produce industry to maintain microbial inactivation efficacy without adding excess amount of free chlorine. The chlorine dosing strategy can be used for fresh produce washing process to enhance the microbial food safety and minimize the DBPs formation potential. © 2018 Institute of Food Technologists®.

Optimization of the liquid biofertilizer production in batch fermentation with by-product from MSG

NASA Astrophysics Data System (ADS)

Namfon, Panjanapongchai; Ratchanok, Sahaworarak; Chalida, Daengbussade

2017-03-01

The long term use of chemical fertilizers destroyed the friability of soil which obviously decreased quantity and quality of crops and especially affect microorganisms living in soils. The bio-fertilizer with microbial consortium is an environmental friendly alternative to solve this bottleneck due to harboring soil microorganisms such as Bacillus sp., Micrococcus sp., Pseudomonas sp., Staphylococcus sp. and Deinococcus sp. produced with natural by-product or waste from industries that is alternative and sustainable such as nutrient-rich (by-product) from Mono Sodium Glutamate (MSG) for producing liquid biofertilizer by batch fermentation. In this work, the concentration of reducing sugar from substrate as main carbon source was evaluated in shake flask with mixed cultures. The optimal conditions were studied comparing with two levels of reducing sugar concentration (10, 20 g/L) and inoculums concentration (10, 20 %v/v) with using (2×2) full factorial design. The results indicated that the by-product from monosodium glutamate is feasible for fermentation and inoculums concentration is mainly influenced the batch fermentation process. Moreover, the combined 20 g/L and 10%v/v were considerably concluded as an optimal condition, of which the concentration of vegetative cells and spores attained at 8.29×109 CFU/mL and 1.97×105 CFU/mL, respectively. Their spores cell yields from reducing sugar (Yx/s) were obtained at 1.22×106 and 3.34×105 CFU/g were markedly different. In conclusion, the liquid Biofertilizer was produced satisfactorily at 20 g/L reducing sugar and 10% v/v inoculums in shake flask culture. Moreover, these results suggested that the by-product from monosodium glutamate is feasible for low-cost substrate in economical scale and environmental-friendly.

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

PubMed

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

2005-11-01

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

Analysis of stability to cheaters in models of antibiotic degrading microbial communities.

PubMed

Szilágyi, András; Boza, Gergely; Scheuring, István

2017-06-21

Antibiotic resistance carried out by antibiotic degradation has been suggested recently as a new mechanism to maintain coexistence of microbial species competing on a single limiting resource, even in well-mixed homogeneous environments. Species diversity and community stability, however, critically depend on resistance against social cheaters, mutants that do not invest in production, but still enjoy the benefits provided by others. Here we investigate how different mutant cheaters affect the stability of antibiotic producing and degrading microbial communities. We consider two cheater types, production and degradation cheaters. We generalize the mixed inhibition-zone and chemostat models introduced previously [Kelsic, E. D., Zhao, J., Vetsigian, K., Kishony, R., 2015. Counteraction of an tibiotic production and degradation stabilizes microbial communities. Nature521, 516-519.] to study the population dynamics of microbial communities in well-mixed environment, and analyze the invasion of different cheaters in these models. We show that production cheaters, mutants that cease producing antibiotics, always destroy coexistence whenever there is a cost of producing these antibiotics. Degradation cheaters, mutants that loose their function of producing extracellular antibiotic degrading molecules, induce community collapse only if the cost of producing the degradation factors is above a critical level. Our analytical studies, supported by numerical simulations, highlight the sensitivity of antibiotic producing and degrading communities to loss-of-function mutants. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

PubMed

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

2017-11-01

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

The role of emerging technologies to ensure the microbial safety of fresh produce, milk and eggs

USDA-ARS?s Scientific Manuscript database

This article reviews emerging techniques that are applied in the produce and dairy industry to ensure product safety. Microbial safety of produce, dairy and egg continues to be a major concern. According to Economic Research Service, USDA the cost of foodborne illnesses in the U.S. tops $15.6 billio...

A Formalized Design Process for Bacterial Consortia That Perform Logic Computing

PubMed Central

Sun, Rui; Xi, Jingyi; Wen, Dingqiao; Feng, Jingchen; Chen, Yiwei; Qin, Xiao; Ma, Yanrong; Luo, Wenhan; Deng, Linna; Lin, Hanchi; Yu, Ruofan; Ouyang, Qi

2013-01-01

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. PMID:23468999

Hydrogen production in single chamber microbial electrolysis cells with different complex substrates.

PubMed

Montpart, Nuria; Rago, Laura; Baeza, Juan A; Guisasola, Albert

2015-01-01

The use of synthetic wastewater containing carbon sources of different complexity (glycerol, milk and starch) was evaluated in single chamber microbial electrolysis cell (MEC) for hydrogen production. The growth of an anodic syntrophic consortium between fermentative and anode respiring bacteria was operationally enhanced and increased the opportunities of these complex substrates to be treated with this technology. During inoculation, current intensities achieved in single chamber microbial fuel cells were 50, 62.5, and 9 A m⁻³ for glycerol, milk and starch respectively. Both current intensities and coulombic efficiencies were higher than other values reported in previous works. The simultaneous degradation of the three complex substrates favored power production and COD removal. After three months in MEC operation, hydrogen production was only sustained with milk as a single substrate and with the simultaneous degradation of the three substrates. The later had the best results in terms of current intensity (150 A m⁻³), hydrogen production (0.94 m³ m⁻³ d⁻¹) and cathodic gas recovery (91%) at an applied voltage of 0.8 V. Glycerol and starch as substrates in MEC could not avoid the complete proliferation of hydrogen scavengers, even under low hydrogen retention time conditions induced by continuous nitrogen sparging.

Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource

PubMed Central

Sun, Shulei; Chen, Jing; Li, Weizhong; Altintas, Ilkay; Lin, Abel; Peltier, Steve; Stocks, Karen; Allen, Eric E.; Ellisman, Mark; Grethe, Jeffrey; Wooley, John

2011-01-01

The Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA, http://camera.calit2.net/) is a database and associated computational infrastructure that provides a single system for depositing, locating, analyzing, visualizing and sharing data about microbial biology through an advanced web-based analysis portal. CAMERA collects and links metadata relevant to environmental metagenome data sets with annotation in a semantically-aware environment allowing users to write expressive semantic queries against the database. To meet the needs of the research community, users are able to query metadata categories such as habitat, sample type, time, location and other environmental physicochemical parameters. CAMERA is compliant with the standards promulgated by the Genomic Standards Consortium (GSC), and sustains a role within the GSC in extending standards for content and format of the metagenomic data and metadata and its submission to the CAMERA repository. To ensure wide, ready access to data and annotation, CAMERA also provides data submission tools to allow researchers to share and forward data to other metagenomics sites and community data archives such as GenBank. It has multiple interfaces for easy submission of large or complex data sets, and supports pre-registration of samples for sequencing. CAMERA integrates a growing list of tools and viewers for querying, analyzing, annotating and comparing metagenome and genome data. PMID:21045053

Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource.

PubMed

Sun, Shulei; Chen, Jing; Li, Weizhong; Altintas, Ilkay; Lin, Abel; Peltier, Steve; Stocks, Karen; Allen, Eric E; Ellisman, Mark; Grethe, Jeffrey; Wooley, John

2011-01-01

The Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA, http://camera.calit2.net/) is a database and associated computational infrastructure that provides a single system for depositing, locating, analyzing, visualizing and sharing data about microbial biology through an advanced web-based analysis portal. CAMERA collects and links metadata relevant to environmental metagenome data sets with annotation in a semantically-aware environment allowing users to write expressive semantic queries against the database. To meet the needs of the research community, users are able to query metadata categories such as habitat, sample type, time, location and other environmental physicochemical parameters. CAMERA is compliant with the standards promulgated by the Genomic Standards Consortium (GSC), and sustains a role within the GSC in extending standards for content and format of the metagenomic data and metadata and its submission to the CAMERA repository. To ensure wide, ready access to data and annotation, CAMERA also provides data submission tools to allow researchers to share and forward data to other metagenomics sites and community data archives such as GenBank. It has multiple interfaces for easy submission of large or complex data sets, and supports pre-registration of samples for sequencing. CAMERA integrates a growing list of tools and viewers for querying, analyzing, annotating and comparing metagenome and genome data.

Economical challenges to microbial producers of butanol: feedstock, butanol ratio and titer.

PubMed

Gu, Yang; Jiang, Yu; Wu, Hui; Liu, Xudong; Li, Zhilin; Li, Jian; Xiao, Han; Shen, Zhaobing; Dong, Hongjun; Yang, Yunliu; Li, Yin; Jiang, Weihong; Yang, Sheng

2011-11-01

Butanol is an important solvent and transport fuel additive, and can be produced by microbial fermentation. Attempts to generate a superior microbial producer of butanol have been made through different metabolic engineering strategies. However, to date, butanol bio-production is still not economically competitive compared to petrochemical-derived production because of its major drawbacks, such as, high cost of the feedstocks, low butanol concentration in the fermentation broth and the co-production of low-value by-products acetone and ethanol. Here we analyze the main bottlenecks in microbial butanol production and summarize relevant advances from recently reported studies. Further needs and directions for developing real industrially applicable strains in butanol production are also discussed. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biotechnological production of limonene in microorganisms.

PubMed

Jongedijk, Esmer; Cankar, Katarina; Buchhaupt, Markus; Schrader, Jens; Bouwmeester, Harro; Beekwilder, Jules

2016-04-01

This mini review describes novel, biotechnology-based, ways of producing the monoterpene limonene. Limonene is applied in relatively highly priced products, such as fragrances, and also has applications with lower value but large production volume, such as biomaterials. Limonene is currently produced as a side product from the citrus juice industry, but the availability and quality are fluctuating and may be insufficient for novel bulk applications. Therefore, complementary microbial production of limonene would be interesting. Since limonene can be derivatized to high-value compounds, microbial platforms also have a great potential beyond just producing limonene. In this review, we discuss the ins and outs of microbial limonene production in comparison with plant-based and chemical production. Achievements and specific challenges for microbial production of limonene are discussed, especially in the light of bulk applications such as biomaterials.

Microbial community changes in hydraulic fracturing fluids and produced water from shale gas extraction.

PubMed

Murali Mohan, Arvind; Hartsock, Angela; Bibby, Kyle J; Hammack, Richard W; Vidic, Radisav D; Gregory, Kelvin B

2013-11-19

Microbial communities associated with produced water from hydraulic fracturing are not well understood, and their deleterious activity can lead to significant increases in production costs and adverse environmental impacts. In this study, we compared the microbial ecology in prefracturing fluids (fracturing source water and fracturing fluid) and produced water at multiple time points from a natural gas well in southwestern Pennsylvania using 16S rRNA gene-based clone libraries, pyrosequencing, and quantitative PCR. The majority of the bacterial community in prefracturing fluids constituted aerobic species affiliated with the class Alphaproteobacteria. However, their relative abundance decreased in produced water with an increase in halotolerant, anaerobic/facultative anaerobic species affiliated with the classes Clostridia, Bacilli, Gammaproteobacteria, Epsilonproteobacteria, Bacteroidia, and Fusobacteria. Produced water collected at the last time point (day 187) consisted almost entirely of sequences similar to Clostridia and showed a decrease in bacterial abundance by 3 orders of magnitude compared to the prefracturing fluids and produced water samplesfrom earlier time points. Geochemical analysis showed that produced water contained higher concentrations of salts and total radioactivity compared to prefracturing fluids. This study provides evidence of long-term subsurface selection of the microbial community introduced through hydraulic fracturing, which may include significant implications for disinfection as well as reuse of produced water in future fracturing operations.

[Characterization of microbial community in produced water from a petroleum reservoir subjected to alkali-surfactant-polymer ASP flooding].

PubMed

Hao, Qin Qin; Shi, Rong Jiu; Hao, Jin Sheng; Zhao, Jin Yi; Li, Guo Qiao; Zhao, Feng; Han, Si Qin; Zhang, Ying

2017-10-01

Injection of alkali, surfactant and polymer (ASP) into oil reservoir can substantially increase oil recovery compared with water-flooding strategy. However, the effects of these agents on the microbial diversity and community structure, which is important for water management and corrosion control in oil industry, are hitherto poorly understood. Here, we disclosed the microbial diversity and community structure in the produced water collected from four producing wells of an ASP-flooded oilfield at Daqing, China, using high-throughput sequencing technique. Results showed that the average pH in produced water was as high as 9.65. The microbial diversity varied from well to well, and the Shannon diversity index was between 2.00 to 3.56. The Proteobacteria (85.5%-98.3%), γ-proteobacteria (83.7%-97.8%), and alkaliphilic Nitrincola (51.8%-82.5%) were the most dominant phylogenetic taxa at the phylum, class, and genus levels, respectively. A total of 12 potentially sulfide-producing genera were detected, and the most abundant taxon was Sulfurospirillum (0.4%-7.4%). The microbial community of ASP-flooded petroleum reservoir was distinct, showing an alkaliphilic or alkalitolerant potential; a reduced diversity and more simple structure were observed compared with those of the water-flooded petroleum reservoirs that were previously reported.

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

PubMed

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

2018-04-27

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

Quinine, Malaria, and the Cinchona Bureau: Marketing Practices and Knowledge Circulation in a Dutch Transoceanic Cinchona–Quinine Enterprise (1920s–30s)

PubMed Central

Roersch Van Der Hoogte, Arjo; Pieters, Toine

2016-01-01

In this study, we will show how a Dutch pharmaceutical consortium of cinchona producers and quinine manufacturers was able to capitalize on one of the first international public health campaigns to fight malaria, thereby promoting the sale of quinine, an antimalarial medicine. During the 1920s and 1930s, the international markets for quinine were controlled by this Dutch consortium, which was a transoceanic cinchona–quinine enterprise centered in the Cinchona Bureau in the Netherlands. We will argue that during the interwar period, the Cinchona Bureau became the decision-making center of this Dutch cinchona–quinine pharmaceutical enterprise and monopolized the production and trade of an essential medicine. In addition, we will argue that capitalizing on the international public health campaign in the fight against malaria by the Dutch cinchona–quinine enterprise via the Cinchona Bureau can be regarded as an early example of corporate colonization of public health by a private pharmaceutical consortium. Furthermore, we will show how commercial interests prevailed over scientific interests within the Dutch cinchona–quinine consortium, thus interfering with and ultimately curtailing the transoceanic circulation of knowledge in the Dutch empire. PMID:26054829

Effect of the polarity reversal frequency in the electrokinetic-biological remediation of oxyfluorfen polluted soil.

PubMed

Barba, Silvia; Villaseñor, José; Rodrigo, Manuel A; Cañizares, Pablo

2017-06-01

This work studies the feasibility of the periodic polarity reversal strategy (PRS) in a combined electrokinetic-biological process for the remediation of clayey soil polluted with a herbicide. Five two-weeks duration electrobioremediation batch experiments were performed in a bench scale set-up using spiked clay soil polluted with oxyfluorfen (20 mg kg -1 ) under potentiostatic conditions applying an electric field between the electrodes of 1.0 V cm -1 (20.0 V) and using PRS with five frequencies (f) ranging from 0 to 6 d -1 . Additionally, two complementary reference tests were done: single bioremediation and single electrokinetic. The microbial consortium used was obtained from an oil refinery wastewater treatment plant and acclimated to oxyfluorfen degradation. Main soil conditions (temperature, pH, moisture and conductivity) were correctly controlled using PRS. On the contrary, the electroosmotic flow clearly decreased as f increased. The uniform soil microbial distribution at the end of the experiments indicated that the microbial activity remained in every parts of the soil after two weeks when applying PRS. Despite the adapted microbial culture was capable of degrade 100% of oxyfluorfen in water, the remediation efficiency in soil in a reference test, without the application of electric current, was negligible. However, under the low voltage gradients and polarity reversal, removal efficiencies between 5% and 15% were obtained, and it suggested that oxyfluorfen had difficulties to interact with the microbial culture or nutrients and that PRS promoted transport of species, which caused a positive influence on remediation. An optimal f value was observed between 2 and 3 d -1 . Copyright © 2017 Elsevier Ltd. All rights reserved.

Microbiology and potential applications of aerobic methane oxidation coupled to denitrification (AME-D) process: A review.

PubMed

Zhu, Jing; Wang, Qian; Yuan, Mengdong; Tan, Giin-Yu Amy; Sun, Faqian; Wang, Cheng; Wu, Weixiang; Lee, Po-Heng

2016-03-01

Aerobic methane oxidation coupled to denitrification (AME-D) is an important link between the global methane and nitrogen cycles. This mini-review updates discoveries regarding aerobic methanotrophs and denitrifiers, as a prelude to spotlight the microbial mechanism and the potential applications of AME-D. Until recently, AME-D was thought to be accomplished by a microbial consortium where denitrifying bacteria utilize carbon intermediates, which are excreted by aerobic methanotrophs, as energy and carbon sources. Potential carbon intermediates include methanol, citrate and acetate. This mini-review presents microbial thermodynamic estimations and postulates that methanol is the ideal electron donor for denitrification, and may serve as a trophic link between methanotrophic bacteria and denitrifiers. More excitingly, new discoveries have revealed that AME-D is not only confined to the conventional synergism between methanotrophic bacteria and denitrifiers. Specifically, an obligate aerobic methanotrophic bacterium, Methylomonas denitrificans FJG1, has been demonstrated to couple partial denitrification with methane oxidation, under hypoxia conditions, releasing nitrous oxide as a terminal product. This finding not only substantially advances the understanding of AME-D mechanism, but also implies an important but unknown role of aerobic methanotrophs in global climate change through their influence on both the methane and nitrogen cycles in ecosystems. Hence, further investigation on AME-D microbiology and mechanism is essential to better understand global climate issues and to develop niche biotechnological solutions. This mini-review also presents traditional microbial techniques, such as pure cultivation and stable isotope probing, and powerful microbial techniques, such as (meta-) genomics and (meta-) transcriptomics, for deciphering linked methane oxidation and denitrification. Although AME-D has immense potential for nitrogen removal from wastewater, drinking water and groundwater, bottlenecks and potential issues are also discussed. Copyright © 2015 Elsevier Ltd. All rights reserved.

Natural attenuation process via microbial oxidation of arsenic in a high Andean watershed.

PubMed

Leiva, Eduardo D; Rámila, Consuelo d P; Vargas, Ignacio T; Escauriaza, Cristian R; Bonilla, Carlos A; Pizarro, Gonzalo E; Regan, John M; Pasten, Pablo A

2014-01-01

Rivers in northern Chile have arsenic (As) concentrations at levels that are toxic for humans and other organisms. Microorganism-mediated redox reactions have a crucial role in the As cycle; the microbial oxidation of As (As(III) to As(V)) is a critical transformation because it favors the immobilization of As in the solid phase. We studied the role of microbial As oxidation for controlling the mobility of As in the extreme environment found in the Chilean Altiplano (i.e., > 4000 meters above sea level (masl) and < 310 mm annual rainfall), which are conditions that have rarely been studied. Our model system was the upper Azufre River sub-basin, where the natural attenuation of As from hydrothermal discharge (pH 4-6) was observed. As(III) was actively oxidized by a microbial consortium, leading to a significant decrease in the dissolved As concentrations and a corresponding increase in the sediment's As concentration downstream of the hydrothermal source. In-situ oxidation experiments demonstrated that the As oxidation required biological activity, and microbiological molecular analysis confirmed the presence of As(III)-oxidizing groups (aroA-like genes) in the system. In addition, the pH measurements and solid phase analysis strongly suggested that the As removal mechanism involved adsorption or coprecipitation with Fe-oxyhydroxides. Taken together, these results indicate that the microorganism-mediated As oxidation contributed to the attenuation of As concentrations and the stabilization of As in the solid phase, therefore controlling the amount of As transported downstream. This study is the first to demonstrate the microbial oxidation of As in Altiplano basins and its relevance in the immobilization of As. © 2013.

Exercise Is More Effective at Altering Gut Microbial Composition and Producing Stable Changes in Lean Mass in Juvenile versus Adult Male F344 Rats

PubMed Central

Mika, Agnieszka; Van Treuren, Will; González, Antonio; Herrera, Jonathan J.; Knight, Rob; Fleshner, Monika

2015-01-01

The mammalian intestine harbors a complex microbial ecosystem that influences many aspects of host physiology. Exposure to specific microbes early in development affects host metabolism, immune function, and behavior across the lifespan. Just as the physiology of the developing organism undergoes a period of plasticity, the developing microbial ecosystem is characterized by instability and may also be more sensitive to change. Early life thus presents a window of opportunity for manipulations that produce adaptive changes in microbial composition. Recent insights have revealed that increasing physical activity can increase the abundance of beneficial microbial species. We therefore investigated whether six weeks of wheel running initiated in the juvenile period (postnatal day 24) would produce more robust and stable changes in microbial communities versus exercise initiated in adulthood (postnatal day 70) in male F344 rats. 16S rRNA gene sequencing was used to characterize the microbial composition of juvenile versus adult runners and their sedentary counterparts across multiple time points during exercise and following exercise cessation. Alpha diversity measures revealed that the microbial communities of young runners were less even and diverse, a community structure that reflects volatility and malleability. Juvenile onset exercise altered several phyla and, notably, increased Bacteroidetes and decreased Firmicutes, a configuration associated with leanness. At the genus level of taxonomy, exercise altered more genera in juveniles than in the adults and produced patterns associated with adaptive metabolic consequences. Given the potential of these changes to contribute to a lean phenotype, we examined body composition in juvenile versus adult runners. Interestingly, exercise produced persistent increases in lean body mass in juvenile but not adult runners. Taken together, these results indicate that the impact of exercise on gut microbiota composition as well as body composition may depend on the developmental stage during which exercise is initiated. PMID:26016739

Natural attenuation of aged tar-oil in soils: A case study from a former gas production site

NASA Astrophysics Data System (ADS)

Ivanov, Pavel; Eickhorst, Thilo; Wehrer, Markus; Georgiadis, Anna; Rennert, Thilo; Eusterhues, Karin; Totsche, Kai Uwe

2017-04-01

Contamination of soils with tar oil occurred on many industrial sites in Europe. The main source of such contamination has been former manufactured gas plants (MGP). As many of them were destroyed during the World War II or abandoned in the second half of the XXth century, the contamination is depleted in volatile and degradable hydrocarbons (HC) but enriched in the heavy oil fractions due to aging processes. We studied a small tar-oil spill in a former MGP reservoir basin. The tar-oil had a total petroleum hydrocarbon (TPH) content of 245 mg/g. At the margin of the spill, vegetation has started to overgrow and intensively root the tar-oil layer. This zone comprised the uppermost 5-7 cm of our profile and contained 28 mg/g of TPH (A-layer)- The layer below the root zone (7-15 cm) was the most contaminated, with 90 mg/g TPH (B-layer). The layer underneath (15-22 cm) had smaller concentrations of 16 mg/g TPH (C-layer). Further down in the profile (D-layer) we found only slightly higher TPH content than in the control samples (1,4 mg/g vs 0,6 mg/g). The polycyclic aromatic hydrocarbons analysis showed the same distribution throughout all layers with highest contents of the PAHs with 4-6 condensed aromatic rings. Direct cell count and extraction of microbial biomass showed that the highly contaminated soil layers A and B had 2-3 times more bacteria than the control soils. CARD-FISH analysis revealed that in samples from layers A and B Archaea were more abundant (12% opposing to 6-7% in control soil). Analysis of bacteria (tested for Alpha-, Beta-, Gamma- and Epsilonproteobacteria and Actinobacteria) showed the dominance of Alphaproteobacteria in the layer A and C both beneath and above the most contaminated layer B. The primers covered the whole microbial consortia in these two layers, leaving almost no unidentified cells. In the most contaminated layer B Alphaproteobacteria amounted only to 20% of the microbial consortium, and almost 40% of the cells remained unidentified, suggesting the presence of other microorganisms using high-molecular weight HC as carbon source. All contaminated layers were found to be enriched in total Fe and both dithionite-extractable and oxalate-extractable Fe. Besides, siderite crystals were identified using FTIR microscopy. The presence of secondary crystalline and poorly crystalline Fe(III)-oxides and secondary Fe(II)-carbonates in the same horizons suggests simultaneous occurrence of oxic and anoxic zones within the porous system of the contaminated layers. Although HC pollution is often considered to inhibit microbial activity in soil, in our study the layers with highest TPH-amounts were the most "alive". We assume that aging processes (the sum of volatilization, dissolution, microbial degradation, chemical oxidation, polymerization and migration) and eventually a long-term microbial adaption to the HC carbon source resulted in the development of a microbial consortium, capable of transforming high-molecular weight HC. Presumably, iron-compounds in the tar oil act as an electron acceptor and trigger HC degradation. However, to unravel natural attenuation processes and degradation pathways it seems mandatory to take into account the soil structure and spatial distribution of microbes.

Microbes mediate carbon and nitrogen retention in shallow photic sediments

NASA Astrophysics Data System (ADS)

Hardison, A.; Anderson, I.; Canuel, E. A.; Tobias, C.; Veuger, B.

2009-12-01

Sediments in shallow coastal bays are sites of intense biogeochemical cycling facilitated by a complex microbial consortium. Unlike deeper coastal environments, much of the benthos is illuminated by sunlight in these bays. As a result, benthic autotrophs such as benthic microalgae (BMA) and macroalgae play an integral role in nutrient cycling. Investigating pathways of carbon (C) and nitrogen (N) flow through individual compartments within the sediment microbial community has previously proved challenging due to methodological difficulties. However, it is now possible using stable isotopes and microbial biomarkers such as fatty acids and amino acids to track C and N flow through individual microbial pools. We investigated the uptake and retention of C and N by bacteria and BMA in a shallow subtidal system. Using bulk and compound specific isotopic analysis, we traced the pathways of dissolved inorganic 13C and 15N under various treatments: 1) in ambient light or dark, 2) from porewater or water column sources, and 3) in the presence or absence of bloom forming nuisance macroalgae. Excess 13C and 15N in THAAs and excess 13C in total PLFAs showed a strong dependence on light. Enrichment of these pools represents uptake by the microbial community, which can include both autotrophic and heterotrophic components. Higher excess 13C in benthic microalgal fatty acids (C20, C22 PUFAs) provides evidence that benthic microalgae were fixing 13C. Aditionally, the ratio of excess 13C in branched fatty acids to microbial fatty acids (BAR) and excess 13C and 15N in D-Ala to L-Ala (D/L-Ala) were low, suggesting dominance by benthic microalgae over bacteria to total label incorporation. Our results support uptake and retention of C and N by the sediment microbial community and indicate a tight coupling between BMA and bacteria in shallow illuminated systems. This uptake is diminished in the presence of macroalgae, likely due to shading and/or nutrient competition. Therefore, macroalgae reduce the retention of C and N within surface sediments, diminishing the role of the microbial community in nutrient cycling processes.

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

PubMed Central

Park, Doo Hyun; Zeikus, J. Gregory

2000-01-01

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

Industry/University Consortium for ATS research

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

Allen, R.P.; Golan, L.P.

1993-11-01

The Industry/University ATS research program is the result of two planning workshops. Workshop I was held April 8--10, 1991 and had the goal of identifying research needs for advanced gas turbine cycles that would permit rapid commercialization of cycles with significant improvements over the machines currently under development, in terms of the cost of electricity produced and the environmental burdens resulting from their use in power producing. Workshop II was held in January 1992 and continued the identification of the research needs to develop advanced gas turbine systems. The goals established for the ATS systems were: (1) efficiency exceeding 60%more » for large utility turbine system and 15% improvement in heat rate for industrial systems; (2) busbar energy costs 10% less than current state of the art and (3) fuel flexible designs. In addition Workshop II participants agreed that an industry driven research consortium was an acceptable mechanism to achieve base technology development needs.« less

Ecological feedback in quorum-sensing microbial populations can induce heterogeneous production of autoinducers

PubMed Central

Bauer, Matthias; Knebel, Johannes; Lechner, Matthias; Pickl, Peter; Frey, Erwin

2017-01-01

Autoinducers are small signaling molecules that mediate intercellular communication in microbial populations and trigger coordinated gene expression via ‘quorum sensing’. Elucidating the mechanisms that control autoinducer production is, thus, pertinent to understanding collective microbial behavior, such as virulence and bioluminescence. Recent experiments have shown a heterogeneous promoter activity of autoinducer synthase genes, suggesting that some of the isogenic cells in a population might produce autoinducers, whereas others might not. However, the mechanism underlying this phenotypic heterogeneity in quorum-sensing microbial populations has remained elusive. In our theoretical model, cells synthesize and secrete autoinducers into the environment, up-regulate their production in this self-shaped environment, and non-producers replicate faster than producers. We show that the coupling between ecological and population dynamics through quorum sensing can induce phenotypic heterogeneity in microbial populations, suggesting an alternative mechanism to stochastic gene expression in bistable gene regulatory circuits. DOI: http://dx.doi.org/10.7554/eLife.25773.001 PMID:28741470

INNOVATIVE MIOR PROCESS UTILIZING INDIGENOUS RESERVOIR CONSTITUENTS

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

D.O. Hitzman; S.A. Bailey

This research program is directed at improving the knowledge of reservoir ecology and developing practical microbial solutions for improving oil production. The goal is to identify indigenous microbial populations which can produce beneficial metabolic products and develop a methodology to stimulate those select microbes with inorganic nutrient amendments to increase oil recovery.This microbial technology has the capability of producing multiple oil releasing agents. The potential of the system will be illustrated and demonstrated by the example of biopolymer production on oil recovery. Research has begun on the program and experimental laboratory work is underway. Polymer-producing cultures have been isolated frommore » produced water samples and initially characterized. Concurrently, a microcosm scale sand-packed column has been designed and developed for testing cultures of interest, including polymer-producing strains. In research that is planned to begin in future work, comparative laboratory studies demonstrating in situ production of microbial products as oil recovery agents will be conducted in sand pack and cores with synthetic and natural field waters at concentrations, flooding rates, and with cultures and conditions representative of oil reservoirs.« less

Independent validation of Swarm Level 2 magnetic field products and `Quick Look' for Level 1b data

NASA Astrophysics Data System (ADS)

Beggan, Ciarán D.; Macmillan, Susan; Hamilton, Brian; Thomson, Alan W. P.

2013-11-01

Magnetic field models are produced on behalf of the European Space Agency (ESA) by an independent scientific consortium known as the Swarm Satellite Constellation Application and Research Facility (SCARF), through the Level 2 Processor (L2PS). The consortium primarily produces magnetic field models for the core, lithosphere, ionosphere and magnetosphere. Typically, for each magnetic product, two magnetic field models are produced in separate chains using complementary data selection and processing techniques. Hence, the magnetic field models from the complementary processing chains will be similar but not identical. The final step in the overall L2PS therefore involves inspection and validation of the magnetic field models against each other and against data from (semi-) independent sources (e.g. ground observatories). We describe the validation steps for each magnetic field product and the comparison against independent datasets, and we show examples of the output of the validation. In addition, the L2PS also produces a daily set of `Quick Look' output graphics and statistics to monitor the overall quality of Level 1b data issued by ESA. We describe the outputs of the `Quick Look' chain.

Temporal and Spatial Differences in Microbial Composition during the Manufacture of a Continental-Type Cheese

PubMed Central

O'Sullivan, Daniel J.; O'Sullivan, Orla; McSweeney, Paul L. H.; Sheehan, Jeremiah J.

2015-01-01

We sought to determine if the time, within a production day, that a cheese is manufactured has an influence on the microbial community present within that cheese. To facilitate this, 16S rRNA amplicon sequencing was used to elucidate the microbial community dynamics of brine-salted continental-type cheese in cheeses produced early and late in the production day. Differences in the microbial composition of the core and rind of the cheese were also investigated. Throughout ripening, it was apparent that cheeses produced late in the day had a more diverse microbial population than their early equivalents. Spatial variation between the cheese core and rind was also noted in that cheese rinds were initially found to have a more diverse microbial population but thereafter the opposite was the case. Interestingly, the genera Thermus, Pseudoalteromonas, and Bifidobacterium, not routinely associated with a continental-type cheese produced from pasteurized milk, were detected. The significance, if any, of the presence of these genera will require further attention. Ultimately, the use of high-throughput sequencing has facilitated a novel and detailed analysis of the temporal and spatial distribution of microbes in this complex cheese system and established that the period during a production cycle at which a cheese is manufactured can influence its microbial composition. PMID:25636841

[Elimination of volatile compounds of leaf tobacco from air emissions using biofiltration].

PubMed

Zagustina, N A; Misharina, T A; Vepritskiĭ, A A; Zhukov, V G; Ruzhitskiĭ, A O; Terenina, M B; Krikunova, N I; Kulikova, A K; Popov, V O

2012-01-01

The composition of the volatile organic compounds (VOCs) of various leaf tobacco brands and their blends has been studied. The differences in the content of nicotine, solanone, tetramethyl hexadecenol, megastigmatrienones, and other compounds, determining the specific tobacco smell, have been revealed. A microbial consortium, which is able to deodorize simulated tobacco emissions and decompose nicotine, has been formed by long-term adaptation to the VOCs of tobacco leaves in a laboratory reactor, functioning as a trickle-bed biofilter. Such a biofilter eliminates 90% of the basic toxic compound (nicotine) and odor-active compounds; the filtration efficiency does not change for tobacco brands with different VOC concentrations or in the presence of foreign substances. The main strains, isolated from the formed consortium and participating in the nicotine decomposition process, belong to the genera Pseudomonas, Bacillus, and Rhodococcus. An examination of the biofilter trickling fluid has shown full decomposition of nicotine and odor-active VOCs. The compounds, revealed in the trickling fluid, did not have any odor and were nontoxic. The obtained results make it possible to conduct scaling of the biofiltration process to eliminate odor from air emissions in the tobacco industry.

Thalassospira permensis sp. nov., a new terrestrial halotolerant bacterium isolated from a naphthalene-utilizing microbial consortium.

PubMed

Plotnikova, E G; Anan'ina, L N; Krausova, V I; Ariskina, E V; Prisyazhnaya, N V; Lebedev, A T; Demakov, V A; Evtushenko, L I

2011-01-01

A halotolerant bacterium, strain SMB34T, was isolated from a naphthalene-utilizing bacterial consortium obtained from primitive technogeneous soil (Vrkhnekamsk salt deposit, Perm region, Russia) by enrichment procedure. The strain itself was unable to degrade naphthalene and grew at NaCl concentrations up to 11% (w/v). The 16S rRNA-based phylogenetic analysis showed that the strain belongs to the genus Thalassospira. The DNA-DNA hybridization values between SMB34T and the type strains of phylogenetically closest species (T. xiamenensis, T. profundimaris and T. tepidiphila) did not exceed 50%. The novel strain could be distinguished from the above species by the cell motility, MALDI/TOF mass spectra of whole cells and a range of physiological and biochemical characteristics. SMB34T also considerably differs from the recently described species T. xianhensis, with the most striking differences in the DNA G + C content (53.7 +/- 1.0 vs. 61.2 +/- 1.0 mol.%) and predominant ubiquinones (Q-10 vs. Q-9). The data obtained suggest strain SMB34T (=VKM B-2527T = NBRC 106175T), designated as the type strain, represents a novel species, named Thalassospira permensis sp. nov.

Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria

NASA Astrophysics Data System (ADS)

Amin, S. A.; Hmelo, L. R.; van Tol, H. M.; Durham, B. P.; Carlson, L. T.; Heal, K. R.; Morales, R. L.; Berthiaume, C. T.; Parker, M. S.; Djunaedi, B.; Ingalls, A. E.; Parsek, M. R.; Moran, M. A.; Armbrust, E. V.

2015-06-01

Interactions between primary producers and bacteria impact the physiology of both partners, alter the chemistry of their environment, and shape ecosystem diversity. In marine ecosystems, these interactions are difficult to study partly because the major photosynthetic organisms are microscopic, unicellular phytoplankton. Coastal phytoplankton communities are dominated by diatoms, which generate approximately 40% of marine primary production and form the base of many marine food webs. Diatoms co-occur with specific bacterial taxa, but the mechanisms of potential interactions are mostly unknown. Here we tease apart a bacterial consortium associated with a globally distributed diatom and find that a Sulfitobacter species promotes diatom cell division via secretion of the hormone indole-3-acetic acid, synthesized by the bacterium using both diatom-secreted and endogenous tryptophan. Indole-3-acetic acid and tryptophan serve as signalling molecules that are part of a complex exchange of nutrients, including diatom-excreted organosulfur molecules and bacterial-excreted ammonia. The potential prevalence of this mode of signalling in the oceans is corroborated by metabolite and metatranscriptome analyses that show widespread indole-3-acetic acid production by Sulfitobacter-related bacteria, particularly in coastal environments. Our study expands on the emerging recognition that marine microbial communities are part of tightly connected networks by providing evidence that these interactions are mediated through production and exchange of infochemicals.

Predicting Species-Resolved Macronutrient Acquisition during Succession in a Model Phototrophic Biofilm Using an Integrated ‘Omics Approach

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

Lindemann, Stephen R.; Mobberley, Jennifer M.; Cole, Jessica K.

The principles governing acquisition and interspecies exchange of nutrients in microbial communities and how those exchanges impact community productivity are poorly understood. Here, we examine energy and macronutrient acquisition in unicyanobacterial consortia for which species-resolved genome information exists for all members, allowing us to use multi-omic approaches to predict species’ abilities to acquire resources and examine expression of resource-acquisition genes during succession. Metabolic reconstruction indicated that a majority of heterotrophic community members lacked the genes required to directly acquire the inorganic nutrients provided in culture medium, suggesting high metabolic interdependency. The sole primary producer in consortium UCC-O, cyanobacterium Phormidium sp.more » OSCR, displayed declining expression of energy harvest, carbon fixation, and nitrate and sulfate reduction proteins but sharply increasing phosphate transporter expression over 28 days. Most heterotrophic members likewise exhibited signs of phosphorus starvation during succession. Though similar in their responses to phosphorus limitation, heterotrophs displayed species-specific expression of nitrogen acquisition genes. These results suggest niche partitioning around nitrogen sources may structure the community when organisms directly compete for limited phosphate. Such niche complementarity around nitrogen sources may increase community diversity and productivity in phosphate-limited phototrophic communities.« less

Degradation of chondroitin sulfate by the gut microbiota of Chinese individuals.

PubMed

Shang, Qingsen; Yin, Yeshi; Zhu, Liying; Li, Guoyun; Yu, Guangli; Wang, Xin

2016-05-01

Oral preparations of chondroitin sulfate (CS) have long been used as anti-osteoarthritis (anti-OA) drugs. However, little is known about the degradation of CS by human gut microbiota. In the present study, degradation profiles of CSA (the main constituent of CS drugs) by the human gut microbiota from six healthy subjects were investigated. Each individual's microbiota had differing degradation activities, but ΔUA-GalNAc4S was the end product in all cases. To elucidate the mechanisms underlying this phenomenon, different CSA-degrading bacteria were isolated from each individual's microbiota and tested for CSA degradation. In addition to Bacteroides thetaiotaomicron J1, Bacteroides thetaiotaomicron 82 and Bacteroides ovatus E3, a new CSA-degrading bacterium, Clostridium hathewayi R4, was isolated and characterized. Interestingly, at least two different CSA-degrading species were identified from each individual's gut microbiota. Predictably, these functional bacteria also had differing degradation rates, but still generated the same end product, ΔUA-GalNAc4S. In addition, the human fecal isolates produced different degradation profiles for CSC, CSD, and CSE, suggesting that CS could be readily metabolized to varying extents by diverse microbial consortiums, which may help to explain the poor bioavailability and unequal efficacy of CS among individuals in OA treatment. Copyright © 2016 Elsevier B.V. All rights reserved.

Biodegradation of engine oil by fungi from mangrove habitat.

PubMed

Ameen, Fuad; Hadi, Sarfaraz; Moslem, Mohamed; Al-Sabri, Ahmed; Yassin, Mohamed A

2015-01-01

The pollution of land and water by petroleum compounds is a matter of growing concern necessitating the development of methodologies, including microbial biodegradation, to minimize the impending impacts. It has been extensively reported that fungi from polluted habitats have the potential to degrade pollutants, including petroleum compounds. The Red Sea is used extensively for the transport of oil and is substantially polluted, due to leaks, spills, and occasional accidents. Tidal water, floating debris, and soil sediment were collected from mangrove stands on three polluted sites along the Red Sea coast of Saudi Arabia and forty-five fungal isolates belonging to 13 genera were recovered from these samples. The isolates were identified on the basis of a sequence analysis of the 18S rRNA gene fragment. Nine of these isolates were found to be able to grow in association with engine oil, as the sole carbon source, under in vitro conditions. These selected isolates and their consortium accumulated greater biomass, liberated more CO2, and produced higher levels of extracellular enzymes, during cultivation with engine oil as compared with the controls. These observations were authenticated by gas chromatography-mass spectrophotometry (GC-MS) analysis, which indicated that many high mass compounds present in the oil before treatment either disappeared or showed diminished levels.

Predicting Species-Resolved Macronutrient Acquisition during Succession in a Model Phototrophic Biofilm Using an Integrated ‘Omics Approach

DOE PAGES

Lindemann, Stephen R.; Mobberley, Jennifer M.; Cole, Jessica K.; ...

2017-06-13

The principles governing acquisition and interspecies exchange of nutrients in microbial communities and how those exchanges impact community productivity are poorly understood. Here, we examine energy and macronutrient acquisition in unicyanobacterial consortia for which species-resolved genome information exists for all members, allowing us to use multi-omic approaches to predict species’ abilities to acquire resources and examine expression of resource-acquisition genes during succession. Metabolic reconstruction indicated that a majority of heterotrophic community members lacked the genes required to directly acquire the inorganic nutrients provided in culture medium, suggesting high metabolic interdependency. The sole primary producer in consortium UCC-O, cyanobacterium Phormidium sp.more » OSCR, displayed declining expression of energy harvest, carbon fixation, and nitrate and sulfate reduction proteins but sharply increasing phosphate transporter expression over 28 days. Most heterotrophic members likewise exhibited signs of phosphorus starvation during succession. Though similar in their responses to phosphorus limitation, heterotrophs displayed species-specific expression of nitrogen acquisition genes. These results suggest niche partitioning around nitrogen sources may structure the community when organisms directly compete for limited phosphate. Such niche complementarity around nitrogen sources may increase community diversity and productivity in phosphate-limited phototrophic communities.« less

Engineering cell factories for producing building block chemicals for bio-polymer synthesis.

PubMed

Tsuge, Yota; Kawaguchi, Hideo; Sasaki, Kengo; Kondo, Akihiko

2016-01-21

Synthetic polymers are widely used in daily life. Due to increasing environmental concerns related to global warming and the depletion of oil reserves, the development of microbial-based fermentation processes for the production of polymer building block chemicals from renewable resources is desirable to replace current petroleum-based methods. To this end, strains that efficiently produce the target chemicals at high yields and productivity are needed. Recent advances in metabolic engineering have enabled the biosynthesis of polymer compounds at high yield and productivities by governing the carbon flux towards the target chemicals. Using these methods, microbial strains have been engineered to produce monomer chemicals for replacing traditional petroleum-derived aliphatic polymers. These developments also raise the possibility of microbial production of aromatic chemicals for synthesizing high-performance polymers with desirable properties, such as ultraviolet absorbance, high thermal resistance, and mechanical strength. In the present review, we summarize recent progress in metabolic engineering approaches to optimize microbial strains for producing building blocks to synthesize aliphatic and high-performance aromatic polymers.

Effect of Mono and Di-rhamnolipids on Biofilms Pre-formed by Bacillus subtilis BBK006.

PubMed

De Rienzo, Mayri A Díaz; Martin, Peter J

2016-08-01

Different microbial inhibition strategies based on the planktonic bacterial physiology have been known to have limited efficacy on the growth of biofilms communities. This problem can be exacerbated by the emergence of increasingly resistant clinical strains. Biosurfactants have merited renewed interest in both clinical and hygienic sectors due to their potential to disperse microbial biofilms. In this work, we explore the aspects of Bacillus subtilis BBK006 biofilms and examine the contribution of biologically derived surface-active agents (rhamnolipids) to the disruption or inhibition of microbial biofilms produced by Bacillus subtilis BBK006. The ability of mono-rhamnolipids (Rha-C10-C10) produced by Pseudomonas aeruginosa ATCC 9027 and the di-rhamnolipids (Rha-Rha-C14-C14) produced by Burkholderia thailandensis E264, and phosphate-buffered saline to disrupt biofilm of Bacillus subtilis BBK006 was evaluated. The biofilm produced by Bacillus subtilis BBK006 was more sensitive to the di-rhamnolipids (0.4 g/L) produced by Burkholderia thailandensis than the mono-rhamnolipids (0.4 g/L) produced by Pseudomonas aeruginosa ATCC 9027. Rhamnolipids are biologically produced compounds safe for human use. This makes them ideal candidates for use in new generations of bacterial dispersal agents and useful for use as adjuvants for existing microbial suppression or eradication strategies.

An investigation of microbial diversity in crude oil & seawater injection systems and microbiologically influenced corrosion (MIC) of linepipe steels under different exposure conditions

NASA Astrophysics Data System (ADS)

AlAbbas, Faisal Mohammed

During oil and gas operations, pipeline networks are subjected to different corrosion deterioration mechanisms that result from the interaction between the fluid process and the linepipe steel. Among these mechanisms is microbiologically influenced corrosion (MIC) that results from accelerated deterioration caused by different indigenous microorganisms that naturally reside in the hydrocarbon and associated seawater injection systems. The focus of this research is to obtain comprehensive understanding of MIC. This work has explored the most essential elements (identifications, implications and mitigations) required to fully understand MIC. Advanced molecular-based techniques, including sequencing of 16S rRNA genes via 454 pyrosequencing methodologies, were deployed to provide in-depth understanding of the microbial diversity associated with crude oil and seawater injection systems and their relevant impact on MIC. Key microbes including sulfate reducing bacteria (SRB) and iron reducing bacteria (IRB) were cultivated from sour oil well field samples. The microbes' phylotypes were identified in the laboratory to gain more thorough understanding of how they impact microbial corrosion. Electrochemical and advanced surface analytical techniques were used for corrosion evaluations of linepipe carbon steels (API 5L X52 and X80) under different exposure conditions. On the identification front, 454 pyrosequencing of both 16S rRNA genes indicated that the microbial communities in the corrosion products obtained from the sour oil pipeline, sweet crude pipeline and seawater pipeline were dominated by bacteria, though archaeal sequences (predominately Methanobacteriaceae and Methanomicrobiaceae) were also identified in the sweet and sour crude oil samples, respectively. The dominant bacterial phylotypes in the sour crude sample included members of the Thermoanaerobacterales, Synergistales, and Syntrophobacterales. In the sweet crude sample, the dominant phylotypes included members of Halothiobacillaceae. In the seawater injection sample, the dominant bacterial phylotypes included members of the Rhodobacterales, Flavobacteriales and Oceanospirillales. Interestingly, common bacterial phylotypes that are related to Thermotogaceae were identified in all investigated samples. The impact of the identified microbial communities on MIC of pipeline system was presented. On the implications front, the influence of field SRB (Desulfomicrobium sp. and Clostridiales.) on the corrosion process was complex. The bacterial activities, metabolic reactions and by-products contributed to the corrosion process. Based on the observations and results, corrosion involves multiple synergistic mechanisms. The MIC vulnerability of X52 was higher than X80 due to microstructural effects. On the other hand, the field IRB consortium (Shewanella oneidensis sp. and Brevibacillus sp.) exhibited inhibitory action on the corrosion process. The maximum corrosion rate was ˜4 mpy in the biotic system and ˜18 mpy in the abiotic system. Corrosion mechanisms were proposed to explain the protective behavior of the IRB consortium. On the special effects front, the influence of remnant magnetic fields (3000 Gauss strength) on MIC by a SRB consortium was investigated. The results confirm substantial increases of bacteria cell attachment, biofilm mass, corrosion and pitting penetration rates under magnetized biotic compared to nonmagnetized biotic conditions. The significant enhancement of MIC under magnetized biotic conditions has been attributed to the synergetic interaction between SRB cells and associated metabolic products with magnetic fields. The effect of magnetic fields on the thermodynamics and kinetics of the bacterial cell attachment and the electrochemical process has been presented. On the mitigation front, this work presented a pioneer study on the inhibition effects of azadirachtin (Neem) extracts of SRB influenced corrosion. The results revealed that Neem extracts reduced the biocorrosion rate by approximately 50%. Neem significantly reduced the contribution of SRB in the corrosion process by minimizing the growth of cells, which subsequently suppressed the production of sulfide, density of sessile cells and development of biofilm. Moreover, the Neem extracts might provide an organic coating that protects the surface against the medium. The work provided by this research will expand the MIC knowledge within the oil and gas industry and will improve monitoring and prevention strategies and direct future research of MIC-related issues, such as microbial injection inhibitors aided with magnetic fields applications and environmentally friendly biocides.

Engineering microbial fatty acid metabolism for biofuels and biochemicals.

PubMed

Marella, Eko Roy; Holkenbrink, Carina; Siewers, Verena; Borodina, Irina

2018-04-01

Traditional oleochemical industry chemically processes animal fats and plant oils to produce detergents, lubricants, biodiesel, plastics, coatings, and other products. Biotechnology offers an alternative process, where the same oleochemicals can be produced from abundant biomass feedstocks using microbial catalysis. This review summarizes the recent advances in the engineering of microbial metabolism for production of fatty acid-derived products. We highlight the efforts in engineering the central carbon metabolism, redox metabolism, controlling the chain length of the products, and obtaining metabolites with different functionalities. The prospects of commercializing microbial oleochemicals are also discussed. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Microbial-Catalyzed Biotransformation of Multifunctional Triterpenoids Derived from Phytonutrients

PubMed Central

Shah, Syed Adnan Ali; Tan, Huey Ling; Sultan, Sadia; Mohd Faridz, Muhammad Afifi Bin; Mohd Shah, Mohamad Azlan Bin; Nurfazilah, Sharifah; Hussain, Munawar

2014-01-01

Microbial-catalyzed biotransformations have considerable potential for the generation of an enormous variety of structurally diversified organic compounds, especially natural products with complex structures like triterpenoids. They offer efficient and economical ways to produce semi-synthetic analogues and novel lead molecules. Microorganisms such as bacteria and fungi could catalyze chemo-, regio- and stereospecific hydroxylations of diverse triterpenoid substrates that are extremely difficult to produce by chemical routes. During recent years, considerable research has been performed on the microbial transformation of bioactive triterpenoids, in order to obtain biologically active molecules with diverse structures features. This article reviews the microbial modifications of tetranortriterpenoids, tetracyclic triterpenoids and pentacyclic triterpenoids. PMID:25003642

Strategies to diagnose and control microbial souring in natural gas storage reservoirs and produced water systems

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

Morris, E.A.; Derr, R.M.; Pope, D.H.

1995-12-31

Hydrogen sulfide production (souring) in natural gas storage reservoirs and produced water systems is a safety and environmental problem that can lead to operational shutdown when local hydrogen sulfide standards are exceeded. Systems affected by microbial souring have historically been treated using biocides that target the general microbial community. However, requirements for more environmentally friendly solutions have led to treatment strategies in which sulfide production can be controlled with minimal impact to the system and environment. Some of these strategies are based on microbial and/or nutritional augmentation of the sour environment. Through research sponsored by the Gas Research Institute (GRI)more » in Chicago, Illinois, methods have been developed for early detection of microbial souring in natural gas storage reservoirs, and a variety of mitigation strategies have been evaluated. The effectiveness of traditional biocide treatment in gas storage reservoirs was shown to depend heavily on the methods by which the chemical is applied. An innovative strategy using nitrate was tested and proved ideal for produced water and wastewater systems. Another strategy using elemental iodine was effective for sulfide control in evaporation ponds and is currently being tested in microbially sour natural gas storage wells.« less

The Consortium for Advancing Renewable Energy Technology (CARET)

NASA Technical Reports Server (NTRS)

Gordon, E. M.; Henderson, D. O.; Buffinger, D. R.; Fuller, C. W.; Uribe, R. M.

1998-01-01

The Consortium for Advancing Renewable Energy (CARET) is a research and education program which uses the theme of renewable energy to build a minority scientist pipeline. CARET is also a consortium of four universities and NASA Lewis Research Center working together to promote science education and research to minority students using the theme of renewable energy. The consortium membership includes the HBCUs (Historically Black Colleges and Universities), Fisk, Wilberforce and Central State Universities as well as Kent State University and NASA Lewis Research Center. The various stages of this pipeline provide participating students experiences with a different emphasis. Some emphasize building enthusiasm for the classroom study of science and technology while others emphasize the nature of research in these disciplines. Still others focus on relating a practical application to science and technology. And, of great importance to the success of the program are the interfaces between the various stages. Successfully managing these transitions is a requirement for producing trained scientists, engineers and technologists. Presentations describing the CARET program have been given at this year's HBCU Research Conference at the Ohio Aerospace Institute and as a seminar in the Solar Circle Seminar series of the Photovoltaic and Space Environments Branch at NASA Lewis Research Center. In this report, we will describe the many positive achievements toward the fulfillment of the goals and outcomes of our program. We will begin with a description of the interactions among the consortium members and end with a description of the activities of each of the member institutions .

Exploring the Association between Alzheimer's Disease, Oral Health, Microbial Endocrinology and Nutrition.

PubMed

Harding, Alice; Gonder, Ulrike; Robinson, Sarita J; Crean, StJohn; Singhrao, Sim K

2017-01-01

Longitudinal monitoring of patients suggests a causal link between chronic periodontitis and the development of Alzheimer's disease (AD). However, the explanation of how periodontitis can lead to dementia remains unclear. A working hypothesis links extrinsic inflammation as a secondary cause of AD. This hypothesis suggests a compromised oral hygiene leads to a dysbiotic oral microbiome whereby Porphyromonas gingivalis , a keystone periodontal pathogen, with its companion species, orchestrates immune subversion in the host. Brushing and chewing on teeth supported by already injured soft tissues leads to bacteremias. As a result, a persistent systemic inflammatory response develops to periodontal pathogens. The pathogens, and the host's inflammatory response, subsequently lead to the initiation and progression of multiple metabolic and inflammatory co-morbidities, including AD. Insufficient levels of essential micronutrients can lead to microbial dysbiosis through the growth of periodontal pathogens such as demonstrated for P. gingivalis under low hemin bioavailability. An individual's diet also defines the consortium of microbial communities that take up residency in the oral and gastrointestinal (GI) tract microbiomes. Their imbalance can lead to behavioral changes. For example, probiotics enriched in Lactobacillus genus of bacteria, when ingested, exert some anti-inflammatory influence through common host/bacterial neurochemicals, both locally, and through sensory signaling back to the brain. Early life dietary behaviors may cause an imbalance in the host/microbial endocrinology through a dietary intake incompatible with a healthy GI tract microbiome later in life. This imbalance in host/microbial endocrinology may have a lasting impact on mental health. This observation opens up an opportunity to explore the mechanisms, which may underlie the previously detected relationship between diet, oral/GI microbial communities, to anxiety, cognition and sleep patterns. This review suggests healthy diet based interventions that together with improved life style/behavioral changes may reduce and/or delay the incidence of AD.

Exploring the Association between Alzheimer’s Disease, Oral Health, Microbial Endocrinology and Nutrition

PubMed Central

Harding, Alice; Gonder, Ulrike; Robinson, Sarita J.; Crean, StJohn; Singhrao, Sim K.

2017-01-01

Longitudinal monitoring of patients suggests a causal link between chronic periodontitis and the development of Alzheimer’s disease (AD). However, the explanation of how periodontitis can lead to dementia remains unclear. A working hypothesis links extrinsic inflammation as a secondary cause of AD. This hypothesis suggests a compromised oral hygiene leads to a dysbiotic oral microbiome whereby Porphyromonas gingivalis, a keystone periodontal pathogen, with its companion species, orchestrates immune subversion in the host. Brushing and chewing on teeth supported by already injured soft tissues leads to bacteremias. As a result, a persistent systemic inflammatory response develops to periodontal pathogens. The pathogens, and the host’s inflammatory response, subsequently lead to the initiation and progression of multiple metabolic and inflammatory co-morbidities, including AD. Insufficient levels of essential micronutrients can lead to microbial dysbiosis through the growth of periodontal pathogens such as demonstrated for P. gingivalis under low hemin bioavailability. An individual’s diet also defines the consortium of microbial communities that take up residency in the oral and gastrointestinal (GI) tract microbiomes. Their imbalance can lead to behavioral changes. For example, probiotics enriched in Lactobacillus genus of bacteria, when ingested, exert some anti-inflammatory influence through common host/bacterial neurochemicals, both locally, and through sensory signaling back to the brain. Early life dietary behaviors may cause an imbalance in the host/microbial endocrinology through a dietary intake incompatible with a healthy GI tract microbiome later in life. This imbalance in host/microbial endocrinology may have a lasting impact on mental health. This observation opens up an opportunity to explore the mechanisms, which may underlie the previously detected relationship between diet, oral/GI microbial communities, to anxiety, cognition and sleep patterns. This review suggests healthy diet based interventions that together with improved life style/behavioral changes may reduce and/or delay the incidence of AD. PMID:29249963

Soil microbial community structure: mechanical disturbance alters soil microbial community

USDA-ARS?s Scientific Manuscript database

Soil microbes are responsible for soil nutrient cycling in both perennial and annual management systems for beef cattle and grain production. In the Southern Plains of Oklahoma, producers plant winter wheat (Triticum aestivum) in rotation with winter canola (Brassica rapa). Producers in the Southern...

Microbial Community Changes in Hydraulic Fracturing Fluids and Produced Water from Shale Gas Extraction

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

Mohan, Arvind Murali; Hartsock, Angela; Bibby, Kyle J

2013-11-19

Microbial communities associated with produced water from hydraulic fracturing are not well understood, and their deleterious activity can lead to significant increases in production costs and adverse environmental impacts. In this study, we compared the microbial ecology in prefracturing fluids (fracturing source water and fracturing fluid) and produced water at multiple time points from a natural gas well in southwestern Pennsylvania using 16S rRNA gene-based clone libraries, pyrosequencing, and quantitative PCR. The majority of the bacterial community in prefracturing fluids constituted aerobic species affiliated with the class Alphaproteobacteria. However, their relative abundance decreased in produced water with an increase inmore » halotolerant, anaerobic/facultative anaerobic species affiliated with the classes Clostridia, Bacilli, Gammaproteobacteria, Epsilonproteobacteria, Bacteroidia, and Fusobacteria. Produced water collected at the last time point (day 187) consisted almost entirely of sequences similar to Clostridia and showed a decrease in bacterial abundance by 3 orders of magnitude compared to the prefracturing fluids and produced water samplesfrom earlier time points. Geochemical analysis showed that produced water contained higher concentrations of salts and total radioactivity compared to prefracturing fluids. This study provides evidence of long-term subsurface selection of the microbial community introduced through hydraulic fracturing, which may include significant implications for disinfection as well as reuse of produced water in future fracturing operations.« less

Connecting genomic alterations to cancer biology with proteomics: the NCI Clinical Proteomic Tumor Analysis Consortium.

PubMed

Ellis, Matthew J; Gillette, Michael; Carr, Steven A; Paulovich, Amanda G; Smith, Richard D; Rodland, Karin K; Townsend, R Reid; Kinsinger, Christopher; Mesri, Mehdi; Rodriguez, Henry; Liebler, Daniel C

2013-10-01

The National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium is applying the latest generation of proteomic technologies to genomically annotated tumors from The Cancer Genome Atlas (TCGA) program, a joint initiative of the NCI and the National Human Genome Research Institute. By providing a fully integrated accounting of DNA, RNA, and protein abnormalities in individual tumors, these datasets will illuminate the complex relationship between genomic abnormalities and cancer phenotypes, thus producing biologic insights as well as a wave of novel candidate biomarkers and therapeutic targets amenable to verification using targeted mass spectrometry methods. ©2013 AACR.

The Integrated Airport: Building a Successful NextGen Testbed

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

Frederick-Recascino, Christina; Sweigard, Doug; Lester, Wade

2009-02-18

This presentation will describe a unique public-private partnership - the Integrated Airport - that was created to engage in research and testing related to NextGen Technology deployment.  NextGen refers to the program that will be initiated to modernize the US National Airspace.  As with any major, multi-decade initiative, such as NextGen, integration of work efforts by multiple partners in the modernization is critical for success.  This talk will focus on the development of the consortium, how the consortium plans for NextGen initiatives, the series of technology demonstrations we have produced and plans for the future of NextGen testing and implementation. 

Innovative MIOR Process Utilizing Indigenous Reservoir Constituents

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

Hitzman, D.O.; Stepp, A.K.

This research program was directed at improving the knowledge of reservoir ecology and developing practical microbial solutions for improving oil production. The goal was to identify indigenous microbial populations which can produce beneficial metabolic products and develop a methodology to stimulate those select microbes with inorganic nutrient amendments to increase oil recovery. This microbial technology has the capability of producing multiple oil-releasing agents. The potential of the system will be illustrated and demonstrated by the example of biopolymer production on oil recovery.

Innovative MIOR Process Utilizing Indigenous Reservoir Constituents

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

Hitzman, D.O.; Bailey, S.A.; Stepp, A.K.

This research program was directed at improving the knowledge of reservoir ecology and developing practical microbial solutions for improving oil production. The goal was to identify indigenous microbial populations which can produce beneficial metabolic products and develop a methodology to stimulate those select microbes with inorganic nutrient amendments to increase oil recovery. This microbial technology has the capability of producing multiple oil releasing agents. The potential of the system will be illustrated and demonstrated by the example of biopolymer production on oil recovery.

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

NASA Astrophysics Data System (ADS)

Schieber, J.

2004-03-01

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

Comparing dependencies of E. coli, Salmonella, and Enterococci survival on temperature in surface waters

USDA-ARS?s Scientific Manuscript database

Microbial water quality is attracting substantial attention due to the documented role of produce in microbial food contamination, shellfish industry concerns, and recreation disruptions. In particular, irrigated produce accounted for nearly half of all food-borne illnesses in the USA from 1998 to 2...

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

NASA Astrophysics Data System (ADS)

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

2017-11-01

The formation of Fe(III) oxides in natural environments occurs in the presence of natural organic matter (OM), resulting in the formation of OM-mineral complexes that form through adsorption or coprecipitation processes. Thus, microbial Fe(III) reduction in natural environments most often occurs in the presence of OM-mineral complexes rather than pure Fe(III) minerals. This study investigated to what extent does the content of adsorbed or coprecipitated OM on ferrihydrite influence the rate of Fe(III) reduction by Shewanella oneidensis MR-1, a model Fe(III)-reducing microorganism, in comparison to a microbial consortium extracted from the acidic, Fe-rich Schlöppnerbrunnen fen. We found that increased OM content led to increased rates of microbial Fe(III) reduction by S. oneidensis MR-1 in contrast to earlier findings with the model organism Geobacter bremensis. Ferrihydrite-OM coprecipitates were reduced slightly faster than ferrihydrites with adsorbed OM. Surprisingly, the complex microbial consortia stimulated by a mixture of electrons donors (lactate, acetate, and glucose) mimics S. oneidensis under the same experimental Fe(III)-reducing conditions suggesting similar mechanisms of electron transfer whether or not the OM is adsorbed or coprecipitated to the mineral surfaces. We also followed potential shifts of the microbial community during the incubation via 16S rRNA gene sequence analyses to determine variations due to the presence of adsorbed or coprecipitated OM-ferrihydrite complexes in contrast to pure ferrihydrite. Community profile analyses showed no enrichment of typical model Fe(III)-reducing bacteria, such as Shewanella or Geobacter sp., but an enrichment of fermenters (e.g., Enterobacteria) during pure ferrihydrite incubations which are known to use Fe(III) as an electron sink. Instead, OM-mineral complexes favored the enrichment of microbes including Desulfobacteria and Pelosinus sp., both of which can utilize lactate and 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.

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

PubMed

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

2018-04-01

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

10 CFR 30.4 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-01-01

... radionuclides for use in producing radioactive drugs within the consortium for noncommercial distributions among... storage sheds, warehouse and shop facilities, utilities, concrete mixing plants, docking and unloading... Rico to prescribe drugs in the practice of medicine; Podiatrist means an individual licensed by a State...

Marketing Education Computer Curriculum. Final Report.

ERIC Educational Resources Information Center

Pittsburgh Univ., PA. School of Education.

A project developed computer software based upon Interstate Distributive Education Curriculum Consortium (IDECC) competency-based materials to produce a new curriculum management system for Pennsylvania secondary marketing education programs. During the project, an advisory committee composed of secondary marketing teachers, business people, and…

A niche for cyanobacteria producing chlorophyll f within a microbial mat.

PubMed

Ohkubo, Satoshi; Miyashita, Hideaki

2017-10-01

Acquisition of additional photosynthetic pigments enables photosynthetic organisms to survive in particular niches. To reveal the ecological significance of chlorophyll (Chl) f, we investigated the distribution of Chl and cyanobacteria within two microbial mats. In a 7-mm-thick microbial mat beneath the running water of the Nakabusa hot spring, Japan, Chl f was only distributed 4.0-6.5 mm below the surface, where the intensity of far-red light (FR) was higher than that of photosynthetically active radiation (PAR). In the same mat, two ecotypes of Synechococcus and two ecotypes of Chl f-producing Leptolyngbya were detected in the upper and deeper layers, respectively. Only the Leptolyngbya strains could grow when FR was the sole light source. These results suggest that the deeper layer of the microbial mat was a habitat for Chl f-producing cyanobacteria, and Chl f enabled them to survive in a habitat with little PAR.

Heavy metal immobilization and microbial community abundance by vegetable waste and pine cone biochar of agricultural soils.

PubMed

Igalavithana, Avanthi Deshani; Lee, Sung-Eun; Lee, Young Han; Tsang, Daniel C W; Rinklebe, Jörg; Kwon, Eilhann E; Ok, Yong Sik

2017-05-01

In order to determine the efficacy of vegetable waste and pine cone biochar for immobilization of metal/metalloid (lead and arsenic) and abundance of microbial community in different agricultural soils, we applied the biochar produced at two different temperatures to two contaminated soils. Biochar was produced by vegetable waste, pine cone, and their mixture (1:1 ww -1 ) at 200 °C (torrefied biomass) and 500 °C (biochar). Contaminated soils were incubated with 5% (ww -1 ) torrefied biomass or biochar. Sequential extraction, thermodynamic modeling, and scanning electron microscopy equipped with energy-dispersive X-ray spectroscopy were used to evaluate the metal immobilization. Microbial communities were characterized by microbial fatty acid profiles and microbial activity was assessed by dehydrogenase activity. Vegetable waste and the mixture of vegetable waste and pine cone biochar exhibited greater ability for Pb immobilization than pine cone biochar and three torrefied biomass, and vegetable waste biochar was found to be most effective. However, torrefied biomass was most effective in increasing both microbial community and dehydrogenase activity. This study confirms that vegetable waste could be a vital biomass to produce biochar to immobilize Pb, and increase the microbial communities and enzyme activity in soils. Biomass and pyrolytic temperature were not found to be effective in the immobilization of As in this study. Copyright © 2017. Published by Elsevier Ltd.

Temporal and spatial differences in microbial composition during the manufacture of a continental-type cheese.

PubMed

O'Sullivan, Daniel J; Cotter, Paul D; O'Sullivan, Orla; Giblin, Linda; McSweeney, Paul L H; Sheehan, Jeremiah J

2015-04-01

We sought to determine if the time, within a production day, that a cheese is manufactured has an influence on the microbial community present within that cheese. To facilitate this, 16S rRNA amplicon sequencing was used to elucidate the microbial community dynamics of brine-salted continental-type cheese in cheeses produced early and late in the production day. Differences in the microbial composition of the core and rind of the cheese were also investigated. Throughout ripening, it was apparent that cheeses produced late in the day had a more diverse microbial population than their early equivalents. Spatial variation between the cheese core and rind was also noted in that cheese rinds were initially found to have a more diverse microbial population but thereafter the opposite was the case. Interestingly, the genera Thermus, Pseudoalteromonas, and Bifidobacterium, not routinely associated with a continental-type cheese produced from pasteurized milk, were detected. The significance, if any, of the presence of these genera will require further attention. Ultimately, the use of high-throughput sequencing has facilitated a novel and detailed analysis of the temporal and spatial distribution of microbes in this complex cheese system and established that the period during a production cycle at which a cheese is manufactured can influence its microbial composition. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

The Multi-Resolution Land Characteristics (MRLC) Consortium: 20 years of development and integration of USA national land cover data

USGS Publications Warehouse

Wickham, James D.; Homer, Collin G.; Vogelmann, James E.; McKerrow, Alexa; Mueller, Rick; Herold, Nate; Coluston, John

2014-01-01

The Multi-Resolution Land Characteristics (MRLC) Consortium demonstrates the national benefits of USA Federal collaboration. Starting in the mid-1990s as a small group with the straightforward goal of compiling a comprehensive national Landsat dataset that could be used to meet agencies’ needs, MRLC has grown into a group of 10 USA Federal Agencies that coordinate the production of five different products, including the National Land Cover Database (NLCD), the Coastal Change Analysis Program (C-CAP), the Cropland Data Layer (CDL), the Gap Analysis Program (GAP), and the Landscape Fire and Resource Management Planning Tools (LANDFIRE). As a set, the products include almost every aspect of land cover from impervious surface to detailed crop and vegetation types to fire fuel classes. Some products can be used for land cover change assessments because they cover multiple time periods. The MRLC Consortium has become a collaborative forum, where members share research, methodological approaches, and data to produce products using established protocols, and we believe it is a model for the production of integrated land cover products at national to continental scales. We provide a brief overview of each of the main products produced by MRLC and examples of how each product has been used. We follow that with a discussion of the impact of the MRLC program and a brief overview of future plans.

Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium

PubMed Central

Freschi, Luca; Jeukens, Julie; Kukavica-Ibrulj, Irena; Boyle, Brian; Dupont, Marie-Josée; Laroche, Jérôme; Larose, Stéphane; Maaroufi, Halim; Fothergill, Joanne L.; Moore, Matthew; Winsor, Geoffrey L.; Aaron, Shawn D.; Barbeau, Jean; Bell, Scott C.; Burns, Jane L.; Camara, Miguel; Cantin, André; Charette, Steve J.; Dewar, Ken; Déziel, Éric; Grimwood, Keith; Hancock, Robert E. W.; Harrison, Joe J.; Heeb, Stephan; Jelsbak, Lars; Jia, Baofeng; Kenna, Dervla T.; Kidd, Timothy J.; Klockgether, Jens; Lam, Joseph S.; Lamont, Iain L.; Lewenza, Shawn; Loman, Nick; Malouin, François; Manos, Jim; McArthur, Andrew G.; McKeown, Josie; Milot, Julie; Naghra, Hardeep; Nguyen, Dao; Pereira, Sheldon K.; Perron, Gabriel G.; Pirnay, Jean-Paul; Rainey, Paul B.; Rousseau, Simon; Santos, Pedro M.; Stephenson, Anne; Taylor, Véronique; Turton, Jane F.; Waglechner, Nicholas; Williams, Paul; Thrane, Sandra W.; Wright, Gerard D.; Brinkman, Fiona S. L.; Tucker, Nicholas P.; Tümmler, Burkhard; Winstanley, Craig; Levesque, Roger C.

2015-01-01

The International Pseudomonas aeruginosa Consortium is sequencing over 1000 genomes and building an analysis pipeline for the study of Pseudomonas genome evolution, antibiotic resistance and virulence genes. Metadata, including genomic and phenotypic data for each isolate of the collection, are available through the International Pseudomonas Consortium Database (http://ipcd.ibis.ulaval.ca/). Here, we present our strategy and the results that emerged from the analysis of the first 389 genomes. With as yet unmatched resolution, our results confirm that P. aeruginosa strains can be divided into three major groups that are further divided into subgroups, some not previously reported in the literature. We also provide the first snapshot of P. aeruginosa strain diversity with respect to antibiotic resistance. Our approach will allow us to draw potential links between environmental strains and those implicated in human and animal infections, understand how patients become infected and how the infection evolves over time as well as identify prognostic markers for better evidence-based decisions on patient care. PMID:26483767

Denitrifying sulfide removal process on high-salinity wastewaters.

PubMed

Liu, Chunshuang; Zhao, Chaocheng; Wang, Aijie; Guo, Yadong; Lee, Duu-Jong

2015-08-01

Denitrifying sulfide removal (DSR) process comprising both heterotrophic and autotrophic denitrifiers can simultaneously convert nitrate, sulfide, and acetate into nitrogen gas, elemental sulfur (S(0)), and carbon dioxide, respectively. Sulfide- and nitrate-laden wastewaters at 2-35 g/L NaCl were treated by DSR process. A C/N ratio of 3:1 was proposed to maintain high S(0) conversion rate. The granular sludge with a compact structure and smooth outer surface was formed. The microbial communities of DSR consortium via high-throughput sequencing method suggested that salinity shifts the predominating heterotrophic denitrifiers at <10 g/L NaCl to autotrophic denitrifiers at >10 g/L NaCl.

Quantitative Monitoring of Microbial Species during Bioleaching of a Copper Concentrate.

PubMed

Hedrich, Sabrina; Guézennec, Anne-Gwenaëlle; Charron, Mickaël; Schippers, Axel; Joulian, Catherine

2016-01-01

Monitoring of the microbial community in bioleaching processes is essential in order to control process parameters and enhance the leaching efficiency. Suitable methods are, however, limited as they are usually not adapted to bioleaching samples and often no taxon-specific assays are available in the literature for these types of consortia. Therefore, our study focused on the development of novel quantitative real-time PCR (qPCR) assays for the quantification of Acidithiobacillus caldus, Leptospirillum ferriphilum, Sulfobacillus thermosulfidooxidans , and Sulfobacillus benefaciens and comparison of the results with data from other common molecular monitoring methods in order to evaluate their accuracy and specificity. Stirred tank bioreactors for the leaching of copper concentrate, housing a consortium of acidophilic, moderately thermophilic bacteria, relevant in several bioleaching operations, served as a model system. The microbial community analysis via qPCR allowed a precise monitoring of the evolution of total biomass as well as abundance of specific species. Data achieved by the standard fingerprinting methods, terminal restriction fragment length polymorphism (T-RFLP) and capillary electrophoresis single strand conformation polymorphism (CE-SSCP) on the same samples followed the same trend as qPCR data. The main added value of qPCR was, however, to provide quantitative data for each species whereas only relative abundance could be deduced from T-RFLP and CE-SSCP profiles. Additional value was obtained by applying two further quantitative methods which do not require nucleic acid extraction, total cell counting after SYBR Green staining and metal sulfide oxidation activity measurements via microcalorimetry. Overall, these complementary methods allow for an efficient quantitative microbial community monitoring in various bioleaching operations.

Quantitative Monitoring of Microbial Species during Bioleaching of a Copper Concentrate

PubMed Central

Hedrich, Sabrina; Guézennec, Anne-Gwenaëlle; Charron, Mickaël; Schippers, Axel; Joulian, Catherine

2016-01-01

Monitoring of the microbial community in bioleaching processes is essential in order to control process parameters and enhance the leaching efficiency. Suitable methods are, however, limited as they are usually not adapted to bioleaching samples and often no taxon-specific assays are available in the literature for these types of consortia. Therefore, our study focused on the development of novel quantitative real-time PCR (qPCR) assays for the quantification of Acidithiobacillus caldus, Leptospirillum ferriphilum, Sulfobacillus thermosulfidooxidans, and Sulfobacillus benefaciens and comparison of the results with data from other common molecular monitoring methods in order to evaluate their accuracy and specificity. Stirred tank bioreactors for the leaching of copper concentrate, housing a consortium of acidophilic, moderately thermophilic bacteria, relevant in several bioleaching operations, served as a model system. The microbial community analysis via qPCR allowed a precise monitoring of the evolution of total biomass as well as abundance of specific species. Data achieved by the standard fingerprinting methods, terminal restriction fragment length polymorphism (T-RFLP) and capillary electrophoresis single strand conformation polymorphism (CE-SSCP) on the same samples followed the same trend as qPCR data. The main added value of qPCR was, however, to provide quantitative data for each species whereas only relative abundance could be deduced from T-RFLP and CE-SSCP profiles. Additional value was obtained by applying two further quantitative methods which do not require nucleic acid extraction, total cell counting after SYBR Green staining and metal sulfide oxidation activity measurements via microcalorimetry. Overall, these complementary methods allow for an efficient quantitative microbial community monitoring in various bioleaching operations. PMID:28066365

Towards a Microbial Thermoelectric Cell

PubMed Central

Rodríguez-Barreiro, Raúl; Abendroth, Christian; Vilanova, Cristina; Moya, Andrés; Porcar, Manuel

2013-01-01

Microbial growth is an exothermic process. Biotechnological industries produce large amounts of heat, usually considered an undesirable by-product. In this work, we report the construction and characterization of the first microbial thermoelectric cell (MTC), in which the metabolic heat produced by a thermally insulated microbial culture is partially converted into electricity through a thermoelectric device optimized for low ΔT values. A temperature of 41°C and net electric voltage of around 250–600 mV was achieved with 1.7 L baker’s yeast culture. This is the first time microbial metabolic energy has been converted into electricity with an ad hoc thermoelectric device. These results might contribute towards developing a novel strategy to harvest excess heat in the biotechnology industry, in processes such as ethanol fermentation, auto thermal aerobic digestion (ATAD) or bioremediation, which could be coupled with MTCs in a single unit to produce electricity as a valuable by-product of the primary biotechnological product. Additionally, we propose that small portable MTCs could be conceived and inoculated with suitable thermophilic of hyperthermophilic starter cultures and used for powering small electric devices. PMID:23468862

The diversity of anti-microbial secondary metabolites produced by fungal endophytes: an interdisciplinary perspective.

PubMed

Mousa, Walaa Kamel; Raizada, Manish N

2013-01-01

Endophytes are microbes that inhabit host plants without causing disease and are reported to be reservoirs of metabolites that combat microbes and other pathogens. Here we review diverse classes of secondary metabolites, focusing on anti-microbial compounds, synthesized by fungal endophytes including terpenoids, alkaloids, phenylpropanoids, aliphatic compounds, polyketides, and peptides from the interdisciplinary perspectives of biochemistry, genetics, fungal biology, host plant biology, human and plant pathology. Several trends were apparent. First, host plants are often investigated for endophytes when there is prior indigenous knowledge concerning human medicinal uses (e.g., Chinese herbs). However, within their native ecosystems, and where investigated, endophytes were shown to produce compounds that target pathogens of the host plant. In a few examples, both fungal endophytes and their hosts were reported to produce the same compounds. Terpenoids and polyketides are the most purified anti-microbial secondary metabolites from endophytes, while flavonoids and lignans are rare. Examples are provided where fungal genes encoding anti-microbial compounds are clustered on chromosomes. As different genera of fungi can produce the same metabolite, genetic clustering may facilitate sharing of anti-microbial secondary metabolites between fungi. We discuss gaps in the literature and how more interdisciplinary research may lead to new opportunities to develop bio-based commercial products to combat global crop and human pathogens.

The Diversity of Anti-Microbial Secondary Metabolites Produced by Fungal Endophytes: An Interdisciplinary Perspective

PubMed Central

Mousa, Walaa Kamel; Raizada, Manish N.

2013-01-01

Endophytes are microbes that inhabit host plants without causing disease and are reported to be reservoirs of metabolites that combat microbes and other pathogens. Here we review diverse classes of secondary metabolites, focusing on anti-microbial compounds, synthesized by fungal endophytes including terpenoids, alkaloids, phenylpropanoids, aliphatic compounds, polyketides, and peptides from the interdisciplinary perspectives of biochemistry, genetics, fungal biology, host plant biology, human and plant pathology. Several trends were apparent. First, host plants are often investigated for endophytes when there is prior indigenous knowledge concerning human medicinal uses (e.g., Chinese herbs). However, within their native ecosystems, and where investigated, endophytes were shown to produce compounds that target pathogens of the host plant. In a few examples, both fungal endophytes and their hosts were reported to produce the same compounds. Terpenoids and polyketides are the most purified anti-microbial secondary metabolites from endophytes, while flavonoids and lignans are rare. Examples are provided where fungal genes encoding anti-microbial compounds are clustered on chromosomes. As different genera of fungi can produce the same metabolite, genetic clustering may facilitate sharing of anti-microbial secondary metabolites between fungi. We discuss gaps in the literature and how more interdisciplinary research may lead to new opportunities to develop bio-based commercial products to combat global crop and human pathogens. PMID:23543048

Microflora of root filled teeth with apical periodontitis in Latvian patients.

PubMed

Mindere, Anda; Kundzina, Rita; Nikolajeva, Vizma; Eze, Daina; Petrina, Zaiga

2010-01-01

The aim of the present study was to investigate the microbial flora of root filled teeth with apical periodontitis and to determine the prevalence of β-lactamase producing strains in isolated bacteria in Latvian patients. 33 root filled teeth with asymptomatic persisting periapical lesions were selected for the present study. During nonsurgical endodontic retreatment, the root filling material was removed and canals were sampled. Determination of microbial species was based on series of biochemical tests using identification kits. All strains of bacteria were tested for β-lactamase production by using chromogenic nitrocefin-impregnated slides. Bacteria were found in 32 (97%) of initial specimens from the teeth. The number of isolated microbial strains in the specimens ranged from one to six (mean 2.7). 79% of the isolated microbial species were Gram-positive bacteria. The most common isolates were Streptococcus (27%), Actinomyces (27%), Staphylococcus (18%), Enterococcus (18%) and Lactobacillus (18%) spp. Yeasts were found as four isolates in 3 cases (9%). β-lactamase-producing bacterial strains were detected in 12 specimens, 36% of the patients. The most common enzyme-producing bacteria belonged to Actinomyces and Staphylococcus spp. The microbial flora in previously treated root canals with apical periodontitis is limited to a small number of predominantly Gram-positive microbial species. The most common isolates are Streptococcus, Actinomyces, Staphylococcus, Enterococcus and Lactobacillus spp. A moderately high prevalence of β-lactamase producing bacterial strains was detected in patients with root filled teeth with apical periodontitis.

Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction: COMMUNITY DATA-DRIVEN METABOLIC NETWORK MODELING

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

Henry, Christopher S.; Bernstein, Hans C.; Weisenhorn, Pamela

Metabolic network modeling of microbial communities provides an in-depth understanding of community-wide metabolic and regulatory processes. Compared to single organism analyses, community metabolic network modeling is more complex because it needs to account for interspecies interactions. To date, most approaches focus on reconstruction of high-quality individual networks so that, when combined, they can predict community behaviors as a result of interspecies interactions. However, this conventional method becomes ineffective for communities whose members are not well characterized and cannot be experimentally interrogated in isolation. Here, we tested a new approach that uses community-level data as a critical input for the networkmore » reconstruction process. This method focuses on directly predicting interspecies metabolic interactions in a community, when axenic information is insufficient. We validated our method through the case study of a bacterial photoautotroph-heterotroph consortium that was used to provide data needed for a community-level metabolic network reconstruction. Resulting simulations provided experimentally validated predictions of how a photoautotrophic cyanobacterium supports the growth of an obligate heterotrophic species by providing organic carbon and nitrogen sources.« less

Screening of a microbial consortium for selective degradation of lignin from tree trimmings.

PubMed

Fang, Xiuxiu; Li, Qiumin; Lin, Yunqin; Lin, Xinlei; Dai, Yiqi; Guo, Zexiang; Pan, Dezhao

2018-04-01

To acquire microbial consortia with effectively precedent degradation of lignin, samples obtained from rotten trunks, rotten stumps and soil near it were screened and isolated after generations of subculture. The dynamic change illustrated that their community structures were affected by pH and tended to be stable after 6 days' cultivation. The desired one, named DM-1, was gained through successive cultivation for over 5 generations, whose high selectivity in lignin degradation was observed within 16 days' cultivation (SV = 2.78). Meanwhile, a remarkable reduction in the fiber crystallinity of tree trimmings (10.35%) resulted from the bio-degradation of DM-1, displayed a greater exposure of cellulose by selective removal of lignin. The diversity analysis of DM-1 was investigated by PCR amplification and 16S rDNA sequencing, indicated that mesorhizobium, cellulosimicrobium, pandoraea, achromobacter and stenotrophomones were the predominant genera. Furthermore, fungi (3 strains), bacteria (4 strains) and actinomycetes (5 strains) constituted 12 strains in total were gained by plate isolation from DM-1. Copyright © 2018 Elsevier Ltd. All rights reserved.

Potential biodegradation of crude petroleum oil by newly isolated halotolerant microbial strains from polluted Red Sea area.

PubMed

Shetaia, Yousseria M H; El Khalik, Wafaa A A; Mohamed, Tarek M; Farahat, Laila A; ElMekawy, Ahmed

2016-10-15

Two microbial isolates from oil polluted Red Sea water in Egypt, designated as RS-Y1 and RS-F3, were found capable of degrading Belayim mix (BX) crude oil. Strains RS-Y1 and RS-F3 were assigned to the genera Lipomyces tetrasporus and Paecilomyces variotii based on their morphological and physiological characteristics. Both isolates were compared for the biodegradation of crude petroleum-oil hydrocarbons in basal salt medium supplemented with 5% (w/v) of BX-crude oil. Gas chromatography profile showed that the biodegradation of total petroleum hydrocarbons (TPHs) inoculated with L. tetrasporus (68.3%) and P. variotii (58.15%) along with their consortium (66%) significantly reduced TPHs levels as compared to the control after 30days. L. tetrasporus (44.5%) was more effective than P. variotii strain (32.89%) in reducing the unresolved complex mixtures (UCM) content from the medium. Both isolates exhibited a strong growth over a wide range of salinity (5-45g/L NaCl). Copyright © 2016 Elsevier Ltd. All rights reserved.

Community dynamics of anaerobic bacteria in deep petroleum reservoirs

NASA Astrophysics Data System (ADS)

Hallmann, Christian; Schwark, Lorenz; Grice, Kliti

2008-09-01

The nature, activity and metabolism of microbes that inhabit the deep subsurface environment are a matter of ongoing debate. Primarily limited by temperature, little is known about secondary factors that restrict or enhance microbial activity or about the extent of a habitable environment deep below the surface. In particular, the degraders of chemically inert organic substrates remain elusive. Petroleum reservoirs can be regarded as natural bioreactors and are ideally suited for the study of microbial metabolism in the deep subsurface. Here we analyse series of oil samples that were biodegraded to different degrees. We find fatty acids after hydrolysis of purified crude oil fractions, indicating the presence of intact phospholipids and suggesting that indigenous bacteria inhabit petroleum reservoirs in sediment depths of up to 2,000m. A major change in bacterial community structure occurs after the removal of n-alkanes, indicating that more than one consortium is responsible for petroleum degradation. Our results suggest that further study of petroleum fluids will help understand bacterial metabolism and diversity in this habitat of the deep subsurface.

Theagalloflavic Acid, a New Pigment Derived from Hexahydroxydiphenoyl Group, and Lignan Oxidation Products Produced by Aerobic Microbial Fermentation of Green Tea.

PubMed

Matsuo, Yosuke; Matsuda, Tomoko; Sugihara, Keisuke; Saito, Yoshinori; Zhang, Ying-Jun; Yang, Chong-Ren; Tanaka, Takashi

2016-01-01

Chinese ripe pu-erh tea is produced by aerobic microbial fermentation of green tea. To clarify the microbial degradation of tea polyphenols, Japanese commercial green tea was mixed with Chinese ripe pu-erh tea, which retains microorganisms, and fermented for 5 d. Chromatographic separation yielded a novel water-soluble yellow pigment termed theagalloflavic acid. Spectroscopic and chemical evidence suggested that this pigment was produced by oxidative ring cleavage of hexahydroxydiphenoyl esters. In addition, two new oxygenated lignin metabolites, (+)-5,5'-dihydroxypinoresinol and 5-hydroxydihydrodehydrodiconiferyl alcohol, were also isolated together with known degradation products of quercetin and tea catechins.

Quinine, Malaria, and the Cinchona Bureau: Marketing Practices and Knowledge Circulation in a Dutch Transoceanic Cinchona-Quinine Enterprise (1920s-30s).

PubMed

Van Der Hoogte, Arjo Roersch; Pieters, Toine

2016-04-01

In this study, we will show how a Dutch pharmaceutical consortium of cinchona producers and quinine manufacturers was able to capitalize on one of the first international public health campaigns to fight malaria, thereby promoting the sale of quinine, an antimalarial medicine. During the 1920s and 1930s, the international markets for quinine were controlled by this Dutch consortium, which was a transoceanic cinchona-quinine enterprise centered in the Cinchona Bureau in the Netherlands. We will argue that during the interwar period, the Cinchona Bureau became the decision-making center of this Dutch cinchona-quinine pharmaceutical enterprise and monopolized the production and trade of an essential medicine. In addition, we will argue that capitalizing on the international public health campaign in the fight against malaria by the Dutch cinchona-quinine enterprise via the Cinchona Bureau can be regarded as an early example of corporate colonization of public health by a private pharmaceutical consortium. Furthermore, we will show how commercial interests prevailed over scientific interests within the Dutch cinchona-quinine consortium, thus interfering with and ultimately curtailing the transoceanic circulation of knowledge in the Dutch empire. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.