DOCSLIB.ORG

Reconstruction of Regulatory and Metabolic

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Reconstruction of Regulatory and Metabolic Open Access Research2004RodionovetVolume al. 5, Issue 11, Article R90 Reconstruction of regulatory and metabolic pathways in comment metal-reducing δ-proteobacteria Dmitry A Rodionov*, Inna Dubchak†, Adam Arkin‡§¶, Eric Alm‡ and Mikhail S Gelfand*¥ Addresses: *Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny per. 19, Moscow 127994, Russia. †Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. ‡Physical Biosciences Division, Lawrence Berkeley § ¶ National Laboratory, Berkeley, CA 94720, USA. Howard Hughes Medical Institute, Berkeley, CA 94720, USA. University of California, reviews Berkeley, CA 94720, USA. ¥State Scientific Center GosniiGenetika, 1st Dorozhny pr. 1, Moscow 117545, Russia. Correspondence: Dmitry A Rodionov. E-mail: [email protected] Published: 22 October 2004 Received: 2 July 2004 Revised: 20 September 2004 Genome Biology 2004, 5:R90 Accepted: 30 September 2004 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2004/5/11/R90 reports © 2004 Rodionov et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Reconstruction<p>Apathways study suggests of the of regulatory geneticthat phylogenetically and and regulatory metabolic diverse factors pathways delta-proteobacteria in several in metal-reducing biosynthesis, have delta-proteobacteriametal homologous ion homeostasis, regulatory stress components.</p> response, and energy metabolism deposited research Abstract Background: Relatively little is known about the genetic basis for the unique physiology of metal- reducing genera in the delta subgroup of the proteobacteria. The recent availability of complete finished or draft-quality genome sequences for seven representatives allowed us to investigate the genetic and regulatory factors in a number of key pathways involved in the biosynthesis of building blocks and cofactors, metal-ion homeostasis, stress response, and energy metabolism using a research refereed combination of regulatory sequence detection and analysis of genomic context. Results: In the genomes of δ-proteobacteria, we identified candidate binding sites for four regulators of known specificity (BirA, CooA, HrcA, sigma-32), four types of metabolite-binding riboswitches (RFN-, THI-, B12-elements and S-box), and new binding sites for the FUR, ModE, NikR, PerR, and ZUR transcription factors, as well as for the previously uncharacterized factors HcpR and LysX. After reconstruction of the corresponding metabolic pathways and regulatory interactions, we identified possible functions for a large number of previously uncharacterized genes covering a wide range of cellular functions. interactions Conclusions: Phylogenetically diverse δ-proteobacteria appear to have homologous regulatory components. This study for the first time demonstrates the adaptability of the comparative genomic approach to de novo reconstruction of a regulatory network in a poorly studied taxonomic group of bacteria. Recent efforts in large-scale functional genomic characterization of Desulfovibrio species will provide a unique opportunity to test and expand our predictions. information Background Bdellovibrio, which prey on other bacteria [1]. In this study, The delta subdivision of proteobacteria is a very diverse group we focus on anaerobic metal-reducing δ-proteobacteria, of Gram-negative microorganisms that include aerobic gen- seven representatives of which have been sequenced recently, era Myxococcus with complex developmental lifestyles and providing an opportunity for comparative genomic analysis. Genome Biology 2004, 5:R90 R90.2 Genome Biology 2004, Volume 5, Issue 11, Article R90 Rodionov et al. http://genomebiology.com/2004/5/11/R90 Within this group, sulfate-reducing bacteria, including Desul- onas palmitatis has been sequenced, resulting in a large fovibrio and Desulfotalea species, are metabolically and eco- number of small scaffolds, the identity of which (acetoxidans logically versatile prokaryotes often characterized by their or palmitatis) has not been determined, and we refer to this ability to reduce sulfate to sulfide [2]. They can be found in sequence set simply as Desulfuromonas. Though draft-qual- aquatic habitats or waterlogged soils containing abundant ity sequence can make it difficult to assert with confidence the organic material and sufficient levels of sulfate, and play a key absence of any particular gene, we have included these role in the global sulfur and carbon cycles [1]. Industrial inter- genomes in our study because they do provide insight as to est in sulfate reducers has focused on their role in corrosion the presence or absence of entire pathways, they can be com- of metal equipment and the souring of petroleum reservoirs, pared to the related finished genome of G. sulfurreducens, while their ability to reduce toxic heavy metals has drawn and because complete genome sequence is not necessary for attention from researchers interested in exploiting this ability the methodology we use to detect regulatory sequences. for bioremediation. Psychrophilic sulfate-reducing Desulfo- talea psychrophila has been isolated from permanently cold In this comprehensive study, we identify a large number of arctic marine sediments [3]. In contrast to sulfate-reducing regulatory elements in these δ-proteobacteria. Some of the bacteria, the genera Geobacter and Desulfuromonas com- corresponding regulons are highly conserved among various prise dissimilative metal-reducing bacteria, which cannot bacteria (for example, riboswitches, BirA, CIRCE), whereas reduce sulfate, but include representatives that require sulfur others are specific only for δ-proteobacteria. We also present as a respiratory electron acceptor for oxidation of acetate to the reconstruction of a number of biosynthetic pathways and carbon dioxide [4]. These bacteria are an important compo- systems for metal-ion homeostasis and stress response in nent of the subsurface biota that oxidizes organic compounds, these bacteria. The most important result of this study is hydrogen or sulfur with the reduction of insoluble Fe(III) identification of a novel regulon involved in sulfate reduction oxides [5], and have also been implicated in corrosion and and energy metabolism in sulfate-reducing bacteria, which is toxic metal reduction. most probably controlled by a regulator from the CRP/FNR family. Knowledge of transcriptional regulatory networks is essential for understanding cellular processes in bacteria. However, experimental data about regulation of gene expression in δ- Results proteobacteria are very limited. Different approaches could The results are organized under four main headings for con- be used for identification of co-regulated genes (regulons). venience. In the first, we analyze a number of specific regu- Transcriptional profiling using DNA microarrays allows one lons for biosynthesis of various amino acids and cofactors in to compare the expression levels of thousands of genes in dif- δ-proteobacteria. Most of them are controlled by RNA regula- ferent experimental conditions, and is a valuable tool for dis- tory elements, or riboswitches, that are highly conserved secting bacterial adaptation to various environments. across bacteria [18]. In the next section we describe several Computational approaches, on the other hand, provide an regulons for the uptake and homeostasis of transition metal opportunity to describe regulons in poorly characterized ions that are necessary for growth. These regulons operate by genomes. Comparison of upstream sequences of genes can, in transcription factors that are homologous to factors in principle, identify co-regulated genes. From large-scale stud- Escherichia coli, but are predicted to recognize entirely dif- ies [6-9] and analyses of individual regulatory systems [10- ferent DNA signals. We then describe two stress-response 14] it is clear that the comparative analysis of binding sites for regulons: heat-shock regulons (σ32 and HrcA/CIRCE), which transcriptional regulators is a powerful approach to the func- operate by regulatory elements conserved in diverse bacteria, tional annotation of bacterial genomes. Additional tech- and newly identified peroxide stress response regulons that niques used in genome context analysis, such as are quite diverse and conserved only in closely related spe- chromosomal gene clustering, protein fusions and co-occur- cies. Finally, we present a completely new global regulon in rence profiles, in combination with metabolic reconstruction, metal-reducing δ-proteobacteria, which includes various allow the inference of functional coupling between genes and genes involved in energy metabolism and sulfate reduction. the prediction of gene function [15]. Biosynthesis and transport of vitamins and amino acids Recent completion of finished and draft quality genome Biotin sequences for δ-proteobacteria provides an opportunity for Biotin (vitamin H) is an essential cofactor for numerous comparative analysis of transcriptional regulation and meta- biotin-dependent carboxylases in a variety of microorgan- bolic pathways in these bacteria. The finished genomes isms [19]. The strict control of biotin biosynthesis is mediated include sulfate-reducing
Load more

Recommended publications
  • Regeneration of Unconventional Natural Gas by Methanogens Co
    www.nature.com/scientificreports OPEN Regeneration of unconventional natural gas by methanogens co‑existing with sulfate‑reducing prokaryotes in deep shale wells in China Yimeng Zhang1,2,3, Zhisheng Yu1*, Yiming Zhang4 & Hongxun Zhang1 Biogenic methane in shallow shale reservoirs has been proven to contribute to economic recovery of unconventional natural gas. However, whether the microbes inhabiting the deeper shale reservoirs at an average depth of 4.1 km and even co-occurring with sulfate-reducing prokaryote (SRP) have the potential to produce biomethane is still unclear. Stable isotopic technique with culture‑dependent and independent approaches were employed to investigate the microbial and functional diversity related to methanogenic pathways and explore the relationship between SRP and methanogens in the shales in the Sichuan Basin, China. Although stable isotopic ratios of the gas implied a thermogenic origin for methane, the decreased trend of stable carbon and hydrogen isotope value provided clues for increasing microbial activities along with sustained gas production in these wells. These deep shale-gas wells harbored high abundance of methanogens (17.2%) with ability of utilizing various substrates for methanogenesis, which co-existed with SRP (6.7%). All genes required for performing methylotrophic, hydrogenotrophic and acetoclastic methanogenesis were present. Methane production experiments of produced water, with and without additional available substrates for methanogens, further confrmed biomethane production via all three methanogenic pathways. Statistical analysis and incubation tests revealed the partnership between SRP and methanogens under in situ sulfate concentration (~ 9 mg/L). These results suggest that biomethane could be produced with more fexible stimulation strategies for unconventional natural gas recovery even at the higher depths and at the presence of SRP.
    [Show full text]
  • Heavy Metal and Sulfate Tolerance Bacteria Isolated from the Mine Drainage and Sediment of Igun, Osun State, Nigeria
    IOSR Journal of Environmental Science, Toxicology and Food Technology (IOSR-JESTFT) e-ISSN: 2319-2402,p- ISSN: 2319-2399.Volume 15, Issue 3 Ser. I (March 2021), PP 36-55 www.iosrjournals.org Heavy Metal and Sulfate Tolerance Bacteria Isolated from the Mine Drainage and Sediment of Igun, Osun State, Nigeria Aransiola M. N.1 Olusola B. O.2 and Fagade O. E.1 1(Department of Microbiology, Faculty of Science, University of Ibadan, Ibadan, Nigeria) 2(Department of Health Sciences, College of Health Professions, Walden University, Minneapolis, USA) Abstract Background: Mine Drainages (MD) are polluted water associated with mining activities which may contain heavy metals and other chemicals which impact biotic and abiotic factors of such environment. Igun area is known for abandoned mine site with MD. Therefore, the objectives of this study are to determine the physicochemical and microbiological properties of an abandoned mine water and sediment at Igun, and evaluate the heavy metals and sulfate ion tolerance of the indigenous bacteria. Materials and Methods: The Igun MD was divided into grids (4x4 m2) and from each grid, water and sediment sample s were purposively collected in February and October of 2014 to 2016. The chemical analyses of the samples were carried out using APHA methods and compared with the NESREA’s recommendation. Microbial analyses of the samples were done using cultural, phenotypic and genomic characteristics to determine the Aerobic Bacteria (AB) and Sulfate Reducing Bacteria (SRB) within the Igun MD. The isolated bacteria were screened for heavy metal and sulfate tolerance using standard methods. Data were analysed using descriptive statistics.
    [Show full text]
  • The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment
    life Article The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment Sierra R. Athen, Shivangi Dubey and John A. Kyndt * College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA; [email protected] (S.R.A.); [email protected] (S.D.) * Correspondence: [email protected] Abstract: The Eastern Nebraska Salt Marshes contain a unique, alkaline, and saline wetland area that is a remnant of prehistoric oceans that once covered this area. The microbial composition of these salt marshes, identified by metagenomic sequencing, appears to be different from well-studied coastal salt marshes as it contains bacterial genera that have only been found in cold-adapted, alkaline, saline environments. For example, Rubribacterium was only isolated before from an Eastern Siberian soda lake, but appears to be one of the most abundant bacteria present at the time of sampling of the Eastern Nebraska Salt Marshes. Further enrichment, followed by genome sequencing and metagenomic binning, revealed the presence of several halophilic, alkalophilic bacteria that play important roles in sulfur and carbon cycling, as well as in nitrogen fixation within this ecosystem. Photosynthetic sulfur bacteria, belonging to Prosthecochloris and Marichromatium, and chemotrophic sulfur bacteria of the genera Sulfurimonas, Arcobacter, and Thiomicrospira produce valuable oxidized sulfur compounds for algal and plant growth, while alkaliphilic, sulfur-reducing bacteria belonging to Sulfurospirillum help balance the sulfur cycle. This metagenome-based study provides a baseline to understand the complex, but balanced, syntrophic microbial interactions that occur in this unique Citation: Athen, S.R.; Dubey, S.; inland salt marsh environment.
    [Show full text]
  • Metagenomes of Native and Electrode-Enriched Microbial Communities from the Soudan Iron Mine Jonathan P
    Metagenomes of native and electrode-enriched microbial communities from the Soudan Iron Mine Jonathan P. Badalamenti and Daniel R. Bond Department of Microbiology and BioTechnology Institute, University of Minnesota - Twin Cities, Saint Paul, Minnesota, USA Twitter: @JonBadalamenti @wanderingbond Summary Approach - compare metagenomes from native and electrode-enriched deep subsurface microbial communities 30 Despite apparent carbon limitation, anoxic deep subsurface brines at the Soudan ) enriched 2 Underground Iron Mine harbor active microbial communities . To characterize these 20 A/cm µ assemblages, we performed shotgun metagenomics of native and enriched samples. enrich ( harvest cells collect inoculate +0.24 V extract 10 Follwing enrichment on poised electrodes and long read sequencing, we recovered Soudan brine electrode 20° C from DNA biodreactors current electrodes from the metagenome the closed, circular genome of a novel Desulfuromonas sp. 0 0 10 20 30 40 filtrate PacBio RS II Illumina HiSeq with remarkable genomic features that were not fully resolved by short read assem- extract time (d) long reads short reads TFF DNA unenriched bly alone. This organism was essentially absent in unenriched Soudan communities, 0.1 µm retentate assembled metagenomes reconstruct long read return de novo complete genome(s) assembly indicating that electrodes are highly selective for putative metal reducers. Native HGAP assembly community metagenomes suggest that carbon cycling is driven by methyl-C me- IDBA_UD 1 hybrid tabolism, in particular methylotrophic methanogenesis. Our results highlight the 3 µm prefilter assembly N4 binning promising potential for long reads in metagenomic surveys of low-diversity environ- borehole N4 binning read trimming and filtering brine de novo ments.
    [Show full text]
  • University of Oklahoma Graduate College Microbial Ecology of Coastal Ecosystems: Investigations of the Genetic Potential For
    UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE MICROBIAL ECOLOGY OF COASTAL ECOSYSTEMS: INVESTIGATIONS OF THE GENETIC POTENTIAL FOR ANAEROBIC HYDROCARBON TRANSFORMATION AND THE RESPONSE TO HYDROCARBON EXPOSURE A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements of the Degree of DOCTOR OF PHILOSOPHY By JAMIE M. JOHNSON DUFFNER Norman, Oklahoma 2017 MICROBIAL ECOLOGY OF COASTAL ECOSYSTEMS: INVESTIGATIONS OF THE GENETIC POTENTIAL FOR ANAEROBIC HYDROCARBON TRANSFORMATION AND THE RESPONSE TO HYDROCARBON EXPOSURE A DISSERTATION APPROVED FOR THE DEPARTMENT OF MICROBIOLOGY AND PLANT BIOLOGY BY ______________________________ Dr. Amy V. Callaghan, Chair ______________________________ Dr. Lee R. Krumholz ______________________________ Dr. Michael J. McInerney ______________________________ Dr. Mark A. Nanny ______________________________ Dr. Boris Wawrik © Copyright by JAMIE M. JOHNSON DUFFNER 2017 All Rights Reserved. This dissertation is dedicated to my husband, Derick, for his unwavering love and support. Acknowledgements I would like to thank my advisor, Dr. Amy Callaghan, for her guidance and support during my time as a graduate student, as well as for her commitment to my success as a scientist. I would also like to thank the members of my doctoral committee for their guidance over the years, particularly that of Dr. Boris Wawrik. I would like to also thank Drs. Josh Cooper, Chris Lyles, and Chris Marks for their friendship and support during my time at OU, both in and outside the lab. iv Table of Contents
    [Show full text]
  • Distribution of Sulfate-Reducing Communities from Estuarine to Marine Bay Waters Yannick Colin, M
    Distribution of Sulfate-Reducing Communities from Estuarine to Marine Bay Waters Yannick Colin, M. Goñi-Urriza, C. Gassie, E. Carlier, M. Monperrus, R. Guyoneaud To cite this version: Yannick Colin, M. Goñi-Urriza, C. Gassie, E. Carlier, M. Monperrus, et al.. Distribution of Sulfate- Reducing Communities from Estuarine to Marine Bay Waters. Microbial Ecology, Springer Verlag, 2017, 73 (1), pp.39-49. 10.1007/s00248-016-0842-5. hal-01499135 HAL Id: hal-01499135 https://hal.archives-ouvertes.fr/hal-01499135 Submitted on 26 Sep 2017 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution - ShareAlike| 4.0 International License Microb Ecol (2017) 73:39–49 DOI 10.1007/s00248-016-0842-5 MICROBIOLOGY OF AQUATIC SYSTEMS Distribution of Sulfate-Reducing Communities from Estuarine to Marine Bay Waters Yannick Colin 1,2 & Marisol Goñi-Urriza1 & Claire Gassie1 & Elisabeth Carlier 1 & Mathilde Monperrus3 & Rémy Guyoneaud1 Received: 23 May 2016 /Accepted: 17 August 2016 /Published online: 31 August 2016 # Springer Science+Business Media New York 2016 Abstract Estuaries are highly dynamic ecosystems in which gradient. The concentration of cultured sulfidogenic microor- freshwater and seawater mix together.
    [Show full text]
  • Phylogenetic and Functional Characterization of Symbiotic Bacteria in Gutless Marine Worms (Annelida, Oligochaeta)
    Phylogenetic and functional characterization of symbiotic bacteria in gutless marine worms (Annelida, Oligochaeta) Dissertation zur Erlangung des Grades eines Doktors der Naturwissenschaften -Dr. rer. nat.- dem Fachbereich Biologie/Chemie der Universität Bremen vorgelegt von Anna Blazejak Oktober 2005 Die vorliegende Arbeit wurde in der Zeit vom März 2002 bis Oktober 2005 am Max-Planck-Institut für Marine Mikrobiologie in Bremen angefertigt. 1. Gutachter: Prof. Dr. Rudolf Amann 2. Gutachter: Prof. Dr. Ulrich Fischer Tag des Promotionskolloquiums: 22. November 2005 Contents Summary ………………………………………………………………………………….… 1 Zusammenfassung ………………………………………………………………………… 2 Part I: Combined Presentation of Results A Introduction .…………………………………………………………………… 4 1 Definition and characteristics of symbiosis ...……………………………………. 4 2 Chemoautotrophic symbioses ..…………………………………………………… 6 2.1 Habitats of chemoautotrophic symbioses .………………………………… 8 2.2 Diversity of hosts harboring chemoautotrophic bacteria ………………… 10 2.2.1 Phylogenetic diversity of chemoautotrophic symbionts …………… 11 3 Symbiotic associations in gutless oligochaetes ………………………………… 13 3.1 Biogeography and phylogeny of the hosts …..……………………………. 13 3.2 The environment …..…………………………………………………………. 14 3.3 Structure of the symbiosis ………..…………………………………………. 16 3.4 Transmission of the symbionts ………..……………………………………. 18 3.5 Molecular characterization of the symbionts …..………………………….. 19 3.6 Function of the symbionts in gutless oligochaetes ..…..…………………. 20 4 Goals of this thesis …….…………………………………………………………..
    [Show full text]
  • 1 Characterization of Sulfur Metabolizing Microbes in a Cold Saline Microbial Mat of the Canadian High Arctic Raven Comery Mast
    Characterization of sulfur metabolizing microbes in a cold saline microbial mat of the Canadian High Arctic Raven Comery Master of Science Department of Natural Resource Sciences Unit: Microbiology McGill University, Montreal July 2015 A thesis submitted to McGill University in partial fulfillment of the requirements of the degree of Master in Science © Raven Comery 2015 1 Abstract/Résumé The Gypsum Hill (GH) spring system is located on Axel Heiberg Island of the High Arctic, perennially discharging cold hypersaline water rich in sulfur compounds. Microbial mats are found adjacent to channels of the GH springs. This thesis is the first detailed analysis of the Gypsum Hill spring microbial mats and their microbial diversity. Physicochemical analyses of the water saturating the GH spring microbial mat show that in summer it is cold (9°C), hypersaline (5.6%), and contains sulfide (0-10 ppm) and thiosulfate (>50 ppm). Pyrosequencing analyses were carried out on both 16S rRNA transcripts (i.e. cDNA) and genes (i.e. DNA) to investigate the mat’s community composition, diversity, and putatively active members. In order to investigate the sulfate reducing community in detail, the sulfite reductase gene and its transcript were also sequenced. Finally, enrichment cultures for sulfate/sulfur reducing bacteria were set up and monitored for sulfide production at cold temperatures. Overall, sulfur metabolism was found to be an important component of the GH microbial mat system, particularly the active fraction, as 49% of DNA and 77% of cDNA from bacterial 16S rRNA gene libraries were classified as taxa capable of the reduction or oxidation of sulfur compounds.
    [Show full text]
  • Archives Des Publications Du CNRC (Nparc)
    NRC Publications Archive (NPArC) Archives des publications du CNRC (NPArC) Effect of 2,4-dinitrotoluene on the anaerobic bacterial community in marine sediment Yang, H.; Zhao, J.-S.; Hawari, J. Publisher’s version / la version de l'éditeur: Journal of Applied Microbiology, 107, 6, pp. 1799-1808, 2009-12 Web page / page Web http://dx.doi.org/10.1111/j.1365-2672.2009.04366.x http://nparc.cisti-icist.nrc-cnrc.gc.ca/npsi/ctrl?action=rtdoc&an=14130357&lang=en http://nparc.cisti-icist.nrc-cnrc.gc.ca/npsi/ctrl?action=rtdoc&an=14130357&lang=fr Access and use of this website and the material on it are subject to the Terms and Conditions set forth at http://nparc.cisti-icist.nrc-cnrc.gc.ca/npsi/jsp/nparc_cp.jsp?lang=en READ THESE TERMS AND CONDITIONS CAREFULLY BEFORE USING THIS WEBSITE. L’accès à ce site Web et l’utilisation de son contenu sont assujettis aux conditions présentées dans le site http://nparc.cisti-icist.nrc-cnrc.gc.ca/npsi/jsp/nparc_cp.jsp?lang=fr LISEZ CES CONDITIONS ATTENTIVEMENT AVANT D’UTILISER CE SITE WEB. Contact us / Contactez nous: [email protected]. Journal of Applied Microbiology ISSN 1364-5072 ORIGINAL ARTICLE Effect of 2,4-dinitrotoluene on the anaerobic bacterial community in marine sediment H. Yang1,2, J.-S. Zhao1 and J. Hawari1 1 Biotechnology Research Institute, National Research Council Canada, Montre´ al, Que´ bec, Canada H4P 2R2 2 College of Life Sciences, Central China Normal University, Wuhan, China Keywords Abstract 2,4-dinitrotoluene, anaerobic, bacterial community, denaturing gradient gel Aims: To study the impact of added 2,4-dinitrotoluene (DNT) on the anaero- electrophoresis, impact, marine sediment.
    [Show full text]
  • (Pelobacter) and Methanococcoides Are Responsible for Choline-Dependent Methanogenesis in a Coastal Saltmarsh Sediment
    The ISME Journal https://doi.org/10.1038/s41396-018-0269-8 ARTICLE Deltaproteobacteria (Pelobacter) and Methanococcoides are responsible for choline-dependent methanogenesis in a coastal saltmarsh sediment 1 1 1 2 3 1 Eleanor Jameson ● Jason Stephenson ● Helen Jones ● Andrew Millard ● Anne-Kristin Kaster ● Kevin J. Purdy ● 4 5 1 Ruth Airs ● J. Colin Murrell ● Yin Chen Received: 22 January 2018 / Revised: 11 June 2018 / Accepted: 26 July 2018 © The Author(s) 2018. This article is published with open access Abstract Coastal saltmarsh sediments represent an important source of natural methane emissions, much of which originates from quaternary and methylated amines, such as choline and trimethylamine. In this study, we combine DNA stable isotope 13 probing with high throughput sequencing of 16S rRNA genes and C2-choline enriched metagenomes, followed by metagenome data assembly, to identify the key microbes responsible for methanogenesis from choline. Microcosm 13 incubation with C2-choline leads to the formation of trimethylamine and subsequent methane production, suggesting that 1234567890();,: 1234567890();,: choline-dependent methanogenesis is a two-step process involving trimethylamine as the key intermediate. Amplicon sequencing analysis identifies Deltaproteobacteria of the genera Pelobacter as the major choline utilizers. Methanogenic Archaea of the genera Methanococcoides become enriched in choline-amended microcosms, indicating their role in methane formation from trimethylamine. The binning of metagenomic DNA results in the identification of bins classified as Pelobacter and Methanococcoides. Analyses of these bins reveal that Pelobacter have the genetic potential to degrade choline to trimethylamine using the choline-trimethylamine lyase pathway, whereas Methanococcoides are capable of methanogenesis using the pyrrolysine-containing trimethylamine methyltransferase pathway.
    [Show full text]
  • Final Report (Posted 2/18)
    FINAL REPORT Post-Remediation Evaluation of EVO Treatment - How Can We Improve Performance? ESTCP Project ER-201581 NOVEMBER 2017 Robert C. Borden Solutions-IES, Inc. Distribution Statement A This document has been cleared for public release Page Intentionally Left Blank This report was prepared under contract to the Department of Defense Environmental Security Technology Certification Program (ESTCP). The publication of this report does not indicate endorsement by the Department of Defense, nor should the contents be construed as reflecting the official policy or position of the Department of Defense. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the Department of Defense. Page Intentionally Left Blank Form Approved REPORT DOCUMENTATION PAGE OMB No. 0704-0188 Public reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing this collection of information. Send comments regarding this burden estimate or any other aspect of this collection of information, including suggestions for reducing this burden to Department of Defense, Washington Headquarters Services, Directorate for Information Operations and Reports (0704-0188), 1215 Jefferson Davis Highway, Suite 1204, Arlington, VA 22202- 4302. Respondents should be aware that notwithstanding any other provision of law, no person shall be subject to any penalty for failing to comply with a collection of information if it does not display a currently valid OMB control number.
    [Show full text]
  • Community Analysis of Biofilms on Flame-Oxidized Stainless Steel
    Eyiuche et al. BMC Microbiology (2017) 17:145 DOI 10.1186/s12866-017-1053-z RESEARCH ARTICLE Open Access Community analysis of biofilms on flame- oxidized stainless steel anodes in microbial fuel cells fed with different substrates Nweze Julius Eyiuche1,2, Shiho Asakawa3, Takahiro Yamashita4, Atsuo Ikeguchi3, Yutaka Kitamura1 and Hiroshi Yokoyama4* Abstract Background: The flame-oxidized stainless steel anode (FO-SSA) is a newly developed electrode that enhances microbial fuel cell (MFC) power generation; however, substrate preference and community structure of the biofilm developed on FO-SSA have not been well characterized. Herein, we investigated the community on FO-SSA using high-throughput sequencing of the 16S rRNA gene fragment in acetate-, starch-, glucose-, and livestock wastewater-fed MFCs. Furthermore, to analyze the effect of the anode material, the acetate-fed community formed on a common carbon-based electrode—carbon-cloth anode (CCA)—was examined for comparison. Results: Substrate type influenced the power output of MFCs using FO-SSA; the highest electricity was generated using acetate as a substrate, followed by peptone, starch and glucose, and wastewater. Intensity of power generation using FO-SSA was related to the abundance of exoelectrogenic genera, namely Geobacter and Desulfuromonas, of the phylum Proteobacteria, which were detected at a higher frequency in acetate-fed communities than in communities fed with other substrates. Lactic acid bacteria (LAB)—Enterococcus and Carnobacterium—were predominant in starch- and glucose-fed communities, respectively. In the wastewater-fed community, members of phylum Planctomycetes were frequently detected (36.2%). Exoelectrogenic genera Geobacter and Desulfuromonas were also detected in glucose-, starch-, and wastewater-fed communities on FO-SSA, but with low frequency (0–3.2%); the lactate produced by Carnobacterium and Enterococcus in glucose- and starch-fed communities might affect exoelectrogenic bacterial growth, resulting in low power output by MFCs fed with these substrates.
    [Show full text]