Microbial Community Analysis of Shallow Subsurface Samples with PCR-Oggf
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Diversity of Rare and Abundant Prokaryotic
Diversity of rare and abundant prokaryotic phylotypes in the Prony hydrothermal field and comparison with other serpentinite-hosted ecosystems Eléonore Frouin, Méline Bes, Bernard Ollivier, Marianne Quéméneur, Anne Postec, Didier Debroas, Fabrice Armougom, Gaël Erauso To cite this version: Eléonore Frouin, Méline Bes, Bernard Ollivier, Marianne Quéméneur, Anne Postec, et al.. Diver- sity of rare and abundant prokaryotic phylotypes in the Prony hydrothermal field and compari- son with other serpentinite-hosted ecosystems. Frontiers in Microbiology, Frontiers Media, 2018, 9, 10.3389/fmicb.2018.00102. hal-01734508 HAL Id: hal-01734508 https://hal.archives-ouvertes.fr/hal-01734508 Submitted on 12 Oct 2018 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| 4.0 International License fmicb-09-00102 February 3, 2018 Time: 13:27 # 1 ORIGINAL RESEARCH published: 06 February 2018 doi: 10.3389/fmicb.2018.00102 Diversity of Rare and Abundant Prokaryotic Phylotypes in the Prony Hydrothermal Field and Comparison with Other Serpentinite-Hosted Ecosystems Eléonore Frouin1, Méline Bes1, Bernard Ollivier1, Marianne Quéméneur1, Anne Postec1, Didier Debroas2, Fabrice Armougom1 and Gaël Erauso1* 1 Aix-Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France, 2 CNRS UMR 6023, Laboratoire “Microorganismes – Génome et Environnement”, Université Clermont Auvergne, Clermont-Ferrand, France The Bay of Prony, South of New Caledonia, represents a unique serpentinite- hosted hydrothermal field due to its coastal situation. -
Microbial Community Structure Dynamics in Ohio River Sediments During Reductive Dechlorination of Pcbs
University of Kentucky UKnowledge University of Kentucky Doctoral Dissertations Graduate School 2008 MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS Andres Enrique Nunez University of Kentucky Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Nunez, Andres Enrique, "MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS" (2008). University of Kentucky Doctoral Dissertations. 679. https://uknowledge.uky.edu/gradschool_diss/679 This Dissertation is brought to you for free and open access by the Graduate School at UKnowledge. It has been accepted for inclusion in University of Kentucky Doctoral Dissertations by an authorized administrator of UKnowledge. For more information, please contact [email protected]. ABSTRACT OF DISSERTATION Andres Enrique Nunez The Graduate School University of Kentucky 2008 MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS ABSTRACT OF DISSERTATION A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the College of Agriculture at the University of Kentucky By Andres Enrique Nunez Director: Dr. Elisa M. D’Angelo Lexington, KY 2008 Copyright © Andres Enrique Nunez 2008 ABSTRACT OF DISSERTATION MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS The entire stretch of the Ohio River is under fish consumption advisories due to contamination with polychlorinated biphenyls (PCBs). In this study, natural attenuation and biostimulation of PCBs and microbial communities responsible for PCB transformations were investigated in Ohio River sediments. Natural attenuation of PCBs was negligible in sediments, which was likely attributed to low temperature conditions during most of the year, as well as low amounts of available nitrogen, phosphorus, and organic carbon. -
Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg -
Hydrogenophaga Electricum Sp. Nov., Isolated from Anodic Biofilms of an Acetate-Fed Microbial Fuel Cell
J. Gen. Appl. Microbiol., 59, 261‒266 (2013) Full Paper Hydrogenophaga electricum sp. nov., isolated from anodic biofilms of an acetate-fed microbial fuel cell Zen-ichiro Kimura and Satoshi Okabe* Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Kita-ku, Sapporo, Hokkaido 060‒8628, Japan (Received October 25, 2012; Accepted April 2, 2013) A Gram-negative, non-spore-forming, rod-shaped bacterial strain, AR20T, was isolated from an- odic biofilms of an acetate-fed microbial fuel cell in Japan and subjected to a polyphasic taxo- nomic study. Strain AR20T grew optimally at pH 7.0‒8.0 and 25°C. It contained Q-8 as the pre- dominant ubiquinone and C16:0, summed feature 3 (C16:1ω7c and/or iso-C15:02OH), and C18:1ω7c as the major fatty acids. The DNA G+C content was 67.1 mol%. A neighbor-joining phylogenetic tree revealed that strain AR20T clustered with three type strains of the genus Hydrogenophaga (H. flava, H. bisanensis and H. pseudoflava). Strain AR20T exhibited 16S rRNA gene sequence similarity values of 95.8‒97.7% to the type strains of the genus Hydrogenophaga. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain AR20T is considered a novel species of the genus Hydrogenophaga, for which the name Hydrogenophaga electricum sp. nov. is pro- posed. The type strain is AR20T (= KCTC 32195T = NBRC 109341T). Key Words—Hydrogenophaga electricum; hydrogenotrophic exoelectrogen; microbial fuel cell Introduction the MFC was analyzed. Results showed that bacteria belonging to the genera Geobacter and Hydrogenoph- Microbial fuel cells (MFCs) are devices that are able aga were abundantly present in the anodic biofilm to directly convert the chemical energy of organic community (Kimura and Okabe, 2013). -
Genome Analysis of Two Bacterial Strains Isolated from Diseased
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 6 September 2020 doi:10.20944/preprints202009.0144.v1 1 Article 2 Genome analysis of two bacterial strains isolated 3 from diseased freshwater sponge reveals the 4 probable cause of its joint domination in microbial 5 community 6 Ivan Petrushin 1,2,*, Sergei Belikov 1 and Lubov Chernogor 1, 7 1 Limnological institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk 664033, Russia; 8 [email protected] 9 2 Irkutsk State University, Irkutsk 664003, Russia; [email protected] 10 * Correspondence: [email protected]; 11 12 Abstract: Endemic freshwater sponges (Demosponges, Lubomirskiidae) dominate in Lake Baikal 13 and are multicellular filter-feeding animals represent a complex consortium of many species of 14 eukaryotes and prokaryotes. In recent years, mass disease and death of the L. baicalensis have been 15 an urgent problem of Lake Baikal. The etiology and ecology of these events remain unknown. 16 Bacteria in microbiomes of diseased sponges of the families Flavobacteriaceae and Oxalobacteraceae 17 were dominant. Both species are opportunistic pathogens common for freshwater ecosystems. The 18 aim of our study is to analyze the genomes of strains Janthinobacterium sp. SLB01 and Flavobacterium 19 sp. SLB02, isolated from diseased sponges to identify the reasons for their joint dominance. The first 20 one attacks the other cells using type VI secretion system, suppress gram-positive bacteria with 21 violacein pigment and regulate its own activity via quorum sensing. It makes the floc and strong 22 biofilm by exopolysaccharide biosynthesis and PEP‐CTERM proteins expression. The second one 23 utilizes the fragments of cell walls produced of polysaccharides. -
Rpon (Σ54) Is Required for Floc Formation but Not for Extracellular Polysaccharide Biosynthesis in a Floc-Forming Aquincola Tertiaricarbonis Strain
Lawrence Berkeley National Laboratory Recent Work Title RpoN (σ54) Is Required for Floc Formation but Not for Extracellular Polysaccharide Biosynthesis in a Floc-Forming Aquincola tertiaricarbonis Strain. Permalink https://escholarship.org/uc/item/9f26h2cp Journal Applied and environmental microbiology, 83(14) ISSN 0099-2240 Authors Yu, Dianzhen Xia, Ming Zhang, Liping et al. Publication Date 2017-07-01 DOI 10.1128/aem.00709-17 Peer reviewed eScholarship.org Powered by the California Digital Library University of California RpoN (σσ54) Is Required for Floc Formation but Not for Extracellular Polysaccharide Biosynthesis in a Floc-Forming Aquincola tertiaricarbonis Strain Dianzhen Yu,a,b Ming Xia,a,b Liping Zhang,a Yulong Song,a You Duan,a,b Tong Yuan,d,f Minjie Yao,c Liyou Wu,d Chunyuan Tian,e Zhenbin Wu,a Xiangzhen Li,c Jizhong Zhou,d Dongru Qiua Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Chinaa ; University of Chinese Academy of Sciences, Beijing, Chinab; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Chinac ; Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USAd; School of Life Sciences and Technology, Hubei Engineering University, Xiaogan, Chinae; College of Life Science, Henan Agricultural University, Zhengzhou, Chinaf ABSTRACT Some bacteria are capable of forming flocs, in which bacterial cells become self-flocculated by secreted extracellular polysaccharides and other biopolymers. The floc-forming bacteria play a central role in activated sludge, which has been widely utilized for the treatment of municipal sewage and industrial wastewater. Here, we use a floc-forming bacterium, Aquincola tertiaricarbonis RN12, as a model to explore the biosynthesis of extracellular polysaccharides and the regulation of floc formation. -
Download/Splitstree5)
bioRxiv preprint doi: https://doi.org/10.1101/2021.05.31.446453; this version posted June 1, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Phylogenetic context using phylogenetic outlines Caner Bagcı1, David Bryant2, Banu Cetinkaya3, and Daniel H. Huson1;4;∗ 1 Algorithms in Bioinformatics, University of T¨ubingen,72076 T¨ubingen,Germany 2 Department of Mathematics, University of Otago, Dunedin, New Zealand 3 Computer Science program, Sabancı University, 34956 Tuzla/Istanbul,_ Turkey 4 Cluster of Excellence: Controlling Microbes to Fight Infection, T¨ubingen,Germany *[email protected] Abstract 1 Microbial studies typically involve the sequencing and assembly of draft genomes for 2 individual microbes or whole microbiomes. Given a draft genome, one first task is to 3 determine its phylogenetic context, that is, to place it relative to the set of related reference 4 genomes. We provide a new interactive graphical tool that addresses this task using Mash 5 sketches to compare against all bacterial and archaeal representative genomes in the 6 GTDB taxonomy, all within the framework of SplitsTree5. The phylogenetic context of the 7 query sequences is then displayed as a phylogenetic outline, a new type of phylogenetic 8 network that is more general that a phylogenetic tree, but significantly less complex than 9 other types of phylogenetic networks. We propose to use such networks, rather than trees, 10 to represent phylogenetic context, because they can express uncertainty in the placement 11 of taxa, whereas a tree must always commit to a specific branching pattern. -
Ample Arsenite Bio-Oxidation Activity in Bangladesh Drinking Water Wells: a Bonanza for Bioremediation?
microorganisms Article Ample Arsenite Bio-Oxidation Activity in Bangladesh Drinking Water Wells: A Bonanza for Bioremediation? 1,2 3 3 1 1, Zahid Hassan , Munawar Sultana , Sirajul I. Khan , Martin Braster , Wilfred F.M. Röling y and Hans V. Westerhoff 1,4,5,* 1 Department of Molecular Cell Biology, Faculty of Science, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands 2 Department of Genetic Engineering and Biotechnology, Jagannath University, Dhaka 1100, Bangladesh 3 Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh 4 Manchester Centre for Integrative Systems Biology (MCISB), School of Chemical Engineering and Analytical Sciences (SCEAS), the University of Manchester, Manchester M13 9PL, UK 5 Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands * Correspondence: h.v.westerhoff@vu.nl; Tel.: +31-205-987-230 Deceased 25 September 2015. y Received: 18 June 2019; Accepted: 31 July 2019; Published: 8 August 2019 Abstract: Millions of people worldwide are at risk of arsenic poisoning from their drinking water. In Bangladesh the problem extends to rural drinking water wells, where non-biological solutions are not feasible. In serial enrichment cultures of water from various Bangladesh drinking water wells, we found transfer-persistent arsenite oxidation activity under four conditions (aerobic/anaerobic; heterotrophic/autotrophic). This suggests that biological decontamination may help ameliorate the problem. The enriched microbial communities were phylogenetically at least as diverse as the unenriched communities: they contained a bonanza of 16S rRNA gene sequences. These related to Hydrogenophaga, Acinetobacter, Dechloromonas, Comamonas, and Rhizobium/Agrobacterium species. In addition, the enriched microbiomes contained genes highly similar to the arsenite oxidase (aioA) gene of chemolithoautotrophic (e.g., Paracoccus sp. -
Rapport Nederlands
Moleculaire detectie van bacteriën in dekaarde Dr. J.J.P. Baars & dr. G. Straatsma Plant Research International B.V., Wageningen December 2007 Rapport nummer 2007-10 © 2007 Wageningen, Plant Research International B.V. Alle rechten voorbehouden. Niets uit deze uitgave mag worden verveelvoudigd, opgeslagen in een geautomatiseerd gegevensbestand, of openbaar gemaakt, in enige vorm of op enige wijze, hetzij elektronisch, mechanisch, door fotokopieën, opnamen of enige andere manier zonder voorafgaande schriftelijke toestemming van Plant Research International B.V. Exemplaren van dit rapport kunnen bij de (eerste) auteur worden besteld. Bij toezending wordt een factuur toegevoegd; de kosten (incl. verzend- en administratiekosten) bedragen € 50 per exemplaar. Plant Research International B.V. Adres : Droevendaalsesteeg 1, Wageningen : Postbus 16, 6700 AA Wageningen Tel. : 0317 - 47 70 00 Fax : 0317 - 41 80 94 E-mail : [email protected] Internet : www.pri.wur.nl Inhoudsopgave pagina 1. Samenvatting 1 2. Inleiding 3 3. Methodiek 8 Algemene werkwijze 8 Bestudeerde monsters 8 Monsters uit praktijkteelten 8 Monsters uit proefteelten 9 Alternatieve analyse m.b.v. DGGE 10 Vaststellen van verschillen tussen de bacterie-gemeenschappen op myceliumstrengen en in de omringende dekaarde. 11 4. Resultaten 13 Monsters uit praktijkteelten 13 Monsters uit proefteelten 16 Alternatieve analyse m.b.v. DGGE 23 Vaststellen van verschillen tussen de bacterie-gemeenschappen op myceliumstrengen en in de omringende dekaarde. 25 5. Discussie 28 6. Conclusies 33 7. Suggesties voor verder onderzoek 35 8. Gebruikte literatuur. 37 Bijlage I. Bacteriesoorten geïsoleerd uit dekaarde en van mycelium uit commerciële teelten I-1 Bijlage II. Bacteriesoorten geïsoleerd uit dekaarde en van mycelium uit experimentele teelten II-1 1 1. -
Cooperative Interaction of Janthinobacterium Sp. SLB01 and Flavobacterium Sp
International Journal of Molecular Sciences Article Cooperative Interaction of Janthinobacterium sp. SLB01 and Flavobacterium sp. SLB02 in the Diseased Sponge Lubomirskia baicalensis Ivan Petrushin 1,2,* , Sergei Belikov 1 and Lubov Chernogor 1 1 Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk 664033, Russia; [email protected] (S.B.); [email protected] (L.C.) 2 Faculty of Business Communication and Informatics, Irkutsk State University, Irkutsk 664033, Russia * Correspondence: [email protected] Received: 31 August 2020; Accepted: 25 October 2020; Published: 30 October 2020 Abstract: Endemic freshwater sponges (demosponges, Lubomirskiidae) dominate in Lake Baikal, Central Siberia, Russia. These sponges are multicellular filter-feeding animals that represent a complex consortium of many species of eukaryotes and prokaryotes. In recent years, mass disease and death of Lubomirskia baicalensis has been a significant problem in Lake Baikal. The etiology and ecology of these events remain unknown. Bacteria from the families Flavobacteriaceae and Oxalobacteraceae dominate the microbiomes of diseased sponges. Both species are opportunistic pathogens common in freshwater ecosystems. The aim of our study was to analyze the genomes of strains Janthinobacterium sp. SLB01 and Flavobacterium sp. SLB02, isolated from diseased sponges to identify the reasons for their joint dominance. Janthinobacterium sp. SLB01 attacks other cells using a type VI secretion system and suppresses gram-positive bacteria with violacein, and regulates its own activity via quorum sensing. It produces floc and strong biofilm by exopolysaccharide biosynthesis and PEP-CTERM/XrtA protein expression. Flavobacterium sp. SLB02 utilizes the fragments of cell walls produced by polysaccharides. These two strains have a marked difference in carbohydrate acquisition. -
Microbial Diversity of a Remote Aviation Fuel Contaminated
ntal & A me na n ly o t ir ic v a Udotong et al., J Environ Anal Toxicol 2015, 5:6 n l T E o Journal of f x o i l c DOI: 10.4172/2161-0525.1000320 o a n l o r g u y o J Environmental & Analytical Toxicology ISSN: 2161-0525 ResearchResearch Article Article OpenOpen Access Access Microbial Diversity of a Remote Aviation Fuel Contaminated Sediment of a Lentic Ecosystem in Ibeno, Nigeria Udotong IR1*, Uko MP1 and Udotong JIR2 1Department of Microbiology, University of Uyo, Uyo, Akwa Ibom State, Nigeria 2Department of Biochemistry, University of Uyo, Uyo, Akwa Ibom State, Nigeria Abstract Environmental pollution from Oil & Gas Exploration & Production (O&G E&P) activities remains one of the major problems in the oil-producing communities of Nigeria. This results from improper oily wastes disposal as well as incessant oil spills in the region. The operator’s lack of responsible business practices in wastes management and the over-dependence of the economy on oil and gas earnings, in the most part, exacerbate the problems of environmental pollution. Government's lack of political will power which treats issues on oil pollution with levity and long period of neglect of these polluted sites leave the environment ecologically destabilized. Studies to ascertain the ecological status of remote aviation fuel-contaminated sediment of a lentic ecosystem in Inua Eyet Ikot village, Ibeno, Nigeria, have been carried out using conventional microbiological culture-dependent methods. This methodology is known to reveal only <1% of the microbial diversity present. These results were therefore considered inaccurate and grossly misleading. -
Physiology and Biochemistry of Aromatic Hydrocarbon-Degrading Bacteria That Use Chlorate And/Or Nitrate As Electron Acceptor
Invitation for the public defense of my thesis Physiology and biochemistry of aromatic hydrocarbon-degrading of aromatic and biochemistry Physiology bacteria that use chlorate and/or nitrate as electron acceptor as electron nitrate and/or use chlorate that bacteria Physiology and biochemistry Physiology and biochemistry of aromatic hydrocarbon-degrading of aromatic hydrocarbon- degrading bacteria that bacteria that use chlorate and/or nitrate as electron acceptor use chlorate and/or nitrate as electron acceptor The public defense of my thesis will take place in the Aula of Wageningen University (Generall Faulkesweg 1, Wageningen) on December 18 2013 at 4:00 pm. This defense is followed by a reception in Café Carré (Vijzelstraat 2, Wageningen). Margreet J. Oosterkamp J. Margreet Paranimphs Ton van Gelder ([email protected]) Aura Widjaja Margreet J. Oosterkamp ([email protected]) Marjet Oosterkamp (911 W Springfield Ave Apt 19, Urbana, IL 61801, USA; [email protected]) Omslag met flap_MJOosterkamp.indd 1 25-11-2013 5:58:31 Physiology and biochemistry of aromatic hydrocarbon-degrading bacteria that use chlorate and/or nitrate as electron acceptor Margreet J. Oosterkamp Thesis-MJOosterkamp.indd 1 25-11-2013 6:42:09 Thesis committee Thesis supervisor Prof. dr. ir. A. J. M. Stams Personal Chair at the Laboratory of Microbiology Wageningen University Thesis co-supervisors Dr. C. M. Plugge Assistant Professor at the Laboratory of Microbiology Wageningen University Dr. P. J. Schaap Assistant Professor at the Laboratory of Systems and Synthetic Biology Wageningen University Other members Prof. dr. L. Dijkhuizen, University of Groningen Prof. dr. H. J. Laanbroek, University of Utrecht Prof.