Genomic and Metabolic Gene Characterization of Bacterial Communities from the Neuse River Estuarine Sytem Using Long Read Metagenomics
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Thèse Morgane Wartel
Faculté des Sciences - Aix-Marseille Université Laboratoire de Chimie Bactérienne 163 Avenue de Luminy - Case 901 31 Chemin Joseph Aiguier 13288 Marseille 13009 Marseille Thèse En vue d’obtenir le grade de Docteur d’Aix-Marseille Université Biologie, spécialité Microbiologie Présentée et soutenue publiquement par Morgane Wartel Le Mercredi 18 Décembre 2013 A novel class of bacterial motors involved in the directional transport of a sugar at the bacterial surface: The machineries of motility and sporulation in Myxococcus xanthus. Une nouvelle classe de moteurs bactériens impliqués dans le transport de macromolécules à la surface bactérienne: Les machineries de motilité et de sporulation de Myxococcus xanthus. Membres du Jury : Dr. Christophe Grangeasse Rapporteur Dr. Patrick Viollier Rapporteur Pr. Pascale Cossart Examinateur Dr. Francis-André Wollman Examinateur Dr. Tâm Mignot Directeur de Thèse Pr. Frédéric Barras Président du Jury Faculté des Sciences - Aix-Marseille Université Laboratoire de Chimie Bactérienne 163 Avenue de Luminy - Case 901 31 Chemin Joseph Aiguier 13288 Marseille 13009 Marseille Thèse En vue d’obtenir le grade de Docteur d’Aix-Marseille Université Biologie, spécialité Microbiologie Présentée et soutenue publiquement par Morgane Wartel Le Mercredi 18 Décembre 2013 A novel class of bacterial motors involved in the directional transport of a sugar at the bacterial surface: The machineries of motility and sporulation in Myxococcus xanthus. Une nouvelle classe de moteurs bactériens impliqués dans le transport de macromolécules à la surface bactérienne: Les machineries de motilité et de sporulation de Myxococcus xanthus. Membres du Jury : Dr. Christophe Grangeasse Rapporteur Dr. Patrick Viollier Rapporteur Pr. Pascale Cossart Examinateur Dr. Francis-André Wollman Examinateur Dr. -
A Web Tool for Hydrogenase Classification and Analysis
bioRxiv preprint doi: https://doi.org/10.1101/061994; this version posted September 16, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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-NC-ND 4.0 International license. 1 HydDB: A web tool for hydrogenase 2 classification and analysis 3 Dan Søndergaarda, Christian N. S. Pedersena, Chris Greeningb, c* 4 5 a Aarhus University, Bioinformatics Research Centre, C.F. Møllers Allé 8, Aarhus 6 DK-8000, Denmark 7 b The Commonwealth Scientific and Industrial Research Organisation, Land and 8 Water Flagship, Clunies Ross Street, Acton, ACT 2060, Australia 9 c Monash University, School of Biological Sciences, Clayton, VIC 2800, Australia 10 11 Correspondence: 12 Dr Chris Greening ([email protected]), Monash University, School of 13 Biological Sciences, Clayton, VIC 2800, Australia 14 Dan Søndergaard ([email protected]), Aarhus University, Bioinformatics Research 15 Centre, C.F. Møllers Allé 8, Aarhus DK-8000, Denmark 1 bioRxiv preprint doi: https://doi.org/10.1101/061994; this version posted September 16, 2016. 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-NC-ND 4.0 International license. 16 Abstract 17 H2 metabolism is proposed to be the most ancient and diverse mechanism of 18 energy-conservation. The metalloenzymes mediating this metabolism, 19 hydrogenases, are encoded by over 60 microbial phyla and are present in all major 20 ecosystems. -
Influencia De La Comunidad Bacteriana En Los Ciclos Biogeoquímicos Del Carbono Y El Nitrógeno En El Ecosistema De Manglar
FACULTAD CIENCIAS DE LA SALUD BACTERIOLOGÍA Y LABORATORIO CLÍNICO BOGOTÁ D.C. 2020 Proyecto: INFLUENCIA DE LA COMUNIDAD BACTERIANA EN LOS CICLOS BIOGEOQUÍMICOS DEL CARBONO Y EL NITRÓGENO EN EL ECOSISTEMA DE MANGLAR Meritoria: _____Si______ Laureada: ___________ Aprobada: ___________ JURADOS _____________________ ________________ ____________________ _________________ _________________________________________________ ASESOR(es) _________ Martha Lucía Posada Buitrago___________________ _________________________________________ ÉTICA, SERVICIO Y SABER INFLUENCIA DE LA COMUNIDAD BACTERIANA EN LOS CICLOS BIOGEOQUÍMICOS DEL CARBONO Y EL NITRÓGENO EN EL ECOSISTEMA DE MANGLAR UNIVERSIDAD COLEGIO MAYOR DE CUNDINAMARCA FACULTAD CIENCIAS DE LA SALUD PROGRAMA BACTERIOLOGÍA Y LABORATORIO CLÍNICO PROYECTO DE GRADO BOGOTÁ D.C 2020 INFLUENCIA DE LA COMUNIDAD BACTERIANA EN LOS CICLOS BIOGEOQUÍMICOS DEL CARBONO Y EL NITRÓGENO EN EL ECOSISTEMA DE MANGLAR Danya Gabriela Ramírez Lozada Nicolás David Rojas Villamil Asesor interno PhD. Martha Lucía Posada Buitrago Monografía para optar al título de Bacteriólogo y Laboratorista Clínico UNIVERSIDAD COLEGIO MAYOR DE CUNDINAMARCA FACULTAD CIENCIAS DE LA SALUD PROGRAMA BACTERIOLOGÍA Y LABORATORIO CLÍNICO PROYECTO DE GRADO BOGOTÁ D.C 2020 INFLUENCIA DE LA COMUNIDAD BACTERIANA EN LOS CICLOS BIOGEOQUÍMICOS DEL CARBONO Y EL NITRÓGENO EN EL ECOSISTEMA DE MANGLAR UNIVERSIDAD COLEGIO MAYOR DE CUNDINAMARCA FACULTAD CIENCIAS DE LA SALUD PROGRAMA BACTERIOLOGÍA Y LABORATORIO CLÍNICO PROYECTO DE GRADO BOGOTÁ D.C 2020 DEDICATORIA A todas las personas y docentes que hicieron parte de nuestro proceso de formación profesional, a nuestras familias y amigos, que nos brindaron su apoyo, tiempo, consejos y paciencia en este camino que no ha culminado y aún está lleno de sueños, esperanzas y metas por alcanzar. AGRADECIMIENTOS Principalmente a nuestras familias porque han sido la base de nuestra formación aportando grandes cosas en nuestras vidas, por confiar y creer en nuestras capacidades y destrezas a lo largo de esta carrera. -
Genomic Signatures of Sex, Selection and Speciation in the Microbial World
Genomic signatures of sex, selection and speciation in the microbial world by B. Jesse Shapiro B.Sc. Biology McGill University, 2003 M.Sc. Integrative Bioscience Oxford University, 2004 SUBMITTED TO THE PROGRAM IN COMPUTATIONAL AND SYSTEMS BIOLOGY IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN COMPUTATIONAL AND SYSTEMS BIOLOGY AT THE MASSACHUSETTS INSTITUTE OF TECHNOLOGY SEPTEMBER 2010 © 2010 Massachusetts Institute of Technology All rights reserved Signature of Author:...……………………………………………………………………………………….. Program in Computational and Systems Biology August 6, 2010 Certified by:…………………………………………………………………………………………………. Eric J. Alm Assistant Professor of Civil and Environmental Engineering and Biological Engineering Thesis Supervisor Accepted by:………………………………………………………………………………………………… Christopher B. Burge Professor of Biology and Biological Engineering Chair, Computational and Systems Biology Ph.D. Graduate Committee 1 Genomic signatures of sex, selection and speciation in the microbial world by B. Jesse Shapiro Submitted to the Program in Computational and Systems Biology on August 6, 2010 in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Computational and Systems Biology ABSTRACT Understanding the microbial world is key to understanding global biogeochemistry, human health and disease, yet this world is largely inaccessible. Microbial genomes, an increasingly accessible data source, provide an ideal entry point. The genome sequences of different microbes may be compared using the tools of population genetics to infer important genetic changes allowing them to diversify ecologically and adapt to distinct ecological niches. Yet the toolkit of population genetics was developed largely with sexual eukaryotes in mind. In this work, I assess and develop tools for inferring natural selection in microbial genomes. -
Genes for Degradation and Utilization of Uronic Acid-Containing Polysaccharides of a Marine Bacterium Catenovulum Sp
Genes for degradation and utilization of uronic acid-containing polysaccharides of a marine bacterium Catenovulum sp. CCB-QB4 Go Furusawa, Nor Azura Azami and Aik-Hong Teh Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia ABSTRACT Background. Oligosaccharides from polysaccharides containing uronic acids are known to have many useful bioactivities. Thus, polysaccharide lyases (PLs) and glycoside hydrolases (GHs) involved in producing the oligosaccharides have attracted interest in both medical and industrial settings. The numerous polysaccharide lyases and glycoside hydrolases involved in producing the oligosaccharides were isolated from soil and marine microorganisms. Our previous report demonstrated that an agar-degrading bacterium, Catenovulum sp. CCB-QB4, isolated from a coastal area of Penang, Malaysia, possessed 183 glycoside hydrolases and 43 polysaccharide lyases in the genome. We expected that the strain might degrade and use uronic acid-containing polysaccharides as a carbon source, indicating that the strain has a potential for a source of novel genes for degrading the polysaccharides. Methods. To confirm the expectation, the QB4 cells were cultured in artificial seawater media with uronic acid-containing polysaccharides, namely alginate, pectin (and saturated galacturonate), ulvan, and gellan gum, and the growth was observed. The genes involved in degradation and utilization of uronic acid-containing polysaccharides were explored in the QB4 genome using CAZy analysis and BlastP analysis. Results. The QB4 cells were capable of using these polysaccharides as a carbon source, and especially, the cells exhibited a robust growth in the presence of alginate. 28 PLs and 22 GHs related to the degradation of these polysaccharides were found in Submitted 5 August 2020 the QB4 genome based on the CAZy database. -
Penaeus Monodon
www.nature.com/scientificreports OPEN Bacterial analysis in the early developmental stages of the black tiger shrimp (Penaeus monodon) Pacharaporn Angthong1,3, Tanaporn Uengwetwanit1,3, Sopacha Arayamethakorn1, Panomkorn Chaitongsakul2, Nitsara Karoonuthaisiri1 & Wanilada Rungrassamee1* Microbial colonization is an essential process in the early life of animal hosts—a crucial phase that could help infuence and determine their health status at the later stages. The establishment of bacterial community in a host has been comprehensively studied in many animal models; however, knowledge on bacterial community associated with the early life stages of Penaeus monodon (the black tiger shrimp) is still limited. Here, we examined the bacterial community structures in four life stages (nauplius, zoea, mysis and postlarva) of two black tiger shrimp families using 16S rRNA amplicon sequencing by a next-generation sequencing. Although the bacterial profles exhibited diferent patterns in each developmental stage, Bacteroidetes, Proteobacteria, Actinobacteria and Planctomycetes were identifed as common bacterial phyla associated with shrimp. Interestingly, the bacterial diversity became relatively stable once shrimp developed to postlarvae (5-day-old and 15-day- old postlarval stages), suggesting an establishment of the bacterial community in matured shrimp. To our knowledge, this is the frst report on bacteria establishment and assembly in early developmental stages of P. monodon. Our fndings showed that the bacterial compositions could be shaped by diferent host developmental stages where the interplay of various host-associated factors, such as physiology, immune status and required diets, could have a strong infuence. Te shrimp aquaculture industry is one of the key sectors to supply food source to the world’s growing pop- ulation. -
Activated Sludge Microbial Community and Treatment Performance of Wastewater Treatment Plants in Industrial and Municipal Zones
International Journal of Environmental Research and Public Health Article Activated Sludge Microbial Community and Treatment Performance of Wastewater Treatment Plants in Industrial and Municipal Zones Yongkui Yang 1,2 , Longfei Wang 1, Feng Xiang 1, Lin Zhao 1,2 and Zhi Qiao 1,2,* 1 School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China; [email protected] (Y.Y.); [email protected] (L.W.); [email protected] (F.X.); [email protected] (L.Z.) 2 China-Singapore Joint Center for Sustainable Water Management, Tianjin University, Tianjin 300350, China * Correspondence: [email protected]; Tel.: +86-22-87402072 Received: 14 November 2019; Accepted: 7 January 2020; Published: 9 January 2020 Abstract: Controlling wastewater pollution from centralized industrial zones is important for reducing overall water pollution. Microbial community structure and diversity can adversely affect wastewater treatment plant (WWTP) performance and stability. Therefore, we studied microbial structure, diversity, and metabolic functions in WWTPs that treat industrial or municipal wastewater. Sludge microbial community diversity and richness were the lowest for the industrial WWTPs, indicating that industrial influents inhibited bacterial growth. The sludge of industrial WWTP had low Nitrospira populations, indicating that influent composition affected nitrification and denitrification. The sludge of industrial WWTPs had high metabolic functions associated with xenobiotic and amino acid metabolism. Furthermore, bacterial richness was positively correlated with conventional pollutants (e.g., carbon, nitrogen, and phosphorus), but negatively correlated with total dissolved solids. This study was expected to provide a more comprehensive understanding of activated sludge microbial communities in full-scale industrial and municipal WWTPs. Keywords: activated sludge; industrial zone; metabolic function; microbial community; wastewater treatment 1. -
Depthwise Microbiome and Isotopic Profiling of a Moderately Saline
www.nature.com/scientificreports OPEN Depthwise microbiome and isotopic profling of a moderately saline microbial mat in a solar saltern Varun Paul1*, Yogaraj Banerjee2, Prosenjit Ghosh2,3 & Susheel Bhanu Busi4 The solar salterns in Tuticorin, India, are man-made, saline to hypersaline systems hosting some uniquely adapted populations of microorganisms and eukaryotic algae that have not been fully characterized. Two visually diferent microbial mats (termed ‘white’ and ‘green’) developing on the reservoir ponds (53 PSU) were isolated from the salterns. Firstly, archaeal and bacterial diversity in diferent vertical layers of the mats were analyzed. Culture-independent 16S rRNA gene analysis revealed that both bacteria and archaea were rich in their diversity. The top layers had a higher representation of halophilic archaea Halobacteriaceae, phylum Chlorofexi, and classes Anaerolineae, Delta- and Gamma- Proteobacteria than the deeper sections, indicating that a salinity gradient exists within the mats. Limited presence of Cyanobacteria and detection of algae-associated bacteria, such as Phycisphaerae, Phaeodactylibacter and Oceanicaulis likely implied that eukaryotic algae and other phototrophs could be the primary producers within the mat ecosystem. Secondly, predictive metabolic pathway analysis using the 16S rRNA gene data revealed that in addition to the regulatory microbial functions, methane and nitrogen metabolisms were prevalent. Finally, stable carbon 13 and nitrogen isotopic compositions determined from both mat samples showed that the δ Corg 15 and δ Norg values increased slightly with depth, ranging from − 16.42 to − 14.73‰, and 11.17 to 13.55‰, respectively. The isotopic signature along the microbial mat profle followed a pattern that is distinctive to the community composition and net metabolic activities, and comparable to saline mats in other salterns. -
A Taxonomic Framework for Emerging Groups of Ecologically
Spring S, Scheuner C, Göker M, Klenk H-P. A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data. Frontiers in Microbiology 2015, 6, 281. Copyright: Copyright © 2015 Spring, Scheuner, Göker and Klenk. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. DOI link to article: http://dx.doi.org/10.3389/fmicb.2015.00281 Date deposited: 07/03/2016 This work is licensed under a Creative Commons Attribution 4.0 International License Newcastle University ePrints - eprint.ncl.ac.uk ORIGINAL RESEARCH published: 09 April 2015 doi: 10.3389/fmicb.2015.00281 A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data Stefan Spring 1*, Carmen Scheuner 1, Markus Göker 1 and Hans-Peter Klenk 1, 2 1 Department Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany, 2 School of Biology, Newcastle University, Newcastle upon Tyne, UK Edited by: Marcelino T. Suzuki, Sorbonne Universities (UPMC) and In recent years a large number of isolates were obtained from saline environments that are Centre National de la Recherche phylogenetically related to distinct clades of oligotrophic marine gammaproteobacteria, Scientifique, France which were originally identified in seawater samples using cultivation independent Reviewed by: Fabiano Thompson, methods and are characterized by high seasonal abundances in coastal environments. -
Microbial Community Composition Reflects Subduction Geochemistry in the Costa Rica Convergent Margin
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Masters Theses Graduate School 5-2019 Microbial Community Composition Reflects Subduction Geochemistry in the Costa Rica Convergent Margin Katherine Marie Fullerton University of Tennessee, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_gradthes Recommended Citation Fullerton, Katherine Marie, "Microbial Community Composition Reflects Subduction Geochemistry in the Costa Rica Convergent Margin. " Master's Thesis, University of Tennessee, 2019. https://trace.tennessee.edu/utk_gradthes/5439 This Thesis is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Masters Theses by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a thesis written by Katherine Marie Fullerton entitled "Microbial Community Composition Reflects Subduction Geochemistry in the Costa Rica Convergent Margin." I have examined the final electronic copy of this thesis for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Master of Science, with a major in Microbiology. Karen G. Lloyd, Major Professor We have read this thesis and recommend its acceptance: Allison Buchan, Frank Loeffler, Ania Sszynkiewicz Accepted for the Council: Dixie L. Thompson Vice Provost -
A Genomic View of Trophic and Metabolic Diversity in Clade-Specific
A genomic view of trophic and metabolic diversity in clade-specic Lamellodysidea sponge microbiomes Sheila Podell ( [email protected] ) University of California San Diego https://orcid.org/0000-0001-7073-5190 Jessica M. Blanton University of California San Diego Aaron Oliver University of California San Diego Michelle A. Schorn Wageningen Universiteit Vinayak Agarwal Georgia Institute of Technology Jason S. Biggs University of Guam Marine Laboratory Bradley S. Moore University of California San Diego Eric E. Allen University of California San Diego Research Keywords: Lamellodysidea, sponge microbiome, cyanosponge, Hormoscilla, PBDE, Methylospongia, Prochloron Posted Date: February 21st, 2020 DOI: https://doi.org/10.21203/rs.2.17204/v2 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Version of Record: A version of this preprint was published on June 23rd, 2020. See the published version at https://doi.org/10.1186/s40168-020-00877-y. Page 1/31 Abstract Background: Marine sponges and their microbiomes contribute signicantly to carbon and nutrient cycling in global reefs, processing and remineralizing dissolved and particulate organic matter. Lamellodysidea herbacea sponges obtain additional energy from abundant photosynthetic Hormoscilla cyanobacterial symbionts, which also produce polybrominated diphenyl ethers (PBDEs) chemically similar to anthropogenic pollutants of environmental concern. Potential contributions of non-Hormoscilla bacteria to Lamellodysidea microbiome metabolism and the synthesis and degradation of additional secondary metabolites are currently unknown. Results: This study has determined relative abundance, taxonomic novelty, metabolic capacities, and secondary metabolite potential in 21 previously uncharacterized, uncultured Lamellodysidea-associated microbial populations by reconstructing near-complete metagenome-assembled genomes (MAGs) to complement 16S rRNA gene amplicon studies. -
Microbial Degradation of Organic Micropollutants in Hyporheic Zone Sediments
Microbial degradation of organic micropollutants in hyporheic zone sediments Dissertation To obtain the Academic Degree Doctor rerum naturalium (Dr. rer. nat.) Submitted to the Faculty of Biology, Chemistry, and Geosciences of the University of Bayreuth by Cyrus Rutere Bayreuth, May 2020 This doctoral thesis was prepared at the Department of Ecological Microbiology – University of Bayreuth and AG Horn – Institute of Microbiology, Leibniz University Hannover, from August 2015 until April 2020, and was supervised by Prof. Dr. Marcus. A. Horn. This is a full reprint of the dissertation submitted to obtain the academic degree of Doctor of Natural Sciences (Dr. rer. nat.) and approved by the Faculty of Biology, Chemistry, and Geosciences of the University of Bayreuth. Date of submission: 11. May 2020 Date of defense: 23. July 2020 Acting dean: Prof. Dr. Matthias Breuning Doctoral committee: Prof. Dr. Marcus. A. Horn (reviewer) Prof. Harold L. Drake, PhD (reviewer) Prof. Dr. Gerhard Rambold (chairman) Prof. Dr. Stefan Peiffer In the battle between the stream and the rock, the stream always wins, not through strength but by perseverance. Harriett Jackson Brown Jr. CONTENTS CONTENTS CONTENTS ............................................................................................................................ i FIGURES.............................................................................................................................. vi TABLES ..............................................................................................................................