Exploring the Cultivable Ectocarpus Microbiome
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1 Microbial Transformations of Organic Chemicals in Produced Fluid From
Microbial transformations of organic chemicals in produced fluid from hydraulically fractured natural-gas wells Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Morgan V. Evans Graduate Program in Environmental Science The Ohio State University 2019 Dissertation Committee Professor Paula Mouser, Advisor Professor Gil Bohrer, Co-Advisor Professor Matthew Sullivan, Member Professor Ilham El-Monier, Member Professor Natalie Hull, Member 1 Copyrighted by Morgan Volker Evans 2019 2 Abstract Hydraulic fracturing and horizontal drilling technologies have greatly improved the production of oil and natural-gas from previously inaccessible non-permeable rock formations. Fluids comprised of water, chemicals, and proppant (e.g., sand) are injected at high pressures during hydraulic fracturing, and these fluids mix with formation porewaters and return to the surface with the hydrocarbon resource. Despite the addition of biocides during operations and the brine-level salinities of the formation porewaters, microorganisms have been identified in input, flowback (days to weeks after hydraulic fracturing occurs), and produced fluids (months to years after hydraulic fracturing occurs). Microorganisms in the hydraulically fractured system may have deleterious effects on well infrastructure and hydrocarbon recovery efficiency. The reduction of oxidized sulfur compounds (e.g., sulfate, thiosulfate) to sulfide has been associated with both well corrosion and souring of natural-gas, and proliferation of microorganisms during operations may lead to biomass clogging of the newly created fractures in the shale formation culminating in reduced hydrocarbon recovery. Consequently, it is important to elucidate microbial metabolisms in the hydraulically fractured ecosystem. -
Metagenomic Insights Into Microbial Metabolisms of a Sulfur-Influenced
bioRxiv preprint doi: https://doi.org/10.1101/2020.01.31.929786; this version posted February 2, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Metagenomic Insights into Microbial Metabolisms of a Sulfur- 2 Influenced Glacial Ecosystem 3 4 Christopher B. Trivedi1,4, Blake W. Stamps1, Graham E. Lau2, Stephen E. Grasby3, Alexis S. 5 Templeton2, John R. Spear1,* 6 7 1Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, 8 80401 USA 9 2Department of Geological Sciences, University of Colorado Boulder, Boulder, CO, 80309 USA 10 3Geological Survey of Canada-Calgary, Calgary, AB, T2L2A7 Canada 11 4GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Potsdam, 12 Brandenburg 14473 Germany 13 *Corresponding author: 14 John R. Spear 15 Colorado School of Mines 16 Department of Civil and Environmental Engineering 17 1500 Illinois Street 18 Golden, Colorado 80401 19 [email protected] 20 21 22 23 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.01.31.929786; this version posted February 2, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 24 Running Title: 25 Metagenomics of a Sulfur-Influenced Glacial Ecosystem 26 27 Abstract 28 Biological sulfur cycling in polar, low-temperature ecosystems is an understudied 29 phenomenon in part due to difficulty of access and the ephemeral nature of such environments. 30 One such environment where sulfur cycling plays an important role in microbial metabolisms is 31 located at Borup Fiord Pass (BFP) in the Canadian High Arctic. -
To Split Or Not to Split: an Opinion on Dividing the Genus Burkholderia
Ann Microbiol (2016) 66:1303–1314 DOI 10.1007/s13213-015-1183-1 REVIEW ARTICLE To split or not to split: an opinion on dividing the genus Burkholderia Paulina Estrada-de los Santos 1 & Fernando Uriel Rojas-Rojas1 & Erika Yanet Tapia-García1 & María Soledad Vásquez-Murrieta1 & Ann M. Hirsch2,3 Received: 27 April 2015 /Accepted: 24 November 2015 /Published online: 23 December 2015 # Springer-Verlag Berlin Heidelberg and the University of Milan 2015 Abstract The genus Burkholderia is a large group of species features, and their relationship with plants as either associative of bacteria that inhabit a wide range of environments. We nitrogen-fixers or legume-nodulating/nitrogen-fixing bacteria. previously recommended, based on multilocus sequence anal- We also propose that a concerted and coordinated effort be ysis, that the genus be separated into two distinct groups—one made by researchers on Burkholderia to determine if a defin- that consists predominantly of human, plant, and animal path- itive taxonomic split of this very large genus is justified, es- ogens, including several opportunistic pathogens, and a sec- pecially now as we describe here for the first time intermediate ond, much larger group of species comprising plant-associated groups based upon their 16S rRNA sequences. We need to beneficial and environmental species that are primarily known learn more about the plant-associated Burkholderia strains not to be pathogenic. This second group of species is found regarding their potential for pathogenicity, especially in those mainly in soils, frequently in association with plants as plant strains intermediate between the two groups, and to discover growth-promoting bacteria. -
Genome Evolution and Phylogenomic Analysis of Candidatus Kinetoplastibacterium, the Betaproteobacterial Endosymbionts of Strigomonas and Angomonas
GBE Genome Evolution and Phylogenomic Analysis of Candidatus Kinetoplastibacterium, the Betaproteobacterial Endosymbionts of Strigomonas and Angomonas Joa˜oM.P.Alves1,3,*, Myrna G. Serrano1,Fla´viaMaiadaSilva2, Logan J. Voegtly1, Andrey V. Matveyev1, Marta M.G. Teixeira2, Erney P. Camargo2, and Gregory A. Buck1 1Department of Microbiology and Immunology and the Center for the Study of Biological Complexity, Virginia Commonwealth University 2Department of Parasitology, ICB, University of Sa˜o Paulo, Sa˜oPaulo,Brazil 3Present address: Sa˜o Paulo, Brazil *Corresponding author: E-mail: [email protected]. Accepted: January 18, 2013 Data deposition: Finished genome sequences and annotations are available from GenBank under accession numbers CP003803, CP003804, CP003805, CP003806, and CP003807. Supplementary table S1, Supplementary Material online, also contains accession numbers to sequences used in the phylogenetic analyses. Abstract It has been long known that insect-infecting trypanosomatid flagellates from the genera Angomonas and Strigomonas harbor bacterial endosymbionts (Candidatus Kinetoplastibacterium or TPE [trypanosomatid proteobacterial endosymbiont]) that supple- ment the host metabolism. Based on previous analyses of other bacterial endosymbiont genomes from other lineages, a stereotypical path of genome evolution in such bacteria over the duration of their association with the eukaryotic host has been characterized. In this work, we sequence and analyze the genomes of five TPEs, perform their metabolic reconstruction, do an extensive phylogenomic analyses with all available Betaproteobacteria, and compare the TPEs with their nearest betaproteobacterial relatives. We also identify a number of housekeeping and central metabolism genes that seem to have undergone positive selection. Our genome structure analyses show total synteny among the five TPEs despite millions of years of divergence, and that this lineage follows the common path of genome evolution observed in other endosymbionts of diverse ancestries. -
Limnobacter Spp. As Newly Detected Phenol-Degraders Among Baltic Sea Surface Water Bacteria Characterised by Comparative Analysi
Systematic and Applied Microbiology 36 (2013) 525–532 Contents lists available at ScienceDirect Systematic and Applied Microbiology jo urnal homepage: www.elsevier.de/syapm Limnobacter spp. as newly detected phenol-degraders among Baltic Sea surface water bacteria characterised by comparative analysis of catabolic genes a,∗ a a a b Eve Vedler , Eeva Heinaru , Jekaterina Jutkina , Signe Viggor , Triinu Koressaar , b a Maido Remm , Ain Heinaru a Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, Tartu 51010, Estonia b Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Street, Tartu 51010, Estonia a r t i c l e i n f o a b s t r a c t Article history: A set of phenol-degrading strains of a collection of bacteria isolated from Baltic Sea surface water was Received 3 April 2013 screened for the presence of two key catabolic genes coding for phenol hydroxylases and catechol 2,3- Received in revised form 10 July 2013 dioxygenases. The multicomponent phenol hydroxylase (LmPH) gene was detected in 70 out of 92 Accepted 17 July 2013 + strains studied, and 41 strains among these LmPH phenol-degraders were found to exhibit catechol 2,3-dioxygenase (C23O) activity. Comparative phylogenetic analyses of LmPH and C23O sequences from Keywords: 56 representative strains were performed. The studied strains were mostly affiliated to the genera Pseu- Phenol-degrading bacteria domonas and Acinetobacter. However, the study also widened the range of phenol-degraders by including Catabolic genes the genus Limnobacter. Furthermore, using a next generation sequencing approach, the LmPH genes of Phylogenetic analysis Limnobacter Limnobacter strains were found to be the most prevalent ones in the microbial community of the Baltic Sea surface water. -
Bacteria in Ballast Water: the Shipping Industry’S
BACTERIA IN BALLAST WATER: THE SHIPPING INDUSTRY’S CONTRIBUTIONS TO THE TRANSPORT AND DISTRIBUTION OF MICROBIAL SPECIES IN TEXAS A Thesis by ELIZABETH B. NEYLAND Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE August 2009 Major Subject: Biology BACTERIA IN BALLAST WATER: THE SHIPPING INDUSTRY’S CONTRIBUTIONS TO THE TRANSPORT AND DISTRIBUTION OF MICROBIAL SPECIES IN TEXAS A Thesis by ELIZABETH B. NEYLAND Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Approved by: Co-Chairs of Committee, Robin Brinkmeyer Susan Golden Committee Members, Michael Benedik Antonietta Quigg Head of Department, Uel J. McMahan August 2009 Major Subject: Biology iii ABSTRACT Bacteria in Ballast Water: The Shipping Industry’s Contributions to the Transport and Distribution of Microbial Species in Texas. (August 2009) Elizabeth B. Neyland, B.S., Texas A&M University Co-Chairs of Advisory Committee: Dr. Robin Brinkmeyer Dr. Susan Golden The transportation of organisms in the ballast water of cargo ships has been recognized as a source of invasive species despite current control measures. Pathogenic bacteria in the ballast tank have been studied but the total diversity of the ballast tank bacterial community has not been examined. This study is the first to characterize the total bacterial community within a ballast tank by constructing a clone library from a ballast water sample from a cargo ship in the Port of Houston, amplified ribosomal rDNA restriction analysis (ARDRA) and phylogenetic analysis. -
Microbiota of Dominant Atlantic Copepods: Pleuromamma Sp. As a Host to a Betaproteobacterial Symbiont
UNIVERSITY OF SOUTHAMPTON Faculty Of Natural And Environmental Sciences School of Ocean and Earth Science Microbiota of dominant Atlantic copepods: Pleuromamma sp. as a host to a betaproteobacterial symbiont by Sara Joan Javornik Cregeen Thesis for the degree of Doctor of Philosophy March 2016 UNIVERSITY OF SOUTHAMPTON ABSTRACT FACULTY OF NATURAL AND ENVIRONMENTAL SCIENCES Ocean and Earth Sciences Thesis for the degree of Doctor of Philosophy MICROBIOTA OF DOMINANT ATLANTIC COPEPODS: PLEUROMAMMA SP. AS A HOST TO A BETAPROTEOBACTERIAL SYMBIONT by Sara Joan Javornik Cregeen Copepods are the most abundant zooplankton group in the ocean and play a pivotal role as grazers of microorganisms and prey for larger animals. Furthermore, they are major contributors to the pool of dissolved organic material in the pelagic and therefore play an important role in the microbial loop. Although biology of copepods has been under investigation for more than a century, few studies have looked at the relationship between copepods and their associated bacteria. Could copepods be perceived as distinctive microbial hotspots in nutrient poor pelagic environment? The microbiota of three Pleuromamma species, an abundant genus of copepods that migrate vertically from surface waters to several hundred meters water depth and back on a daily basis was investigated using various molecular and morphological techniques. The focus was on the differences in the bacterial community composition of these copepods along the Atlantic Meridional Transect, which traverses major oceanic biomes such as the subtropical gyres and the equatorial convergence region. Additionally, the community structure and stable isotope composition of the likely microplankton food source as well as the Pleuromamma copepods was assessed along the same cruise transect. -
The Influence of Bacteria on the Adaptation to Changing Environments in Ectocarpus : a Systems Biology Approach Hetty Kleinjan
The influence of bacteria on the adaptation to changing environments in Ectocarpus : a systems biology approach Hetty Kleinjan To cite this version: Hetty Kleinjan. The influence of bacteria on the adaptation to changing environments in Ectocar- pus : a systems biology approach. Molecular biology. Sorbonne Université, 2018. English. NNT : 2018SORUS267. tel-02868508 HAL Id: tel-02868508 https://tel.archives-ouvertes.fr/tel-02868508 Submitted on 15 Jun 2020 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. Sorbonne Université ED 227 - Sciences de la Nature et de l'Homme : écologie & évolution Laboratoire de Biologie Intégrative des Modèles Marins Equipe Biologie des algues et interactions avec l'environnement The influence of bacteria on the adaptation to changing environments in Ectocarpus: a systems biology approach Par Hetty KleinJan Thèse de doctorat en Biologie Marine Dirigée par Simon Dittami et Catherine Boyen Présentée et soutenue publiquement le 24 septembre 2018 Devant un jury composé de : Pr. Ute Hentschel Humeida, Rapportrice GEOMAR, Kiel, Germany Dr. Suhelen Egan, Rapportrice UNSW Sydney, Australia Dr. Fabrice Not, Examinateur Sorbonne Université – CNRS Dr. David Green, Examinateur SAMS, Oban, UK Dr. Aschwin Engelen, Examinateur CCMAR, Faro, Portugal Dr. -
Proteotyping Environmental Microorganisms by Phylopeptidomics: Case Study Screening Water from a Radioactive Material Storage Pool
microorganisms Article Proteotyping Environmental Microorganisms by Phylopeptidomics: Case Study Screening Water from a Radioactive Material Storage Pool Karim Hayoun 1,2, Olivier Pible 1, Pauline Petit 3, François Allain 1, Virginie Jouffret 1 , Karen Culotta 1, Corinne Rivasseau 4 , Jean Armengaud 1,* and Béatrice Alpha-Bazin 1 1 Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, SPI, Université Paris Saclay, F-30200 Bagnols-sur-Cèze, France; [email protected] (K.H.); [email protected] (O.P.); [email protected] (F.A.); virginie.jouff[email protected] (V.J.); [email protected] (K.C.); [email protected] (B.A.-B.) 2 Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Université de Montpellier, F-30207 Bagnols-sur-Cèze, France 3 CEA, CNRS, INRA, Université Grenoble Alpes, Institut de Biosciences et Biotechnologies de Grenoble, UMR5168, F-38000 Grenoble, France; [email protected] 4 CEA-Saclay, DRF/Joliot/SB2SM/BBC, I2BC, 91191 Gif-sur-Yvette, France; [email protected] * Correspondence: [email protected]; Tel.: +33-466-79-62-77 Received: 22 August 2020; Accepted: 1 October 2020; Published: 4 October 2020 Abstract: The microbial diversity encompassed by the environmental biosphere is largely unexplored, although it represents an extensive source of new knowledge and potentially of novel enzymatic catalysts for biotechnological applications. Todetermine the taxonomy of microorganisms, proteotyping by tandem mass spectrometry has proved its efficiency. Its latest extension, phylopeptidomics, adds a biomass quantitation perspective for mixtures of microorganisms. Here, we present an application of phylopeptidomics to rapidly and sensitively screen microorganisms sampled from an industrial environment, i.e., a pool where radioactive material is stored. -
Genome Analysis of a Limnobacter Sp. Identified in an Anaerobic
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Frontiers - Publisher Connector ORIGINAL RESEARCH published: 08 December 2016 doi: 10.3389/fmars.2016.00257 Genome Analysis of a Limnobacter sp. Identified in an Anaerobic Methane-Consuming Cell Consortium Ying Chen 1, 2, 3, Xiaoyuan Feng 1, 2, Ying He 1, 2 and Fengping Wang 1, 2* 1 State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China, 2 State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, China, 3 Department of Biochemistry and Molecular Biology, Guilin Medical University, Guilin, China Species of Limnobacter genus are widespread in a variety of environments, yet knowledges upon their metabolic potentials and mechanisms of environmental adaptation are limited. In this study, a cell aggregate containing Limnobacter and anaerobic methanotrophic archaea (ANME) was captured from an enriched anaerobic methane oxidizing (AOM) microbial community. A genomic bin of Limnobacter was obtained and analyzed, which provides the first metabolic insights into Limnobacter from an AOM environment. This Limnobacter was found to contain genes involved in the Edited by: Sandie M. Degnan, Embden-Meyerhof pathway, the citrate cycle, citronellol degradation, and transporters of University of Queensland, Australia various organic substances, indicating a potentially heterotrophic lifestyle. A number of Reviewed by: genes involved in sulfur oxidization, oxidative phosphorylation and ethanol fermentation Haiwei Luo, that serve both aerobic and anaerobic purposes have been found in Limnobacter. This The Chinese University of Hong Kong, Hong Kong work suggests that in the AOM environment, Limnobacter strains may live on the organic Rui Zhang, substances produced through AOM activity and subsequently may contribute to the Xiamen University, China Roland Hatzenpichler, AOM community by providing sulfate from sulfur oxidation. -
The Revised Manuscript Characteristics Of
The revised manuscript Characteristics of bacterial community in fog water at Mt. Tai: similarity and disparity under polluted and non-polluted fog episodes 5 Min Wei 1, Caihong Xu1, Jianmin Chen1,2,*, Chao Zhu1, Jiarong Li1 1 Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji’nan 250100, China 2 Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP), Fudan Tyndall Centre, Department of Environmental Science & Engineering, Fudan 10 University, Shanghai 200433, China Correspondence to: JM.Chen ([email protected]) Abstract: Bacteria, widely distributed in atmospheric bioaerosols, are indispensable components 15 in fog/clouds and play an important role in atmospheric hydrological cycle. However, limited acknowledge is acquired about bacterial community structure and function, especially for the increasing air pollution events in North China Plain. Here we presented a comprehensive characterization of bacterial community composition and function, variation and environmental influence on fog water collected at Mt. Tai 20 under polluted and non-polluted fog episodes from 24 Jul to 23 Aug 2014. Using the Miseq 16S rRNA gene sequencing, the facts that fog water harbored a highly diverse bacterial community and the predominant phyla of Proteobacteria, Bacteroidetes, Cyanobacteria and Firmicutes were investigated. The presence of bacterial taxa survived in low temperature, radiation and poor nutrients conditions were encountered 25 in fog water, suggesting the well adaption to extreme environment. Bacterial gene 1 functions predicted from 16S rRNA gene using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) suggested the pathways relating to metabolism and disease infections are significantly correlated to the predominant genera. -
Letter to the Editor Bacterial Communities Associated with An
646 Biomed Environ Sci, 2014; 27(8): 646-650 Letter to the Editor Bacterial Communities Associated with An Occurrence of Colored Water in An Urban Drinking Water Distribution System* WU Hui Ting1,2,△, MI Zi Long1,2,△, ZHANG Jing Xu3, CHEN Chao1,2, and XIE Shu Guang3,# This study aimed to investigate bacterial majority of urban areas reported the occurrence of community in an urban drinking water distribution colored water, but the water quality in some areas system (DWDS) during an occurrence of colored was still normal, without perceptible color. Water water. Variation in the bacterial community samples were collected from three colored water diversity and structure was observed among the points A, B and C, and a normal point D (as a different waters, with the predominance of reference point). All water samples were Proteobacteria. While Verrucomicrobia was also a immediately processed after collection. The major phylum group in colored water. Limnobacter physicochemical features of the four water samples was the major genus group in colored water, but are shown in Table S1. Undibacterium predominated in normal tap water. For analysis of aquatic bacterial community, The coexistence of Limnobacter as well as water samples (5 L) were filtered through 0.22-µm Sediminibacterium and Aquabacterium might pore-size membranes (diameter 50 mm; Millipore, contribute to the formation of colored water. USA). The membrane filters stored at -20 °C for The drinking water distribution system (DWDS) further molecular analysis. DNA samples were is mainly composed of iron and steel pipes in many extracted using the E.Z.N.A.® Water DNA kit (Omega, countries that are subject to corrosion during USA) according to the manufacturer’s protocol.