Microbial Ecology of Expanding Oxygen Minimum Zones
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A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium Smegmatis Is Involved in De Novo Cysteine Biosynthesis
University of Arkansas, Fayetteville ScholarWorks@UARK Theses and Dissertations 5-2020 A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium smegmatis is Involved in de novo Cysteine Biosynthesis Saroj Kumar Mahato University of Arkansas, Fayetteville Follow this and additional works at: https://scholarworks.uark.edu/etd Part of the Cell Biology Commons, Molecular Biology Commons, and the Pathogenic Microbiology Commons Citation Mahato, S. K. (2020). A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium smegmatis is Involved in de novo Cysteine Biosynthesis. Theses and Dissertations Retrieved from https://scholarworks.uark.edu/etd/3639 This Thesis is brought to you for free and open access by ScholarWorks@UARK. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of ScholarWorks@UARK. For more information, please contact [email protected]. A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium smegmatis is Involved in de novo Cysteine Biosynthesis A thesis submitted in partial fulfillment of the requirement for the degree of Master of Science in Cell and Molecular Biology by Saroj Kumar Mahato Purbanchal University Bachelor of Science in Biotechnology, 2016 May 2020 University of Arkansas This thesis is approved for recommendation to the Graduate Council. ___________________________________ Young Min Kwon, Ph.D. Thesis Director ___________________________________ ___________________________________ Suresh Thallapuranam, Ph.D. Inés Pinto, Ph.D. Committee Member Committee Member ABSTRACT Mycobacteria include serious pathogens of humans and animals. Mycolicibacterium smegmatis is a non-pathogenic model that is widely used to study core mycobacterial metabolism. This thesis explores mycobacterial pathways of cysteine biosynthesis by generating and study of genetic mutants of M. smegmatis. Published in vitro biochemical studies had revealed three independent routes to cysteine synthesis in mycobacteria involving separate homologs of cysteine synthase, namely CysK1, CysK2, and CysM. -
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. -
Exploring Antibiotic Susceptibility, Resistome and Mobilome Structure of Planctomycetes from Gemmataceae Family
sustainability Article Exploring Antibiotic Susceptibility, Resistome and Mobilome Structure of Planctomycetes from Gemmataceae Family Anastasia A. Ivanova *, Kirill K. Miroshnikov and Igor Y. Oshkin Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, 119071 Moscow, Russia; [email protected] (K.K.M.); [email protected] (I.Y.O.) * Correspondence: [email protected] Abstract: The family Gemmataceae accomodates aerobic, chemoorganotrophic planctomycetes with large genome sizes, is mostly distributed in freshwater and terrestrial environments. However, these bacteria have recently also been found in locations relevant to human health. Since the antimi- crobial resistance genes (AMR) from environmental resistome have the potential to be transferred to pathogens, it is essential to explore the resistant capabilities of environmental bacteria. In this study, the reconstruction of in silico resistome was performed for all nine available gemmata genomes. Furthermore, the genome of the newly isolated yet-undescribed strain G18 was sequenced and added to all analyses steps. Selected genomes were screened for the presence of mobile genetic elements. The flanking location of mobilizable genomic milieu around the AMR genes was of particular in- terest since such colocalization may appear to promote the horizontal gene transfer (HGT) events. Moreover the antibiotic susceptibility profile of six phylogenetically distinct strains of Gemmataceae planctomycetes was determined. Citation: Ivanova, A.A.; Keywords: planctomycetes; Gemmataceae; antibiotic resistance profile; resistome; mobilome Miroshnikov, K.K.; Oshkin, I.Y. Exploring Antibiotic Susceptibility, Resistome and Mobilome Structure of Planctomycetes from Gemmataceae 1. Introduction Family. Sustainability 2021, 13, 5031. Several decades ago humanity faced the global issue of growing antibiotic resistance https://doi.org/10.3390/su13095031 of bacterial pathogens in clinic [1–5]. -
Expanding the Chlamydiae Tree
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 2040 Expanding the Chlamydiae tree Insights into genome diversity and evolution JENNAH E. DHARAMSHI ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6214 ISBN 978-91-513-1203-3 UPPSALA urn:nbn:se:uu:diva-439996 2021 Dissertation presented at Uppsala University to be publicly examined in A1:111a, Biomedical Centre (BMC), Husargatan 3, Uppsala, Tuesday, 8 June 2021 at 13:15 for the degree of Doctor of Philosophy. The examination will be conducted in English. Faculty examiner: Prof. Dr. Alexander Probst (Faculty of Chemistry, University of Duisburg-Essen). Abstract Dharamshi, J. E. 2021. Expanding the Chlamydiae tree. Insights into genome diversity and evolution. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 2040. 87 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-513-1203-3. Chlamydiae is a phylum of obligate intracellular bacteria. They have a conserved lifecycle and infect eukaryotic hosts, ranging from animals to amoeba. Chlamydiae includes pathogens, and is well-studied from a medical perspective. However, the vast majority of chlamydiae diversity exists in environmental samples as part of the uncultivated microbial majority. Exploration of microbial diversity in anoxic deep marine sediments revealed diverse chlamydiae with high relative abundances. Using genome-resolved metagenomics various marine sediment chlamydiae genomes were obtained, which significantly expanded genomic sampling of Chlamydiae diversity. These genomes formed several new clades in phylogenomic analyses, and included Chlamydiaceae relatives. Despite endosymbiosis-associated genomic features, hosts were not identified, suggesting chlamydiae with alternate lifestyles. Genomic investigation of Anoxychlamydiales, newly described here, uncovered genes for hydrogen metabolism and anaerobiosis, suggesting they engage in syntrophic interactions. -
8.4 the Significance of Ocean Deoxygenation for Continental Margin Mesopelagic Communities J
8.4 The significance of ocean deoxygenation for continental margin mesopelagic communities J. Anthony Koslow 8.4 The significance of ocean deoxygenation for continental margin mesopelagic communities J. Anthony Koslow Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia and Scripps Institution of Oceanography, University of California, SD, La Jolla, CA 92093 USA. Email: [email protected] Summary • Global climate models predict global warming will lead to declines in midwater oxygen concentrations, with greatest impact in regions of oxygen minimum zones (OMZ) along continental margins. Time series from these regions indicate that there have been significant changes in oxygen concentration, with evidence of both decadal variability and a secular declining trend in recent decades. The areal extent and volume of hypoxic and suboxic waters have increased substantially in recent decades with significant shoaling of hypoxic boundary layers along continental margins. • The mesopelagic communities in OMZ regions are unique, with the fauna noted for their adaptations to hypoxic and suboxic environments. However, mesopelagic faunas differ considerably, such that deoxygenation and warming could lead to the increased dominance of subtropical and tropical faunas most highly adapted to OMZ conditions. • Denitrifying bacteria within the suboxic zones of the ocean’s OMZs account for about a third of the ocean’s loss of fixed nitrogen. Denitrification in the eastern tropical Pacific has varied by about a factor of 4 over the past 50 years, about half due to variation in the volume of suboxic waters in the Pacific. Continued long- term deoxygenation could lead to decreased nutrient content and hence decreased ocean productivity and decreased ocean uptake of carbon dioxide (CO2). -
Spatiotemporal Dynamics of Marine Bacterial and Archaeal Communities in Surface Waters Off the Northern Antarctic Peninsula
Spatiotemporal dynamics of marine bacterial and archaeal communities in surface waters off the northern Antarctic Peninsula Camila N. Signori, Vivian H. Pellizari, Alex Enrich Prast and Stefan M. Sievert The self-archived postprint version of this journal article is available at Linköping University Institutional Repository (DiVA): http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-149885 N.B.: When citing this work, cite the original publication. Signori, C. N., Pellizari, V. H., Enrich Prast, A., Sievert, S. M., (2018), Spatiotemporal dynamics of marine bacterial and archaeal communities in surface waters off the northern Antarctic Peninsula, Deep-sea research. Part II, Topical studies in oceanography, 149, 150-160. https://doi.org/10.1016/j.dsr2.2017.12.017 Original publication available at: https://doi.org/10.1016/j.dsr2.2017.12.017 Copyright: Elsevier http://www.elsevier.com/ Spatiotemporal dynamics of marine bacterial and archaeal communities in surface waters off the northern Antarctic Peninsula Camila N. Signori1*, Vivian H. Pellizari1, Alex Enrich-Prast2,3, Stefan M. Sievert4* 1 Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo (USP). Praça do Oceanográfico, 191. CEP: 05508-900 São Paulo, SP, Brazil. 2 Department of Thematic Studies - Environmental Change, Linköping University. 581 83 Linköping, Sweden 3 Departamento de Botânica, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ). Av. Carlos Chagas Filho, 373. CEP: 21941-902. Rio de Janeiro, Brazil 4 Biology Department, Woods Hole Oceanographic Institution (WHOI). 266 Woods Hole Road, Woods Hole, MA 02543, United States. *Corresponding authors: Camila Negrão Signori Address: Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo, São Paulo, Brazil. -
Metaproteomics Reveals Differential Modes of Metabolic Coupling Among Ubiquitous Oxygen Minimum Zone Microbes
Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes Alyse K. Hawleya, Heather M. Brewerb, Angela D. Norbeckb, Ljiljana Paša-Tolicb, and Steven J. Hallama,c,d,1 aDepartment of Microbiology and Immunology, cGraduate Program in Bioinformatics, and dGenome Sciences and Technology Training Program, University of British Columbia, Vancouver, BC, Canada V6T 1Z3; and bBiological and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352 Edited by Edward F. DeLong, Massachusetts Institute of Technology, Cambridge, MA, and approved June 10, 2014 (received for review November 26, 2013) Marine oxygen minimum zones (OMZs) are intrinsic water column transformations in nonsulfidic OMZs, providing evidence for features arising from respiratory oxygen demand during organic a cryptic sulfur cycle with the potential to drive inorganic carbon matter degradation in stratified waters. Currently OMZs are expand- fixation processes (13). Indeed, many of the key microbial players ing due to global climate change with resulting feedback on marine implicated in nitrogen and sulfur transformations in OMZs, in- ecosystem function. Here we use metaproteomics to chart spatial cluding Thaumarchaeota, Nitrospina, Nitrospira, Planctomycetes, and temporal patterns of gene expression along defined redox and SUP05/ARCTIC96BD-19 Gammaproteobacteria have the gradients in a seasonally stratified fjord to better understand metabolic potential for inorganic carbon fixation (14–19), and -
Development of the Equine Hindgut Microbiome in Semi-Feral and Domestic Conventionally-Managed Foals Meredith K
Tavenner et al. Animal Microbiome (2020) 2:43 Animal Microbiome https://doi.org/10.1186/s42523-020-00060-6 RESEARCH ARTICLE Open Access Development of the equine hindgut microbiome in semi-feral and domestic conventionally-managed foals Meredith K. Tavenner1, Sue M. McDonnell2 and Amy S. Biddle1* Abstract Background: Early development of the gut microbiome is an essential part of neonate health in animals. It is unclear whether the acquisition of gut microbes is different between domesticated animals and their wild counterparts. In this study, fecal samples from ten domestic conventionally managed (DCM) Standardbred and ten semi-feral managed (SFM) Shetland-type pony foals and dams were compared using 16S rRNA sequencing to identify differences in the development of the foal hindgut microbiome related to time and management. Results: Gut microbiome diversity of dams was lower than foals overall and within groups, and foals from both groups at Week 1 had less diverse gut microbiomes than subsequent weeks. The core microbiomes of SFM dams and foals had more taxa overall, and greater numbers of taxa within species groups when compared to DCM dams and foals. The gut microbiomes of SFM foals demonstrated enhanced diversity of key groups: Verrucomicrobia (RFP12), Ruminococcaceae, Fusobacterium spp., and Bacteroides spp., based on age and management. Lactic acid bacteria Lactobacillus spp. and other Lactobacillaceae genera were enriched only in DCM foals, specifically during their second and third week of life. Predicted microbiome functions estimated computationally suggested that SFM foals had higher mean sequence counts for taxa contributing to the digestion of lipids, simple and complex carbohydrates, and protein. -
Recurring Patterns in Bacterioplankton Dynamics During Coastal Spring
RESEARCH ARTICLE Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms Hanno Teeling1*†, Bernhard M Fuchs1*†, Christin M Bennke1‡, Karen Kru¨ ger1, Meghan Chafee1, Lennart Kappelmann1, Greta Reintjes1, Jost Waldmann1, Christian Quast1, Frank Oliver Glo¨ ckner1, Judith Lucas2, Antje Wichels2, Gunnar Gerdts2, Karen H Wiltshire3, Rudolf I Amann1* 1Max Planck Institute for Marine Microbiology, Bremen, Germany; 2Biologische Anstalt Helgoland, Alfred Wegener Institute for Polar and Marine Research, Helgoland, Germany; 3Alfred Wegener Institute for Polar and Marine Research, List auf Sylt, Germany Abstract A process of global importance in carbon cycling is the remineralization of algae biomass by heterotrophic bacteria, most notably during massive marine algae blooms. Such blooms can trigger secondary blooms of planktonic bacteria that consist of swift successions of distinct *For correspondence: hteeling@ mpi-bremen.de (HT); bfuchs@mpi- bacterial clades, most prominently members of the Flavobacteriia, Gammaproteobacteria and the bremen.de (BMF); ramann@mpi- alphaproteobacterial Roseobacter clade. We investigated such successions during spring bremen.de (RIA) phytoplankton blooms in the southern North Sea (German Bight) for four consecutive years. Dense sampling and high-resolution taxonomic analyses allowed the detection of recurring patterns down † These authors contributed to the genus level. Metagenome analyses also revealed recurrent patterns at the functional level, in equally to this work particular with respect to algal polysaccharide degradation genes. We, therefore, hypothesize that Present address: ‡Section even though there is substantial inter-annual variation between spring phytoplankton blooms, the Biology, Leibniz Institute for accompanying succession of bacterial clades is largely governed by deterministic principles such as Baltic Sea Research, substrate-induced forcing. -
Climate-Driven Deoxygenation Elevates Fishing Vulnerability for The
RESEARCH ARTICLE Climate-driven deoxygenation elevates fishing vulnerability for the ocean’s widest ranging shark Marisa Vedor1,2, Nuno Queiroz1,3†*, Gonzalo Mucientes1,4, Ana Couto1, Ivo da Costa1, Anto´ nio dos Santos1, Frederic Vandeperre5,6,7, Jorge Fontes5,7, Pedro Afonso5,7, Rui Rosa2, Nicolas E Humphries3, David W Sims3,8,9†* 1CIBIO/InBIO, Universidade do Porto, Campus Agra´rio de Vaira˜ o, Vaira˜ o, Portugal; 2MARE, Laborato´rio Marı´timo da Guia, Faculdade de Cieˆncias da Universidade de Lisboa, Av. Nossa Senhora do Cabo, Cascais, Portugal; 3Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, United Kingdom; 4Instituto de Investigaciones Marinas, Consejo Superior de Investigaciones Cientı´ficas (IIM-CSIC), Vigo, Spain; 5IMAR – Institute of Marine Research, Departamento de Oceanografia e Pescas, Universidade dos Ac¸ores, Horta, Portugal; 6MARE – Marine and Environmental Sciences Centre, Faculdade de Cieˆncias da Universidade de Lisboa, Lisbon, Portugal; 7Okeanos - Departamento de Oceanografia e Pescas, Universidade dos Ac¸ores, Horta, Portugal; 8Centre for Biological Sciences, Highfield Campus, University of Southampton, Southampton, United Kingdom; 9Ocean and Earth Science, National Oceanography Centre Southampton, Waterfront Campus, University of Southampton, Southampton, United Kingdom *For correspondence: [email protected] (NQ); Abstract Climate-driven expansions of ocean hypoxic zones are predicted to concentrate [email protected] (DWS) pelagic fish in oxygenated surface layers, but how expanding hypoxia and fisheries will interact to affect threatened pelagic sharks remains unknown. Here, analysis of satellite-tracked blue sharks †These authors contributed equally to this work and environmental modelling in the eastern tropical Atlantic oxygen minimum zone (OMZ) shows shark maximum dive depths decreased due to combined effects of decreasing dissolved oxygen Competing interests: The (DO) at depth, high sea surface temperatures, and increased surface-layer net primary production. -
Ocean Deoxygenation and Copepods: Coping with Oxygen Minimum Zone Variability
Biogeosciences, 17, 2315–2339, 2020 https://doi.org/10.5194/bg-17-2315-2020 © Author(s) 2020. This work is distributed under the Creative Commons Attribution 4.0 License. Ocean deoxygenation and copepods: coping with oxygen minimum zone variability Karen F. Wishner1, Brad Seibel2, and Dawn Outram1 1Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA 2College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA Correspondence: Karen F. Wishner ([email protected]) Received: 27 September 2019 – Discussion started: 28 October 2019 Revised: 31 March 2020 – Accepted: 2 April 2020 – Published: 24 April 2020 Abstract. Increasing deoxygenation (loss of oxygen) of compression concept). These distribution depths changed by the ocean, including expansion of oxygen minimum zones tens to hundreds of meters depending on the species, oxygen (OMZs), is a potentially important consequence of global profile, and phenomenon. For example, at the lower oxycline, warming. We examined present-day variability of vertical the depth of maximum abundance for Lucicutia hulsemannae distributions of 23 calanoid copepod species in the East- shifted from ∼ 600 to ∼ 800 m, and the depth of diapause for ern Tropical North Pacific (ETNP) living in locations with Eucalanus inermis shifted from ∼ 500 to ∼ 775 m, in an ex- different water column oxygen profiles and OMZ inten- panded OMZ compared to a thinner OMZ, but remained at sity (lowest oxygen concentration and its vertical extent in similar low oxygen levels in -
Card Uses a Minor Groove Wedge Mechanism to Stabilize the RNA
1 CarD uses a minor groove wedge mechanism to stabilize the RNA 2 polymerase open promoter complex 3 4 Brian Bae1, James Chen1, Elizabeth Davis1, Katherine Leon1, Seth A. Darst1,*, 5 Elizabeth A. Campbell1,* 6 7 1The Rockefeller University, Laboratory for Molecular Biophysics, 1230 York Avenue, New York, 8 NY 10065, USA. 9 10 *Correspondence to: E-mail: [email protected], [email protected] 11 12 Present Address: Elizabeth Davis, The University of Minnesota School of Medicine, 13 420 Delaware St. SE, Minneapolis, MN 55455, USA; Katherine Leon, Department of 14 Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, GCIS 15 W219 Chicago, IL 60637, USA. 16 17 2 18 Abstract A key point to regulate gene expression is at transcription initiation, and 19 activators play a major role. CarD, an essential activator in Mycobacterium tuberculosis, 20 is found in many bacteria, including Thermus species, but absent in Escherichia coli. To 21 delineate the molecular mechanism of CarD, we determined crystal structures of 22 Thermus transcription initiation complexes containing CarD. The structures show CarD 23 interacts with the unique DNA topology presented by the upstream double- 24 stranded/single-stranded DNA junction of the transcription bubble. We confirm that our 25 structures correspond to functional activation complexes, and extend our understanding 26 of the role of a conserved CarD Trp residue that serves as a minor groove wedge, 27 preventing collapse of the transcription bubble to stabilize the transcription initiation 28 complex. Unlike E. coli RNAP, many bacterial RNAPs form unstable promoter 29 complexes, explaining the need for CarD.