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Supplementary Information Comparative Microbiome and Metabolome Analyses of the Marine Tunicate Ciona intestinalis from Native and Invaded Habitats Caroline Utermann 1, Martina Blümel 1, Kathrin Busch 2, Larissa Buedenbender 1, Yaping Lin 3,4, Bradley A. Haltli 5, Russell G. Kerr 5, Elizabeta Briski 3, Ute Hentschel 2,6, Deniz Tasdemir 1,6* 1 GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany 2 Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Duesternbrooker Weg 20, 24105 Kiel, Germany 3 Research Group Invasion Ecology, Research Unit Experimental Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Duesternbrooker Weg 20, 24105 Kiel, Germany 4 Chinese Academy of Sciences, Research Center for Eco-Environmental Sciences, 18 Shuangqing Rd., Haidian District, Beijing, 100085, China 5 Department of Chemistry, University of Prince Edward Island, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada 6 Faculty of Mathematics and Natural Sciences, Kiel University, Christian-Albrechts-Platz 4, Kiel 24118, Germany * Corresponding author: Deniz Tasdemir ([email protected]) This document includes: Supplementary Figures S1-S11 Figure S1. Genotyping of C. intestinalis with the mitochondrial marker gene COX3-ND1. Figure S2. Influence of the quality filtering steps on the total number of observed read pairs from amplicon sequencing. Figure S3. Rarefaction curves of OTU abundances for C. intestinalis and seawater samples. Figure S4. Multivariate ordination plots of the bacterial community associated with C. intestinalis. Figure S5. Across sample type and geographic origin comparison of the C. intestinalis associated microbiome. -
Short Communication Production of Dibromomethane and Changes in the Bacterial Community in Bromoform-Enriched Seawater
Microbes Environ. Vol. 34, No. 2, 215-218, 2019 https://www.jstage.jst.go.jp/browse/jsme2 doi:10.1264/jsme2.ME18027 Short Communication Production of Dibromomethane and Changes in the Bacterial Community in Bromoform-Enriched Seawater TAKAFUMI KATAOKA1*, ATSUSHI OOKI2, and DAIKI NOMURA2 1Faculty of Marine Science and Technology, Fukui Prefectural University, 1–1 Gakuen-cho Obama, Fukui, 917–0003, Japan; and 2Faculty of Fisheries Sciences, Hokkaido University, 3–1–1, Minato-cho, Hakodate, Hokkaido 041–8611, Japan (Received February 27, 2018—Accepted December 13, 2018—Published online February 15, 2019) The responses of bacterial communities to halocarbon were examined using a 28-d incubation of bromoform- and methanol- enriched subarctic surface seawater. Significant increases were observed in dibromomethane concentrations and bacterial 16S rRNA gene copy numbers in the treated substrates incubated for 13 d. The accumulated bacterial community was investigated by denaturing gradient gel electrophoresis and amplicon analyses. The dominant genotypes corresponded to the genera Roseobacter, Lentibacter, and Amylibacter; the family Flavobacteriaceae; and the phylum Planctomycetes, including methylotrophs of the genus Methylophaga and the family Methylophilaceae. Therefore, various phylotypes responded along with the dehalogenation processes in subarctic seawater. Key words: dibromomethane (CH2Br2), dehalogenation, bacterial community, denaturing gradient gel electrophoresis, subarctic Pacific Brominated, very short-lived halocarbons, such as bromoform identify the bacteria phylotypes involved in CH2Br2 production (CHBr3) and dibromomethane (CH2Br2), with atmospheric as a response to this addition using a 28-d incubation. lifetimes of 24 and 123 d, respectively (25), are potentially Seawater samples were collected from the eastern coast of significant contributors to catalytic ozone loss in the troposphere Hokkaido, the northern area of Japan, located in the subarctic and lower stratosphere (12). -
Effect of Environmental Variations on Bacterial Communities Dynamics
Effect of environmental variations on bacterial communities dynamics : evolution and adaptation of bacteria as part of a microbial observatory in the Bay of Brest and the Iroise Sea Clarisse Lemonnier To cite this version: Clarisse Lemonnier. Effect of environmental variations on bacterial communities dynamics : evolution and adaptation of bacteria as part of a microbial observatory in the Bay of Brest and the Iroise Sea. Ecosystems. Université de Bretagne occidentale - Brest, 2019. English. NNT : 2019BRES0030. tel-02953054 HAL Id: tel-02953054 https://tel.archives-ouvertes.fr/tel-02953054 Submitted on 29 Sep 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. THESE DE DOCTORAT DE L'UNIVERSITE DE BRETAGNE OCCIDENTALE COMUE UNIVERSITE BRETAGNE LOIRE ECOLE DOCTORALE N° 598 Sciences de la Mer et du littoral Spécialité : Microbiologie Par Clarisse LEMONNIER Effet des changements environnementaux sur la dynamique des communautés microbiennes : évolution et adaptation des bactéries dans le cadre du développement de l’Observatoire Microbien en Rade de -
Host-Microbe Symbiosis in the Marine Sponge Halichondria Panicea
Host-microbe symbiosis in the marine sponge Halichondria panicea Stephen Knobloch Faculty of Life and Environmental Sciences University of Iceland 2019 Host-microbe symbiosis in the marine sponge Halichondria panicea Stephen Knobloch Dissertation submitted in partial fulfilment of a Philosophiae Doctor degree in Biology PhD Committee Viggó Þór Marteinsson Ragnar Jóhannsson Eva Benediktsdóttir Opponents Detmer Sipkema Ólafur Sigmar Andrésson Faculty of Life and Environmental Sciences School of Engineering and Natural Sciences University of Iceland Reykjavik, May 2019 Host-microbe symbiosis in the marine sponge Halichondria panicea Bacterial symbiosis in H. panicea Dissertation submitted in partial fulfilment of a Philosophiae Doctor degree in Biology Copyright © 2019 Stephen Knobloch All rights reserved Faculty of Life and Environmental Sciences School of Engineering and Natural Sciences University of Iceland Askja, Sturlugata 7 101, Reykjavik Iceland Telephone: +354 525 4000 Bibliographic information: Stephen Knobloch, 2019, Host-microbe symbiosis in the marine sponge Halichondria panicea, PhD dissertation, Faculty of Life and Environmental Sciences, University of Iceland, 204 pp. ISBN: 978-9935-9438-8-0 Author ORCID: 0000-0002-0930-8592 Printing: Háskólaprent Reykjavik, Iceland, May 2019 Abstract Sponges (phylum Porifera) are considered one of the oldest extant lineages of the animal kingdom. Their close association with microorganism makes them suitable for studying early animal-microbe symbiosis and expanding our understanding of host-microbe interactions through conserved mechanisms. Moreover, many sponges and sponge- associated microorganisms produce bioactive compounds, making them highly relevant for the biotechnology and pharmaceutical industry. So far, however, it has not been possible to grow biotechnologically relevant sponge species or isolate their obligate microbial symbionts for these purposes. -
Amylibacter Kogurei Sp. Nov., a Novel Marine Alphaproteobacterium Isolated from the Coastal Sea Surface Microlayer of a Marine Inlet
TAXONOMIC DESCRIPTION Wong et al., Int J Syst Evol Microbiol 2018;68:2872–2877 DOI 10.1099/ijsem.0.002911 Amylibacter kogurei sp. nov., a novel marine alphaproteobacterium isolated from the coastal sea surface microlayer of a marine inlet Shu-Kuan Wong,1,* Susumu Yoshizawa,1 Yu Nakajima,1 Marie Johanna Cuadra,2 Yuichi Nogi,3 Keiji Nakamura,4 Hideto Takami,3 Yoshitoshi Ogura,4 Tetsuya Hayashi,4 Hiroshi Xavier Chiura1 and Koji Hamasaki1 Abstract A novel Gram-negative bacterium, designated 4G11T, was isolated from the sea surface microlayer of a marine inlet. On the basis of 16S rRNA gene sequence analysis, the strain showed the closest similarity to Amylibacter ulvae KCTC 32465T (99.0 %). However, DNA–DNA hybridization values showed low DNA relatedness between strain 4G11T and its close phylogenetic neighbours, Amylibacter marinus NBRC 110140T (8.0±0.4 %) and Amylibacter ulvae KCTC 32465T (52.9±0.9 %). T T Strain 4G11 had C18 : 1,C16 : 0 and C18 : 2 as the major fatty acids. The only isoprenoid quinone detected for strain 4G11 was ubiquinone-10. The major polar lipids were phosphatidylglycerol, phosphatidylcholine, one unidentified polar lipid, one unidentified phospholipid and one unidentified aminolipid. The DNA G+C content of strain 4G11T was 50.0 mol%. Based on phenotypic and chemotaxonomic characteristics and analysis of the 16S rRNA gene sequence, the novel strain should be assigned to a novel species, for which the name Amylibacter kogurei sp. nov. is proposed. The type strain of Amylibacter kogurei is 4G11T (KY463497=KCTC 52506T=NBRC 112428T). The genus Amylibacter from the family Rhodobacteracaea the University of Tokyo’s Misaki Marine Biological Station was first proposed by Teramoto and Nishijima [1] as an aer- (35 09.5¢ N 139 36.5¢ E) at Misaki, Japan. -
Seasonal Dynamics of Prokaryotes and Their
Seasonal dynamics of prokaryotes and their associations with diatoms in the Southern Ocean as revealed by an autonomous sampler Yan Liu, Stephane Blain, Olivier Crispi, Mathieu Rembauville, Ingrid Obernosterer To cite this version: Yan Liu, Stephane Blain, Olivier Crispi, Mathieu Rembauville, Ingrid Obernosterer. Seasonal dy- namics of prokaryotes and their associations with diatoms in the Southern Ocean as revealed by an autonomous sampler. Environmental Microbiology, Society for Applied Microbiology and Wiley- Blackwell, In press, 10.1111/1462-2920.15184. hal-02917040 HAL Id: hal-02917040 https://hal.archives-ouvertes.fr/hal-02917040 Submitted on 18 Aug 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. Seasonal dynamics of prokaryotes and their associations with diatoms in the Southern Ocean as revealed by an autonomous sampler Yan Liu1,2, Stéphane Blain1, Olivier Crispi1, Mathieu Rembauville1, Ingrid Obernosterer1* 5 1Sorbonne Université, CNRS, Laboratoire d’Océanographie Microbienne (LOMIC), 66650 Banyuls-sur-Mer, France 2College of Marine -
Complete Genome Sequence of Lutibacter Profundi LP1T Isolated
Wissuwa et al. Standards in Genomic Sciences (2017) 12:5 DOI 10.1186/s40793-016-0219-x SHORT GENOME REPORT Open Access Complete genome sequence of Lutibacter profundi LP1T isolated from an Arctic deep- sea hydrothermal vent system Juliane Wissuwa1,2, Sven Le Moine Bauer1,2, Ida Helene Steen1,2 and Runar Stokke1,2* Abstract Lutibacter profundi LP1T within the family Flavobacteriaceae was isolated from a biofilm growing on the surface of a black smoker chimney at the Loki’s Castle vent field, located on the Arctic Mid-Ocean Ridge. The complete genome of L. profundi LP1T is the first genome to be published within the genus Lutibacter. L. profundi LP1T consists of a single 2,966,978 bp circular chromosome with a GC content of 29.8%. The genome comprises 2,537 protein-coding genes, 40 tRNA species and 2 rRNA operons. The microaerophilic, organotrophic isolate contains genes for all central carbohydrate metabolic pathways. However, genes for the oxidative branch of the pentose-phosphate-pathway, the glyoxylate shunt of the tricarboxylic acid cycle and the ATP citrate lyase for reverse TCA are not present. L. profundi LP1T utilizes starch, sucrose and diverse proteinous carbon sources. In accordance, the genome harbours 130 proteases and 104 carbohydrate-active enzymes, indicating a specialization in degrading organic matter. Among a small arsenal of 24 glycosyl hydrolases, which offer the possibility to hydrolyse diverse poly- and oligosaccharides, a starch utilization cluster was identified. Furthermore, a variety of enzymes may be secreted via T9SS and contribute to the hydrolytic variety of the microorganism. Genes for gliding motility are present, which may enable the bacteria to move within the biofilm. -
Lutibacter Holmesii Sp. Nov., a Marine Bacterium of the Family
International Journal of Systematic and Evolutionary Microbiology (2015), 65, 3991–3996 DOI 10.1099/ijsem.0.000525 Lutibacter holmesii sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from the sea urchin Strongylocentrotus intermedius, and emended description of the genus Lutibacter Olga I. Nedashkovskaya,1,2 Stefanie Van Trappen,3 Natalia V. Zhukova2,4 and Paul De Vos3 Correspondence 1G.B. Elyakov Pacific Institute of Bioorganic Chemistry of the Far-Eastern Branch of the Russian Olga I. Nedashkovskaya Academy of Sciences, Prospekt 100 Let Vladivostoku 159, 690022 Vladivostok, Russia [email protected] 2Far Easten Federal University, Sukhanova St. 8, 690091 Vladivostok, Russia or 3BCCM/LMG Bacteria Collection, and Laboratory of Microbiology, Ghent University, Ledeganck- [email protected] straat 35, B-9000 Ghent, Belgium 4A.V. Zhirmunsky Institute of Marine Biology of the Far Eastern Branch of the Russian Academy of Science, Pal’chevskogo St. 17, 690032 Vladivostok, Russia Seven Gram-staining-negative, strictly aerobic, pale-yellow-pigmented, rod-shaped and non- motile strains were isolated from the sea urchin Strongylocentrotus intermedius collected from Troitsa Bay, Sea of Japan. Phylogenetic analyses based on 16S rRNA gene sequences showed that these isolates were affiliated with the family Flavobacteriaceae. The novel isolates showed 99.9–100 % 16S rRNA gene sequence similarity to each other and were closely related to the type strains of the recognized members of the genus Lutibacter with sequence similarities of 95.8–98.4 %. The G+C content of the genomic DNA was 35–36 mol%. DNA–DNA relatedness among the sea urchin isolates was 95–99 % and between strain KMM 6277T and its most closely related type strains, Lutibacter agarilyticus KCTC 23842T and Lutibacter litoralis JCM T 13034 , was 38 and 27 %, respectively. -
Supplementary Fig. 5
PFspades_M3_96_0.952241;Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Mitochondria;NA Matam_M3_6315;Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Mitochondria;NA PFspades_M3_102_1.274286;Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Mitochondria;NA PFspades_M2_93_1.298496;Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Mitochondria;NA Matam_M4_5440;Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Mitochondria;NAPFspades_M4_75_1.305007;Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Mitochondria;NA 0.999 A Matam_M3_6487;Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Mitochondria;NA PFspades_M2_97_0.823083;Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Mitochondria;NA 0.841 0.876 Matam_M3_5437;Bacteria;Proteobacteria;Gammaproteobacteria;SAR86Matam_M3_5438;Bacteria;Proteobacteria;Gammaproteobacteria;SAR86 clade;NA;NA clade;NA;NA 0.787 Matam_M2_1930;Bacteria;Proteobacteria;Gammaproteobacteria;SAR86 clade;NA;NA Matam_M3_3768;Bacteria;Proteobacteria;Gammaproteobacteria;SAR86 clade;NA;NA Matam_M3_1904;Bacteria;Proteobacteria;Gammaproteobacteria;SAR86 clade;NA;NA Matam_M2_1678;Bacteria;Proteobacteria;Gammaproteobacteria;SAR86 clade;NA;NA Matam_M2_1258;Bacteria;Proteobacteria;Alphaproteobacteria;NA;NA;NA Matam_M4_1919;Bacteria;Proteobacteria;Gammaproteobacteria;SAR86 clade;NA;NA Matam_M3_1916;Bacteria;Proteobacteria;Gammaproteobacteria;SAR86 clade;NA;NA 1.000 Matam_M2_1974;Bacteria;Proteobacteria;Gammaproteobacteria;SAR86 clade;NA;NA Matam_M2_1403;Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Pseudoalteromonadaceae;Pseudoalteromonas -
Graduate School Thesis Template
A GLOBAL COMPARISON OF THE BACTERIAL COMMUNITIES OF BILGE WATER, BOAT SURFACES, AND EXTERNAL PORT WATER By Laura G. Schaerer A THESIS Submitted in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE In Biological Sciences MICHIGAN TECHNOLOGICAL UNIVERSITY 2019 © 2019 Laura G. Schaerer This thesis has been approved in partial fulfillment of the requirements for the Degree of MASTER OF SCIENCE in Biological Sciences. Department of Biological Sciences Thesis Advisor: Stephen Techtmann Committee Member: Amy Marcarelli Committee Member: Jennifer Becker Department Chair: Chandrashekhar Joshi Table of Contents Preface..................................................................................................................................v Acknowledgements ............................................................................................................ vi Abstract ............................................................................................................................. vii 1 Introduction .................................................................................................................9 1.1 Ships as a vector for transport of microorganisms .........................................11 1.2 Port Microbiomes ...........................................................................................14 1.3 Bacteria in Ballast water are an Emerging Problem .......................................16 1.4 Ballast Tanks are a Selective Environment ....................................................17 -
Summer Marine Bacterial Community Composition of the Western Antarctic Peninsula
San Jose State University SJSU ScholarWorks Master's Projects Master's Theses and Graduate Research Spring 5-26-2021 Summer Marine Bacterial Community Composition of the Western Antarctic Peninsula Codey Phoun Follow this and additional works at: https://scholarworks.sjsu.edu/etd_projects Part of the Bioinformatics Commons SUMMER MARINE BACTERIAL COMMUNITY COMPOSITION OF THE WESTERN ANTARCTIC PENINSULA Summer Marine Bacterial Community Composition of the Western Antarctic Peninsula A Project Presented to the Department of Computer Science San José State University In Partial Fulfillment of the Requirements for the Degree Master of Science By Codey Phoun May 2021 SUMMER MARINE BACTERIAL COMMUNITY COMPOSITION OF THE WESTERN ANTARCTIC PENINSULA ABSTRACT The Western Antarctic Peninsula has experienced dramatic warming due to climate change over the last 50 years and the consequences to the marine microbial community are not fully clear. The marine bacterial community are fundamental contributors to biogeochemical cycling of nutrients and minerals in the ocean. Molecular data of bacteria from the surface waters of the Western Antarctic Peninsula are lacking and most existing studies do not capture the annual variation of bacterial community dynamics. In this study, 15 different 16S rRNA gene amplicon samples covering 3 austral summers were processed and analyzed to investigate the marine bacterial community composition and its changes over the summer season. Between the 3 summer seasons, a similar pattern of dominance in relative community composition by the classes of Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes was observed. Alphaproteobacteria were mainly composed of the order Rhodobacterales and increased in relative abundance as the summer progressed. Gammaproteobacteria were represented by a wide array of taxa at the order level. -
Host-Specific Symbioses and the Microbial Prey of a Pelagic Tunicate
www.nature.com/ismecomms ARTICLE OPEN Host-specific symbioses and the microbial prey of a pelagic tunicate (Pyrosoma atlanticum) ✉ Anne W. Thompson 1 , Anna C. Ward 2, Carey P. Sweeney 1 and Kelly R. Sutherland 2 © The Author(s) 2021 Pyrosomes are widely distributed pelagic tunicates that have the potential to reshape marine food webs when they bloom. However, their grazing preferences and interactions with the background microbial community are poorly understood. This is the first study of the marine microorganisms associated with pyrosomes undertaken to improve the understanding of pyrosome biology, the impact of pyrosome blooms on marine microbial systems, and microbial symbioses with marine animals. The diversity, relative abundance, and taxonomy of pyrosome-associated microorganisms were compared to seawater during a Pyrosoma atlanticum bloom in the Northern California Current System using high-throughput sequencing of the 16S rRNA gene, microscopy, and flow cytometry. We found that pyrosomes harbor a microbiome distinct from the surrounding seawater, which was dominated by a few novel taxa. In addition to the dominant taxa, numerous more rare pyrosome-specific microbial taxa were recovered. Multiple bioluminescent taxa were present in pyrosomes, which may be a source of the iconic pyrosome luminescence. We also discovered free-living marine microorganisms in association with pyrosomes, suggesting that pyrosome feeding impacts all microbial size classes but preferentially removes larger eukaryotic taxa. This study demonstrates that microbial symbionts and microbial prey are central to pyrosome biology. In addition to pyrosome impacts on higher trophic level marine food webs, the work suggests that pyrosomes also alter marine food webs at the microbial level through feeding and seeding of the marine microbial communities with their symbionts.