DOCSLIB.ORG

Graduate School Thesis Template

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
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 1.5 Biofilms Cause Complications .......................................................................18 1.6 Bilge Water as a Means of Transport .............................................................19 1.7 Current Water Regulations .............................................................................21 1.8 Conclusions ....................................................................................................23 2 A Global comparison of the microbial communities of bilge water, boat surfaces and external port water.......................................................................................................26 2.1 Materials and Methods ...................................................................................28 2.1.1 Sample Collection .............................................................................28 2.1.2 DNA extraction and sequencing library preparation ........................30 2.1.3 16S rRNA sequence analysis ............................................................31 2.1.4 Statistical Analysis of 16S rRNA reads ............................................31 2.2 Results ............................................................................................................35 2.2.1 Overall Microbial Community Diversity ..........................................35 2.2.2 Differences in abundance between boat and port water ...................38 2.2.3 Pathogens in bilge water and on boat surfaces .................................40 2.2.4 The microbial community in the bilge is influenced by the microbial community in the water .................................. Error! Bookmark not defined. 2.2.5 Quantifying the proportion of the water as a source in boat microbiomes ...................................................................................................44 2.3 Discussion ......................................................................................................47 iii 3 Sources of Boat Microbial Communities ..................................................................54 4 Works Cited ..............................................................................................................78 A Chapter 2 Supplemental Material .............................................................................88 B Copyright documentation.......................................... Error! Bookmark not defined. iv Preface This thesis is submitted for a Master of Science degree at Michigan Technological University. The research described in this document was supervised by Dr. Stephen Techtmann in the Department of Biological Sciences at Michigan Technological University between January 2018 and December 2019. The work described in this document is original, to the best of my knowledge, aside from references to previous work. Chapter 2, A global comparison of the bacterial communities of bilge water, boat surfaces, and external port water, has been accepted for publication in Applied and Environmental Microbiology. This study was designed by Stephen Techtmann. Sample collection was done by Stephen Techtmann, Ryan Ghannam, and Timothy Butler. Ryan Ghannam performed most of the library preparation and pre-processing of sequencing reads discussed in Chapter 2. Chapter 3 is in preparation for future publication. This experiment was also designed by Stephen Techtmann. Sample collection was done by Paige Webb and Annika Corazzol. v Acknowledgements This work was made possible by funding from the DARPA Young Faculty Award D16AP00146. I would like to acknowledge the captains and crews of the vessels involved in this work. Particularly, Gian Marco Luna, Grazia Quero, Thorsten Brinkhoff, and Stanley Lau for provision of vessels and help in sample collection. Additionally, I would like to thank Jamey Anderson and Chris Pinnow from the MTU Great Lakes Research Center for help with sample collection in the Great Lakes ports. I would like to thank the Techtmann lab for their help with this research project. In particular, I would like to acknowledge Timothy Butler and Ryan Ghannam for their involvement in this project. I would also like to acknowledge my committee members and thank them for their advice and guidance during my time as Michigan Technological University as a Masters’ student. In particular, I would like to thank my advisor, Steve Techtmann for always pushing me to be a better scientist with his positive encouragement. Lastly, I would like to thank my family for their love and support throughout my education. Most of all, I would like to acknowledge my husband, Charles, for all he has done to help me with this achievement, because I would not have been able to do this without him. vi Abstract Each year, hundreds of thousands of boats travel across the globe carrying over 80% of the world’s cargo. With all of these boats traveling all over the world, it is important to understand the organisms which live in and on the boats. This study looks at the extent to which bacteria can colonize ships. The potential for microbes from the water to colonize boats is an understudied, yet important topic which affects ecosystems and human health. Because of increasingly affordable metagenomic tools, it is now possible to characterize microbial communities in more detail than has been affordable and or practical in the past. Ballast water is intentionally taken onto a ship to increase stability and safety, and it has been shown to be a key vector in the spread of some non-native species. Because bacteria are ubiquitous in most environments, they have potential to be transported on ships in additional ways. Bilge water collects at the bottom of all boats and is another potential vector for the spread of non-native species. Additionally, bacteria frequently colonize underwater surfaces, making the outside surfaces of a boat another likely location for colonization by water microbes. Using a large data set collected from 20 ports in five regions of the world (Asia, Europe, east and west coasts U.S.A. and Great Lakes U.S.A.) we explore how the boat microbial community is similar to the water. We do this with microbial diversity analysis and source tracking software. The results from the source tracking software showed on average 40% of the bilge bacterial community and 52% of the hull bacterial community were sourced from the water. This suggests that microbes from the port water colonize a boat and have potential to travel with that boat. Source tracking analysis attributed an average of 60% of the bilge bacterial community and 48% of the hull bacterial community to unknown sources. To further quantify these vii unknown sources, we investigated air and dock as potential sources to the boat microbiome. After analysis with source tracking software, we showed that air contributed minimally to the boat microbiome (<1%) while dock contributed to the hull and transom of the boat (14-64%). This suggests that the dock may be an underappreciated source of microorganisms to the boat microbial community. In conclusion, this study shows that the microbial community of a boat is strongly influenced by its surroundings. We show that several sources (water, dock and air) contribute to the boat microbial community. viii 1 A Brief History of Invasive Species and Ballast Water Human activity has resulted in the spread of many organisms around the globe. Not every species that is displaced becomes invasive, but many displaced organisms do have long lasting impacts on ecosystems1. Throughout recent history, many species have been moved around the world at speeds which would be impossible without anthropogenic influence. According to the Federal Invasive Species Advisory Committee, an invasive species is an alien species which is likely to cause economic or environmental harm or is likely to have a negative impact on human health2. Once a species is in a non-native ecosystem, it is possible for the non-native species to become invasive
Load more

Recommended publications
  • 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.
    [Show full text]
  • Artificial Neural Network Analysis of Microbial Diversity in the Central and Southern Adriatic
    www.nature.com/scientificreports OPEN Artifcial neural network analysis of microbial diversity in the central and southern Adriatic Sea Danijela Šantić1*, Kasia Piwosz2, Frano Matić1, Ana Vrdoljak Tomaš1, Jasna Arapov1, Jason Lawrence Dean3, Mladen Šolić1, Michal Koblížek3,4, Grozdan Kušpilić1 & Stefanija Šestanović1 Bacteria are an active and diverse component of pelagic communities. The identifcation of main factors governing microbial diversity and spatial distribution requires advanced mathematical analyses. Here, the bacterial community composition was analysed, along with a depth profle, in the open Adriatic Sea using amplicon sequencing of bacterial 16S rRNA and the Neural gas algorithm. The performed analysis classifed the sample into four best matching units representing heterogenic patterns of the bacterial community composition. The observed parameters were more diferentiated by depth than by area, with temperature and identifed salinity as important environmental variables. The highest diversity was observed at the deep chlorophyll maximum, while bacterial abundance and production peaked in the upper layers. The most of the identifed genera belonged to Proteobacteria, with uncultured AEGEAN-169 and SAR116 lineages being dominant Alphaproteobacteria, and OM60 (NOR5) and SAR86 being dominant Gammaproteobacteria. Marine Synechococcus and Cyanobium- related species were predominant in the shallow layer, while Prochlorococcus MIT 9313 formed a higher portion below 50 m depth. Bacteroidota were represented mostly by uncultured lineages (NS4, NS5 and NS9 marine lineages). In contrast, Actinobacteriota were dominated by a candidatus genus Ca. Actinomarina. A large contribution of Nitrospinae was evident at the deepest investigated layer. Our results document that neural network analysis of environmental data may provide a novel insight into factors afecting picoplankton in the open sea environment.
    [Show full text]
  • Supplementary Information
    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.
    [Show full text]
  • Distinct Relationships Between Fluorescence in Situ Hybridization
    Systematic and Applied Microbiology 42 (2019) 126000 Contents lists available at ScienceDirect Systematic and Applied Microbiology jou rnal homepage: http://www.elsevier.com/locate/syapm Distinct relationships between fluorescence in situ hybridization and 16S rRNA gene- and amplicon-based sequencing data of bacterioplankton lineages a b b a a Insa Bakenhus , Bernd Wemheuer , Pinar Akyol , Helge-Ansgar Giebel , Leon Dlugosch , b a,∗ Rolf Daniel , Meinhard Simon a Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129 Oldenburg, Germany b Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany a r t i c l e i n f o a b s t r a c t Article history: Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) and amplicon sequencing Received 6 April 2019 of the total (16S rRNA gene) and potentially active (16S rRNA transcripts), community are the major Received in revised form 21 June 2019 state of the art approaches for assessing the composition of bacterial communities in marine pelagic and Accepted 28 June 2019 other ecosystems. However, CARD-FISH and amplicon sequencing methods have not yet been directly compared to assess the composition of bacterioplankton communities. Therefore, these approaches were Keywords: used to study the composition of bacterial communities in two North Sea seawater mesocosm experi- Bacteria ments supplemented with diatom-derived organic matter (OM). All approaches revealed Proteobacteria CARD-FISH and Bacteroidetes as major components of the bacterioplankton communities.
    [Show full text]
  • 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).
    [Show full text]
  • 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
    [Show full text]
  • [Article] JMLS
    한국해양생명과학회지[Journal of Marine Life Science] June 2021; 6(1): 9-22 [Article] JMLS http://jmls.or.kr Bacterial Communities from the Water Column and the Surface Sediments along a Transect in the East Sea Jeong-Kyu Lee, Keun-Hyung Choi* Department of Marine Environmental Science, Chungnam National University, Daejeon 34134, Korea Corresponding Author We determined the composition of water and sediment bacterial assemblages from the Keun-Hyung Choi East Sea using 16S rRNA gene sequencing. Total bacterial reads were greater in surface waters (<100 m) than in deep seawaters (>500 m) and sediments. However, total OTUs, Department of Marine Environmental bacterial diversity, and evenness were greater in deep seawaters than in surface waters Science, Chungnam National University, with those in the sediment comparable to the deep sea waters. Proteobacteria was the Daejeon 34134, Korea most dominant bacterial phylum comprising 67.3% of the total sequence reads followed E-mail : [email protected] by Bacteriodetes (15.8%). Planctomycetes, Verrucomicrobia, and Actinobacteria followed all together consisting of only 8.1% of the total sequence. Candidatus Pelagibacter ubique considered oligotrophic bacteria, and Planctomycetes copiotrophic bacteria showed an Received : March 22, 2021 opposite distribution in the surface waters, suggesting a potentially direct competition for Revised : April 12, 2021 available resources by these bacteria with different traits. The bacterial community in the Accepted : April 26, 2021 warm surface waters were well separated from the other deep cold seawater and sediment samples. The bacteria exclusively associated with deep sea waters was Actinobacteriacea, known to be prevalent in the deep photic zone. The bacterial group Chromatiales and Lutibacter were those exclusively associated with the sediment samples.
    [Show full text]
  • Taxonomic Hierarchy of the Phylum Proteobacteria and Korean Indigenous Novel Proteobacteria Species
    Journal of Species Research 8(2):197-214, 2019 Taxonomic hierarchy of the phylum Proteobacteria and Korean indigenous novel Proteobacteria species Chi Nam Seong1,*, Mi Sun Kim1, Joo Won Kang1 and Hee-Moon Park2 1Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea 2Department of Microbiology & Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea *Correspondent: [email protected] The taxonomic hierarchy of the phylum Proteobacteria was assessed, after which the isolation and classification state of Proteobacteria species with valid names for Korean indigenous isolates were studied. The hierarchical taxonomic system of the phylum Proteobacteria began in 1809 when the genus Polyangium was first reported and has been generally adopted from 2001 based on the road map of Bergey’s Manual of Systematic Bacteriology. Until February 2018, the phylum Proteobacteria consisted of eight classes, 44 orders, 120 families, and more than 1,000 genera. Proteobacteria species isolated from various environments in Korea have been reported since 1999, and 644 species have been approved as of February 2018. In this study, all novel Proteobacteria species from Korean environments were affiliated with four classes, 25 orders, 65 families, and 261 genera. A total of 304 species belonged to the class Alphaproteobacteria, 257 species to the class Gammaproteobacteria, 82 species to the class Betaproteobacteria, and one species to the class Epsilonproteobacteria. The predominant orders were Rhodobacterales, Sphingomonadales, Burkholderiales, Lysobacterales and Alteromonadales. The most diverse and greatest number of novel Proteobacteria species were isolated from marine environments. Proteobacteria species were isolated from the whole territory of Korea, with especially large numbers from the regions of Chungnam/Daejeon, Gyeonggi/Seoul/Incheon, and Jeonnam/Gwangju.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • Bacterial Diversity in the Gorgonian Coral Eunicella Labiata and How
    Dominic Eriksson Bacterial diversity of the gorgonian coral Eunicella labiata: how much can we cultivate? UNIVERSIDADE DO ALGARVE Faculdade de Ciências e Tecnologia 2017 Dominic Eriksson Bacterial diversity of the gorgonian coral Eunicella labiata: how much can we cultivate? Mestrado em Biologia Marinha Supervisors: Prof. Dr. Ester Serrão Co-supervisor Prof. Dr. Rodrigo Costa UNIVERSIDADE DO ALGARVE Faculdade de Ciências e Tecnologia 2017 Abstract: Bacterial communities inhabiting non-calcified gorgonian corals (Octocorallia, Gorgoniidae) are apparently unique in taxonomic composition and may benefit their host by several means, including chemical defense and nutrient provision. However, in spite of their distinct phylogenetic diversity, the gorgonian symbiotic consortium has thus far been scarcely addressed, and thus the microbiota of several gorgonian hosts remains uncharted. This thesis describes the bacterial diversity found in the gorgonian host Eunicella labiata, determines its degree of uniqueness in comparison with the structure of the surrounding bacterioplankton and reveals the readily cultivatable fraction within this symbiotic consortium. To this end, a custom methodological approach was employed allowing direct comparison between the “total” and “cultivatable” bacterial community inhabiting E. labiata using massive Illumina sequencing of 16S rRNA gene amplicons. The 16S rRNA gene Operational Taxonomic Units (OTUs) were established at a cut-off of 97% gene similarity. Biodiversity indices such as the Shannon-Wiener were highest in the bacterial community obtained from seawater. A Tukey Honest Post Hoc test determined significant differences between biodiversity indices and sample categories. A closer look into taxonomic profiles and the relative abundances of dominant genera, clearly showed differences between microhabitats, with Candidatus Actinomarina dominating the seawater samples whereas within Ruegeria and Endozoicomonas represented the dominant fraction within E.
    [Show full text]
  • Seasonal Dynamics of Prokaryotes and Their Associations with Diatoms in the Southern Ocean As Revealed by an Autonomous Sampler
    1 Environmental Microbiology Archimer September 2020, Volume 22, Issue 9, Pages 3968-3984 https://doi.org/10.1111/1462-2920.15184 https://archimer.ifremer.fr https://archimer.ifremer.fr/doc/00643/75475/ Seasonal dynamics of prokaryotes and their associations with diatoms in the Southern Ocean as revealed by an autonomous sampler Liu Yan 1, 2, Blain Stéphane 1, Crispi Olivier 1, Rembauville Mathieu 1, Obernosterer Ingrid 1, * 1 CNRS, Laboratoire d'Océanographie Microbienne (LOMIC)Sorbonne Université 66650 Banyuls‐sur‐ Mer ,France 2 College of Marine Life SciencesOcean University of China Qingdao 266003 ,China * Corresponding author : Ingrid Obernosterer, email address : [email protected] Abstract : The Southern Ocean remains one of the least explored marine environments. The investigation of temporal microbial dynamics has thus far been hampered by the limited access to this remote ocean. We present here high‐resolution seasonal observations of the prokaryotic community composition during phytoplankton blooms induced by natural iron fertilization. A total of 18 seawater samples was collected by a moored remote autonomous sampler over 4 months at 5‐11 day intervals in offshore surface waters (central Kerguelen Plateau). Illumina sequencing of the 16S rRNA gene revealed that among the most abundant ASVs, SAR92 and Aurantivirga were the first bloom responders, Pseudomonadaceae, Nitrincolaceae, and Polaribacter had successive peaks during the spring bloom decline, and Amylibacter increased in relative abundance later in the season. SAR11 and SUP05 were abundant prior to and after the blooms. Using network analysis, we identified two groups of diatoms representative of the spring and summer bloom that had opposite correlation patterns with prokaryotic taxa.
    [Show full text]