Short Communication Production of Dibromomethane and Changes in the Bacterial Community in Bromoform-Enriched Seawater
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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. -
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 -
[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. -
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 -
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. -
Rarefaction Curves of Mock Communities, After Subsampling to 6,800 Sequences but Prior to Removing Rare Otus (See Results and Methods for Complete Details)
SI Figure 1: Rarefaction curves of mock communities, after subsampling to 6,800 sequences but prior to removing rare OTUs (see Results and Methods for complete details). Solid line represents the mean and dashed lines indicate the range of all eight replicate mock communities; rarefaction curves of Even and Bloom communities were very similar and therefore are combined here. Note that the color scheme here is altered to distinguish the overlapping V4-5 and V3-4 lines. A: Full range of data. B: Subset of panel A, with restricted axes for detail. Dotted black line indicates 22 OTUs, the number of cloned 16S genes added to the mock communities. SI Figure 2: Log2-fold ratios of observed OTU relative abundance to expected, in Even and Bloom communities. Solid line is a 1:1 ratio. A: V4-5. B: V4. C: V3-4. D: V1-2. SI Figure 3: Mock community results – log2-fold ratio to expected values in Bloom mock community (mean of four replicates; error bars indicate range). “Other” columns indicate sequences that could not be assigned to an expected clone. As log2-fold ratios cannot accommodate zero values, samples were adjusted as follows: for samples with mean observed relative abundance = 0 and expected > 0, the log2-fold ratio was set to -10, without error bars, which was an arbitrary value more negative than any observed; for samples with observed > 0 and expected = 0, the expected value was set to 0.0001, which is less than 1 sequence per 6800, for calculations; for individual replicates with observed = 0 and expected > 0, where other replicates had observed > 0, relative abundance was set to 0.0001 for calculations. -
A001 Sandarakinorhabdus Ruber Sp. Nov., and Sandarakinorhabdus Oryzae Sp
A001 Sandarakinorhabdus ruber sp. nov., and Sandarakinorhabdus oryzae sp. nov., Isolated from Rice Paddy Soil Geon-Yeong Cho1, Min-Jung Park1, and Kyung-Sook Whang1,2* 1Department of Microbial & Nano Materials, Mokwon University, 2Institute of Microbial Ecology and Resources, Mokwon University A Gram-stain-negative, motile, rods-shaped, aerobic bacteria, designated strain MO-4T and NM-18T, were isolated from rice paddy soil in south Korea. The two strains grew at pH 5.0–11.0 (optimum, pH 8.0), at 15–45°C (optimum, 37°C ) and at salinities of 0–1.5% (w/v) NaCl (optimum, 0.4% NaCl). Phylogenetic analyses based on 16S rRNA gene sequences comparisons showed that the two isolates belonged to the genus Sandarakinorhabdus with sequence similarity of 98.6 to 97.6 %. And the similarity between strain MO-4T and NM-18T showed 97.3%. Average nucleotide identity values between MO-4T and NM-18T was lower than 82.0%, and that of between the two strains and closet relatives, S. limnophila so42T and S. caynobacteriorum TH057T 84.31 to 85.73%. The major fatty acids T T were iso-C18:1 ω7c and summed features 3. The G+C content of strains MO-4 and NM-18 , obtained from genome sequencing data, were 67.6 mol% and 66.6 mol%, respectively. On the basis of polyphasic analysis from this study, strains MO-4T and NM-18T represents a novel species of the genus Sandarakinorhabdus, for which the names Sandarakinorhabdus ruber sp. nov. (type strain NM-4T = KACC 21378 = NBRC 113957), Sandarakinorhabdus oryzae sp.