PDF (Figs S1-S3)
Total Page：16
File Type：pdf, Size：1020Kb
Load more
Recommended publications
-
Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations
fmicb-09-02879 December 1, 2018 Time: 14:0 # 1 ORIGINAL RESEARCH published: 04 December 2018 doi: 10.3389/fmicb.2018.02879 Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations Klervi Crenn, Delphine Duffieux and Christian Jeanthon* CNRS, Sorbonne Université, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Roscoff, France Interactions between phytoplankton and bacteria play a central role in mediating biogeochemical cycling and food web structure in the ocean. The cosmopolitan diatoms Thalassiosira and Chaetoceros often dominate phytoplankton communities in marine systems. Past studies of diatom-bacterial associations have employed community- level methods and culture-based or natural diatom populations. Although bacterial assemblages attached to individual diatoms represents tight associations little is known on their makeup or interactions. Here, we examined the epibiotic bacteria of 436 Thalassiosira and 329 Chaetoceros single cells isolated from natural samples and Edited by: collection cultures, regarded here as short- and long-term associations, respectively. Matthias Wietz, Epibiotic microbiota of single diatom hosts was analyzed by cultivation and by cloning- Alfred Wegener Institut, Germany sequencing of 16S rRNA genes obtained from whole-genome amplification products. Reviewed by: The prevalence of epibiotic bacteria was higher in cultures and dependent of the host Lydia Jeanne Baker, Cornell University, United States species. Culture approaches demonstrated that both diatoms carry distinct bacterial Bryndan Paige Durham, communities in short- and long-term associations. Bacterial epibonts, commonly University of Washington, United States associated with phytoplankton, were repeatedly isolated from cells of diatom collection *Correspondence: cultures but were not recovered from environmental cells. -
Fluviicola Taffensis Type Strain (RW262)
Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262). Permalink https://escholarship.org/uc/item/9tc6n0sm Journal Standards in genomic sciences, 5(1) ISSN 1944-3277 Authors Woyke, Tanja Chertkov, Olga Lapidus, Alla et al. Publication Date 2011-10-01 DOI 10.4056/sigs.2124912 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2011) 5:21-29 DOI:10.4056/sigs.2124912 Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262T) Tanja Woyke1, Olga Chertkov1, Alla Lapidus1, Matt Nolan1, Susan Lucas1, Tijana Glavina Del Rio1, Hope Tice1, Jan-Fang Cheng1, Roxanne Tapia1,2, Cliff Han1,2, Lynne Goodwin1,2, Sam Pitluck1, Konstantinos Liolios1, Ioanna Pagani1, Natalia Ivanova1, Marcel Huntemann1, Konstantinos Mavromatis1, Natalia Mikhailova1, Amrita Pati1, Amy Chen3, Krishna Palaniappan3, Miriam Land1,4, Loren Hauser1,4, Evelyne-Marie Brambilla5, Manfred Rohde6, Romano Mwirichia7, Johannes Sikorski5, Brian J. Tindall5, Markus Göker5, James Bristow1, Jonathan A. Eisen1,7, Victor Markowitz4, Philip Hugenholtz1,9, Hans-Peter Klenk5, and Nikos C. Kyrpides1* 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 3 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 4 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 5 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 6 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 7 Jomo Kenyatta University of Agriculture and Technology, Kenya 8 University of California Davis Genome Center, Davis, California, USA 9 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia *Corresponding author: Nikos C. -
Owenweeksia Hongkongensis UST20020801T
Lawrence Berkeley National Laboratory Recent Work Title Genome sequence of the orange-pigmented seawater bacterium Owenweeksia hongkongensis type strain (UST20020801(T)). Permalink https://escholarship.org/uc/item/8734g6jx Journal Standards in genomic sciences, 7(1) ISSN 1944-3277 Authors Riedel, Thomas Held, Brittany Nolan, Matt et al. Publication Date 2012-10-01 DOI 10.4056/sigs.3296896 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2012) 7:120-130 DOI:10.4056/sigs.3296896 Genome sequence of the orange-pigmented seawater bacterium Owenweeksia hongkongensis type strain (UST20020801T) Thomas Riedel1, Brittany Held2,3, Matt Nolan2, Susan Lucas2, Alla Lapidus2, Hope Tice2, Tijana Glavina Del Rio2, Jan-Fang Cheng2, Cliff Han2,3, Roxanne Tapia2,3, Lynne A. Goodwin2,3, Sam Pitluck2, Konstantinos Liolios2, Konstantinos Mavromatis2, Ioanna Pagani2, Natalia Ivanova2, Natalia Mikhailova2, Amrita Pati2, Amy Chen4, Krishna Palaniappan4, Manfred Rohde1, Brian J. Tindall6, John C. Detter2,3, Markus Göker6, Tanja Woyke2, James Bristow2, Jonathan A. Eisen2,7, Victor Markowitz4, Philip Hugenholtz2,8, Hans-Peter Klenk6*, and Nikos C. Kyrpides2 1 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 2 DOE Joint Genome Institute, Walnut Creek, California, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 5 Oak -
Assessment of the Dynamics of Microbial Community Associated with Tetraselmis Suecica Culture Under Different LED Lights Using N
J. Microbiol. Biotechnol. (2019), 29(12), 1957–1968 https://doi.org/10.4014/jmb.1910.10046 Research Article Review jmb Assessment of the Dynamics of Microbial Community Associated with Tetraselmis suecica Culture under Different LED Lights Using Next-Generation Sequencing Su-Jeong Yang1†, Hyun-Woo Kim1†, Seok-Gwan Choi2, Sangdeok Chung2, Seok Jin Oh3, Shweta Borkar4, and Hak Jun Kim4* 1Interdisciplinary Program of Biomedical, Mechanical and Electrical Engineering, Pukyong National University, Busan 48513, Republic of Korea 2National Institute of Fisheries Science (NIFS), Busan 46083, Republic of Korea 3Department of Oceanography, Pukyong National University, Busan 48513, Republic of Korea 4Department of Chemistry, Pukyong National University, Busan 48513, Republic of Korea Received: October 21, 2019 Revised: November 11, 2019 Tetraselmis is a green algal genus, some of whose species are important in aquaculture as well Accepted: November 14, 2019 as biotechnology. In algal culture, fluorescent lamps, traditional light source for culturing First published online: algae, are now being replaced by a cost-effective light-emitting diodes (LEDs). In this study, November 18, 2019 we investigated the effect of LED light of different wavelengths (white, red, yellow, and blue) *Corresponding author on the growth of Tetraselmis suecica and its associated microbial community structures using Phone: +82-51-629-5926 the next-generation sequencing (NGS). The fastest growth rate of T. suecica was shown in the Fax: +82-51-629-5930 Email: [email protected] red light, whereas the slowest was in yellow. The highest OTUs (3426) were identified on day 0, whereas the lowest ones (308) were found on day 15 under red light. -
Crenn Et Al. 2018.Pdf
Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations Klervi Crenn, Delphine Duffieux, Christian Jeanthon To cite this version: Klervi Crenn, Delphine Duffieux, Christian Jeanthon. Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations. Frontiers in Microbiology, Frontiers Media, 2018, 9, pp.2879. 10.3389/fmicb.2018.02879. hal-02130560 HAL Id: hal-02130560 https://hal.archives-ouvertes.fr/hal-02130560 Submitted on 15 May 2019 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. fmicb-09-02879 December 1, 2018 Time: 14:0 # 1 ORIGINAL RESEARCH published: 04 December 2018 doi: 10.3389/fmicb.2018.02879 Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations Klervi Crenn, Delphine Duffieux and Christian Jeanthon* CNRS, Sorbonne Université, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Roscoff, France Interactions between phytoplankton and bacteria play a central role in mediating biogeochemical cycling and food web structure in the ocean. The cosmopolitan diatoms Thalassiosira and Chaetoceros often dominate phytoplankton communities in marine systems. Past studies of diatom-bacterial associations have employed community- level methods and culture-based or natural diatom populations. -
Abstract Tracing Hydrocarbon
ABSTRACT TRACING HYDROCARBON CONTAMINATION THROUGH HYPERALKALINE ENVIRONMENTS IN THE CALUMET REGION OF SOUTHEASTERN CHICAGO Kathryn Quesnell, MS Department of Geology and Environmental Geosciences Northern Illinois University, 2016 Melissa Lenczewski, Director The Calumet region of Southeastern Chicago was once known for industrialization, which left pollution as its legacy. Disposal of slag and other industrial wastes occurred in nearby wetlands in attempt to create areas suitable for future development. The waste creates an unpredictable, heterogeneous geology and a unique hyperalkaline environment. Upgradient to the field site is a former coking facility, where coke, creosote, and coal weather openly on the ground. Hydrocarbons weather into characteristic polycyclic aromatic hydrocarbons (PAHs), which can be used to create a fingerprint and correlate them to their original parent compound. This investigation identified PAHs present in the nearby surface and groundwaters through use of gas chromatography/mass spectrometry (GC/MS), as well as investigated the relationship between the alkaline environment and the organic contamination. PAH ratio analysis suggests that the organic contamination is not mobile in the groundwater, and instead originated from the air. 16S rDNA profiling suggests that some microbial communities are influenced more by pH, and some are influenced more by the hydrocarbon pollution. BIOLOG Ecoplates revealed that most communities have the ability to metabolize ring structures similar to the shape of PAHs. Analysis with bioinformatics using PICRUSt demonstrates that each community has microbes thought to be capable of hydrocarbon utilization. The field site, as well as nearby areas, are targets for habitat remediation and recreational development. In order for these remediation efforts to be successful, it is vital to understand the geochemistry, weathering, microbiology, and distribution of known contaminants. -
Supplement of Biogeosciences, 13, 5527–5539, 2016 Doi:10.5194/Bg-13-5527-2016-Supplement © Author(S) 2016
Supplement of Biogeosciences, 13, 5527–5539, 2016 http://www.biogeosciences.net/13/5527/2016/ doi:10.5194/bg-13-5527-2016-supplement © Author(s) 2016. CC Attribution 3.0 License. Supplement of Seasonal changes in the D / H ratio of fatty acids of pelagic microorganisms in the coastal North Sea Sandra Mariam Heinzelmann et al. Correspondence to: Sandra Mariam Heinzelmann ([email protected]) The copyright of individual parts of the supplement might differ from the CC-BY 3.0 licence. Figure legends Supplementary Figure S1 Phylogenetic tree of 16S rRNA gene sequence reads assigned to Bacteroidetes. Scale bar indicates 0.10 % estimated sequence divergence. Groups containing sequences are highlighted. Figure S2 Phylogenetic tree of 16S rRNA gene sequence reads assigned to Alphaproteobacteria. Scale bar indicates 0.10 % estimated sequence divergence. Groups containing sequences are highlighted. Figure S3 Phylogenetic tree of 16S rRNA gene sequence reads assigned to Gammaproteobacteria. Scale bar indicates 0.10 % estimated sequence divergence. Groups containing sequences are highlighted. Figure S4 δDwater versus salinity of North Sea SPM sampled in 2013. Bacteroidetes figS01 group including Prevotellaceae Bacteroidaceae_Bacteroides RH-aaj90h05 RF16 S24-7 gir-aah93ho Porphyromonadaceae_1 ratAN060301C Porphyromonadaceae_2 3M1PL1-52 termite group Porphyromonadaceae_Paludibacter EU460988, uncultured bacterium, red kangaroo feces Porphyromonadaceae_3 009E01-B-SD-P15 Rikenellaceae MgMjR-022 BS11 gut group Rs-E47 termite group group including termite group FTLpost3 ML635J-40 aquatic group group including gut group vadinHA21 LKC2.127-25 Marinilabiaceae Porphyromonadaceae_4 Sphingobacteriia_Sphingobacteriales_1 group including Cytophagales Bacteroidetes Incertae Sedis_Unknown Order_Unknown Family_Prolixibacter WCHB1-32 SB-1 vadinHA17 SB-5 BD2-2 Ika-33 VC2.1 Bac22 Flavobacteria_Flavobacteriales including e.g. -
Bacterioplankton Diversity and Distribution in Relation To
bioRxiv preprint doi: https://doi.org/10.1101/2021.06.08.447544; this version posted June 8, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Bacterioplankton Diversity and Distribution in Relation to Phytoplankton Community Structure in the Ross Sea surface waters Angelina Cordone1, Giuseppe D’Errico2, Maria Magliulo1,§, Francesco Bolinesi1*, Matteo Selci1, Marco Basili3, Rocco de Marco3, Maria Saggiomo4, Paola Rivaro5, Donato Giovannelli1,2,3,6,7,8* and Olga Mangoni1,9 1 Department of Biology, University of Naples Federico II, Naples, Italy 2 Department of Life Sciences, DISVA, Polytechnic University of Marche, Ancona, Italy 3 National Research Council – Institute of Marine Biological Resources and Biotechnologies CNR-IRBIM, Ancona, Italy 4 Stazione Zoologica Anton Dohrn, Naples, Italy 5 Department of Chemistry and Industrial Chemistry, University of Genoa, Genoa, Italy 6 Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ, USA 7 Marine Chemistry & Geochemistry Department - Woods Hole Oceanographic Institution, MA, USA 8 Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan § now at University of Essex, Essex, UK 9 Consorzio Nazionale Interuniversitario delle Scienze del Mare (CoNISMa), Rome, Italy *corresponding author: Francesco Bolinesi [email protected] Donato Giovannelli [email protected] Keywords: bacterial diversity, bacterioplankton, phytoplankton, Ross Sea, Antarctica Abstract Primary productivity in the Ross Sea region is characterized by intense phytoplankton blooms whose temporal and spatial distribution are driven by changes in environmental conditions as well as interactions with the bacterioplankton community. -
Genome-Based Taxonomic Classification Of
ORIGINAL RESEARCH published: 20 December 2016 doi: 10.3389/fmicb.2016.02003 Genome-Based Taxonomic Classification of Bacteroidetes Richard L. Hahnke 1 †, Jan P. Meier-Kolthoff 1 †, Marina García-López 1, Supratim Mukherjee 2, Marcel Huntemann 2, Natalia N. Ivanova 2, Tanja Woyke 2, Nikos C. Kyrpides 2, 3, Hans-Peter Klenk 4 and Markus Göker 1* 1 Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany, 2 Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA, USA, 3 Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia, 4 School of Biology, Newcastle University, Newcastle upon Tyne, UK The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for Edited by: assessing their taxonomy based on the principles of phylogenetic classification and Martin G. Klotz, Queens College, City University of trees inferred from genome-scale data. No significant conflict between 16S rRNA gene New York, USA and whole-genome phylogenetic analysis is found, whereas many but not all of the Reviewed by: involved taxa are supported as monophyletic groups, particularly in the genome-scale Eddie Cytryn, trees. Phenotypic and phylogenomic features support the separation of Balneolaceae Agricultural Research Organization, Israel as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new John Phillip Bowman, class Saprospiria from Chitinophagia. -
Shifts in the Structure of Rhizosphere Bacterial Communities of Avocado After Fusarium Dieback
Rhizosphere 18 (2021) 100333 Contents lists available at ScienceDirect Rhizosphere journal homepage: www.elsevier.com/locate/rhisph Shifts in the structure of rhizosphere bacterial communities of avocado after Fusarium dieback Alix A. Bejarano-Bolívar a, Araceli Lamelas a,b, Eneas Aguirre von Wobeser c, Diana Sanchez-Rangel´ d, Alfonso M´endez-Bravo e, Akif Eskalen f, Fr´ed´erique Reverchon g,* a Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., Xalapa, Veracruz, M´exico b Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de Val`encia, Val`encia, Espana~ c CONACYT - Centro de Investigacion´ en Alimentacion´ y Desarrollo A.C., Pachuca, Hidalgo, Mexico d CONACYT - Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., Xalapa, Veracruz, Mexico e CONACYT - Escuela Nacional de Estudios Superiores Unidad Morelia, Laboratorio Nacional de Analisis´ y Síntesis Ecologica,´ Universidad Nacional Autonoma´ de M´exico, Morelia, Michoacan,´ Mexico f Department of Plant Pathology, Universidad de California – Davis, Davis, CA, United States g Red de Estudios Moleculares Avanzados, Centro Regional Del Bajío, Instituto de Ecología, A.C., Patzcuaro,´ Michoacan,´ Mexico ARTICLE INFO ABSTRACT Keywords: The rhizosphere microbiome is critical for plant growth and protection against plant pathogens. However, Biological control rhizosphere microbial communities are likely to be restructured upon plant infection by fungal pathogens. Our Fusarium kuroshium objective was to determine the shifts in rhizosphere bacterial communities of avocado trees (Persea americana Microbial diversity Mill.) after Fusarium dieback (FD), a disease triggered by the symbiotic fungi of invasive ambrosia beetles Persea americana (Euwallacea kuroshio and Euwallacea sp. nr. fornicatus), using 16S rDNA gene amplicon sequencing and a culture- Rhizosphere core microbiome dependent approach. -
Systematic Bacteriology Second Edition
BERGEY’S MANUAL® OF Systematic Bacteriology Second Edition Volume Four The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes BERGEY’S MANUAL® OF Systematic Bacteriology Second Edition Volume Four The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes Noel R. Krieg, James T. Staley, Daniel R. Brown, Brian P. Hedlund, Bruce J. Paster, Naomi L. Ward, Wolfgang Ludwig and William B. Whitman EDITORS, VOLUME FOUR William B. Whitman DIRECTOR OF THE EDITORIAL OFFICE Aidan C. Parte MANAGING EDITOR EDITORIAL BOARD Michael Goodfellow, Chairman, Peter Kämpfer, Vice Chairman, Jongsik Chun, Paul De Vos, Fred A. Rainey and William B. Whitman WITH CONTRIBUTIONS FROM 129 COLLEAGUES William B. Whitman Bergey’s Manual Trust Department of Microbiology 527 Biological Sciences Building University of Georgia Athens, GA 30602-2605 USA ISBN: 978-0-387-95042-6 e-ISBN: 978-0-387-68572-4 DOI: 10.1007/978-0-387-68572-4 Springer New York Dordrecht Heidelberg London Library of Congress Control Number: 2010936277 © 2010, 1984–1989 Bergey’s Manual Trust Bergey’s Manual is a registered trademark of Bergey’s Manual Trust. All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. -
Heterotrophic Bacteria from Brackish Water of the Southern Baltic Sea
Heterotrophic bacteria OCEANOLOGIA, 48 (4), 2006. pp. 525–543. from brackish water of C 2006, by Institute of the southern Baltic Oceanology PAS. Sea: biochemical and KEYWORDS molecular identification Heterotrophic bacteria and characterisation* Polyphasic study Brackish water Agnieszka Cabaj1,∗ Katarzyna Palińska2 Alicja Kosakowska1 Julianna Kurlenda3 1 Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, PL–81–712 Sopot, Poland; e-mail: [email protected] ∗corresponding author 2 Institute for Chemistry and Biology of the Marine Environment, AG Geomicrobiology, Carl von Ossietzky University, PO Box 2503, D–26111 Oldenburg, Germany 3 Department of Clinical Bacteriology, Provincial Technical Hospital, Nowe Ogrody 1–6, PL–80–803 Gdańsk, Poland Received 28 June 2006, revised 8 November 2006, accepted 13 November 2006. Abstract Six bacterial strains isolated from the surface water of the southern Baltic Sea were described on the basis of their morphological, physiological and biochemical features, and were classified on the basis of 16S rDNA sequence analysis. Comparative analyses of the 16S rDNA sequences of five of the six bacterial strains * The study was partially supported by the Centre of Excellence for Shelf Seas Sciences, Institute of Oceanology PAS, FP5 programme, contract No EFK3-CT 2002-80004, as a part of the statutory activities of the Institute of Oceanology PAS (grant No II.3) and by the Polish State Committee for Scientific Research (grant No 2 PO4E 026 30, 2006–2008). The complete text of the paper is available at http://www.iopan.gda.pl/oceanologia/ 526 A. Cabaj, K. Palińska, A. Kosakowska, J. Kurlenda examined displayed a ≥ 98% similarity to the sequences available in the NCBI GenBank.