Marine Ecology Progress Series 389:45
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Muricauda Ruestringensis Type Strain (B1T)
Standards in Genomic Sciences (2012) 6:185-193 DOI:10.4056/sigs.2786069 Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda T ruestringensis type strain (B1 ) Marcel Huntemann1, Hazuki Teshima1,2, Alla Lapidus1, Matt Nolan1, Susan Lucas1, Nancy Hammon1, Shweta Deshpande1, Jan-Fang Cheng1, Roxanne Tapia1,2, Lynne A. Goodwin1,2, Sam Pitluck1, Konstantinos Liolios1, Ioanna Pagani1, Natalia Ivanova1, Konstantinos Mavromatis1, Natalia Mikhailova1, Amrita Pati1, Amy Chen3, Krishna Palaniappan3, Miriam Land1,4 Loren Hauser1,4, Chongle Pan1,4, Evelyne-Marie Brambilla5, Manfred Rohde6, Stefan Spring5, Markus Göker5, John C. Detter1,2, James Bristow1, Jonathan A. Eisen1,7, Victor Markowitz3, Philip Hugenholtz1,8, Nikos C. Kyrpides1, Hans-Peter Klenk5*, and Tanja Woyke1 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 Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany 6 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 7 University of California Davis Genome Center, Davis, California, USA 8 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia *Corresponding author: Hans-Peter Klenk ([email protected]) Keywords: facultatively anaerobic, non-motile, Gram-negative, mesophilic, marine, chemo- heterotrophic, Flavobacteriaceae, GEBA Muricauda ruestringensis Bruns et al. 2001 is the type species of the genus Muricauda, which belongs to the family Flavobacteriaceae in the phylum Bacteroidetes. The species is of inter- est because of its isolated position in the genomically unexplored genus Muricauda, which is located in a part of the tree of life containing not many organisms with sequenced genomes. -
Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341 -
Bacterial Oxygen Production in the Dark
HYPOTHESIS AND THEORY ARTICLE published: 07 August 2012 doi: 10.3389/fmicb.2012.00273 Bacterial oxygen production in the dark Katharina F. Ettwig*, Daan R. Speth, Joachim Reimann, Ming L. Wu, Mike S. M. Jetten and JanT. Keltjens Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands Edited by: Nitric oxide (NO) and nitrous oxide (N2O) are among nature’s most powerful electron Boran Kartal, Radboud University, acceptors. In recent years it became clear that microorganisms can take advantage of Netherlands the oxidizing power of these compounds to degrade aliphatic and aromatic hydrocar- Reviewed by: bons. For two unrelated bacterial species, the “NC10” phylum bacterium “Candidatus Natalia Ivanova, Lawrence Berkeley National Laboratory, USA Methylomirabilis oxyfera” and the γ-proteobacterial strain HdN1 it has been suggested Carl James Yeoman, Montana State that under anoxic conditions with nitrate and/or nitrite, monooxygenases are used for University, USA methane and hexadecane oxidation, respectively. No degradation was observed with *Correspondence: nitrous oxide only. Similarly, “aerobic” pathways for hydrocarbon degradation are employed − Katharina F.Ettwig, Department of by (per)chlorate-reducing bacteria, which are known to produce oxygen from chlorite (ClO ). Microbiology, Institute for Water and 2 Wetland Research, Radboud In the anaerobic methanotroph M. oxyfera, which lacks identifiable enzymes for nitrogen University Nijmegen, formation, substrate activation in the presence of nitrite was directly associated with both Heyendaalseweg 135, 6525 AJ oxygen and nitrogen formation. These findings strongly argue for the role of NO, or an Nijmegen, Netherlands. e-mail: [email protected] oxygen species derived from it, in the activation reaction of methane. -
17-S. Prabhu Rekha.Indd
Polish Journal of Microbiology 2014, Vol. 63, No 1, 115–119 SHORT COMMUNICATION Zeaxanthin Biosynthesis by Members of the Genus Muricauda SUDHARSHAN PRABHU, P.D. REKHA and A.B. ARUN* Yenepoya Research Centre, Yenepoya University, Deralakatte, Mangalore, Karnataka State, India Submitted 3 March 2013, revised 3 May 2013, accepted 16 November 2013 Abstract Zeaxanthin, a C40 xanthophyll carotenoid, has potential biological applications in nutrition and human health. In this study we characterized carotenoid composition in 5 taxonomically related marine bacterial isolates from the genus Muricauda. The pigment was characterized using high performance liquid chromatography (HPLC) and mass spectrometry, which confirmed the presence of all-trans-zeaxanthin. Muricauda strains produced zeaxanthin as a predominant carotenoid. M. flavescens JCM 11812T produced highest yield (4.4 ± 0.2 mg L–1) when cultured on marine broth at 32°C for 72 h. This is the first report on the presence of zeaxanthin among the majority of species from the genus Muricauda. K e y w o r d s: Flavobacteriaceae, Muricauda, marine bacteria, zeaxanthin Zeaxanthin is a potential biomolecule having anti- duce characteristic orange-yellow pigmented colonies oxidant, anticancer properties and is known to prevent (Lee et al., 2012; Arun et al., 2009; Hwang et al., 2009; age related macular degeneration (Krinsky et al., 2003). Lee et al., 2012). M. lutaonensis CC-HSB-11T isolated Apart from plant sources, microbes have been found as from a coastal hot-spring was first reported to produce an important source of carotenoids particularly zeaxan- high amounts of zeaxanthin (Hameed et al., 2011). thin (Hameed et al., 2011). -
Flavobacterium Gliding Motility: from Protein Secretion to Cell Surface Adhesin Movements
University of Wisconsin Milwaukee UWM Digital Commons Theses and Dissertations August 2019 Flavobacterium Gliding Motility: From Protein Secretion to Cell Surface Adhesin Movements Joseph Johnston University of Wisconsin-Milwaukee Follow this and additional works at: https://dc.uwm.edu/etd Part of the Biology Commons, Microbiology Commons, and the Molecular Biology Commons Recommended Citation Johnston, Joseph, "Flavobacterium Gliding Motility: From Protein Secretion to Cell Surface Adhesin Movements" (2019). Theses and Dissertations. 2202. https://dc.uwm.edu/etd/2202 This Dissertation is brought to you for free and open access by UWM Digital Commons. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of UWM Digital Commons. For more information, please contact [email protected]. FLAVOBACTERIUM GLIDING MOTILITY: FROM PROTEIN SECRETION TO CELL SURFACE ADHESIN MOVEMENTS by Joseph J. Johnston A Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Biological Sciences at The University of Wisconsin-Milwaukee August 2019 ABSTRACT FLAVOBACTERIUM GLIDING MOTILITY: FROM PROTEIN SECRETION TO CELL SURFACE ADHESIN MOVEMENTS by Joseph J. Johnston The University of Wisconsin-Milwaukee, 2019 Under the Supervision of Dr. Mark J. McBride Flavobacterium johnsoniae exhibits rapid gliding motility over surfaces. At least twenty genes are involved in this process. Seven of these, gldK, gldL, gldM, gldN, sprA, sprE, and sprT encode proteins of the type IX protein secretion system (T9SS). The T9SS is required for surface localization of the motility adhesins SprB and RemA, and for secretion of the soluble chitinase ChiA. This thesis demonstrates that the gliding motility proteins GldA, GldB, GldD, GldF, GldH, GldI and GldJ are also essential for secretion. -
The Role of Territorial Grazers in Coral Reef Trophic Dynamics from Microbes to Apex Predators
ResearchOnline@JCU This file is part of the following reference: Casey, Jordan Marie (2015) The role of territorial grazers in coral reef trophic dynamics from microbes to apex predators. PhD thesis, James Cook University. Access to this file is available from: http://researchonline.jcu.edu.au/41148/ The author has certified to JCU that they have made a reasonable effort to gain permission and acknowledge the owner of any third party copyright material included in this document. If you believe that this is not the case, please contact [email protected] and quote http://researchonline.jcu.edu.au/41148/ The role of territorial grazers in coral reef trophic dynamics from microbes to apex predators Thesis submitted by Jordan Marie Casey April 2015 For the degree of Doctor of Philosophy ARC Centre of Excellence for Coral Reef Studies College of Marine and Environmental Sciences James Cook University ! Acknowledgements First and foremost, I thank my supervisory team, Sean Connolly, J. Howard Choat, and Tracy Ainsworth, for their continuous intellectual support throughout my time at James Cook University. It was invaluable to draw upon the collective insights and constructive criticisms of an ecological modeller, an ichthyologist, and a microbiologist. I am grateful to each of my supervisors for their unique contributions to this PhD thesis. I owe many thanks to all of the individuals that assisted me in the field: Kristen Anderson, Andrew Baird, Shane Blowes, Simon Brandl, Ashley Frisch, Chris Heckathorn, Mia Hoogenboom, Oona Lönnstedt, Chris Mirbach, Chiara Pisapia, Justin Rizzari, and Melanie Trapon. I also thank the directors and staff of Lizard Island Research Station and the Research Vessel James Kirby for efficiently facilitating my research trips. -
Temperature Responses of Heterotrophic Bacteria in Co-Culture with a Red Sea Synechococcus Strain
Temperature Responses of Heterotrophic Bacteria in Co-culture With a Red Sea Synechococcus Strain Item Type Article Authors Labban, Abbrar; Palacio, Antonio S.; García, Francisca C.; Hadaidi, Ghaida A.; Ansari, Mohd Ikram; López-Urrutia, Ángel; Alonso-Sáez, Laura; Hong, Pei-Ying; Moran, Xose Anxelu G. Citation Labban, A., Palacio, A. S., García, F. C., Hadaidi, G., Ansari, M. I., López-Urrutia, Á., … Morán, X. A. G. (2021). Temperature Responses of Heterotrophic Bacteria in Co-culture With a Red Sea Synechococcus Strain. Frontiers in Microbiology, 12. doi:10.3389/fmicb.2021.612732 Eprint version Publisher's Version/PDF DOI 10.3389/fmicb.2021.612732 Publisher Frontiers Media SA Journal Frontiers in Microbiology Rights This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Download date 01/10/2021 21:10:52 Item License https://creativecommons.org/licenses/by/4.0/ Link to Item http://hdl.handle.net/10754/669159 fmicb-12-612732 May 4, 2021 Time: 23:46 # 1 ORIGINAL RESEARCH published: 10 May 2021 doi: 10.3389/fmicb.2021.612732 Temperature Responses of Heterotrophic Bacteria in Co-culture With a Red Sea Synechococcus Strain Abbrar Labban1,2, Antonio S. Palacio3, Francisca C. García4, Ghaida Hadaidi1, Mohd I. Ansari1, Ángel López-Urrutia5, Laura Alonso-Sáez3, Pei-Ying Hong2 and Xosé Anxelu G. -
Characteristics of Genome Evolution in Obligate Insect Symbionts, Including The
Characteristics of genome evolution in obligate insect symbionts, including the description of a recently identified obligate extracellular symbiont. Thesis Presented in Partial Fulfillment of the Requirements for the Degree Master of Science in the Graduate School of The Ohio State University By Laura Jean Kenyon, B.S. Graduate Program in Evolution, Ecology, and Organismal Biology The Ohio State University 2015 Thesis Committee: Norman Johnson Andy Michel Kelly Wrighton Zakee L. Sabree, Advisor Copyright by Laura Jean Kenyon 2015 Abstract Animal-bacterial symbioses have shaped the evolution of all eukaryotic organisms. All symbioses have in common a long-term association and therefore provide valuable insight into the evolution and diversification of both partners. Insect-bacterial mutualisms represent the most extreme natural partnerships known, showing evidence of coevolution and obligate interdependence between the partners. Early investigations of plant sap-feeding insects, in particular, revealed tissues of unknown function inhabited by bacteria and insects void of their symbionts revealed reduced host fitness compared to symbiotic insects. Due to the obligate nature of the relationships, endosymbiotic bacteria are uncultivable, but complete genome sequencing suggests bacterial mutualists metabolic capabilities and likely contribution to the mutualisms, typically nutrient provisioning. A well-supported pattern of bacterial genome evolution for obligate mutualists is extreme genome reduction, likely due to relaxed selection upon genes that are not required in the stable environment of the host, leading to an accumulation of deleterious mutations in these genes, and eventually to their complete loss, leaving only those genes that are required for the relatively-stable life-style and for maintenance of the symbiosis. -
Salinity and Time Can Alter Epibacterial Communities of an Invasive Seaweed
fmicb-10-02870 January 6, 2020 Time: 15:52 # 1 ORIGINAL RESEARCH published: 15 January 2020 doi: 10.3389/fmicb.2019.02870 Salinity and Time Can Alter Epibacterial Communities of an Invasive Seaweed Mahasweta Saha1,2,3*, Robert M. W. Ferguson2, Shawn Dove4,5, Sven Künzel6, Rafael Meichssner7,8, Sven C. Neulinger9, Finn Ole Petersen10 and Florian Weinberger1 1 Benthic Ecology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany, 2 The School of Life Sciences, University of Essex, Colchester, United Kingdom, 3 Marine Ecology and Biodiversity, Plymouth Marine Laboratory, Plymouth, United Kingdom, 4 Centre for Biodiversity and Environment Research, University College London, London, United Kingdom, 5 Institute of Zoology, Zoological Society of London, London, United Kingdom, 6 Max Planck Institute for Evolutionary Biology, Plön, Germany, 7 Department of Biology, Botanical Institute, Christian-Albrechts-University, Kiel, Germany, 8 Coastal Research & Management, Kiel, Germany, 9 omics2view.consulting GbR, Kiel, Germany, 10 Department of Biology, Institute for General Microbiology, Christian-Albrechts-University, Kiel, Germany The establishment of epibacterial communities is fundamental to seaweed health and Edited by: fitness, in modulating ecological interactions and may also facilitate adaptation to Olga Lage, University of Porto, Portugal new environments. Abiotic factors like salinity can determine bacterial abundance, Reviewed by: growth and community composition. However, influence of salinity as a driver of Hanzhi Lin, epibacterial community composition (until species level) has not been investigated for University of Maryland Center for Environmental Science (UMCES), seaweeds and especially under long time scales. We also do not know how abiotic United States stressors may influence the ‘core’ bacterial species of seaweeds. -
Microbiome Species Average Counts (Normalized) Veillonella Parvula
Table S2. Bacteria and virus detected with RN OLP Microbiome Species Average Counts (normalized) Veillonella parvula 3435527.229 Rothia mucilaginosa 1810713.571 Haemophilus parainfluenzae 844236.8342 Fusobacterium nucleatum 825289.7789 Neisseria meningitidis 626843.5897 Achromobacter xylosoxidans 415495.0883 Atopobium parvulum 205918.2297 Campylobacter concisus 159293.9124 Leptotrichia buccalis 123966.9359 Megasphaera elsdenii 87368.48455 Prevotella melaninogenica 82285.23784 Selenomonas sputigena 77508.6755 Haemophilus influenzae 76896.39289 Porphyromonas gingivalis 75766.09645 Rothia dentocariosa 64620.85367 Candidatus Saccharimonas aalborgensis 61728.68147 Aggregatibacter aphrophilus 54899.61834 Prevotella intermedia 37434.48581 Tannerella forsythia 36640.47285 Streptococcus parasanguinis 34865.49274 Selenomonas ruminantium 32825.83925 Streptococcus pneumoniae 23422.9219 Pseudogulbenkiania sp. NH8B 23371.8297 Neisseria lactamica 21815.23198 Streptococcus constellatus 20678.39506 Streptococcus pyogenes 20154.71044 Dichelobacter nodosus 19653.086 Prevotella sp. oral taxon 299 19244.10773 Capnocytophaga ochracea 18866.69759 [Eubacterium] eligens 17926.74096 Streptococcus mitis 17758.73348 Campylobacter curvus 17565.59393 Taylorella equigenitalis 15652.75392 Candidatus Saccharibacteria bacterium RAAC3_TM7_1 15478.8893 Streptococcus oligofermentans 15445.0097 Ruminiclostridium thermocellum 15128.26924 Kocuria rhizophila 14534.55059 [Clostridium] saccharolyticum 13834.76647 Mobiluncus curtisii 12226.83711 Porphyromonas asaccharolytica 11934.89197 -
Muricauda Chongwuensis Sp. Nov., Isolated from Coastal Seawater of China
Muricauda Chongwuensis Sp. Nov., Isolated From Coastal Seawater of China Ming-Xia Chen ( [email protected] ) Huaqiao University https://orcid.org/0000-0001-9420-9339 Xiao-Yu He Huaqiao University He-Yang Li Third Institute of Oceanography, Ministry of Natural Resources Research Article Keywords: Muricauda chongwuensis, nonobligate bacterial predator, polyphasic taxonomy Posted Date: June 22nd, 2021 DOI: https://doi.org/10.21203/rs.3.rs-631001/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/17 Abstract In the course of screening for bacterial predator, a Gram-negative, non-agellated, gliding, long rod- shaped and yellow-pigmented bacterium, designated strain HICWT, was isolated from coastal seawater of China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HICWT represented a member of the genus Muricauda and showed the highest sequence similarity to M. aquimarina JCM11811T (98.8%) and M. ruestringensis DSM13258T (98.1%). NaCl was required for growth. Optimum growth occurred at 25–30 oC, 2.0–3.0% (w/v) NaCl with pH 7.0. Strain HICWT showed some similar characteristics to the nonobligate bactertal predators, the cells can attach the prey cells. Strain HICWT contained MK-6 as the predominant respiratory quinone and had iso-C15:0, iso-C15:1 G and iso-C17:0 3-OH as the major cellular fatty acids. The polar lipids contained phosphatidylethanolamine (PE), three unknown phospholipids (PL1–PL3), one unknown aminolipids (AL) and three unknown polar lipids (L1– L3). The genome size of strain HICWT was approximately 3.8 Mbp, with a G+C content of 41.4%. -
Molecular Biological and Physiological Investigations of Heterotrophic Bacteria Associated with Marine Filamentous Cyanobacteria
Molecular Biological and Physiological Investigations of Heterotrophic Bacteria Associated with Marine Filamentous Cyanobacteria Dissertation zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) dem Fachbereich Biologie / Chemie der Universität Bremen vorgelegt von Annina E. Hube Stade November 2009 1. Gutachter: Prof. Dr. Ulrich Fischer 2. Gutachter: PD Dr. Jens Harder Tag des Promotionskolloquiums: 16. Dezember 2009 2 Table of contents Table of contents Table of contents ........................................................................................................................ 3 List of abbreviations................................................................................................................... 4 Abstract ...................................................................................................................................... 5 Zusammenfassung...................................................................................................................... 7 1 Introduction ........................................................................................................................ 9 1.1 The Baltic Sea ............................................................................................................. 9 1.2 Bloom forming and benthic Baltic Sea cyanobacteria.............................................. 10 1.3 Cyanobacteria and heterotrophic bacteria................................................................. 12 1.4 Aerobic anoxygenic phototrophic