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Article-Associated Bac- Teria and Colony Isolation in Soft Agar Medium for Bacteria Unable to Grow at the Air-Water Interface
Biogeosciences, 8, 1955–1970, 2011 www.biogeosciences.net/8/1955/2011/ Biogeosciences doi:10.5194/bg-8-1955-2011 © Author(s) 2011. CC Attribution 3.0 License. Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea C. Jeanthon1,2, D. Boeuf1,2, O. Dahan1,2, F. Le Gall1,2, L. Garczarek1,2, E. M. Bendif1,2, and A.-C. Lehours3 1Observatoire Oceanologique´ de Roscoff, UMR7144, INSU-CNRS – Groupe Plancton Oceanique,´ 29680 Roscoff, France 2UPMC Univ Paris 06, UMR7144, Adaptation et Diversite´ en Milieu Marin, Station Biologique de Roscoff, 29680 Roscoff, France 3CNRS, UMR6023, Microorganismes: Genome´ et Environnement, Universite´ Blaise Pascal, 63177 Aubiere` Cedex, France Received: 21 April 2011 – Published in Biogeosciences Discuss.: 5 May 2011 Revised: 7 July 2011 – Accepted: 8 July 2011 – Published: 20 July 2011 Abstract. Aerobic anoxygenic phototrophic (AAP) bac- detected in the eastern basin, reflecting the highest diver- teria play significant roles in the bacterioplankton produc- sity of pufM transcripts observed in this ultra-oligotrophic tivity and biogeochemical cycles of the surface ocean. In region. To our knowledge, this is the first study to document this study, we applied both cultivation and mRNA-based extensively the diversity of AAP isolates and to unveil the ac- molecular methods to explore the diversity of AAP bacte- tive AAP community in an oligotrophic marine environment. ria along an oligotrophic gradient in the Mediterranean Sea By pointing out the discrepancies between culture-based and in early summer 2008. Colony-forming units obtained on molecular methods, this study highlights the existing gaps in three different agar media were screened for the production the understanding of the AAP bacteria ecology, especially in of bacteriochlorophyll-a (BChl-a), the light-harvesting pig- the Mediterranean Sea and likely globally. -
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. -
DMSP) Demethylation Enzyme Dmda in Marine Bacteria
Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria Laura Hernández1, Alberto Vicens2, Luis E. Eguiarte3, Valeria Souza3, Valerie De Anda4 and José M. González1 1 Departamento de Microbiología, Universidad de La Laguna, La Laguna, Spain 2 Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, Vigo, Spain 3 Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico D.F., Mexico 4 Department of Marine Sciences, Marine Science Institute, University of Texas Austin, Port Aransas, TX, USA ABSTRACT Dimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton and bacteria, is primarily degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSP- producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: (1) a recent common ancestor of DmdA and GcvT, (2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and (3) an enzymatic adaptation for utilizing DMSP in marine bacteria prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and Submitted 6 April 2020 functional divergence driven by positive selection before a coevolution between Accepted 12 August 2020 Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA Published 10 September 2020 by horizontal gene transfer prior to an environment with higher DMSP. -
Appendix 1. Validly Published Names, Conserved and Rejected Names, And
Appendix 1. Validly published names, conserved and rejected names, and taxonomic opinions cited in the International Journal of Systematic and Evolutionary Microbiology since publication of Volume 2 of the Second Edition of the Systematics* JEAN P. EUZÉBY New phyla Alteromonadales Bowman and McMeekin 2005, 2235VP – Valid publication: Validation List no. 106 – Effective publication: Names above the rank of class are not covered by the Rules of Bowman and McMeekin (2005) the Bacteriological Code (1990 Revision), and the names of phyla are not to be regarded as having been validly published. These Anaerolineales Yamada et al. 2006, 1338VP names are listed for completeness. Bdellovibrionales Garrity et al. 2006, 1VP – Valid publication: Lentisphaerae Cho et al. 2004 – Valid publication: Validation List Validation List no. 107 – Effective publication: Garrity et al. no. 98 – Effective publication: J.C. Cho et al. (2004) (2005xxxvi) Proteobacteria Garrity et al. 2005 – Valid publication: Validation Burkholderiales Garrity et al. 2006, 1VP – Valid publication: Vali- List no. 106 – Effective publication: Garrity et al. (2005i) dation List no. 107 – Effective publication: Garrity et al. (2005xxiii) New classes Caldilineales Yamada et al. 2006, 1339VP VP Alphaproteobacteria Garrity et al. 2006, 1 – Valid publication: Campylobacterales Garrity et al. 2006, 1VP – Valid publication: Validation List no. 107 – Effective publication: Garrity et al. Validation List no. 107 – Effective publication: Garrity et al. (2005xv) (2005xxxixi) VP Anaerolineae Yamada et al. 2006, 1336 Cardiobacteriales Garrity et al. 2005, 2235VP – Valid publica- Betaproteobacteria Garrity et al. 2006, 1VP – Valid publication: tion: Validation List no. 106 – Effective publication: Garrity Validation List no. 107 – Effective publication: Garrity et al. -
IJSEM-19May2017 Accept (002)
Monaibacterium marinum, gen. nov, sp. nov, a new member of the ANGOR UNIVERSITY Alphaproteobacteria isolated from seawater of Menai Straits, Wales, UK Chernikova, Tatyana; Dallimore, James; Lunsdorf, Heinrich; Heipieper, Hermann J.; Golyshin, Peter International Journal of Systematic Evolutionary Microbiology DOI: 10.1099/ijsem.0.002111 PRIFYSGOL BANGOR / B Published: 01/09/2017 Peer reviewed version Cyswllt i'r cyhoeddiad / Link to publication Dyfyniad o'r fersiwn a gyhoeddwyd / Citation for published version (APA): Chernikova, T., Dallimore, J., Lunsdorf, H., Heipieper, H. J., & Golyshin, P. (2017). Monaibacterium marinum, gen. nov, sp. nov, a new member of the Alphaproteobacteria isolated from seawater of Menai Straits, Wales, UK. International Journal of Systematic Evolutionary Microbiology, 67, 3310-3317. https://doi.org/10.1099/ijsem.0.002111 Hawliau Cyffredinol / General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. 25. Sep. 2021 1 Monaibacterium marinum, gen. nov, sp. -
Roseobacter Clade Bacteria Are Abundant in Coastal Sediments and Encode a Novel Combination of Sulfur Oxidation Genes
The ISME Journal (2012) 6, 2178–2187 & 2012 International Society for Microbial Ecology All rights reserved 1751-7362/12 www.nature.com/ismej ORIGINAL ARTICLE Roseobacter clade bacteria are abundant in coastal sediments and encode a novel combination of sulfur oxidation genes Sabine Lenk1, Cristina Moraru1, Sarah Hahnke2,4, Julia Arnds1, Michael Richter1, Michael Kube3,5, Richard Reinhardt3,6, Thorsten Brinkhoff2, Jens Harder1, Rudolf Amann1 and Marc Mumann1 1Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany; 2Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany and 3Max Planck Institute for Molecular Genetics, Berlin, Germany Roseobacter clade bacteria (RCB) are abundant in marine bacterioplankton worldwide and central to pelagic sulfur cycling. Very little is known about their abundance and function in marine sediments. We investigated the abundance, diversity and sulfur oxidation potential of RCB in surface sediments of two tidal flats. Here, RCB accounted for up to 9.6% of all cells and exceeded abundances commonly known for pelagic RCB by 1000-fold as revealed by fluorescence in situ hybridization (FISH). Phylogenetic analysis of 16S rRNA and sulfate thiohydrolase (SoxB) genes indicated diverse, possibly sulfur-oxidizing RCB related to sequences known from bacterioplankton and marine biofilms. To investigate the sulfur oxidation potential of RCB in sediments in more detail, we analyzed a metagenomic fragment from a RCB. This fragment encoded the reverse dissimilatory sulfite reductase (rDSR) pathway, which was not yet found in RCB, a novel type of sulfite dehydro- genase (SoeABC) and the Sox multi-enzyme complex including the SoxCD subunits. This was unexpected as soxCD and dsr genes were presumed to be mutually exclusive in sulfur-oxidizing prokaryotes. -
Metagenome-Assembled Genomes of Phytoplankton Communities Across
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.16.154583; this version posted June 17, 2020. 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. 1 Metagenome-assembled genomes of phytoplankton 2 communities across the Arctic Circle 3 4 A. Duncan1, K. Barry2, C. Daum2, E. Eloe-Fadrosh2, S. Roux2, , S. G. Tringe2, K. Schmidt3, K. U. 5 Valentin4, N. Varghese2, I. V. Grigoriev2, R. Leggett5, V. M ou lt on 1, T. Mock3* 6 7 1School of Computing Sciences, University of East Anglia, Norwich Research Park, NR47TJ, 8 Norwich, U.K. 9 2DOE-Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, U.S.A. 10 3School of Environmental Sciences, University of East Anglia, Norwich Research Park, NR47TJ, 11 Norwich, U.K. 12 4Alfred-Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570 13 Bremerhaven, Germany 14 5Earlham Institute, Norwich Research Park, Norwich, NR4 7UG, U.K. 15 16 * Correspondence to: [email protected] 17 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.16.154583; this version posted June 17, 2020. 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. 18 Abstract 19 Phytoplankton communities significantly contribute to global biogeochemical cycles of elements 20 and underpin marine food webs. -
The Onset of Microbial Associations in the Coral Pocillopora Meandrina
The ISME Journal (2009) 3, 685–699 & 2009 International Society for Microbial Ecology All rights reserved 1751-7362/09 $32.00 www.nature.com/ismej ORIGINAL ARTICLE The onset of microbial associations in the coral Pocillopora meandrina Amy Apprill1,2, Heather Q Marlow3, Mark Q Martindale3 and Michael S Rappe´1 1Hawaii Institute of Marine Biology, SOEST, University of Hawaii, Kaneohe, HI, USA; 2Department of Oceanography, SOEST, University of Hawaii, Honolulu, HI, USA and 3Kewalo Marine Laboratory, Pacific Biomedical Research Center, University of Hawaii, Honolulu, HI, USA Associations between healthy adult reef-building corals and bacteria and archaea have been observed in many coral species, but the initiation of their association is not understood. We investigated the onset of association between microorganisms and Pocillopora meandrina, a coral that vertically seeds its eggs with symbiotic dinoflagellates before spawning. We compared the bacterial communities associated with prespawned oocyte bundles, spawned eggs, and week old planulae using multivariate analyses of terminal restriction fragment length polymorphisms of SSU rRNA genes, which revealed that the composition of bacteria differed between these life stages. Additionally, planulae raised in ambient seawater and seawater filtered to reduce the microbial cell density harbored dissimilar bacterial communities, though SSU rRNA gene clone libraries showed that planulae raised in both treatments were primarily associated with different members of the Roseobacter clade of Alphaproteobacteria. Fluorescent in situ hybridization with an oligonucleotide probe suite targeting all bacteria and one oligonucleotide probe targeting members of the Roseobacter clade was used to localize the bacterial cells. Only planulae greater than 3 days old were observed to contain internalized bacterial cells, and members of the Roseobacter clade were detected in high abundance within planula tissues exposed to the ambient seawater treatment. -
Biofilm Plasmids with a Rhamnose Operon Are Widely Distributed Determinants of the ‘Swim-Or-Stick’ Lifestyle in Roseobacters
The ISME Journal (2016) 10, 2498–2513 © 2016 International Society for Microbial Ecology All rights reserved 1751-7362/16 OPEN www.nature.com/ismej ORIGINAL ARTICLE Biofilm plasmids with a rhamnose operon are widely distributed determinants of the ‘swim-or-stick’ lifestyle in roseobacters Victoria Michael1, Oliver Frank1, Pascal Bartling, Carmen Scheuner, Markus Göker, Henner Brinkmann and Jörn Petersen Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany Alphaproteobacteria of the metabolically versatile Roseobacter group (Rhodobacteraceae) are abundant in marine ecosystems and represent dominant primary colonizers of submerged surfaces. Motility and attachment are the prerequisite for the characteristic ‘swim-or-stick’ lifestyle of many representatives such as Phaeobacter inhibens DSM 17395. It has recently been shown that plasmid curing of its 65-kb RepA-I-type replicon with 420 genes for exopolysaccharide biosynthesis including a rhamnose operon results in nearly complete loss of motility and biofilm formation. The current study is based on the assumption that homologous biofilm plasmids are widely distributed. We analyzed 33 roseobacters that represent the phylogenetic diversity of this lineage and documented attachment as well as swimming motility for 60% of the strains. All strong biofilm formers were also motile, which is in agreement with the proposed mechanism of surface attachment. We established transposon mutants for the four genes of the rhamnose operon from P. inhibens and proved its crucial role in biofilm formation. In the Roseobacter group, two-thirds of the predicted biofilm plasmids represent the RepA-I type and their physiological role was experimentally validated via plasmid curing for four additional strains. -
Understanding Microbial Community Dynamics to Improve Optimal Microbiome Selection Robyn J
Wright et al. Microbiome (2019) 7:85 https://doi.org/10.1186/s40168-019-0702-x RESEARCH Open Access Understanding microbial community dynamics to improve optimal microbiome selection Robyn J. Wright1*, Matthew I. Gibson2,3 and Joseph A. Christie-Oleza1* Abstract Background: Artificial selection of microbial communities that perform better at a desired process has seduced scientists for over a decade, but the method has not been systematically optimised nor the mechanisms behind its success, or failure, determined. Microbial communities are highly dynamic and, hence, go through distinct and rapid stages of community succession, but the consequent effect this may have on artificially selected communities is unknown. Results: Using chitin as a case study, we successfully selected for microbial communities with enhanced chitinase activities but found that continuous optimisation of incubation times between selective transfers was of utmost importance. The analysis of the community composition over the entire selection process revealed fundamental aspects in microbial ecology: when incubation times between transfers were optimal, the system was dominated by Gammaproteobacteria (i.e. main bearers of chitinase enzymes and drivers of chitin degradation), before being succeeded by cheating, cross-feeding and grazing organisms. Conclusions: The selection of microbiomes to enhance a desired process is widely used, though the success of artificially selecting microbial communities appears to require optimal incubation times in order to avoid the loss of the desired trait as a consequence of an inevitable community succession. A comprehensive understanding of microbial community dynamics will improve the success of future community selection studies. Keywords: Artificial microbiome selection, Microbial communities, Microbial ecology, Polymer degradation, Chitin degradation, Ecological succession, Microbial community dynamics Background [3]. -
Microdiversity and Temporal Dynamics of Marine Bacterial Dimethylsulfoniopropionate Genes
Environmental Microbiology (2019) 00(00), 00–00 doi:10.1111/1462-2920.14560 Microdiversity and temporal dynamics of marine bacterial dimethylsulfoniopropionate genes Brent Nowinski,1 Jessie Motard-Côté,2,3 co-occurred with haptophytes. This in situ study of Marine Landa,1† Christina M. Preston,4 the drivers of DMSP fate in a coastal ecosystem Christopher A. Scholin,4 James M. Birch,4 demonstrates for the first time correlations between Ronald P. Kiene2,3 and Mary Ann Moran 1* specific groups of bacterial DMSP degraders and 1Department of Marine Sciences, University of Georgia, phytoplankton taxa. Athens, GA, 30602, USA. 2 Department of Marine Sciences, University of South Introduction Alabama, Mobile, AL, 36688, USA. 3Dauphin Island Sea Lab, Dauphin Island, AL, The phytoplankton-produced organic sulfur compound 36528, USA. dimethylsulfoniopropionate (DMSP) plays a major role in 4Monterey Bay Aquarium Research Institute, Moss marine microbial food webs as a source of reduced sulfur Landing, CA, 95039, USA. and carbon (Kiene et al., 2000), and its degradation has impacts on ocean–atmosphere sulfur flux (Andreae, 1990). Marine bacteria can catabolize DMSP using the Summary demethylation pathway, wherein sulfur is routed to metha- Dimethylsulfoniopropionate (DMSP) is an abundant nethiol and potentially incorporated into biomass; or using organic sulfur metabolite produced by many phyto- the cleavage pathway, in which case sulfur is routed to the plankton species and degraded by bacteria via two dis- gas dimethylsulfide (DMS) with implications for atmo- tinct pathways with climate-relevant implications. We spheric aerosol dynamics and cloud formation (Charlson assessed the diversity and abundance of bacteria pos- et al., 1987; Quinn and Bates, 2011). -
Supplementary Information 1 2 Population Differentiation Of
1 Supplementary Information 2 3 Population Differentiation of Rhodobacteraceae Along Coral Compartments 4 Danli Luo, Xiaojun Wang, Xiaoyuan Feng, Mengdan Tian, Sishuo Wang, Sen-Lin Tang, Put 5 Ang Jr, Aixin Yan, Haiwei Luo 6 7 8 9 10 11 This PDF file includes: 12 Text 1. Supplementary methods 13 Text 2. Supplementary results 14 Figures S1 to S13 15 Supplementary references 16 17 Text 1. Supplementary methods 18 1.1 Coral sample collection and processing 19 1.2 Bacterial isolation 20 1.3 Genome sequencing, assembly and annotation 21 1.4 Ortholog prediction and phylogenomic tree construction 22 1.5 Analysis of population structure in core genomes 23 1.6 Inference of novel allelic replacement with external lineages in core genomes 24 1.7 Differentiation in the accessory genome and inference of evolutionary history 25 1.8 Identification of pseudogenes in the fla1 flagellar gene cluster 26 1.9 The physiological assays 27 1.10 Test of compartmentalization and dispersal limitation 28 1.11 Estimating the origin time for the Rhodobacteraceae and the Ruegeria populations 29 Text 2. Supplementary results 30 2.1 Population differentiation at the core genomes of the Ruegeria population 31 2.2 The Ruegeria population differentiation at the physiological level 32 2.3 Metabolic potential for utilizing other substrates by the mucus clade of the Ruegeria 33 population 34 2.4 Metabolic potential of the mucus clade in the Ruegeria population underlying 35 microbial interactions in the densely-populated mucus habitat 36 2.5 Adaptation of the skeleton clade in the Ruegeria population to the periodically 37 anoxic skeleton habitat 38 39 40 Text 1.