Understanding Microbial Community Dynamics to Improve Optimal Microbiome Selection Robyn J
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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. -
How to Cite Complete Issue More Information About This
Revista Internacional de Contaminación Ambiental ISSN: 0188-4999 [email protected] Universidad Nacional Autónoma de México México Luis-Villaseñor, Irasema E.; Zamudio-Armenta, Olga O.; Voltolina, Domenico; Rochin- Arenas, Jesús A.; Gómez-Gil, Bruno; Audelo-Naranjo, Juan M.; Flores-Higuera, Francisco A. BACTERIAL COMMUNITIES OF THE OYSTERS Crassostrea corteziensis AND C. sikamea OF COSPITA BAY, SINALOA, MEXICO Revista Internacional de Contaminación Ambiental, vol. 34, no. 2, 2018, May-July, pp. 203-213 Universidad Nacional Autónoma de México México DOI: https://doi.org/10.20937/RICA.2018.34.02.02 Available in: https://www.redalyc.org/articulo.oa?id=37056657002 How to cite Complete issue Scientific Information System Redalyc More information about this article Network of Scientific Journals from Latin America and the Caribbean, Spain and Journal's webpage in redalyc.org Portugal Project academic non-profit, developed under the open access initiative Rev. Int. Contam. Ambie. 34 (2) 203-213, 2018 DOI: 10.20937/RICA.2018.34.02.02 BACTERIAL COMMUNITIES OF THE OYSTERS Crassostrea corteziensis AND C. sikamea OF COSPITA BAY, SINALOA, MEXICO Irasema E. LUIS-VILLASEÑOR1*, Olga O. ZAMUDIO-ARMENTA1, Domenico VOLTOLINA2, Jesús A. ROCHIN-ARENAS1, Bruno GÓMEZ-GIL3, Juan M. AUDELO-NARANJO1 y Francisco A. FLORES-HIGUERA1 1 Universidad Autónoma de Sinaloa, Facultad de Ciencias del Mar, Paseo Claussen s/n, Mazatlán, Sinaloa, México 2 Centro de Investigaciones Biológicas del Noroeste, Apartado 1132, Mazatlán, Sinaloa, México 3 Centro de Investigación en Alimentación y Desarrollo, Unidad Mazatlán, Apartado 711, Mazatlán, Sinaloa, México * Author for correspondence; [email protected] (Received December 2016; accepted September 2017) Key words: bacteria, cultured oysters, wild oysters ABSTRACT This work aimed to quantify the bacterial loads and determine the taxonomic composi- tion of the microbial communities of oysters Crassostrea corteziensis and C. -
Large Scale Biogeography and Environmental Regulation of 2 Methanotrophic Bacteria Across Boreal Inland Waters
1 Large scale biogeography and environmental regulation of 2 methanotrophic bacteria across boreal inland waters 3 running title : Methanotrophs in boreal inland waters 4 Sophie Crevecoeura,†, Clara Ruiz-Gonzálezb, Yves T. Prairiea and Paul A. del Giorgioa 5 aGroupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), 6 Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, Québec, Canada 7 bDepartment of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, 8 Catalunya, Spain 9 Correspondence: Sophie Crevecoeur, Canada Centre for Inland Waters, Water Science and Technology - 10 Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, 11 Burlington, Ontario, Canada, e-mail: [email protected] 12 † Current address: Canada Centre for Inland Waters, Water Science and Technology - Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, Burlington, Ontario, Canada 1 13 Abstract 14 Aerobic methanotrophic bacteria (methanotrophs) use methane as a source of carbon and energy, thereby 15 mitigating net methane emissions from natural sources. Methanotrophs represent a widespread and 16 phylogenetically complex guild, yet the biogeography of this functional group and the factors that explain 17 the taxonomic structure of the methanotrophic assemblage are still poorly understood. Here we used high 18 throughput sequencing of the 16S rRNA gene of the bacterial community to study the methanotrophic 19 community composition and the environmental factors that influence their distribution and relative 20 abundance in a wide range of freshwater habitats, including lakes, streams and rivers across the boreal 21 landscape. Within one region, soil and soil water samples were additionally taken from the surrounding 22 watersheds in order to cover the full terrestrial-aquatic continuum. -
Metaproteomics Characterization of the Alphaproteobacteria
Avian Pathology ISSN: 0307-9457 (Print) 1465-3338 (Online) Journal homepage: https://www.tandfonline.com/loi/cavp20 Metaproteomics characterization of the alphaproteobacteria microbiome in different developmental and feeding stages of the poultry red mite Dermanyssus gallinae (De Geer, 1778) José Francisco Lima-Barbero, Sandra Díaz-Sanchez, Olivier Sparagano, Robert D. Finn, José de la Fuente & Margarita Villar To cite this article: José Francisco Lima-Barbero, Sandra Díaz-Sanchez, Olivier Sparagano, Robert D. Finn, José de la Fuente & Margarita Villar (2019) Metaproteomics characterization of the alphaproteobacteria microbiome in different developmental and feeding stages of the poultry red mite Dermanyssusgallinae (De Geer, 1778), Avian Pathology, 48:sup1, S52-S59, DOI: 10.1080/03079457.2019.1635679 To link to this article: https://doi.org/10.1080/03079457.2019.1635679 © 2019 The Author(s). Published by Informa View supplementary material UK Limited, trading as Taylor & Francis Group Accepted author version posted online: 03 Submit your article to this journal Jul 2019. Published online: 02 Aug 2019. Article views: 694 View related articles View Crossmark data Citing articles: 3 View citing articles Full Terms & Conditions of access and use can be found at https://www.tandfonline.com/action/journalInformation?journalCode=cavp20 AVIAN PATHOLOGY 2019, VOL. 48, NO. S1, S52–S59 https://doi.org/10.1080/03079457.2019.1635679 ORIGINAL ARTICLE Metaproteomics characterization of the alphaproteobacteria microbiome in different developmental and feeding stages of the poultry red mite Dermanyssus gallinae (De Geer, 1778) José Francisco Lima-Barbero a,b, Sandra Díaz-Sanchez a, Olivier Sparagano c, Robert D. Finn d, José de la Fuente a,e and Margarita Villar a aSaBio. -
Evolution of Methanotrophy in the Beijerinckiaceae&Mdash
The ISME Journal (2014) 8, 369–382 & 2014 International Society for Microbial Ecology All rights reserved 1751-7362/14 www.nature.com/ismej ORIGINAL ARTICLE The (d)evolution of methanotrophy in the Beijerinckiaceae—a comparative genomics analysis Ivica Tamas1, Angela V Smirnova1, Zhiguo He1,2 and Peter F Dunfield1 1Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada and 2Department of Bioengineering, School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, China The alphaproteobacterial family Beijerinckiaceae contains generalists that grow on a wide range of substrates, and specialists that grow only on methane and methanol. We investigated the evolution of this family by comparing the genomes of the generalist organotroph Beijerinckia indica, the facultative methanotroph Methylocella silvestris and the obligate methanotroph Methylocapsa acidiphila. Highly resolved phylogenetic construction based on universally conserved genes demonstrated that the Beijerinckiaceae forms a monophyletic cluster with the Methylocystaceae, the only other family of alphaproteobacterial methanotrophs. Phylogenetic analyses also demonstrated a vertical inheritance pattern of methanotrophy and methylotrophy genes within these families. Conversely, many lateral gene transfer (LGT) events were detected for genes encoding carbohydrate transport and metabolism, energy production and conversion, and transcriptional regulation in the genome of B. indica, suggesting that it has recently acquired these genes. A key difference between the generalist B. indica and its specialist methanotrophic relatives was an abundance of transporter elements, particularly periplasmic-binding proteins and major facilitator transporters. The most parsimonious scenario for the evolution of methanotrophy in the Alphaproteobacteria is that it occurred only once, when a methylotroph acquired methane monooxygenases (MMOs) via LGT. -
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. -
Genomic Evidence of the Illumination Response Mechanism and Evolutionary History of Magnetotactic Bacteria Within the Rhodospiri
Wang et al. BMC Genomics (2019) 20:407 https://doi.org/10.1186/s12864-019-5751-9 RESEARCH ARTICLE Open Access Genomic evidence of the illumination response mechanism and evolutionary history of magnetotactic bacteria within the Rhodospirillaceae family Yinzhao Wang1,2,3* , Giorgio Casaburi4, Wei Lin2, Ying Li5, Fengping Wang1 and Yongxin Pan2,3 Abstract Background: Magnetotactic bacteria (MTB) are ubiquitous in natural aquatic environments. MTB can produce intracellular magnetic particles, navigate along geomagnetic field, and respond to light. However, the potential mechanism by which MTB respond to illumination and their evolutionary relationship with photosynthetic bacteria remain elusive. Results: We utilized genomes of the well-sequenced genus Magnetospirillum, including the newly sequenced MTB strain Magnetospirillum sp. XM-1 to perform a comprehensive genomic comparison with phototrophic bacteria within the family Rhodospirillaceae regarding the illumination response mechanism. First, photoreceptor genes were identified in the genomes of both MTB and phototrophic bacteria in the Rhodospirillaceae family, but no photosynthesis genes were found in the MTB genomes. Most of the photoreceptor genes in the MTB genomes from this family encode phytochrome-domain photoreceptors that likely induce red/far-red light phototaxis. Second, illumination also causes damage within the cell, and in Rhodospirillaceae, both MTB and phototrophic bacteria possess complex but similar sets of response and repair genes, such as oxidative stress response, -
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.