DOCSLIB.ORG

Genome Sequence of the Exopolysaccharide-Producing

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Genome Sequence of the Exopolysaccharide-Producing Genome sequence of the exopolysaccharide-producing Salipiger mucosus type strain (DSM 16094 T ), a moderately halophilic member of the Roseobacter clade Thomas Riedel, Stefan Spring, Anne Fiebig, Jörn Petersen, Nikos C Kyrpides, Markus Göker, Hans-Peter Klenk To cite this version: Thomas Riedel, Stefan Spring, Anne Fiebig, Jörn Petersen, Nikos C Kyrpides, et al.. Genome sequence of the exopolysaccharide-producing Salipiger mucosus type strain (DSM 16094 T ), a moderately halophilic member of the Roseobacter clade. Standards in Genomic Sciences, 2014, 9 (3), pp.1333- 1345. 10.4056/sigs.4909790. hal-01230507 HAL Id: hal-01230507 https://hal.sorbonne-universite.fr/hal-01230507 Submitted on 18 Nov 2015 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. Distributed under a Creative Commons Attribution| 4.0 International License Standards in Genomic Sciences (2014) 9: 1331-1343 DOI:10.4056/sigs.4909790 Genome sequence of the exopolysaccharide-producing Salipiger mucosus type strain (DSM 16094T), a moderately halophilic member of the Roseobacter clade Thomas Riedel1,2, Stefan Spring3, Anne Fiebig3, Jörn Petersen3, Nikos C. Kyrpides4, Markus Göker3*, Hans-Peter Klenk3 1Sorbonne Universités, UPMC Univ Paris 06, USR 3579, LBBM, Observatoire Océanologique, Banyuls/Mer, France 2 CNRS, USR 3579, LBBM, Observatoire Océanologique, Banyuls/Mer, France 3 Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany* Correspondence: Markus Göker ([email protected]) Keywords: aerobic, chemoheterotrophic, rod-shaped, photosynthesis, extrachromosomal el- ements, OmniLog phenotyping, Roseobacter clade, Rhodobacteraceae, Alphaproteobacteria. Salipiger mucosus Martínez-Cànovas et al. 2004 is the type species of the genus Salipiger, a moderately halophilic and exopolysaccharide-producing representative of the Roseobacter lineage within the alphaproteobacterial family Rhodobacteraceae. Members of this family were shown to be the most abundant bacteria especially in coastal and polar waters, but were also found in microbial mats and sediments. Here we describe the features of the S. mucosus strain DSM 16094T together with its genome sequence and annotation. The 5,689,389-bp genome sequence consists of one chromosome and several extrachromosomal elements. It contains 5,650 protein-coding genes and 95 RNA genes. The genome of S. mucosus DSM 16094T was sequenced as part of the activities of the Transregional Collabora- tive Research Center 51 (TRR51) funded by the German Research Foundation (DFG). Introduction be moderate halophiles, which are adapted to a The Roseobacter clade is a very heterogeneous wide range of salinities and were found to pro- group of marine Alphaproteobacteria that plays an duce special compounds like compatible solutes, important role in the global carbon cycle and oth- halophilic enzymes or exopolysaccharides [7-9]. er biogeochemical processes [1]. Members of this Strain A3T (= DSM 16094T = LMG 22090T = CECT group form an allegedly monophyletic, physiologi- 5855T) represents the type strain of S. mucosus cally heterogeneous, as well as metabolically ver- (initially proposed as ‘S. muscescens’) in the mono- satile group of bacterioplankton [1]. They are typic genus Salipiger [10] and was isolated from known to live in the open ocean, especially in saline soil bordering a saltern on the Mediterrane- coastal areas, where they have been found many an Sea coast at Calblanque (Spain) [7]. The genus times in symbiosis with algae, in microbial mats, name Salipiger was derived from the Latin noun sediments, or associated with invertebrates, but sal, salis (‘salt’) and the Latin adjective piger (‘la- representatives of this lineage were also isolated zy’) [10]. The species epithet mucosus refers to the from marine environments like polar waters or Latin adjective mucosus (‘slimy, mucous’) [10]. sea ice [1-4], which is also presented and reflected Current PubMed records do not indicate any fol- by their genome sequences [2]. Whereas some low-up research with strain A3T after the initial members of the Roseobacter clade contain the description of S. mucosus [7] and the characteriza- pigment bacteriochlorophyll a and are capable of tion of its exopolysaccharide [11]. aerobic anoxygenic photophosphorylation, other In this study we analyzed the genome sequence of members were found to transform S. mucosus DSM 16094T, which was selected for dimethylsulfonylpropionate into dimethylsulfide sequencing under the auspices of the German Re- [4-6]. search Foundation (DFG) Transregio-SFB51 Some representatives of the Roseobacter lineage Roseobacter grant because of its phylogenetic po- such as Salipiger mucosus A3T are also known to sition [12] and was also a candidate for the Ge- The Genomic Standards Consortium Salipiger mucosus sp. nov. nomic Encyclopedia of Archaea and Bacteria [13]. quence (AY527274), which contains two ambigu- We present a description of the genomic sequenc- ous base calls. ing and annotation and present a summary classi- fication together with a set of features for strain Morphology and physiology DSM 16094T, including novel aspects of its pheno- Cells of strain A3T are pleomorphic and stain type. Gram-negative (Figure 2). They are 1 µm in width and 2.0-2.5 µm in length. Motility was not ob- Classification and features served. They live a strictly aerobic and chemohet- erotrophic lifestyle. Colonies grown on MY solid 16S rRNA gene analysis medium are circular, convex, cream-colored and The single genomic 16S rRNA gene sequence of S. mucoid, whereas in liquid medium their growth is mucosus DSM 16094T was compared with the uniform. Cells are encapsulated. They are moder- Greengenes database for determining the ately halophilic, and capable of growth in a mix- weighted relative frequencies of taxa and (trun- ture of sea salts from 0.5 to 20% (w/v), whereas cated) keywords as previously described [14]. The the optimum is between 3 and 6% (w/v) sea salts. most frequently occurring genera were Salipiger When using NaCl instead of sea salts, optimal (21.2%), Pelagibaca (17.1%), Roseovarius growth occurs at a salt concentration of 9-10% (17.0%), Marinovum (13.1%) and Roseobacter (w/v). Cells of strain A3T grow within a tempera- (9.5%) (30 hits in total). Regarding the single hit ture range of 20-40°C and at a pH range between 6 to sequences from members of the species, the av- and 10. Growth does not occur under anaerobic erage identity within high scoring pairs (HSPs) conditions either by fermentation, fumarate or ni- was 100.0%, whereas the average coverage by trate reduction or photoheterotrophy. Cells are cy- HSPs was 97.2%. Regarding the two hits to se- tochrome oxidase and catalase positive. quences from other members of the genus, the av- Polyhydroxyalkanoates (PHA) are stored as re- erage identity within HSPs was 98.4%, whereas serve material within the cells. H2S is produced the average coverage by HSPs was 99.0%. Among from L-cysteine. Selenite reduction, gluconate oxi- all other species, the one yielding the highest dation and phosphatase were observed. Urea and score was 'Salipiger bermudensis' (DQ178660), Tween 20 are hydrolyzed. A variety of tested or- which corresponded to an identity of 96.8% and a ganic compounds were neither metabolized nor HSP coverage of 99.9%. (Note that the Greengenes sustained growth; for details see [7]. database uses the INSDC (= EMBL/NCBI/DDBJ) The utilization of carbon compounds by S. annotation, which is not an authoritative source mucosus DSM 16094T grown at 28°C was also de- for nomenclature or classification). The highest- termined for this study using Generation-III scoring environmental sequence was AB302369 microplates in an OmniLog phenotyping device (Greengenes short name 'Hydrocarbon-Degrading (BIOLOG Inc., Hayward, CA, USA). The microplates Indonesian Seawater seawater isolate B44-2B44-2 were inoculated with a cell suspension at a cell str. B44-2'), which showed an identity of 97.4% density of 95-96% turbidity and dye IF-A. Further and an HSP coverage of 95.4%. The most frequent- additives were vitamins, micronutrient and sea- ly occurring keywords within the labels of all en- salt solutions, which had to be added for dealing vironmental samples that yielded hits were 'aquat, with such marine bacteria [29]. The plates were rank' (4.9%), 'microbi' (3.7%), 'harbour, newport' sealed with parafilm to avoid a loss of fluid. The (3.3%), 'water' (2.7%) and 'seawat' (2.4%) (219 exported measurement data were further ana- hits in total) and in line with the habitat from lyzed with the opm package for R [30,31], using its which strain A3T was isolated. Environmental functionality for statistically estimating parame- samples that yielded hits of a higher score than ters from the respiration curves such as the max- the highest scoring species were not found. imum height, and automatically translating these Figure 1 shows the phylogenetic neighborhood of values into negative, ambiguous, and positive re- S. mucosus strain DSM 16094T in a 16S rRNA gene actions. The reactions
Load more

Recommended publications
  • Physiology of Dimethylsulfoniopropionate Metabolism
    PHYSIOLOGY OF DIMETHYLSULFONIOPROPIONATE METABOLISM IN A MODEL MARINE ROSEOBACTER, Silicibacter pomeroyi by JAMES R. HENRIKSEN (Under the direction of William B. Whitman) ABSTRACT Dimethylsulfoniopropionate (DMSP) is a ubiquitous marine compound whose degradation is important in carbon and sulfur cycles and influences global climate due to its degradation product dimethyl sulfide (DMS). Silicibacter pomeroyi, a member of the a marine Roseobacter clade, is a model system for the study of DMSP degradation. S. pomeroyi can cleave DMSP to DMS and carry out demethylation to methanethiol (MeSH), as well as degrade both these compounds. Dif- ferential display proteomics was used to find proteins whose abundance increased when chemostat cultures of S. pomeroyi were grown with DMSP as the sole carbon source. Bioinformatic analysis of these genes and their gene clusters suggested roles in DMSP metabolism. A genetic system was developed for S. pomeroyi that enabled gene knockout to confirm the function of these genes. INDEX WORDS: Silicibacter pomeroyi, Ruegeria pomeroyi, dimethylsulfoniopropionate, DMSP, roseobacter, dimethyl sulfide, DMS, methanethiol, MeSH, marine, environmental isolate, proteomics, genetic system, physiology, metabolism PHYSIOLOGY OF DIMETHYLSULFONIOPROPIONATE METABOLISM IN A MODEL MARINE ROSEOBACTER, Silicibacter pomeroyi by JAMES R. HENRIKSEN B.S. (Microbiology), University of Oklahoma, 2000 B.S. (Biochemistry), University of Oklahoma, 2000 A Dissertation Submitted to the Graduate Faculty of The University of Georgia in Partial Fulfillment of the Requirements for the Degree DOCTOR OF PHILOSOPHY ATHENS, GEORGIA 2008 cc 2008 James R. Henriksen Some Rights Reserved Creative Commons License Version 3.0 Attribution-Noncommercial-Share Alike PHYSIOLOGY OF DIMETHYLSULFONIOPROPIONATE METABOLISM IN A MODEL MARINE ROSEOBACTER, Silicibacter pomeroyi by JAMES R.
    [Show full text]
  • Horizontal Operon Transfer, Plasmids, and the Evolution of Photosynthesis in Rhodobacteraceae
    The ISME Journal (2018) 12:1994–2010 https://doi.org/10.1038/s41396-018-0150-9 ARTICLE Horizontal operon transfer, plasmids, and the evolution of photosynthesis in Rhodobacteraceae 1 2 3 4 1 Henner Brinkmann ● Markus Göker ● Michal Koblížek ● Irene Wagner-Döbler ● Jörn Petersen Received: 30 January 2018 / Revised: 23 April 2018 / Accepted: 26 April 2018 / Published online: 24 May 2018 © The Author(s) 2018. This article is published with open access Abstract The capacity for anoxygenic photosynthesis is scattered throughout the phylogeny of the Proteobacteria. Their photosynthesis genes are typically located in a so-called photosynthesis gene cluster (PGC). It is unclear (i) whether phototrophy is an ancestral trait that was frequently lost or (ii) whether it was acquired later by horizontal gene transfer. We investigated the evolution of phototrophy in 105 genome-sequenced Rhodobacteraceae and provide the first unequivocal evidence for the horizontal transfer of the PGC. The 33 concatenated core genes of the PGC formed a robust phylogenetic tree and the comparison with single-gene trees demonstrated the dominance of joint evolution. The PGC tree is, however, largely incongruent with the species tree and at least seven transfers of the PGC are required to reconcile both phylogenies. 1234567890();,: 1234567890();,: The origin of a derived branch containing the PGC of the model organism Rhodobacter capsulatus correlates with a diagnostic gene replacement of pufC by pufX. The PGC is located on plasmids in six of the analyzed genomes and its DnaA- like replication module was discovered at a conserved central position of the PGC. A scenario of plasmid-borne horizontal transfer of the PGC and its reintegration into the chromosome could explain the current distribution of phototrophy in Rhodobacteraceae.
    [Show full text]
  • An Updated Genome Annotation for the Model Marine Bacterium Ruegeria Pomeroyi DSS-3 Adam R Rivers, Christa B Smith and Mary Ann Moran*
    Rivers et al. Standards in Genomic Sciences 2014, 9:11 http://www.standardsingenomics.com/content/9/1/11 SHORT GENOME REPORT Open Access An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3 Adam R Rivers, Christa B Smith and Mary Ann Moran* Abstract When the genome of Ruegeria pomeroyi DSS-3 was published in 2004, it represented the first sequence from a heterotrophic marine bacterium. Over the last ten years, the strain has become a valuable model for understanding the cycling of sulfur and carbon in the ocean. To ensure that this genome remains useful, we have updated 69 genes to incorporate functional annotations based on new experimental data, and improved the identification of 120 protein-coding regions based on proteomic and transcriptomic data. We review the progress made in understanding the biology of R. pomeroyi DSS-3 and list the changes made to the genome. Keywords: Roseobacter,DMSP Introduction Genome properties Ruegeria pomeroyi DSS-3 is an important model organ- The R. pomeroyi DSS-3 genome contains a 4,109,437 bp ism in studies of the physiology and ecology of marine circular chromosome (5 bp shorter than previously re- bacteria [1]. It is a genetically tractable strain that has ported [1]) and a 491,611 bp circular megaplasmid, with been essential for elucidating bacterial roles in the mar- a G + C content of 64.1 (Table 3). A detailed description ine sulfur and carbon cycles [2,3] and the biology and of the genome is found in the original article [1]. genomics of the marine Roseobacter clade [4], a group that makes up 5–20% of bacteria in ocean surface waters [5,6].
    [Show full text]
  • Roseovarius Azorensis Sp. Nov., Isolated from Seawater At
    Author version: Antonie van Leeuwenhoek, vol.105(3); 2014; 571-578 Roseovarius azorensis sp. nov., isolated from seawater at Espalamaca, Azores Raju Rajasabapathy • Chellandi Mohandass • Syed Gulam Dastager • Qing Liu • Thi-Nhan Khieu • Chu Ky Son • Wen-Jun Li • Ana Colaco Raju Rajasabapathy · Chellandi Mohandass* Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa 403 004, India. E-mail: [email protected] Syed Gulam Dastager NCIM Resource Center, CSIR-National Chemical Laboratory, Dr. Homi Bhabha road, Pune 411 008, India Qing Liu · Thi-Nhan Khieu · Wen-Jun Li Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan 650091, P.R. China Thi-Nhan Khieu · Chu Ky Son School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Vietnam Ana Colaco IMAR-Department of Oceanography and Fisheries, University Açores, Cais de Sta Cruz, 9901-862, Horta, Portugal Abstract A Gram-negative, motile, non-spore forming, rod shaped aerobic bacterium, designated strain SSW084T, was isolated from a surface seawater sample collected at Espalamaca (38°33’N; 28°39’W), Azores. Growth was found to occur from 15 – 40 °C (optimum 30 °C), at pH 7.0 – 9.0 (optimum pH 7.0) and with 25 to 100 % seawater or 0.5 – 7.0 % NaCl in the presence of Mg2+ and Ca2+; no growth was found with NaCl alone. Colonies on seawater nutrient agar (SWNA) were observed to be punctiform, white, convex, circular, smooth, and translucent. Strain SSW084T did not grow on Zobell Marine Agar (ZMA) and tryptic soy agar (TSA) even when seawater supplemented. The major respiratory quinone was found to be Q-10 and the G+C content was determined to be 61.9 mol%.
    [Show full text]
  • Genomic Analyses of Two Alteromonas Stellipolaris Strains Reveal Traits
    www.nature.com/scientificreports OPEN Genomic analyses of two Alteromonas stellipolaris strains reveal traits with potential Received: 7 August 2018 Accepted: 27 November 2018 biotechnological applications Published: xx xx xxxx Marta Torres1,2,3, Kar-Wai Hong4, Teik-Min Chong4, José Carlos Reina1, Kok-Gan Chan 4,5, Yves Dessaux3 & Inmaculada Llamas 1,2 The Alteromonas stellipolaris strains PQQ-42 and PQQ-44, previously isolated from a fsh hatchery, have been selected on the basis of their strong quorum quenching (QQ) activity, as well as their ability to reduce Vibrio-induced mortality on the coral Oculina patagonica. In this study, the genome sequences of both strains were determined and analyzed in order to identify the mechanism responsible for QQ activity. Both PQQ-42 and PQQ-44 were found to degrade a wide range of N-acylhomoserine lactone (AHL) QS signals, possibly due to the presence of an aac gene which encodes an AHL amidohydrolase. In addition, the diferent colony morphologies exhibited by the strains could be related to the diferences observed in genes encoding cell wall biosynthesis and exopolysaccharide (EPS) production. The PQQ-42 strain produces more EPS (0.36 g l−1) than the PQQ-44 strain (0.15 g l−1), whose chemical compositions also difer. Remarkably, PQQ-44 EPS contains large amounts of fucose, a sugar used in high-value biotechnological applications. Furthermore, the genome of strain PQQ-42 contained a large non- ribosomal peptide synthase (NRPS) cluster with a previously unknown genetic structure. The synthesis of enzymes and other bioactive compounds were also identifed, indicating that PQQ-42 and PQQ-44 could have biotechnological applications.
    [Show full text]
  • Photosynthesis Is Widely Distributed Among Proteobacteria As Demonstrated by the Phylogeny of Puflm Reaction Center Proteins
    fmicb-08-02679 January 20, 2018 Time: 16:46 # 1 ORIGINAL RESEARCH published: 23 January 2018 doi: 10.3389/fmicb.2017.02679 Photosynthesis Is Widely Distributed among Proteobacteria as Demonstrated by the Phylogeny of PufLM Reaction Center Proteins Johannes F. Imhoff1*, Tanja Rahn1, Sven Künzel2 and Sven C. Neulinger3 1 Research Unit Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany, 2 Max Planck Institute for Evolutionary Biology, Plön, Germany, 3 omics2view.consulting GbR, Kiel, Germany Two different photosystems for performing bacteriochlorophyll-mediated photosynthetic energy conversion are employed in different bacterial phyla. Those bacteria employing a photosystem II type of photosynthetic apparatus include the phototrophic purple bacteria (Proteobacteria), Gemmatimonas and Chloroflexus with their photosynthetic relatives. The proteins of the photosynthetic reaction center PufL and PufM are essential components and are common to all bacteria with a type-II photosynthetic apparatus, including the anaerobic as well as the aerobic phototrophic Proteobacteria. Edited by: Therefore, PufL and PufM proteins and their genes are perfect tools to evaluate the Marina G. Kalyuzhanaya, phylogeny of the photosynthetic apparatus and to study the diversity of the bacteria San Diego State University, United States employing this photosystem in nature. Almost complete pufLM gene sequences and Reviewed by: the derived protein sequences from 152 type strains and 45 additional strains of Nikolai Ravin, phototrophic Proteobacteria employing photosystem II were compared. The results Research Center for Biotechnology (RAS), Russia give interesting and comprehensive insights into the phylogeny of the photosynthetic Ivan A. Berg, apparatus and clearly define Chromatiales, Rhodobacterales, Sphingomonadales as Universität Münster, Germany major groups distinct from other Alphaproteobacteria, from Betaproteobacteria and from *Correspondence: Caulobacterales (Brevundimonas subvibrioides).
    [Show full text]
  • Trimethylamine N-Oxide Metabolism by Abundant Marine Heterotrophic Bacteria
    Trimethylamine N-oxide metabolism by abundant marine heterotrophic bacteria Ian Lidburya, J. Colin Murrellb, and Yin Chena,1 aSchool of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom; and bSchool of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom Edited* by Mary E. Lidstrom, University of Washington, Seattle, WA, and approved January 8, 2014 (received for review September 27, 2013) Trimethylamine N-oxide (TMAO) is a common osmolyte found in marine bacteria are not known. It has previously been suggested a variety of marine biota and has been detected at nanomolar that in Methylocella silvestris, a TMA-degrading soil bacterium, an concentrations in oceanic surface waters. TMAO can serve as an aminotransferase protein containing a conserved C-terminal tet- important nutrient for ecologically important marine heterotro- rahydrofolate (THF)-binding domain (Msil_3603) is probably in- phic bacteria, particularly the SAR11 clade and marine Roseobacter volved in the metabolism of TMAO, because this polypeptide was clade (MRC). However, the enzymes responsible for TMAO catab- highly enriched in TMA-grown cells and TMAO is a known in- termediate of TMA metabolism by TMA monooxygenase, Tmm, olism and the membrane transporter required for TMAO uptake + in this bacterium (TMA + NADPH + O + H → TMAO + H O + into microbial cells have yet to be identified. We show here that + 2 2 the enzyme TMAO demethylase (Tdm) catalyzes the first step in NADP ) (13). It is hypothesized that TMAO is further metab- TMAO degradation. This enzyme represents a large group of pro- olized to ammonium and formaldehyde, which serve as N and teins with an uncharacterized domain (DUF1989).
    [Show full text]
  • A059p283.Pdf
    Vol. 59: 283–293, 2010 AQUATIC MICROBIAL ECOLOGY Published online April 21 doi: 10.3354/ame01398 Aquat Microb Ecol High diversity of Rhodobacterales in the subarctic North Atlantic Ocean and gene transfer agent protein expression in isolated strains Yunyun Fu1,*, Dawne M. MacLeod1,*, Richard B. Rivkin2, Feng Chen3, Alison Buchan4, Andrew S. Lang1,** 1Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John’s, Newfoundland A1B 3X9, Canada 2Ocean Sciences Centre, Memorial University of Newfoundland, Marine Lab Road, St. John’s, Newfoundland A1C 5S7, Canada 3Center of Marine Biotechnology, University of Maryland Biotechnology Institute, 236-701 East Pratt St., Baltimore, Maryland 21202, USA 4Department of Microbiology, University of Tennessee, M409 Walters Life Sciences, Knoxville, Tennessee 37914, USA ABSTRACT: Genes encoding gene transfer agent (GTA) particles are well conserved in bacteria of the order Rhodobacterales. Members of this order are abundant in diverse marine environments, fre- quently accounting for as much as 25% of the total bacterial community. Conservation of the genes encoding GTAs allows their use as diagnostic markers of Rhodobacterales in biogeographical stud- ies. The first survey of the diversity of Rhodobacterales based on the GTA major capsid gene was con- ducted in a warm temperate estuarine ecosystem, the Chesapeake Bay, but the biogeography of Rhodobacterales has not been explored extensively. This study investigates Rhodobacterales diver- sity in the cold subarctic water near Newfoundland, Canada. Our results suggest that the subarctic region of the North Atlantic contains diverse Rhodobacterales communities in both winter and sum- mer, and that the diversity of the Rhodobacterales community in the summer Newfoundland coastal water is higher than that found in the Chesapeake Bay, in either the summer or winter.
    [Show full text]
  • Downloaded from the Functional Gene Pipeline and Repository (Fungene, Accessed on 9 January 2021)
    microorganisms Article Bacterial Dimethylsulfoniopropionate Biosynthesis in the East China Sea Ji Liu 1,2,†, Yunhui Zhang 1,†, Jingli Liu 1,2, Haohui Zhong 1, Beth T. Williams 2, Yanfen Zheng 1, Andrew R. J. Curson 2, Chuang Sun 1, Hao Sun 1, Delei Song 1, Brett Wagner Mackenzie 3, Ana Bermejo Martínez 2, Jonathan D. Todd 1,2,* and Xiao-Hua Zhang 1,4,* 1 College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; [email protected] (J.L.); [email protected] (Y.Z.); [email protected] (J.L.); [email protected] (H.Z.); [email protected] (Y.Z.); [email protected] (C.S.); [email protected] (H.S.); [email protected] (D.S.) 2 School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; [email protected] (B.T.W.); [email protected] (A.R.J.C.); [email protected] (A.B.M.) 3 Department of Surgery, School of Medicine, The University of Auckland, Auckland 1142, New Zealand; [email protected] 4 Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China * Correspondence: [email protected] (J.D.T.); [email protected] (X.-H.Z.) † These authors contributed equally to this work. Abstract: Dimethylsulfoniopropionate (DMSP) is one of Earth’s most abundant organosulfur molecules. Recently, many marine heterotrophic bacteria were shown to produce DMSP, but few studies have Citation: Liu, J.; Zhang, Y.; Liu, J.; combined culture-dependent and independent techniques to study their abundance, distribution, Zhong, H.; Williams, B.T.; Zheng, Y.; diversity and activity in seawater or sediment environments.
    [Show full text]
  • CGM-18-001 Perseus Report Update Bacterial Taxonomy Final Errata
    report Update of the bacterial taxonomy in the classification lists of COGEM July 2018 COGEM Report CGM 2018-04 Patrick L.J. RÜDELSHEIM & Pascale VAN ROOIJ PERSEUS BVBA Ordering information COGEM report No CGM 2018-04 E-mail: [email protected] Phone: +31-30-274 2777 Postal address: Netherlands Commission on Genetic Modification (COGEM), P.O. Box 578, 3720 AN Bilthoven, The Netherlands Internet Download as pdf-file: http://www.cogem.net → publications → research reports When ordering this report (free of charge), please mention title and number. Advisory Committee The authors gratefully acknowledge the members of the Advisory Committee for the valuable discussions and patience. Chair: Prof. dr. J.P.M. van Putten (Chair of the Medical Veterinary subcommittee of COGEM, Utrecht University) Members: Prof. dr. J.E. Degener (Member of the Medical Veterinary subcommittee of COGEM, University Medical Centre Groningen) Prof. dr. ir. J.D. van Elsas (Member of the Agriculture subcommittee of COGEM, University of Groningen) Dr. Lisette van der Knaap (COGEM-secretariat) Astrid Schulting (COGEM-secretariat) Disclaimer This report was commissioned by COGEM. The contents of this publication are the sole responsibility of the authors and may in no way be taken to represent the views of COGEM. Dit rapport is samengesteld in opdracht van de COGEM. De meningen die in het rapport worden weergegeven, zijn die van de auteurs en weerspiegelen niet noodzakelijkerwijs de mening van de COGEM. 2 | 24 Foreword COGEM advises the Dutch government on classifications of bacteria, and publishes listings of pathogenic and non-pathogenic bacteria that are updated regularly. These lists of bacteria originate from 2011, when COGEM petitioned a research project to evaluate the classifications of bacteria in the former GMO regulation and to supplement this list with bacteria that have been classified by other governmental organizations.
    [Show full text]
  • Genomic Analysis of the Evolution of Phototrophy Among Haloalkaliphilic Rhodobacterales
    GBE Genomic Analysis of the Evolution of Phototrophy among Haloalkaliphilic Rhodobacterales Karel Kopejtka1,2,Ju¨rgenTomasch3, Yonghui Zeng4, Martin Tichy1, Dimitry Y. Sorokin5,6,and Michal Koblızek1,2,* 1Laboratory of Anoxygenic Phototrophs, Institute of Microbiology, CAS, Center Algatech, Trebon, Czech Republic 2Faculty of Science, University of South Bohemia, Ceske ´ Budejovice, Czech Republic 3Research Group Microbial Communication, Helmholtz Centre for Infection Research, Braunschweig, Germany 4Aarhus Institute of Advanced Studies, Aarhus, Denmark 5Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia 6Department of Biotechnology, Delft University of Technology, The Netherlands *Corresponding author: E-mail: [email protected]. Accepted: July 26, 2017 Data deposition: This project has been deposited at NCBI GenBank under the accession numbers: GCA_001870665.1, GCA_001870675.1, GCA_001884735.1. Abstract A characteristic feature of the order Rhodobacterales is the presence of a large number of photoautotrophic and photo- heterotrophic species containing bacteriochlorophyll. Interestingly, these phototrophic species are phylogenetically mixed with chemotrophs. To better understand the origin of such variability, we sequenced the genomes of three closely related haloalkaliphilic species, differing in their phototrophic capacity and oxygen preference: the photoheterotrophic and faculta- tively anaerobic bacterium Rhodobaca barguzinensis, aerobic photoheterotroph Roseinatronobacter
    [Show full text]
  • Data-Mining of Antibiotic Resistance Genes Provides Insight Into the Community
    bioRxiv preprint doi: https://doi.org/10.1101/246033; this version posted January 10, 2018. 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-NC-ND 4.0 International license. 1 Data-mining of Antibiotic Resistance Genes Provides Insight into the Community 2 Structure of Ocean Microbiome 3 Shiguang Hao1,$, Pengshuo Yang1,$, Maozhen Han1,$, Junjie Xu1, Shaojun Yu1, Chaoyun 4 Chen1, Wei-Hua Chen1, Houjin Zhang1,*, Kang Ning1,* 5 1Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life 6 Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 7 430074, China 8 9 $ These authors contributed equally to this work. 10 * Corresponding author. E-mail: [email protected], [email protected]. 11 1 bioRxiv preprint doi: https://doi.org/10.1101/246033; this version posted January 10, 2018. 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-NC-ND 4.0 International license. 12 Abstract 13 Background：Antibiotics have been spread widely in environments, asserting profound 14 effects on environmental microbes as well as antibiotic resistance genes (ARGs) within these 15 microbes. Therefore, investigating the associations between ARGs and bacterial communities 16 become an important issue for environment protection. Ocean microbiomes are potentially 17 large ARG reservoirs, but the marine ARG distribution and its associations with bacterial 18 communities remain unclear.
    [Show full text]