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Veseli I, DeMers MA, Cooper ZS, Schechter MS, Miller S, Weber L, Smith CB, Rodriguez LT, Schroer WF, McIlvin MR, Lopez PZ, Saito M, Dyhrman S, Eren AM, Moran MA, Braakman R. Digital Microbe: a genome-informed data integration framework for team science on emerging model organisms. Sci Data 2024; 11:967. [PMID: 39232008 PMCID: PMC11374999 DOI: 10.1038/s41597-024-03778-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 08/13/2024] [Indexed: 09/06/2024] Open
Abstract
The remarkable pace of genomic data generation is rapidly transforming our understanding of life at the micron scale. Yet this data stream also creates challenges for team science. A single microbe can have multiple versions of genome architecture, functional gene annotations, and gene identifiers; additionally, the lack of mechanisms for collating and preserving advances in this knowledge raises barriers to community coalescence around shared datasets. "Digital Microbes" are frameworks for interoperable and reproducible collaborative science through open source, community-curated data packages built on a (pan)genomic foundation. Housed within an integrative software environment, Digital Microbes ensure real-time alignment of research efforts for collaborative teams and facilitate novel scientific insights as new layers of data are added. Here we describe two Digital Microbes: 1) the heterotrophic marine bacterium Ruegeria pomeroyi DSS-3 with > 100 transcriptomic datasets from lab and field studies, and 2) the pangenome of the cosmopolitan marine heterotroph Alteromonas containing 339 genomes. Examples demonstrate how an integrated framework collating public (pan)genome-informed data can generate novel and reproducible findings.
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Affiliation(s)
- Iva Veseli
- Helmholtz Institute for Functional Marine Biodiversity, 26129, Oldenburg, Germany
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27570, Bremerhaven, Germany
| | - Michelle A DeMers
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Zachary S Cooper
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Matthew S Schechter
- Committee on Microbiology, The University of Chicago, Chicago, IL, 60637, USA
| | - Samuel Miller
- Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Laura Weber
- Woods Hole Oceanographic Institution, Falmouth, MA, 02543, USA
| | - Christa B Smith
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Lidimarie T Rodriguez
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611-0180, USA
| | - William F Schroer
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
| | | | - Paloma Z Lopez
- Woods Hole Oceanographic Institution, Falmouth, MA, 02543, USA
| | - Makoto Saito
- Woods Hole Oceanographic Institution, Falmouth, MA, 02543, USA
| | - Sonya Dyhrman
- Lamont-Doherty Earth Observatory, and the Department of Earth and Environmental Sciences, Columbia University, New York, NY, 10032, USA
| | - A Murat Eren
- Helmholtz Institute for Functional Marine Biodiversity, 26129, Oldenburg, Germany.
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27570, Bremerhaven, Germany.
- Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, 02543, USA.
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.
- Marine 'Omics Bridging Group, Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany.
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA.
| | - Rogier Braakman
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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Robertson JM, Garza EA, Stubbusch AKM, Dupont CL, Hwa T, Held NA. Marine bacteria Alteromonas spp. require UDP-glucose-4-epimerase for aggregation and production of sticky exopolymer. mBio 2024; 15:e0003824. [PMID: 38958440 PMCID: PMC11325263 DOI: 10.1128/mbio.00038-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 05/23/2024] [Indexed: 07/04/2024] Open
Abstract
The physiology and ecology of particle-associated marine bacteria are of growing interest, but our knowledge of their aggregation behavior and mechanisms controlling their association with particles remains limited. We have found that a particle-associated isolate, Alteromonas sp. ALT199 strain 4B03, and the related type-strain A. macleodii 27126 both form large (>500 μm) aggregates while growing in rich medium. A non-clumping variant (NCV) of 4B03 spontaneously arose in the lab, and whole-genome sequencing revealed a partial deletion in the gene encoding UDP-glucose-4-epimerase (galEΔ308-324). In 27126, a knock-out of galE (ΔgalE::kmr) resulted in a loss of aggregation, mimicking the NCV. Microscopic analysis shows that both 4B03 and 27126 rapidly form large aggregates, whereas their respective galE mutants remain primarily as single planktonic cells or clusters of a few cells. Strains 4B03 and 27126 also form aggregates with chitin particles, but their galE mutants do not. Alcian Blue staining shows that 4B03 and 27126 produce large transparent exopolymer particles (TEP), but their galE mutants are deficient in this regard. This study demonstrates the capabilities of cell-cell aggregation, aggregation of chitin particles, and production of TEP in strains of Alteromonas, a widespread particle-associated genus of heterotrophic marine bacteria. A genetic requirement for galE is evident for each of the above capabilities, expanding the known breadth of requirement for this gene in biofilm-related processes. IMPORTANCE Heterotrophic marine bacteria have a central role in the global carbon cycle. Well-known for releasing CO2 by decomposition and respiration, they may also contribute to particulate organic matter (POM) aggregation, which can promote CO2 sequestration via the formation of marine snow. We find that two members of the prevalent particle-associated genus Alteromonas can form aggregates comprising cells alone or cells and chitin particles, indicating their ability to drive POM aggregation. In line with their multivalent aggregation capability, both strains produce TEP, an excreted polysaccharide central to POM aggregation in the ocean. We demonstrate a genetic requirement for galE in aggregation and large TEP formation, building our mechanistic understanding of these aggregative capabilities. These findings point toward a role for heterotrophic bacteria in POM aggregation in the ocean and support broader efforts to understand bacterial controls on the global carbon cycle based on microbial activities, community structure, and meta-omic profiling.
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Affiliation(s)
- Jacob M Robertson
- Division of Biological Sciences, UC San Diego, La Jolla, California, USA
| | - Erin A Garza
- Microbial and Environmental Genomics, J Craig Venter Institute, La Jolla, California, USA
| | - Astrid K M Stubbusch
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Earth Sciences, Geological Institute, ETH Zurich, Zurich, Switzerland
| | - Christopher L Dupont
- Microbial and Environmental Genomics, J Craig Venter Institute, La Jolla, California, USA
| | - Terence Hwa
- Division of Biological Sciences, UC San Diego, La Jolla, California, USA
- Department of Physics, UC San Diego, La Jolla, California, USA
| | - Noelle A Held
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Biological Sciences, Marine and Environmental Biology Section, University of Southern California, Los Angeles, California, USA
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Goux M, Demonceaux M, Hendrickx J, Solleux C, Lormeau E, Fredslund F, Tezé D, Offmann B, André-Miral C. Sucrose phosphorylase from Alteromonas mediterranea: Structural insight into the regioselective α-glucosylation of (+)-catechin. Biochimie 2024; 221:13-19. [PMID: 38199518 DOI: 10.1016/j.biochi.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/12/2024]
Abstract
Sucrose phosphorylases, through transglycosylation reactions, are interesting enzymes that can transfer regioselectively glucose from sucrose, the donor substrate, onto acceptors like flavonoids to form glycoconjugates and hence modulate their solubility and bioactivity. Here, we report for the first time the structure of sucrose phosphorylase from the marine bacteria Alteromonas mediterranea (AmSP) and its enzymatic properties. Kinetics of sucrose hydrolysis and transglucosylation capacities on (+)-catechin were investigated. Wild-type enzyme (AmSP-WT) displayed high hydrolytic activity on sucrose and was devoid of transglucosylation activity on (+)-catechin. Two variants, AmSP-Q353F and AmSP-P140D catalysed the regiospecific transglucosylation of (+)-catechin: 89 % of a novel compound (+)-catechin-4'-O-α-d-glucopyranoside (CAT-4') for AmSP-P140D and 92 % of (+)-catechin-3'-O-α-d-glucopyranoside (CAT-3') for AmSP-Q353F. The compound CAT-4' was fully characterized by NMR and mass spectrometry. An explanation for this difference in regiospecificity was provided at atomic level by molecular docking simulations: AmSP-P140D was found to preferentially bind (+)-catechin in a mode that favours glucosylation on its hydroxyl group in position 4' while the binding mode in AmSP-Q353F favoured glucosylation on its hydroxyl group in position 3'.
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Affiliation(s)
- Marine Goux
- Nantes Université, CNRS, US2B, UMR 6286, F-44000, Nantes, France
| | - Marie Demonceaux
- Nantes Université, CNRS, US2B, UMR 6286, F-44000, Nantes, France
| | - Johann Hendrickx
- Nantes Université, CNRS, US2B, UMR 6286, F-44000, Nantes, France
| | - Claude Solleux
- Nantes Université, CNRS, US2B, UMR 6286, F-44000, Nantes, France
| | - Emilie Lormeau
- Nantes Université, CNRS, US2B, UMR 6286, F-44000, Nantes, France
| | - Folmer Fredslund
- DTU Biosustain, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark
| | - David Tezé
- DTU Biosustain, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark
| | - Bernard Offmann
- Nantes Université, CNRS, US2B, UMR 6286, F-44000, Nantes, France.
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Srivastava P, Tyagi A, Bhardwaj C, Kumari A, Kaur H, Seth S, Kaur A, Panigrahi I, Dayal D, Pramanik S, Mandal K. SHOX Variations in Idiopathic Short Stature in North India and a Review of Cases from Asian Countries. J Clin Res Pediatr Endocrinol 2024; 16:41-49. [PMID: 37750395 PMCID: PMC10938528 DOI: 10.4274/jcrpe.galenos.2023.2023-3-13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 09/17/2023] [Indexed: 09/27/2023] Open
Abstract
Objective Short stature homeobox (SHOX) haploinsufficiency underlies idiopathic short stature (ISS) and Leri-Weill dyschondrosteosis. The worldwide prevalence of SHOX variations in ISS varies from 2.5% to 15.0%. The aim of this study was to assess the implication of SHOX variation in ISS in North Indians and compare this with other cases of SHOX variations from Asian population. Methods SHOX gene analysis was carried out by multiplex ligation-dependent probe amplification followed by Sanger sequencing in 54 patients with variable phenotypes. Comparison with other reports in a meta-analysis comprising the current study and 11 previous studies (n=979) was performed. Results SHOX analysis resulted in 12.9% positivity (7.4% deletions and 5.5% duplications). SHOX association was seen significantly related to gender, with predominance in females (p=0.047). Short arms and forearms were the only significantly associated trait seen in 51.9% of children. The overall prevalence of SHOX variation was 15.2% in Asians with ISS. No significant difference was found in geographical region-specific analysis. Conclusion This study summarises findings from the last decade and provides an updated picture of the prevalence of SHOX variations in Asians, emphasizing their potential as therapeutic targets in ISS patients. Further high quality, large investigations including functional validation is warranted to validate this association.
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Affiliation(s)
- Priyanka Srivastava
- Advanced Pediatrics Centre (APC), Postgraduate Institute of Medical Education & Research (PGIMER), Genetic Metabolic Unit, Chandigarh, India
| | - Ankita Tyagi
- Advanced Pediatrics Centre (APC), Postgraduate Institute of Medical Education & Research (PGIMER), Genetic Metabolic Unit, Chandigarh, India
| | - Chitra Bhardwaj
- Advanced Pediatrics Centre (APC), Postgraduate Institute of Medical Education & Research (PGIMER), Genetic Metabolic Unit, Chandigarh, India
| | - Anu Kumari
- Advanced Pediatrics Centre (APC), Postgraduate Institute of Medical Education & Research (PGIMER), Genetic Metabolic Unit, Chandigarh, India
| | - Harvinder Kaur
- Advanced Pediatrics Centre (APC), Postgraduate Institute of Medical Education & Research (PGIMER), Child Growth and Anthropology Unit, Chandigarh, India
| | - Saurabh Seth
- Advanced Pediatrics Centre (APC), Postgraduate Institute of Medical Education & Research (PGIMER), Genetic Metabolic Unit, Chandigarh, India
| | - Anupriya Kaur
- Advanced Pediatrics Centre (APC), Postgraduate Institute of Medical Education & Research (PGIMER), Genetic Metabolic Unit, Chandigarh, India
| | - Inusha Panigrahi
- Advanced Pediatrics Centre (APC), Postgraduate Institute of Medical Education & Research (PGIMER), Genetic Metabolic Unit, Chandigarh, India
| | - Devi Dayal
- Advanced Pediatrics Centre, Postgraduate Institute of Medical Education & Research (PGIMER), Pediatric Endocrinology Unit, Chandigarh, India
| | | | - Kausik Mandal
- Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS), Department of Medical Genetics, Lucknow, India
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Emsley SA, Loughran RM, Shlafstein MD, Pfannmuller KM, De La Flor YT, Lein CG, Dove NC, Koyack MJ, Oline DK, Hanson TE, Videau P, Saw JH, Ushijima B. Fluctibacter corallii gen. nov., sp. nov., isolated from the coral Montipora capitata on a reef in Kāne'ohe Bay, O'ahu, Hawai'i, reclassification of Aestuariibacter halophilus as Fluctibacter halophilus comb. nov., and Paraglaciecola oceanifecundans as a later heterotypic synonym of Paraglaciecola agarilytica. Antonie Van Leeuwenhoek 2024; 117:45. [PMID: 38424217 DOI: 10.1007/s10482-024-01934-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 01/25/2024] [Indexed: 03/02/2024]
Abstract
Strain AA17T was isolated from an apparently healthy fragment of Montipora capitata coral from the reef surrounding Moku o Lo'e in Kāne'ohe Bay, O'ahu, Hawai'i, USA, and was taxonomically evaluated using a polyphasic approach. Comparison of a partial 16S rRNA gene sequence found that strain AA17T shared the greatest similarity with Aestuariibacter halophilus JC2043T (96.6%), and phylogenies based on 16S rRNA gene sequences grouped strain AA17T with members of the Aliiglaciecola, Aestuariibacter, Lacimicrobium, Marisediminitalea, Planctobacterium, and Saliniradius genera. To more precisely infer the taxonomy of strain AA17T, a phylogenomic analysis was conducted and indicated that strain AA17T formed a monophyletic clade with A. halophilus JC2043T, divergent from Aestuariibacter salexigens JC2042T and other related genera. As a result of monophyly and multiple genomic metrics of genus demarcation, strain AA17T and A. halophilus JC2043T comprise a distinct genus for which the name Fluctibacter gen. nov. is proposed. Based on a polyphasic characterisation and identifying differences in genomic and taxonomic data, strain AA17T represents a novel species, for which the name Fluctibacter corallii sp. nov. is proposed. The type strain is AA17T (= LMG 32603 T = NCTC 14664T). This work also supports the reclassification of A. halophilus as Fluctibacter halophilus comb. nov., which is the type species of the Fluctibacter genus. Genomic analyses also support the reclassification of Paraglaciecola oceanifecundans as a later heterotypic synonym of Paraglaciecola agarilytica.
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Affiliation(s)
- Sarah A Emsley
- Department of Biology, Southern Oregon University, Ashland, OR, USA
| | - Rachel M Loughran
- Microbiology Graduate Program, University of Delaware, Newark, DE, USA
| | | | | | - Yesmarie T De La Flor
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA
| | | | | | - Marc J Koyack
- School of Arts and Sciences, Gwynedd Mercy University, Gwynedd Valley, PA, USA
| | - David K Oline
- Department of Biology, Southern Oregon University, Ashland, OR, USA
| | - Thomas E Hanson
- Microbiology Graduate Program, University of Delaware, Newark, DE, USA
- School of Marine Science and Policy and Delaware Biotechnology Institute, University of Delaware, Delaware, USA
| | - Patrick Videau
- Department of Biology, Southern Oregon University, Ashland, OR, USA
- AgBiome, Research Triangle Park, NC, USA
| | - Jimmy H Saw
- Department of Biological Sciences, The George Washington University, Washington, DC, USA.
| | - Blake Ushijima
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA.
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Gautam P, Cusick KD. Development of a real-time quantitative PCR assay for detection and quantification of the marine bacterium Alteromonas macleodii from coastal environments. J Microbiol Methods 2023; 204:106629. [PMID: 36460091 DOI: 10.1016/j.mimet.2022.106629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 11/16/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022]
Abstract
Alteromonas macleodii is a ubiquitous marine bacterial species found in a variety of habitats that displays both planktonic and particle-associated lifestyles. Transcriptomic studies demonstrate that, even when present at low abundance, it can make significant contributions to biogeochemical cycles, and its specific association with key marine phytoplankton species indicates other ecological roles as well. It has also been shown to be one of the early colonizers of copper-treated marine vessels. There currently exist no rapid, reliable molecular assays for the detection and quantification of A. macleodii from its different environments. We developed a real-time PCR assay, specific to A. macleodii. This assay targets the DNA gyrase B subunit (gyrB) gene, which occurs as a single copy in the genome. The assay possesses an amplification efficiency of 94.3%, with a limit of detection of 2.5 gyrB copies per μL. Assay specificity was validated by melt curve analysis, followed by sequencing of the amplified product. The assay was specific to thirteen A. macleodii strains and did not amplify other marine bacteria, including Roseobacter denitrificans, Silicibacter sp. TM1040, Vibrio coralliilyticus, Vibrio harveyi, and Vibrio alginolyticus. It also did not amplify Alteromonas mediterranea, a close relative that can occur in the same environment as A. macleodii. This assay was used to determine the presence and abundance of A. macleodii from a range of coastal habitats. The assay was also used to monitor the A. macleodii growth in biofilm and planktonic cultures over time in the presence of elevated copper. This assay provides a rapid and reliable means to assess the presence and abundance of a ubiquitous marine bacterium that, even at low abundance, has been shown to make significant contributions to key marine processes.
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Affiliation(s)
- Pratima Gautam
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21225, USA
| | - Kathleen D Cusick
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21225, USA.
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Haro-Moreno JM, López-Pérez M, Rodriguez-Valera F. Enhanced Recovery of Microbial Genes and Genomes From a Marine Water Column Using Long-Read Metagenomics. Front Microbiol 2021; 12:708782. [PMID: 34512586 PMCID: PMC8430335 DOI: 10.3389/fmicb.2021.708782] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/30/2021] [Indexed: 12/12/2022] Open
Abstract
Third-generation sequencing has penetrated little in metagenomics due to the high error rate and dependence for assembly on short-read designed bioinformatics. However, second-generation sequencing metagenomics (mostly Illumina) suffers from limitations, particularly in the assembly of microbes with high microdiversity and retrieval of the flexible (adaptive) fraction of prokaryotic genomes. Here, we have used a third-generation technique to study the metagenome of a well-known marine sample from the mixed epipelagic water column of the winter Mediterranean. We have compared PacBio Sequel II with the classical approach using Illumina Nextseq short reads followed by assembly to study the metagenome. Long reads allow for efficient direct retrieval of complete genes avoiding the bias of the assembly step. Besides, the application of long reads on metagenomic assembly allows for the reconstruction of much more complete metagenome-assembled genomes (MAGs), particularly from microbes with high microdiversity such as Pelagibacterales. The flexible genome of reconstructed MAGs was much more complete containing many adaptive genes (some with biotechnological potential). PacBio Sequel II CCS appears particularly suitable for cellular metagenomics due to its low error rate. For most applications of metagenomics, from community structure analysis to ecosystem functioning, long reads should be applied whenever possible. Specifically, for in silico screening of biotechnologically useful genes, or population genomics, long-read metagenomics appears presently as a very fruitful approach and can be analyzed from raw reads before a computationally demanding (and potentially artifactual) assembly step.
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Affiliation(s)
- Jose M. Haro-Moreno
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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Feng X, Yan W, Wang A, Ma R, Chen X, Lin TH, Chen YL, Wei S, Jin T, Jiao N, Zhang R. A Novel Broad Host Range Phage Infecting Alteromonas. Viruses 2021; 13:v13060987. [PMID: 34073246 PMCID: PMC8228385 DOI: 10.3390/v13060987] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 12/24/2022] Open
Abstract
Bacteriophages substantially contribute to bacterial mortality in the ocean and play critical roles in global biogeochemical processes. Alteromonas is a ubiquitous bacterial genus in global tropical and temperate waters, which can cross-protect marine cyanobacteria and thus has important ecological benefits. However, little is known about the biological and ecological features of Alteromonas phages (alterophages). Here, we describe a novel alterophage vB_AmeP-R8W (R8W), which belongs to the Autographiviridae family and infects the deep-clade Alteromonas mediterranea. R8W has an equidistant and icosahedral head (65 ± 1 nm in diameter) and a short tail (12 ± 2 nm in length). The genome size of R8W is 48,825 bp, with a G + C content of 40.55%. R8W possesses three putative auxiliary metabolic genes encoding proteins involved in nucleotide metabolism and DNA binding: thymidylate synthase, nucleoside triphosphate pyrophosphohydrolase, and PhoB. R8W has a rapid lytic cycle with a burst size of 88 plaque-forming units/cell. Notably, R8W has a wide host range, such that it can infect 35 Alteromonas strains; it exhibits a strong specificity for strains isolated from deep waters. R8W has two specific receptor binding proteins and a compatible holin-endolysin system, which contribute to its wide host range. The isolation of R8W will contribute to the understanding of alterophage evolution, as well as the phage-host interactions and ecological importance of alterophages.
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Affiliation(s)
- Xuejin Feng
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Wei Yan
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
- College of Marine Science and Technology, China University of Geosciences, Wuhan 430074, China
| | - Anan Wang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Ruijie Ma
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Xiaowei Chen
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Ta-Hui Lin
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Yi-Lung Chen
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Shuzhen Wei
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
| | - Tao Jin
- Guangzhou Magigene Biotechnology Co., Ltd., Guangzhou 510000, China;
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
- Correspondence: (N.J.); (R.Z.)
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (X.F.); (W.Y.); (A.W.); (R.M.); (X.C.); (T.-H.L.); (Y.-L.C.); (S.W.)
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China
- Correspondence: (N.J.); (R.Z.)
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Kim YO, Park IS, Park S, Yoon JH. Alteromonas ponticola sp. nov., a gammaproteobacterium isolated from seawater. Int J Syst Evol Microbiol 2020; 70:6396-6401. [DOI: 10.1099/ijsem.0.004545] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
A Gram-stain-negative, aerobic, non-spore-forming, non-motile and ovoid or rod-shaped bacterial strain, MYP5T, was isolated from seawater in Jeju island of South Korea. MYP5T grew optimally at 30–35 °C and in the presence of 2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that MYP5T fell within the clade enclosed by the type strains of species of the genus
Alteromonas
, clustering with the type strains of
Alteromonas confluentis
and
Alteromonas halophila
. MYP5T exhibited the highest 16S rRNA gene sequence similarity value (98.0 %) to the type strain of
A. confluentis
and similarities of 95.1–97.9 % to the type strains of the other species of the genus
Alteromonas
. ANI and dDDH values of genomic sequences between MYP5T and the type strains of 22 species of the genus
Alteromonas
were 66.8–70.5 % and 18.6–27.5 %, respectively. The DNA G+C content of MYP5T, determined from the genome sequence, was 46.1 %. MYP5T contained Q-8 as the predominant ubiquinone and C18 : 1 ω7c, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and 10-methyl C17 : 0 as the major fatty acids. The major polar lipids of MYP5T were phosphatidylethanolamine and phosphatidylglycerol. Distinguishing phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that MYP5T is separated from species of the genus
Alteromonas
. On the basis of the data presented, MYP5T is considered to represent a novel species of the genus
Alteromonas
, for which the name Alteromonas ponticola sp. nov. is proposed. The type strain is MYP5T (=KCTC 82144T=NBRC 114354T).
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Affiliation(s)
- Young-Ok Kim
- Biotechnology Research Division, National Institute of Fisheries Science (NIFS), Gijang, Busan 46083, South Korea
| | - In-Suk Park
- Biotechnology Research Division, National Institute of Fisheries Science (NIFS), Gijang, Busan 46083, South Korea
| | - Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon 16419, South Korea
- Biotechnology Research Division, National Institute of Fisheries Science (NIFS), Gijang, Busan 46083, South Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon 16419, South Korea
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10
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Chen M, Song Y, Feng X, Tang K, Jiao N, Tian J, Zhang Y. Genomic Characteristics and Potential Metabolic Adaptations of Hadal Trench Roseobacter and Alteromonas Bacteria Based on Single-Cell Genomics Analyses. Front Microbiol 2020; 11:1739. [PMID: 32793171 PMCID: PMC7393951 DOI: 10.3389/fmicb.2020.01739] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 07/03/2020] [Indexed: 11/30/2022] Open
Abstract
Heterotrophic bacteria such as those from the Roseobacter group and genus Alteromonas dominate the hadal zones of oceans; however, we know little about the genomic characteristics and potential metabolic adaptations of hadal trench-dwelling bacteria. Here, we report multiple single amplified genomes (SAGs) belonging to Roseobacter and Alteromonas, recovered from the hadal zone of the Mariana Trench. While phylogenetic analyses show that these hadal SAGs cluster with their surface relatives, an analysis of genomic recruitment indicates that they have higher relative abundances in the hadal zone of the Mariana Trench. Comparative genomic analyses between the hadal SAGs and reference genomes of closely related shallow-water relatives indicate that genes involved in the mobilome (prophages and transposons) are overrepresented among the unique genes of the hadal Roseobacter and Alteromonas SAGs; the functional proteins encoded by this category of genes also shows higher amino acid sequence variation than those encoded by other gene sets within the Roseobacter SAGs. We also found that genes involved in cell wall/membrane/envelope biogenesis, transcriptional regulation, and metal transport may be important for the adaptation of hadal Roseobacter and Alteromonas lineages. These results imply that the modification of cell surface-related proteins and transporters is the major direction of genomic evolution in Roseobacter and Alteromonas bacteria adapting to the hadal environment, and that prophages and transposons may be the key factors driving this process.
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Affiliation(s)
- Mingming Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Yu Song
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Xiaoyuan Feng
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Jiwei Tian
- Physical Oceanography Laboratory, Ocean University of China, Qingdao, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
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11
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Complete genome sequence of Alteromonas pelagimontana 5.12 T, a marine exopolysaccharide-producing bacterium isolated from hydrothermally influenced deep-sea sediment of eastern Southwest Indian Ridge. Mar Genomics 2020; 55:100804. [PMID: 32665084 DOI: 10.1016/j.margen.2020.100804] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/24/2020] [Accepted: 06/30/2020] [Indexed: 11/21/2022]
Abstract
The whole genome of Alteromonas pelagimontana 5.12T, a psychrotolerant deep-sea bacterium isolated from the sediment sample of eastern Southwest Indian Ridge, was sequenced and analysed for understanding its metabolic capacities and biosynthesis potential of natural products. The circular genome contained 4.3 Mb with a GC content of 42.6 mol%. Genomic data mining revealed a gene cluster for heavy metal resistance (czcABC, acrB, arsR1, copA, nikA, mntH, mntP), exopolysaccharides (EPS; epsCDEFHLM) and polyhydroxyalkanoates (PHA; phbC) production, as well as genes involved in complex polysaccharide degradation. Genes that could allow strain 5.12T to cope with acid stress (ibaG) and heat shock (ibpA, hslR) were observed along with ten chaperone-encoding genes which could possibly play vital role in adaptability of this strain to the hydrothermally influenced environment. Gene clusters for secondary metabolite production such as bacteriocin and arylpolyene were also predicted. Thus, genome sequencing and data mining provided insights into the molecular mechanisms involved in the adaptation to hydrothermally influenced deep-sea environment that could promote further experimental exploration.
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12
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Shen X, Zhu S, Dong B, Chen Y, Xue Z, Ren N, Chen T, Chen X, Yang J, Chen J. Alteromonas profundi sp. nov., isolated from the Indian Ocean. Int J Syst Evol Microbiol 2020; 70:4531-4536. [PMID: 32614764 DOI: 10.1099/ijsem.0.004308] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative bacterium, designated 345S023T, was isolated from a sea water sample from the Indian Ocean. The results of 16S rRNA gene sequence analysis revealed that 345S023T represents a member of the genus Alteromonas, with closely related type strains Alteromonas fortis 1T (98.7 %), Alteromonas hispanica F-32T (98.6 %) and Alteromonas genovensis LMG 24078T (98.6 %). Up-to-date bacterial core gene set analysis revealed that 345S023T formed a phyletic lineage with Alteromonas australica H 17T. The case for 345S023T representing a novel species was supported by genomic results. Pairwise in silico DNA-DNA hybridization and average nucleotide identity values were much lower than the proposed and generally accepted species boundaries. Strain 345S023T contains ubiquinone-8 (Q-8) as the sole isoprenoid quinone, summed featured 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c as the dominant cellular fatty acids (>10 %), and phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. The genome of strain 345S023T consisted of a 4.4 Mb chromosome with a DNA G+C content of 44.4 %. On the basis of these genomic, chemotaxonomic and phenotypic characteristics, we propose a novel species: Alteromonas profundi sp. nov. The type strain is 345S023T(=JCM 33893T=MCCC 1K04570T).
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Affiliation(s)
- Xudong Shen
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Sidong Zhu
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Bingxia Dong
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Yong Chen
- Institute of Respiratory and Disease, Shenzhen People's Hospital, Shenzhen 518020, PR China
| | - Zehao Xue
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Na Ren
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Ting Chen
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Xiunuan Chen
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Jifang Yang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Jigang Chen
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
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13
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Huang H, Mo K, Li S, Dongmei S, Zhu J, Zou X, Hu Y, Bao S. Alteromonas portus sp. nov., an alginate lyase-excreting marine bacterium. Int J Syst Evol Microbiol 2020; 70:1516-1521. [DOI: 10.1099/ijsem.0.003884] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An alginate lyase-excreting bacterium, designated strain HB161718T, was isolated from coastal sand collected from Tanmen Port in Hainan, PR China. Cells were Gram-stain-negative rods and motile with a single polar flagellum. Its major isoprenoid quinone was ubiquinone 8 (Q-8), and its cellular fatty acid profile mainly consisted of C16 : 1 ω7c and/or C16 : 1 ω6c, C18 : 1 ω6c and/or C18 : 1 ω7c, C16 : 0, C17 : 0 10-methyl and C16 : 0 N alcohol. The G+C content of the genomic DNA was 44.1 mol%. 16S rRNA gene sequence analysis suggested that strain HB161718T belonged to the genus
Alteromonas
, sharing 99.5, 99.4, 99.2, 98.9 and 98.5 % sequence similarities to its closest relatives,
Alteromonas macleodii
JCM 20772T,
Alteromonas gracilis
9a2T,
Alteromonas australica
H17T,
Alteromonas marina
SW-47T and
Alteromonas mediterranea
DET, respectively. The low values of DNA–DNA hybridization and average
nucleotide identity showed that it formed a distinct genomic species. The combined phenotypic and molecular features supported the conclusion that strain HB161718T represents a novel species of the genus
Alteromonas
, for which the name Alteromonas portus sp. nov. is proposed. The type strain is HB161718T (=CGMCC 1.13585T=JCM 32687T).
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Affiliation(s)
- Huiqin Huang
- Hainan Provincial Key Laboratory for Functional Component Research and Utilization of Marine Bioresources, Haikou 571101, Hainan, PR China
- Institute of Tropical Biosciences and Biotechnology, Hainan Academy of Tropical Agricultural Resources, CATAS, Haikou 571101, PR China
| | - Kunlian Mo
- Hainan Provincial Key Laboratory for Functional Component Research and Utilization of Marine Bioresources, Haikou 571101, Hainan, PR China
- Institute of Tropical Biosciences and Biotechnology, Hainan Academy of Tropical Agricultural Resources, CATAS, Haikou 571101, PR China
| | - Shuang Li
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163000, Hainan, PR China
- Institute of Tropical Biosciences and Biotechnology, Hainan Academy of Tropical Agricultural Resources, CATAS, Haikou 571101, PR China
| | - Sun Dongmei
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, 163000, Hainan, PR China
| | - Jun Zhu
- Hainan Provincial Key Laboratory for Functional Component Research and Utilization of Marine Bioresources, Haikou 571101, Hainan, PR China
- Institute of Tropical Biosciences and Biotechnology, Hainan Academy of Tropical Agricultural Resources, CATAS, Haikou 571101, PR China
| | - Xiaoxiao Zou
- Hainan Provincial Key Laboratory for Functional Component Research and Utilization of Marine Bioresources, Haikou 571101, Hainan, PR China
- Institute of Tropical Biosciences and Biotechnology, Hainan Academy of Tropical Agricultural Resources, CATAS, Haikou 571101, PR China
| | - Yonghua Hu
- Institute of Tropical Biosciences and Biotechnology, Hainan Academy of Tropical Agricultural Resources, CATAS, Haikou 571101, PR China
- Hainan Provincial Key Laboratory for Functional Component Research and Utilization of Marine Bioresources, Haikou 571101, Hainan, PR China
| | - Shixiang Bao
- Institute of Tropical Biosciences and Biotechnology, Hainan Academy of Tropical Agricultural Resources, CATAS, Haikou 571101, PR China
- Hainan Provincial Key Laboratory for Functional Component Research and Utilization of Marine Bioresources, Haikou 571101, Hainan, PR China
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14
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Zhang D, Gui J, Zheng S, Zhu X, Wu S, Tian Y, Lai Q, Xu H. Marisediminitalea mangrovi gen. nov., sp. nov., isolated from marine mangrove sediment, and reclassification of Aestuariibacter aggregatus as Marisediminitalea aggregata comb. nov. Int J Syst Evol Microbiol 2020; 70:457-464. [PMID: 31626587 DOI: 10.1099/ijsem.0.003773] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain GS-14T was isolated from a mangrove sediment sample collected at Beilun Estuary National Nature Reserve, Guangxi Province, PR China. Cells were Gram-stain-negative, strictly aerobic and rod-shaped with a polar flagellum. Optimal growth occurred in the presence of 3-6 % (w/v) NaCl, at pH 6-8 and at a temperature of 37 °C. The predominant polar lipids were phosphatidylglycerol and phosphatidylethanolamine. Ubiquinone 8 (Q-8) was the sole respiratory quinone. The major fatty acids (>10 % of the total fatty acids) were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The DNA G+C content was 47.6 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain GS-14T had the highest sequence similarity to Aestuariibacter aggregatus WH169T (96.63 %), Aliiglaciecola coringensis AK49T (96.56 %) and Alteromonas lipolytica JW12T (96.22 %). In addition, the OrthoANIu value and dDDH values calculated from the genomes of strain GS-14T and A. aggregatus WH169T were 79.5 and 21.9 %, respectively. Based on the polyphasic taxonomic results, strain GS-14T is considered to represent a novel species in a new genus, for which the name Marisediminitalea mangrovi gen. nov., sp. nov. is proposed. The type strain of Marisediminitalea mangrovi is GS-14T (=KCTC 72401T=MCCC 1K03622T). Because Aestuariibacter aggregatus WH169T clustered with strain GS-14T in the phylogenetic trees and was clearly separated from the two species within the genus Aestuariibacter, it is reclassified as a member of the genus Marisediminitalea as Marisediminitalea aggregata comb. nov. (type strain WH169T=CGMCC 1.8995T=LMG 25283T). The type species of the genus Marisediminitalea is Marisediminitalea aggregata gen. nov., comb. nov.
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Affiliation(s)
- Danyang Zhang
- State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen, Fujian, 361102, PR China.,Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Jiali Gui
- State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen, Fujian, 361102, PR China.,Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Sisi Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Xiaoying Zhu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Shiyin Wu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, 361005, PR China
| | - Hong Xu
- State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen, Fujian, 361102, PR China.,Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, PR China
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15
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Barbeyron T, Zonta E, Le Panse S, Duchaud E, Michel G. Alteromonas fortis sp. nov., a non-flagellated bacterium specialized in the degradation of iota-carrageenan, and emended description of the genus Alteromonas. Int J Syst Evol Microbiol 2019; 69:2514-2521. [DOI: 10.1099/ijsem.0.003533] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Tristan Barbeyron
- 1CNRS / Sorbonne Université, UMR 8227 Integrative Biology of Marine Models (LBI2M), research group of Marine Glycobiology, Station Biologique de Roscoff (SBR), 29680 Roscoff, Brittany, France
| | - Erwann Zonta
- 1CNRS / Sorbonne Université, UMR 8227 Integrative Biology of Marine Models (LBI2M), research group of Marine Glycobiology, Station Biologique de Roscoff (SBR), 29680 Roscoff, Brittany, France
| | - Sophie Le Panse
- 2CNRS / Sorbonne Université, FR 2424 Research and training in marine biology, Merimage platform, Station Biologique de Roscoff (SBR), 29680 Roscoff, Brittany, France
| | - Eric Duchaud
- 3INRA VIM-UR0892 Molecular Immunology and Virology, research group of Infection and Immunity of Fish, Research Center of Jouy-en-Josas, F-78352 Jouy-en-Josas, Ile-de-France, France
| | - Gurvan Michel
- 1CNRS / Sorbonne Université, UMR 8227 Integrative Biology of Marine Models (LBI2M), research group of Marine Glycobiology, Station Biologique de Roscoff (SBR), 29680 Roscoff, Brittany, France
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16
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Liu J, Zheng Y, Lin H, Wang X, Li M, Liu Y, Yu M, Zhao M, Pedentchouk N, Lea-Smith DJ, Todd JD, Magill CR, Zhang WJ, Zhou S, Song D, Zhong H, Xin Y, Yu M, Tian J, Zhang XH. Proliferation of hydrocarbon-degrading microbes at the bottom of the Mariana Trench. MICROBIOME 2019; 7:47. [PMID: 30975208 PMCID: PMC6460516 DOI: 10.1186/s40168-019-0652-3] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 02/22/2019] [Indexed: 05/09/2023]
Abstract
BACKGROUND The Mariana Trench is the deepest known site in the Earth's oceans, reaching a depth of ~ 11,000 m at the Challenger Deep. Recent studies reveal that hadal waters harbor distinctive microbial planktonic communities. However, the genetic potential of microbial communities within the hadal zone is poorly understood. RESULTS Here, implementing both culture-dependent and culture-independent methods, we perform extensive analysis of microbial populations and their genetic potential at different depths in the Mariana Trench. Unexpectedly, we observed an abrupt increase in the abundance of hydrocarbon-degrading bacteria at depths > 10,400 m in the Challenger Deep. Indeed, the proportion of hydrocarbon-degrading bacteria at > 10,400 m is the highest observed in any natural environment on Earth. These bacteria were mainly Oleibacter, Thalassolituus, and Alcanivorax genera, all of which include species known to consume aliphatic hydrocarbons. This community shift towards hydrocarbon degraders was accompanied by increased abundance and transcription of genes involved in alkane degradation. Correspondingly, three Alcanivorax species that were isolated from 10,400 m water supplemented with hexadecane were able to efficiently degrade n-alkanes under conditions simulating the deep sea, as did a reference Oleibacter strain cultured at atmospheric pressure. Abundant n-alkanes were observed in sinking particles at 2000, 4000, and 6000 m (averaged 23.5 μg/gdw) and hadal surface sediments at depths of 10,908, 10,909, and 10,911 m (averaged 2.3 μg/gdw). The δ2H values of n-C16/18 alkanes that dominated surface sediments at near 11,000-m depths ranged from - 79 to - 93‰, suggesting that these sedimentary alkanes may have been derived from an unknown heterotrophic source. CONCLUSIONS These results reveal that hydrocarbon-degrading microorganisms are present in great abundance in the deepest seawater on Earth and shed a new light on potential biological processes in this extreme environment.
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Affiliation(s)
- Jiwen Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yanfen Zheng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Heyu Lin
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Xuchen Wang
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Qingdao, 266100, China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Yang Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Meng Yu
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Qingdao, 266100, China
| | - Meixun Zhao
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Qingdao, 266100, China
| | - Nikolai Pedentchouk
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - David J Lea-Smith
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | | | - Wei-Jia Zhang
- Laboratory of Deep Sea Microbial Cell Biology, Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Shun Zhou
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Delei Song
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Haohui Zhong
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yu Xin
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Qingdao, 266100, China
| | - Min Yu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Jiwei Tian
- Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao, 266100, China.
- Marine Dynamic Process and Climate Function Laboratory, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Xiao-Hua Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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17
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Ye MQ, Han JR, Wang C, Du ZJ. Alteromonas sediminis sp. nov., isolated from sediment in a sea cucumber culture pond. Int J Syst Evol Microbiol 2019; 69:1579-1584. [PMID: 30900969 DOI: 10.1099/ijsem.0.003358] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel strain, U0105T, was isolated from marine sediment of the coast of Weihai, China. The bacterium was aerobic, Gram-stain-negative, oxidase-positive, catalase-positive, rod-shaped and motile. Growth was observed at salinities of 1.0-6.0 % (w/v) NaCl (optimum with 2.0-3.0 %), temperatures of 20-40 °C (optimum at 37 °C) and pH of 6.5-9.5 (optimum at pH 7.0-7.5). The isolate could not reduce nitrate to nitrite. It could hydrolyse starch and Tweens 20, 40 and 60, but not casein or cellulose. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain U0105T belonged to the genus Alteromonas, with highest sequence similarity to Alteromonas aestuariivivens KCTC 52655T (97.1 %). The average nucleotide identity value and the digital DNA-DNA hybridization value between strain U0105T and A. aestuariivivens KCTC 52655T were 69.2 % and 21.2 %, respectively. Strain U0105T was found to contain Q-8 as the sole menaquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c as the major fatty acids. The major polar lipids were identified as phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the chromosomal DNA was 45.3 mol%. The combined genotypic and phenotypic data show that strain U0105T represents a novel species of the genus Alteromonas, for which the name Alteromonas sediminis sp. nov. is proposed. The type strain is U0105T (=KCTC 62080T=MCCC 1H00299T).
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Affiliation(s)
- Meng-Qi Ye
- 1College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Ji-Ru Han
- 1College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Chong Wang
- 1College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Zong-Jun Du
- 2State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.,1College of Marine Science, Shandong University, Weihai 264209, PR China
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18
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Sun C, Xamxidin M, Wu YH, Cheng H, Wang CS, Xu XW. Alteromonas alba sp. nov., a marine bacterium isolated from seawater of the West Pacific Ocean. Int J Syst Evol Microbiol 2019; 69:278-284. [DOI: 10.1099/ijsem.0.003151] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Cong Sun
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Maripat Xamxidin
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Yue-Hong Wu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Hong Cheng
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Chun-Sheng Wang
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, PR China
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19
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Lin D, Chen Y, Zhu S, Yang J, Chen J. Alteromonas indica sp. nov., isolated from surface seawater from the Indian Ocean. Int J Syst Evol Microbiol 2018; 68:3881-3885. [DOI: 10.1099/ijsem.0.003078] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Danqiu Lin
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Yong Chen
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Sidong Zhu
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Jifang Yang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Jigang Chen
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
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20
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Peoples LM, Donaldson S, Osuntokun O, Xia Q, Nelson A, Blanton J, Allen EE, Church MJ, Bartlett DH. Vertically distinct microbial communities in the Mariana and Kermadec trenches. PLoS One 2018; 13:e0195102. [PMID: 29621268 PMCID: PMC5886532 DOI: 10.1371/journal.pone.0195102] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/17/2018] [Indexed: 01/13/2023] Open
Abstract
Hadal trenches, oceanic locations deeper than 6,000 m, are thought to have distinct microbial communities compared to those at shallower depths due to high hydrostatic pressures, topographical funneling of organic matter, and biogeographical isolation. Here we evaluate the hypothesis that hadal trenches contain unique microbial biodiversity through analyses of the communities present in the bottom waters of the Kermadec and Mariana trenches. Estimates of microbial protein production indicate active populations under in situ hydrostatic pressures and increasing adaptation to pressure with depth. Depth, trench of collection, and size fraction are important drivers of microbial community structure. Many putative hadal bathytypes, such as members related to the Marinimicrobia, Rhodobacteraceae, Rhodospirilliceae, and Aquibacter, are similar to members identified in other trenches. Most of the differences between the two trench microbiomes consists of taxa belonging to the Gammaproteobacteria whose distributions extend throughout the water column. Growth and survival estimates of representative isolates of these taxa under deep-sea conditions suggest that some members may descend from shallower depths and exist as a potentially inactive fraction of the hadal zone. We conclude that the distinct pelagic communities residing in these two trenches, and perhaps by extension other trenches, reflect both cosmopolitan hadal bathytypes and ubiquitous genera found throughout the water column.
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Affiliation(s)
- Logan M. Peoples
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of America
| | - Sierra Donaldson
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of America
| | - Oladayo Osuntokun
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of America
| | - Qing Xia
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of America
- Department of Soil Science, North Carolina State University, Raleigh, NC, United States of America
| | - Alex Nelson
- Center for Microbial Oceanography: Research and Education, C-MORE Hale, University of Hawaiʻi at Mānoa, Honolulu, HI, United States of America
| | - Jessica Blanton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of America
| | - Eric E. Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of America
| | - Matthew J. Church
- Center for Microbial Oceanography: Research and Education, C-MORE Hale, University of Hawaiʻi at Mānoa, Honolulu, HI, United States of America
- Flathead Lake Biological Station, University of Montana, Polson, MT, United States of America
| | - Douglas H. Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of America
- * E-mail:
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21
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Jin QW, Hu YH, Sun L. Alteromonas oceani sp. nov., isolated from deep-sea sediment of a hydrothermal field. Int J Syst Evol Microbiol 2018; 68:657-662. [DOI: 10.1099/ijsem.0.002560] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Qian-wen Jin
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, PR China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Yong-hua Hu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, PR China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Li Sun
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, PR China
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22
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Nóbrega MS, Silva BS, Leomil L, Tschoeke DA, Campeão ME, Garcia GD, Dias GA, Vieira VV, Thompson CC, Thompson FL. Description of Alteromonas abrolhosensis sp. nov., isolated from sea water of Abrolhos Bank, Brazil. Antonie van Leeuwenhoek 2018; 111:1131-1138. [PMID: 29349565 DOI: 10.1007/s10482-018-1016-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 01/10/2018] [Indexed: 11/29/2022]
Abstract
Two Gram-negative, motile, aerobic bacteria isolated from waters of the Abrolhos Bank were classified through a whole genome-based taxonomy. Strains PEL67ET and PEL68C shared 99% 16S rRNA and dnaK sequence identity with Alteromonas marina SW-47T and Alteromonas macleodii ATCC 27126T. In silico DNA-DNA Hybridization, i.e. genome-to-genome distance (GGD), average amino acid identity (AAI) and average nucleotide identity (ANI) showed that PEL67ET and PEL68C had identity values between 33-36, 86-88 and 83-84%, and 85-86 and 83%, respectively, towards their close neighbors A. macleodii ATCC 27126T and A. marina SW-47T. The DNA G + C contents of PEL67ET and PEL68C were 44.5%. The phenotypic features that differentiate PEL67ET and PEL68C strains from their close neighbors were assimilation of galactose and activity of phosphatase, and lack of mannitol, maltose, acetate, xylose and glycerol assimilation and lack of lipase, α and β-glucosidase activity. The new species Alteromonas abrolhosensis is proposed. The type strain is PEL67ET (= CBAS 610T = CAIM 1925T).
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Affiliation(s)
- Maria S Nóbrega
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Bruno S Silva
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Luciana Leomil
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Diogo Antonio Tschoeke
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil.,Núcleo em Ecologia e Desenvolvimento Sócio-Ambiental de Macaé (NUPEM), Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil.,SAGE-COPPE, Federal University of Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Mariana E Campeão
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | - Gizele D Garcia
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil.,Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil
| | - Graciela A Dias
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil
| | | | - Cristiane C Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil. .,CCS/IB/BIOMAR, Lab. de Microbiologia, Cidade Universitária, Av. Carlos Chagas Filho 373. Sala 102, Bloco A, Rio de Janeiro, RJ, CEP 21941-599, Brazil.
| | - Fabiano L Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio De Janeiro, RJ, Brazil. .,SAGE-COPPE, Federal University of Rio de Janeiro, Rio De Janeiro, RJ, Brazil. .,CCS/IB/BIOMAR, Lab. de Microbiologia, Cidade Universitária, Av. Carlos Chagas Filho 373. Sala 102, Bloco A, Rio de Janeiro, RJ, CEP 21941-599, Brazil.
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23
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Sinha RK, Krishnan KP, Singh A, Thomas FA, Jain A, John Kurian P. Alteromonas pelagimontana sp. nov., a marine exopolysaccharide-producing bacterium isolated from the Southwest Indian Ridge. Int J Syst Evol Microbiol 2017; 67:4032-4038. [DOI: 10.1099/ijsem.0.002245] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Rupesh Kumar Sinha
- National Centre for Antarctic and Ocean Research, Headland Sada, Vasco da Gama, Goa, India
| | - K. P. Krishnan
- National Centre for Antarctic and Ocean Research, Headland Sada, Vasco da Gama, Goa, India
| | - Archana Singh
- National Centre for Antarctic and Ocean Research, Headland Sada, Vasco da Gama, Goa, India
| | - Femi Anna Thomas
- National Centre for Antarctic and Ocean Research, Headland Sada, Vasco da Gama, Goa, India
| | - Anand Jain
- National Centre for Antarctic and Ocean Research, Headland Sada, Vasco da Gama, Goa, India
| | - P. John Kurian
- National Centre for Antarctic and Ocean Research, Headland Sada, Vasco da Gama, Goa, India
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24
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Alteromonas aestuariivivens sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2017; 67:2791-2797. [DOI: 10.1099/ijsem.0.002023] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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25
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Cusick KD, Dale JR, Fitzgerald LA, Little BJ, Biffinger JC. Adaptation to copper stress influences biofilm formation in Alteromonas macleodii. BIOFOULING 2017; 33:505-519. [PMID: 28604167 DOI: 10.1080/08927014.2017.1329423] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 05/09/2017] [Indexed: 06/07/2023]
Abstract
An Alteromonas macleodii strain was isolated from copper-containing coupons incubated in surface seawater (Key West, FL, USA). In addition to the original isolate, a copper-adapted mutant was created and maintained with 0.78 mM Cu2+. Biofilm formation was compared between the two strains under copper-amended and low-nutrient conditions. Biofilm formation was significantly increased in the original isolate under copper amendment, while biofilm formation was significantly higher in the mutant under low-nutrient conditions. Biofilm expression profiles of diguanylate cyclase (DGC) genes, as well as genes involved in secretion, differed between the strains. Comparative genomic analysis demonstrated that both strains possessed a large number of gene attachment harboring cyclic di-GMP synthesis and/or degradation domains. One of the DGC genes, induced at very high levels in the mutant, possessed a degradation domain in the original isolate that was lacking in the mutant. The genetic and transcriptional mechanisms contributing to biofilm formation are discussed.
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Affiliation(s)
- Kathleen D Cusick
- a Chemistry Department , US Naval Research Laboratory , Washington , DC , USA
| | - Jason R Dale
- b Geosciences Division , US Naval Research Laboratory, Stennis Space Center , Mississippi , MS , USA
| | - Lisa A Fitzgerald
- c Chemistry Department , US Naval Research Laboratory , Washington , DC , USA
| | - Brenda J Little
- b Geosciences Division , US Naval Research Laboratory, Stennis Space Center , Mississippi , MS , USA
| | - Justin C Biffinger
- c Chemistry Department , US Naval Research Laboratory , Washington , DC , USA
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26
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Shi XL, Wu YH, Jin XB, Wang CS, Xu XW. Alteromonas lipolytica sp. nov., a poly-beta-hydroxybutyrate-producing bacterium isolated from surface seawater. Int J Syst Evol Microbiol 2017; 67:237-242. [DOI: 10.1099/ijsem.0.001604] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Xiao-Lai Shi
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012, PR China
| | - Yue-Hong Wu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012, PR China
| | - Xiong-Bin Jin
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012, PR China
| | - Chun-Sheng Wang
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012, PR China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, Hangzhou, 310012, PR China
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27
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Abstract
We have examined a collection of the free-living marine bacterium Alteromonas genomes with cores diverging in average nucleotide identities ranging from 99.98% to 73.35%, i.e., from microbes that can be considered members of a natural clone (like in a clinical epidemiological outbreak) to borderline genus level. The genomes were largely syntenic allowing a precise delimitation of the core and flexible regions in each. The core was 1.4 Mb (ca. 30% of the typical strain genome size). Recombination rates along the core were high among strains belonging to the same species (37.7-83.7% of all nucleotide polymorphisms) but they decreased sharply between species (18.9-5.1%). Regarding the flexible genome, its main expansion occurred within the boundaries of the species, i.e., strains of the same species already have a large and diverse flexible genome. Flexible regions occupy mostly fixed genomic locations. Four large genomic islands are involved in the synthesis of strain-specific glycosydic receptors that we have called glycotypes. These genomic regions are exchanged by homologous recombination within and between species and there is evidence for their import from distant taxonomic units (other genera within the family). In addition, several hotspots for integration of gene cassettes by illegitimate recombination are distributed throughout the genome. They code for features that give each clone specific properties to interact with their ecological niche and must flow fast throughout the whole genus as they are found, with nearly identical sequences, in different species. Models for the generation of this genomic diversity involving phage predation are discussed.
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Affiliation(s)
- Mario López-Pérez
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
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28
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Fadeev E, De Pascale F, Vezzi A, Hübner S, Aharonovich D, Sher D. Why Close a Bacterial Genome? The Plasmid of Alteromonas Macleodii HOT1A3 is a Vector for Inter-Specific Transfer of a Flexible Genomic Island. Front Microbiol 2016; 7:248. [PMID: 27014193 PMCID: PMC4781885 DOI: 10.3389/fmicb.2016.00248] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 02/15/2016] [Indexed: 12/20/2022] Open
Abstract
Genome sequencing is rapidly becoming a staple technique in environmental and clinical microbiology, yet computational challenges still remain, leading to many draft genomes which are typically fragmented into many contigs. We sequenced and completely assembled the genome of a marine heterotrophic bacterium, Alteromonas macleodii HOT1A3, and compared its full genome to several draft genomes obtained using different reference-based and de novo methods. In general, the de novo assemblies clearly outperformed the reference-based or hybrid ones, covering >99% of the genes and representing essentially all of the gene functions. However, only the fully closed genome (∼4.5 Mbp) allowed us to identify the presence of a large, 148 kbp plasmid, pAM1A3. While HOT1A3 belongs to A. macleodii, typically found in surface waters (“surface ecotype”), this plasmid consists of an almost complete flexible genomic island (fGI), containing many genes involved in metal resistance previously identified in the genomes of Alteromonas mediterranea (“deep ecotype”). Indeed, similar to A. mediterranea, A. macleodii HOT1A3 grows at concentrations of zinc, mercury, and copper that are inhibitory for other A. macleodii strains. The presence of a plasmid encoding almost an entire fGI suggests that wholesale genomic exchange between heterotrophic marine bacteria belonging to related but ecologically different populations is not uncommon.
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Affiliation(s)
- Eduard Fadeev
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa Haifa, Israel
| | - Fabio De Pascale
- Department of Biology and CRIBI Biotechnology Centre, University of Padua Padova, Italy
| | - Alessandro Vezzi
- Department of Biology and CRIBI Biotechnology Centre, University of Padua Padova, Italy
| | - Sariel Hübner
- Department of Botany and Biodiversity Research Centre, University of British ColumbiaVancouver, Canada; The Department of Evolutionary and Environmental Biology, University of HaifaHaifa, Israel
| | - Dikla Aharonovich
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa Haifa, Israel
| | - Daniel Sher
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa Haifa, Israel
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Jin HM, Jeong HI, Kim KH, Hahn Y, Madsen EL, Jeon CO. Genome-wide transcriptional responses of Alteromonas naphthalenivorans SN2 to contaminated seawater and marine tidal flat sediment. Sci Rep 2016; 6:21796. [PMID: 26887987 PMCID: PMC4757865 DOI: 10.1038/srep21796] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 02/01/2016] [Indexed: 11/09/2022] Open
Abstract
A genome-wide transcriptional analysis of Alteromonas naphthalenivorans SN2 was performed to investigate its ecophysiological behavior in contaminated tidal flats and seawater. The experimental design mimicked these habitats that either added naphthalene or pyruvate; tidal flat-naphthalene (TF-N), tidal flat-pyruvate (TF-P), seawater-naphthalene (SW-N), and seawater-pyruvate (SW-P). The transcriptional profiles clustered by habitat (TF-N/TF-P and SW-N/SW-P), rather than carbon source, suggesting that the former may exert a greater influence on genome-wide expression in strain SN2 than the latter. Metabolic mapping of cDNA reads from strain SN2 based on KEGG pathway showed that metabolic and regulatory genes associated with energy metabolism, translation, and cell motility were highly expressed in all four test conditions, probably highlighting the copiotrophic properties of strain SN2 as an opportunistic marine r-strategist. Differential gene expression analysis revealed that strain SN2 displayed specific cellular responses to environmental variables (tidal flat, seawater, naphthalene, and pyruvate) and exhibited certain ecological fitness traits -- its notable PAH degradation capability in seasonally cold tidal flat might be reflected in elevated expression of stress response and chaperone proteins, while fast growth in nitrogen-deficient and aerobic seawater probably correlated with high expression of glutamine synthetase, enzymes utilizing nitrite/nitrate, and those involved in the removal of reactive oxygen species.
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Affiliation(s)
- Hyun Mi Jin
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea.,Freshwater Bioresources Utilization Division, Nakdonggang National Institute of Biological Resources, Gyeongsangbuk-do 37242, Republic of Korea
| | - Hye Im Jeong
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Kyung Hyun Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Yoonsoo Hahn
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Eugene L Madsen
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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30
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Zhong ZP, Liu Y, Wang F, Zhou YG, Liu HC, Liu ZP. Lacimicrobium alkaliphilum gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from a salt lake. Int J Syst Evol Microbiol 2016; 66:422-429. [DOI: 10.1099/ijsem.0.000735] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Zhi-Ping Zhong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Ying Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Fang Wang
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100089, PR China
| | - Yu-Guang Zhou
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hong-Can Liu
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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31
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Mi Jin H, Hyun Kim K, Ok Jeon C. Alteromonas naphthalenivorans sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from tidal-flat sediment. Int J Syst Evol Microbiol 2015; 65:4208-4214. [DOI: 10.1099/ijsem.0.000563] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative and halotolerant bacterium, designated SN2T, capable of biodegrading polycyclic aromatic hydrocarbons, was isolated from a tidal flat contaminated with crude oil in Korea. Cells were strictly aerobic, catalase- and oxidase-positive, motile rods, with a single polar flagellum. Growth was observed at 4–37 °C (optimum, 25–30 °C) at pH 6.0–9.0 (optimum, pH 7.0–7.5) and in the presence of 0.5–9.0 % (w/v) NaCl (optimum, 2.0 %). Only ubiquinone 8 was detected as the isoprenoid quinone, and summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0, C18 : 1ω7c and C12 : 0 were observed as the major cellular fatty acids. The major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, a glycolipid, an aminolipid and three unidentified lipids. The DNA G+C content was 43.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SN2T formed a phylogenetic lineage with Alteromonas stellipolaris and Alteromonas addita within the genus Alteromonas, which was consistent with multilocus phylogenetic and MALDI-TOF MS analyses. Strain SN2T was most closely related to the type strains of A. stellipolaris, A. addita and Alteromonas macleodii, with 16S rRNA gene sequence similarities of 99.5, 99.3 and 98.4 % and DNA–DNA relatedness of 48.7 ± 6.6, 24.9 ± 7.5 and 27.9 ± 8.4 %, respectively. In conclusion, strain SN2T represents a novel species of the genus Alteromonas, for which the name Alteromonas naphthalenivorans sp. nov. is proposed. The type strain is SN2T ( = KCTC 11700BPT = JCM 17741T = KACC 18427T).
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Affiliation(s)
- Hyun Mi Jin
- Department of Life Science, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Kyung Hyun Kim
- Department of Life Science, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 156-756, Republic of Korea
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32
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Draft Genome Sequence of Alteromonas macleodii Strain MIT1002, Isolated from an Enrichment Culture of the Marine Cyanobacterium Prochlorococcus. GENOME ANNOUNCEMENTS 2015; 3:3/4/e00967-15. [PMID: 26316635 PMCID: PMC4551879 DOI: 10.1128/genomea.00967-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Alteromonas spp. are heterotrophic gammaproteobacteria commonly found in marine environments. We present here the draft genome sequence of Alteromonas macleodii MIT1002, which was isolated from an enrichment culture of the marine cyanobacterium Prochlorococcus NATL2A. This genome contains a mixture of features previously seen only within either the “surface” or “deep” Alteromonas ecotype.
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33
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Neumann AM, Balmonte JP, Berger M, Giebel HA, Arnosti C, Voget S, Simon M, Brinkhoff T, Wietz M. Different utilization of alginate and other algal polysaccharides by marine Alteromonas macleodii ecotypes. Environ Microbiol 2015; 17:3857-68. [PMID: 25847866 DOI: 10.1111/1462-2920.12862] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/29/2015] [Indexed: 10/23/2022]
Abstract
The marine bacterium Alteromonas macleodii is a copiotrophic r-strategist, but little is known about its potential to degrade polysaccharides. Here, we studied the degradation of alginate and other algal polysaccharides by A. macleodii strain 83-1 in comparison to other A. macleodii strains. Cell densities of strain 83-1 with alginate as sole carbon source were comparable to those with glucose, but the exponential phase was delayed. The genome of 83-1 was found to harbour an alginolytic system comprising five alginate lyases, whose expression was induced by alginate. The alginolytic system contains additional CAZymes, including two TonB-dependent receptors, and is part of a 24 kb genomic island unique to the A. macleodii 'surface clade' ecotype. In contrast, strains of the 'deep clade' ecotype contain only a single alginate lyase in a separate 7 kb island. This difference was reflected in an eightfold greater efficiency of surface clade strains to grow on alginate. Strain 83-1 furthermore hydrolysed laminarin, pullulan and xylan, and corresponding polysaccharide utilization loci were detected in the genome. Alteromonas macleodii alginate lyases were predominantly detected in Atlantic Ocean metagenomes. The demonstrated hydrolytic capacities are likely of ecological relevance and represent another level of adaptation among A. macleodii ecotypes.
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Affiliation(s)
- Anna M Neumann
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, 26129, Germany
| | - John P Balmonte
- Department of Marine Sciences, University of North Carolina, 3117 Venable Hall, Chapel Hill, NC, USA
| | - Martine Berger
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, 26129, Germany
| | - Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, 26129, Germany
| | - Carol Arnosti
- Department of Marine Sciences, University of North Carolina, 3117 Venable Hall, Chapel Hill, NC, USA
| | - Sonja Voget
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, 37077, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, 26129, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, 26129, Germany
| | - Matthias Wietz
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, 26129, Germany
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Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2015. [DOI: 10.1099/ijs.0.000178] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, Givat Ram, 91904 Jerusalem, Israel
| | - George M. Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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