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Borchert E, García-Moyano A, Sanchez-Carrillo S, Dahlgren TG, Slaby BM, Bjerga GEK, Ferrer M, Franzenburg S, Hentschel U. Deciphering a Marine Bone-Degrading Microbiome Reveals a Complex Community Effort. mSystems 2021; 6:e01218-20. [PMID: 33563781 PMCID: PMC7883544 DOI: 10.1128/msystems.01218-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/20/2021] [Indexed: 11/29/2022] Open
Abstract
The marine bone biome is a complex assemblage of macro- and microorganisms; however, the enzymatic repertoire to access bone-derived nutrients remains unknown. The bone matrix is a composite material made up mainly of organic collagen and inorganic hydroxyapatite. We conducted field experiments to study microbial assemblages that can use organic bone components as nutrient source. Bovine and turkey bones were deposited at 69 m depth in a Norwegian fjord (Byfjorden, Bergen). Metagenomic sequence analysis was used to assess the functional potential of microbial assemblages from bone surface and the bone-eating worm Osedax mucofloris, which is a frequent colonizer of whale falls and known to degrade bone. The bone microbiome displayed a surprising taxonomic diversity revealed by the examination of 59 high-quality metagenome-assembled genomes from at least 23 bacterial families. Over 700 genes encoding enzymes from 12 relevant enzymatic families pertaining to collagenases, peptidases, and glycosidases putatively involved in bone degradation were identified. Metagenome-assembled genomes (MAGs) of the class Bacteroidia contained the most diverse gene repertoires. We postulate that demineralization of inorganic bone components is achieved by a timely succession of a closed sulfur biogeochemical cycle between sulfur-oxidizing and sulfur-reducing bacteria, causing a drop in pH and subsequent enzymatic processing of organic components in the bone surface communities. An unusually large and novel collagen utilization gene cluster was retrieved from one genome belonging to the gammaproteobacterial genus Colwellia IMPORTANCE Bones are an underexploited, yet potentially profitable feedstock for biotechnological advances and value chains, due to the sheer amounts of residues produced by the modern meat and poultry processing industry. In this metagenomic study, we decipher the microbial pathways and enzymes that we postulate to be involved in bone degradation in the marine environment. We here demonstrate the interplay between different bacterial community members, each supplying different enzymatic functions with the potential to cover an array of reactions relating to the degradation of bone matrix components. We identify and describe a novel gene cluster for collagen utilization, which is a key function in this unique environment. We propose that the interplay between the different microbial taxa is necessary to achieve the complex task of bone degradation in the marine environment.
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Affiliation(s)
- Erik Borchert
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Research Unit Marine Symbioses, Kiel, Germany
| | | | | | - Thomas G Dahlgren
- NORCE Norwegian Research Centre, Bergen, Norway
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Beate M Slaby
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Research Unit Marine Symbioses, Kiel, Germany
| | | | | | - Sören Franzenburg
- IKMB, Institute of Clinical Molecular Biology, University of Kiel, Kiel, Germany
| | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Research Unit Marine Symbioses, Kiel, Germany
- Christian-Albrechts University of Kiel, Kiel, Germany
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Liu A, Zhang YJ, Cheng P, Peng YJ, Blom J, Xue QJ. Whole genome analysis calls for a taxonomic rearrangement of the genus Colwellia. Antonie van Leeuwenhoek 2020; 113:919-931. [DOI: 10.1007/s10482-020-01405-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/11/2020] [Indexed: 02/06/2023]
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Park S, Park JM, Yoon JH. Colwellia ponticola sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2019; 69:3062-3067. [PMID: 31310197 DOI: 10.1099/ijsem.0.003590] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, motile and rod-shaped bacterial strain, designated OISW-25T, was isolated from seawater in Republic of Korea. Strain OISW-25T grew optimally at 25 °C and in the presence of 2.0 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences showed that strain OISW-25T fell within the clade comprising the type strains of Colwellia species. Strain OISW-25T exhibited 16S rRNA gene sequence similarity values of 97.5, 97.2 and 97.1 % to the type strains of C. piezophila, C. maris and C. psychrerythraea, respectively, and of 93.6-96.6 % to the type strains of the other Colwellia species. The average nucleotide identity values between strain OISW-25T and C. piezophila ATCC BAA-637T and two non-type strains of C. psychrerythraea were 78.16-79.35 % and DNA-DNA relatedness value of strain OISW-25T with the type strain of C. maris was 17 %. The DNA G+C content of strain OISW-25T was 39.2 mol% (HPLC) or 38.7 mol% (genome data). Strain OISW-25T contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 0 as the major fatty acids. The major polar lipids of strain OISW-25T were phosphatidylethanolamine and phosphatidylglycerol. Distinguished phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that strain OISW-25T is distinct from Colwellia species. On the basis of the data presented, strain OISW-25T is considered to represent a novel species of the genus Colwellia, for which the name Colwellia ponticola sp. nov. is proposed. The type strain is OISW-25T (=KCTC 62426T=NBRC 113187T).
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Affiliation(s)
- Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, South Korea
| | - Ji-Min Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, South Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, South Korea
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Christiansen L, Bech PK, Schultz-Johansen M, Martens HJ, Stougaard P. Colwellia echini sp. nov., an agar- and carrageenan-solubilizing bacterium isolated from sea urchin. Int J Syst Evol Microbiol 2018; 68:687-691. [PMID: 29388544 DOI: 10.1099/ijsem.0.002568] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterial strain, A3T, was isolated from the intestines of the sea urchin Strongylocentrotus droebachiensis collected in Øresund, Denmark. The strain was Gram-reaction-negative, rod-shaped and facultatively anaerobic, and displayed growth at 5-25 °C (optimum 20 °C), pH 7-9 (optimum at pH 7) and 1-6 % (w/v) NaCl (optimum 3 %). Furthermore, strain A3T grew on agar, agarose, κ-carrageenan, alginate and laminarin as sole carbon source. Complete liquefaction of agar and κ-carrageenan was observed on solid plate media as a result of enzymatic activities. Major fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The respiratory quinones were determined to be ubiquinones Q-8 (92 %) and Q-7 (8 %), and polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 36.9 mol%. Phylogenetical analyses based on the 16S rRNA gene showed that the bacterium was affiliated with the genus Colwellia within the Alteromonadaceae of the Gammaproteobacteria. The level of 16S rRNA gene sequence similarity between strain A3T and its closest relatives in the genus Colwellia (C. psychrerythraea ATCC 27364T and C. asteriadis KMD 002T) was 97.5 %. The average nucleotide identity between strain A3T and other members of Colwellia was 78.6-80.5 %, and DNA-DNA hybridization prediction revealed values of less than 23 % relatedness between strain A3T and other Colwellia species. The phenotypic, phylogenetic and genomic analyses support the hypothesis that strain A3T represents a novel species of the genus Colwellia, for which the name Colwellia echini sp. nov. is proposed. The type strain is A3T (=LMG 30125T=NCIMB 15095T).
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Affiliation(s)
- Line Christiansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Pernille Kjersgaard Bech
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Mikkel Schultz-Johansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Helle Juel Martens
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Peter Stougaard
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
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The complete genome sequence of Colwellia sp. NB097-1 reveals evidence for the potential genetic basis for its adaptation to cold environment. Mar Genomics 2018; 37:54-57. [PMID: 33250129 DOI: 10.1016/j.margen.2017.11.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/24/2017] [Accepted: 11/25/2017] [Indexed: 11/20/2022]
Abstract
Colwellia sp. NB097-1, isolated from a marine sediment sample from the Bering Sea, is a psychrophilic bacterium whose optimal and maximal growth temperatures were 13 and 25°C, respectively. Here, we present the complete genome of Colwellia sp. NB097-1, which was 4,661,274bp in length with a GC content of 38.5%. The genome provided evidence for the potential genetic basis for its adaptation to a cold environment, such as producing compatible solutes and cold-shock proteins, increasing membrane fluidity and synthesizing glycogen. Some cold-adaptive proteases were also detected in the genome of Colwellia sp. NB097-1. Protease activity analysis further showed that extracellular proteases of Colwellia sp. NB097-1 remained active at low temperatures. The complete genome sequence may be helpful to reveal how this strain survives at low temperature and to find cold-adaptive proteases that may be useful to industry.
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Zhang C, Guo W, Wang Y, Chen X. Colwellia beringensis sp. nov., a psychrophilic bacterium isolated from the Bering Sea. Int J Syst Evol Microbiol 2017; 67:5102-5107. [PMID: 29068274 DOI: 10.1099/ijsem.0.002423] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram stain-negative, motile and rod-shaped bacterial strain, designated NB097-1T, was isolated from a marine sediment sample collected from the Bering Sea, and subjected to a polyphasic taxonomic study. Strain NB097-1T grew at 0-25 °C, with an optimum growth temperature of 10-13 °C. Phylogenetic trees reconstructed based on 16S rRNA gene sequences indicated that strain NB097-1T belonged to the genus Colwellia. Strain NB097-1T exhibited 16S rRNA gene sequence similarities of 98.6, 98.5, 98.0, 97.2 and 96.8 % with the type strains of Colwellia mytili, C. sediminilitoris, C. aestuarii, C. polaris and C. chukchiensis, respectively. Strain NB097-1T had Q-8 as the major respiratory quinone and contained summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 as the major fatty acids. The major polar lipids detected in strain NB097-1T were phosphatidylglycerol and phosphatidylethanolamine. The genomic DNA G+C content of strain NB097-1T was 38.5 mol%, and its average nucleotide identity values with the type strains of C. mytili, C. sediminilitoris, C. aestuarii, C. polaris and C. chukchiensis were 77.30, 78.99, 78.82, 80.66 and 75.77 %, respectively. On the basis of phenotypic, chemotaxonomic and phylogenetic properties, together with average nucleotide identity value data, strain NB097-1T represents a novel species of the genus Colwellia, for which the name Colwellia beringensis sp. nov. is proposed. The type strain is NB097-1T (=MCCC 1A11668T=KCTC 52554T).
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Affiliation(s)
- Cong Zhang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, PR China
| | - Wenbin Guo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, PR China
| | - Yuguang Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, PR China
| | - Xinhua Chen
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen 361005, PR China.,College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China.,Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, PR China
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