Colwellia chukchiensis sp. nov., a psychrotolerant bacterium isolated from the Arctic Ocean

Deciphering a Marine Bone-Degrading Microbiome Reveals a Complex Community Effort

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.

Colwellia ponticola sp. nov., isolated from seawater

A Gram-stain-negative, aerobic, motile and rod-shaped bacterial strain, designated OISW-25^T, was isolated from seawater in Republic of Korea. Strain OISW-25^T 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-25^T fell within the clade comprising the type strains of Colwellia species. Strain OISW-25^T 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-25^T and C. piezophila ATCC BAA-637^T and two non-type strains of C. psychrerythraea were 78.16-79.35 % and DNA-DNA relatedness value of strain OISW-25^T with the type strain of C. maris was 17 %. The DNA G+C content of strain OISW-25^T was 39.2 mol% (HPLC) or 38.7 mol% (genome data). Strain OISW-25^T contained Q-8 as the predominant ubiquinone and summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c) and C_16 : 0 as the major fatty acids. The major polar lipids of strain OISW-25^T were phosphatidylethanolamine and phosphatidylglycerol. Distinguished phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that strain OISW-25^T is distinct from Colwellia species. On the basis of the data presented, strain OISW-25^T 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-25^T (=KCTC 62426^T=NBRC 113187^T).

Colwellia echini sp. nov., an agar- and carrageenan-solubilizing bacterium isolated from sea urchin

A novel bacterial strain, A3^T, 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 A3^T 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 A3^T and its closest relatives in the genus Colwellia (C. psychrerythraea ATCC 27364^T and C. asteriadis KMD 002^T) was 97.5 %. The average nucleotide identity between strain A3^T and other members of Colwellia was 78.6-80.5 %, and DNA-DNA hybridization prediction revealed values of less than 23 % relatedness between strain A3^T and other Colwellia species. The phenotypic, phylogenetic and genomic analyses support the hypothesis that strain A3^T represents a novel species of the genus Colwellia, for which the name Colwellia echini sp. nov. is proposed. The type strain is A3^T (=LMG 30125^T=NCIMB 15095^T).

Draft Genome Sequences of Two Psychrotolerant Strains, Colwellia polaris MCCC 1C00015T and Colwellia chukchiensis CGMCC 1.9127T

Colwellia polaris MCCC 1C00015T and Colwellia chukchiensis CGMCC 1.9127T are psychrotolerant bacteria isolated from the Canadian Basin and Chukchi Sea, respectively. Here, we report the draft genome sequences of C. polaris MCCC 1C00015T and C. chukchiensis CGMCC 1.9127T, which will help reveal how they adapt to cold environments.

Colwellia beringensis sp. nov., a psychrophilic bacterium isolated from the Bering Sea

A Gram stain-negative, motile and rod-shaped bacterial strain, designated NB097-1^T, was isolated from a marine sediment sample collected from the Bering Sea, and subjected to a polyphasic taxonomic study. Strain NB097-1^T 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 NB097-1^T belonged to the genus Colwellia. Strain NB097-1^T 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 NB097-1^T 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 NB097-1^T were phosphatidylglycerol and phosphatidylethanolamine. The genomic DNA G+C content of strain NB097-1^T 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 NB097-1^T represents a novel species of the genus Colwellia, for which the name Colwellia beringensis sp. nov. is proposed. The type strain is NB097-1^T (=MCCC 1A11668^T=KCTC 52554^T).

Colwellia mytili sp. nov., isolated from mussel Mytilus edulis

A Gram-stain-negative, aerobic, motile and rod-shaped bacterial strain, designated RA2-7T, was isolated from a mussel (Mytilus edulis) collected from the South Sea, South Korea, and subjected to a taxonomic study using a polyphasic approach. Strain RA2-7T grew optimally at 20 °C, at pH 7.0-8.0 and in the presence of 2.0-3.0 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences showed that strain RA2-7T belonged to the genus Colwellia. Strain RA2-7T exhibited 16S rRNA gene sequence similarity values of 98.3, 98.0 and 97.5 % to the type strains of Colwellia sediminilitoris, Colwellia aestuarii and Colwellia polaris, respectively, and of 94.5-96.5 % to the type strains of the other species of the genus Colwellia. Strain RA2-7T contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 as the major fatty acids. The major polar lipids detected in strain RA2-7T were phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content of strain RA2-7T was 39.0±0.04 mol% and its DNA-DNA relatedness values with the type strains of C. sediminilitoris, C. aestuarii and C. polaris were 14-19 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain RA2-7T is separated from recognized species of the genus Colwellia. On the basis of the data presented, strain RA2-7T is considered to represent a novel species of the genus Colwellia, for which the name Colwellia mytili sp. nov. is proposed. The type strain is RA2-7T (=KCTC 52417T=NBRC 112381T).

Colwellia sediminilitoris sp. nov., isolated from a tidal flat

A Gram-stain-negative, aerobic, motile and rod-shaped or ovoid bacterial strain, designated YSM-23T, was isolated from a tidal flat on the South Sea in South Korea, and subjected to a polyphasic taxonomic study. Strain YSM-23T grew optimally at 30 °C, at pH 7.0-8.0 and in the presence of 1.0-2.0 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences showed that strain YSM-23T represented a member of the genus Colwellia. Strain YSM-23T exhibited 16S rRNA gene sequence similarity values of 98.0, 97.4 and 97.3 % to the type strains of Colwellia aestuarii, Colwellia polaris and Colwellia chukchiensis, respectively, and of 94.5-96.8 % to the type strains of the other species of the genus Colwellia. Strain YSM-23T contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the major fatty acid. The major polar lipids detected in strain YSM-23T were phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content of strain YSM-23T was 43.8±0.08 mol% and its DNA-DNA relatedness values with the type strain of C. aestuarii, C. polaris and C. chukchiensis were 10±3.5-22±4.9 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain YSM-23T is separated from species of the genus Colwelliawith validly published names. On the basis of the data presented, strain YSM-23T is considered to represent a novel species of the genus Colwellia, for which the name Colwellia sediminilitoris sp. nov. is proposed. The type strain is YSM-23T (=KCTC 52213T=NBRC 111994T).

Colwellia aquaemaris sp. nov., isolated from the Cynoglossus semilaevis culture tank in a recirculating mariculture system

A Gram-staining-negative, heterotrophic, facultatively anaerobic bacterium, designated S1T, was isolated from the Cynoglossus semilaevis culture pond in a recirculating mariculture system in Tianjin, China. The taxonomy of strain S1T was studied by using a polyphasic approach. Cells of strain S1T were non-spore-forming, curved rods, 0.4–0.6 µm wide and 1.2–2.0 µm long, and motile by means of a single polar flagellum. The strain was positive for oxidase and catalase activities. Strain S1T was able to grow at 4–30 °C (optimum, 25 °C), at pH 5.5–10.0 (optimum, pH 6.5–7.5) and in the presence of 1–5 % (w/v) NaCl (optimum, 2 %). Strain S1T contained Q-8 as the sole respiratory quinone and C16 : 1ω7c/C16 : 1ω6c and C16 : 0 as the predominant cellular fatty acids. The genomic DNA G+C content was 40.1 mol% (T m). Phylogenetic analysis based on 16S rRNA gene sequences placed strain S1T in the genus Colwellia , and it formed a distinct lineage in the phylogenetic tree together with Colwellia meonggei MA1-3T, Colwellia aestuarii SMK-10T, Colwellia polaris 537T and Colwellia chukchiensis BCw111T, with 97.7, 96.1, 95.9 and 95.0 % 16S rRNA gene sequence similarity to these strains, respectively. DNA–DNA relatedness of strain S1T to Colwellia meonggei MA1-3T was 23.5±3.6 %. On the basis of the phylogenetic and phenotypic evidence, strain S1T is considered to represent a novel species of the genus Colwellia , for which the name Colwellia aquaemaris sp. nov. is proposed. The type strain is S1T ( = CGMCC 1.12165T = JCM 18479T).