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Antarcticibacterium arcticum sp. nov., a bacterium isolated from marine sediment of the Canadian Beaufort Sea

2020-06-01T00:00:00Z

Title: Antarcticibacterium arcticum sp. nov., a bacterium isolated from marine sediment of the Canadian Beaufort Sea Authors: Lee, Yung Mi; Baek, Kiwoon; Lee, Dong-Hun; Park, Yerin; Shin, Seung Chul; Jin, Young Keun Abstract: A Gram-staining-negative, aerobic, yellow-pigmented, flexirubin-negative, rod-shaped, and non-motile bacterial strain, PAMC 28998T, was isolated from the marine sediment of the Canadian Beaufort Sea. Strain PAMC 28998T grew at 437 C (optimally at 25 C), at pH 7.09.0 (optimally at 7.5) and in the presence of 1.010.0 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain PAMC 28998T belongs to the genus Antarcticibacterium showing the highest sequence similarity (96.8 %) with A. flavum JB01H24T. Average nucleotide identity and the genome-to-genome distance between PAMC 28998T and the most closely related species A. flavum JB01H24T were 74.1 % and 18.5 %, respectively, indicating that strain PAMC 28998T is clearly distinguished from A. flavum. The genomic DNA G+C content calculated from genome sequences was 39.8 mol%. The major fatty acids (>10 %) were iso-C15:0 (19.5 %), anteiso-C15:0 (18.0 %), iso-C16:0 (11.6 %), summed feature 3 (C16:1 ω6c and/or C16:1 ω7c) (11.4 %). The major polar lipids were phosphatidylethanolamine, aminoglycolipid, two unidentified aminolipids, three unidentified phospholipids, and four unidentified lipids. The major respiratory quinone was MK-6. Based on the phylogenetic, genomic, and phenotypic data presented, strain PAMC 28998T is considered to represent a novel species of the genus Antarcticibacterium, for which the name Antarcticibacterium arcticum sp. nov. is proposed with the strain PAMC 28998T (= KCCM 43316 T = JCM 33514T).

Upwarding gas source and postgenetic processes in the shallow sediments from the ARAON Mounds, Chukchi Sea

2020-04-01T00:00:00Z

Title: Upwarding gas source and postgenetic processes in the shallow sediments from the ARAON Mounds, Chukchi Sea Authors: Kim, Ji-Hoon; Hachikubo, Akihiro; Kida, Masato; Minami, Hirotsugu; Lee, Dong-Hun; Jin, Young Keun; Ryu, Jong-Sik; Lee, Yung Mi; Hur, Jin; Park, Myong-Ho; Kim, Young-Gyun; Kang, Moo-Hee; Park, Sanghee; Chen, Meilian; Kang, Seung-Goo; Kim, Sookwan Abstract: The methane (CH4) emission from the Arctic Ocean is crucial to understand global carbon cycle. Here, we investigated sulfate (SO42) in pore water and compositional and isotopic gas signatures at ARAON Mounds (hydrate/nonhydrate-bearing sites) and background site in the Chukchi Sea. Sulfate-methane transition (SMT) did not reach at the background site but occurred at shallow depths (3.3 m below the seafloor) at all ARAON Mounds sites. The SO42 profiles at ARAON Mounds also clearly indicate the unsteady state due to upward gas migration by high flux at the hydrate-bearing sites compared to the nonhydrate-bearing sites. The isotopic signatures of gas samples at the hydrate-bearing sites and below the SMT at the nonhydrate-bearing sites reflect thermogenic source transported across at least 1 km through faults/fractures in the Chukchi Sea. The headspace (HS) gas samples above/near the SMT at the nonhydrate-bearing sites are affected by the biogenic CH4 with enriched 12C; they indicate biogenic or thermogenic/biogenic mixed sources. The thermogenic gases below the SMT at ARAON Mounds have high C1/C2þ ratios (>300), much higher than those of normal thermogenic gases in offshore shallow sediments (<100), due to postgenetic processes during migration. The carbon isotopic fractionation (13CCO2 - 13CCH4) in HS samples of the background site and ARAON Mounds above the SMT are consistent with the biogenic gas range generated via microbial CO2 reduction. However, εc below the SMT is anomalously low (1342‰) and is higher at the hydrate-bearing sites than at the nonhydrate-bearing sites. We postulate that this low εc is explained by the two-phase fluid transport model of Kim et al. (2012) and that gas hydrates highly influence this value. We suggest that εc can be used as a powerful geochemical proxy for the upward gas migration and gas hydrate occurrence in shallow marine sediment systems.

Complete genome sequence of Antarcticibacterium flavum JB01H24T from an Antarctic marine sediment

2020-04-01T00:00:00Z

Title: Complete genome sequence of Antarcticibacterium flavum JB01H24T from an Antarctic marine sediment Authors: Lee, Yung Mi; Jin, Young Keun; Shin, Seung Chul Abstract: Antarcticibacterium flavum JB01H24T was isolated from a marine sediment of the Ross Sea, Antarctica. Whole-genome sequencing of the strain Antarcticibacterium flavum JB01H24T was achieved using PacBio RS II platform. The resulting complete genome comprised of one closed, complete chromosome of 4,319,074 base pairs with a 40.87% G+C content, where genomic analyses demonstrated that it is constituted mostly javascript:void(null);by putative ORFs with unknown functions, representing a novel genetic feature. It is the first complete genome sequence of the Antarcticibacterium strain.

Bacterial endosymbiont of Oligobrachia sp. (Frenulata) from an active mud volcano in the Canadian Beaufort Sea

2019-12-01T00:00:00Z

Title: Bacterial endosymbiont of Oligobrachia sp. (Frenulata) from an active mud volcano in the Canadian Beaufort Sea Authors: Lee, Yung Mi; Noh, Hyun-Ju; Lee, Dong-Hun; Kim, Junghyun; Jin, Young Keun; Paull, Charles Abstract: Siboglinid tubeworms of the genus Oligobrachia that thrive in obligatory association with endosymbionts have been predominantly observed in Arctic and high-latitude Atlantic cold seeps. Metabolic features of endosymbionts provide fundamental understanding for the survival strategy of tubeworms in cold seeps. However, no information on the bacterial endosymbionts of tubeworms from the Canadian Beaufort Sea was available until now. In this study, we investigated the phylogeny and metabolic potential of a bacterial endosymbiont of siboglinid tubeworms from an active mud volcano in the Canadian Beaufort Sea using Illumina MiSeq sequencing of 16S rRNA gene amplicons. The siboglinid tubeworm shared 99.9% 18S rRNA gene sequence similarity with Oligobrachia haakonmosbiensis and 99.7%？99.8% mitochondrial cytochrome C oxidase subunit I gene (COI) similarity with members of Oligobrachia sp. CPL-clade and was designated 'Oligobrachia sp. BS1'. The endosymbiont of Oligobrachia sp. BS1, which belongs to the Gammaproteobacteria, was most closely related to endosymbionts of Oligobrachia sp. CPL-clade, revealing the close relationships between the endosymbionts and their hosts. The bacterial endosymbiont of Oligobrachia sp. BS1 contained the key gene required for sulfur oxidation, aprA gene encoding the α-subunit of adenosine 1,5-phosphosulfate reductase, suggesting that this endosymbiont is capable of using sulfide as an energy source. The bacterial endosymbiont of an Oligobrachia species from an active mud volcano in the Canadian Beaufort Sea presented here expands our knowledge of the identities and thiotrophic metabolism of endosymbionts that are associated with hosts that dominate a wide range of methane seep habitats in the Arctic.