@article {1743, title = {Methanocaldococcus bathoardescens sp. nov., a hyperthermophilic methanogen isolated from a volcanically active deep-sea hydrothermal vent.}, journal = {Int J Syst Evol Microbiol}, volume = {65}, year = {2015}, month = {2015 Apr}, pages = {1280-3}, abstract = {

A hyperthermophilic methanogen, strain JH146(T), was isolated from 26 {\textdegree}C hydrothermal vent fluid emanating from a crack in basaltic rock at Marker 113 vent, Axial Seamount in the northeastern Pacific Ocean. It was identified as an obligate anaerobe that uses only H2 and CO2 for growth. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain is more than 97\% similar to other species of the genus Methanocaldococcus . Therefore, overall genome relatedness index analyses were performed to establish that strain JH146(T) represents a novel species. For each analysis, strain JH146(T) was most similar to Methanocaldococcus sp. FS406-22, which can fix N2 and also comes from Marker 113 vent. However, strain JH146(T) differs from strain FS406-22 in that it cannot fix N2. The average nucleotide identity score for strain JH146(T) was 87\%, the genome-to-genome direct comparison score was 33-55\% and the species identification score was 93\%. For each analysis, strain JH146(T) was below the species delineation cut-off. Full-genome gene synteny analysis showed that strain JH146(T) and strain FS406-22 have 97\% genome synteny, but strain JH146(T) was missing the operons necessary for N2 fixation and assimilatory nitrate reduction that are present in strain FS406-22. Based on its whole genome sequence, strain JH146(T) is suggested to represent a novel species of the genus Methanocaldococcus for which the name Methanocaldococcus bathoardescens is proposed. The type strain is JH146(T) ( = DSM 27223(T) = KACC 18232(T)).

}, keywords = {DNA, Bacterial, Hydrothermal Vents, Methanocaldococcus, Molecular Sequence Data, Pacific Ocean, Phylogeny, RNA, Ribosomal, 16S, Seawater, Sequence Analysis, DNA}, issn = {1466-5034}, doi = {10.1099/ijs.0.000097}, author = {Stewart, Lucy C and Jung, Jong-Hyun and Kim, You-Tae and Kwon, Soon-Wo and Park, Cheon-Seok and Holden, James F} } @article {1410, title = {Thermococcus paralvinellae sp. nov. and Thermococcus cleftensis sp. nov. of hyperthermophilic heterotrophs from deep-sea hydrothermal vents.}, journal = {Int J Syst Evol Microbiol}, volume = {64}, year = {2014}, month = {2014 Nov}, pages = {3655-9}, abstract = {

Two heterotrophic hyperthermophilic strains, ES1(T) and CL1(T), were isolated from Paralvinella sp. polychaete worms collected from active hydrothermal vent chimneys in the north-eastern Pacific Ocean. Both were obligately anaerobic and produced H2S in the presence of elemental sulfur and H2. Complete genome sequences are available for both strains. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strains are more than 97\% similar to most other species of the genus Thermococcus. Therefore, overall genome relatedness index analyses were performed to establish that these strains are novel species. For each analysis, strain ES1(T) was determined to be most similar to Thermococcus barophilus MP(T), while strain CL1(T) was determined to be most similar to Thermococcus sp. 4557. The average nucleotide identity scores for these strains were 84\% for strain ES1(T) and 81\% for strain CL1(T), genome-to-genome direct comparison scores were 23\% for strain ES1(T) and 47\% for strain CL1(T), and the species identification scores were 89\% for strain ES1(T) and 88\% for strain CL1(T). For each analysis, strains ES1(T) and CL1(T) were below the species delineation cut-off. Therefore, based on their whole genome sequences, strains ES1(T) and CL1(T) are suggested to represent novel species of the genus Thermococcus for which the names Thermococcus paralvinellae sp. nov. and Thermococcus cleftensis sp. nov. are proposed, respectively. The type strains are ES1(T) ( =DSM 27261(T) =KACC 17923(T)) and CL1(T) ( =DSM 27260(T) =KACC 17922(T)).

}, keywords = {Animals, DNA, Archaeal, Hydrothermal Vents, Molecular Sequence Data, Pacific Ocean, Phylogeny, Polychaeta, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Thermococcus}, issn = {1466-5034}, doi = {10.1099/ijs.0.066100-0}, author = {Hensley, Sarah A and Jung, Jong-Hyun and Park, Cheon-Seok and Holden, James F} } @article {1207, title = {Complete genome sequence of the hyperthermophilic archaeon Pyrococcus sp. strain ST04, isolated from a deep-sea hydrothermal sulfide chimney on the Juan de Fuca Ridge.}, journal = {J Bacteriol}, volume = {194}, year = {2012}, month = {2012 Aug}, pages = {4434-5}, abstract = {

Pyrococcus sp. strain ST04 is a hyperthermophilic, anaerobic, and heterotrophic archaeon isolated from a deep-sea hydrothermal sulfide chimney on the Endeavour Segment of the Juan de Fuca Ridge in the northeastern Pacific Ocean. To further understand the distinct characteristics of this archaeon at the genome level (polysaccharide utilization at high temperature and ATP generation by a Na(+) gradient), the genome of strain ST04 was completely sequenced and analyzed. Here, we present the complete genome sequence analysis results of Pyrococcus sp. ST04 and report the major findings from the genome annotation, with a focus on its saccharolytic and metabolite production potential.

}, keywords = {Adenosine Triphosphate, Anaerobiosis, DNA, Archaeal, Genome, Archaeal, Heterotrophic Processes, Hydrothermal Vents, Molecular Sequence Data, Pacific Ocean, Polysaccharides, Pyrococcus, Seawater, Sequence Analysis, DNA, Sodium Chloride, Sulfides}, issn = {1098-5530}, doi = {10.1128/JB.00824-12}, author = {Jung, Jong-Hyun and Lee, Ju-Hoon and Holden, James F and Seo, Dong-Ho and Shin, Hakdong and Kim, Hae-Yeong and Kim, Wooki and Ryu, Sangryeol and Park, Cheon-Seok} }