Spirochaeta psychrophila sp. nov., a psychrophilic spirochaete isolated from subseafloor sediment, and emended description of the genus Spirochaeta

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2798-2804 ◽  
Author(s):  
Masayuki Miyazaki ◽  
Sanae Sakai ◽  
Yuko Yamanaka ◽  
Yumi Saito ◽  
Ken Takai ◽  
...  

An obligately anaerobic, psychrophilic spirochaete, strain MO-SPC1T, was isolated from a methanogenic microbial community grown in a continuous-flow bioreactor. Originally, this community was obtained from subseafloor sediments off the Shimokita Peninsula of Japan in the north-western Pacific Ocean. The cells were motile, Gram-stain-negative, helical, 0.25–0.55×3.6–15 µm, with a wavelength of approximately 0.5–0.6 µm. Strain MO-SPC1T grew at 0–18 °C (optimally at 15 °C), at pH 6.0–7.5 (optimally at pH 6.8–7.0) and in 20–70 g NaCl l−1 (optimally at 30–40 NaCl l−1). The strain grew chemo-organotrophically with mono-, di- and polysaccharides. The major end products of glucose fermentation were acetate, ethanol, hydrogen and carbon dioxide. The abundant polar lipids of strain MO-SPC1T were diphosphatidylglycerol, phosphatidylglycerol, unknown phospholipids and an unknown lipid. The major cellular fatty acids (>5 % of the total) were C14 : 0, C16 : 0, iso-C13 : 0, iso-C14 : 0, iso-C15 : 0, anteiso-C13 : 0 and anteiso-C15 : 0. To the best of our knowledge, this is the first report of the fatty acids iso-C13 : 0 and anteiso-C13 : 0 from a species of the genus Spirochaeta . Isoprenoid quinones were not found. The G+C content of the genomic DNA was 39.8 mol%. 16S rRNA gene sequence-based phylogenetic analysis showed that strain MO-SPC1T was affiliated with the genus Spirochaeta , and its closest relatives were Spirochaeta isovalerica MA-2T (95.6 % sequence identity) and Spirochaeta litoralis R1T (89.4 %). Based on its phenotypic characteristics and phylogenetic traits, strain MO-SPC1T is placed in a separate taxon at the level of a novel species within the genus Spirochaeta, for which the name Spirochaeta psychrophila sp. nov. is proposed, reflecting its true psychrophilic physiology. The type strain is MO-SPC1T ( = JCM 17280T = DSM 23951T). To our knowledge, this is the first report of an isolate of the phylum Spirochaetes from a deep-sea sedimentary environment, and of an obligately psychrophilic nature.

2012 ◽  
Vol 62 (Pt_5) ◽  
pp. 1075-1080 ◽  
Author(s):  
Masayuki Miyazaki ◽  
Osamu Koide ◽  
Tohru Kobayashi ◽  
Kozue Mori ◽  
Shigeru Shimamura ◽  
...  

A novel, facultatively anaerobic bacterium (strain JAM-BA0501T) was isolated from a deep subseafloor sediment sample at a depth of 247 m below seafloor off the Shimokita Peninsula of Japan in the north-western Pacific Ocean (Site C9001, 1180 m water depth). Cells of strain JAM-BA0501T were Gram-negative, filamentous, non-spore-forming and motile on solid medium by gliding. Phylogenetic analysis based on the 16S rRNA gene sequence of strain JAM-BA0501T indicated a distant relationship to strains representing genera within the order Bacteroidales , such as Alkaliflexus imshenetskii Z-7010T (91.1 % similarity), Marinilabilia salmonicolor ATCC 19041T (86.2 %) and Anaerophaga thermohalophila Fru22T (89.3 %). The new isolate produced isoprenoid quinones with menaquinone MK-7 as the major component, and the predominant fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The DNA G+C content of the isolate was 42.9 mol%. Based on its taxonomic distinctiveness, strain JAM-BA0501T is considered to represent a novel species of a new genus within the family Marinilabiliaceae , for which the name Geofilum rubicundum gen. nov., sp. nov. is proposed. The type strain of Geofilum rubicundum is JAM-BA0501T ( = JCM 15548T  = NCIMB 14482T).


2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4147-4154 ◽  
Author(s):  
Masayuki Miyazaki ◽  
Sanae Sakai ◽  
Kirsti M. Ritalahti ◽  
Yayoi Saito ◽  
Yuko Yamanaka ◽  
...  

An anaerobic, psychrophilic bacterium, strain MO-SPC2T, was isolated from a methanogenic microbial community in a continuous-flow bioreactor that was established from subseafloor sediments collected from off the Shimokita Peninsula of Japan in the north-western Pacific Ocean. Cells were pleomorphic: spherical, annular, curved rod, helical and coccoid cell morphologies were observed. Motility only occurred in helical cells. Strain MO-SPC2T grew at 0–17 °C (optimally at 9 °C), at pH 6.0–8.0 (optimally at pH 6.8–7.2) and in 20–40 g NaCl l−1 (optimally at 20–30 NaCl l−1). The strain grew chemo-organotrophically with mono-, di- and polysaccharides. The major end products of glucose fermentation were acetate, ethanol, hydrogen and carbon dioxide. The abundant polar lipids of strain MO-SPC2T were phosphatidylglycolipids, phospholipids and glycolipids. The major cellular fatty acids were C14 : 0, C16 : 0 and C16 : 1ω9. Isoprenoid quinones were not detected. The G+C content of the DNA was 32.3 mol%. 16S rRNA gene-based phylogenetic analysis showed that strain MO-SPC2T was affiliated with the genus Sphaerochaeta within the phylum Spirochaetes , and its closest relatives were Sphaerochaeta pleomorpha GrapesT (88.4 % sequence identity), Sphaerochaeta globosa BuddyT (86.7 %) and Sphaerochaeta coccoides SPN1T (85.4 %). Based on phenotypic characteristics and phylogenetic traits, strain MO-SPC2T is considered to represent a novel species of the genus Sphaerochaeta , for which the name Sphaerochaeta multiformis sp. nov. is proposed. The type strain is MO-SPC2T ( = JCM 17281T = DSM 23952T). An emended description of the genus Sphaerochaeta is also proposed.


2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2133-2139 ◽  
Author(s):  
S. Shivaji ◽  
P. Vishnu Vardhan Reddy ◽  
S. S. S. Nageshwara Rao ◽  
Zareena Begum ◽  
Poorna Manasa ◽  
...  

A novel Gram-stain-negative, horseshoe-shaped, non-motile bacterium, designated strain M12-11BT, was isolated from a marine sediment sample collected at a depth of 200 m from Kongsfjorden, Svalbard. The colony colour was orangish red due to the presence of carotenoids. Fatty acids were dominated by branched and unsaturated fatty acids (90.8 %), with a high abundance of iso-C15 : 0 (14.9 %), anteiso-C15 : 0 (11.4 %), iso-C15 : 1 G (13.1 %), C15 : 1ω6c (5.4 %), C17 : 1ω6c (6.7 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 9.3 %) and summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1ω9c; 5.9 %). Strain M12-11BT contained MK-7 as the major respiratory quinone. The polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, one unidentified aminolipid and three unidentified lipids. Based on 16S rRNA gene sequence similarities, the type strains of Cyclobacterium amurskyense , Cyclobacterium marinum and Cyclobacterium lianum were most closely related to M12-11BT with sequence similarities of 98.2, 96.8 and 93.3 %, respectively. Other members of the family Cyclobacteriaceae had sequence similarities of <92.0 %. However, DNA–DNA hybridization with Cyclobacterium amurskyense KCTC 12363T and Cyclobacterium marinum DSM 745T showed relatedness values of only 24.5 and 32.5 % with respect to strain M12-11BT. Based on the results of DNA–DNA hybridization experiments and phenotypic and chemotaxonomic data, it appears that strain M12-11BT represents a novel species of the genus Cyclobacterium , for which the name Cyclobacterium qasimii sp. nov. is proposed; the type strain is M12-11BT ( = KCTC 23011T = NBRC 106168T) and it has a DNA G+C content of 40.5 mol%.


Author(s):  
Yuxin Chen ◽  
Arisa Nishihara ◽  
Takao Iino ◽  
Moriya Ohkuma ◽  
Shin Haruta

A novel nitrogen-fixing fermentative bacterium, designated as YA01T, was isolated from Nakabusa hot springs in Japan. The short-rod cells of strain YA01T were Gram-positive and non-sporulating. Phylogenetic trees of the 16S rRNA gene sequence and concatenated sequences of 40 single-copy ribosomal genes revealed that strain YA01T belonged to the genus Caldicellulosiruptor and was closely related to Caldicellulosiruptor hydrothermalis 108T, Caldicellulosiruptor bescii DSM 6725T and Caldicellulosiruptor kronotskyensis 2002T. The 16S rRNA gene sequence of strain YA01T shares less than 98.1 % identity to the known Caldicellulosiruptor species. The G+C content of the genomic DNA was 34.8 mol%. Strain YA01T shares low genome-wide average nucleotide identity (90.31–91.10 %), average amino acid identity (91.45–92.10 %) and <70 % digital DNA–DNA hybridization value (41.8–44.2 %) with the three related species of the genus Caldicellulosiruptor . Strain YA01T grew at 50–78 °C (optimum, 70 °C) and at pH 5.0–9.5 (optimum, pH 6.5). Strain YA01T mainly produced acetate by consuming d(+)-glucose as a carbon source. The main cellular fatty acids were iso-C17 : 0 (35.7 %), C16 : 0 (33.3 %), DMA16 : 0 (6.6 %) and iso-C15 : 0 (5.9 %). Based on its distinct phylogenetic position, biochemical and physiological characteristics, and the major cellular fatty acids, strain YA01T is considered to represent a novel species of the genus Caldicellulosiruptor for which the name Caldicellulosiruptor diazotrophicus sp. nov. is proposed (type strain YA01T=DSM 112098T=JCM 34253T).


2020 ◽  
Vol 70 (4) ◽  
pp. 2657-2663 ◽  
Author(s):  
Shasha Wang ◽  
Lijing Jiang ◽  
Xuewen Liu ◽  
Suping Yang ◽  
Zongze Shao

Strains 1-1NT and GYSZ_1T were isolated from marine sediments collected from the coast of Xiamen, PR China. Cells of the two strains were Gram-stain-negative, rod-shaped or slightly curved. Strain 1-1NT was non-motile, whereas strain GYSZ_1T was motile by means of one polar flagellum. The temperature, pH and salinity concentration ranges for growth of 1-1NT were 10–45 °C (optimum 30 °C), pH 5.5–8.0 (optimum 7.0) and 0–90 g l−1 NaCl (optimum 50 g l−1), while the growth of GYSZ_1T occurred at 4–45 °C (optimum 33 °C), pH 5.0–8.5 (optimum 6.5) and 5–90 g l−1 NaCl (optimum 20 g l−1). The two novel isolates were obligate chemolithoautotrophs capable of growth using hydrogen, thiosulfate, sulfide or elemental sulfur as the sole energy source, and nitrate, elemental sulfur or molecular oxygen as an electron acceptor. The major fatty acids of 1-1NT were C16 : 1ω7c, C16 : 0, C18 : 1ω7c and C18 : 0, while the predominant fatty acids of strain GYSZ_1T were C16 : 1ω7c, C16 : 0, C18 : 1ω7c and C14 : 0 3-OH. The DNA G+C contents of 1-1NT and GYSZ_1T were 34.5 mol% and 33.2 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that 1-1NT and GYSZ_1T represented members of the genus Sulfurimonas , with the highest sequence similarities to Sulfurimonas crateris SN118T (97.4 %) and Sulfurimonas denitrificans DSM 1251T (94.7 %), respectively. However, 1-1NT and GYSZ_1T shared 95.5 % similarity of 16S rRNA gene sequences, representing different species of the genus Sulfurimonas . On the basis of the physiological properties and the results of phylogenetic analyses, including average nucleotide identity and in silico DNA–DNA hybridization values, strains 1-1NT and GYSZ_1T represent two novel species within the genus Sulfurimonas , for which the names Sulfurimonas xiamenensis sp. nov. and Sulfurimonas lithotrophica sp. nov. are proposed, with the type strains 1-1NT (=MCCC 1A14514T=KCTC 15851T) and GYSZ_1T (=MCCC 1A14739T=KCTC 15853T), respectively. Our results also justify an emended description of the genus Sulfurimonas .


Author(s):  
Lei-Lei Yang ◽  
Hong-Can Liu ◽  
Qing Liu ◽  
Yu-Hua Xin

Two Gram-stain-positive, aerobic, rod-shaped, pink and light pink colony-forming bacteria, designated as Hz2T and MDT2-14T, respectively, were isolated from glacier cryoconite samples. Comparisons based on 16S rRNA gene sequences showed that strains Hz2T and MDT2-14T take Arthrobacter bussei KR32T and Arthrobacter zhaoguopingii J391T as their closest neighbours, respectively. The average nucleotide identity values between the two novel strains and their closest relatives were 83.56 and 93.06 %, respectively. The two strains contain MK-9(H2) as their predominant menaquinone. The polar lipids of both strains were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and an unidentified glycolipid. The major fatty acids of strain Hz2T were anteiso-C15 : 0, summed feature 3 (comprising C16 : 1  ω7c and/or C16 : 1  ω6c) and iso-C15 : 0, while the major fatty acids of strain MDT2-14T were anteiso-C15 : 0 and anteiso-C17 : 0. Based on these data, we propose two novel species, Arthrobacter cheniae sp. nov. (Hz2T = CGMCC 1.9262T=NBRC 113086T) and Arthrobacter frigidicola sp. nov. (MDT2-14T=CGMCC 1.9882T=NBRC 113089T).


Author(s):  
Hiroyuki Sawada ◽  
Takashi Fujikawa ◽  
Shigeru Osada ◽  
Mamoru Satou

Five phytopathogenic bacterial strains, MAFF 301449T, MAFF 301450, MAFF 301451, MAFF 301452, and MAFF 301453, which were isolated from bud blight lesions of cyclamen (Cyclamen persicum Mill.) in Miyagi, Japan, were subjected to polyphasic taxonomic characterisation. The cells were Gram-reaction-negative, aerobic, non-spore-forming, motile with one to five polar flagella, and rod-shaped. Analysis of 16S rRNA gene sequences showed that they belong to the genus Pseudomonas , with Pseudomonas extremaustralis 14-3T (99.79 % sequence similarity), Pseudomonas trivialis DSM 14937T (99.79 %), Pseudomonas poae DSM 14936T (99.72 %), and Pseudomonas antarctica CMS 35T (99.72 %) as their relatives. The genomic DNA G+C content was 60.3 mol% and the major fatty acids (>5 % of the total fatty acids) were C16 : 0, summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), and C17 : 0 cyclo. Phylogenetic analysis using the rpoD gene sequences and phylogenomic analyses based on the whole genome sequences demonstrated that the strains are members of the Pseudomonas fluorescens subgroup, but form a monophyletic and robust clade separated from their relatives. Average nucleotide identity and digital DNA–DNA hybridisation analyses with the closely related Pseudomonas species corroborated their novel species status. The strains were differentiated from their relatives by phenotypic characteristics, pathogenicity towards cyclamen, cellular fatty acid composition, and whole-cell MALDI-TOF mass spectrometry profiles. Based on the phenotypic, chemotaxonomic, and genotypic data obtained, we conclude that the strains represent a novel Pseudomonas species, for which we propose the name Pseudomonas cyclaminis sp. nov.; the type strain is MAFF 301449T (=ICMP 23720T).


2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2436-2441 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Soo-Jin Kim ◽  
Yun-Hee Jang ◽  
Moriyuki Hamada ◽  
Tomohiko Tamura ◽  
...  

A Gram-positive, aerobic, rod-shaped bacterial strain, 5116S-4T, was isolated from an air sample collected in Suwon city, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this strain was a new member of the family Microbacteriaceae . The sequence similarities of this strain to the members of the family Microbacteriaceae were less than 97 %, with the highest values observed with Cryobacterium mesophilum MSL-15T (96.3 %), Cryobacterium roopkundense RuGl7T (96.2 %), Labedella gwakjiensis KSW2-17T (96.2 %), Cryobacterium luteum Hh15T (96.2 %), Cryobacterium psychrophilum DSM 4854T (96.2 %), Klugiella xanthotipulae 44C3T (96.0 %) and Amnibacterium kyonggiense KSL51201-037T (96.0 %). According to the phylogenetic tree, strain 5116S-4T formed a cluster with A. kyonggiense KSL51201-037T, Labedella gwakjiensis KSW2-17T and Lysinimonas soli SGM3-12T (95.3 % sequence similarity) on the support of high bootstrap values. Cells were motile with single polar flagellum and showed optimum growth at 30 °C and pH 7 without NaCl. Predominant cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. Polar lipids were diphosphatidylglycerol, dimannosyldiacylglycerol, phosphatidylglycerol, one unknown glycolipid, one unknown phospholipid and one unknown lipid. The acyl type of the cell-wall muramic acid was the acetyl type. Peptidoglycan was supposed to be the type B1 with 2,4-diaminobutyric acid on position 3. Strain 5116S-4T was clearly distinguishable from the phylogenetically related genera in the family Microbacteriaceae in terms of chemotaxonomic characteristics. On the basis of the chemotaxonomic and phylogenetic characteristics, a novel genus and species are proposed, Naasia aerilata gen. nov., sp. nov. The type strain of Naasia aerilata is 5116S-4T ( = KACC 15517T  = NBRC 108725T).


2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 413-419 ◽  
Author(s):  
Yochan Joung ◽  
Haneul Kim ◽  
Heeyoung Kang ◽  
Beom-Il Lee ◽  
Tae-Seok Ahn ◽  
...  

A non-motile, yellow–orange-pigmented bacterial strain, designated HME6664T, was isolated from Lake Soyang, Republic of Korea. The major fatty acids of strain HME6664T were summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c; 44.7 %) and iso-C15 : 0 (20.2 %). The DNA G+C content was 40.8 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HME6664T formed a lineage within the genus Mucilaginibacter . Strain HME6664T was closely related to Mucilaginibacter ximonensis (96.7 %), Mucilaginibacter dorajii (96.5 %) and Mucilaginibacter lappiensis (96.3 %). On the basis of the evidence presented in this study, strain HME6664T represents a novel species of the genus Mucilaginibacter , for which the name Mucilaginibacter soyangensis sp. nov., is proposed. The type strain is HME6664T ( = KCTC 23261T = CECT 7824T).


2012 ◽  
Vol 62 (Pt_5) ◽  
pp. 1191-1198 ◽  
Author(s):  
Kathrin I. Mohr ◽  
Ronald O. Garcia ◽  
Klaus Gerth ◽  
Herbert Irschik ◽  
Rolf Müller

A novel starch-degrading myxobacterium designated NOSO-4T (new organism of the Sorangiineae strain 4) was isolated in 1995 from a soil sample containing plant residues, collected in Lucknow, Uttar Pradesh, India. The novel bacterium shows typical myxobacterial characteristics such as Gram-negative, rod-shaped vegetative cells, swarming colonies, fruiting body-like aggregates and bacteriolytic activity. The strain is mesophilic, strictly aerobic and chemoheterotrophic. Based on 16S rRNA gene sequences, NOSO-4T shows highest similarity (96.2 %) with the unidentified bacterial strain O29 (accession no. FN554397), isolated from leek (Allium porrum) rhizosphere, and to the myxobacteria Jahnella thaxteri (88.9 %) and Chondromyces pediculatus (88.5 %). Major fatty acids are C17 : 1 2-OH, C20 : 4ω6 (arachidonic acid), and the straight-chain fatty acids C17 : 0, C15 : 0 and C16 : 0. The genomic DNA G+C content of the novel isolate is 66.8 mol%. It is proposed that strain NOSO-4T represents a novel species in a new genus, i.e. Sandaracinus amylolyticus gen. nov., sp. nov., but also belongs to a new family, Sandaracinaceae fam. nov. The type strain of the type species, S. amylolyticus sp. nov., is NOSO-4T ( = DSM 53668T = NCCB 100362T).


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