Georgenia sediminis sp. nov., a moderately thermophilic actinobacterium isolated from sediment

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4243-4247 ◽  
Author(s):  
Zhi-Qing You ◽  
Jie Li ◽  
Sheng Qin ◽  
Xin-Peng Tian ◽  
Fa-Zuo Wang ◽  
...  
Keyword(s):  
Type Species ◽  
Minor Component ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Content Type ◽  
Moderately Thermophilic ◽  
Link Type ◽  
Nacl Concentration ◽  
Ph Range ◽  
A Minor

A Gram-stain-positive actinobacterium, designated strain SCSIO 15020T, was isolated from sediment of the South China Sea, and characterized by using a polyphasic approach. The temperature range for growth was 24–60 °C, with optimal growth occurring at 50 °C. The pH range for growth was 6–10 (optimum pH 8–9). The NaCl concentration range for growth was 0–5 % (w/v). The peptidoglycan type was A4α. Polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and an unknown polar lipid. The major menaquinone was MK-8(H4); MK-7(H4) was present as a minor component. The major fatty acids (>5 %) were anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0. The DNA G+C content of strain SCSIO 15020T was 73.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SCSIO 15020T belonged to the genus Georgenia , with the closest neighbours being Georgenia muralis 1A-CT (96.3 % similarity), Georgenia thermotolerans TT02-04T (95.7 %) and Georgenia ruanii YIM 004T (95.6 %). Based on evidence from the present polyphasic study, strain SCSIO 15020T is considered to represent a novel species of the genus Georgenia , for which the name Georgenia sediminis sp. nov. is proposed. The type strain is SCSIO 15020T ( = DSM 25884T = NBRC 108941T).

scholarly journals Tessaracoccus lapidicaptus sp. nov., an actinobacterium isolated from the deep subsurface of the Iberian pyrite belt

2014 ◽  
Vol 64 (Pt_10) ◽  
pp. 3546-3552 ◽  
Author(s):  
Fernando Puente-Sánchez ◽  
Mónica Sánchez-Román ◽  
Ricardo Amils ◽  
Víctor Parro
Keyword(s):  
Type Species ◽  
Optimal Growth ◽  
Iberian Pyrite Belt ◽  
Cellular Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Optimal Value ◽  
Ph Range

A novel actinobacterium, designated IPBSL-7T, was isolated from a drilling core 297 m deep obtained from the Iberian Pyrite Belt. The strain was isolated anaerobically using nitrate as the electron acceptor. 16S rRNA gene sequence analysis revealed that it was related to Tessaracoccus flavescens SST-39T (95.7 % similarity), Tessaracoccus bendigoensis Ben 106T (95.7 %), Tessaracoccus lubricantis KSS-17SeT (95.6 %) and Tessaracoccus oleiagri SL014B-20A1T (95.0 %), while its similarity to any other member of the family Propionibacteriaceae was less than 94 %. Cells were non-motile, non-spore-forming, Gram-positive, oval to rod-shaped, and often appeared in pairs or small groups. The strain was facultatively anaerobic, oxidase-negative, catalase-positive and capable of reducing nitrate. Colonies were circular, convex, smooth and colourless. The organism could grow at between 15 and 40 °C, with an optimal growth at 37 °C. The pH range for growth was from pH 6 to 9, with pH 8 being the optimal value. Strain IPBSL-7T had peptidoglycan type A3-γ′, with ll-diaminopimelic acid as the diagnostic diamino-acid and glycine at position 1 of the peptide subunit. The dominant menaquinone was MK-9(H4) (93.8 %). The major cellular fatty acid was anteiso-C15 : 0 (55.0 %). The DNA G+C content was 70.3 mol%. On the basis of phenotypic and phylogenetic results, strain IPBSL-7T can be differentiated from previously described species of the genus Tessaracoccus and, therefore, represents a novel species, for which the name Tessaracoccus lapidicaptus sp. nov. is proposed. The type strain is IPBSL-7T ( = CECT 8385T = DSM 27266T).

scholarly journals Cohnella nanjingensis sp. nov., an extracellular polysaccharide-producing bacterium isolated from soil

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3320-3324 ◽  
Author(s):  
Zhi Huang ◽  
Ya-jun Yu ◽  
Yuan-yuan Bao ◽  
Li Xia ◽  
Xia-fang Sheng ◽  
...  
Keyword(s):  
Type Species ◽  
Minor Component ◽  
Extracellular Polysaccharide ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Bacterium Strain ◽  
A Minor

A Gram-stain-positive, rod-shaped, endospore-forming bacterium, strain D45T, was isolated from soil in Nanjing, China. The organism grew optimally at 30 °C, pH 7.0 and with 0 % NaCl (w/v). The 16S rRNA gene sequence of the isolate showed similarities lower than 97 % with respect to species of the genus Cohnella . The predominant respiratory quinone was MK-7, with MK-6 present as a minor component; anteiso-C15 : 0 and iso-C16 : 0 were the major fatty acids. The polar lipids of strain D45T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two aminophospholipids, four phospholipids, two glycolipids, one aminolipid and two lipids. The DNA G+C content was 59.5 mol%. DNA–DNA hybridization of the isolate with two reference strains showed relatedness values of 33.4 % with Cohnella ginsengisoli DSM 18997T and 25.8 % with Cohnella thermotolerans DSM 17683T. The phylogenetic, chemotaxonomic and phenotypic data supported the classification of strain D45T as a representative of a novel species of the genus Cohnella , for which the name Cohnella nanjingensis sp. nov. is proposed. The type strain is D45T ( = CCTCC AB 2014067T = DSM 28246T).

scholarly journals Vulcanisaeta thermophila sp. nov., a hyperthermophilic and acidophilic crenarchaeon isolated from solfataric soil

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 201-205 ◽  
Author(s):  
Kyung June Yim ◽  
In-Tae Cha ◽  
Jin-Kyu Rhee ◽  
Hye Seon Song ◽  
Dong-Wook Hyun ◽  
...  
Keyword(s):  
Type Species ◽  
Optimal Growth ◽  
The Philippines ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Mayon Volcano ◽  
Final Electron ◽  
The Republic ◽  
Ph Range

An anaerobic, rod-shaped, hyperthermophilic and acidophilic crenarchaeon, designated strain CBA1501T, was isolated from solfataric soil of the Mayon volcano in the Republic of the Philippines. Phylogenetic analysis showed that strain CBA1501T is affiliated with the genus Vulcanisaeta in the phylum Crenarchaeota . DNA sequence similarities between the 16S rRNA gene of strain CBA1501T and those of Vulcanisaeta distributa IC-017T and Vulcanisaeta souniana IC-059T were 98.5 and 97.4 %, respectively. Strain CBA1501T grew between 75–90 °C, over a pH range of 4.0–6.0 and in the presence of 0–1.0 % (w/v) NaCl, with optimal growth occurring at 85 °C, pH 5.0, and with 0 % (w/v) NaCl. Fumarate, malate, oxidized glutathione, sulfur and thiosulfate were used as final electron acceptors, but FeCl3, nitrate and sulfate were not. The DNA G+C content of strain CBA1501T was 43.1 mol%. On the basis of polyphasic taxonomic analysis, strain CBA1501T represents a novel species of the genus Vulcanisaeta in the phylum Crenarchaeota , for which we propose the name Vulcanisaeta thermophila sp. nov. The type strain is CBA1501T ( = ATCC BAA-2415T = JCM 17228T).

Oceanirhabdus sediminicola gen. nov., sp. nov., an anaerobic bacterium isolated from sea sediment

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4277-4283 ◽  
Author(s):  
Ruo-Xi Pi ◽  
Wen-Wu Zhang ◽  
Ming-Xu Fang ◽  
Yan-Zhou Zhang ◽  
Tian-Tian Li ◽  
...  
Keyword(s):  
Type Species ◽  
Anaerobic Bacterium ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Fermentation Products ◽  
Content Type ◽  
Link Type ◽  
Nacl Concentration

A novel anaerobic bacterium, designated NH-JN4T was isolated from a sediment sample collected in the South China Sea. Cells were Gram-stain-positive, spore-forming, peritrichous and rod-shaped (0.5–1.2×2.2–7 µm). The temperature and pH ranges for growth were 22–42 °C and pH 6.0–8.5. Optimal growth occurred at 34–38 °C and pH 6.5–7.0. The NaCl concentration range for growth was 0.5–6 % (w/v) with an optimum of 2.5 %. Catalase and oxidase were not produced. Substrates which could be utilized were peptone, tryptone, yeast extract, beef extract and glycine. Main fermentation products from PYG medium were formate, acetate, butyrate and ethanol. Strain NH-JN4T could utilize sodium sulfite as an electron acceptor. No respiratory quinone was detected. The predominant fatty acids were anteiso-C15 : 0, C16 : 0, iso-C15 : 0, anteiso-C17 : 0 and C16 : 0 DMA. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and glycolipids. The DNA G+C content was 35.8 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain NH-JN4T was a member of family Clostridiaceae , and was most closely related to Clostridium limosum ATCC 25620T, Clostridium proteolyticum DSM 3090T, Clostridium histolyticum ATCC 19401T and Clostridium tepidiprofundi SG 508T, showing 94.0, 93.0, 92.9 and 92.3 % sequence similarity, respectively. On the basis of phenotypic, genotypic and chemotaxonomic properties, strain NH-JN4T represents a novel species of a new genus in the family Clostridiaceae , for which the name Oceanirhabdus sediminicola gen. nov., sp. nov. is proposed. The type strain of the type species is NH-JN4T ( = JCM 18501T = CCTCC AB 2013103T = KCTC 15322T).

scholarly journals Halovivax limisalsi sp. nov., an extremely halophilic archaeon from hypersaline mud

2014 ◽  
Vol 64 (Pt_10) ◽  
pp. 3422-3426 ◽  
Author(s):  
Mohammad Ali Amoozegar ◽  
Ali Makhdoumi-Kakhki ◽  
Maliheh Mehrshad ◽  
Siavash Riazi ◽  
Antonio Ventosa
Keyword(s):  
Type Species ◽  
Optimal Growth ◽  
Rpob Gene ◽  
Hypersaline Lake ◽  
Rrna Gene ◽  
Halophilic Archaeon ◽  
Content Type ◽  
Link Type ◽  
Extremely Halophilic Archaeon ◽  
Ph Range

A Gram-stain-negative, cream‐pigmented, motile, extremely halophilic archaeon, designated strain IC38T, was isolated from a saline mud sample taken from a hypersaline lake, Aran-Bidgol, in Iran. The strain required at least 2.5 M NaCl for growth. However, MgCl2 was not required. Optimal growth occurred with 4.3 M NaCl and 0.2 M MgCl2. The optimum pH and temperature for growth were pH 7.0 and 35 °C, respectively, and strain IC38T was able to grow over a pH range of 6.5–9.0, and a temperature range of 25–45 °C. Analysis of the 16S rRNA gene sequence revealed that strain IC38T clustered with the two species of the genus Halovivax , Halovivax asiaticus EJ-46T and Halovivax ruber XH-70T, with sequence similarities of 96.4 % and 96.1 %, respectively. The similarities between the rpoB′ gene of the novel strain and Halovivax asiaticus and Halovivax ruber were 90.7 % and 90.3 %, respectively. The polar lipid pattern of strain IC38T consisted of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. Three unidentified glycolipids and two minor phospholipids were also observed. The DNA G+C content of strain IC38T was 62.6 mol%. On the basis of the phylogenetic analysis, as well as the biochemical and physiological characteristics, the new isolate is suggested to be a representative of a novel species of the genus Halovivax , for which the name Halovivax limisalsi sp. nov. is proposed. The type strain of Halovivax limisalsi is IC38T ( = IBRC-M 10022T = KCTC 4051T).

scholarly journals Mizugakiibacter sediminis gen. nov., sp. nov., isolated from a freshwater lake

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 3983-3987 ◽  
Author(s):  
Hisaya Kojima ◽  
Riho Tokizawa ◽  
Manabu Fukui
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Freshwater Lake ◽  
Rrna Gene ◽  
Optimum Growth ◽  
Phenotypic Properties ◽  
Content Type ◽  
Moderately Thermophilic ◽  
Link Type ◽  
Ph Range

A novel, moderately thermophilic, bacterial strain (skMP5T) was isolated from sediment of a freshwater lake in Japan. The cells were rod-shaped, motile and Gram-stain-negative. Growth was observed at temperatures ranging from 25 to 52 °C, with optimum growth observed at 48–50 °C. The pH range for growth was pH 5.0–8.2, with optimum growth at pH 6.0–7.0. The G+C content of genomic DNA was 72 mol%. The major components in the fatty acid profile were iso-C17 : 0 and iso-C17 : 1ω9c. The predominant isoprenoid quinone of the strain was ubiquinone Q-8. The strain was facultatively anaerobic, and reduced nitrate to nitrite under anoxic conditions. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate was a member of the family Xanthomonadaceae within the class Gammaproteobacteria , showing highest sequence similarity with Tahibacter aquaticus RaM5-2 (93.6 %) and Metallibacterium scheffleri DKE6T (93.3 %). On the basis of phylogenetic and phenotypic properties, strain skMP5T represents a novel species of a new genus, Mizugakiibacter sediminis gen. nov., sp. nov. The type strain of the type species is skMP5T ( = DSM 27098T = NBRC 109608T).

Litorilinea aerophila gen. nov., sp. nov., an aerobic member of the class Caldilineae , phylum Chloroflexi , isolated from an intertidal hot spring

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1149-1154 ◽  
Author(s):  
Varsha Kale ◽  
Snædís H. Björnsdóttir ◽  
Ólafur H. Friðjónsson ◽  
Sólveig K. Pétursdóttir ◽  
Sesselja Ómarsdóttir ◽  
...  
Keyword(s):  
Type Species ◽  
Hot Spring ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Phenotypic Differences ◽  
Link Type ◽  
Fermentative Growth ◽  
Distinct Lineage ◽  
Ph Range

A thermophilic, aerobic, Gram-stain-negative, filamentous bacterium, strain PRI-4131T, was isolated from an intertidal hot spring in Isafjardardjup, NW Iceland. The strain grew chemo-organotrophically on various carbohydrates. The temperature range for growth was 40–65 °C (optimum 55 °C), the pH range was pH 6.5–9.0 (optimum pH 7.0) and the NaCl range was 0–3 % (w/v) (optimum 0.5 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain PRI-4131T represented a distinct lineage within the class Caldilineae of the phylum Chloroflexi. The highest levels of sequence similarity, about 91 %, were with Caldilinea aerophila STL-6-O1T and Caldilinea tarbellica D1-25-10-4T. Fermentative growth was not observed for strain PRI-4131T, which, in addition to other characteristics, distinguished it from the two Caldilinea species. Owing to both phylogenetic and phenotypic differences from the described members of the class Caldilineae , we propose to accommodate strain PRI-4131T in a novel species in a new genus, Litorilinea aerophila gen. nov., sp. nov. The type strain of Litorilinea aerophila is PRI-4131T ( = DSM 25763T  = ATCC BAA-2444T).

Rhizobium paknamense sp. nov., isolated from lesser duckweeds (Lemna aequinoctialis)

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3823-3828 ◽  
Author(s):  
Chokchai Kittiwongwattana ◽  
Chitti Thawai
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Low Levels ◽  
Sequence Similarity Analysis ◽  
Ph Range

A Gram-stain-negative, rod-shaped bacterium was isolated and designated strain L6-8T during a study of endophytic bacterial communities in lesser duckweed (Lemna aequinoctialis). Cells of strain L6-8T were motile with peritrichous flagella. The analysis of the nearly complete 16S rRNA gene sequence indicated that strain L6-8T was phylogenetically related to species of the genus Rhizobium . Its closest relatives were Rhizobium borbori DN316T (97.6 %), Rhizobium oryzae Alt 505T (97.3 %) and Rhizobium pseudoryzae J3-A127T (97.0 %). The sequence similarity analysis of housekeeping genes recA, glnII, atpD and gyrB showed low levels of sequence similarity (<91.5 %) between strain L6-8T and other species of the genus Rhizobium with validly published names. The pH range for growth was 4.0–9.0 (optimum 6.0–7.0), and the temperature range for growth was 20–45 °C (optimum 30 °C). Strain L6-8T tolerated NaCl up to 2 % (w/v) (optimum 1 % NaCl). The predominant components of cellular fatty acids were C19 : 0 cyclo ω8c (31.32 %), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 25.39 %) and C16 : 0 (12.03 %). The DNA G+C content of strain L6-8T was 60.4 mol% (T m). nodC and nifH were not amplified in strain L6-8T. DNA–DNA relatedness between strain L6-8T and R. borbori DN316T, R. oryzae Alt505T and R. pseudoryzae J3-A127T was between 11.2 and 18.3 %. Based on the sequence similarity analyses, phenotypic, biochemical and physiological characteristics and DNA–DNA hybridization, strain L6-8T could be readily distinguished from its closest relatives and represents a novel species of the genus Rhizobium , for which the name Rhizobium paknamense sp. nov. is proposed. The type strain is L6-8T ( = NBRC 109338T = BCC 55142T).

scholarly journals Salinibaculum litoreum gen. nov., sp. nov., isolated from salted brown alga Laminaria

2020 ◽  
Vol 70 (4) ◽  
pp. 2879-2887 ◽  
Author(s):  
Dong Han ◽  
Heng-Lin Cui
Keyword(s):  
Brown Alga ◽  
Type Species ◽  
Sequence Similarity ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Pr China ◽  
A Minor

A novel Gram-stain-negative, aerobic and rod-shaped halophilic archaeon, designated HD8-45T, was isolated from the red brine of salted brown alga Laminaria produced at Dalian, PR China. According to the results of 16S rRNA gene and rpoB′ gene sequence comparisons, strain HD8-45T showed the highest sequence similarity to the corresponding genes of Salinirussus salinus YGH44T (95.1 and 85.2 % similarities, respectively), Halovenus aranensis EB27T (91.2 and 86.0 % similarities, respectively). The low sequence similarity and the phylogeny implied the novel generic status of strain HD8-45T. Genomic relatedness analyses showed that strain HD8-45T were clearly distinguished from other species in the order Halobacteriales , with average nucleotide identity, amino acid identity and in silico DNA–DNA hybridization values not more than 75.1, 65.6 and 21.5 %. The polar lipid pattern contained phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, two major glycolipids and two minor glycolipids. The two major glycolipids and a minor glycolipid were chromatographically identical to disulfated mannosyl glucosyl diether, sulfated mannosyl glucosyl diether and mannosyl glucosyl diether, respectively. The major respiratory quinones were menaquinone MK-8 and MK-8(H2). The DNA G+C content was 62.0 mol% (Tm ) and 61.9 mol% (genome). All these results showed that strain HD8-45T represents a novel species of a new genus in the order Halobacteriales , for which the name Salinibaculum litoreum gen. nov., sp. nov. is proposed. The type strain of Salinibaculum litoreum is HD8-45T (=CGMCC 1.15328T=JCM 31107T).

Crassaminicella thermophila sp. nov., a moderately thermophilic bacterium isolated from a deep-sea hydrothermal vent chimney and emended description of the genus Crassaminicella

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Xue-Gong Li ◽  
Jin Lin ◽  
Shi-Jie Bai ◽  
Jie Dai ◽  
Ze-Xi Jiao ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Hydrothermal Vent ◽  
Type Species ◽  
Rrna Gene ◽  
Chromosomal Dna ◽  
Content Type ◽  
Moderately Thermophilic ◽  
Link Type ◽  
Emended Description

A novel moderately thermophilic, anaerobic, heterotrophic bacterium (strain SY095T) was isolated from a hydrothermal vent chimney located on the Southwest Indian Ridge at a depth of 2730 m. Cells were Gram-stain-positive, motile, straight to slightly curved rods forming terminal endospores. SY095T was grown at 45–60 °C (optimum 50–55 °C), pH 6.0–7.5 (optimum 7.0), and in a salinity of 1–4.5 % (w/v) NaCl (optimum 2.5 %). Substrates utilized by SY095T included fructose, glucose, maltose, N-acetyl glucosamine and tryptone. Casamino acid and amino acids (glutamate, glutamine, lysine, methionine, serine and histidine) were also utilized. The main end products from glucose fermentation were acetate, H2 and CO2. Elemental sulphur, sulphate, thiosulphate, sulphite, fumarate, nitrate, nitrite and Fe(III) were not used as terminal electron acceptors. The predominant cellular fatty acids were C14 : 0 (60.5%) and C16 : 0 (7.6 %). The main polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, five unidentified phospholipids and two unidentified aminophospholipids. No respiratory quinones were detected. The chromosomal DNA G+C content was 30.8 mol%. The results of phylogenetic analysis of the 16S rRNA gene sequences indicated that SY095T was closely related to Crassaminicella profunda Ra1766HT (95.8 % 16S rRNA gene sequence identity). SY095T exhibited 78.1 % average nucleotide identity (ANI) to C. profunda Ra1766HT. The in silico DNA–DNA hybridization (DDH) value indicated that SY095T shared 22.7 % DNA relatedness with C. profunda Ra1766HT. On the basis of its phenotypic, genotypic and phylogenetic characteristics, SY095T is suggested to represent a novel species of the genus Crassaminicella , for which the name Crassaminicella thermophila sp. nov. is proposed. The type strain is SY095T (=JCM 34213=MCCC 1K04191). An emended description of the genus Crassaminicella is also proposed.

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