scholarly journals Alkalibaculum sporogenes sp. nov., isolated from a terrestrial mud volcano and emended description of the genus Alkalibaculum

2020 ◽  
Vol 70 (9) ◽  
pp. 4914-4919 ◽  
Author(s):  
M.A. Khomyakova ◽  
A.Y. Merkel ◽  
D.A. Petrova ◽  
E.A. Bonch-Osmolovskaya ◽  
A.I. Slobodkin
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Mud Volcano ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Emended Description ◽  
Bacterium Strain ◽  
Ph Range

A novel anaerobic, endospore-forming bacterium (strain M08 DMBT) was isolated from a terrestrial mud volcano (Taman Peninsula, Russia). Cells of the strain were motile rods 1.3–2.0 µm long and 0.4 µm in diameter. The temperature range for growth was 5–42 °C, with an optimum at 30 °C. The pH range for growth was H 6.5–11.0, with an optimum at pH 8.0. Growth of strain M08 DMBT was observed at NaCl concentrations of 0–5.0 % (w/v) with an optimum at 1.0 %. Strain M08 DMBT utilized 3,4-dimethoxybenzoic acid, 2-methoxyphenol, carbon monoxide, glucose, fructose, mannose, xylose and yeast extract. The end product of glucose fermentation was acetate. The DNA G+C content of strain M08 DMBT was 32.3 mol% (obtained via whole genome sequencing). The closest phylogenetic relative of strain M08 DMBT was Alkalibaculum bacchi (family Eubacteriaceae , class Clostridia ) with 95.17 % 16S rRNA gene sequence similarity. Based on the phenotypic, genotypic and phylogenetic characteristics of the isolate, strain M08 DMBT is considered to represent a novel species of the genus Alkalibaculum , for which the name Alkalibaculum sporogenes sp. nov. is proposed. The type strain of Alkalibaculum sporogenes is M08 DMBT (=KCTC 15840T=VKM B-3387T).

scholarly journals Methanolobus halotolerans sp. nov., isolated from the saline Lake Tus in Siberia

2020 ◽  
Vol 70 (10) ◽  
pp. 5586-5593 ◽  
Author(s):  
Ya Shen ◽  
Sheng-Chung Chen ◽  
Mei-Chin Lai ◽  
Hsing-Hua Huang ◽  
Hsiu-Hui Chiu ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Saline Lake ◽  
Novel Species ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Ph Range ◽  
Genomic Relatedness

A halotolerant, psychrotolerant and methylotrophic methanogen, strain SY-01T, was isolated from the saline Lake Tus in Siberia. Cells of strain SY-01T were non-motile, cocci and 0.8–1.0 µm in diameter. The only methanogenic substrate utilized by strain SY-01T was methanol. The temperature range of growth for strain SY-01T was from 4 to 40 °C and the optimal temperature for growth was 30 °C. The pH range of growth was from pH 7.2 to 9.0, with optimal growth at pH 8.0. The NaCl range of growth was 0–1.55 M with optimal growth at 0.51 M NaCl. The G+C content of the genome of strain SY-01T was 43.6 mol % as determined by genome sequencing. Phylogenetic analysis revealed that strain SY-01T was most closely related to Methanolobus zinderi SD1T (97.3 % 16S rRNA gene sequence similarity), and had 95.5–97.2 % similarities to other Methanolobus species with valid names. Genome relatedness between strain SY-01T and DSM 21339T was computed using average nucleotide identity and digital DNA–DNAhybridization, which yielded values of 79.7 and 21.7 %, respectively. Based on morphological, phenotypic, phylogenetic and genomic relatedness data presented here, it is evident that strain SY-01T represents a novel species of the genus Methanolobus , and the name Methanolobus halotolerans sp. nov. is proposed. The type strain is SY-01T (=BCRC AR10051T=NBRC 113166 T=DSM 107642T).

scholarly journals Spirosoma oryzae sp. nov., isolated from rice soil and emended description of the genus Spirosoma

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3230-3234 ◽  
Author(s):  
Jae-Hyung Ahn ◽  
Hang-Yeon Weon ◽  
Soo-Jin Kim ◽  
Seung-Beom Hong ◽  
Soon-Ja Seok ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rice Soil ◽  
Content Type ◽  
Link Type ◽  
Emended Description ◽  
Unknown Phospholipid ◽  
Sequence Similarities

A bacterial strain, designated RHs22T, was isolated from a soil sample cultivated with rice in the Suwon region of South Korea. The cells were aerobic, Gram-stain-negative, non-spore-forming, non-flagellated rods or occasionally filaments. The strain grew at 10–37 °C (optimum, 28–30 °C), at pH 5.0–10.0 (optimum, 7.0) and in the presence of 0–1 % (w/v) NaCl (optimum, 0 %). Phylogenetically, the strain was closely related to members of the genus Spirosoma , as its 16S rRNA gene sequence had similarity of 90.3–92.1 % with respect to those of members of the genus Spirosoma , showing the highest sequence similarity with Spirosoma panaciterrae DSM 21099T. Strain RHs22T revealed relatively low sequence similarities of less than 90 % with all the other species with validly published names. It contained MK-7 as the predominant menaquinone and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 1ω5c, iso-C15 : 0 and iso-C17 : 0 3-OH as the main fatty acids. The polar lipids of strain RHs22T were phosphatidylethanolamine, one unknown aminolipid, two unknown aminophospholipids, one unknown phospholipid and five unknown lipids. The DNA G+C content was 57.0 mol%. Phylogenetic, phenotypic and chemotaxonomic data obtained in this study indicate that strain RHs22T represents a novel species of the genus Spirosoma , for which the name Spirosoma oryzae sp. nov. is proposed. The type strain is RHs22T ( = KACC 17324T = DSM 28354T). An emended description of the genus Spirosoma is also proposed.

scholarly journals Dysgonomonas termitidis sp. nov., isolated from the gut of the subterranean termite Reticulitermes speratus

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 681-685 ◽  
Author(s):  
Ajeng K. Pramono ◽  
Mitsuo Sakamoto ◽  
Takao Iino ◽  
Yuichi Hongoh ◽  
Moriya Ohkuma
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Reticulitermes Speratus ◽  
Content Type ◽  
Optimum Growth Temperature ◽  
Link Type ◽  
Bacterium Strain ◽  
Sequence Similarity Analysis

A facultatively anaerobic, Gram-stain-negative, non-motile and rod-shaped bacterium, strain N-10T, was isolated from the gut of the termite Reticulitermes speratus. Strain N-10T was closely related to Dysgonomonas gadei JCM 16698T according to 16S rRNA gene sequence similarity analysis (98 %) and DNA–DNA relatedness value (≤61.3 %). The optimum growth temperature of strain N-10T was 30 °C, which was distinct from that (37 °C) of known species of the genus Dysgonomonas . Growth of strain N-10T was inhibited on medium containing 5 or 20 % bile, unlike other species of the genus Dysgonomonas . In addition, acid production in the API 20A system and enzymic reactions in the Rapid ID 32A system of strain N-10T differed from those of other species of the genus Dysgonomonas . Based on these characteristics, strain N-10T represents a novel species of the genus Dysgonomonas , for which the name Dysgonomonas termitidis sp. nov. is proposed. The type strain is N-10T ( = JCM 30204T = CCUG 66188T).

Alkalibacter mobilis sp. nov., an anaerobic bacterium isolated from a coastal lake

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Maria Khomyakova ◽  
Alexander Merkel ◽  
Andrei Novikov ◽  
Alexandra Klyukina ◽  
Alexander Slobodkin
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Coastal Lake ◽  
Content Type ◽  
Link Type ◽  
Bacterium Strain ◽  
Ph Range ◽  
Alkaliphilic Bacterium

A novel anaerobic chemoorganotrophic, facultatively alkaliphilic bacterium (strain M17 DMBT) was isolated from a coastal lake (Golubitsckoe, Taman Peninsula, Russia). Cells were motile rods, 1.6–2.1 µm long and 0.45 µm in diameter. The temperature range for growth was 14–42 °C, with an optimum at 30 °C. The pH range for growth was pH 5.5–10.0, with an optimum at pH 8.0–8.5. Growth of strain M17 DMBT was observed at NaCl concentrations of 1–12 % (w/v) with optimum growth at 1.5–2.0 %. Strain M17 MBTutilized glucose, fructose, sucrose, ribose, mannose, raffinose, arabinose, dextrin, yeast extract, peptone, carbon monoxide, vanillic acid and 3,4-dimethoxybenzoic acid. The end products from glucose fermentation were acetate and ethanol. The DNA G+C content of strain M17 DMBT was 39.1 mol%. The closest phylogenetic relative of strain M17 DMBT was Alkalibacter saccharofermentans with 97.8 % 16S rRNA gene sequence similarity. The OrthoANI value between M17 DMBT and A. saccharofermentans was 70.4 %. Based on the phenotypic, genotypic and phylogenetic characteristics of the isolate, strain M17 DMBT is considered to represent a novel species of the genus Alkalibacter for which the name Alkalibacter mobilis sp. nov. is proposed. The type strain of Alkalibacter mobilis is M17 DMBT (=KCTC 15920T=VKM B-3408T).

Pseudomonas guangdongensis sp. nov., isolated from an electroactive biofilm, and emended description of the genus Pseudomonas Migula 1894

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4599-4605 ◽  
Author(s):  
Guiqin Yang ◽  
Luchao Han ◽  
Junlin Wen ◽  
Shungui Zhou
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Emended Description

A Gram-negative, straight to slightly curved rod-shaped bacterium, motile with peritrichous flagella, designated SgZ-6T, was isolated from an electroactive biofilm and was characterized by means of a polyphasic approach. Growth occurred with 0–5.0 % (w/v) NaCl (optimum 1 %), at pH 6.0–10.0 (optimum pH 7.0) and at 10–42 °C (optimum 30 °C) in trypticase soya broth. Phylogenetic analyses based on the 16S rRNA and gyrB genes identified the isolate as a member of a novel species of the genus Pseudomonas . Strain SgZ-6T exhibited the highest 16S rRNA gene sequence similarity to ‘ Pseudomonas linyingensis’ CGMCC 1.10701 (97.5 %), followed by Pseudomonas sagittaria JCM 18195T (97.4 %), P. oleovorans subsp. lubricantis DSM 21016T (96.6 %), P. tuomuerensis JCM 14085T (96.5 %) and P. alcaliphila JCM 10630T (96.4 %). Strain SgZ-6T showed the highest gyrB gene sequence similarity of 93.7 % to ‘P. linyingensis’ CGMCC 1.10701 among all type strains of genus Pseudomonas . DNA–DNA pairing studies showed that strain SgZ-6T displayed 47.1 and 40.3 % relatedness to ‘P. linyingensis’ CGMCC 1.10701 and P. sagittaria JCM 18195T, respectively. The major isoprenoid quinone was ubiquinone 9 (Q-9). The whole-cell fatty acids consisted mainly of summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The DNA G+C content of the genomic DNA was 68.1 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain SgZ-6T is proposed to represent a novel species of the genus Pseudomonas , for which the name Pseudomonas guangdongensis sp. nov. is proposed. The type strain is SgZ-6T ( = CCTCC AB 2012022T = KACC 16606T). An emended description of the genus Pseudomonas is also proposed.

scholarly journals Ercella succinigenes gen. nov., sp. nov., an anaerobic succinate-producing bacterium

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2449-2454 ◽  
Author(s):  
Antonie H. van Gelder ◽  
Diana Z. Sousa ◽  
W. Irene C. Rijpstra ◽  
Jaap S. Sinninghe Damsté ◽  
Alfons J. M. Stams ◽  
...  
Keyword(s):  
New Genus ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Curved Rods ◽  
Bacterium Strain ◽  
Ph Range

A novel anaerobic succinate-producing bacterium, strain ZWBT, was isolated from sludge collected from a biogas desulfurization bioreactor (Eerbeek, the Netherlands). Cells were non-spore-forming, motile, slightly curved rods (0.4–0.5 µm in diameter and 2–3 µm in length), and stained Gram-negative. The temperature range for growth was 25–40 °C, with an optimum at 37 °C. The pH range for growth was 7.0–9.0, with an optimum at pH 7.5. Strain ZWBT was able to ferment glycerol and several carbohydrates mainly to H2, succinate and acetate. Sulfur and fumarate could be used as electron acceptors by strain ZWBT. The G+C content of the genomic DNA was 37.6 mol%. The most abundant fatty acids were iso-C14 : 0 and iso-C16 : 0 DMA. On the basis of 16S rRNA gene sequence similarity, strain ZWBT belongs to the family Ruminococcaceae and it is distantly related to Saccharofermentans acetigenes JCM 14006T (92.1 %). Based on the physiological features and phylogenetic analysis, strain ZWBT represents a novel species of a new genus, for which the name Ercella succinigenes gen. nov., sp. nov. is proposed. The type strain of Ercella succinigenes is ZWBT ( = DSM 27333T = JCM 19283T).

scholarly journals Flavisolibacter rigui sp. nov., isolated from freshwater of an artificial reservoir and emended description of the genus Flavisolibacter

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4038-4042 ◽  
Author(s):  
Keun Sik Baik ◽  
Mi Sun Kim ◽  
Ji Hee Lee ◽  
Sang Suk Lee ◽  
Wan-Taek Im ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gram Stain ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Emended Description

A non-motile and rod-shaped bacterium, designated strain 02SUJ3T, was isolated from freshwater collected from the Juam Reservoir (Republic of Korea). Cells were Gram-stain-negative, aerobic, oxidase-negative and catalase-positive. The major fatty acids were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The strain contained MK-7 as the major isoprenoid quinone. The main polar lipid was phosphatidylethanolamine. The DNA G+C content was 46.4 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain 02SUJ3T forms an independent lineage within the genus Flavisolibacter with low sequence similarity to Flavisolibacter ginsengiterrae Gsoil 492T and Flavisolibacter ginsengisoli Gsoil 643T (95.7 %). Phenotypic characteristics distinguished strain 02SUJ3T from members of the genus Flavisolibacter . On the basis of the evidence presented in this study, strain 02SUJ3T is considered to represent a novel species, for which the name Flavisolibacter rigui sp. nov. is proposed. The type strain is 02SUJ3T ( = JCM 17515T = KCTC 23328T). An emended description of the genus Flavisolibacter is also provided.

scholarly journals Rhizobium rhizoryzae sp. nov., isolated from rice roots

2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1373-1377 ◽  
Author(s):  
Xiao-Xia Zhang ◽  
Xue Tang ◽  
Rizwan Ali Sheirdil ◽  
Lei Sun ◽  
Xiao-Tong Ma
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type ◽  
The 16S Rrna Gene

Two strains (J3-AN59T and J3-N84) of Gram-stain-negative, aerobic and rod-shaped bacteria were isolated from the roots of fresh rice plants. The 16S rRNA gene sequence similarity results showed that the similarity between strains J3-AN59T and J3-N84 was 100 %. Both strains were phylogenetically related to members of the genus Rhizobium , and they were most closely related to Rhizobium tarimense ACCC 06128T (97.43 %). Similarities in the sequences of housekeeping genes between strains J3-AN59T and J3-N84 and those of recognized species of the genus Rhizobium were less than 90 %. The polar lipid profiles of both strains were predominantly composed of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unknown aminophospholipid. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The DNA G+C contents of J3-AN59T and J3-N84 were 55.7 and 57.1 mol%, respectively. The DNA–DNA relatedness value between J3-AN59T and J3-N84 was 89 %, and strain J3-AN59T showed 9 % DNA–DNA relatedness to R. tarimense ACCC 06128T, the most closely related strain. Based on this evidence, we found that J3-AN59T and J3-N84 represent a novel species in the genus Rhizobium and we propose the name Rhizobium rhizoryzae sp. nov. The type strain is J3-AN59T ( = ACCC 05916T = KCTC 23652T).

Rhodanobacter denitrificans sp. nov., isolated from nitrate-rich zones of a contaminated aquifer

2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2457-2462 ◽  
Author(s):  
Om Prakash ◽  
Stefan J. Green ◽  
Puja Jasrotia ◽  
Will A. Overholt ◽  
Andy Canion ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Contaminated Aquifer ◽  
Content Type ◽  
Link Type ◽  
Characteristic Features

Bacterial strains 2APBS1T and 116-2 were isolated from the subsurface of a nuclear legacy waste site where the sediments are co-contaminated with large amounts of acids, nitrate, metal radionuclides and other heavy metals. A combination of physiological and genetic assays indicated that these strains represent the first member of the genus Rhodanobacter shown to be capable of complete denitrification. Cells of strain 2APBS1T and 116-2 were Gram-negative, non-spore-forming rods, 3–5 µm long and 0.25–0.5 µm in diameter. The isolates were facultative anaerobes, and had temperature and pH optima for growth of 30 °C and pH 6.5; they were able to tolerate up to 2.0 % NaCl, although growth improved in its absence. Strains 2APBS1T and 116-2 contained fatty acid and quinone (ubiquinone-8; 100 %) profiles that are characteristic features of the genus Rhodanobacter . Although strains 2APBS1T and 116-2 shared high 16S rRNA gene sequence similarity with Rhodanobacter thiooxydans LCS2T (>99 %), levels of DNA–DNA relatedness between these strains were substantially below the 70 % threshold used to designate novel species. Thus, based on genotypic, phylogenetic, chemotaxonomic and physiological differences, strains 2APBS1T and 116-2 are considered to represent a single novel species of the genus Rhodanobacter , for which the name Rhodanobacter denitrificans sp. nov. is proposed. The type strain is 2APBS1T ( = DSM 23569T = JCM 17641T).

scholarly journals Chitinimonas viridis sp. nov., isolated from a mesotrophic artificial lake

2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1123-1126 ◽  
Author(s):  
Yochan Joung ◽  
Beom-Il Lee ◽  
Heeyoung Kang ◽  
Haneul Kim ◽  
Kiseong Joh
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Artificial Lake ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Bacterium Strain

A Gram-staining-negative, rod-shaped bacterium, strain HMD2169T, was isolated from a mesotrophic artificial lake in Korea. Strain HMD2169T grew in the presence of 0–3.0 % (w/v) NaCl, at pH 5–10 and at 20–37 °C. The predominant quinone of strain HMD2169T was ubiquinone (UQ)-8. The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, two unidentified aminolipids and two unidentified lipids. The DNA G+C content was 59.8 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HMD2169T was a representative of a lineage within the genus Chitinimonas . Strain HMD2169T was closely related to Chitinimonas taiwanensis (95.8 % sequence similarity) and Chitinimonas koreensis (94.6 %). On the basis of the evidence presented in this study, strain HMD2169T is a representative of a novel species of the genus Chitinimonas , for which the name Chitinimonas viridis sp. nov. is proposed with the type strain HMD2169T ( = KCTC 22839T = CECT 7703T).

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