scholarly journals Sandaracinus amylolyticus gen. nov., sp. nov., a starch-degrading soil myxobacterium, and description of Sandaracinaceae fam. nov.

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).

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4396-4401 ◽  
Author(s):  
Jung-Eun Yang ◽  
Heung-Min Son ◽  
Jung Min Lee ◽  
Heon-Sub Shin ◽  
Sang-Yong Park ◽  
...  

A Gram-reaction-negative, strictly aerobic, non-motile, non-spore-forming and rod-shaped bacterial strain, designated THG-45T, was isolated from soil of a ginseng field of Pocheon province in the Republic of Korea and its taxonomic position was investigated by a polyphasic approach. Growth occurred at 4–30 °C, at pH 5.5–9.0 and with 0–2 % (w/v) NaCl on nutrient agar. On the basis of 16S rRNA gene sequence similarity, strain THG-45T was shown to belong to the genus Pedobacter and was related to Pedobacter borealis G-1T (98.8 %), P. alluvionis NWER-II11T (97.9 %), P. agri PB92T (97.9 %), P. terrae DS-57T (97.5 %), P. suwonensis 15-52T (97.4 %), P. sandarakinus DS-27T (97.0 %) and P. soli 15-51T (97.0 %), but DNA relatedness between strain THG-45T and these strains was below 36 %. The G+C content of the genomic DNA was 39 mol%. The only isoprenoid quinone detected in strain THG-45T was menaquinone-7 (MK-7). The predominant fatty acids were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c) and iso-C17 : 0 3-OH, and the major polar lipids were phosphatidylethanolamine and an unidentified aminophosphoglycolipid. Phenotypic data and phylogenetic inference supported the affiliation of strain THG-45T to the genus Pedobacter , and a number of biochemical tests differentiated strain THG-45T from the recognized species of the genus Pedobacter . Therefore, the novel isolate represents a novel species, for which the name Pedobacter ginsenosidimutans sp. nov. is proposed, with THG-45T as the type strain ( = KACC 14530T = JCM 16721T).


2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1562-1567 ◽  
Author(s):  
Mohammad Ali Amoozegar ◽  
Ali Makhdoumi-Kakhki ◽  
Mohadaseh Ramezani ◽  
Mahdi Moshtaghi Nikou ◽  
Seyed Abolhassan Shahzadeh Fazeli ◽  
...  

A novel, Gram-staining-negative, non-pigmented, rod-shaped, strictly aerobic, extremely halophilic bacterium, designated strain IA16T, was isolated from the mud of the hypersaline Lake Aran-Bidgol, in Iran. Cells of strain IA16T were not motile. Growth occurred with 2.5–5.2 M NaCl (optimum 3.4 M), at pH 6.0–8.0 (optimum pH 7.0) and at 30–50 °C (optimum 40 °C). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain IA16T belonged in the family Rhodospirillaceae and that its closest relatives were Rhodovibrio sodomensis DSM 9895T (91.6 % sequence similarity), Rhodovibrio salinarum NCIMB 2243T (91.2 %), Pelagibius litoralis CL-UU02T (88.9 %) and Fodinicurvata sediminis YIM D82T (88.7 %). The novel strain’s major cellular fatty acids were C19 : 0 cyclo ω7c and C18 : 0 and its polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, four unidentified phospholipids, three unidentified aminolipids and two other unidentified lipids. The cells of strain IA16T contained the ubiquinone Q-10. The G+C content of the novel strain’s genomic DNA was 67.0 mol%. The physiological, biochemical and phylogenetic differences between strain IA16T and other previously described taxa indicate that the strain represents a novel species in a new genus within the family Rhodospirillaceae , for which the name Limimonas halophila gen. nov., sp. nov. is proposed. The type strain of Limimonas halophila is IA16T ( = IBRC-M 10018T  = DSM 25584T).


2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2223-2228 ◽  
Author(s):  
Gabriel Paiva ◽  
Pedro Abreu ◽  
Diogo Neves Proença ◽  
Susana Santos ◽  
Maria Fernanda Nobre ◽  
...  

Bacterial strain M47C3BT was isolated from the endophytic microbial community of a Pinus pinaster tree branch from a mixed grove of pines. Phylogenetic analysis of 16S rRNA gene sequences showed that this organism represented one distinct branch within the family Sphingobacteriaceae , most closely related to the genus Mucilaginibacter . Strain M47C3BT formed a distinct lineage, closely related to Mucilaginibacter dorajii KACC 14556T, with which it shared 97.2 % 16S rRNA gene sequence similarity. The other members of the genus Mucilaginibacter included in the same clade were Mucilaginibacter lappiensis ATCC BAA-1855T sharing 97.0 % similarity and Mucilaginibacter composti TR6-03T that had a lower similarity (95.7 %). The novel strain was Gram-staining-negative, formed rod-shaped cells, grew optimally at 26 °C and at pH 7, and was able to grow with up to 0.3 % (w/v) NaCl. The respiratory quinone was menaquinone 7 (MK-7) and the major fatty acids of the strain were summed feature 3 (C16 : 1ω7c/iso-C15 : 0 2-OH), iso-C15 : 0 and iso-C17 : 0 3-OH, representing 73.5 % of the total fatty acids. The major components of the polar lipid profile of strain M47C3BT consisted of phosphatidylethanolamine, three unidentified aminophospholipids, one unidentified aminolipid and three unidentified polar lipids. The G+C content of the DNA was 40.6 mol%. On the basis of the phylogenetic analysis and physiological and biochemical characteristics we propose the name Mucilaginibacter pineti sp. nov. for the novel species represented by strain M47C3BT ( = CIP 110632T = LMG 28160T).


2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1235-1240 ◽  
Author(s):  
Tong Yu ◽  
Qi Yin ◽  
Xiangyu Song ◽  
Rui Zhao ◽  
Xiaochong Shi ◽  
...  

A novel Gram-stain-negative, rod-shaped, non-flagellated, strictly aerobic strain with gliding motility, designated SW024T, was isolated from surface seawater of the South Pacific Gyre (26° 29′ S 137° 56′ W) during the Integrated Ocean Drilling Program Expedition 329. Phylogenetic analyses based on 16S rRNA gene sequences showed that the novel strain was related most closely to Aquimarina muelleri KMM 6020T, Aquimarina macrocephali JAMB N27T, Aquimarina addita JC2680T, Aquimarina mytili PSC33T, Aquimarina intermedia KMM 6258T, Aquimarina latercula ATCC 23177T, Aquimarina spongiae A6T, Aquimarina agarilytica ZC1T and Aquimarina brevivitae SMK-19T (96.1, 95.5, 95.0, 94.4, 94.3, 94.0, 93.4, 93.3 and 93.2 % similarities, respectively), demonstrating that the novel strain belonged to the genus Aquimarina . The DNA G+C content of strain SW024T was 30.8 mol%. The major respiratory quinone of strain SW024T was MK-6. The dominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G, C16 : 0 10-methyl and/or iso-C17 : 1ω9c, and iso-C15 : 0 3-OH. The polar lipids of strain SW024T were phosphatidylethanolamine, three unknown aminolipids and five unknown polar lipids. On the basis of combined phenotypic and phylogenetic analyses, strain SW024T represents a novel species of the genus Aquimarina , for which the name Aquimarina longa sp. nov. is proposed. The type strain is SW024T ( = CGMCC 1.11007T = JCM 17859T). An emended description of A. muelleri is also proposed.


2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3854-3860 ◽  
Author(s):  
Masanori Tohno ◽  
Maki Kitahara ◽  
Tomohiro Irisawa ◽  
Takaharu Masuda ◽  
Ryuichi Uegaki ◽  
...  

Two bacterial strains, designated IWT246T and IWT248, were isolated from orchardgrass (Dactylis glomerata L.) silage from Iwate prefecture, Japan, and examined for a taxonomic study. Both organisms were rod-shaped, Gram-stain-positive, catalase-negative, facultatively anaerobic and homofermentative. The cell wall did not contain meso-diaminopimelic acid and the major fatty acids were C18 : 1ω9c and C19 cyclo 9,10/:1. Comparative analyses of 16S rRNA, pheS and rpoA gene sequences revealed that these strains were novel and belonged to the genus Lactobacillus . Based on 16S rRNA gene sequence similarity, the isolates were most closely related to the type strains of the following members of the genus Lactobacillus : Lactobacillus coryniformis subsp. coryniformis (96.7 % similarity), L. coryniformis subsp. torquens (96.6 %), L. bifermentans (95.5 %) and L. rennini (94.1 %). However, the 16S rRNA gene sequences of both IWT246T and IWT248 were 99.7 % similar to that of ‘ Lactobacillus backi’ JCM 18665; this name has not been validly published. Genotypic, phenotypic and chemotaxonomic analyses confirmed that these novel strains occupy a unique taxonomic position. DNA–DNA hybridization experiments demonstrated genotypic separation of the novel isolates from related Lactobacillus species. The name Lactobacillus iwatensis sp. nov. is proposed for the novel isolates, with strain IWT246T ( = JCM 18838T = DSM 26942T) as the type strain. Our results also suggest that ‘L. backi’ does represent a novel Lactobacillus species. The cells did not contain meso-diaminopimelic acid in their cell-wall peptidoglycan and the major fatty acids were C16 : 0, C19 cyclo 9,10/:1 and summed feature 10 (one or more of C18 : 1ω11c, C18 : 1ω9t, C18 : 1ω6t and unknown ECL 17.834). We therefore propose the corrected name Lactobacillus backii sp. nov., with the type strain JCM 18665T ( = LMG 23555T = DSM 18080T = L1062T).


2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4134-4140 ◽  
Author(s):  
Iftikhar Ahmed ◽  
Saira Abbas ◽  
Takuji Kudo ◽  
Muhammad Iqbal ◽  
Toru Fujiwara ◽  
...  

A Gram-stain-positive, strictly aerobic, non-motile, coccoid bacterium, designated NCCP-154T, was isolated from citrus leaf canker lesions and was subjected to a polyphasic taxonomic study. Strain NCCP-154T grew at 10–37 °C (optimum 30 °C) and at pH 7.0–8.0 (optimum pH 7.0). The novel strain exhibited tolerance of UV irradiation (>1000 J m−2). Based on 16S rRNA gene sequence analysis, strain NCCP-154T showed the highest similarity to Deinococcus gobiensis CGMCC 1.7299T (98.8 %), and less than 94 % similarity to other closely related taxa. The chemotaxonomic data [major menaquinone, MK-8; cell-wall peptidoglycan type, A3β (Orn–Gly2); major fatty acids, summed feature 3 (C16 : 1ω7c/iso-C15 : 0 2-OH; 35.3 %) followed by C16 : 0 (12.7 %), iso-C17 : 1ω9c (9.2 %), C17 : 1ω8c (7.4 %) and iso-C17 : 0 (6.9 %); major polar lipids made up of several unidentified phosphoglycolipids and glycolipids and an aminophospholipid, and mannose as the predominant whole-cell sugar] also supported the affiliation of strain NCCP-154T to the genus Deinococcus . The level of DNA–DNA relatedness between strain NCCP-154T and D. gobiensis JCM 16679T was 63.3±3.7 %. The DNA G+C content of strain NCCP-154T was 70.0 mol%. Based on the phylogenetic analyses, DNA–DNA hybridization and physiological and biochemical characteristics, strain NCCP-154T can be differentiated from species with validly published names. Therefore, it represents a novel species of the genus Deinococcus . The name Deinococcus citri sp. nov. is proposed, with the type strain NCCP-154T ( = JCM 19024T = DSM 24791T = KCTC 13793T).


2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2844-2850 ◽  
Author(s):  
Sathiyaraj Srinivasan ◽  
Jae-Jin Lee ◽  
Sangyong Lim ◽  
Minho Joe ◽  
Myung Kyum Kim

A Gram-staining-positive, strictly aerobic, spherical, non-motile, red-pigmented bacterium, designated strain MK03T, was isolated from a soil sample collected in South Korea. The taxonomic position of the novel strain was investigated using a polyphasic approach. In phylogenetic analyses based on 16S rRNA gene sequences, strain MK03T was placed in a clade formed by members of the genus Deinococcus in the family Deinococcaceae and appeared to be most closely related to Deinococcus aerolatus 5516T-9T (97.4 % sequence similarity), Deinococcus marmoris AA-63T (97.2 %), Deinococcus radiopugnans ATCC 19172T (97.2 %) and Deinococcus saxicola AA-1444T (96.9 %). The genomic DNA G+C content of the novel strain was 64.5 mol%. The chemotaxonomic characteristics of strain MK03T were typical of members of the genus Deinococcus : MK-8 was identified as the predominant respiratory quinine, the major fatty acids were C16 : 1ω7c, C15 : 1ω6c, C16 : 0 and C15 : 0, ornithine was found to be the diamino acid in the cell-wall peptidoglycan and the novel strain showed resistance to gamma radiation, with a D10 value (i.e. the dose required to reduce the bacterial population by 10-fold) in excess of 9 kGy. In hybridization experiments, only low DNA–DNA relatedness values (11.6–34.5 %) were recorded between the novel strain and its closest relatives in the genus Deinococcus . Based on the phylogenetic, chemotaxonomic, phenotypic and DNA–DNA relatedness data, strain MK03T represents a novel species of the genus Deinococcus , for which the name Deinococcus humi sp. nov. is proposed. The type strain is MK03T ( = KCTC 13619T  = JCM 17915T).


2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1421-1426 ◽  
Author(s):  
Byoung-Jun Yoon ◽  
Dong-Heon Lee ◽  
Duck-Chul Oh

A Gram-staining-negative, yellow-pigmented, non-motile, strictly aerobic, rod-shaped bacterium, designated strain CNU001T, was isolated from seawater collected on the coast of Jeju Island, South Korea, and subjected to a polyphasic taxonomic study. The temperature, pH and NaCl ranges for growth were 10–30 °C, pH 6.0–10.0 and 2.0–5.0 %, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CNU001T belonged to the genus Erythrobacter in the family Erythrobacteraceae , with Erythrobacter longus DSM 6997T (96.6 % sequence similarity), Erythrobacter gaetbuli SW-161T (96.3 %), Erythrobacter vulgaris 022 2-10T (96.2 %), Erythrobacter nanhaisediminis T30T (96.1 %) and other members of the genus Erythrobacter (<96.0 %) identified as the novel strain’s closest relatives. The major cellular fatty acids were C18 : 1ω7c and C17 : 1ω6c. The polar lipids were found to be diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, one sphingoglycolipid, one unidentified aminolipid and six other unidentified lipids. The major respiratory quinone was ubiquinone-10 (UQ-10) and the genomic DNA G+C content of the novel strain was 58.9 mol%. On the basis of phenotypic, phylogenetic and genotypic data, strain CNU001T represents a novel species within the genus Erythrobacter , for which the name Erythrobacter jejuensis sp. nov. is proposed. The type strain is CNU001T ( = KCTC 23090T  = JCM 16677T).


2020 ◽  
Vol 70 (7) ◽  
pp. 4409-4415 ◽  
Author(s):  
Soon Dong Lee ◽  
In Seop Kim ◽  
Young-Ju Kim ◽  
Yochan Joung

A Gram-reaction-positive, strictly aerobic, catalase-positive, oxidase-negative, non-motile actinobacterium, designated C1-24T, was isolated from a soil sample collected inside a natural cave. The organism exhibited a rod–coccus developmental cycle during its growth phase. Results of 16S rRNA gene-based phylogenetic analysis showed that the novel strain belonged to the genus Rhodococcus and formed a distinct sublineage at the base of the radiation including a Rhodococcus enclensis–Rhodococcus kroppenstedtii–Rhodococcus corynebacterioides–Rhodococcus trifoli cluster. In the results of phylogenomic analysis, the novel strain was loosely associated to Rhodococcus corynebacterioides . The closest relatives were Rhodococcus qingshengii (98.01 % 16S rRNA gene sequence similarity) and Rhodococcus degradans (98.01 %). The genome size was 5.66 Mbp and the DNA G+C content was 64.30 mol%. Whole-cell hydrolysates contained meso-diaminopimelic acid, arabinose and galactose as the diagnostic diamino acid and sugars. MK-8(H2) was the predominant menaquinone. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, an unidentified glycolipid and three unidentified phospholipids. Mycolic acids were present. The major fatty acids were C16 : 0, C18 : 1  ω9c, C16 : 1  ω7c and/or C16 : 1  ω6c and 10-methyl C18 : 0. Digital DNA–DNA hybridization and average nucleotide identity values revealed that the novel strain should be assigned to a different species. Based on the combined data obtained here, strain C1-24T (=KACC 19964T=DSM 109484T) represents a new species of the genus Rhodococcus , for which Rhodococcus cavernicola sp. nov. is proposed. Also, it is proposed that R. degradans is a later heterosynonym of R. qingshengii based on analyses of 16S rRNA gene and whole-genome sequences.


2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 1030-1034 ◽  
Author(s):  
Jing Huang ◽  
Zhi Huang ◽  
Zhen-Dong Zhang ◽  
Lin-Yan He ◽  
Xia-Fang Sheng

A novel type of mineral-weathering bacterium was isolated from purplish soils collected from Yanting (Sichuan, south-western China). Cells of strain 1007T were Gram-stain-negative and rod-shaped, motile and yellow-pigmented. The isolate was strictly aerobic, catalase- and oxidase-positive, and grew optimally at 28-30 °C and pH 6.0-7.0. The genomic DNA G+C content of strain 1007T was 67±0.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 1007T belonged to the genus Sphingomonas and was most closely related to Sphingomonas pruni IFO 15498T (97.3 %), Sphingomonas mali IFO 15500T (97.2 %), Sphingomonas japonica KC7T (97.2 %) and Sphingomonas koreensis JSS26T (97.0 %). This affiliation of strain 1007T to the genus Sphingomonas was confirmed by the presence of Q-10 as the major ubiquinone, sphingoglycolipid, C14 : 0 2-OH and by the absence of 3-hydroxy fatty acids. The major polyamine was homospermidine. The main cellular fatty acids included summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. Based on the low level of DNA–DNA relatedness (ranging from 26.1 % to 58.7 %) to these type strains of species of the genus Sphingomonas and unique phenotypic characteristics, strain 1007T represents a novel species of the genus Sphingomonas , for which the name Sphingomonas yantingensis sp. nov. is proposed. The type strain is 1007T ( = DSM 27244T = JCM 19201T = CCTCC AB 2013146T).


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