scholarly journals Description of Domibacillus indicus sp. nov., isolated from ocean sediments and emended description of the genus Domibacillus

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3010-3015 ◽  
Author(s):  
Avinash Sharma ◽  
Sunil Kumar Dhar ◽  
Om Prakash ◽  
Venkata Ramana Vemuluri ◽  
Vishal Thite ◽  
...  

A novel Gram-stain-positive, spore-forming, aerobic, non-motile, rod-shaped bacterium designated strain SD111T that forms red-pigmented colonies was isolated from a marine sediment sample (collected from 5 m depth) from Lakshadweep, India. Strain SD111T grew well on seawater agar at pH 6–10 (optimum pH 7.5±0.2). It showed maximum (97.6 %) 16S rRNA gene sequence similarity and formed a monophyletic clade with Domibacillus robiginosus WS 4628T ( = DSM 25058T). The genomic DNA G+C content was 37.4 mol% and the strain showed 37.7 % DNA–DNA relatedness to D. robiginosus DSM 25058T. The major fatty acids were anteiso-C15 : 0, C16 : 0, iso-C15 : 0 and iso-C16 : 0 and MK-6 was the predominant quinone. The polar lipid profile of strain SD111T consisted of unidentified phospholipids (PL1 and PL2), phosphatidylglycerol (PG) and diphosphatidylglycerol (DPG). The cell wall contained meso-diaminopimelic acid and the peptidoglycan was of A1γ type. Glucose and ribose were detected as major cell-wall sugars. Results from polyphasic studies indicated that SD111T represents a novel species of the genus Domibacillus for which the name Domibacillus indicus sp. nov. is proposed. The type strain is SD111T ( = MCC 2255T = DSM 28032T).

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 230-235 ◽  
Author(s):  
P. Kämpfer ◽  
K. Martin ◽  
W. Dott

Two Gram-stain-positive, non-endospore-forming actinobacteria (Ca8Tand Ca14) were isolated from a bioreactor with extensive phosphorus removal. Based on 16S rRNA gene sequence similarity comparisons, strains Ca8T and Ca14 were shown to belong to the genus Gordonia and were most closely related to Gordonia hirsuta DSM 44140T (98.0 % sequence similarity) and Gordonia hydrophobica DSM 44015T (97.2 %). In comparison with the sequences of the type strains of all other species of the genus Gordonia tested, similarities were below 97 %. The quinone systems of the strains were determined to consist predominantly of MK-9H2. The polar lipid profile for both organisms consisted of diphosphatidylglycerol, phosphatidylglycerol, phospatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. Whole-organism hydrolysates contained meso-diaminopimelic acid as the diamino acid of the peptidoglycan; mycolic acids were detected as well. These chemotaxonomic traits and the major fatty acids, which were C16 : 1 cis-9, C16 : 0 and C18 : 1 and tuberculostearic acid strongly supported the grouping of strains Ca8T and Ca14 into the genus Gordonia . The two strains showed a DNA–DNA similarity of 96 %. DNA–DNA hybridizations of strain Ca8T with G. hirsuta DSM 44140T and G. hydrophobica DSM 44015T resulted in values of 26.3 and 25.0 %, respectively. These results and those of the physiological and biochemical tests allowed a clear phenotypic differentiation of strains Ca8T and Ca14 from the most closely related species of the genus Gordonia . It is concluded that strains Ca8T and Ca14 represent a novel species, for which the name Gordonia phosphorivorans sp. nov. is proposed, with the type strain Ca8T ( = DSM 45630T = CCUG 61533T = CCM 7957T = LMG 26648T).


2020 ◽  
Vol 70 (5) ◽  
pp. 3234-3240 ◽  
Author(s):  
Sihui Zhang ◽  
Xiaoxia Wang ◽  
Jing Yang ◽  
Shan Lu ◽  
Xin-He Lai ◽  
...  

Two novel Gram-stain-positive, irregular rod-shaped actinomycetes, S-1144T and 4053, were isolated from leaves of Lamiophlomis rotata on the Qinghai–Tibet Plateau, PR China. Cells were aerobic, catalase-positive and oxidase-negative. Colonies on Reasoner’s 2A agar were light yellow, circular, shiny, smooth and convex after 2 days of incubation. The isolates grew optimally at 25 °C, pH 7.5 and with 0 % (w/v) NaCl. The results of polyphasic analyses indicated that strain S-1144T belonged to the genus Nocardioides and its close phylogenetic neighbours (16S rRNA gene sequence similarity) were Nocardioides litoris DSM 103718T (98.4 %), Nocardioides rubriscoriae DSM 23986T (98.2%) and Nocardioides plantarum DSM 11054T (97.8 %). The genome of strain S-1144T showed less than 70 % digital DNA–DNA hybridization and < 95–96 % average nucleotide identity values to the above reference strains. The DNA G+C content of strain S-1144T was 73.5 mol%. MK-8(H4) was the predominant respiratory quinone (96.0 %) and llLL-2,6-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The polar lipid profile of strain S-1144T consisted of diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids, one unidentified glycolipid and one unidentified lipid. The major cellular fatty acids were iso-C16 : 0, C17 : 1  ω8c, C17 : 0 and C18 : 1  ω9c. On the basis of obtained data, strain S-1144T represented a novel species of the genus Nocardioides , for which the name Nocardioides dongxiaopingii sp. nov. is proposed. The type strain is S-1144T (=CGMCC 4.7568T=JCM 33469T).


2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2693-2697 ◽  
Author(s):  
Syed G. Dastager ◽  
Rahul Mawlankar ◽  
Shan-Kun Tang ◽  
Srinivasan Krishnamurthi ◽  
V. Venkata Ramana ◽  
...  

A novel actinobacterial strain, designated, NIO-1009T, was isolated from a marine sediment sample collected from Chorao Island, Goa, India. Phylogenetic analysis comparisons based on 16S rRNA gene sequences between strain NIO-1009T and other members of the genus Rhodococcus revealed that strain NIO-1009T had the closest sequence similarity to Rhodococcus kroppenstedtii DSM 44908T and Rhodococcus corynebacterioides DSM 20151T with 99.2 and 99.1 %, respectively. Furthermore, DNA–DNA hybridization results showed that R. kroppenstedtii DSM 44908T and R. corynebacterioides DSM 20151T were 39.5 (3.0 %) and 41.7 (2.0 %) with strain NIO-1009T, respectively, which were well below the 70 % limit for any novel species proposal. Phylogenetically strain NIO-1009T forms a stable clade with and R. kroppenstedtii DSM 44908T and R. corynebacterioides DSM 20151T with 100 % bootstrap values. Strain NIO-1009T contained meso-diaminopimelic acid as the diagnostic diamino acid and galactose and arabinose as the cell wall sugars. The major fatty acids were C16 : 0, C18 : 1ω9c, C16 : 1(ω6c and/or ω7c) and 10-methyl C18 : 0. The only menaquinone detected was MK-8(H2), while the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and one unknown phospholipid. The G+C content of the genomic DNA was 66.9 mol%. The phenotypic and genotypic data showed that strain NIO-1009T warrants recognition as a novel species of the genus Rhodococcus for which the name Rhodococcus enclensis sp. nov., is proposed; the type strain is NIO-1009T ( = NCIM 5452T = DSM 45688T).


2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 152-157 ◽  
Author(s):  
Yingshun Cui ◽  
Myung-Suk Kang ◽  
Sung-Geun Woo ◽  
Long Jin ◽  
Kwang Kyu Kim ◽  
...  

A Gram-reaction-positive, non-spore-forming, aerobic actinobacterial strain (2C6-41T) was isolated from the activated sludge from an industrial wastewater treatment plant in Daegu, South Korea. Its taxonomic position was investigated by using a polyphasic approach. On the basis of 16S rRNA gene sequence similarity, closest phylogenetic relatives to strain 2C6-41T were Brevibacterium pityocampae DSM 21720T (97.2 %), Brevibacterium salitolerans KCTC 19616T (96.7 %), Brevibacterium album KCTC 19173T (96.2 %) and Brevibacterium samyangense KCCM 42316T (96.2 %). The DNA G+C content of strain 2C6-41T was 66.4 mol%. Chemotaxonomic data, which included MK-8(H2) as the major menaquinone; meso-diaminopimelic acid, glutamic acid and alanine as cell-wall amino acids; ribose, mannose and glucose as major cell-wall sugars; and anteiso-C15 : 0, anteiso-C17 : 0, C16 : 0 and iso-C15 : 0 as major fatty acids, supported the affiliation of strain 2C6-41T to the genus Brevibacterium . The aromatic ring cleavage enzyme catechol 1,2-dioxygenase was not detected in strain 2C6-41T, but catechol 2,3-dioxygenase was detected. The results of physiological and biochemical tests, and the low level of DNA–DNA relatedness to the closest phylogenetic relative enabled strain 2C6-41T to be differentiated genotypically and phenotypically from recognized species of the genus Brevibacterium . The isolate is therefore considered to represent a novel species in the genus Brevibacterium , for which the name Brevibacterium daeguense sp. nov. is proposed. The type strain is 2C6-41T ( = KCTC 19800T = JCM 17458T).


2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 3007-3012 ◽  
Author(s):  
Nareeluk Nakaew ◽  
Rungroch Sungthong ◽  
Akira Yokota ◽  
Saisamorn Lumyong

A novel actinomycete, designated strain PT708T, was isolated from cave soil collected in Pha Tup Cave Forest Park, Nan province, Thailand. It produced compounds with antimicrobial and anticancer activities. Its chemotaxonomic properties were consistent with those of members of the genus Nonomuraea . The major menaquinone was MK-9(H4), with minor amounts of MK-9(H6), MK-9(H2), MK-10(H2) and MK-8(H4). The polar lipid profile contained phosphatidylmonomethylethanolamine, diphosphatidylglycerol, hydroxy-phosphatidylmonomethylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol mannoside and phosphatidylinositol. The major fatty acids were iso-C16 : 0, 10-methyl C17 : 0, C16 : 0 and C17 : 1ω6c. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain PT708T belonged to the genus Nonomuraea and was most closely related to Nonomuraea rhizophila YIM 67092T (98.50 % sequence similarity) and Nonomuraea rosea GW 12687T (98.30 %). The genomic DNA G+C content of strain PT708T was 73.3 mol%. Unlike the recognized members of the genus Nonomuraea , the novel strain formed single spores at the tips of aerial hyphae. Based on the phenotypic, phylogenetic and genotypic evidence, strain PT708T represents a novel species of the genus Nonomuraea , for which the name Nonomuraea monospora sp. nov. is proposed. The type strain is PT708T ( = TISTR 1910T = JCM 16114T).


2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 531-536 ◽  
Author(s):  
Pil Soo Kim ◽  
Na-Ri Shin ◽  
Dong-Wook Hyun ◽  
Joon Yong Kim ◽  
Tae Woong Whon ◽  
...  

A novel Gram-stain-positive, non-motile, facultatively anaerobic and rod-shaped bacterium, strain PSPT56T, was isolated from the gastrointestinal tract of a pen shell (Atrina pectinata). Optimal growth of strain PSPT56T was ascertained to occur at 30 °C, pH 8.0 and in the presence of 1–2 % (w/v) NaCl. The strain was catalase-positive and oxidase-negative. The major cellular fatty acids were C18 : 1ω9c, C16 : 0, C17 : 1ω8c and C17 : 0. Tuberculostearic acid was not present. The major cell-wall sugars were ribose, galactose, glucose and arabinose. Peptidoglycan amino acids were meso-diaminopimelic acid, alanine and glutamic acid. The predominant isoprenoid quinone was MK-8(H2). Strain PSPT56T contained phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid, two unidentified lipids and two unidentified amino-lipids. Mycolic acids were detected as constitutive components of the cell wall. A phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain PSPT56T was most closely related to Corynebacterium testudinoris M935/96/4T and Corynebacterium felinum M714/95/5T with 98.69 % and 97.01 % similarity, respectively. DNA–DNA hybridization experiments indicated less than 29.9 % relatedness to the phylogenetically closest species. The G+C content of genomic DNA was 67.6 mol%. The phenotypic, phylogenetic and genotypic analyses indicated that strain PSPT56T represents a novel species within the genus Corynebacterium , for which the name Corynebacterium atrinae is proposed. The type strain is PSPT56T ( = KACC 17525T = JCM 19266T).


Author(s):  
Nisachon Tedsree ◽  
Somboon Tanasupawat ◽  
Boonchoo Sritularak ◽  
Nattakorn Kuncharoen ◽  
Kittisak Likhitwitayawuid

Three novel actinomycete strains, designated as DR6-1T, DR6-2 and DR6-4, isolated from the roots of Dendrobium heterocarpum Lindl in Thailand were studied using a polyphasic taxonomic approach. The strains grew at 20–37 °C, at pH 5–10 and with 5 % (w/v) NaCl. They contained meso-diaminopimelic acid in the cell-wall peptidoglycan and MK-9(H4) was a major menaquinone. Arabinose and galactose were the major sugars in the cell wall. The predominant cellular fatty acids were iso-C16 : 0 and iso-C15 : 0. The detected polar lipids were diphosphatidylglycerol, hydroxyphosphatidylethanolamine, phosphatidylethanolamine, phosphatidylinositol and phosphatidylglycerol. Strains DR6-1T, DR6-2 and DR6-4 shared 99.9–100 % 16S rRNA gene sequence similarity and were closely related to Amycolatopsis echigonensis JCM 21831T (98.7-98.8%). The approximate genome size of strain DR6-1T was 9.6 Mb with a G+C content of 69.6 mol%. The ANIb and dDDH values between genomic sequences of strain DR6-1T and Amycolatopsis echigonensis JCM21831T, Amycolatopsis rubida JCM 10871T and Amycolatopsis nivea KCTC 39515T were 90.55, 92.25, 92.60%, and 47.20, 52.10 and 52.50%, respectively. Based on the phenotypic, chemotaxonomic and genotypic characteristics, it has been concluded that strains DR6-1T, DR6-2 and DR6-4 represent a novel species of the genus Amycolatopsis for which the name Amycolatopsis dendrobii sp. nov. is proposed. The type strain is DR6-1T (=JCM 33742T=KCTC 49546T=TISTR 2840T).


Author(s):  
Stefanie P. Glaeser ◽  
Christian Rückert ◽  
Usama Ramadan Abdelmohsen ◽  
Anika Winkler ◽  
Jochen Blom ◽  
...  

A Gram-stain-positive bacterium, strain RV15T, forming an extensively branched substrate mycelium and aerial hyphae that differentiate into spiral chains of spores, was isolated from a marine sponge Dysidea tupha collected from Rovinj (Croatia). Comparison of 16S rRNA gene sequences showed that strain RV15T is a member of the genus Streptomyces with highest sequence similarity to the type strains of Streptomyces caeruleatus (98.8 %), Streptomyces cyaneochromogenes (98.6 %) and Streptomyces shaanxiensis (98.5 %). Sequence similarities to all other Streptomyces types strains were below 98.5 %. The multilocus sequence analysis-based evolutionary distance, the average nucleotide identity value and the genome-to-genome distance of strain RV15T and the type strain of S. caeruleatus were clearly below the species cut-off values. Strain RV15T exhibited a quinone system composed of the major menaquinones MK-9(H4), MK-9(H6) and MK-9(H2), typical for the genus Streptomyces . The polar lipid profile of strain RV15T consisted of the predominant compounds diphosphatidylglycerol and phosphatidylethanolamine, moderate amounts of phosphatidylinositol, phosphatidylinositol mannoside, an unidentified lipid and an unidentified phospholipid. Major polyamines were spermine and spermidine. The diagnostic diaminoacid of the peptidoglycan was meso-diaminopimelic acid. The major fatty acids were iso C16 : 0, anteiso C17 : 1 ω9c and anteiso C17 : 0. The results of physiological and biochemical tests allowed further phenotypic differentiation of strain RV15T from its most-related species and hence clearly merits species status. We propose the name Streptomyces dysideae sp. nov. with the type strain RV15T (=DSM 42110T=LMG 27702T).


2020 ◽  
Vol 70 (7) ◽  
pp. 4358-4363 ◽  
Author(s):  
Yan-Juan Lei ◽  
Zhan-Feng Xia ◽  
Xiao-Xia Luo ◽  
Li-Li Zhang

A novel Gram-positive, aerobic and motile endophytic actinomycete, designated TRM 65233T, was isolated from the root of Peganum harmala L. collected from Xinjiang Uygur Autonomous Region of China. The isolate had white aerial mycelium and brown substrate mycelium on Gause’s synthetic agar. Growth occurred at 10–40 °C, pH 6–9 with NaCl concentration of 0–6 % (w/v). Strain TRM 65233T contained meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The whole-cell hydrolysates included glucose and galactose as the major whole-cell sugars. The menaquinones were MK-9 (H4) and MK-7. The major cellular fatty acids were iso-C16 : 0, iso-C15 : 0 and anteiso-C17 : 0. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phospholipids, phosphatidylinositol and one unidentified lipid. Strain TRM 65233T showed the highest 16S rRNA gene sequence similarity to Actinokineospora cianjurensis BTCC B-558T (98.13 %), Actinokineospora auranticolor IFO 16518T (98.06 %), Actinokineospora spheciospongiae EG49T (97.99 %), Actinokineospora baliensis ID03-0561T (97.97 %), Actinokineospora mzabensis PAL84T (97.95 %) and Actinokineospora bangkokensis 44EHWT (97.06 %). The isolate was distinguished from these phylogenetically related strains by digital DNA–DNA hybridization and average nucleotide identity analyses and by a range of physiological and biochemical characteristics. The G+C content of the genomic DNA was 72.6 mol%. On the basis of polyphasic taxonomic data, strain TRM 65233T represents a novel species of the genus Actinokineospora , for which the name Actinokineospora pegani sp. nov. is proposed. The type strain is TRM 65233T (KCTC 49342=CCTCC AA 2019050).


2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 2011-2017 ◽  
Author(s):  
Anil Sazak ◽  
Mustafa Camas ◽  
Cathrin Spröer ◽  
Hans-Peter Klenk ◽  
Nevzat Sahin

A novel actinobacterium, strain A8036T, isolated from soil, was investigated by using a polyphasic taxonomic approach. The organism formed extensively branched substrate hyphae that generated spiral chains of spores with irregular surfaces. The cell wall contained meso-diaminopimelic acid (type III) and cell-wall sugars were glucose, madurose, mannose and ribose. The predominant menaquinones were MK-9(H6) and MK-9(H4). The phospholipids were diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The major cellular fatty acids were iso-C16 : 0, C17 : 1 cis9, C16 : 0, C15 : 0 and 10-methyl C17 : 0. Based on 16S rRNA gene sequence analysis, the closest phylogenetic neighbours of strain A8036T were Actinomadura meyerae DSM 44715T (99.23 % similarity), Actinomadura bangladeshensis DSM 45347T (98.9 %) and Actinomadura chokoriensis DSM 45346T (98.3 %). However, DNA–DNA relatedness and phenotypic data demonstrated that strain A8036T could be clearly distinguished from the type strains of all closely related Actinomadura species. Strain A8036T is therefore considered to represent a novel species of the genus Actinomadura , for which the name Actinomadura geliboluensis sp. nov. is proposed. The type strain is A8036T ( = DSM 45508T = KCTC 19868T).


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