Jatrophihabitans soli sp. nov., isolated from soil

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1759-1763 ◽  
Author(s):  
Soo-Jin Kim ◽  
Ji-Young Moon ◽  
Jun-Muk Lim ◽  
Moriyuki Hamada ◽  
Jae-Hyung Ahn ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Content Type ◽  
Link Type ◽  
Diamino Acid ◽  
The 16S Rrna Gene

One bacterial strain, designated KIS75-12T, isolated from a soil sample collected from Wonsando island located in Boryeong city, Republic of Korea, was characterized as aerobic, Gram-stain-positive, non-flagellated and a short rod. It grew between temperatures of 15–37 °C, pH 4–9 and 0–3.0 % (w/v) NaCl. The 16S rRNA gene analysis showed the strain was moderately related to Jatrophihabitans endophyticus S9-650T (97.7 %) and revealed low sequence similarity (≤94.7 %) with all the other species with validly published names. Its major fatty acid was iso-C16 : 0. The predominant menaquinone of strain KIS75-12T was MK-9(H4). The polar lipids consisted of diphosphatidylglycerol and several small amounts of phosphatidylinositol, aminolipids and glycolipid. The peptidoglycan contained meso-A2pm as diagnostic diamino acid and the peptidoglycan type is A4γ. The genomic DNA G+C content of the type strain was 72.1 mol%. The combined phenotypic, chemotaxonomic and phylogenetic data showed that strain KIS75-12T could be clearly distinguished from the only member of the genus Jatrophihabitans , J. endophyticus . Therefore, the results of this study indicate the existence of a representative of a novel species of the genus Jatrophihabitans , for which we propose the name Jatrophihabitans soli sp. nov., with strain KIS75-12T ( = KACC 17298T = DSM 45908T  =  NBRC 109658T) as the type strain. An emended description of the genus Jatrophihabitans is also given.

Genome based reclassification of Deinococcus swuensis as a heterotypic synonym of Deinococcus radiopugnans

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Priya Lakra ◽  
Helianthous Verma ◽  
Chandni Talwar ◽  
Durgesh Narain Singh ◽  
Nirjara Singhvi ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Species Delineation ◽  
16S Rrna Gene Analysis ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Deinococcus species are widely studied due to their utility in bioremediation of sites contaminated with radioactive elements. In the present study, we re-evaluated the taxonomic placement of two species of the genus Deinococcus namely D. swuensis DY59T and D. radiopugnans ATCC 19172T based on whole genome analyses. The 16S rRNA gene analysis revealed a 99.58% sequence similarity between this species pair that is above the recommended threshold value for species delineation. These two species also clustered together in both the 16S rRNA gene and core genome based phylogenies depicting their close relatedness. Furthermore, more than 98% of genes were shared between D. swuensi s DY59T and D. radiopugnans ATCC 19172T. Interestingly, D. swuensis DY59T and D. radiopugnans ATCC 19172T shared high genome similarity in different genomic indices. They displayed an average nucleotide identity value of 97.63%, an average amino acid identity value of 97% and a digital DNA–DNA hybridization value equal to 79.50%, all of which are well above the cut-off for species delineation. Altogether, based on these evidences, D. swuensis DY59T and D. radiopugnans ATCC 19172T constitute a single species. Hence, as per the priority of publication, we propose that Deinococcus swuensis Lee et al. 2015 should be reclassified as a later heterotypic synonym of Deinococcus radiopugnans .

Roseimicrobium gellanilyticum gen. nov., sp. nov., a new member of the class Verrucomicrobiae

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 1982-1986 ◽  
Author(s):  
Shigeto Otsuka ◽  
Hiroyuki Ueda ◽  
Taku Suenaga ◽  
Yoshihito Uchino ◽  
Moriyuki Hamada ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Verrucomicrobium Spinosum ◽  
The 16S Rrna Gene

The taxonomic properties of strain DC2a-G7T, a Gram-negative, ovoid to rod-shaped, gellan gum-lysing bacterium, were examined. The 16S rRNA gene sequence similarity showed that DC2a-G7T is a member of the phylum Verrucomicrobia and the closest type strain of a species with a validly published name is Verrucomicrobium spinosum DSM 4136T, with a sequence similarity of 91.2 %. In addition to this similarity value lower than 95 %, the absence of prostheca, the orangey-red colony colour and the compositions of the major menaquinones and polar lipids also supported the differentiation of this bacterium from the genus Verrucomicrobium . Here, we propose the name Roseimicrobium gellanilyticum gen. nov., sp. nov. for the isolate. The type strain of Roseimicrobium gellanilyticum is DC2a-G7T ( = NBRC 108606T = DSM 25532T).

scholarly journals Paraburkholderia dioscoreae sp. nov., a novel plant associated growth promotor

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Johannes B. Herpell ◽  
Sarah Vanwijnsberghe ◽  
Charlotte Peeters ◽  
Florian Schindler ◽  
Lena Fragner ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Distinctive Features ◽  
Link Type ◽  
Novel Bacterium ◽  
A Genome ◽  
The 16S Rrna Gene

A novel bacterium, designated strain Msb3T, was recently isolated from leaves of the yam family plant Dioscorea bulbifera (Dioscoreaceae). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that this strain belonged to the genus Paraburkholderia with Paraburkholderia xenovorans as nearest validly named neighbour taxon (99.3 % sequence similarity towards the P. xenovorans type strain). Earlier genome sequence analysis revealed a genome of 8.35 Mb in size with a G+C content of 62.5 mol%, which was distributed over two chromosomes and three plasmids. Here, we confirm that strain Msb3T represents a novel Paraburkholderia species. In silico DNA–DNA hybridization and average nucleotide identity (OrthoANIu) analyses towards P. xenovorans LB400T yielded 58.4 % dDDH and 94.5 % orthoANIu. Phenotypic and metabolic characterization revealed growth at 15 °C on tryptic soy agar, growth in the presence of 1 % NaCl and the lack of assimilation of phenylacetic acid as distinctive features. Together, these data demonstrate that strain Msb3T represents a novel species of the genus Paraburkholderia, for which we propose the name Paraburkholderia dioscoreae sp. nov. The type strain is Msb3T (=LMG 31881T, DSM 111632T, CECT 30342T).

scholarly journals Marmoricola solisilvae sp. nov. and Marmoricola terrae sp. nov., isolated from soil and emended description of the genus Marmoricola

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1825-1830 ◽  
Author(s):  
Soo-Jin Kim ◽  
Jun-Muk Lim ◽  
Moriyuki Hamada ◽  
Jae-Hyung Ahn ◽  
Hang-Yeon Weon ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Bridge Type ◽  
Diamino Acid ◽  
Sequence Similarities

Two strains of species of the genus Marmoricola , designated KIS18-7T and JOS5-1T, were isolated from soil samples in Korea. The 16S rRNA gene sequence of strain KIS18-7T showed highest similarities with Marmoricola scoriae Sco-D01T (97.8 %), Marmoricola aequoreus SST-45T (97.6 %) and Marmoricola aurantiacus BC 361T (97.3 %), and strain JOS5-1T had highest sequence similarities with M. aequoreus SST-45T (97.5 %) and Marmoricola bigeumensis MSL-05T (97.3 %). The sequence similarity between KIS18-7T and JOS5-1T was 98.1 %. Phylogenetic analysis showed that these strains grouped with species of the genus Marmoricola . The major fatty acids of strain KIS18-7T were iso-C16 : 0 and C17 : 1ω8c, and C17 : 1ω8c, C18 : 0 10-methyl (TBSA), C18 : 1ω9c, C17 : 0 10-methyl and C16 : 0 2-OH for strain JOS5-1T. Strain KIS18-7T contained the polar lipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylcholine, while strain JOS5-1T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, one unknown aminolipid and two unknown phospholipids. The peptidoglycan of both strains contained ll-diaminopimelic acid as the diagnostic diamino acid and a single glycine residue as the interpeptide bridge (type A3γ). The major menaquinone of both strains was MK-8(H4). The G+C contents of the DNA of strains KIS18-7T and JOS5-1T were 68.0 mol% and 62.9 mol%, respectively. These data demonstrate that strains KIS18-7T and JOS5-1T are representatives of two novel species of the genus Marmoricola , for which the names Marmoricola solisilvae sp. nov. (type strain KIS18-7T = KACC 17307T = DSM 27140T = NBRC 109601T) and Marmoricola terrae sp. nov. (type strain JOS5-1T = KACC 17308T = DSM 27141T = NBRC 109602T) are proposed.

Spelaeicoccus albus gen. nov., sp. nov., an actinobacterium isolated from a natural cave

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 3958-3963 ◽  
Author(s):  
Soon Dong Lee
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Mycolic Acids ◽  
Link Type ◽  
Diamino Acid ◽  
Unknown Phospholipid

A novel Gram-stain-positive, non-endospore-forming, coccoid actinobacterium, designated strain D3-40T, was isolated from the soil of a natural cave and characterized by means of a polyphasic taxonomic analysis. 16S rRNA gene sequence analysis showed that strain D3-40T is a member of the suborder Micrococcineae and forms a distinct branch at the base of a Brevibacteriaceae cluster. Its closest relative is the type strain of Brevibacterium samyangense (95.7 % sequence similarity). The chemotaxonomic characteristics were as follows: the cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid; the major menaquinone was MK-9(H2); the polar lipids consisted of phosphatidylglycerol, phosphatidylinositol, an unknown glycolipid and an unknown phospholipid; the major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0, C16 : 0 and cyclohexyl-C17 : 0; mycolic acids were absent. The G+C content of the DNA was 64.3 mol%. On the basis of morphological, chemotaxonomic and phylogenetic data, it is suggested that the organism represents a novel species of a new genus within the family Brevibacteriaceae , for which the name Spelaeicoccus albus gen. nov., sp. nov. is proposed. The type strain of the type species is D3-40T ( = KCTC 29141T = DSM 26341T).

scholarly journals Pseudoseohaeicola caenipelagi gen. nov., sp. nov., isolated from a tidal flat

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1819-1824 ◽  
Author(s):  
Sooyeon Park ◽  
Ji-Min Park ◽  
Chul-Hyung Kang ◽  
Song-Gun Kim ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Strain ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, non-motile, aerobic and pleomorphic bacterium, designated BS-W13T, was isolated from a tidal flat on the South Sea, South Korea, and its taxonomic position was investigated using a polyphasic approach. Strain BS-W13T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 1.0–2.0 % (w/v) NaCl. Neighbour-joining and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain BS-W13T clustered with the type strain of Seohaeicola saemankumensis , showing the highest sequence similarity (95.96 %) to this strain. Strain BS-W13T exhibited 16S rRNA gene sequence similarity values of 95.95, 95.91, 95.72 and 95.68 % to the type strains of Sulfitobacter donghicola , Sulfitobacter porphyrae , Sulfitobacter mediterraneus and Roseobacter litoralis , respectively. Strain BS-W13T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The polar lipid profile of strain BS-W13T, containing phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid as major components, was distinguishable from those of some phylogenetically related taxa. The DNA G+C content of strain BS-W13T was 58.1 mol%. The phylogenetic data and differential chemotaxonomic and other phenotypic properties revealed that strain BS-W13T constitutes a novel genus and species within family Rhodobacteraceae of the class Alphaproteobacteria , for which the name Pseudoseohaeicola caenipelagi gen. nov., sp. nov. is proposed. The type strain is BS-W13T ( = KCTC 42349T = CECT 8724T).

Nocardiopsis coralli sp. nov. a novel actinobacterium isolated from the coral Galaxea astreata

2021 ◽  
Vol 71 (6) ◽  
Author(s):  
Fenfa Li ◽  
Qingyi Xie ◽  
Shuangqing Zhou ◽  
Fandong Kong ◽  
Yun Xu ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Phosphatidylinositol Mannosides

Strain HNM0947T, representing a novel actinobacterium, was isolated from the coral Galaxea astreata collected from the coast of Wenchang, Hainan, China. The strain was found to have morphological and chemotaxonomic characteristics consistent with the genus Nocardiopsis . The organism formed abundant fragmented substrate mycelia and aerial mycelia which differentiated into non-motile, rod-shaped spores. Whole-cell hydrolysates contained meso-diaminopimelic acid and no diagnostic sugars. The major menaquinones were MK-10(H8), MK-10(H6) and MK-10(H4). The major phospholipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The major fatty acids were iso-C16:0, anteiso-C17:0, C18:0, C18:0 10-methyl (TBSA) and anteiso-C15:0. The G+C content was 71.3 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain HNM0947T belonged to the genus Nocardiopsis and shared highest sequence similarity to Nocardiopsis salina YIM 90010T (98.8%), Nocardiopsis xinjiangensis YIM 90004T(98.5%) and Nocardiopsis kunsanensis DSM 44524T (98.3%). The strain HNM0947T was distinguished from its closest type strain by low average nucleotide identity (90.8%) and dDDH values (60.4%) respectively. Based on genotypic, chemotaxonomic and phenotypic characteristics, it was concluded that strain HNM0947T represents a novel species of the genus Nocardiopsis whose name was proposed as Nocardiopsis coralli sp. nov. The type strain was HNM0947T (=CCTCC AA 2020015 T=KCTC 49525 T).

Aquabacterium soli sp. nov., a novel bacterium isolated from soil under the long-term application of bifenthrin

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Lina Sun ◽  
Wei Chen ◽  
Kaihua Huang ◽  
Weiguang Lyu ◽  
Xinhua Gao
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Content Type ◽  
Link Type ◽  
Novel Bacterium ◽  
Pr China

Strain SJQ9T, an aerobic bacterium isolated from a soil sample collected in Shanghai, PR China, was characterized using a polyphasic approach. It grew optimally at pH 7.0, 30–35 °C and in the presence of 1 % (w/v) NaCl. A comparative analysis of 16S rRNA gene sequences showed that strain SJQ9T fell within the genus Aquabacterium . The closest phylogenetic relatives of strain SJQ9T were Aquabacterium citratiphilum DSM 11900T (98.6 % sequence similarity) and Aquabacterium commune DSM 11901T (96.4 %). Cells of the strain were Gram-stain-negative, motile, non-spore-forming, rod-shaped and positive for oxidase activity and negative for catalase. The chemotaxonomic properties of strain SJQ9T were consistent with those of the genus Aquabacterium : the major fatty acid was summed feature 3 (C16 : 1  ω6c and/or C16 : 1  ω7c). The isoprenoid quinone was Q-8. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 65.7 mol%. Strain SH9T exhibited a DNA–DNA relatedness level of 34±2 % with A. citratiphilum DSM 11900T and 28±3 % with A. commune DSM 11901T. Based on the obtained data, strain SJQ9T represents a novel species of the genus Aquabacterium , for which the name Aquabacterium soli sp. nov. is proposed. The type strain is SJQ9T (=JCM 33106T=CCTCC AB 2018284T).

Leucobacter soli sp. nov., from soil amended with humic acid

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Peter Kämpfer ◽  
John A. McInroy ◽  
Dominique Clermont ◽  
Meina Neumann-Schaal ◽  
Alexis Criscuolo ◽  
...  
Keyword(s):  
Humic Acid ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Polar Lipid Profile ◽  
Phenotypic Differentiation ◽  
Content Type ◽  
Link Type ◽  
Diamino Acid

A Gram-positive, non-spore-forming actinobacterium (IMT-300T) was isolated from soil amended with humic acid in Malvern, AL, USA. This soil has been used for 50+years for the cultivation of earthworms for use as fish bait. Based on 16S rRNA gene sequence similarity studies, strain IMT-300T was shown to belong to the genus Leucobacter and was closely related to the type strain of ‘Leucobacter margaritiformis’ L1T (97.8%). Similarity to all other type strains of Leucobacter species was lower than 97.2 %. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the IMT-300T genome assembly and those of the closest relative Leucobacter type strain were 81.4 and 23.3 % ( Leucobacter chironomi ), respectively. The peptidoglycan of strain IMT-300T contained l-2,4-diaminobutyric acid as the diagnostic diamino acid. In addition, glycine, d- and l-alanine and d-glutamic acid were found. The peptidoglycan type represents a variant of B2δ (B11). The major quinones were menaquinones MK-10 and MK-11. The polar lipid profile consisted of the major lipids diphosphatidylglycerol, phosphatidylglycerol and moderate to minor amounts of two unidentified phospholipids, two unidentified glycolipids and an unidentified aminophospholipid. The polyamine pattern contained major amounts of spermidine and spermine. Strain IMT-300T contained the major fatty acids C15 : 0 anteiso, C16 : 0 iso and C17 : 0 anteiso, like other members of the genus Leucobacter . The results of ANI and dDDH analyses and physiological and biochemical tests allowed a genotypic and phenotypic differentiation of strain IMT-300T from the most closely related Leucobacter species. Strain IMT-300T represents a novel Leucobacter species, for which we propose the name Leucobacter soli sp. nov., with the type strain IMT-300T (CIP 111803T=DSM 110505T=CCM 9020T=LMG 31600T).

scholarly journals Haloactinopolyspora alkaliphila sp. nov., and emended description of the genus Haloactinopolyspora

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1945-1951 ◽  
Author(s):  
Yong-Guang Zhang ◽  
Qing Liu ◽  
Hong-Fei Wang ◽  
Dao-Feng Zhang ◽  
Yuan-Ming Zhang ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
North West ◽  
Link Type ◽  
Hybridization Data ◽  
Actinomycete Strain ◽  
Diamino Acid

A facultatively alkaliphilic actinomycete strain, designated EGI 80088T, was isolated from a saline-alkali soil sample from Xinjiang province, north-west China, and subjected to a polyphasic taxonomic characterization. Strain EGI 80088T formed fragmented aerial hyphae and short spore chains, and rod-like spores aggregated at maturity. Whole-cell hydrolysates of the isolate contained ll-diaminopimelic acid as the diagnostic diamino acid, and glucosamine, mannose, galactose, glucose and rhamnose as the marker sugars. The major fatty acids identified (>5 %) were anteiso-C15 : 0, iso-C15 : 0, summed feature 4 (iso-C17 : 1I/anteiso-C17 : 1B), iso-C16 : 0 and anteiso-C17 : 0. The predominant menaquinone was MK-9(H4). The G+C content of the genomic DNA of strain EGI 80088T was 70.6 mol%. EGI 80088T showed the highest 16S rRNA gene sequence similarity to its closest phylogenetic neighbour Haloactinopolyspora alba YIM 93246T (98.5 %). The DNA–DNA relatedness value of the strain EGI 80088T and H. alba YIM 93246T was 59.3±5.2 %. On the basis of morphological, chemotaxonomic and phylogenetic characteristics and DNA–DNA hybridization data, strain EGI 80088T represents a novel species of the genus Haloactinopolyspora , for which the name Haloactinopolyspora alkaliphila sp. nov. (type strain EGI 80088T = BCRC 16946T = JCM 19128T) is proposed. The description of the genus Haloactinopolyspora has also been emended.

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