Xenorhabdus ishibashii sp. nov., isolated from the entomopathogenic nematode Steinernema aciari

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1690-1695 ◽  
Author(s):  
Ryusei Kuwata ◽  
Li-hong Qiu ◽  
Wen Wang ◽  
Yuki Harada ◽  
Mutsuhiro Yoshida ◽  
...  

Gram-negative bacteria of the genus Xenorhabdus exhibit a mutualistic association with steinernematid entomopathogenic nematodes and a pathogenic relationship with insects. Here we describe two isolates of the entomopathogenic nematode Steinernema aciari collected from China and Japan. 16S rRNA gene sequence similarity and phylogenetic analysis indicated that the isolates obtained from S. aciari belonged to the genus Xenorhabdus . Multilocus sequence analysis based on five universal protein-coding gene sequences revealed that the isolates were closely related to Xenorhabdus ehlersii DSM 16337T and Xenorhabdus griffiniae ID10T but that they exhibited <97 % sequence similarity with these reference strains, which indicated that the isolates were distinct from previously described species. Based on these genetic differences and several differential phenotypic traits, we propose that the isolates represent a novel species of the genus Xenorhabdus , for which we propose the name Xenorhabdus ishibashii sp. nov. The type strain is GDh7T ( = DSM 22670T  = CGMCC 1.9166T).

2020 ◽  
Vol 70 (10) ◽  
pp. 5296-5303 ◽  
Author(s):  
Kenika Lipun ◽  
Wee Fei Aaron Teo ◽  
Paweena Suksaard ◽  
Wasu Pathom-aree ◽  
Kannika Duangmal

A novel actinobacterium, designated strain NN258T, was isolated from a cave soil sample collected from a karst cave at Khao No-Khao Kaeo, Nakhon Sawan province, Thailand. The morphological, chemotaxonomic and phylogenetic characteristics were consistent with its classification in the genus Nonomuraea . Strain NN258T showed the highest 16S rRNA gene sequence similarity values to Nonomuraea candida HMC10T, Nonomuraea mesophila 6K102T, Nonomuraea rubra DSM 43768T, Nonomuraea diastatica KC712T and Nonomuraea helvata IFO 14681T. The strain formed an extensively branched substrate and aerial mycelia. The whole-cell hydrolysates contained meso-diaminopimelic acid as the diagnostic diamino acid, with glucose, madurose, mannose and ribose as the whole-cell sugars. The polar lipids were diphosphatidylglycerol, phosphotidylmethylethanolamine, phosphatidylethanolamine, hydroxy-phosphatidylmonomethylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, two unidentified phospholipids, three unidentified sugar-containing phosphoaminolipids, an unidentified glycolipid and two unidentified lipids. The predominant menaquinone was MK-9(H4), with minor amounts of MK-9(H0), MK-9(H2) and MK-9(H6). Major cellular fatty acids (>10%) were iso-C16 : 0 and 10-methyl-C17 : 0. The G+C content of the genomic DNA was 71.0 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strain NN258T and the reference strains were 79.9–80.9 % and 26.1–27.0 %, respectively. On the basis of phenotypic, genotypic and phylogenetic data, strain NN258T represents a novel species of the genus Nonomuraea , for which the name Nonomuraea antri sp. nov. is proposed. The type strain is NN258T (=TBRC 11478T=NBRC 114269T).


2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 1761-1765 ◽  
Author(s):  
Patrick Tailliez ◽  
Sylvie Pagès ◽  
Steve Edgington ◽  
Lukasz M. Tymo ◽  
Alan G. Buddie

A symbiotic bacterium, strain IMI 397775T, was isolated from the insect-pathogenic nematode Steinernema australe. On the basis of 16S rRNA gene sequence similarity, this bacterial isolate was shown to belong to the genus Xenorhabdus , in agreement with the genus of its nematode host. The accurate phylogenetic position of this new isolate was defined using a multigene approach and showed that isolate IMI 397775T shares a common ancestor with Xenorhabdus doucetiae FRM16T and Xenorhabdus romanii PR06-AT, the symbiotic bacteria associated with Steinernema diaprepesi and Steinernema puertoricense, respectively. The nucleotide identity (less than 97 %) between isolate IMI 397775T, X. doucetiae FRM16T and X. romanii PR06-AT calculated for the concatenated sequences of five gene fragments encompassing 4275 nt, several phenotypic traits and the difference between the upper temperatures that limit growth of these three bacteria allowed genetic and phenotypic differentiation of isolate IMI 397775T from the two closely related species. Strain IMI 397775T therefore represents a novel species, for which the name Xenorhabdus magdalenensis sp. nov. is proposed, with the type strain IMI 397775T ( = DSM 24915T).


2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1611-1616 ◽  
Author(s):  
Syed G. Dastager ◽  
Rahul Mawlankar ◽  
Vidya V. Sonalkar ◽  
Meghana N. Thorat ◽  
Poonam Mual ◽  
...  

A Gram-stain-positive bacterium, designated strain NIO-1109T, was isolated from a marine sediment sample from Chorao Island, Goa, India. Phenotypic and chemotaxonomic characteristics and data from phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NIO-1109T was related to the genus Exiguobacterium . Strain NIO-1109T exhibited >98.0 % 16S rRNA gene sequence similarity with respect to Exiguobacterium indicum HHS 31T (99.5 %) and Exiguobacterium acetylicum NCIMB 9889T (99.1 %); the type strains of other species showed <98 % similarity. Levels of DNA–DNA relatedness between strain NIO-1109T and E. acetylicum DSM 20416T and E. indicum LMG 23471T were less than 70 % (33.0±2.0 and 37±3.2 %, respectively). Strain NIO-1109T also differed from these two closely related species in a number of phenotypic traits. Based on phenotypic, chemotaxonomic and phylogenetic data, strain NIO-1109T is considered to represent a novel species of the genus Exiguobacterium , for which the name Exiguobacterium enclense sp. nov. is proposed. The type strain is NIO-1109T ( = NCIM 5457T = DSM 25128T = CCTCC AB 2011124T).


Author(s):  
Ram Hari Dahal ◽  
Dhiraj Kumar Chaudhary ◽  
Dong-Uk Kim ◽  
Jaisoo Kim

A yellow-coloured, Gram-stain-negative, non-sporulating, psychrotolerant and motile bacterium, designated AR-3-1T, was isolated from the Arctic soil of Cambridge Bay, Nunavut, Canada. Strain AR-3-1T could grow at 4–32 °C and pH 5.0– 11.0. Phylogenetic analysis based on its 16S rRNA gene sequence indicated that strain AR-3-1T formed a lineage within the family Sphingomonadaceae and clustered as a member of the genus Sphingobium . The closest members within this genus were Sphingobium cupriresistens CU4T (98.1 % sequence similarity), Sphingobium vermicomposti VC-230T (97.6 %) and Sphingobium lactosutens DS20T (97.5 %). The only respiratory quinone was the ubiquinone Q-10. Spermidine was the predominant polyamine. The principal cellular fatty acids were summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), summed feature 3 (iso-C15  : 0 2-OH and/or C16  : 1 ω7c), C16 : 0 and C14 : 0 2-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, sphingoglycolipid and phosphoglycolipid. The DNA G+C content was 63.1 %. The average nucleotide identity and in silico DNA–DNA hybridization relatedness values between strain AR-3-1T and its most closely related genus members were ≤89.6 and 39.6 %, respectively. The genome was 5 162 327 bp long, with 83 scaffolds and 4824 protein-coding genes. The genome showed six putative biosynthetic gene clusters responsible for various secondary metabolites. Based on this polyphasic study, strain AR-3-1T represents a novel species within the genus Sphingobium , for which the name Sphingobium psychrophilum sp. nov. is proposed. The type strain is AR-3-1T (=KACC 21613T=NBRC 114604T).


2020 ◽  
Vol 70 (12) ◽  
pp. 6044-6051 ◽  
Author(s):  
Nesrine Lenchi ◽  
Adriana Anzil ◽  
Pierre Servais ◽  
Salima Kebbouche-Gana ◽  
Mohamed Lamine Gana ◽  
...  

A non-motile, straight-rod-shaped, Gram-stain-positive and facultative anaerobic bacterium (i.e., strain G1T) was isolated from production waters from an Algerian oilfield. Growth was observed in the presence of 0.3–3.5 % (w/v) NaCl, at 20–50 °C and at pH 6.0–9.0. Results of phylogenetic analyses based on 16S rRNA gene sequences showed that strain G1T belonged to the genus Microbacterium . Strain G1 T was closely related to Microbacterium oxydans (DSM 20578T) and Microbacterium maritypicum (DSM 12512T) with 99.8 % sequence similarity and to Microbacterium saperdae (DSM 20169T) with 99.6 % sequence similarity. Strain G1 T contained MK9, MK10, MK11, MK12 and MK13 as respiratory quinones, and phosphatidylglycerol, diphosphatidylglycerol and glycolipid as the major polar lipids. The major cellular fatty acids were anteiso-C15:0, iso-C16:0 and anteiso-C17:0. The estimated DNA G+C content was 69.57 mol% based on its draft genome sequence. Genome annotation of strain G1T predicted the presence of 3511 genes, of which 3483 were protein-coding and 47 were tRNA genes. The DNA–DNA hybridization (DDH) and average nucleotide identity (ANI) values between strain G1T and M. oxydans (DSM 20578T) and M. maritypicum (DSM 12512T) were in both cases far below the respective species boundary thresholds (27.5 and 28.0 % for DDH; and 84.40 and 84.82% for ANI, respectively). Based on the data presented above, strain G1T was considered to represent a novel species for which the name Microbacterium algeriense is proposed with the type strain G1T (=DSM 109018T=LMG 31276T).


Author(s):  
Geeta Chhetri ◽  
Jiyoun Kim ◽  
Inhyup Kim ◽  
Minchung Kang ◽  
Taegun Seo

In the present study, in an attempt to explore the diversity of bacteria in the roots of rice plants, a Gram-stain-negative, motile, facultatively anaerobic, non-pigmented, catalase-positive, oxidase-negative and rod-shaped bacterium with polar flagella was isolated. Phylogenetic analysis based on 16S rRNA gene sequences revealed highest sequence similarity to Limnohabitans parvus KCTC 42859T (98.2%) followed by Limnohabitans curvus KCTC 42562T (98%), Limnohabitans planktonicicus II-D5T (97.9%) and Limnohabitans australis MWH-BRAZ-DAM2DT (97.4%). Growth of strain JUR4T occurred at 10–37 °C (optimum, 30 °C), at pH 5.5–8.0 (optimum, 6.5–7) and in the presence of 0–0.2% NaCl (optimum, 0%, w/v). The genome size of strain JUR4T was found to be 3.34 Mb containing 3139 predicted protein-coding genes with a DNA G+C content of 61.5 mol%. The digital DNA–DNA hybridization and average nucleotide identity values between the genome sequence of strain JUR4T and closely related reference strains were 21.0–24.8% and 74.7–81.4%, respectively. Strain JUR4T contained diphosphatidylglycerol, phoshatidylethanolamine, one unidentified phosphoglycolipid, one unidentified aminophosphoglycolipid, one unidentified phospholipid and seven unidentified glycolipids. The major fatty acids were C16:0 and summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c), and ubiquinone Q-8 was the sole isoprenoid quinone. So far, all species belonging to the genus Limnohabitans have been described as non-motile and devoid of flagella. All species were isolated from freshwater and are therefore denoted as planktonic bacteria. This present study introduces a novel motile member of Limnohabitans isolated from the root of rice plant, and introduces the genes associated with motility and methyl-accepting chemotaxis proteins. Phylogenetic, phenotypic, chemotaxonomic and genotypic data clearly indicates that strain JUR4T represents a novel species of the genus Limnohabitans for which the name Limnohabitans radicicola sp. nov. is proposed. The type strain is JUR4T (=KACC 21745T=NBRC 114484T).


2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3877-3884 ◽  
Author(s):  
Celine De Maesschalck ◽  
Filip Van Immerseel ◽  
Venessa Eeckhaut ◽  
Siegrid De Baere ◽  
Margo Cnockaert ◽  
...  

Strains LMG 27428T and LMG 27427 were isolated from the caecal content of a chicken and produced butyric, lactic and formic acids as major metabolic end products. The genomic DNA G+C contents of strains LMG 27428T and LMG 27427 were 40.4 and 38.8 mol%. On the basis of 16S rRNA gene sequence similarity, both strains were most closely related to the generically misclassified Streptococcus pleomorphus ATCC 29734T. Strain LMG 27428T could be distinguished from S. pleomorphus ATCC 29734T based on production of more lactic acid and less formic acid in M2GSC medium, a higher DNA G+C content and the absence of activities of acid phosphatase and leucine, arginine, leucyl glycine, pyroglutamic acid, glycine and histidine arylamidases, while strain LMG 27428 was biochemically indistinguishable from S. pleomorphus ATCC 29734T. The novel genus Faecalicoccus gen. nov. within the family Erysipelotrichaceae is proposed to accommodate strains LMG 27428T and LMG 27427. Strain LMG 27428T ( = DSM 26963T) is the type strain of Faecalicoccus acidiformans sp. nov., and strain LMG 27427 ( = DSM 26962) is a strain of Faecalicoccus pleomorphus comb. nov. (type strain LMG 17756T = ATCC 29734T = DSM 20574T). Furthermore, the nearest phylogenetic neighbours of the genus Faecalicoccus are the generically misclassified Eubacterium cylindroides DSM 3983T (94.4 % 16S rRNA gene sequence similarity to strain LMG 27428T) and Eubacterium biforme DSM 3989T (92.7 % 16S rRNA gene sequence similarity to strain LMG 27428T). We present genotypic and phenotypic data that allow the differentiation of each of these taxa and propose to reclassify these generically misnamed species of the genus Eubacterium formally as Faecalitalea cylindroides gen. nov., comb. nov. and Holdemanella biformis gen. nov., comb. nov., respectively. The type strain of Faecalitalea cylindroides is DSM 3983T = ATCC 27803T = JCM 10261T and that of Holdemanella biformis is DSM 3989T = ATCC 27806T = CCUG 28091T.


2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1819-1824 ◽  
Author(s):  
Sooyeon Park ◽  
Ji-Min Park ◽  
Chul-Hyung Kang ◽  
Song-Gun Kim ◽  
Jung-Hoon Yoon

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).


2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1149-1154 ◽  
Author(s):  
Varsha Kale ◽  
Snædís H. Björnsdóttir ◽  
Ólafur H. Friðjónsson ◽  
Sólveig K. Pétursdóttir ◽  
Sesselja Ómarsdóttir ◽  
...  

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).


2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 516-521 ◽  
Author(s):  
Gaiyun Zhang ◽  
Yubian Zhang ◽  
Xijie Yin ◽  
Shuang Wang

A Gram-staining-positive, aerobic, motile and non-spore-forming actinobacteria, designated strain F10T, was isolated from a deep-sea sediment of the western Pacific Ocean. Phylogenetic and phenotypic properties of the organism supported that it belonged to the genus Nesterenkonia . Strain F10T shared highest 16S rRNA gene sequence similarity of 96.8 % with Nesterenkonia aethiopica DSM 17733T, followed by Nesterenkonia xinjiangensis YIM 70097T (96.7 %) and Nesterenkonia alba CAAS 252T (96.6 %). The organism grew at 4–50 °C, at pH 7.0–12.0 and in the presence of 0–12 % (w/v) NaCl, with optimal growth occurring at 40 °C, at pH 9.0 and in the presence of 1 % (w/v) NaCl. The peptidoglycan type was A4(alpha), l-Lys–Gly–l-Glu. The polar lipid profile of strain F10T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unknown glycolipids and two unknown lipids. The isolate contained MK-9 (92 %) and MK-8 (5.8 %) as the major components of the menaquinone system, and anteiso-C17 : 0 (50.9 %) and anteiso-C15 : 0 (29.8 %) as the predominant fatty acids. The G+C content of the genomic DNA of strain F10T was 66.2 mol%. Based on phenotypic, genotypic and phylogenetic analyses, strain F10T represents a novel species of the genus Nesterenkonia for which the name Nesterenkonia alkaliphila sp. nov. is proposed. The type strain is F10T ( = LMG 28112T = CGMCC 1.12781T = JCM 19766T = MCCC 1A09946T).


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