scholarly journals Description of Xenorhabdus khoisanae sp. nov., the symbiont of the entomopathogenic nematode Steinernema khoisanae

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3220-3224 ◽  
Author(s):  
Tiarin Ferreira ◽  
Carol A. van Reenen ◽  
Akihito Endo ◽  
Cathrin Spröer ◽  
Antoinette P. Malan ◽  
...  

Bacterial strain SF87T, and additional strains SF80, SF362 and 106-C, isolated from the nematode Steinernema khoisanae, are non-bioluminescent Gram-reaction-negative bacteria that share many of the carbohydrate fermentation reactions recorded for the type strains of recognized Xenorhabdus species. Based on 16S rRNA gene sequence data, strain SF87T is shown to be closely related (98 % similarity) to Xenorhabdus hominickii DSM 17903T. Nucleotide sequences of strain SF87 obtained from the recA, dnaN, gltX, gyrB and infB genes showed 96–97 % similarity with Xenorhabdus miraniensis DSM 17902T . However, strain SF87 shares only 52.7 % DNA–DNA relatedness with the type strain of X. miraniensis , confirming that it belongs to a different species. Strains SF87T, SF80, SF362 and 106-C are phenotypically similar to X. miraniensis and X. beddingii , except that they do not produce acid from aesculin. These strains are thus considered to represent a novel species of the genus Xenorhabdus , for which the name Xenorhabdus khoisanae sp. nov. is proposed. The type strain is SF87T ( = DSM 25463T = ATCC BAA-2406T).

2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1245-1251 ◽  
Author(s):  
Tiago Domingues Zucchi ◽  
Geok Yuan Annie Tan ◽  
Avinash Naga Venkata Bonda ◽  
Sarah Frank ◽  
Jenileima Devi Kshetrimayum ◽  
...  

The taxonomic positions of three thermophilic actinomycetes isolated from arid soil samples were established by using a polyphasic approach. The organisms had chemical and morphological features that were consistent with their classification in the genus Amycolatopsis . 16S rRNA gene sequence data supported the classification of the isolates in the genus Amycolatopsis and showed that they formed distinct branches in the Amycolatopsis methanolica subclade. DNA–DNA relatedness studies between the isolates and their phylogenetic neighbours showed that they belonged to distinct genomic species. The three isolates were readily distinguished from one another and from the type strains of species classified in the A. methanolica subclade based on a combination of phenotypic properties and by genomic fingerprinting. Consequently, it is proposed that the three isolates be classified in the genus Amycolatopsis as representatives of Amycolatopsis granulosa sp. nov. (type strain GY307T = NCIMB 14709T = NRRL B-24844T), Amycolatopsis ruanii sp. nov. (type strain NMG112T = NCIMB 14711T = NRRL B-24848T) and Amycolatopsis thermalba sp. nov. (type strain SF45T = NCIMB 14705T = NRRL B-24845T).


2020 ◽  
Vol 70 (12) ◽  
pp. 6301-6306
Author(s):  
Sooyeon Park ◽  
Seo Yeon Lee ◽  
Wonyong Kim ◽  
Jung-Hoon Yoon

A Gram-stain-negative, aerobic, non-spore-forming, motile by single polar flagellum and ovoid or rod-shaped bacterial strain, designated JBTF-M23T, was isolated from tidal flat sediment collected from the Yellow Sea, Republic of Korea. Neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain JBTF-M23T fell within the clade comprising the type strains of Pseudoalteromonas species, clustering with the type strains of P. byunsanensis and P. amylolytica . Strain JBTF-M23T exhibited the highest 16S rRNA gene sequence similarity value (98.6 %) to the type strain of P. rubra and sequence similarities of 98.3 and 97.7 % to the type strains of P. byunsanensis and P. amylolytica, respectively. The DNA G+C content of strain JBTF-M23T from genomic sequence data was 41.98 %. The ANI and dDDH values between strain JBTF-M23T and the type strains of P. rubra , P. byunsanensis and P. amylolytica were 71.3–76.6 and 19.4–19.9 %, respectively. Strain JBTF-M23T contained Q-8 as the predominant ubiquinone and C16 : 1  ω7c and/or C16 : 1  ω6c, C16 : 0 and C18 : 1  ω7c as the major fatty acids. The major polar lipids of strain JBTF-M23T were phosphatidylethanolamine and one unidentified aminolipid. Distinguished phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that strain JBTF-M23T is separated from recognized Pseudoalteromonas species. On the basis of the data presented, strain JBTF-M23Tis considered to represent a novel species of the genus Pseudoalteromonas , for which the name Pseudoalteromonas caenipelagi sp. nov. is proposed. The type strain is JBTF-M23T(=KACC 19900T=NBRC 113647T).


2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1841-1846 ◽  
Author(s):  
Sooyeon Park ◽  
Ji-Min Park ◽  
Chul-Hyung Kang ◽  
Jung-Hoon Yoon

A Gram-stain-negative, non-motile, aerobic, curved-to-spiral-rod-shaped bacterium, designated AH-MY2T, was isolated from a tidal flat on Aphae island in the sea to the south-west of South Korea, and its taxonomic position was investigated using a polyphasic taxonomic approach. Strain AH-MY2T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain AH-MY2T clustered with the type strain of Terasakiella pusilla and that this cluster joined the clade comprising the type strains of species of the genus Thalassospira . Strain AH-MY2T exhibited 16S rRNA gene sequence similarity values of 90.6 % to the type strain of Terasakiella pusilla and of less than 91.0 % to the type strains of other species with validly published names. Strain AH-MY2T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids detected in strain AH-MY2T were phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminolipids and one unidentified glycolipid. The DNA G+C content of strain AH-MY2T was 56.0 mol%. The phylogenetic data and differential chemotaxonomic and other phenotypic properties revealed that strain AH-MY2T represented a novel genus and species within the family Rhodospirillaceae of the class Alphaproteobacteria , for which the name Aestuariispira insulae gen. nov., sp. nov. is proposed. The type strain of Aestuariispira insulae is AH-MY2T ( = KCTC 32577T = CECT 8488T).


2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 219-223 ◽  
Author(s):  
P. Schumann ◽  
R. Pukall ◽  
C. Spröer ◽  
E. Stackebrandt

16S rRNA gene sequences deposited for the type strains of Paraoerskovia marina (CTT-37T; GenBank accession no. AB445007) and Koreibacter algae (DSW-2T; FM995611) show a similarity of 100 %. Consequently, the type strains were subjected to a polyphasic recharacterization under direct comparison in order to clarify their taxonomic position. PvuII RiboPrint patterns and quantitative ratios of cellular fatty acids revealed strain-specific differences between P. marina DSM 21750T ( = CTT-37T) and K. algae DSM 22126T ( = DSW-2T). The percentage of DNA–DNA binding of 94 % indicated that the two type strains belong to the same genomospecies. Agreement in the peptidoglycan structure and polar lipid pattern, highly similar fatty acid profiles and MALDI-TOF mass spectra, the ability to produce acid from the same carbon sources, corresponding enzymic activities and DNA G+C contents of 70.8±0.3 mol%, in addition to the consistent characteristics reported in the original descriptions, support the view that the two strains should be affiliated to the same species. According to Rules 38 and 42 of the Bacteriological Code, Koreibacter algae should be reclassified as later heterotypic synonym of Paraoerskovia marina , and the descriptions of the genus Paraoerskovia Khan et al. 2009 and of Paraoerskovia marina Khan et al. 2009 are emended accordingly.


Author(s):  
Marvin A. Altamia ◽  
J. Reuben Shipway ◽  
David Stein ◽  
Meghan A. Betcher ◽  
Jennifer M. Fung ◽  
...  

Here, we describe three endosymbiotic bacterial strains isolated from the gills of the shipworm, Bankia setacea (Teredinidae: Bivalvia). These strains, designated as Bs08T, Bs12T and Bsc2T, are Gram-stain-negative, microaerobic, gammaproteobacteria that grow on cellulose and a variety of substrates derived from lignocellulose. Phenotypic characterization, phylogeny based on 16S rRNA gene and whole genome sequence data, amino acid identity and percentage of conserved proteins analyses, show that these strains are novel and may be assigned to the genus Teredinibacter . The three strains may be differentiated and distinguished from other previously described Teredinibacter species based on a combination of four characteristics: colony colour (Bs12T, purple; others beige to brown), marine salt requirement (Bs12T, Bsc2T and Teredinibacter turnerae strains), the capacity for nitrogen fixation (Bs08T and T. turnerae strains) and the ability to respire nitrate (Bs08T). Based on these findings, we propose the names Teredinibacter haidensis sp. nov. (type strain Bs08T=ATCC TSD-121T=KCTC 62964T), Teredinibacter purpureus sp. nov. (type strain Bs12T=ATCC TSD-122T=KCTC 62965T) and Teredinibacter franksiae sp. nov. (type strain Bsc2T=ATCC TSD-123T=KCTC 62966T).


2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2600-2606 ◽  
Author(s):  
Laure Mondani ◽  
Laurie Piette ◽  
Richard Christen ◽  
Dipankar Bachar ◽  
Catherine Berthomieu ◽  
...  

An actinobacterial strain, designated ViU22T, was isolated from a natural uranium-rich soil and was studied using a polyphasic approach. Cells formed orange-pigmented colonies, were rod-shaped, Gram-positive (non-staining method), non-motile and non-spore-forming. This organism grew in 0–4.5 % (w/v) NaCl and at 15–37 °C, with optimal growth occurring in 0.5 % (w/v) NaCl and at 30 °C. Comparative 16S rRNA gene sequence analysis revealed that the strain ViU22T belonged to the genus Microbacterium . It exhibited highest 16S rRNA gene sequence similarity with the type strains of Microbacterium testaceum (98.14 %) and Microbacterium binotii (98.02 %). The DNA–DNA relatedness of strains ViU22T with the most closely related type strains Microbacterium testaceum and Microbacterium binotii DSM 19164T was 20.10 % (±0.70) and 28.05 % (±0.35), respectively. Strain ViU22T possessed a type B2β peptidoglycan with partial substitution of glutamic acid by 3-hydroxy glutamic acid. The major menaquinones were MK-11 and MK-12. Major polar lipids detected in the strain ViU22T were diphosphatidylglycerol, phosphatidylglycerol, an unknown phospholipid and unknown glycolipids. The predominant fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0, a pattern reported for other Microbacterium species. The major cell-wall sugars were galactose, xylose and mannose and the DNA G+C content was 71 mol%. Together, the DNA–DNA hybridization results and the differentiating phenotypic characteristics, showed that strain ViU22T should be classified as the type strain of a novel species within the genus Microbacterium , for which the name Microbacterium lemovicicum sp. nov. is proposed. The type strain is ViU22T ( = ATCC BAA-2396T = CCUG 62198T = DSM 25044T).


2012 ◽  
Vol 62 (Pt_8) ◽  
pp. 1825-1831 ◽  
Author(s):  
Young-Ok Kim ◽  
Sooyeon Park ◽  
Bo-Hye Nam ◽  
So-Jung Kang ◽  
Young-Baek Hur ◽  
...  

A Gram-negative, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated MA1-1T, was isolated from a sea squirt (Halocynthia roretzi) collected from the South Sea, Korea. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain MA1-1T is phylogenetically closely related to Litoreibacter species and to Thalassobacter arenae . It exhibited 16S rRNA gene sequence similarities of 97.3, 97.1 and 97.3 % to the type strains of Litoreibacter albidus , Litoreibacter janthinus and T. arenae , respectively. Strain MA1-1T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the predominant fatty acid. The polar lipid profile of strain MA1-1T was similar to those of the type strains of L. albidus and L. janthinus . T. arenae was found to be phylogenetically and chemotaxonomically more closely related to Litoreibacter species and strain MA1-1T than to Thalassobacter stenotrophicus , the type species of the genus Thalassobacter . The DNA G+C content of strain MA1-1T was 57.9 mol%, and DNA–DNA relatedness to the type strains of the two Litoreibacter species and T. arenae was 9–14 %. Differential phenotypic properties, together with the observed phylogenetic and genetic distinctiveness, distinguished strain MA1-1T from the two Litoreibacter species and T. arenae . On the basis of the data presented, strain MA1-1T is considered to represent a novel species of the genus Litoreibacter , for which the name Litoreibacter meonggei sp. nov. is proposed. The type strain is MA1-1T ( = KCTC 23699T  = CCUG 61486T). In this study, it is also proposed that Thalassobacter arenae is reclassified as a member of the genus Litoreibacter , Litoreibacter arenae comb. nov. (type strain GA2-M15T  = DSM 19593T  = KACC 12675T). An emended description of the genus Litoreibacter is also presented.


2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 3943-3949 ◽  
Author(s):  
Yong-Taek Jung ◽  
Sooyeon Park ◽  
Jung-Sook Lee ◽  
Jung-Hoon Yoon

A Gram-stain-negative, coccoid- or oval-shaped, gliding bacterial strain, designated HDW-31T, belonging to the class Alphaproteobacteria , was isolated from seawater of the Yellow Sea, Korea, and was subjected to a taxonomic study using a polyphasic approach. Strain HDW-31T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2–3 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain HDW-31T fell within the clade comprising the genus Altererythrobacter , clustering with the type strains of Altererythrobacter luteolus and Altererythrobacter gangjinensis , with which strain HDW-31T exhibited 97.0 and 96.0 % sequence similarity values, respectively. Sequence similarities to the type strains of the other recognized species of the genus Altererythrobacter were 93.5–96.0 %. The DNA G+C content was 57.9 mol% and mean DNA–DNA relatedness between strain HDW-31T and the type strain of A. luteolus was 5.3 %. Strain HDW-31T contained Q-10 as the predominant ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and C16 : 0 as the major fatty acids. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, a sphingoglycolipid, two unidentified glycolipids and an unidentified lipid. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, demonstrated that strain HDW-31T is distinguishable from recognized species of the genus Altererythrobacter . On the basis of the data presented, strain HDW-31T is considered to represent a novel species of the genus Altererythrobacter , for which the name Altererythrobacter aestiaquae sp. nov. is proposed. The type strain is HDW-31T ( = KCTC 42006T = CECT 8527T).


2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 839-843 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Soo-Young Lee ◽  
Yong-Taek Jung ◽  
Jung-Sook Lee ◽  
...  

A Gram-stain-negative, non-motile, non-spore-forming, aerobic, rod-shaped bacterial strain, designated DPG-28T, was isolated from seawater on the southern coast of Korea. Strain DPG-28T grew optimally at 30 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain DPG-28T formed a coherent cluster with members of the genera Marivita and Gaetbulicola , with which it exhibited sequence similarity values of 97.8–98.5 %. The DNA G+C content of strain DPG-28T was 65.1 mol%. The predominant ubiquinone of strain DPG-28T was ubiquinone-10 (Q-10), consistent with data for the genera Marivita and Gaetbulicola . The cellular fatty acid profiles of strain DPG-28T and the type strains of Marivita cryptomonadis , Marivita litorea and Gaetbulicola byunsanensis were essentially similar in that the common predominant fatty acid was C18 : 1ω7c. Major polar lipids found in strain DPG-28T and the type strains of M. cryptomonadis , M. litorea and G. byunsanensis were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and an unidentified aminolipid. From these data, it is proposed that Gaetbulicola byunsanensis be reclassified as a member of the genus Marivita , for which the name Marivita byunsanensis comb. nov. is proposed, with the type strain SMK-114T ( = CCUG 57612T  = KCTC 22632T), and that strain DPG-28T be classified in the genus Marivita . Differential phenotypic properties and genetic distinctiveness of strain DPG-28T demonstrated that this strain is distinguishable from M. cryptomonadis , M. litorea and G. byunsanensis . On the basis of the data presented, strain DPG-28T is considered to represent a novel species of the genus Marivita , for which the name Marivita hallyeonensis sp. nov. is proposed. The type strain is DPG-28T ( = KCTC 23421T  = CCUG 60522T). An emended description of the genus Marivita is also provided.


2020 ◽  
Vol 70 (9) ◽  
pp. 4867-4873 ◽  
Author(s):  
Guang-Da Feng ◽  
Jun Zhang ◽  
Wendi Chen ◽  
Sheng-Nan Wang ◽  
Honghui Zhu

Two novel strains, designated 92R-1T and 9PBR-1T, were isolated from abandoned lead–zinc ore collected in Meizhou, Guangdong Province, PR China. Phylogenetic analyses based on 16S rRNA gene sequences showed that they fell into the genus of Hymenobacte r and formed two distinct lineages. Strain 92R-1T was most closely related to Hymenobacter wooponensis JCM 19491T (98.7 %) and Hymenobacter gelipurpurascens LMG 21873T (98.5 %), while strain 9PBR-1T was most closely related to Hymenobacter chitinivorans LMG 21951T (99.0 %), Hymenobacter elongatus JCM 17223T (98.7 %) and Hymenobacter aquaticus JCM 31653T (98.1 %). Strain 92R-1Tshared average nucleotide identity values of 80.0–83.7 % and digital DNA–DNA hybridization values of 23.1–27.1 % with its closely related type strains, respectively, while strain 9PBR-1T shared corresponding values of 80.3–83.2 % and 23.6–26.7 % with its closely related type strains, respectively. The two novel strains could be clearly distinguished from their closely related type strains by enzyme activities and substrates assimilation, respectively. Both of them took iso-C15:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), summed feature 4 (iso-C17:1 I and/or anteiso-C17:1 B) and C16:1 ω5c as major fatty acids, and showed clear differences from their closely relatives in the contents of several components. They contained menaquinone 7 as the major respiratory quinone and phosphatidylethanolamine as the dominant polar lipid. The G+C contents of strains 92R-1T and 9PBR-1T were 56.7 and 59.5 mol%, respectively. The results clearly supported that strains 92R-1T and 9PBR-1T represent two distinct novel species within the genus Hymenobacter , for which the names Hymenobacter fodinae sp. nov. (type strain 92R-1T=GDMCC 1.1493T=JCM 32697T) and Hymenobacter metallicola sp. nov. (type strain 9PBR-1T=GDMCC 1.1491T=JCM 32698T) are proposed.


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