Halopelagius fulvigenes sp. nov., a halophilic archaeon isolated from a lake

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2192-2196 ◽  
Author(s):  
Bing-Bing Liu ◽  
Shu-Kun Tang ◽  
Heng-Lin Cui ◽  
Yong-Guang Zhang ◽  
Li Li ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Type Species ◽  
Sequence Similarity ◽  
Halophilic Archaea ◽  
Rrna Gene ◽  
Content Type ◽  
North West ◽  
Link Type ◽  
Taxonomic Characterization ◽  
The 16S Rrna Gene

Two extremely halophilic archaea, designated YIM 94188T and YIM 94189, were isolated from Qijiaojing lake in Xinjiang province, north-west China and subjected to taxonomic characterization using a polyphasic approach. The cells of the two strains were coccoid, non-motile and Gram-stain-negative. Colonies were pink–white-pigmented and aerobic. Growth occurred at 10–30 % (w/v) NaCl, 20–55 °C and pH 6.0–8.0 (optimum: 20–25 % NaCl, 37–42 °C, pH 6.5–7.0). Magnesium was necessary for growth in the range of 0.2–1.2 M. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that the two strains belonged to the genus Halopelagius showing 98.5 % sequence similarity to the closest phylogenetic neighbour, Halopelagius inordinatus RO5-2T. In addition, the DNA–DNA hybridization values of strains YIM 94188T and YIM 94189 to Halopelagius inordinatus RO5-2T were 35.7 % and 37.7 %, respectively. Polar lipid analyses revealed that the two strains contained phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1) and mannosyl glucosyl diether (DGD-1). The DNA G+C contents of strains YIM 94188T and YIM 94189 were 66.3 mol% and 64.6 mol%, respectively. On the basis of physiological and chemotaxonomic data, and phylogenetic analysis, strains YIM 94188T and YIM 94189 were classified as representing a novel species in the genus Halopelagius . The name Halopelagius fulvigenes sp. nov. is proposed, with YIM 94188T ( = CCTCC AB 2010456T = JCM 17506T) as the type strain.

Sanguibacter suaedae sp. nov., isolated from the root of Suaeda aralocaspica in north-west PR China

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Qin Ma ◽  
Rui-Feng Lei ◽  
Yu-Qian Li ◽  
Dilireba Abudourousuli ◽  
Zulihumaer Rouzi ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
North West ◽  
Link Type ◽  
Pr China ◽  
Genome Analyses ◽  
Wall Characteristic

A bacterial strain, designated YZGR15T, was isolated from the root of an annual halophyte Suaeda aralocaspica, collected from the southern edge of the Gurbantunggut desert, north-west PR China. Cells of the isolate were Gram-stain-positive, facultatively anaerobic, irregular rods. Growth occurred at 4–42 °C (optimum, 30–37 °C), at pH 6.0–9.0 (optimum, pH 7.0–7.5) and in the presence of 0–9 % (w/v) NaCl (optimum, 2–5 %). Phylogenetic analysis using 16S rRNA gene sequences indicated that strain YZGR15T showed the highest sequence similarity to Sanguibacter keddieii (98.27 %), Sanguibacter antarcticus (98.20 %) and Sanguibacter inulinus (98.06 %). Results of genome analyses of strain YZGR15T indicated that the genome size was 3.16 Mb, with a genomic DNA G+C content of 71.9 mol%. Average nucleotide identity and digital DNA–DNA hybridization values between strain YZGR15Tand three type strains were in the range of 76.5–77.8 % and 20.0–22.2 %, respectively. Analysis of the cellular component of strain YZGR15T revealed that the primary fatty acids were anteiso-C15 : 0, C16 : 0, C14 : 0 and iso-C16 : 0 and the polar lipids included diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids and two unidentified glycolipids. The cell-wall characteristic amino acids were glutamic acid, alanine and an unknown amino acid. The whole-cell sugars for the strain were mannose, ribose, rhamnose, glucose and an unidentified sugar. The predominant respiratory quinone was MK-9(H4). Based on the results of genomic, phylogenetic, phenotypic and chemotaxonomic analyses, strain YZGR15T represents a novel species of the genus Sanguibacter , for which the name Sanguibacter suaedae sp. nov. is proposed. The type strain is YZGR15T (=CGMCC 1.18691T=KCTC 49659T)

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.

scholarly journals Nonomuraea solani sp. nov., an actinomycete isolated from eggplant root (Solanum melongena L.)

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2418-2423 ◽  
Author(s):  
Xiangjing Wang ◽  
Junwei Zhao ◽  
Chongxi Liu ◽  
Jidong Wang ◽  
Yue Shen ◽  
...  
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Solanum Melongena ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Phenotypic Differentiation ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

A novel actinomycete, designated strain NEAU-Z6T, was isolated from eggplant (Solanum melongena L.) root. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain NEAU-Z6T belonged to the genus Nonomuraea , with highest sequence similarity to Nonomuraea monospora PT 708T (98.83 %), Nonomuraea rosea GW 12687T (98.55 %) and Nonomuraea rhizophila YIM 67092T (98.02 %). Sequence similarities between strain NEAU-Z6T and other species of the genus Nonomuraea ranged from 97.94 % ( Nonomuraea candida HMC10T) to 96.30 % ( Nonomuraea wenchangensis 210417T). Key morphological, physiological and chemotaxonomic characteristics of strain NEAU-Z6T were congruent with the description of the genus Nonomuraea . The G+C content of the genomic DNA was 64.51 mol%. DNA–DNA relatedness and comparative analysis of physiological, biochemical and chemotaxonomic data allowed genotypic and phenotypic differentiation of strain NEAU-Z6T from closely related species. Thus, strain NEAU-Z6T represents a novel species of the genus Nonomuraea , for which the name Nonomuraea solani sp. nov. is proposed. The type strain is NEAU-Z6T ( = CGMCC 4.7037T = DSM 45729T).

Sphingomonas indica sp. nov., isolated from hexachlorocyclohexane (HCH)-contaminated soil

2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2997-3002 ◽  
Author(s):  
Neha Niharika ◽  
Swati Jindal ◽  
Jasvinder Kaur ◽  
Rup Lal
Keyword(s):  
Phylogenetic Analysis ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Total Dna ◽  
Physiological Tests

A bacterial strain, designated Dd16T, was isolated from a hexachlorocyclohexane (HCH) dumpsite at Lucknow, India. Cells of strain Dd16T were Gram-stain-negative, non-motile, rod-shaped and yellow-pigmented. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain belonged to the genus Sphingomonas in the family Sphingomonadaceae , as it showed highest sequence similarity to Sphingomonas asaccharolytica IFO 15499T (95.36 %), Sphingosinicella vermicomposti YC7378T (95.30), ‘Sphingomonas humi’ PB323 (95.20 %), Sphingomonas sanxanigenens NX02T (95.14 %) and Sphingomonas desiccabilis CP1DT (95.00 %). The major fatty acids were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) C14 : 0 2-OH, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The polar lipid profile of strain Dd16T also corresponded to those reported for species of the genus Sphingomonas (phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, and a sphingoglycolipid), again supporting its identification as a member of the genus Sphingomonas . The predominant respiratory quinone was ubiquinone Q10, and sym-homospermidine was the major polyamine observed. The total DNA G+C content of strain Dd16T was 65.8 mol%. The results obtained on the basis of phenotypic characteristics and phylogenetic analysis and after biochemical and physiological tests, clearly distinguished strain Dd16T from closely related members of the genus Sphingomonas . Thus, strain Dd16T represents a novel species of the genus Sphingomonas for which the name Sphingomonas indica sp. nov. is proposed. The type strain is Dd16T ( = DSM 25434T = CCM 7882T).

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 .

scholarly journals Rhizobium rhizoryzae sp. nov., isolated from rice roots

2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1373-1377 ◽  
Author(s):  
Xiao-Xia Zhang ◽  
Xue Tang ◽  
Rizwan Ali Sheirdil ◽  
Lei Sun ◽  
Xiao-Tong Ma
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type ◽  
The 16S Rrna Gene

Two strains (J3-AN59T and J3-N84) of Gram-stain-negative, aerobic and rod-shaped bacteria were isolated from the roots of fresh rice plants. The 16S rRNA gene sequence similarity results showed that the similarity between strains J3-AN59T and J3-N84 was 100 %. Both strains were phylogenetically related to members of the genus Rhizobium , and they were most closely related to Rhizobium tarimense ACCC 06128T (97.43 %). Similarities in the sequences of housekeeping genes between strains J3-AN59T and J3-N84 and those of recognized species of the genus Rhizobium were less than 90 %. The polar lipid profiles of both strains were predominantly composed of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unknown aminophospholipid. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The DNA G+C contents of J3-AN59T and J3-N84 were 55.7 and 57.1 mol%, respectively. The DNA–DNA relatedness value between J3-AN59T and J3-N84 was 89 %, and strain J3-AN59T showed 9 % DNA–DNA relatedness to R. tarimense ACCC 06128T, the most closely related strain. Based on this evidence, we found that J3-AN59T and J3-N84 represent a novel species in the genus Rhizobium and we propose the name Rhizobium rhizoryzae sp. nov. The type strain is J3-AN59T ( = ACCC 05916T = KCTC 23652T).

Transfer of Bacillus schlegelii to a novel genus and proposal of Hydrogenibacillus schlegelii gen. nov., comb. nov.

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1723-1727 ◽  
Author(s):  
Peter Kämpfer ◽  
Stefanie P. Glaeser ◽  
Hans-Jürgen Busse
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Novel Genus ◽  
Content Type ◽  
Link Type ◽  
Bacillus Schlegelii ◽  
The 16S Rrna Gene

Analysis of the 16S rRNA gene sequences of species currently assigned to the genus Bacillus has shown an extensive intrageneric phylogenetic heterogeneity. The 16S rRNA gene sequence of Bacillus schlegelii ATCC 43741T shows only 82.2–85.9 % sequence similarity to type strains of other members of the genus Bacillus and <88.5 % sequence similarity to recognised species of the most closely related genera, Calditerricola (88.4–88.5 %), Planifilum (87.3–87.8 %) and Caldalkalibacillus (87.2−87.9 %). Furthermore, B. schlegelii ATCC 43741T could not be assigned to an existing family by phylogenetic analysis. The predominant menaquinone was MK-7. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, one unidentified phospholipid and two unidentified glycolipids. The major fatty acids were iso-C16 : 0, C16 : 0, iso-C17 : 0 and anteiso-C17 : 0. Both the polar lipid profile and the fatty acid composition clearly distinguished B. schlegelii DSM 2000T from the type species of the genus Bacillus , Bacillus subtilis . Hence, there is no evidence for a clear phenotypic grouping of this organism into the genus Bacillus nor to the genera Calditerricola , Caldalkalibacillus or Planifilum . A proposal is made to transfer Bacillus schlegelii to a novel genus and species, Hydrogenibacillus schlegelii gen. nov., comb. nov., and to emend the species description. The type strain of the type species is DSM 2000T ( = ATCC 43741T = CCUG 26017T = CIP 106933T).

Microbacterium karelineae sp. nov. isolated from a halophyte plant in the Taklamakan desert

2021 ◽  
Vol 71 (2) ◽  
Author(s):  
Qi-hui Zhu ◽  
Cai-ling Yang ◽  
Xiao-xia Luo ◽  
Li-li Zhang ◽  
Zhan-feng Xia
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
West China ◽  
Content Type ◽  
Taklamakan Desert ◽  
North West ◽  
Link Type ◽  
Diamino Acid ◽  
The 16S Rrna Gene

A bacterial strain, designated TRM 80801T, was isolated from the Karelinea in Taklamakan desert, Xinjiang Uygur Autonomous Region, north-west China. Cells were Gram-stain-positive, aerobic, non-motile, short rods. Strain TRM 80801T grew at 4–50 °C, with optimum growth at 28 °C, and grew at pH 6.0–11.0 and 1–15 % (w/v) NaCl. Phylogenetic analyses of the 16S rRNA gene sequences placed strain TRM 80801T within the genus Microbacterium with the highest similarities to Microbacterium suaedae YZYP 306T (98.97 %) and Microbacterium indicum BBH6T (98.17 %), respectively. The DNA G+C content of TRM 80801T is 69.38 mol%. The cell-wall peptidoglycan contained the amino acids ornithine, glutamic acid, glycine and alanine, the diagnostic diamino acid was ornithine. The acyl type of the peptidoglycan was glycolyl. Whole-cell sugars were ribose, mannose, glucose, rhamnose and galactose. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The predominant menaquinones were MK-10, MK-11 and MK-12. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol. The whole-genome average nucleotide identity (ANI) value between strain TRM 80801T and Microbacterium suaedae YZYP 306T is 70.2 %. On the basis of the evidence presented in this study, strain TRM 80801T is representative of a novel species in the genus Microbacterium , for which the name Microbacterium karelineae sp. nov. is proposed. The type strain is TRM 80801T (=CCTCC AB 2019248T=KCTC 49357T).

Mucilaginibacter inviolabilis sp. nov., isolated from the phycosphere of Haematococcus lacustris NIES 144 culture

2021 ◽  
Author(s):  
Sang-Ah Lee ◽  
Ve Van Le ◽  
So-Ra Ko ◽  
Nakyeong Lee ◽  
Hee-Mock Oh ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Haematococcus Lacustris ◽  
The 16S Rrna Gene

A Gram-stain-negative, non-motile, rod-shaped, aerobic bacterial strain, designated HC2T, was isolated from the phycosphere of Haematococcus lacustris NIES 144 culture. Strain HC2T was able to grow at pH 4.5–8.0, at 4–32 °C and in the presence of 0–2 % (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain HC2T was affiliated to the genus Mucilaginibacter and shared the highest sequence similarity with Mucilaginibacter lappiensis ANJKI2T (98.20 %) and Mucilaginibacter sabulilitoris SMS-12T (98.06 %). Strain HC2T contained summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and iso-C15 : 0 as the major fatty acids (>10.0 %). The major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid, two unidentified aminolipids and four unidentified lipids. The respiratory quinone was menaquinone 7 (MK-7). The genomic DNA G+C content was 42.0 %. On the basis of the phenotypic, chemotaxonomic and phylogenetic characteristics, strain HC2T represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter inviolabilis sp. nov. is proposed. The type strain is HC2T (=KCTC 82084T=JCM 34116T).

Mariniflexile jejuense sp. nov., isolated from the junction between seawater and a freshwater spring, and emended description of the genus Mariniflexile

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1329-1334 ◽  
Author(s):  
Yong-Taek Jung ◽  
Jung-Hoon Yoon
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Emended Description ◽  
Freshwater Spring

A Gram-negative, non-spore-forming, non-flagellated, motile-by-gliding rod, designated SSK2-3T, was isolated from the junction between seawater and a freshwater spring at Jeju island, South Korea. Strain SSK2-3T grew optimally at 25–30 °C, at pH 7.0–7.5 and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SSK2-3T clustered with type strains of species of the genus Mariniflexile , with which it exhibited 97.2–97.8 % 16S rRNA gene sequence similarity. Sequence similarity between the isolate and the other strains used in the phylogenetic analysis was <95.6 %. Strain SSK2-3T contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C15 : 1 G and C15 : 0 as the major fatty acids. The major polar lipids of strain SSK2-3T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain SSK2-3T was 32.4 mol%. DNA–DNA relatedness between the isolate and Mariniflexile gromovii KCTC 12570T, Mariniflexile fucanivorans DSM 18792T and Mariniflexile aquimaris HWR-17T was 19, 15 and 20 %, respectively. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain SSK2-3T is separate from other members of the genus Mariniflexile . On the basis of the data presented, strain SSK2-3T is considered to represent a novel species of the genus Mariniflexile , for which the name Mariniflexile jejuense sp. nov. is proposed. The type strain is SSK2-3T ( = KCTC 23958T  = CCUG 62414T). An emended description of the genus Mariniflexile is given.

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