scholarly journals Flavobacterium panici sp. nov. isolated from the rhizosphere of the switchgrass Panicum virgatum

2020 ◽  
Vol 70 (11) ◽  
pp. 5824-5831 ◽  
Author(s):  
Peter Kämpfer ◽  
S. P. Glaeser ◽  
John A. McInroy ◽  
Jia Xu ◽  
Hans-Jürgen Busse ◽  
...  

A Gram-staining-negative non endospore-forming strain, PXU-55T, was isolated from the rhizosphere of the switchgrass Panicum virgatum and studied in detail to determine its taxonomic position. The results of 16S rRNA gene sequence analysis indicated that the isolate represented a member of the genus Flavobacterium . The isolate shared highest 16S rRNA gene sequence similarities with the type strains of Flavobacterium chungangense (98.78 %) and Flavobacterium chilense (98.64 %). The average nucleotide identity (ANI) and in silico DNA–DNA hybridization (isDDH) values between the PXU-55T genome assembly and the ones of the most closely related type strains of species of the genus Flavobacterium were 87.3 and 31.9% ( Flavobacterium defluvii ), and 86.1 and 29.9% ( Flavobacterium johnsoniae ). Menaquinone MK-6 was the major respiratory quinone. As major polar lipids, phosphatidylethanolamine, an ornithine lipid and the unidentified polar lipids L2, L3 and L4 lacking a functional group were found. Moderate to minor amounts of another ornithine lipid, the unidentified lipid L1 and a glycolipid were present, as well. The major polyamine is sym-homospermidine. The fatty acid profiles contained major amounts of iso-C15:0, iso-C15:0 3-OH, iso-C17:0 3-OH, C15:0, summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH) and various hydroxylated fatty acids in smaller amounts, among them iso C16:0 3-OH, C16:0 3-OH and C15:0 3-OH, which supported the classification of the isolate as a member of the genus Flavobacterium . Physiological and biochemical characterisation and ANI calculations with the type strains of the most closely related species allowed a clear phenotypic and genotypic differentiation of the strain. For this reason, we propose that strain PXU-55T (=CIP 111646T=CCM 8914T) represents a novel species with the name Flavobacterium panici sp. nov.

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 945-951 ◽  
Author(s):  
Yong-Taek Jung ◽  
Jung-Hoon Yoon

A Gram-stain-negative, non-motile, rod- or coccoid-shaped bacterial strain, designated HD-22T, belonging to the class Alphaproteobacteria , was isolated from a tidal flat sediment of the Yellow Sea, Korea, and was subjected to a polyphasic taxonomic study. Strain HD-22T grew optimally at pH 7.0–8.0, at 25 °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 HD-22T fell within the clade comprising species of the genus Jannaschia , clustering with the type strains of Jannaschia helgolandensis , Jannaschia donghaensis and Jannaschia rubra , with which it exhibited highest 16S rRNA gene sequence similarity (97.6–98.2 %). Levels of 16S rRNA gene sequence similarity between strain HD-22T and the type strains of the other species of the genus Jannaschia were in the range 94.4–97.5 %. The DNA G+C content was 64.6 mol% and mean DNA–DNA relatedness values between strain HD-22T and the type strains of J. helgolandensis , J. donghaensis and J. rubra were 42.1, 40.1 and 27.0 %, respectively. Strain HD-22T contained Q-10 as the predominant ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as the major fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, demonstrated that strain HD-22T is distinguishable from recognized species of the genus Jannaschia . On the basis of the data presented, strain HD-22T is considered to represent a novel species of the genus Jannaschia , for which the name Jannaschia faecimaris sp. nov. is proposed. The type strain is HD-22T ( = KCTC 32179T = CCUG 63415T).


2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4118-4123 ◽  
Author(s):  
Sooyeon Park ◽  
Yong-Taek Jung ◽  
Jung-Hoon Yoon

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, designated D1-W3T, was isolated from tidal flat sediment of the South Sea, South Korea, and subjected to a taxonomic study using a polyphasic approach. Strain D1-W3T grew optimally at pH 7.0–8.0, at 25 °C and in the presence of 2 % (w/v) NaCl. Neighbour-joining phylogenetic analyses based on 16S rRNA gene sequences revealed that strain D1-W3T fell within the clade comprising species of the genus Loktanella , clustering with the type strains of Loktanella tamlensis , Loktanella rosea and Loktanella maricola , with which it exhibited the highest 16S rRNA gene sequence similarity values (98.1–98.2 %). The 16S rRNA gene sequence similarity values between strain D1-W3T and the type strains of other species of the genus Loktanella were in the range 93.5–96.5 %. The DNA G+C content of strain D1-W3T was 58.1 mol% and the mean DNA–DNA hybridization values with L. tamlensis KCTC 12722T, L. rosea LMG 22534T and L. maricola DSW-18T were 13–25 %. Strain D1-W3T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the predominant fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and one unidentified aminolipid. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, showed that strain D1-W3T could be differentiated from other species of the genus Loktanella . On the basis of the data presented, strain D1-W3T represents a novel species of the genus Loktanella , for which the name Loktanella sediminilitoris sp. nov. is proposed. The type strain is D1-W3T ( = KCTC 32383T = CECT 8284T).


2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2383-2387 ◽  
Author(s):  
Huili Pang ◽  
Maki Kitahara ◽  
Zhongfang Tan ◽  
Yanping Wang ◽  
Guangyong Qin ◽  
...  

Characterization and identification of strain CW 1 ( = JCM 17161) isolated from corn silage were performed. Strain CW 1 was a Gram-positive, catalase-negative and homofermentative rod that produced the dl-form of lactic acid. This strain exhibited more than 99.6 % 16S rRNA gene sequence similarity and greater than 82 % DNA–DNA reassociation with type strains of Lactobacillus kimchii , L. bobalius and L. paralimentarius . To clarify the taxonomic positions of these type strains, phenotypic characterization, 16S rRNA gene sequencing, ribotyping and DNA–DNA relatedness were examined. The three type strains displayed different l-arabinose, lactose, melibiose, melezitose, raffinose and N-acetyl-β-glucosaminidase fermentation patterns. Phylogenetic analysis showed that L. paralimentarius is a closer neighbour of L. kimchii and L. bobalius , sharing 99.5–99.9 % 16S rRNA gene sequence similarity, which was confirmed by the high DNA–DNA relatedness (≥82 %) between L. paralimentarius JCM 10415T, L. bobalius JCM 16180T and L. kimchii JCM 10707T. Therefore, it is proposed that L. kimchii and L. bobalius should be reclassified as later synonyms of L. paralimentarius .


Author(s):  
Peter Kämpfer ◽  
Hans-Jürgen Busse ◽  
Stefanie P. Glaeser ◽  
Dominique Clermont ◽  
Alexis Criscuolo ◽  
...  

A Gram-stain-positive, non-motile, non-spore-forming, coccus (strain Do 184T) was isolated from exhaust air of a turkey fattening plant on mannitol salt agar. The strain shared high 16S rRNA gene sequence similarity to the type strains of Jeotgalicoccus aerolatus (98.0%) followed by Jeotgalicoccus marinus (97.2%) and Jeotgalicoccus huakuii (97.1%). All other 16S rRNA gene sequence similarities to species of the genus Jeotgalicoccus were below 97%. The average nucleotide identities (ANI) between the Do 184T genome assembly and the ones of type strains of species of the genus Jeotgalicoccus were far below the 95% species delineation cutoff value, ranging from 79.47% ( J. marinus DSM 19772T) to 75.30% ( J. pinnipedialis CIP 107946T). The quinone system of Do 184T, the polar lipid profile, the polyamine pattern and the fatty acid profile were in congruence with those reported for other species of the genus Jeotgalicoccus and thus supported the affiliation of Do 184T to this genus. Do 184T represents a novel species, for which the name Jeotgalicoccus meleagridis sp. nov. is proposed, with the type strain Do 184T (=LMG 31100T=CCM 8918T=CIP 111649T). In addition, data on genome sequences of Jeotgalicoccus halophilus C1-52T =CGMCC 1.8911T=NBRC 105788T and Jeotgalicoccus aerolatus MPA-33T=CCM 7679T=CCUG 57953T=DSM 22420T=CIP 111750T indicate that both isolates represent the same species. Pairwise ANI between the genomes of these two strains lead to similarities of 98.98–99.05 %. These results indicate that these strains represent members of the same species. Due to priority of publication it is proposed that Jeotgalicoccus halophilus is reclassified as Jeotgalicoccus aerolatus .


2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3841-3847 ◽  
Author(s):  
Peter Kämpfer ◽  
Stefanie Glaeser ◽  
Hans-Jürgen Busse ◽  
Tobias Eisenberg ◽  
Holger Scholz

A Gram-stain-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacterium (B1315T) was isolated from the placenta of a sheep with abortion. On the basis of 16S rRNA gene sequence analyses the strain was assigned to the Brucella – Ochrobactrum – Paenochrobactrum – Pseudochrobactrum group with 94.5–94.8 %, 94.3–96.1 %, 95.0–95.1 %, and 95.9–96.1 % sequence similarities to type strains of species of the four genera, respectively. Phylogenetic trees indicated a close relationship to the type strains of Ochrobactrum gallinifaecis and Ochrobactrum oryzae (95.9 and 96.1 % sequence similarity, respectively). Chemotaxonomic data confirmed the allocation of strain B1315T to the family Brucellaceae (quinone system: ubiquinone Q-10 and major fatty acids: C18 : 1ω7c and C19 : 0 cyclo ω8c). The polar lipid profile contained the major lipids diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and the unidentified but unique phospholipid PL7. The polyamine pattern of strain B1315T contained the major polyamines spermidine and putrescine. On the basis of the 16S rRNA gene and recA sequence phylogeny and chemotaxonomic data strain B1315T was clearly different from the genera Brucella , Ochrobactrum , Paenochrobactrum and Pseudochrobactrum . On the basis of these data we propose the novel genus Falsochrobactrum gen. nov. with the type species Falsochrobactrum ovis sp. nov. with the type strain B1315T ( = CCM 8460T = LMG 27356T.) The taxonomic allocation of O. gallinifaecis , which grouped inconsistently together with strain B1315T on the basis of 16S rRNA gene sequence data, but shows the chemotaxonomic features of the genus Ochrobactrum , remains to be clarified.


2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1559-1565 ◽  
Author(s):  
Radha Vaddavalli ◽  
Sneha Peddi ◽  
Srilekha Yadav Kothagauni ◽  
Zareena Begum ◽  
Bhagyanarayana Gaddam ◽  
...  

A novel actinomycete strain, designated VRC122T, was isolated from a Callistemon citrinus rhizosphere sample collected from New Delhi, India, and its taxonomic status was determined by using a polyphasic approach. Strain VRC122T was a Gram-stain-positive, aerobic, non-motile, non-acid–alcohol-fast strain. Phylogenetic analysis based on 16S rRNA gene sequences showed the strain was placed in a well-separated sub-branch within the genus Saccharopolyspora . The highest levels of 16S rRNA gene sequence similarity were found with Saccharopolyspora hirsuta subsp. kobensis JCM 9109T (98.71 %), Saccharopolyspora antimicrobica I05-00074T (98.69 %) and Saccharopolyspora jiangxiensis W12T (98.66 %); 16S rRNA gene sequence similarities with type strains of all other species of the genus Saccharopolyspora were below 98 %. Chemosystematic studies revealed that it contained meso-diaminopimelic acid. Arabinose and galactose were the predominant whole-cell sugars. Diagnostic polar lipids were diphosphatidylglycerol, phosphatidylinositol and phosphatidylcholine. MK-9(H6) was the predominant menaquinone. C14 : 0, C16 : 0, iso-C15 : 0, iso-C16 : 0, iso-C17 : 0, anteiso-C15 : 0, anteiso-C17 : 0, C17 : 0 cyclo and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) were the major cellular fatty acids. The G+C content of the genomic DNA was 69.5 mol%. The results of DNA–DNA hybridization (30 %, 22 % and 25 %, respectively) with type strains of the above-mentioned species, in combination with differences in physiological and biochemical data supported that strain VRC122T represents a novel species of the genus Saccharopolyspora , for which the name Saccharopolyspora indica sp. nov., is proposed. The type strain is VRC122T ( = KCTC 29208T = MTCC 11564T = MCC 2206T = ATCC BAA-2551T).


2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2532-2537 ◽  
Author(s):  
Poonam Vashist ◽  
Yuichi Nogi ◽  
Sanjeev C. Ghadi ◽  
Pankaj Verma ◽  
Yogesh S. Shouche

A rod-shaped, Gram-negative, non-motile, aerobic and non-endospore forming bacterium, designated strain DD-13T, was isolated from the mangrove ecosystem of Goa, India. Strain DD-13T degraded polysaccharides such as agar, alginate, chitin, cellulose, laminarin, pectin, pullulan, starch, carrageenan, xylan and β-glucan. The optimum pH and temperature for growth was 7 and 36 °C, respectively. The strain grew optimally in the presence of 3 % NaCl (w/v). The DNA G+C content was 61.4 mol%. The predominant fatty acid of strain DD-13T was iso-C15 : 0. Ubiquinone-8 was detected as the major respiratory lipoquinone. Phylogenetic studies based on 16S rRNA gene sequence analysis demonstrated that strain DD-13T formed a coherent cluster with species of the genus Microbulbifer . Strain DD-13T exhibited 16S rRNA gene sequence similarity levels of 98.9–97.1 % with Microbulbifer hydrolyticus IRE-31T, Microbulbifer salipaludis JCM 11542T, Microbulbifer agarilyticus JAMB A3T, Microbulbifer celer KCTC 12973T and Microbulbifer elongatus DSM 6810T. However, the level of DNA–DNA relatedness between strain DD-13T and the five type strains of these species of the genus Microbulbifer were in the range of 26–33 %. Additionally, strain DD-13T demonstrates several phenotypic differences from these type strains of species of the genus Microbulbifer . Thus strain DD-13T represents a novel species of the genus Microbulbifer , for which the name Microbulbifer mangrovi sp. nov. is proposed with the type strain DD-13T ( = KCTC 23483T = JCM 17729T).


2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2062-2067 ◽  
Author(s):  
Yong-Taek Jung ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon

A Gram-negative, motile, rod-shaped bacterial strain, designated HDW-15T, was isolated from seawater of the Yellow Sea, Korea, and subjected to a polyphasic taxonomic study. Strain HDW-15T grew optimally at pH 7.0–8.0, at 25 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain HDW-15T fell within the clade comprising Marinomonas species, joining the type strain of Marinomonas arctica , with which it exhibited highest 16S rRNA gene sequence similarity (97.7 %). The 16S rRNA gene sequence similarity values between strain HDW-15T and the type strains of other Marinomonas species were in the range 93.7–97.2 %. Mean DNA–DNA relatedness values between strain HDW-15T and the type strains of M. arctica , Marinomonas polaris and Marinomonas pontica were 5.0–9.9 %. The DNA G+C content of the isolate was 48.7 mol%. Strain HDW-15T contained Q-8 as the predominant ubiquinone and C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C16 : 0 as the major fatty acids. The major polar lipids found in strain HDW-15T were phosphatidylglycerol and phosphatidylethanolamine. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, showed that strain HDW-15T can be differentiated from other Marinomonas species. On the basis of the data presented, strain HDW-15T is considered to represent a novel species of the genus Marinomonas , for which the name Marinomonas hwangdonensis sp. nov. is proposed. The type strain is HDW-15T ( = KCTC 23661T = CCUG 61321T).


2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 175-180 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Yong-Taek Jung ◽  
Jung-Sook Lee

A Gram-negative, non-motile, rod-shaped bacterial strain, designated DPG-5T, was isolated from seawater of the South Sea, Korea and subjected to a study using a polyphasic taxonomic approach. Strain DPG-5T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. Neighbour-joining phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DPG-5T fell within the clade comprising members of the genus Loktanella , and formed a cluster with the type strains of Loktanella rosea , Loktanella maricola , Loktanella koreensis and Loktanella tamlensis , with which it exhibited highest 16S rRNA gene sequence similarity values of 96.7, 96.5, 96.2 and 96.7 %, respectively. The 16S rRNA gene sequence similarity values between strain DPG-5T and the type strains of the other species of the genus Loktanella were in the range of 94.4–96.0 %. The DNA G+C content of strain DPG-5T was 57.6 mol%. Strain DPG-5T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and 11-methyl C18 : 1ω7c as the major fatty acids. The major polar lipids found in strain DPG-5T were phosphatidylcholine and phosphatidylglycerol. Differential phenotypic properties, together with the phylogenetic distinctiveness, showed that strain DPG-5T is differentiated from other species of the genus Loktanella . On the basis of the data presented, strain DPG-5T is considered to represent a novel species of the genus Loktanella , for which the name Loktanella litorea sp. nov. is proposed. The type strain is DPG-5T ( = KCTC 23883T = CCUG 62113T).


2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1736-1742 ◽  
Author(s):  
Peter Kämpfer ◽  
Hans-Jürgen Busse ◽  
John A. McInroy ◽  
Stefanie P. Glaeser

A yellow-pigmented, Gram-negative, rod-shaped, non-spore-forming bacterium (strain JM-1070T) was isolated as a presumptive endophyte from internal stem tissue of a healthy corn stem. Phylogenetic analyses based on the 16S rRNA gene sequence placed strain JM-1070T in the monophyletic cluster of the genus Mucilaginibacter , with closest affiliation to the type strains of Mucilaginibacter composti (98 % similarity) and Mucilaginibacter calamicampi (97.2 %). 16S rRNA gene sequence similarity to type strains of other species of the genus Mucilaginibacter was 93.4–96.0 %. DNA–DNA hybridizations between strain JM-1070T and the type strains M. composti LMG 23497T and M. calamicampi CCUG 63418T showed low relatedness values of 13 % (reciprocal 18 %) and 52 % (reciprocal 54.4 %). Major respiratory quinones were menaquinones MK-6 and MK-7. The predominant fatty acids (>15 %) were iso-C15 : 0, iso-C15 : 0 2-OH/C16 : 1ω7c (measured as summed feature 3) and iso-C17 : 0 3-OH. Several other iso-branched and hydroxylated fatty acids were detected. The polar lipid profile was composed of the major components phosphatidylethanolamine and an unidentified aminophospholipid. The polyamine pattern contained predominantly sym-homospermidine. Characterization by 16S rRNA gene sequencing, physiological parameters and polyamine, ubiquinone, polar lipid and fatty acid compositions revealed that strain JM-1070T represents a novel species of the genus Mucilaginibacter . For this reason, we propose the name Mucilaginibacter auburnensis sp. nov., with the type strain JM-1070T ( = CIP 110694T = LMG 28078T).


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