scholarly journals Genome Analysis of Endobacterium cerealis, a Novel Genus and Species Isolated from Zea mays Roots in North Spain

2020 ◽  
Vol 8 (6) ◽  
pp. 939
Author(s):  
Esther Menéndez ◽  
Jose David Flores-Félix ◽  
Martha Helena Ramírez-Bahena ◽  
Jose M. Igual ◽  
Paula García-Fraile ◽  
...  
Keyword(s):  
Zea Mays ◽  
Phylogenetic Analyses ◽  
Hydrolytic Enzymes ◽  
Plant Colonization ◽  
Rrna Gene ◽  
Novel Genus ◽  
Phenotypic Differences ◽  
Novel Genus And Species ◽  
Definition Of ◽  
Type Strains

In the present work, we analyse the genomic and phenotypic characteristics of a strain named RZME27T isolated from roots of a Zea mays plant grown in Spain. The phylogenetic analyses of 16S rRNA gene and whole genome sequences showed that the strain RZME27T clustered with the type strains of Neorhizobium galegae and Pseudorhizobium pelagicum from the family Rhizobiaceae. This family encompasses several genera establishing symbiosis with legumes, but the genes involved in nodulation and nitrogen fixation are absent in its genome. Nevertheless, genes related to plant colonization, such as those involved in motility, chemotaxis, quorum sensing, exopolysaccharide biosynthesis and hydrolytic enzymes production were found. The comparative pangenomic analyses showed that 78 protein clusters present in the strain RZME27T were not found in the type strains of its closest relatives N. galegae and P. pelagicum. The calculated average nucleotide identity (ANI) values between the strain RZME27T and the type strains of N. galegae and P. pelagicum were 75.61% and 75.1%, respectively, similar or lower than those found for other genera from family Rhizobiaceae. Several phenotypic differences were also found, highlighting the absence of the fatty acid C19:0 cyclo ω8c and propionate assimilation. These results support the definition of a novel genus and species named Endobacterium cerealis gen. nov. sp. nov. whose type strain is RZME27T.

scholarly journals Flavicella marina gen. nov., sp. nov., a carotenoid-producing bacterium from surface seawater

2015 ◽  
Vol 65 (Pt_3) ◽  
pp. 799-804 ◽  
Author(s):  
Maki Teramoto ◽  
Miyuki Nishijima
Keyword(s):  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Surface Seawater ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Novel Genus And Species ◽  
Bacterium Strain ◽  
Kochi Prefecture ◽  
Type Strains

A Gram-stain-negative, non-motile, mesophilic, aerobic, rod-shaped or spherical bacterium, strain 2A-7T, was isolated from surface seawater at Muroto city, Kochi prefecture, Japan. The strain produced a pigment(s), the absorption spectrum of which closely resembled that of β-carotene. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain fell within the family Flavobacteriaceae and clustered distantly with the type strains of species of the genus Lutibacter (up to 93.9 % similarity). The DNA G+C content was 34.1 mol%. The major fatty acids were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The major polar lipids were phosphatidylethanolamine and three unidentified lipids. Menaquinone 6 was detected as the sole isoprenoid quinone. On the basis of phenotypic, genotypic and chemotaxonomic data, strain 2A-7T represents a novel genus and species, for which the name Flavicella marina gen. nov., sp. nov. is proposed. The type strain of Flavicella marina is 2A-7T ( = NBRC 110145T = KCTC 42197T).

scholarly journals Puniceicoccus vermicola gen. nov., sp. nov., a novel marine bacterium, and description of Puniceicoccaceae fam. nov., Puniceicoccales ord. nov., Opitutaceae fam. nov., Opitutales ord. nov. and Opitutae classis nov. in the phylum ‘Verrucomicrobia’

2007 ◽  
Vol 57 (3) ◽  
pp. 532-537 ◽  
Author(s):  
Yoe-Jin Choo ◽  
Kiyoung Lee ◽  
Jaeho Song ◽  
Jang-Cheon Cho
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Novel Genus ◽  
Marine Isolate ◽  
Novel Genus And Species

A Gram-negative, chemoheterotrophic, facultatively anaerobic coccus, designated IMCC1545T, was isolated from the digestive tract of a marine clamworm, Periserrula leucophryna, inhabiting a tidal flat of the Yellow Sea. Cells of strain IMCC1545T are non-motile, dividing by binary fission. The predominant fatty acids are anteiso-C15 : 0 and C18 : 0. The respiratory quinone is menaquinone-7 and the DNA G+C content is 52.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences using three treeing algorithms revealed that the strain formed a novel genus-level lineage within the phylum ‘Verrucomicrobia’. The most closely related named organisms to strain IMCC1545T are ‘Fucophilus fucoidanolyticus’ SI-1234 (86.5 % 16S rRNA gene sequence similarity), Alterococcus agarolyticus ADT3T (81.8 %) and Opitutus terrae PB90-1T (80.3 %), which belong to subdivision 4 of the ‘Verrucomicrobia’. Subdivision 4 of the ‘Verrucomicrobia’ (here named Opitutae classis nov.) was divided into two clades, a clade containing strain IMCC1545T and a clade containing Opitutus terrae. From the taxonomic data obtained in this study, it is proposed that the new marine isolate be placed into a novel genus and species named Puniceicoccus vermicola gen. nov., sp. nov. (the type strain of Puniceicoccus vermicola is IMCC1545T=KCCM 42343T=NBRC 101964T) within Puniceicoccaceae fam. nov and Puniceicoccales ord. nov in the class Opitutae. The family Opitutaceae fam. nov. and order Opitutales ord. nov. are also formally proposed.

scholarly journals Demequina aestuarii gen. nov., sp. nov., a novel actinomycete of the suborder Micrococcineae, and reclassification of Cellulomonas fermentans Bagnara et al. 1985 as Actinotalea fermentans gen. nov., comb. nov.

2007 ◽  
Vol 57 (1) ◽  
pp. 151-156 ◽  
Author(s):  
Hana Yi ◽  
Peter Schumann ◽  
Jongsik Chun
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Novel Genus ◽  
Novel Genus And Species

An actinobacterial strain containing demethylmenaquinone DMK-9(H4) as the diagnostic isoprenoid quinone was isolated from a tidal flat sediment sample, from South Korea. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain JC2054T represents a distinct phyletic line within the suborder Micrococcineae of the order Actinomycetales. The closest phylogenetic neighbour was Cellulomonas fermentans, with 94.7 % 16S rRNA gene sequence similarity. The novel isolate was strictly aerobic and slightly halophilic, with optimum growth occurring in 2–4 % (w/v) NaCl. Cells were non-motile, non-sporulating and rod-shaped. The peptidoglycan type was of the A-type of cross-linkage. l-ornithine was the diamino acid and d-glutamate represented the N-terminus of the interpeptide bridge. The predominant fatty acids were anteiso-branched and straight-chain fatty acids. The major polar lipids were phosphatidylinositol, diphosphatidylglycerol and an unknown phospholipid. The menaquinone composition of C. fermentans was determined to be MK-10(H4), MK-9(H4) and MK-8(H4) in the ratio 56 : 2 : 1. On the basis of the polyphasic evidence presented in this study, it is proposed that strain JC2054T should be classified as representing a novel genus and species of the suborder Micrococcineae, with the name Demequina aestuarii gen. nov., sp. nov. The type strain is JC2054T (=IMSNU 14027T=KCTC 9919T=JCM 12123T). In addition, it was clear from the phylogenetic analysis and chemotaxonomic data that C. fermentans does not belong to the genus Cellulomonas or any other recognized genera. Therefore, C. fermentans should be reclassified as representing a novel genus, for which the name Actinotalea fermentans gen. nov., comb. nov. is proposed, with strain DSM 3133T (=ATCC 43279T=CFBP 4259T=CIP 103003T=NBRC 15517T=JCM 9966T=LMG 16154T) as the type strain.

scholarly journals Mariniflexile gromovii gen. nov., sp. nov., a gliding bacterium isolated from the sea urchin Strongylocentrotus intermedius

2006 ◽  
Vol 56 (7) ◽  
pp. 1635-1638 ◽  
Author(s):  
Olga I. Nedashkovskaya ◽  
Seung Bum Kim ◽  
Jangryul Kwak ◽  
Valery V. Mikhailov ◽  
Kyung Sook Bae
Keyword(s):  
Phylogenetic Analyses ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Novel Genus And Species ◽  
Respective Type ◽  
Gliding Bacterium ◽  
Type Strains ◽  
Sequence Similarities

A marine bacterium, designated strain KMM 6038T, was subjected to taxonomic analysis via a polyphasic approach. Cells of the strain were heterotrophic, orange-pigmented, Gram-negative and motile by means of gliding. 16S rRNA gene sequence analysis indicated that strain KMM 6038T was closely related to the type species of the genera Algibacter and Yeosuana, members of the family Flavobacteriaceae, with sequence similarities of 93.8 and 93.6 % to the respective type strains. However, several chemotaxonomic and phenotypic characteristics, such as the cellular fatty acid profile (iso-C15 : 0, anteiso-C15 : 0, iso-C15 : 1, C15 : 0, C15 : 1 ω6c, iso-C15 : 0 3-OH and iso-C17 : 0 3-OH) and the low G+C content of the DNA (35.7 mol%), indicated that the strain should be separated from these two genera. From the results of phenotypic, genotypic, chemotaxonomic and phylogenetic analyses, the bacterium should be classified as representing a novel genus and species, for which the name Mariniflexile gromovii gen. nov., sp. nov. is proposed. The type strain of Mariniflexile gromovii is KMM 6038T (=KCTC 12570T=LMG 22578T).

scholarly journals Litoricolaceae fam. nov., to include Litoricola lipolytica gen. nov., sp. nov., a marine bacterium belonging to the order Oceanospirillales

2007 ◽  
Vol 57 (8) ◽  
pp. 1793-1798 ◽  
Author(s):  
Hana Kim ◽  
Yoe-Jin Choo ◽  
Jang-Cheon Cho
Keyword(s):  
Sequence Data ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Novel Genus ◽  
New Family ◽  
Novel Genus And Species ◽  
Marine Strain ◽  
Distinct Phylogenetic Lineage ◽  
Sequence Similarities

A Gram-negative, non-motile, chemoheterotrophic, facultatively aerobic, short-rod-shaped bacterium, designated IMCC1097T, was isolated from coastal seawater (10 m depth) of the East Sea, Korea. The temperature, pH and NaCl ranges for growth were 15–30 °C, pH 5.0–10.0 and 1.5–10 % NaCl. The colonies of the strain were very small, having a mean diameter of 0.05 mm. 16S rRNA gene sequence data indicated that the strain was most closely related to genera within the class Gammaproteobacteria. Members of the most closely related genera showed less than 90 % sequence similarity and included Saccharospirillum (89.3 %), Oleiphilus (88.7 %), Reinekea (88.2 %), Alcanivorax (86.4–87.6 %) and Zooshikella (87.6 %), which represent five different families of the order Oceanospirillales. Phylogenetic analyses showed that this marine strain represented a distinct phylogenetic lineage in the order Oceanospirillales and could not be assigned to any of the defined families in the order. The predominant fatty acids were C16 : 1 ω7c and/or iso-C15 : 0 2-OH, C18 : 1 ω7c and C10 : 0 3-OH, and the DNA G+C content was 57.9 mol%. These chemotaxonomic properties, together with phenotypic characteristics, served to differentiate the strain from phylogenetically closely related genera. The very low sequence similarities (<90 %) and distant relationships between IMCC1097T and members of the order Oceanospirillales suggested that the strain merited classification within a novel genus within a novel family in the order. On the basis of taxonomic evidence collected in this study, a novel genus and species are proposed, Litoricola lipolytica gen. nov., sp. nov., within a new family Litoricolaceae fam. nov. Strain IMCC1097T (=KCCM 42360T =NBRC 102074T) is the type strain of Litoricola lipolytica.

Flavobacterium akiainvivens sp. nov., from decaying wood of Wikstroemia oahuensis, Hawai‘i, and emended description of the genus Flavobacterium

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3280-3286 ◽  
Author(s):  
Iris Kuo ◽  
Jimmy Saw ◽  
Durrell D. Kapan ◽  
Stephanie Christensen ◽  
Kenneth Y. Kaneshiro ◽  
...  
Keyword(s):  
Type Species ◽  
Original Description ◽  
Gliding Motility ◽  
Rrna Gene ◽  
Content Type ◽  
Phenotypic Differences ◽  
Whole Cells ◽  
Link Type ◽  
Decaying Wood ◽  
Type Strains

Strain IK-1T was isolated from decaying tissues of the shrub Wikstroemia oahuensis collected on O‘ahu, Hawai‘i. Cells were rods that stained Gram-negative. Gliding motility was not observed. The strain was oxidase-negative and catalase-positive. Zeaxanthin was the major carotenoid. Flexirubin-type pigments were not detected. The most abundant fatty acids in whole cells of IK-1T grown on R2A were iso-C15 : 0 and one or both of C16 : 1ω7c and C16 : 1ω6c. Based on comparisons of the nucleotide sequence of the 16S rRNA gene, the closest neighbouring type strains were Flavobacterium rivuli WB 3.3-2T and Flavobacterium subsaxonicum WB 4.1-42T, with which IK-1T shares 93.84 and 93.67 % identity, respectively. The G+C content of the genomic DNA was 44.2 mol%. On the basis of distance from its nearest phylogenetic neighbours and phenotypic differences, the species Flavobacterium akiainvivens sp. nov. is proposed to accommodate strain IK-1T ( = ATCC BAA-2412T = CIP 110358T) as the type strain. The description of the genus Flavobacterium is emended to reflect the DNA G+C contents of Flavobacterium akiainvivens IK-1T and other species of the genus Flavobacterium described since the original description of the genus.

Novosphingobium decolorationis sp. nov., an aniline blue-decolourizing bacterium isolated from East Pacific sediment

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Xiunuan Chen ◽  
Bingxia Dong ◽  
Ting Chen ◽  
Na Ren ◽  
Jing Wang ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Cellular Fatty Acid ◽  
Aniline Blue ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
East Pacific ◽  
Type Strains

Aniline blue-decolourizing bacterial strain 502str22T, isolated from sediment collected in the East Pacific, was subjected to characterization by a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain 502str22T belongs to the genus Novosphingobium , with closely related type strains ‘ Novosphingobium profundi ’ F72T (97.6%), N. mathurense SM117T (97.1%) and N. arvoryzae Jyi-02T (97.0%). Digital DNA–DNA hybridization and average nucleotide identity values between strain 502str22T and closely related type strains were 20.3–24.8% and 74.1–81.9%, respectively. The major cellular fatty acid (>10%) was C18:1 ω7c. The polar lipid profile consisted of a mixture of phosphatidylcholine, one sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylethanolamine. The DNA G+C content of strain 502str22T was 65.5 mol%. The polyphasic taxonomic results indicated that strain 502str22T represents a novel species of the genus Novosphingobium , for which the name Novosphingobium decolorationis sp. nov is proposed. The type strain is 502str22T (=KCTC 82134T= MCCC 1K04799 T).

Namhaeicola litoreus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from seawater

2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2163-2168 ◽  
Author(s):  
Yong-Taek Jung ◽  
Ji-Hoon Kim ◽  
So-Jung Kang ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Type Strains

A Gram-staining-negative, non-flagellated, non-gliding and pleomorphic bacterial strain, designated DPG-25T, was isolated from seawater in a seaweed farm in the South Sea in Korea and its taxonomic position was investigated by using a polyphasic approach. Strain DPG-25T grew optimally at 25 °C, at pH 7.0–7.5 and in the presence of 2 % (w/v) NaCl. Flexirubin-type pigments were not produced. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DPG-25T formed a cluster with the type strains of Actibacter sediminis , Aestuariicola saemankumensis and Lutimonas vermicola . Strain DPG-25T exhibited 16S rRNA gene sequence similarity values of 95.3, 93.1 and 93.6 % to the type strains of Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola , respectively. Strain DPG-25T contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain DPG-25T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content was 39.9 mol%. Differential phenotypic properties and the phylogenetic distinctiveness of strain DPG-25T demonstrated that this strain is distinguishable from Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola . On the basis of the data presented here, strain DPG-25T represents a novel species in a novel genus of the family Flavobacteriaceae , for which the name Namhaeicola litoreus gen. nov., sp. nov. is proposed. The type strain of Namhaeicola litoreus is DPG-25T ( = KCTC 23702T  = CCUG 61485T).

scholarly journals Amycolatopsis xylanica sp. nov., isolated from soil

2010 ◽  
Vol 60 (9) ◽  
pp. 2124-2128 ◽  
Author(s):  
Jie Chen ◽  
Jin-Jin Su ◽  
Yu-Zhen Wei ◽  
Qiu-Ping Li ◽  
Li-Yan Yu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Taxonomic Status ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Qinghai Province ◽  
Phenotypic Differences ◽  
Separate Branch ◽  
Type Strains ◽  
Sequence Similarities

An actinomycete, designated CPCC 202699T, was isolated from soil in Qinghai province, China, and its taxonomic status was established. Strain CPCC 202699T contained meso-diaminopimelic acid in its peptidoglycan, arabinose and galactose as the diagnostic sugars in whole-cell hydrolysates, a phospholipid pattern consisting mainly of phosphatidylethanolamine, phosphatidylmethylethanolamine and phosphatidylcholine, MK-9(H4) as the predominant menaquinone and iso-C16 : 0 (18.8 %), iso-C15 : 0 (18.1 %), iso-C14 : 0 (14.2 %), C16 : 1 cis9 (10.9 %) and C17 : 1 cis9 (10.3 %) as the major fatty acids. In the phylogenetic tree based on 16S rRNA gene sequences, strain CPCC 202699T formed a separate branch within the genus Amycolatopsis. However, strain CPCC 202699T showed low 16S rRNA gene sequence similarities (<97.0 %) with type strains of species with validly published names in the genus Amycolatopsis. On the basis of genotypic and phenotypic differences from the closest phylogenetic neighbours of strain CPCC 202699T, a novel species, Amycolatopsis xylanica sp. nov., is proposed. The type strain is CPCC 202699T (=DSM 45285T =KCTC 19581T =CCM 7627T).

Aestuariisphingobium litorale Li et al. 2020 is a later heterotypic synonym of Chakrabartia godavariana Jani et al. 2019

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Peng Wang ◽  
Yuxin Gao
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Single Species ◽  
Rrna Gene ◽  
Genomic Comparison ◽  
Content Type ◽  
Link Type ◽  
Type Strains

Chakrabartia godavariana PRB40T was compared with Aestuariisphingobium litorale SYSU M10002T to examine the taxonomic relationship between the two type strains. The 16S rRNA gene sequence of C. godavariana PRB40T had high similarity (99.8 %) to that of A. litorale SYSU M10002T. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the two strains formed a tight cluster within the genus Chakrabartia . A draft genomic comparison between the two strains revealed an average nucleotide identity of 97.3 % and a digital DNA–DNA hybridization estimate of 79.5±2.9 %, strongly indicating that the two strains represented a single species. In addition, neither strain displayed any striking differences in metabolic, physiological or chemotaxonomic features. Therefore, we propose that Aestuariisphingobium litorale is a later heterotypic synonym of Chakrabartia godavariana .

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