scholarly journals Pantanalinema gen. nov. and Alkalinema gen. nov.: novel pseudanabaenacean genera (Cyanobacteria) isolated from saline–alkaline lakes

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 298-308 ◽  
Author(s):  
Marcelo Gomes Marçal Vieira Vaz ◽  
Diego Bonaldo Genuário ◽  
Ana Paula Dini Andreote ◽  
Camila Francieli Silva Malone ◽  
Célia Leite Sant’Anna ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Reconstruction ◽  
Intergenic Spacer ◽  
Gliding Motility ◽  
23S Rrna ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Code Of Nomenclature ◽  
Group B

The genus Leptolyngbya Anagnostidis & Komárek (1988) was described from a set of strains identified as ‘LPP-group B’. The morphology within this group is not particularly informative and underestimates the group’s genetic diversity. In the present study, two new pseudanabaenacean genera related to Leptolyngbya morphotypes, Pantanalinema gen. nov. and Alkalinema gen. nov., are described under the provisions of the International Code of Nomenclature for Algae, Fungi and Plants, based on a polyphasic approach. Pantanalinema gen. nov. (type species Pantanalinema rosaneae sp. nov.) has sheaths and trichomes with slight gliding motility, which distinguish this genus from Alkalinema gen. nov. (type species Alkalinema pantanalense sp. nov.), which possesses trichomes arranged in an ornate (interwoven) pattern. 16S rRNA gene sequences of strains of Pantanalinema and Alkalinema exhibited low identity to each other (≤91.6 %) and to other sequences from known pseudanabaenacean genera (≤94.3 and 93.7 %, respectively). In a phylogenetic reconstruction, six sequences from strains of Pantanalinema and four from strains of Alkalinema formed two separate and robust clades (99 % bootstrap value), with the genera Oculatella and Phormidesmis, respectively, as the closest related groups. 16S–23S rRNA intergenic spacer sequences and secondary structures of strains of Pantanalinema and Alkalinema did not correspond to any previous descriptions. The strains of Pantanalinema and Alkalinema were able to survive and produce biomass at a range of pH (pH 4–11) and were also able to alter the culture medium to pH values ranging from pH 8.4 to 9.9. These data indicate that cyanobacterial communities in underexplored environments, such as the Pantanal wetlands, are promising sources of novel taxa.

scholarly journals Bradyrhizobium erythrophlei sp. nov. and Bradyrhizobium ferriligni sp. nov., isolated from effective nodules of Erythrophleum fordii

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1831-1837 ◽  
Author(s):  
Yao Yao ◽  
Xin Hua Sui ◽  
Xiao Xia Zhang ◽  
En Tao Wang ◽  
Wen Xn Chen
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Intergenic Spacer ◽  
23S Rrna ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Erythrophleum Fordii ◽  
Slow Growing

Six slow-growing rhizobial strains isolated from effective nodules of Erythrophleum fordii were classified into the genus Bradyrhizobium based on their 16S rRNA gene sequences. The results of multilocus sequence analysis of recA, glnII and gyrB genes and 16S–23S rRNA intergenic spacer (IGS) sequence phylogeny indicated that the six strains belonged to two novel species, represented by CCBAU 53325T and CCBAU 51502T, which were consistent with the results of DNA–DNA hybridization; CCBAU 53325T had 17.65–25.59 % relatedness and CCBAU 51502T had 22.69–44.58 % relatedness with five closely related type strains, Bradyrhizobium elkanii USDA 76T, B. pachyrhizi LMG 24246T, B. lablabi CCBAU 23086T, B. jicamae LMG 24556T and B. japonicum USDA 6T. In addition, analysis of phenotypic characteristics and fatty acid profiles also distinguished the test strains from defined species of Bradyrhizobium . Two novel species, Bradyrhizobium erythrophlei sp. nov., represented by the type strain CCBAU 53325T ( = HAMBI 3614T = CGMCC 1.13002T = LMG 28425T), and Bradyrhizobium ferriligni sp. nov., represented by the type strain CCBAU 51502T ( = HAMBI 3613T = CGMCC 1.13001T), are proposed to accommodate the strains.

scholarly journals Leuconostoc mesenteroides subsp. suionicum subsp. nov.

2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1548-1551 ◽  
Author(s):  
Chun Tao Gu ◽  
Fang Wang ◽  
Chun Yan Li ◽  
Fei Liu ◽  
Gui Cheng Huo
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Leuconostoc Mesenteroides ◽  
Sequence Similarity ◽  
Intergenic Spacer ◽  
23S Rrna ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Strains LMG 8159 and LMG 11499 were reclassified by a polyphasic approach, including 16S rRNA gene sequence analysis, 16S–23S rRNA intergenic spacer (IGS) sequence analysis, (GTG)5-PCR fingerprinting, RAPD fingerprinting, fatty acid methyl ester analysis and an analysis of phenotypic features using API 50 CH. The two strains were closely related to the type strains of the three defined subspecies of Leuconostoc mesenteroides , showing 99.7–99.9 % 16S rRNA gene sequence similarity, 99.2 % 16S–23S rRNA gene intergenic spacer sequence similarity, 97.1–97.4 % pheS gene sequence similarity and 98.0–98.2 % rpoA gene sequence similarity. Low atpA gene sequence similarity (91.4–91.7 %), (GTG)5-PCR fingerprinting, RAPD fingerprinting, fatty acid compositions and phenotypic features allowed us to differentiate strains LMG 8159 and LMG 11499 from all established subspecies within L. mesenteroides . Based upon the data obtained in the present and previous studies, a novel subspecies is proposed within the species L. mesenteroides , Leuconostoc mesenteroides subsp. suionicum subsp. nov., with the type strain LMG 8159T ( = ATCC 9135T  = DSM 20241T  = NCIMB 6992T).

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.

Xenorhabdus lircayensis sp. nov., the symbiotic bacterium associated with the entomopathogenic nematode Steinernema unicornum

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Carlos Castaneda-Alvarez ◽  
Simona Prodan ◽  
Alan Zamorano ◽  
Ernesto San-Blas ◽  
Erwin Aballay
Keyword(s):  
New Species ◽  
Type Species ◽  
Entomopathogenic Nematode ◽  
Phylogenetic Reconstruction ◽  
Symbiotic Bacterium ◽  
Rrna Gene ◽  
Species List ◽  
Content Type ◽  
Link Type ◽  
Bacterium Strain

Xenorhabdus is a symbiotic group of bacteria associated with entomopathogenic nematodes of the family Steinernematidae. Although the described Steirnernema species list is extensive, not all their symbiotic bacteria have been identified. One single motile, Gram-negative and non-spore-forming rod-shaped symbiotic bacterium, strain VLST, was isolated from the entomopathogenic nematode Steinernema unicornum. Analyses of the 16S rRNA gene determined that the VLST isolate belongs to the genus Xenorhabdus , and its closest related species is Xenorhabdus szentirmaii DSM 16338T (98.2 %). Deeper analyses using the whole genome for phylogenetic reconstruction indicate that VLST exhibits a unique clade in the genus. Genomic comparisons considering digital DNA–DNA hybridization (dDDH) values confirms this result, showing that the VLST values are distant enough from the 70 % threshold suggested for new species, sharing 30.7, 30.5 and 30.3 % dDDH with Xenorhabdus khoisanae MCB, Xenorhabdus koppenhoeferi DSM 18168T and Xenorhabdus miraniensis DSM 18168T, respectively, as the closest species. Detailed physiological, biochemical and chemotaxonomic tests of the VLST isolate reveal consistent differences from previously described Xenorhabdus species. Phylogenetic, physiological, biochemical and chemotaxonomic approaches show that VLST represents a new species of the genus Xenorhabdus , for which the name Xenorhabdus lircayensis sp. nov. (type strain VLST=CCCT 20.04T=DSM 111583T) is proposed.

scholarly journals Neisseria oralis sp. nov., isolated from healthy gingival plaque and clinical samples

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1323-1328 ◽  
Author(s):  
William J. Wolfgang ◽  
Teresa V. Passaretti ◽  
Reashma Jose ◽  
Jocelyn Cole ◽  
An Coorevits ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
23S Rrna ◽  
Clinical Samples ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Link Type

A polyphasic analysis was undertaken of seven independent isolates of Gram-negative cocci collected from pathological clinical samples from New York, Louisiana, Florida and Illinois and healthy subgingival plaque from a patient in Virginia, USA. The 16S rRNA gene sequence similarity among these isolates was 99.7–100 %, and the closest species with a validly published name was Neisseria lactamica (96.9 % similarity to the type strain). DNA–DNA hybridization confirmed that these isolates are of the same species and are distinct from their nearest phylogenetic neighbour, N. lactamica . Phylogenetic analysis of 16S and 23S rRNA gene sequences indicated that the novel species belongs in the genus Neisseria . The predominant cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C18 : 1ω7c. The cellular fatty acid profile, together with other phenotypic characters, further supports the inclusion of the novel species in the genus Neisseria . The name Neisseria oralis sp. nov. (type strain 6332T  = DSM 25276T  = LMG 26725T) is proposed.

scholarly journals Genome sequence analyses show that Neisseria oralis is the same species as ‘ Neisseria mucosa var. heidelbergensis’

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3920-3926 ◽  
Author(s):  
Julia S. Bennett ◽  
Keith A. Jolley ◽  
Martin C. J. Maiden
Keyword(s):  
Genome Sequence ◽  
Type Species ◽  
Whole Genome Sequence ◽  
23S Rrna ◽  
Rrna Gene ◽  
Whole Genome ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Neisseria Mucosa

Phylogenies generated from whole genome sequence (WGS) data provide definitive means of bacterial isolate characterization for typing and taxonomy. The species status of strains recently defined with conventional taxonomic approaches as representing Neisseria oralis was examined by the analysis of sequences derived from WGS data, specifically: (i) 53 Neisseria ribosomal protein subunit (rps) genes (ribosomal multi-locus sequence typing, rMLST); and (ii) 246 Neisseria core genes (core genome MLST, cgMLST). These data were compared with phylogenies derived from 16S and 23S rRNA gene sequences, demonstrating that the N. oralis strains were monophyletic with strains described previously as representing ‘ Neisseria mucosa var. heidelbergensis’ and that this group was of equivalent taxonomic status to other well-described species of the genus Neisseria . Phylogenetic analyses also indicated that Neisseria sicca and Neisseria macacae should be considered the same species as Neisseria mucosa and that Neisseria flavescens should be considered the same species as Neisseria subflava . Analyses using rMLST showed that some strains currently defined as belonging to the genus Neisseria were more closely related to species belonging to other genera within the family; however, whole genome analysis of a more comprehensive selection of strains from within the family Neisseriaceae would be necessary to confirm this. We suggest that strains previously identified as representing ‘ N. mucosa var. heidelbergensis’ and deposited in culture collections should be renamed N. oralis . Finally, one of the strains of N. oralis was able to ferment lactose, due to the presence of β-galactosidase and lactose permease genes, a characteristic previously thought to be unique to Neisseria lactamica , which therefore cannot be thought of as diagnostic for this species; however, the rMLST and cgMLST analyses confirm that N. oralis is most closely related to N. mucosa .

scholarly journals Mycoplasma anserisalpingitidis sp. nov., isolated from European domestic geese (Anser anser domesticus) with reproductive pathology

2020 ◽  
Vol 70 (4) ◽  
pp. 2369-2381 ◽  
Author(s):  
Dmitriy V. Volokhov ◽  
Dénes Grózner ◽  
Miklós Gyuranecz ◽  
Naola Ferguson-Noel ◽  
Yamei Gao ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

In 1983, Mycoplasma sp. strain 1220 was isolated in Hungary from the phallus lymph of a gander with phallus inflammation. Between 1983 and 2017, Mycoplasma sp. 1220 was also identified and isolated from the respiratory tract, liver, ovary, testis, peritoneum and cloaca of diseased geese in several countries. Seventeen studied strains produced acid from glucose and fructose but did not hydrolyse arginine or urea, and all grew under aerobic, microaerophilic and anaerobic conditions at 35 to 37 ˚C in either SP4 or pleuropneumonia-like organism medium supplemented with glucose and serum. Colonies on agar showed a typical fried-egg appearance and transmission electron microscopy revealed a typical mycoplasma cellular morphology. Molecular characterization included analysis of the following genetic loci: 16S rRNA, 23S rRNA, 16S–23S rRNA ITS, rpoB, rpoC, rpoD, uvrA, parC, topA, dnaE, fusA and pyk. The genome was sequenced for type strain 1220T. The 16S rRNA gene sequences of studied strains of Mycoplasma sp. 1220 shared 99.02–99.19 % nucleotide similarity with M. anatis strains but demonstrated ≤95.00–96.70 % nucleotide similarity to the 16S rRNA genes of other species of the genus Mycoplasma . Phylogenetic, average nucleotide and amino acid identity analyses revealed that the novel species was most closely related to Mycoplasma anatis . Based on the genetic data, we propose a novel species of the genus Mycoplasma , for which the name Mycoplasma anserisalpingitidis sp. nov. is proposed with the type strain 1220T (=ATCC BAA-2147T=NCTC 13513T=DSM 23982T). The G+C content is 26.70 mol%, genome size is 959110 bp.

Flavobacterium ummariense sp. nov., isolated from hexachlorocyclohexane-contaminated soil, and emended description of Flavobacterium ceti Vela et al. 2007

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2674-2679 ◽  
Author(s):  
Pushp Lata ◽  
Devi Lal ◽  
Rup Lal
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Contaminated Soil ◽  
Type Species ◽  
Gliding Motility ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type ◽  
Emended Description

A Gram-negative, strictly aerobic, yellow bacterial strain, designated DS-12T, was isolated from hexachlorocyclohexane-contaminated soil in Lucknow, Uttar Pradesh, India. Strain DS-12T showed the highest 16S rRNA gene sequence similarity with Flavobacterium ceti 454-2T (94.2 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-12T belonged to the genus Flavobacterium . Strain DS-12T produced flexirubin-type pigments. Gliding motility was not observed. The major fatty acids of strain DS-12T were iso-C15 : 0 (48.0 %), summed feature 9 (comprising iso-C17 : 1ω9c and/or C16 : 0 10-methyl; 19.3 %), iso-C17 : 0 3-OH (8.5 %) and summed feature 3 (comprising one or more of C16 : 1ω7c, C16 : 1ω6c and iso-C15 : 0 2-OH; 7.2 %). The only respiratory quinone was menaquinone-6 and the major polyamine was homospermidine. Strain DS-12T contained phosphatidyldimethylethanolamine, phosphatidylserine, phosphatidylethanolamine, one unknown phospholipid and one unknown aminolipid. The DNA G+C content was 37.4 mol%. Phylogenetic inference and phenotypic properties indicated that strain DS-12T represents a novel species of the genus Flavobacterium , for which the name Flavobacterium ummariense sp. nov. is proposed. The type strain is DS-12T ( = CCM 7847T  = MTCC 10766T). An emended description of Flavobacterium ceti is also given.

Streptococcus dentisani sp. nov., a novel member of the mitis group

2014 ◽  
Vol 64 (Pt_1) ◽  
pp. 60-65 ◽  
Author(s):  
Anny Camelo-Castillo ◽  
Alfonso Benítez-Páez ◽  
Pedro Belda-Ferre ◽  
Raúl Cabrera-Rubio ◽  
Alex Mira
Keyword(s):  
Type Species ◽  
Spherical Shape ◽  
Culture Collection ◽  
23S Rrna ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
23S Rrna Gene ◽  
Tooth Surfaces ◽  
Streptococcal Species

Genomic, taxonomic and biochemical studies were performed on two strains of α-haemolytic streptococci that showed them to be clustered with major members of the Streptococcus mitis group. These Gram-stain-positive strains were isolated from tooth surfaces of caries-free humans and showed the classical spherical shape of streptococcal species growing in chains. Sequence analysis from concatenated 16S and 23S rRNA gene and sodA genes showed that these strains belonged to the mitis group, but both of them clustered into a new phylogenetic branch. The genomes of these two isolates were sequenced, and whole-genome average nucleotide identity (ANI) demonstrated that these strains significantly differed from any streptococcal species, showing ANI values under 91 % even when compared with the phylogenetically closest species such as Streptococcus oralis and S. mitis . Biochemically, the two isolates also showed distinct metabolic features relative to closely related species, like α-galactosidase activity. From the results of the present study, the name Streptococcus dentisani sp. nov. is proposed to accommodate these novel strains, which have been deposited in open collections at the Spanish type Culture Collection (CECT) and Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures (DSMZ), being respectively identified as Streptococcus dentisani Str. 7746 ( = CECT 8313 = DSM 27089) and Streptococcus dentisani Str. 7747T ( = CECT 8312T = DSM 27088T).

Epibacterium ulvae gen. nov., sp. nov., epibiotic bacteria isolated from the surface of a marine alga

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1589-1596 ◽  
Author(s):  
Anahit Penesyan ◽  
Sven Breider ◽  
Peter Schumann ◽  
Brian J. Tindall ◽  
Suhelen Egan ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Marine Alga ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

Two Gram-reaction-negative, rod-shaped, motile bacteria, designated strains U82 and U95T, were isolated from the marine alga Ulva australis collected at Sharks Point, Clovelly, a rocky intertidal zone near Sydney, Australia. Both strains were oxidase- and catalase-positive, formed brown- to black-pigmented colonies and required NaCl for growth. Phylogenetic analysis based on nearly complete 16S rRNA gene sequences revealed that these strains belong to the Roseobacter clade within the Alphaproteobacteria . The 16S rRNA genes of both strains were identical across the sequenced 1326 nt, but showed differences in the intergenic spacer region (ITS) between the 16S and the 23S rRNA genes. At the genomic level the DNA G+C contents of strains U82 and U95T were identical (52.6 mol%) and they had a DNA–DNA hybridization value of 83.7 %, suggesting that these strains belong to the same species. The closest described phylogenetic neighbour to strains U82 and U95T was Thalassobius aestuarii DSM 15283T with 95.8 % 16S rRNA gene sequence similarity. Other close relatives include further species of the genera Thalassobius and Shimia . Strains U82 and U95T were negative for bacteriochlorophyll a production, showed antibacterial activity towards other marine bacteria, were resistant to the antibiotics gentamicin and spectinomycin and were unable to hydrolyse starch or gelatin. The major fatty acids (>1 %) were 18 : 1ω7c, 16 : 0, 18 : 2, 10 : 0 3-OH, 12 : 0, 20 : 1 2-OH and 18 : 0. The polar lipid pattern indicated the presence of phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids and four unidentified phospholipids. Both strains produced ubiquinone 10 (Q-10) as the sole respiratory lipoquinone. Based on their phenotypic and phylogenetic characteristics, it is suggested that strains U82 and U95T are members of a novel species within a new genus for which the name Epibacterium ulvae gen. nov., sp. nov. is proposed. The type strain of the type species is U95T ( = DSM 24752T = LMG 26464T).

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