Polynucleobacter sp. SHI2
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB15085 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| DRR428553_subreads.fastq.gz | Fastqsanger.gz | |||
| DRR428554_subreads.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 3 of 3 |
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Project description:Polynucleobacter sp. subcluster PnecC bacterioplankton isolate genome sequencing and assembly
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Project description:Polynucleobacter sp. subcluster PnecB bacterioplankton isolates genome sequencing and assembly
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Project description:Genome comparisons based on average nucleotide identity (ANI) values of four strains currently classified as Polynucleobacter necessarius subsp. asymbioticus resulted in ANI values of 75.7-78.4 %, suggesting that each of those strains represents a separate species. The species P. necessarius was proposed by Heckmann and Schmidt in 1987 to accommodate obligate endosymbionts of ciliates affiliated with the genus Euplotes. The required revision of this species is, however, hampered by the fact, that this species is based only on a description and lacks a type strain available as pure culture. Furthermore, the ciliate culture Euplotes aediculatus ATCC 30859, on which the description of the species was based, is no longer available. We found another Euplotes aediculatus culture (Ammermann) sharing the same origin with ATCC 30859 and proved the identity of the endosymbionts contained in the two cultures. A multilocus sequence comparison approach was used to estimate if the four strains currently classified as Polynucleobacternecessarius subsp. asymbioticus share ANI values with the endosymbiont in the Ammermann culture above or below the threshold for species demarcation. A significant correlation (R2 0.98, P<0.0001) between multilocus sequence similarity and ANI values of genome-sequenced strains enabled the prediction that it is highly unlikely that these four strains belong to the species P. necessarius. We propose reclassification of strains QLW-P1DMWA-1T (=DSM 18221T=CIP 109841T), MWH-MoK4T (=DSM 21495T=CIP 110977T), MWH-JaK3T (=DSM 21493T=CIP 110976T) and MWH-HuW1T (=DSM 21492T=CIP 110978T) as Polynucleobacter asymbioticus comb. nov., Polynucleobacter duraquae sp. nov., Polynucleobacter yangtzensis sp. nov. and Polynucleobacter sinensis sp. nov., respectively.
| S-EPMC5018217 | biostudies-literature
Project description:Strains MWH-EgelM1-30-B4T and MWH-Feld-100T were isolated from the water columns of two freshwater systems. Both strains represent delicate bacteria not easy to work with in laboratory experiments. Phylogenetic analyses of the 16S rRNA genes suggested that both strains were affiliated with the genus Polynucleobacter. Both strains share 16S rRNA gene sequence similarities of >99 % with eight free-living Polynucleobacter type strains, all affiliated with the cryptic species complex PnecC. The full-length 16S rRNA gene sequences of the two strains differ only in two and three positions, respectively, from the sequence of the closest related Polynucleobacter type strain. Genome sequencing of both strains revealed relatively small genome sizes of 2.0 Mbp and G+C contents of 45 mol%. Phylogenetic analyses based on nucleotide sequences of 319 shared protein-encoding genes consistently placed the two strains in taxon PnecC but did not suggest an affiliation with one of the previously described species. Pairwise analyses of whole genome average nucleotide identities (gANI) with representatives of all previously described Polynucleobacter species resulted in both cases throughout in values <80 %. Pairwise comparison of the genomes of the two new strains resulted in gANI values of 83.3 %. All gANI analyses clearly suggested that strains MWH-EgelM1-30-B4T and MWH-Feld-100T represent two novel Polynucleobacter species. We propose for these novel species the names Polynucleobacter hirudinilacicola sp. nov. and Polynucleobacter campilacus sp. nov. and strains MWH-EgelM1-30-B4T (=DSM 23911T=LMG 30144T) and MWH-Feld-100T (=DSM 24007T=LMG 29705T) as the type strains, respectively.
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Project description:Aurantimicrobium sp. bacterioplankton isolate genome sequencing and assembly
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Project description:Limnohabitans sp. bacterioplankton isolate genome sequencing and assembly
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Project description:The genus Polynucleobacter (family Burkholderiaceae) is phylogenetically subdivided into at least four subclusters. One of those, subcluster PnecC, was recognized as a cryptic species complex. Here we test by comparative genome analyses whether subcluster PnecD, currently solely represented by the species Polynucleobactercosmopolitanus, also represents such a cryptic species complex. The genome sequences of the two P. cosmopolitanus strains, MWH-MoIso2T and MWH-VicM1, were determined. The latter strain was also characterized in the previous description of P. cosmopolitanus. These two strains originate from a temperate lake located in Austria and from the large tropical Lake Victoria located in East Africa, respectively. Strains MWH-MoIso2T and MWH-VicM1 possess quite small genomes of 1.78 and 1.63 Mbp, respectively, and share similar G+C values of 44.1 and 43.1 mol%, respectively. Both strains encode only a single copy of the ribosomal operon, and their 16S rRNA genes differ only in four positions, equalling a sequence similarity of 99.74 %. Both genomes possess characteristics indicating evolutionary genome streamlining, such as high coding densities of 93.9 and 94.6 % of bases, respectively. Average nucleotide identity (ANI) comparisons of the genomes of the two strains resulted in a value of 78.4 %, suggesting that each of the strains represents a separate species. Our investigation suggests that PnecD represents an additional cryptic species complex within the genus Polynucleobacter that was not resolved by 16S rRNA gene sequence analyses. We propose reclassification of strain MWH-VicM1 as Polynucleobacter victoriensis sp. nov., with type strain MWH-VicM1T(=DSM 21486T=JCM 32005T).
| S-EPMC6150420 | biostudies-literature
Project description:Strain AM-8B5(T), isolated from Lake Sevan in Armenia, was characterized phenotypically, chemotaxonomically and phylogenetically. This chemo-organoheterotrophic, aerobic, facultatively anaerobic, catalase- and oxidase-positive, non-motile strain grew on NSY medium at NaCl concentrations of 0.0-0.2 % (w/v) and at 4-30 °C. Whole-cell fatty acids were dominated by summed feature 3 (including C(16 : 1)ω7c and iso-C(15 : 0) 2-OH), C(16 : 0) and C(18 : 1)ω7c. C(12 : 0) 2-OH and C(16 : 1) 2-OH were the only hydroxylated fatty acids detected. Phylogenetic analysis as well as phenotypic and chemotaxonomic similarities indicated that the novel isolate was affiliated with the genus Polynucleobacter. 16S rRNA gene similarity values with the four previously described Polynucleobacter species ranged from 96.2 to 98.7 %. DNA-DNA hybridization experiments showed that the isolate did not belong to any of the previously described Polynucleobacter species. The isolate could be distinguished from all previously established Polynucleobacter species based on chemotaxonomic and phenotypic traits. The bacterium possessed a free-living lifestyle and represents a group of bacteria inhabiting the water column of many freshwater lakes. Based on the revealed phylogeny, and chemotaxonomic and phenotypic differences to previously described Polynucleobacter species, it is proposed that the isolate represents a novel species, Polynucleobacter difficilis sp. nov.; the type strain is AM-8B5(T) ( = DSM 22349(T) = CIP 110078(T)).
| S-EPMC4266013 | biostudies-literature
Project description:Polynucleobacter Genome sequencing and assembly
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Project description:Polynucleobacter Genome sequencing and assembly
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