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Complete genome sequence of the thermophilic Acidobacteria, Pyrinomonas methylaliphatogenes type strain K22(T).

Lee KC, Morgan XC, Power JF, Dunfield PF, Huttenhower C, Stott MB - Stand Genomic Sci (2015)

Bottom Line: Its cell membrane is dominated by iso-branching fatty acids, and up to 40 % of its lipid content is membrane-spanning and ether lipids.It is obligately aerobic, thermophilic, moderately acidophilic, and non-spore-forming.The 3,788,560 bp genome of P. methylaliphatogenes K22(T) has a G + C content of 59.36 % and contains 3,189 protein-encoding and 55 non-coding RNA genes.

View Article: PubMed Central - PubMed

Affiliation: GNS Science, Extremophiles Research Group, Taupō, New Zealand.

ABSTRACT
Strain K22(T) is the type species of the recently- described genus Pyrinomonas, in subdivision 4 of the phylum Acidobacteria (Int J Syst Evol Micr. 2014; 64(1):220-7). It was isolated from geothermally-heated soil from Mt. Ngauruhoe, New Zealand, using low-nutrient medium. P. methylaliphatogenes K22(T) has a chemoheterotrophic metabolism; it can hydrolyze a limited range of simple carbohydrates and polypeptides. Its cell membrane is dominated by iso-branching fatty acids, and up to 40 % of its lipid content is membrane-spanning and ether lipids. It is obligately aerobic, thermophilic, moderately acidophilic, and non-spore-forming. The 3,788,560 bp genome of P. methylaliphatogenes K22(T) has a G + C content of 59.36 % and contains 3,189 protein-encoding and 55 non-coding RNA genes. Genomic analysis was consistent with nutritional requirements; in particular, the identified transporter classes reflect the oligotrophic nature of this strain.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree based on 16S rRNA gene sequences of Pyrinomonas methylaliphatogenes K22T (highlighted) and other cultivated strains and clonal phylotypes within the phylum Acidobacteria. Four of the acidobacterial subdivisions are included. The tree was constructed via a Bayesian inference model (MrBayes), using Markov Chain Monte Carlo (MCMC - 2,000,000 resamples, four chains, temperature = 0.5) sampling methods to calculate posterior distributions of trees in the ARB software environment. Posterior probability values ≥ 90 % are indicated by open circles, ≥80 % by filled circles, and ≥70 % by open diamonds. The scale bar represents a 0.1 change per nucleotide position. Strains whose genomes have been sequenced, are marked with an asterisk; G. fermentans H5T (NZ_AUAU00000000), H. foetida TMBS4T (AGSB00000000), C. thermophilum BT (CP002414), P. methylaliphatogenes K22T (CBXV000000000), Candidatus ‘S. usitatus’ Ellin6076 (CP000473), Candidatus ‘K. versatilis’ Ellin345 (CP000360), Acidobacterium capsulatum ATCC 51196T (CP001472), Edaphobacter aggregans Wbg-1T (JQKI00000000), Granulicella mallensis MP5ACTX9T (CP003130), Granulicella tundricola MP5ACTX9T (CP002480), Terriglobus roseus KBS63T (CP003379), and Terriglobus saanensis SP1PR4T (CP002467). The phylotypes strains used as an outgroup included Thermoanaerobaculum aquaticum MP-01T (JX4200244), Dictyoglomus thermophilum H-6-12T (X69194), Caldisericum exile AZM16c01T (AB428365), Hydrogenobacter hydrogenophilus Z-829T (Z30424), Thermodesulfobacterium thermophilum DSM 1276T (AF334601), Deinococcus roseus TDMA-uv51 (AB264136), Truepera radiovicrix RQ-24T (DQ022076), Thermus aquaticus YT-1 (L09663), and Thermus scotoductus SE-1T (AF032127)
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Fig1: Phylogenetic tree based on 16S rRNA gene sequences of Pyrinomonas methylaliphatogenes K22T (highlighted) and other cultivated strains and clonal phylotypes within the phylum Acidobacteria. Four of the acidobacterial subdivisions are included. The tree was constructed via a Bayesian inference model (MrBayes), using Markov Chain Monte Carlo (MCMC - 2,000,000 resamples, four chains, temperature = 0.5) sampling methods to calculate posterior distributions of trees in the ARB software environment. Posterior probability values ≥ 90 % are indicated by open circles, ≥80 % by filled circles, and ≥70 % by open diamonds. The scale bar represents a 0.1 change per nucleotide position. Strains whose genomes have been sequenced, are marked with an asterisk; G. fermentans H5T (NZ_AUAU00000000), H. foetida TMBS4T (AGSB00000000), C. thermophilum BT (CP002414), P. methylaliphatogenes K22T (CBXV000000000), Candidatus ‘S. usitatus’ Ellin6076 (CP000473), Candidatus ‘K. versatilis’ Ellin345 (CP000360), Acidobacterium capsulatum ATCC 51196T (CP001472), Edaphobacter aggregans Wbg-1T (JQKI00000000), Granulicella mallensis MP5ACTX9T (CP003130), Granulicella tundricola MP5ACTX9T (CP002480), Terriglobus roseus KBS63T (CP003379), and Terriglobus saanensis SP1PR4T (CP002467). The phylotypes strains used as an outgroup included Thermoanaerobaculum aquaticum MP-01T (JX4200244), Dictyoglomus thermophilum H-6-12T (X69194), Caldisericum exile AZM16c01T (AB428365), Hydrogenobacter hydrogenophilus Z-829T (Z30424), Thermodesulfobacterium thermophilum DSM 1276T (AF334601), Deinococcus roseus TDMA-uv51 (AB264136), Truepera radiovicrix RQ-24T (DQ022076), Thermus aquaticus YT-1 (L09663), and Thermus scotoductus SE-1T (AF032127)

Mentions: Phylogenetic distances of closest-related phylotypes and cultivated subdivision 4 acidobacterial strains were determined by aligning the representative near full length 16S rRNA gene sequences (all sequences were > 1,400 nucleotides in length) and calculating sequence similarity via a pair-wise alignment within the ARB software environment [11]. Analysis showed that the 16S rRNA gene sequence of P. methylaliphatogenes K22T (AM749787) is 85 % similar to B. fastidiosa strain A2-16T (JQ309130), and is 84 % similar to both A. famidurans strain A22_HD_4HT (KF245634), and A. kavangonensis Ac_23_E3T (KF245633) [3, 4, 9]. In addition, P. methylaliphatogenes K22T shares 85 % 16S rRNA gene sequence similarity with both Ellin6075 (AY234727) [7] and C. thermophilum BT (EF531339) [8]. The most closely-related phylotypes to P. methylaliphatogenes K22T are two sequences from clonal libraries of environmental 16S rRNA genes (EU490264, EU490279) retrieved from geothermal soils on Mt. Erebus, Antarctica [12]; both of these shared 95 % 16S rRNA gene sequence similarity with P. methylaliphatogenes K22T. Phylogenetic comparison (Fig. 1) showed that P. methylaliphatogenes K22T is a taxonomically-distinct genus and species of subdivision 4 in the phylum Acidobacteria.Fig. 1


Complete genome sequence of the thermophilic Acidobacteria, Pyrinomonas methylaliphatogenes type strain K22(T).

Lee KC, Morgan XC, Power JF, Dunfield PF, Huttenhower C, Stott MB - Stand Genomic Sci (2015)

Phylogenetic tree based on 16S rRNA gene sequences of Pyrinomonas methylaliphatogenes K22T (highlighted) and other cultivated strains and clonal phylotypes within the phylum Acidobacteria. Four of the acidobacterial subdivisions are included. The tree was constructed via a Bayesian inference model (MrBayes), using Markov Chain Monte Carlo (MCMC - 2,000,000 resamples, four chains, temperature = 0.5) sampling methods to calculate posterior distributions of trees in the ARB software environment. Posterior probability values ≥ 90 % are indicated by open circles, ≥80 % by filled circles, and ≥70 % by open diamonds. The scale bar represents a 0.1 change per nucleotide position. Strains whose genomes have been sequenced, are marked with an asterisk; G. fermentans H5T (NZ_AUAU00000000), H. foetida TMBS4T (AGSB00000000), C. thermophilum BT (CP002414), P. methylaliphatogenes K22T (CBXV000000000), Candidatus ‘S. usitatus’ Ellin6076 (CP000473), Candidatus ‘K. versatilis’ Ellin345 (CP000360), Acidobacterium capsulatum ATCC 51196T (CP001472), Edaphobacter aggregans Wbg-1T (JQKI00000000), Granulicella mallensis MP5ACTX9T (CP003130), Granulicella tundricola MP5ACTX9T (CP002480), Terriglobus roseus KBS63T (CP003379), and Terriglobus saanensis SP1PR4T (CP002467). The phylotypes strains used as an outgroup included Thermoanaerobaculum aquaticum MP-01T (JX4200244), Dictyoglomus thermophilum H-6-12T (X69194), Caldisericum exile AZM16c01T (AB428365), Hydrogenobacter hydrogenophilus Z-829T (Z30424), Thermodesulfobacterium thermophilum DSM 1276T (AF334601), Deinococcus roseus TDMA-uv51 (AB264136), Truepera radiovicrix RQ-24T (DQ022076), Thermus aquaticus YT-1 (L09663), and Thermus scotoductus SE-1T (AF032127)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4644332&req=5

Fig1: Phylogenetic tree based on 16S rRNA gene sequences of Pyrinomonas methylaliphatogenes K22T (highlighted) and other cultivated strains and clonal phylotypes within the phylum Acidobacteria. Four of the acidobacterial subdivisions are included. The tree was constructed via a Bayesian inference model (MrBayes), using Markov Chain Monte Carlo (MCMC - 2,000,000 resamples, four chains, temperature = 0.5) sampling methods to calculate posterior distributions of trees in the ARB software environment. Posterior probability values ≥ 90 % are indicated by open circles, ≥80 % by filled circles, and ≥70 % by open diamonds. The scale bar represents a 0.1 change per nucleotide position. Strains whose genomes have been sequenced, are marked with an asterisk; G. fermentans H5T (NZ_AUAU00000000), H. foetida TMBS4T (AGSB00000000), C. thermophilum BT (CP002414), P. methylaliphatogenes K22T (CBXV000000000), Candidatus ‘S. usitatus’ Ellin6076 (CP000473), Candidatus ‘K. versatilis’ Ellin345 (CP000360), Acidobacterium capsulatum ATCC 51196T (CP001472), Edaphobacter aggregans Wbg-1T (JQKI00000000), Granulicella mallensis MP5ACTX9T (CP003130), Granulicella tundricola MP5ACTX9T (CP002480), Terriglobus roseus KBS63T (CP003379), and Terriglobus saanensis SP1PR4T (CP002467). The phylotypes strains used as an outgroup included Thermoanaerobaculum aquaticum MP-01T (JX4200244), Dictyoglomus thermophilum H-6-12T (X69194), Caldisericum exile AZM16c01T (AB428365), Hydrogenobacter hydrogenophilus Z-829T (Z30424), Thermodesulfobacterium thermophilum DSM 1276T (AF334601), Deinococcus roseus TDMA-uv51 (AB264136), Truepera radiovicrix RQ-24T (DQ022076), Thermus aquaticus YT-1 (L09663), and Thermus scotoductus SE-1T (AF032127)
Mentions: Phylogenetic distances of closest-related phylotypes and cultivated subdivision 4 acidobacterial strains were determined by aligning the representative near full length 16S rRNA gene sequences (all sequences were > 1,400 nucleotides in length) and calculating sequence similarity via a pair-wise alignment within the ARB software environment [11]. Analysis showed that the 16S rRNA gene sequence of P. methylaliphatogenes K22T (AM749787) is 85 % similar to B. fastidiosa strain A2-16T (JQ309130), and is 84 % similar to both A. famidurans strain A22_HD_4HT (KF245634), and A. kavangonensis Ac_23_E3T (KF245633) [3, 4, 9]. In addition, P. methylaliphatogenes K22T shares 85 % 16S rRNA gene sequence similarity with both Ellin6075 (AY234727) [7] and C. thermophilum BT (EF531339) [8]. The most closely-related phylotypes to P. methylaliphatogenes K22T are two sequences from clonal libraries of environmental 16S rRNA genes (EU490264, EU490279) retrieved from geothermal soils on Mt. Erebus, Antarctica [12]; both of these shared 95 % 16S rRNA gene sequence similarity with P. methylaliphatogenes K22T. Phylogenetic comparison (Fig. 1) showed that P. methylaliphatogenes K22T is a taxonomically-distinct genus and species of subdivision 4 in the phylum Acidobacteria.Fig. 1

Bottom Line: Its cell membrane is dominated by iso-branching fatty acids, and up to 40 % of its lipid content is membrane-spanning and ether lipids.It is obligately aerobic, thermophilic, moderately acidophilic, and non-spore-forming.The 3,788,560 bp genome of P. methylaliphatogenes K22(T) has a G + C content of 59.36 % and contains 3,189 protein-encoding and 55 non-coding RNA genes.

View Article: PubMed Central - PubMed

Affiliation: GNS Science, Extremophiles Research Group, Taupō, New Zealand.

ABSTRACT
Strain K22(T) is the type species of the recently- described genus Pyrinomonas, in subdivision 4 of the phylum Acidobacteria (Int J Syst Evol Micr. 2014; 64(1):220-7). It was isolated from geothermally-heated soil from Mt. Ngauruhoe, New Zealand, using low-nutrient medium. P. methylaliphatogenes K22(T) has a chemoheterotrophic metabolism; it can hydrolyze a limited range of simple carbohydrates and polypeptides. Its cell membrane is dominated by iso-branching fatty acids, and up to 40 % of its lipid content is membrane-spanning and ether lipids. It is obligately aerobic, thermophilic, moderately acidophilic, and non-spore-forming. The 3,788,560 bp genome of P. methylaliphatogenes K22(T) has a G + C content of 59.36 % and contains 3,189 protein-encoding and 55 non-coding RNA genes. Genomic analysis was consistent with nutritional requirements; in particular, the identified transporter classes reflect the oligotrophic nature of this strain.

No MeSH data available.


Related in: MedlinePlus