Limits...
Draft genome sequence of Lampropedia cohaerens strain CT6 T isolated from arsenic rich microbial mats of a Himalayan hot water spring

View Article: PubMed Central - PubMed

ABSTRACT

Lampropedia cohaerens strain CT6T, a non-motile, aerobic and coccoid strain was isolated from arsenic rich microbial mats (temperature ~45 °C) of a hot water spring located atop the Himalayan ranges at Manikaran, India. The present study reports the first genome sequence of type strain CT6T of genus Lampropedia cohaerens. Sequencing data was generated using the Illumina HiSeq 2000 platform and assembled with ABySS v 1.3.5. The 3,158,922 bp genome was assembled into 41 contigs with a mean GC content of 63.5 % and 2823 coding sequences. Strain CT6T was found to harbour genes involved in both the Entner-Duodoroff pathway and non-phosphorylated ED pathway. Strain CT6T also contained genes responsible for imparting resistance to arsenic, copper, cobalt, zinc, cadmium and magnesium, providing survival advantages at a thermal location. Additionally, the presence of genes associated with biofilm formation, pyrroloquinoline-quinone production, isoquinoline degradation and mineral phosphate solubilisation in the genome demonstrate the diverse genetic potential for survival at stressed niches.

No MeSH data available.


Related in: MedlinePlus

Maximum-Likelihood phylogenetic tree based on 16S rRNA gene sequences of L. cohaerens strain CT6T and its nearest phylogenetic neighbours based on blast-n similarity. All phylogenetic neighbours belong to the family Comamonadaceae. The tree was computed using the Jukes and Cantor model. Bootstrap values (>70 %) calculated for 1000 subsets are shown at branch points. Bar 2 substitutions per 100 nucleotide positions. *Not validly published
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC5015223&req=5

Fig2: Maximum-Likelihood phylogenetic tree based on 16S rRNA gene sequences of L. cohaerens strain CT6T and its nearest phylogenetic neighbours based on blast-n similarity. All phylogenetic neighbours belong to the family Comamonadaceae. The tree was computed using the Jukes and Cantor model. Bootstrap values (>70 %) calculated for 1000 subsets are shown at branch points. Bar 2 substitutions per 100 nucleotide positions. *Not validly published

Mentions: L. cohaerens was characterized by using a polyphasic approach with the integration of genotypic, phenotypic and chemotaxonomic methods [6]. This Gram-stain-negative, aerobic bacterial strain, forms white, smooth colonies with irregular margins on LB agar [6]. Transmission electron microscopy (TEM) revealed coccoid, unflagellated cells approximately 0.62 μm × 0.39 μm in dimension (Fig. 1). Summary characteristics are mentioned in Table 1. The slightly thermophilic and arsenic tolerant L. cohaerens strain CT6 can tolerate temperature in the range 20–55 °C and can tolerate arsenic trioxide up to 80 parts per billion [6]. The NaCl tolerance for strain CT6T was tested as 1–3 % (w/v) and pH range as 6–9. Biofilm formation is observed in LB media, inspiring its etymology. L. cohaerens showed closest phylogenetic similarity to “L. puyangensis 2-binT” (96.4 %) and L. hyalinaATCC 11041T (95.4 %) on the basis of 16S rRNA gene sequences. A maximum-likelihood [14] phylogenetic tree based on Jukes-Cantor [15] model using MEGA version 6 [16] constructed with closely related members of family Comamonadaceae on the basis of Blast-n [17] of 16S rRNA gene placed strain CT6T along with the members of genus Lampropedia with bootstrap [18] confidence value of 98 % (Fig. 2). Positive biochemical tests included the hydrolysis of tween 20, tween 80 and starch and utilization of capric acid, malic acid, citric acid, xanthine and hypoxanthine [6]. Catalase test was positive whereas oxidase test was negative [6]. The most prominent fatty acid methyl esters were C16:0, summed feature 8 (C18:1ω7c/C18:1ω6c), C14:0, C19:0ω8c cyclo and summed feature 3 (C16:1ω7c/C16:1ω6c) [6]. The major polar lipids detected in strain CT6T were phosphatidylethanolamine, phosphatidylglycerol and a glycolipid [6]. Strain CT6T demonstrated the presence of putrescine, 2-hydroxyputrescine and spermidine as the major polyamines and ubiquinone-8 as the major quinone [6].Fig. 1


Draft genome sequence of Lampropedia cohaerens strain CT6 T isolated from arsenic rich microbial mats of a Himalayan hot water spring
Maximum-Likelihood phylogenetic tree based on 16S rRNA gene sequences of L. cohaerens strain CT6T and its nearest phylogenetic neighbours based on blast-n similarity. All phylogenetic neighbours belong to the family Comamonadaceae. The tree was computed using the Jukes and Cantor model. Bootstrap values (>70 %) calculated for 1000 subsets are shown at branch points. Bar 2 substitutions per 100 nucleotide positions. *Not validly published
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC5015223&req=5

Fig2: Maximum-Likelihood phylogenetic tree based on 16S rRNA gene sequences of L. cohaerens strain CT6T and its nearest phylogenetic neighbours based on blast-n similarity. All phylogenetic neighbours belong to the family Comamonadaceae. The tree was computed using the Jukes and Cantor model. Bootstrap values (>70 %) calculated for 1000 subsets are shown at branch points. Bar 2 substitutions per 100 nucleotide positions. *Not validly published
Mentions: L. cohaerens was characterized by using a polyphasic approach with the integration of genotypic, phenotypic and chemotaxonomic methods [6]. This Gram-stain-negative, aerobic bacterial strain, forms white, smooth colonies with irregular margins on LB agar [6]. Transmission electron microscopy (TEM) revealed coccoid, unflagellated cells approximately 0.62 μm × 0.39 μm in dimension (Fig. 1). Summary characteristics are mentioned in Table 1. The slightly thermophilic and arsenic tolerant L. cohaerens strain CT6 can tolerate temperature in the range 20–55 °C and can tolerate arsenic trioxide up to 80 parts per billion [6]. The NaCl tolerance for strain CT6T was tested as 1–3 % (w/v) and pH range as 6–9. Biofilm formation is observed in LB media, inspiring its etymology. L. cohaerens showed closest phylogenetic similarity to “L. puyangensis 2-binT” (96.4 %) and L. hyalinaATCC 11041T (95.4 %) on the basis of 16S rRNA gene sequences. A maximum-likelihood [14] phylogenetic tree based on Jukes-Cantor [15] model using MEGA version 6 [16] constructed with closely related members of family Comamonadaceae on the basis of Blast-n [17] of 16S rRNA gene placed strain CT6T along with the members of genus Lampropedia with bootstrap [18] confidence value of 98 % (Fig. 2). Positive biochemical tests included the hydrolysis of tween 20, tween 80 and starch and utilization of capric acid, malic acid, citric acid, xanthine and hypoxanthine [6]. Catalase test was positive whereas oxidase test was negative [6]. The most prominent fatty acid methyl esters were C16:0, summed feature 8 (C18:1ω7c/C18:1ω6c), C14:0, C19:0ω8c cyclo and summed feature 3 (C16:1ω7c/C16:1ω6c) [6]. The major polar lipids detected in strain CT6T were phosphatidylethanolamine, phosphatidylglycerol and a glycolipid [6]. Strain CT6T demonstrated the presence of putrescine, 2-hydroxyputrescine and spermidine as the major polyamines and ubiquinone-8 as the major quinone [6].Fig. 1

View Article: PubMed Central - PubMed

ABSTRACT

Lampropedia cohaerens strain CT6T, a non-motile, aerobic and coccoid strain was isolated from arsenic rich microbial mats (temperature ~45 °C) of a hot water spring located atop the Himalayan ranges at Manikaran, India. The present study reports the first genome sequence of type strain CT6T of genus Lampropedia cohaerens. Sequencing data was generated using the Illumina HiSeq 2000 platform and assembled with ABySS v 1.3.5. The 3,158,922 bp genome was assembled into 41 contigs with a mean GC content of 63.5 % and 2823 coding sequences. Strain CT6T was found to harbour genes involved in both the Entner-Duodoroff pathway and non-phosphorylated ED pathway. Strain CT6T also contained genes responsible for imparting resistance to arsenic, copper, cobalt, zinc, cadmium and magnesium, providing survival advantages at a thermal location. Additionally, the presence of genes associated with biofilm formation, pyrroloquinoline-quinone production, isoquinoline degradation and mineral phosphate solubilisation in the genome demonstrate the diverse genetic potential for survival at stressed niches.

No MeSH data available.


Related in: MedlinePlus