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

ABSTRACT: Lampropedia cohaerens strain CT6(T), 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 CT6(T) 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 CT6(T) was found to harbour genes involved in both the Entner-Duodoroff pathway and non-phosphorylated ED pathway. Strain CT6(T) 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.

SUBMITTER: Tripathi C

PROVIDER: S-EPMC5015223 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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

Tripathi Charu C Mahato Nitish K NK Rani Pooja P Singh Yogendra Y Kamra Komal K Lal Rup R

Standards in genomic sciences 20160907 1

Lampropedia cohaerens strain CT6(T), 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 CT6(T) 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 ...[more]

PMID: 27610214

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Project description:Omics approaches employed to study biological molecules have revolutionized environmental microbiology and elevated our understanding of ecological processes in the biosphere. However, conventional omics applications often lead to the loss of information about macromolecular organization of the molecules within the cellular context. This can be a significant disadvantage since many proteins are functional only as macromolecular complexes in particular structural forms. A great example is bacterial contractile injection system (CIS), a syringe-like protein complex whose function is the translocation of molecules into a target cell to affect its state, often inducing lysis. Since the function of CIS is tightly linked to its intracellular localization, proteomics cannot confidently predict the function of novel uncharacterized CISs in natura. To overcome this challenge, we have developed a cryo-electron tomography workflow as a technique complementing metagenomics and proteomics. Additionally, we developed an immuno-electron microscopy protocol to identify and quantify CIS particles in environmental samples. Using this approach, we discovered a novel bacterial CIS in thermophilic multicellular Chloroflexota bacteria populating hot spring mats worldwide. We found that this system is similar phylogenetically and structurally to a recently described cytoplasmic CIS, which was found in multicellular Streptomyces and has been shown to be involved in cell cycle regulation. Interestingly, using our approaches, we have discovered that Chloroflexota cells produce different numbers of CIS particles depending on the mat micro-niches they occupy. In agreement with this, we observed that CIS was also non-constitutively expressed under laboratory conditions. Motivated by this discovery, we searched and analyzed similar CIS in extremophilic bacteria from other lineages. Overall, we have gained an understanding that bacterial cytoplasmic CIS is an overlooked cellular feature of the extremophilic bacteria, which is potentially involved in the cell fate control or intraspecies interaction within microbial community.

Project description:The Sembawang Hot Spring in Singapore lies at the foot of a major regional geological feature called the Bentong-Raub Suture Zone. Amid an extensively managed surface geothermal park, an undisturbed hot spring emerges with source water at 61°C, pH 6.8, and 1 mg/L dissolved sulfide. A small main pool at the source supported orange-green benthic flocs, whereas the outflow channel with gradually less extreme environmental stress supported extensive vivid green microbial mats. Microscopy revealed that cyanobacterial morphotypes were distinct in flocs and mats at several intervals along the environmental gradient, and we describe a spiraling pattern in the oscillatorian cyanobacteria that may reflect response to poly-extreme stress. Estimation of diversity using 16S rRNA gene sequencing revealed assemblages that were dominated by phototrophic bacteria. The most abundant taxa in flocs at 61°C/1 mg/L sulfide were Roseiflexus sp. and Thermosynechococcus elongatus, whilst the mats at 45.7-55.3°C/0-0.5 mg/L sulfide were dominated by Oscillatoriales cyanobacterium MTP1 and Chloroflexus sp. Occurrence of diverse chemoautotrophs and heterotrophs reflected known thermal ranges for taxa, and of note was the high abundance of thermophilic cellulolytic bacteria that likely reflected the large allochthonous leaf input. A clear shift in ASV-defined putative ecotypes occurred along the environmental stress gradient of the hot spring and overall diversity was inversely correlated to environmental stress. Significant correlations for abiotic variables with observed biotic diversity were identified for temperature, sulfide, and carbonate. A network analysis revealed three putative modules of biotic interactions that also reflected the taxonomic composition at intervals along the environmental gradient. Overall, the data indicated that three distinct microbial communities were supported within a small spatial scale along the poly-extreme environmental gradient. The findings add to the growing inventory of hot spring microbiomes and address an important biogeographic knowledge gap for the region.

Dataset Information

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

Publications

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

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