Draft Genome Sequence of Methylophaga lonarensis MPLT, a Haloalkaliphilic (Non-Methane-Utilizing) Methylotroph.

Methylophaga lonarensis strain MPL(T) is a haloalkaliphilic methylotroph isolated from Lonar Lake, a saline and alkaline lake in Maharashtra, India. Strain MPL(T) utilizes methanol as its sole carbon and energy source. Here, we present the draft genome sequence of M. lonarensis MPL(T) (VKM B-2684(T) = MCC 1002(T)).

GENOME ANNOUNCEMENT

Members of the genus Methylophaga are known for their ability to utilize one-carbon compounds (C1) and have been isolated mostly from habitats of low water activity (1). Four previously described genome sequences of Methylophaga spp. have provided insights into the metabolic potential of marine Methylophaga strains (2–4).

Methylophaga lonarensis strain MPLT was isolated from Lonar Lake, a saline and alkaline ecosystem that is located in Buldhana district, Maharashtra, India (5). Strain MPLT is a moderately haloalkaliphilic methylotroph that assimilates carbon via the ribulose monophosphate (RuMP) pathway. Methylophaga spp. were previously shown to actively assimilate methanol in the Lonar Lake sediments (6). The genome of M. lonarensis was sequenced in order to gain a better understanding of the genetic potential of haloalkaliphilic methylotrophs.

The draft genome of M. lonarensis MPLT, determined by a whole-genome shotgun approach using Ion torrent PGM (200-bp single-end shotgun sequencing, 1,572,266 assembled reads), is 2,637,625 bp with coverage of 80.7×. Assembly of sequencing reads was done using MIRA assembler v3.4.0 with the default parameters (7). After assembly, a total of 116 contigs were obtained with a mean G+C content of 49.7%, which is in agreement with experimental data (G+C content of 50.0% [5]). Annotation was done using RAST server, an automated annotation system (8).

The chromosome of M. lonarensis MPLT harbors 2,614 protein-coding genes. Fifty-five RNA genes, with six rRNA operons (four 5S rRNA and one each for 23S and 16S rRNA), were identified using RNAmmer v1.2 (9). Twenty-five genes encoding putative cytochrome bc1 complex and three genes for terminal oxidase cbb3 were found. The gene clusters responsible for methanol oxidation (mxaFJDIACKL) were identified. Genetic potential for osmoregulation was confirmed by the presence of genes encoding enzymes associated with ectoine biosynthesis and sucrose accumulation. Genes involved in pyrroloquinoline quinone biosynthesis (pqqBCDE) and genes encoding methylamine dehydrogenase (mauABDEF) were identified.

Genes encoding enzymes of the Entner-Doudoroff variant of the RuMP pathway, the tricarboxylic acid (TCA) cycle, the pentose phosphate pathway, sulfur metabolism, and nitrogen metabolism were detected. Key genes associated with the serine- or the ribulose-bisphosphate-pathway of C1 assimilation were absent, in agreement with enzyme assay data (5). Extrachromosomal elements, such as phages, prophages, and plasmids, were not detected in the draft genome. Future in-depth analysis of the M. lonarensis MPLT genome along with other Methylophaga genomes will shed light on the biotechnological potential of these methylotrophs and also help to understand how they adapt to environments of low water activity.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at GenBank under the accession no. APHR00000000. The version described in this paper is the first version, accession no. APHR01000000.