Genome Sequence of Exiguobacterium antarcticum B7, Isolated from a Biofilm in Ginger Lake, King George Island, Antarctica

Abstract

Exiguobacterium antarcticum is a psychotropic bacterium isolated for the first time from microbial mats of Lake Fryxell in Antarctica. Many organisms of the genus Exiguobacterium are extremophiles and have properties of biotechnological interest, e.g., the capacity to adapt to cold, which make this genus a target for discovering new enzymes, such as lipases and proteases, in addition to improving our understanding of the mechanisms of adaptation and survival at low temperatures. This study presents the genome of E. antarcticum B7, isolated from a biofilm sample of Ginger Lake on King George Island, Antarctic peninsula.

GENOME ANNOUNCEMENT

The genus Exiguobacterium consists of many species isolated from diverse habitats over a wide temperature range (−12 to 55°C), such as glacial ice, hot springs, plant rhizospheres, Siberian permafrost, tropical soils, and temperate soils (11). These species' adaptation to cold requires cellular modifications that may have possible industrial applications. Thermal acclimation proteins and enzymes, such as proteases, lipases, and cellulases, can be used as follows: in the food industry as food additives and flavoring agents, as biosensors, in environmental bioremediation, and in the pharmaceutical industry, among others (5, 9).

Exiguobacterium antarcticum is a Gram-positive bacterium that is mobile by peritrichous flagella but does not form spores and exhibits bright orange, convex colonies with varied sizes and shapes in bacillary morphology when grown on tryptone soy agar (TSA) at 25°C (3). This organism was isolated for the first time from microbial mats of Lake Fryxell, Antarctica (1) and has been named strain H2^T (DSM 14480^T; EMBL accession no. AJ297437). Moreover, studies of the biodiversity and biogeography of the genus Exiguobacterium, such as analysis by pulsed-field gel electrophoresis (PFGE), have contributed to classifying this species and estimating that the genome of strain H2^T is approximately 2,550,800 bp according to the PFGE results (14).

Thus, we present the first complete genome of E. antarcticum B7, isolated from a microbial biofilm at Ginger Lake, located on King George Island, Antarctic peninsula. This strain was subjected to two sequence analyses using two methods to construct genomic libraries on the SOLiD platform (mate paired and fragments), which generated 89,195,902 reads 25 bp in size and 71,239,854 reads 50 bp in size, respectively. The quality control of the raw data was assessed using the Quality assessment program (10), and a quality filter with Phred 20 was applied.

The filtered and corrected data set totaled 61,981,355 and 39,811,567 reads for the mate-paired and fragment libraries, corresponding to genomic coverages of 499× and 642×, respectively, considering the 3.1-Mb size of the Exiguobacterium sibiricum 255-15 (CP001022) reference genome.

To assemble the data, we adopted a de novo approach using the Velvet (16) and Edena programs (6). The best assembly results with Velvet and Edena were grouped for a total of 21,878 contigs, which were ordered and aligned using the reference genome through CLC Genomics Workbench 4.7.1. A scaffold with 1,187 contiguous sequences, totaling 2,665,352 bases, was thus obtained. The remaining gaps were closed by recursive alignments with unmapped contigs and short reads not used in the de novo assembly, followed by manual strand editing (2, 13).

For the functional genome annotation, open reading frame (ORF) prediction was obtained using the Glimmer program (http://www.cbcb.umd.edu/software/glimmer/). The RNAmmer program (7) was used to predict rRNAs. The tRNAscan-SE program (8) was used to identify tRNAs, and the RFAM database (4) was searched to predict other noncoding RNAs (ncRNAs). Domains and protein families were predicted with InterproScan software (15), and the annotations were manually curated in the Artemis program (12).

The E. antarcticum B7 genome has a size of 2,815,863 bp, a GC content of 47.48%, 2,772 coding sequences (CDSs), 9 rRNA operons, 66 tRNAs, 52 ncRNAs, and 76 pseudogenes.

Nucleotide sequence accession number.

The genome sequence obtained in this study has been deposited in the GenBank database under accession number CP003063.1.