Complete genome sequence of Exiguobacterium profundum TSS-3 isolated from an extremely saline-alkaline spring located in Ixtapa, Chiapas-México

ABSTRACT We report the complete genome sequence of Exiguobacterium profundum TSS-3, a strain isolated from the sediment of an extremely saline-alkaline spring located in Ixtapa, Chiapas-México (16° 47´ LN and 92° 54´ LO). Its genome is composed of a 2.8-Mb chromosome and a small 4.6-Kb plasmid.

KEYWORDS plant growth-promoting bacteria, Exiguobacterium profundum, NaCl resistant E xiguobacterium strains have been isolated from different environments such as glaciers, seawater, soils, hydrothermal vents, industrial affluents, salt lakes, and rhizosphere plants (1,2). Many strains in this genus have characteristics with potential for use in agriculture, industry, and bioremediation (3).
The spring sediment was collected in 2018 with sterilized 3L Van Dorn bottles (https://vimeo.com/365895946) at a depth of 1 m from the saltwater in a 17-m-deep well, following the Mexican standard NOM-021-RECNAT-2000 (4). One gram of sediment was resuspended in 50 mL of sterile water; it was diluted up to 10 −6 and plated in lysogeny broth (LB) medium (5) to obtain isolated colonies. A colony designated TSS-3 was streak purified twice and stored at −70°C in LB containing 30% (vol/vol) glycerol. A glycerol-recovered colony was used to inoculate 5 mL of liquid LB; it was incubated overnight at 30°C for DNA extraction. The DNA was obtained with the "DNA Isolation Kit for Cells and Tissues" from Roche, following the company's instructions. Libraries were prepared with "TruSeq Nano DNA, read length 2 × 151 bp" and "SQK-LSK109" Kits for the Novaseq 6000 platform and Oxford Nanopore Technologies, respectively. Different aliquots of the same DNA were used for sequencing with both methods. No size was selected for Nanopore; only a large fragment buffer was used in the final library wash. The flow cell chemistry for Nanopore was R9.4.1, and the basecaller used was Guppy v6.4.6+ae70e8f. The Nanopore N50 read length was 21,898 bp. A pre-assembly read QC was made with Trim Galore v2.5 for Illumina sequences (https://www.bioinformat ics.babraham.ac.uk/projects/trim_galore/). Unicycler hybrid assembler v0.4.8 was used to get the complete and closed genome, with 24, 269,912 and 64,387 reads for Illumina and Nanopore, respectively (6). Genome coverage was 420×. Genome annotation was performed using the NCBI Prokaryotic Genome Annotation Pipeline Gene (7). Clusters of Orthologous Groups were obtained using CD-Search (Conserved Domain Search Service) from the NCBI database, and hits were accepted with an E-value ≤1e−10 6 . Default parameters were used for all software unless otherwise specified.
The TSS-3 strain has a 2.8-Mb chromosome and a small 4.6-Kb plasmid, which were confirmed by alkaline lysis (8). The predicted CDS were 2,900 and 6, with a GC content of 48.16% and 43.9% for the chromosome and small plasmid, respectively.
The species was confirmed with an ANI value of 96% against Exiguobacterium profundum type strain 10C T with the accession number ASM2523463v1 (9, 10). Exiguo bacterium reference genomes were downloaded from the NCBI database, and the PYANI v0.2.12 program was used to calculate the ANI value with the option "ANIm (ANImum mer)" (11).
Genes annotated as cardiolipin synthase and the seven-gene operon involved in the Na+/H+ antiporter function could help strain TSS-3 to grow in extreme salinity conditions since it has been reported that some strains require them to grow in saline environments (12)(13)(14)(15). The E. profundum TSS-3 genome shows different genes such as proteases, amylases, pullulanases, and neopullulunases that could have a wide application in industry.

ACKNOWLEDGMENTS
This project was funded by Tecnológico Nacional de México (TNM, México; 14094.22 P and 13529.22 P). We thank Michael Dunn for reading the manuscript.