Complete genome sequence of a Salimicrobium sp. PL1-032A isolated from the pink hypersaline Pearse Lakes, Rottnest Island, Western Australia

TL;DR

Scientists sequenced the genome of a new salt-loving microbe from a hypersaline lake in Western Australia.

Contribution

This study provides the complete genome sequence of a new Salimicrobium species from an extreme hypersaline environment.

Findings

The genome is a single chromosome of 2,705,688 base pairs with 47.2% GC content.

The isolate contributes to understanding extremophiles and the Pearse Lakes ecosystem.

Abstract

Salimicrobium sp. PL1-032A was isolated from Pearse Lakes, Western Australia. The sequenced genome consists of a single chromosome (2,705,688  bp) with a GC content of 47.2%. The isolation of Salimicrobium sp. PL1-032A contributes to the collection of culturable extremophiles and offers potential insight into the Pearse Lakes biome.

Figures

Dendro-unweighted pair group method with arithmetic mean (UPGMA) tree displaying the relatedness of Salimicrobium sp. PL1-032A to related species based on ANIb values. The ANIb values were generated using JSpeciesWS (11) and imported into DendroUPGMA, and the tree was constructed using a similarity matrix (Pearson’s correlation coefficient) within the algorithm (14). The tree was exported from MEGA11 in Newick format and imported into tvBOT (https://www.tvBOT.html) (15). The superscript T indicates type strains and Marinococcus halophilus KCTC 2843T used as an outgroup (16).

Tables

TABLE 1. General feature of the genome of Salimicrobium sp. PL1-032A (Accession: CP139874) from Prokaryotic Genome Annotation Pipeline

	Data from
Feature	GenBank annotation
Total no. of genes	2,795
No. protein-coding sequences	2,506
No. of rRNA operons	7
5s	7
16s	7
23s	7
No. of tRNA genes	67
No. of other RNA genes	4
Locus tag prefix	U0355_

Full text

ANNOUNCEMENT

Salimicrobium are typically Gram-positive, non-motile cocci, endospore-forming, moderate halophiles found in hypersaline lakes (1, 2). Rottnest Island (~30.4 km offshore from Perth, Western Australia) hosts athalassic soda-hypersaline lakes, including Pearse Lakes (3). Here, we report the complete genome sequence of a Salimicrobium sp. PL1-032A, isolated from Pearse Lakes in May 2022, when the lakes had a pH of 8.0 ± 0.01 and salinity of 20.1% ± 1.44%.

Water samples were collected (S 32° 0′ 22.281″ E 115° 30′ 44.484″) and stored at 4°C before cultivation. Water samples (1,500 mL) were centrifuged at 4,500 × g for 10 minutes and streaked from the cell pellet on adapted lysogeny broth containing (per liter) 10.0 g bacto-tryptone, 5.0 g bacto-yeast extract, 150.0 g NaCl, and 2.4 g HEPES (pH 7.8) (4). Single colonies were re-streaked until pure cultures were obtained and cryopreserved (15% glycerol, −80°C). Genomic DNA (gDNA) was extracted from stationary-phase culture using the CTAB (2%) (5) and was sequenced using Oxford Nanopore Technology (ONT). The ONT library was prepared according to the ONT ligation native barcoding gDNA library protocol (SQK-NBD114.24) (https://nanoporetech.com/protocols) with a FLO-PRO114M flow cell (R10.4.1) on the PromethION 2 platform. Guppy [v6.5.7 (6)] was used for base-calling sequenced data with a read-pass-filter quality score cutoff value of 9 and a minimum length of 1,500 bp. Nineteen thousand two hundred twenty-seven reads were generated (146,068,268 bp) providing an average coverage of 54× and a N50 value of 14,731 bp determined with NanoStat [v1.6.0 (7)]. ONT long reads were assembled using Flye [v2.9.2 (8)] using default parameters, with nine iterations to provide a single circular chromosome (2,705,688 bp with 47.2% GC content). A quantitative genome assembly assessment was performed using BUSCO [v5.4.6 (9)] and CheckM [v1.2.2 (10)], providing a completeness score of 91.5% and 99.78% (0.22% contamination), respectively. Average nucleotide identity analysis using BLAST (ANIb) showed below the cutoff value (>95%) with the closest relative (83.4%) Salimicrobium halophilum DSM 4771^T^ (GCF_900100295.1) (11–13) (Fig. 1).

Dendro-unweighted pair group method with arithmetic mean (UPGMA) tree displaying the relatedness of Salimicrobium sp. PL1-032A to related species based on ANIb values. The ANIb values were generated using JSpeciesWS (11) and imported into DendroUPGMA, and the tree was constructed using a similarity matrix (Pearson’s correlation coefficient) within the algorithm (14). The tree was exported from MEGA11 in Newick format and imported into tvBOT (https://www.tvBOT.html) (15). The superscript T indicates type strains and Marinococcus halophilus KCTC 2843T used as an outgroup (16).

Gene calling and annotation of the generated chromosomal sequence were performed using the NCBI Prokaryotic Genome Annotation Pipeline (Table 1) [v6.6 (17)]. The isolation of Salimicrobium sp. PL1-032A and completion of the genome could provide knowledge about the extreme Pearse Lakes biome (18).