
==== Front
Microbiol Resour Announc
Microbiol Resour Announc
mra
Microbiology Resource Announcements
2576-098X
American Society for Microbiology 1752 N St., N.W., Washington, DC

39162484
mra00361-24
10.1128/mra.00361-24
mra.00361-24
Genome Sequences
environmental-microbiologyEnvironmental MicrobiologyComplete genome sequence of a Salimicrobium sp. PL1-032A isolated from the pink hypersaline Pearse Lakes, Rottnest Island, Western Australia
https://orcid.org/0009-0001-3808-8672
Young Crystal E. 1 2 C.Young@murdoch.edu.au

Alattas Hussain 2
https://orcid.org/0000-0001-6110-6982
Scott Colin 1 3
Murphy Daniel V. 1
Tiwari Ravi 1 2
https://orcid.org/0000-0002-3780-8965
Reeve Wayne G. 1 2
1 Bioplastic Innovation Hub, Food Futures Institute, Murdoch University , Murdoch, Western Australia, Australia
2 School of Medical, Molecular and Forensic Sciences, Murdoch University , Murdoch, Western Australia, Australia
3 CSIRO Environment, Black Mountain Science and Innovation Park , Canberra, Australia
Editor Maresca Julia A. SUNY College of Environmental Science and Forestry , Syracuse, New York, USA

Address correspondence to Crystal E. Young, C.Young@murdoch.edu.au
The authors declare no conflict of interest.

9 2024
20 8 2024
20 8 2024
13 9 e00361-2407 4 2024
19 6 2024
Copyright © 2024 Young et al.
2024
Young et al.
https://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

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.

KEYWORDS

halophiles
extremophiles
environmental microbiology
cover-dateSeptember 2024
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pmcANNOUNCEMENT

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 4771T (GCF_900100295.1) (11–13) (Fig. 1).

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).

Phylogenetic tree of Halobacillus, Thalassobacillus, Salimicrobium, and Marinococcus bacterial species. Branch lengths show evolutionary distance (scale 0.01). Image highlights Salimicrobium species, PL1-032A.

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).

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_	

ACKNOWLEDGMENTS

This project was funded by a Murdoch University RTP scholarship (C.Y.) and a top-up scholarship through the CSIRO-Murdoch University-Industry Bioplastics Innovation Hub (C.Y.). H.A. was supported by a Murdoch University International Postgraduate Scholarship. We acknowledge the Western Australia Department of Biodiversity, Conservation, and Attractions for the sampling permits. We acknowledge the Rottnest Island Authority for logistical assistance and access to Pearse Lakes. We also acknowledge the Whadjuk Noongar people as the original custodians of Wadjemup (Rottnest Island) and their continued connection to the island and its waters, and we pay our respects to elders past, present, and emerging.

DATA AVAILABILITY

The Salimicrobium sp. PL1-022A whole-genome sequence (CP139874) has been deposited in the GenBank database (NCBI) under BioSample: SAMN38237613 within BioProject: PRJNA1039979. ONT long reads were deposited in SRA (SRR26991452).
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