Abstract
The halophilic genus Joostella is one of the least-studied genera in the family of Flavobacteriaceae. So far, only two species were taxonomically identified with limited genomic analysis in the aspect of application has been reported. Joostella atrarenae M1-2T was previously isolated from a seashore sample and it is the second discovered species of the genus Joostella. In this project, the genome of J. atrarenae M1-2T was sequenced using NovaSeq 6000. The final assembled genome is comprised of 71 contigs, a total of 3,983,942 bp, a GC ratio of 33.2%, and encoded for 3,416 genes. The 16S rRNA gene sequence of J. atrarenae M1-2T shows 97.3% similarity against J. marina DSM 19592T. Genome-genome comparison between the two strains by ANI, dDDH, AAI, and POCP shows values of 80.8%, 23.3%, 83.4%, and 74.1% respectively. Pan-genome analysis shows that strain M1-2T and J. marina DSM 19592T shared a total of 248 core genes. Taken together, strain M-2T and J. marina DSM 19592T belong to the same genus but are two different species. CAZymes analysis revealed that strain M1-2T harbors 109 GHs, 40 GTs, 5 PLs, 9 CEs, and 6 AAs. Among these CAZymes, while 5 genes are related to cellulose degradation, 12 and 24 genes are found to encode for xylanolytic enzymes and other hemicellulases that involve majorly in the side chain removal of the lignocellulose structure, respectively. Furthermore, both the intracellular and extracellular crude extracts of strain M1-2T exhibited enzymatic activities against CMC, xylan, pNPG, and pNPX substrates, which corresponding to endoglucanase, xylanase, β-glucosidase, and β-xylosidase, respectively. Collectively, description of genome coupled with the enzyme assay results demonstrated that J. atrarenae M1-2T has a role in lignocellulosic biomass degradation, and the strain could be useful for lignocellulosic biorefining.
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Data availability
All data generated or analyzed during this study are included in this published article. Accession Numbers: The whole-genome sequence of J. atrarenae M1-2T can be accessed via National Center for Biotechnology Information (NCBI) database, either with BioProject accession number PRJNA694488, BioSample accession number SAMN17525809, or Genbank accession number JAETXX000000000. The raw sequence data from the sequencing was also deposited in NCBI Sequence Read Archive (SRA) database with accession number SRR15341968.
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Acknowledgements
K.J.L. is a post-doctoral researcher of Universiti Teknologi Malaysia funded by NFIS 2020-2021. M.R.Z. and C.W.L.H. would like to thank Zamalah Program of Universiti Teknologi Malaysia for scholarship support.
Funding
This work was supported by the Ministry of Higher Education Malaysia under Fundamental Research Grant Scheme (FRGS/1/2019/WAB13/UTM/02/1) as main sponsor. This work was also supported by Newton Fund Impact Scheme (NFIS) 2020–2021 from Malaysian Industry-Government Group for High Technology with project ID 536423090 (RADIS cost centre number:4B568).
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K.J.L. performed the genome analysis and wrote the manuscript. M.R.Z. and C.W.L.H. collected the sequencing data and carried out the enzyme assay experiments. M.C.Y.T. reviewed and edited the manuscript. C.S.C. conceived the project. All authors reviewed and approved the final manuscript.
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Liew, K.J., Zakaria, M.R., Hong, C.W.L. et al. Draft genome sequence of Joostella atrarenae M1-2T with cellulolytic and hemicellulolytic ability. 3 Biotech 13, 50 (2023). https://doi.org/10.1007/s13205-023-03472-8
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DOI: https://doi.org/10.1007/s13205-023-03472-8