Genomic insights on carotenoid synthesis by extremely halophilic archaea Haloarcula rubripromontorii BS2, Haloferax lucentense BBK2 and Halogeometricum borinquense E3 isolated from the solar salterns of India

Oren, A. Halophilic microbial communities and their environments. Curr. Opin. Biotechnol. 33, 119–124. https://doi.org/10.1016/j.copbio.2015.02.005 (2015).Article 
CAS 
PubMed 

Google Scholar 
Ventosa, A. & Nieto, J. J. Biotechnological applications and potentialities of halophilic microorganisms. World J. Microbiol. Biotechnol. 11, 85–94. https://doi.org/10.1007/BF00339138 (1995).Article 
CAS 
PubMed 

Google Scholar 
de Lourdes Moreno, M., Sánchez-Porro, C., García, M. T. & Mellado, E. Carotenoids’ production from halophilic bacteria. In Microbial Carotenoids from Bacteria and Microalgae: Methods and Protocols (ed. Barredo, J.-L.) 207–217 (Humana, 2012).Chapter 

Google Scholar 
Salgaonkar, B. B. & Rodrigues, R. a study on the halophilic archaeal diversity from the food grade iodised crystal salt from a saltern of India. Microbiology (N Y) 88, 709–719. https://doi.org/10.1134/S002626171906016X (2019).Article 
CAS 

Google Scholar 
Oren, A. & Rodrı́guez-Valera, F. The contribution of halophilic Bacteria to the red coloration of saltern crystallizer ponds (1). FEMS Microbiol Ecol 36, 123–130. https://doi.org/10.1111/j.1574-6941.2001.tb00832.x (2001).Article 
CAS 
PubMed 

Google Scholar 
Amoozegar, M. A., Siroosi, M., Atashgahi, S., Smidt, H. & Ventosa, A. Systematics of haloarchaea and biotechnological potential of their hydrolytic enzymes. Microbiology (N Y) 163, 623–645. https://doi.org/10.1099/mic.0.000463 (2017).Article 
CAS 

Google Scholar 
Yang, Y. et al. Complete biosynthetic pathway of the C50 carotenoid bacterioruberin from lycopene in the extremely halophilic archaeon Haloarcula japonica. J. Bacteriol. 197, 1614–1623. https://doi.org/10.1128/JB.02523-14 (2015).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Yatsunami, R. et al. Identification of carotenoids from the extremely halophilic archaeon Haloarcula japonica. Front. Microbiol. 5, 100. https://doi.org/10.3389/fmicb.2014.00100 (2014).Article 
PubMed 
PubMed Central 

Google Scholar 
Heider, S. A. E., Wolf, N., Hofemeier, A., Peters-Wendisch, P. & Wendisch, V. F. Optimization of the IPP precursor supply for the production of lycopene, decaprenoxanthin and astaxanthin by Corynebacterium glutamicum. Front. Bioeng. Biotechnol. 2, 28. https://doi.org/10.3389/fbioe.2014.00028 (2014).Article 
PubMed 
PubMed Central 

Google Scholar 
Rodrigo-Baños, M., Garbayo, I., Vílchez, C., Bonete, M. J. & Martínez-Espinosa, R. M. Carotenoids from haloarchaea and their potential in biotechnology. Mar. Drugs 13, 5508–5532. https://doi.org/10.3390/md13095508 (2015).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Montero-Lobato, Z. et al. Optimization of growth and carotenoid production by haloferax mediterranei using response surface methodology. Mar. Drugs 16, 372. https://doi.org/10.3390/md16100372 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Kelly, M. & Jensen, S. L. Bacterial carotenoids. XXVI. C50-carotenoids. 2 Bacterioruberin. Acta Chem. Scand. 21, 2578–2580. https://doi.org/10.3891/acta.chem.scand.21-2578 (1967).Article 
CAS 
PubMed 

Google Scholar 
Giani, M., Garbayo, I., Vílchez, C. & Martínez-Espinosa, R. M. Haloarchaeal carotenoids: Healthy novel compounds from extreme environments. Mar. Drugs 17, 524. https://doi.org/10.3390/md17090524 (2019).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Fang, C.-J., Ku, K.-L., Lee, M.-H. & Su, N.-W. Influence of nutritive factors on C50 carotenoids production by Haloferax mediterranei ATCC 33500 with two-stage cultivation. Bioresour. Technol. 101, 6487–6493. https://doi.org/10.1016/j.biortech.2010.03.044 (2010).Article 
CAS 
PubMed 

Google Scholar 
Chen, C. W., Hsu, S. H., Lin, M. T. & Hsu, Y. H. Mass production of C50 carotenoids by Haloferax mediterranei in using extruded rice bran and starch under optimal conductivity of brined medium. Bioprocess Biosyst. Eng. 38, 2361–2367. https://doi.org/10.1007/s00449-015-1471-y (2015).Article 
CAS 
PubMed 

Google Scholar 
Grivard, A. et al. Archaea carotenoids: Natural pigments with unexplored innovative potential. Mar. Drugs 20, 524. https://doi.org/10.3390/md20080524 (2022).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Miller, N. J., Sampson, J., Candeias, L. P., Bramley, P. M. & Rice-Evans, C. A. Antioxidant activities of carotenes and xanthophylls. FEBS Lett. 384, 240–242. https://doi.org/10.1016/0014-5793(96)00323-7 (1996).Article 
CAS 
PubMed 

Google Scholar 
Albrecht, M., Takaichi, S., Steiger, S., Wang, Z. Y. & Sandmann, G. Novel hydroxycarotenoids with improved antioxidative properties produced by gene combination in Escherichia coli. Nat. Biotechnol. 18, 843–846. https://doi.org/10.1038/78443 (2000).Article 
CAS 
PubMed 

Google Scholar 
Saito, T., Miyabe, Y., Ide, H. & Yamamoto, O. Hydroxyl radical scavenging ability of bacterioruberin. Radiat. Phys. Chem. 50, 267–269. https://doi.org/10.1016/S0969-806X(97)00036-4 (1997).Article 
ADS 
CAS 

Google Scholar 
Stahl, W. & Sies, H. (2005). Bioactivity and protective effects of natural carotenoids. Biochimica et Biophysica Acta (BBA) – Molecular Basis of Disease. 1740, 101–107. https://doi.org/10.1016/j.bbadis.2004.12.006Hwang, C. Y., Cho, E. S., Rhee, W. J., Kim, E. & Seo, M. J. Genomic and physiological analysis of C50 carotenoid-producing novel Halorubrum ruber sp. nov. J. Microbiol. 60, 1007–1020. https://doi.org/10.1007/s12275-022-2173-1 (2022).Article 
CAS 
PubMed 

Google Scholar 
Hwang, C. Y., Cho, E. S., Yoon, D. J. & Seo, M. J. Halobellus ruber sp. Nov., a deep red-pigmented extremely halophilic archaeon isolated from a Korean solar saltern. Antonie Van Leeuwenhoek 114, 997–1011. https://doi.org/10.1007/s10482-021-01571-1 (2021).Article 
CAS 
PubMed 

Google Scholar 
Mani, K., Salgaonkar, B. B. & Braganca, J. M. Culturable halophilic archaea at the initial and crystallization stages of salt production in a natural solar saltern of Goa. India. Aquat Biosyst.. 8, 15. https://doi.org/10.1186/2046-9063-8-15 (2012).Article 
CAS 
PubMed 

Google Scholar 
Salgaonkar, B. B. & Bragança, J. M. Biosynthesis of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) by Halogeometricum borinquense strain E3. Int. J. Biol. Macromol. 78, 339–346. https://doi.org/10.1016/j.ijbiomac.2015.04.016 (2015).Article 
CAS 
PubMed 

Google Scholar 
Andrews, S. FastQC: a quality control tool for high throughput sequence data. www.bioinformatics.babraham.ac.uk/projects/fastqc/ (2010).Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890. https://doi.org/10.1093/bioinformatics/bty560 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Souvorov, A., Agarwala, R. & Lipman, D. SKESA: Strategic k-mer extension for scrupulous assemblies. Genome Biol. 19, 153. https://doi.org/10.1186/s13059-018-1540-z (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055. https://doi.org/10.1101/gr.186072.114 (2015).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. QUAST: Quality assessment tool for genome assemblies. Bioinformatics 29, 1072–1075. https://doi.org/10.1093/bioinformatics/btt086 (2013).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Seemann, T. Prokka: Rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069. https://doi.org/10.1093/bioinformatics/btu153 (2014).Article 
CAS 
PubMed 

Google Scholar 
Aziz, R. K. et al. The RAST server: Rapid annotations using subsystems technology. BMC Genomics 9, 75. https://doi.org/10.1186/1471-2164-9-75 (2008).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Overbeek, R. et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucl. Acids Res. 42, D206–D214. https://doi.org/10.1093/nar/gkt1226 (2014).Article 
CAS 
PubMed 

Google Scholar 
Törönen, P., Medlar, A. & Holm, L. PANNZER2: A rapid functional annotation web server. Nucl. Acids Res. 46, W84–W88. https://doi.org/10.1093/nar/gky350 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Kanehisa, M., Sato, Y. & Morishima, K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J. Mol. Biol. 428, 726–731. https://doi.org/10.1016/j.jmb.2015.11.006 (2016).Article 
CAS 
PubMed 

Google Scholar 
Grant, J. R. et al. Proksee: In-depth characterization and visualization of bacterial genomes. Nucl. Acids Res. 51, W484–W492. https://doi.org/10.1093/nar/gkad326 (2023).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Buchfink, B., Reuter, K. & Drost, H. G. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat. Methods 18, 366–368. https://doi.org/10.1038/s41592-021-01101-x (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Conesa, A. & Götz, S. Blast2GO: A comprehensive suite for functional analysis in plant genomics. Int. J. Plant Genomics 2008, 619832. https://doi.org/10.1155/2008/619832 (2008).Article 
CAS 
PubMed 

Google Scholar 
Ye, J. et al. WEGO 2.0: A web tool for analyzing and plotting GO annotations, 2018 update. NucL. Acids Res. 46, W71–W75. https://doi.org/10.1093/nar/gky400 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Blin, K. et al. antiSMASH 7.0: New and improved predictions for detection, regulation, chemical structures and visualisation. Nucl. Acids Res 51, W46–W50. https://doi.org/10.1093/nar/gkad344 (2023).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Couvin, D. et al. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucl. Acids Res. 46, W246–W251. https://doi.org/10.1093/nar/gky425 (2018).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Carattoli, A. et al. In silico detection and typing of plasmids using plasmidfinder and plasmid multilocus sequence typing. Antimicrob. Agents Chemother. 58, 3895–3903. https://doi.org/10.1128/AAC.02412-14 (2014).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Arndt, D. et al. PHASTER: A better, faster version of the PHAST phage search tool. Nucl. Acids Res. 44, W16–W21. https://doi.org/10.1093/nar/gkw387 (2016).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Zhou, Y., Liang, Y., Lynch, K. H., Dennis, J. J. & Wishart, D. S. PHAST: A fast phage search tool. Nucl. Acids Res. 39, W347–W352. https://doi.org/10.1093/nar/gkr485 (2011).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Yoon, S. H. et al. Introducing EzBioCloud: A taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int. J. Syst. Evol. Microbiol. 67, 1613–1617. https://doi.org/10.1099/ijsem.0.001755 (2017).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Saitou, N. & Nei, M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454 (1987).Article 
CAS 
PubMed 

Google Scholar 
Tamura, K. & Nei, M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10, 512–526. https://doi.org/10.1093/oxfordjournals.molbev.a040023 (1993).Article 
CAS 
PubMed 

Google Scholar 
Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Bio.l Evol. 35, 1547–1549. https://doi.org/10.1093/molbev/msy096 (2018).Article 
CAS 

Google Scholar 
Yoon, S. H., Ha, S. M., Lim, J., Kwon, S. & Chun, J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110, 1281–1286. https://doi.org/10.1007/s10482-017-0844-4 (2017).Article 
CAS 
PubMed 

Google Scholar 
Meier-Kolthoff, J. P., Carbasse, J. S., Peinado-Olarte, R. L. & Göker, M. TYGS and LPSN: A database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucl. Acids Res. 50, D801–D807. https://doi.org/10.1093/nar/gkab902 (2022).Article 
CAS 
PubMed 

Google Scholar 
Lee, I., Ouk Kim, Y., Park, S. C. & Chun, J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int. J. Syst. Evol. Microbiol. 66, 1100–1103. https://doi.org/10.1099/ijsem.0.000760 (2016).Article 
CAS 
PubMed 

Google Scholar 
Lynch, E. A. et al. Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux. PLoS ONE 7, e41389. https://doi.org/10.1371/journal.pone.0041389 (2012).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Dummer, A. M. et al. Bacterioopsin-mediated regulation of bacterioruberin biosynthesis in Halobacterium salinarum. J. Bacteriol. 193, 5658–5667. https://doi.org/10.1128/JB.05376-11 (2011).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Giani, M., Miralles-Robledillo, J. M., Peiró, G., Pire, C. & Martínez-Espinosa, R. M. Deciphering pathways for carotenogenesis in haloarchaea. Molecules 25, 1197. https://doi.org/10.3390/molecules25051197 (2020).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar