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Comparative Genomics of the Genus Methanohalophilus, Including a Newly Isolated Strain From Kebrit Deep in the Red Sea
Copyright policy )Comparative Genomics of the Genus Methanohalophilus, Including a Newly Isolated Strain From Kebrit Deep in the Red Sea
Halophilic methanogens play an important role in the carbon cycle in hypersaline environments, but are under-represented in culture collections. In this study, we describe a novel Methanohalophilus strain that was isolated from the sulfide-rich brine-seawater interface of Kebrit Deep in the Red Sea. Based on physiological and phylogenomic features, strain RSK, which is the first methanogenic archaeon to be isolated from a deep hypersaline anoxic brine lake of the Red Sea, represents a novel species of this genus. In order to compare the genetic traits underpinning the adaptations of this genus in diverse hypersaline environments, we sequenced the genome of strain RSK and compared it with genomes of previously isolated and well characterized species in this genus (Methanohalophilus mahii, Methanohalophilus halophilus, Methanohalophilus portucalensis, and Methanohalophilus euhalobius). These analyses revealed a highly conserved genomic core of greater than 93% of annotated genes (1490 genes) containing pathways for methylotrophic methanogenesis, osmoprotection through salt-out strategy, and oxidative stress response, among others. Despite the high degree of genomic conservation, species-specific differences in sulfur and glycogen metabolisms, viral resistance, amino acid, and peptide uptake machineries were also evident. Thus, while Methanohalophilus species are found in diverse extreme environments, each genotype also possesses adaptive traits that are likely relevant in their respective hypersaline habitats.
- University of Giessen Germany
- University of Florida United States
- Pennsylvania State University United States
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Saudi Arabia Saudi Arabia
- King Abdullah University of Science and Technology (KAUST) Saudi Arabia
Microsoft Academic Graph classification: Comparative genomics biology Strain (biology) Library science Methanohalophilus biology.organism_classification Genus Methanohalophilus
Library of Congress Subject Headings: lcsh:QR1-502 lcsh:Microbiology
Microbiology (medical), comparative genomics, methanogenic archaea, Microbiology, red sea, Methanohalophilus, deep-sea brine
Microbiology (medical), comparative genomics, methanogenic archaea, Microbiology, red sea, Methanohalophilus, deep-sea brine
Microsoft Academic Graph classification: Comparative genomics biology Strain (biology) Library science Methanohalophilus biology.organism_classification Genus Methanohalophilus
Library of Congress Subject Headings: lcsh:QR1-502 lcsh:Microbiology
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Alam, I., Antunes, A., Kamau, A. A., Ba alawi, W., Kalkatawi, M., Stingl, U., et al. (2013). INDIGO - integrated data warehouse of MIcrobial GenOmes with examples from the Red Sea extremophiles. PLoS One 8:e82210. doi: 10.1371/ journal.pone.0082210
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Antunes, A., Alam, I., Simões, M. F., Daniels, C., Ferreira, A. J. S., Siam, R., et al. (2015). First Insights into the viral communities of the deep-sea aoxic brines of the Red Sea. Genom. Proteom. Bioinform. 13, 304-309. doi: 10.1016/j.gpb.2015. 06.004 [OpenAIRE]
Antunes, A., Ngugi, D. K., and Stingl, U. (2011). Microbiology of the Red Sea (and other) deep-sea anoxic brine lakes. Environ. Microbiol. Rep. 3, 416-433. doi: 10.1111/j.1758-2229.2011.00264.x
Araya-Secchi, R., Garate, J. A., Holmes, D. S., and Perez-Acle, T. (2011). Molecular dynamics study of the archaeal aquaporin AqpM. BMC Genomics 12(Suppl. 4):S8. doi: 10.1186/1471-2164-12-S4-S8
Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., et al. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455-477. doi: 10.1089/cmb.2012. 0021
Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., et al. (2007). CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1712. doi: 10.1126/science.1138140 [OpenAIRE]
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Boone, D. R., Mathrani, I. M., Liu, Y., Menaia, J. A. G. F., Mah, R. A., and Boone, J. E. (1993). Isolation and characterization of Methanohalophilus portucalensis sp. nov. and DNA reassociation study of the genus Methanohalophilus. Int. J. Syst. Bacteriol. 43, 430-437. doi: 10.1099/00207713-43-3-430
Borin, S., Brusetti, L., Mapelli, F., D'Auria, G., Brusa, T., Marzorati, M., et al. (2009). Sulfur cycling and methanogenesis primarily drive microbial colonization of the highly sulfidic Urania deep hypersaline basin. Proc. Natl. Acad. Sci. U.S.A. 106, 9151-9156. doi: 10.1073/pnas.0811984106 [OpenAIRE]
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Citations provided by BIP!Popularity provided by BIP!- University of Giessen Germany
- University of Florida United States
- Pennsylvania State University United States
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Saudi Arabia Saudi Arabia
- King Abdullah University of Science and Technology (KAUST) Saudi Arabia
- DSM (Netherlands) Netherlands
- Florida Southern College United States
- University of Pennsylvania United States
- King Abdullah University of Science and Technology Saudi Arabia
- Department of Biochemistry and Molecular Biology Pennsylvania State University United States
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Saudi Arabia Saudi Arabia
Halophilic methanogens play an important role in the carbon cycle in hypersaline environments, but are under-represented in culture collections. In this study, we describe a novel Methanohalophilus strain that was isolated from the sulfide-rich brine-seawater interface of Kebrit Deep in the Red Sea. Based on physiological and phylogenomic features, strain RSK, which is the first methanogenic archaeon to be isolated from a deep hypersaline anoxic brine lake of the Red Sea, represents a novel species of this genus. In order to compare the genetic traits underpinning the adaptations of this genus in diverse hypersaline environments, we sequenced the genome of strain RSK and compared it with genomes of previously isolated and well characterized species in this genus (Methanohalophilus mahii, Methanohalophilus halophilus, Methanohalophilus portucalensis, and Methanohalophilus euhalobius). These analyses revealed a highly conserved genomic core of greater than 93% of annotated genes (1490 genes) containing pathways for methylotrophic methanogenesis, osmoprotection through salt-out strategy, and oxidative stress response, among others. Despite the high degree of genomic conservation, species-specific differences in sulfur and glycogen metabolisms, viral resistance, amino acid, and peptide uptake machineries were also evident. Thus, while Methanohalophilus species are found in diverse extreme environments, each genotype also possesses adaptive traits that are likely relevant in their respective hypersaline habitats.