Diversity of the Genus and Proposal of 19 Novel Species Isolated from Glaciers

Overview

Journal Front Microbiol

Specialty Microbiology

Date 2023 Apr 6

PMID 37020720

Authors

Qing Liu

Lei-Lei Yang

Yu-Hua Xin

Affiliations

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Abstract

The bacterial genus includes at present 14 species that live in cryospheric environments. In this study, we analyzed 101 genomes of with pure cultures obtained from GenBank. They could be classified into 44 species based on average nucleotide identity (ANI) analysis, showing the diversity of . Among these, 19 strains in our laboratory were isolated from the glacier samples in China. The pairwise ANI values of these 19 strains and known species were <95%, indicating that they represented 19 novel species. The comparative genomic analysis showed significant differences in gene content between the two groups with a maximum growth temperature ( ) of ≤ 20°C and a of >20°C. A comprehensive and robust phylogenetic tree, including 14 known species and 19 novel species, was constructed and showed five phylogenetic branches based on 265 concatenated single-copy gene sequences. The parameter had a strong phylogenetic signal, indicating that the temperature adaptation of was largely through vertical transfer rather than horizontal gene transfer and was affected by selection. Furthermore, using polyphasic taxonomy combined with phylogenomic analysis, we proposed 19 novel species of the genus by the following 19 names: sp. nov., sp. nov., sp. nov., sp. nov., sp. nov., sp. nov., sp. nov., sp. nov., sp. nov., sp. nov., sp. nov., sp. nov., sp. nov., sp. nov., sp. nov., sp. nov., sp. nov., sp. nov., and sp. nov. Overall, the taxonomy and genomic analysis can improve our knowledge of phenotypic diversity, genetic diversity, and evolutionary characteristics of .

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References

Liu Q, Song W, Zhou Y, Dong X, Xin Y . Phenotypic divergence of thermotolerance: Molecular basis and cold adaptive evolution related to intrinsic DNA flexibility of glacier-inhabiting Cryobacterium strains. Environ Microbiol. 2020; 22(4):1409-1420. DOI: 10.1111/1462-2920.14957. View

Blomberg S, Garland Jr T, Ives A . Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution. 2003; 57(4):717-45. DOI: 10.1111/j.0014-3820.2003.tb00285.x. View

Jain C, Rodriguez-R L, Phillippy A, Konstantinidis K, Aluru S . High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018; 9(1):5114. PMC: 6269478. DOI: 10.1038/s41467-018-07641-9. View

Liu Q, Yang L, Liu H, Zhang G, Xin Y . gen. nov., sp. nov., a novel member of the family isolated from a glacier. Int J Syst Evol Microbiol. 2021; 71(7). DOI: 10.1099/ijsem.0.004886. View

Contreras-Moreira B, Vinuesa P . GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl Environ Microbiol. 2013; 79(24):7696-701. PMC: 3837814. DOI: 10.1128/AEM.02411-13. View

Polz M, Alm E, Hanage W . Horizontal gene transfer and the evolution of bacterial and archaeal population structure. Trends Genet. 2013; 29(3):170-5. PMC: 3760709. DOI: 10.1016/j.tig.2012.12.006. View

Liu Q, Liu H, Zhou Y, Xin Y . Microevolution and Adaptive Strategy of Psychrophilic Species sp. nov. Isolated From Glaciers. Front Microbiol. 2019; 10:1069. PMC: 6538692. DOI: 10.3389/fmicb.2019.01069. View

Liu Q, Liu H, Zhang J, Zhou Y, Xin Y . Cryobacterium levicorallinum sp. nov., a psychrophilic bacterium isolated from glacier ice. Int J Syst Evol Microbiol. 2013; 63(Pt 8):2819-2822. DOI: 10.1099/ijs.0.046896-0. View

Liu Q, Xin Y, Chen X, Liu H, Zhou Y, Chen W . Cryobacterium aureum sp. nov., a psychrophilic bacterium isolated from glacier ice collected from the ice tongue surface. Int J Syst Evol Microbiol. 2018; 68(4):1173-1176. DOI: 10.1099/ijsem.0.002647. View

10.

Liu Q, Tian J, Liu H, Zhou Y, Xin Y . sp. nov., a psychrophilic bacterium isolated from glacier ice. Int J Syst Evol Microbiol. 2019; 69(10):3276-3280. DOI: 10.1099/ijsem.0.003620. View

11.

Kimura M . A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980; 16(2):111-20. DOI: 10.1007/BF01731581. View

12.

Galperin M, Wolf Y, Makarova K, Vera Alvarez R, Landsman D, Koonin E . COG database update: focus on microbial diversity, model organisms, and widespread pathogens. Nucleic Acids Res. 2020; 49(D1):D274-D281. PMC: 7778934. DOI: 10.1093/nar/gkaa1018. View

13.

Boenigk J, Jost S, Stoeck T, Garstecki T . Differential thermal adaptation of clonal strains of a protist morphospecies originating from different climatic zones. Environ Microbiol. 2007; 9(3):593-602. DOI: 10.1111/j.1462-2920.2006.01175.x. View

14.

Yang L, Liu H, Liu Q, Xin Y . and sp. nov., isolated from a glacier. Int J Syst Evol Microbiol. 2021; 71(12). DOI: 10.1099/ijsem.0.005177. View

15.

Boenigk J, Pfandl K, Garstecki T, Harms H, Novarino G, Chatzinotas A . Evidence for geographic isolation and signs of endemism within a protistan morphospecies. Appl Environ Microbiol. 2006; 72(8):5159-64. PMC: 1538753. DOI: 10.1128/AEM.00601-06. View

16.

Reddy G, Pradhan S, Manorama R, Shivaji S . Cryobacterium roopkundense sp. nov., a psychrophilic bacterium isolated from glacial soil. Int J Syst Evol Microbiol. 2009; 60(Pt 4):866-870. DOI: 10.1099/ijs.0.011775-0. View

17.

Kim M, Oh H, Park S, Chun J . Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol. 2014; 64(Pt 2):346-351. DOI: 10.1099/ijs.0.059774-0. View

18.

Liu Y, Vick-Majors T, Priscu J, Yao T, Kang S, Liu K . Biogeography of cryoconite bacterial communities on glaciers of the Tibetan Plateau. FEMS Microbiol Ecol. 2017; 93(6). DOI: 10.1093/femsec/fix072. View

19.

Silva B, Antunes C, Andrade F, Silva E, Grande J, Luis A . Prokaryotic and eukaryotic diversity in hydrothermal continental systems. Arch Microbiol. 2021; 203(7):3751-3766. DOI: 10.1007/s00203-021-02416-1. View

20.

Liu Q, Zhou Y, Xin Y . High diversity and distinctive community structure of bacteria on glaciers in China revealed by 454 pyrosequencing. Syst Appl Microbiol. 2015; 38(8):578-85. DOI: 10.1016/j.syapm.2015.09.005. View