5,587
Views
0
CrossRef citations to date
0
Altmetric
Research Article

Genetic analysis of the frozen microbiome at 7900 m a.s.l., on the South Col of Sagarmatha (Mount Everest)

ORCID Icon, , , , &
Article: 2164999 | Received 01 Jul 2022, Accepted 01 Jan 2023, Published online: 16 Feb 2023

References

  • Aalismail, N. A., D. K. Ngugi, R. Díaz-Rúa, I. Alam, M. Cusack, and C. M. Duarte. 2019. Functional metagenomic analysis of dust-associated microbiomes above the Red Sea. Scientific Reports 9:13741. doi:10.1038/s41598-019-50194-0.
  • Aguirre, M., and M. D. Collins. 1992. Phylogenetic analysis of Alloiococcus otitis gen. nov., sp. nov., an organism from human middle ear fluid. International Journal of Systematic and Evolutionary Microbiology 42:79–17. doi:10.1099/00207713-42-1-79.
  • Ahmad, T., G. Gupta, A. Sharma, B. Kaur, M. A. El-Sheikh, and M. N. Alyemeni. 2021. Metagenomic analysis exploring taxonomic and functional diversity of bacterial communities of a Himalayan urban freshwater lake. PLOS ONE 16:e0248116. doi:10.1371/journal.pone.0248116.
  • Alonso-Vega, P., L. Carro, E. Martínez-Molina, and M. E. Trujillo. 2011. Auraticoccus monumenti gen. nov., sp. nov., an Actinomycete isolated from a deteriorated sandstone monument. International Journal of Systematic and Evolutionary Microbiology 61:1098–103. doi:10.1099/ijs.0.024257-0.
  • Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. Journal of Molecular Biology 215:403–10. doi:10.1016/S0022-2836(05)80360-2.
  • Amato, P., M. Parazols, M. Sancelme, P. Laj, G. Mailhot, and A. Delort. 2007. Microorganisms isolated from the water phase of tropospheric clouds at the Puy de Dôme: Major groups and growth abilities at low temperatures. FEMS Microbiology Ecology 59:242–54. doi:10.1111/j.1574-6941.2006.00199.x.
  • Archer, S. D. J., K. C. Lee, T. Caruso, T. Maki, C. K. Lee, S. C. Cary, D. A. Cowan, F. T. Maestre, and S. B. Pointing. 2019. Airborne microbial transport limitation to isolated Antarctic soil habitats. Nature Microbiology 4:925–32. doi:10.1038/s41564-019-0370-4.
  • Atlas, R. M. 2004. Handbook of microbiological media. Boca Raton, FL: CRC press.
  • Babalola, O. O., B. M. Kirby, M. Le Roes-Hill, A. E. Cook, S. C. Cary, S. G. Burton, and D. A. Cowan. 2009. Phylogenetic analysis of Actinobacterial populations associated with Antarctic Dry Valley mineral soils. Environmental Microbiology 11:566–76. doi:10.1111/j.1462-2920.2008.01809.x.
  • Becher, D., K. Hempel, S. Sievers, D. Zühlke, J. Pané-Farré, A. Otto, S. Fuchs, D. Albrecht, J. Bernhardt, S. Engelmann, et al. 2009. A proteomic view of an important human pathogen – Towards the quantification of the entire Staphylococcus aureus proteome. PLOS ONE 4:e8176. doi:10.1371/journal.pone.0008176.
  • Bellemain, E., T. Carlsen, C. Brochmann, E. Coissac, P. Taberlet, and H. Kauserud. 2010. ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiology 10:189. doi:10.1186/1471-2180-10-189.
  • Breitenbach, R., D. Silbernagl, J. Toepel, H. Sturm, W. J. Broughton, G. L. Sassaki, and A. A. Gorbushina. 2018. Corrosive extracellular polysaccharides of the rock-inhabiting model fungus Knufia petricola. Extremophiles 22:165–75. doi:10.1007/s00792-017-0984-5.
  • Bryant, J. A., C. Lamanna, H. Morlon, A. J. Kerkhoff, B. J. Enquist, and J. L. Green. 2008. Microbes on mountainsides: Contrasting elevational patterns of bacterial and plant diversity. Proceedings of the National Academy of Sciences 105:11505–11. doi:10.1073/pnas.0801920105.
  • Busarakam, K., A. T. Bull, M. E. Trujillo, R. Riesco, V. Sangal, G. P. van Wezel, and M. Goodfellow. 2016. Modestobacter caceresii sp. nov., novel Actinobacteria with an insight into their adaptive mechanisms for survival in extreme hyper-arid Atacama Desert soils. Systematic and Applied Microbiology 39:243–51. doi:10.1016/j.syapm.2016.03.007.
  • Callahan, B. J., P. J. McMurdie, M. J. Rosen, A. W. Han, A. A. Johnson, and S. P. Holmes. 2016. DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods 13:581–83. doi:10.1038/nmeth.3869.
  • Caporaso, J. G., C. L. Lauber, W. A. Walters, D. Berg-Lyons, J. Huntley, N. Fierer, S. M. Owens, J. Betley, L. Fraser, M. Bauer, et al. 2012. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. The ISME Journal 6:1621–24. doi:10.1038/ismej.2012.8.
  • Cheema, M. T., J. Ye, F. Li, Q. Lu, M. Abbas, I. Sajid, D. Huang, S. Liu, and C. Sun. 2020. Auraticoccus cholistanensis sp. nov., an Actinomycete isolated from soil of the Cholistan Desert, and emended description of the genus Auraticoccus. International Journal of Systematic and Evolutionary Microbiology 70:3179–85. doi:10.1099/ijsem.0.004152.
  • Costello, E. K., S. R. P. Halloy, S. C. Reed, P. Sowell, and S. K. Schmidt. 2009. Fumarole-supported islands of biodiversity within a hyperarid, high-elevation landscape on Socompa Volcano, Puna de Atacama, Andes. Applied and Environmental Microbiology 75:735–47. doi:10.1128/AEM.01469-08.
  • Cowan, D. A., T. P. Makhalanyane, P. G. Dennis, and D. W. Hopkins. 2014. Microbial ecology and biogeochemistry of continental Antarctic soils. Frontiers in Microbiology 5:154. doi:10.3389/fmicb.2014.00154.
  • Delgado-Baquerizo, M., A. M. Oliverio, T. E. Brewer, A. Benavent-González, D. J. Eldridge, R. D. Bardgett, F. T. Maestre, B. K. Singh, and N. Fierer. 2018. A global atlas of the dominant bacteria found in soil. Science 359:320–25. doi:10.1126/science.aap9516.
  • Dragone, N. B., M. A. Diaz, I. D. Hogg, W. B. Lyons, W. A. Jackson, D. H. Wall, B. J. Adams, and N. Fierer. 2021. Exploring the boundaries of microbial habitability in soil. Journal of Geophysical Research: Biogeosciences 126:e2020JG006052. doi:10.1029/2020JG006052.
  • Dragone, N. B., J. B. Henley, H. Holland-Moritz, M. Diaz, I. D. Hogg, W. B. Lyons, D. H. Wall, B. J. Adams, and N. Fierer. 2022. Elevational constraints on the composition and genomic attributes of soil microbial communities in Antarctica. mSystems 7:e01330–21. doi:10.1128/msystems.01330-21.
  • Duarte, A. W. F., J. A. Dos Santos, M. V. Vianna, J. M. F. Vieira, V. H. Mallagutti, F. J. Inforsato, L. C. P. Wentzel, L. D. Lario, A. Rodrigues, F. C. Pagnocca, et al. 2018. Cold-adapted enzymes produced by fungi from terrestrial and marine Antarctic environments. Critical Reviews in Biotechnology 38:600–19. doi:10.1080/07388551.2017.1379468.
  • Dunitz, M. I., J. M. Lang, G. Jospin, A. E. Darling, J. A. Eisen, and D. A. Coil. 2015. Swabs to genomes: A comprehensive workflow. PeerJ 3:e960. doi:10.7717/peerj.960.
  • Edgar, R. C. 2004. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32:1792–97. doi:10.1093/nar/gkh340.
  • Egan, S., S. Kjelleberg, and C. Holmström. 2015. Pseudoalteromonas ulvae sp. nov., a bacterium with antifouling activities isolated from the surface of a marine alga. International Journal of Systematic and Evolutionary Microbiology 51:1499–504. doi:10.1099/00207713-51-4-1499.
  • Escapa, I. F., T. Chen, Y. Huang, P. Gajare, F. E. Dewhirst, and K. P. Lemon. 2018. New insights into human nostril microbiome from the Expanded Human Oral Microbiome Database (EHOMD): A resource for the microbiome of the human aerodigestive tract. Msystems 3:e00187–18. doi:10.1128/mSystems.00187-18.
  • Essoussi, I., F. Ghodhbane-Gtari, H. Amairi, H. Sghaier, A. Jaouani, L. Brusetti, D. Daffonchio, A. Boudabous, and M. Gtari. 2010. Esterase as an enzymatic signature of Geodermatophilaceae adaptability to Sahara Desert stones and monuments. Journal of Applied Microbiology 108:1723–32. doi:10.1111/j.1365-2672.2009.04580.x.
  • Freeman, K. R., A. P. Martin, D. Karki, R. C. Lynch, M. S. Mitter, A. F. Meyer, J. E. Longcore, D. R. Simmons, and S. K. Schmidt. 2009. Evidence that chytrids dominate fungal communities in high-elevation soils. Proceedings of the National Academy of Sciences 106:18315–20. doi:10.1073/pnas.0907303106.
  • Gevers, D., R. Knight, J. F. Petrosino, K. Huang, A. L. McGuire, B. W. Birren, K. E. Nelson, O. White, B. A. Methé, and C. Huttenhower. 2012. The Human Microbiome Project: A community resource for the healthy human microbiome. PLOS Biology 10:e1001377. doi:10.1371/journal.pbio.1001377.
  • Ghareeb, H., A. Becker, T. Iven, I. Feussner, and J. Schirawski. 2011. Sporisorium reilianum infection changes inflorescence and branching architectures of maize. Plant Physiology 156:2037–52. doi:10.1104/pp.111.179499.
  • Golinska, P., M. Montero-Calasanz, M. Świecimska, A. Yaramis, J. M. Igual, A. T. Bull, and M. Goodfellow. 2020. Modestobacter excelsi sp. nov., a novel Actinobacterium isolated from a high altitude Atacama Desert soil. Systematic and Applied Microbiology 43:126051. doi:10.1016/j.syapm.2019.126051.
  • Grice, E. A., and J. A. Segre. 2011. The skin microbiome. Nature Reviews. Microbiology 9:244–53. doi:10.1038/nrmicro2537.
  • Harwood, V., C. Staley, B. D. Badgley, K. Borges, and A. Korajkic. 2014. Microbial source tracking markers for detection of fecal contamination in environmental waters: Relationships between pathogens and human health outcomes. FEMS Microbiology Reviews 38:1–40. doi:10.1111/1574-6976.12031.
  • Hezbri, K., F. Ghodhbane-Gtari, M. Montero-Calasanz, I. Nouioui, M. Rohde, C. Spröer, P. Schumann, H. Klenk, and M. Gtari. 2016. Geodermatophilus pulveris sp. nov., a gamma-radiation-resistant Actinobacterium isolated from the Sahara Desert. International Journal of Systematic and Evolutionary Microbiology 66:3828–34. doi:10.1099/ijsem.0.001272.
  • Ibironke, O., L. R. McGuinness, S. Lu, Y. Wang, S. Hussain, C. P. Weisel, and L. J. Kerkhof. 2020. Species-level evaluation of the human respiratory microbiome. GigaScience 9:giaa038. doi:10.1093/gigascience/giaa038.
  • Ishiguro, E. E. 1969. The microbiology of Mount Everest soils. PhD Diss., San Francisco State College.
  • Ishiguro, E. E., and D. W. Fletcher. 1975. Characterization of Geodermatophilus strains isolated from high altitude Mount Everest soils. Mikrobiologika 12:99–108.
  • Ishiguro, E. E., and R. S. Wolfe. 1970. Control of morphogenesis in Geodermatophilus: Ultrastructural studies. Journal of Bacteriology 104:566–80. doi:10.1128/jb.104.1.566-580.1970.
  • Joergensen, R. G., and C. Emmerling. 2006. Methods for evaluating human impact on soil microorganisms based on their activity, biomass, and diversity in agricultural soils. Journal of Plant Nutrition and Soil Science 169:295–309. doi:10.1002/jpln.200521941.
  • Kang, S., Q. Zhang, Y. Zhang, W. Guo, Z. Ji, M. Shen, S. Wang, X. Wang, L. Tripathee, Y. Liu, et al. 2022. Warming and thawing in the Mt. Everest region: A review of climate and environmental changes. Earth-Science Reviews 225:103911. doi:10.1016/j.earscirev.2021.103911.
  • Kennedy, H. F., D. Morrison, M. E. Kaufmann, M. S. Jackson, J. Bagg, B. E. S. Gibson, C. G. Gemmell, and J. R. Michie. 2000. Origins of Staphylococcus epidermidis and Streptococcus oralis causing bacteraemia in a bone marrow transplant patient. Journal of Medical Microbiology 49:367–70. doi:10.1099/0022-1317-49-4-367.
  • King, A. J., K. R. Freeman, K. F. McCormick, R. C. Lynch, C. Lozupone, R. Knight, and S. K. Schmidt. 2010. Biogeography and habitat modelling of high-alpine bacteria. Nature Communications 1:53. doi:10.1038/ncomms1055.
  • Klepa, M. S., L. C. F. Helene, G. O’Hara, and M. Hungria. 2021. Bradyrhizobium agreste sp. nov., Bradyrhizobium glycinis sp. nov. and Bradyrhizobium diversitatis sp. Nov., isolated from a biodiversity hotspot of the genus Glycine in Western Australia. International Journal of Systematic and Evolutionary Microbiology 71:004742. doi:10.1099/ijsem.0.004742.
  • Ko, K. S., S. Lim, S. Jung, J. M. Yoon, J. Y. Choi, and J. Song. 2011. Sequence type 72 meticillin-resistant Staphylococcus aureus isolates from humans, raw meat and soil in South Korea. Journal of Medical Microbiology 60:442–45. doi:10.1099/jmm.0.026484-0.
  • Leff, J. 2016. mctoolsR. v.1.1. GitHub. https://github.com/leffj/mctoolsr/
  • Letunic, I., and P. Bork. 2016. Interactive tree of life (ITOL) v3: An online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Research 44:W242–W245. doi:10.1093/nar/gkw290.
  • Liu, Y. Q., T. D. Yao, S. C. Kang, N. Z. Jiao, Y. H. Zeng, S. J. Huang, and T. W. Luo. 2007. Microbial community structure in major habitats above 6000 m on Mount Everest. Chinese Science Bulletin 52:2350–57. doi:10.1007/s11434-007-0360-4.
  • Lorite, M. J., J. Tachil, J. Sanjuán, O. Meyer, and E. J. Bedmar. 2000. Carbon monoxide dehydrogenase activity in Bradyrhizobium japonicum. Applied and Environmental Microbiology 66:1871–76. doi:10.1128/AEM.66.5.1871-1876.2000.
  • Lynch, R. C., A. J. King, M. E. Farías, P. Sowell, C. Vitry, and S. K. Schmidt. 2012. The potential for microbial life in the highest-elevation (>6000 m.a.s.l.) mineral soils of the Atacama Region. Journal of Geophysical Research 117:G02028. doi:10.1029/2012JG001961.
  • Maki, T., K. C. Lee, K. Kawai, K. Onishi, C. S. Hong, Y. Kurosaki, M. Shinoda, K. Kai, Y. Iwasaka, S. D. J. Archer, et al. 2019. Aeolian dispersal of bacteria associated with desert dust and anthropogenic particles over continental and oceanic surfaces. Journal of Geophysical Research: Atmospheres 124:5579–88. doi:10.1029/2018JD029597.
  • Mandic-Mulec, I., P. Stefanic, and J. D. van Elsas. 2015. Ecology of Bacillaceae. Microbiology Spectrum 3:3–2. doi:10.1128/microbiolspec.TBS-0017-2013.
  • Margesin, R., M. Jud, D. Tscherko, and F. Schinner. 2009. Microbial communities and activities in alpine and subalpine soils. FEMS Microbiology Ecology 67:208–18. doi:10.1111/j.1574-6941.2008.00620.x.
  • Margesin, R., and V. Miteva. 2011. Diversity and ecology of psychrophilic microorganisms. Research in Microbiology 162:346–61. doi:10.1016/j.resmic.2010.12.004.
  • Matthews, T., L. B. Perry, I. Koch, D. Aryal, A. Khadka, D. Shrestha, K. Abernathy, A. C. Elmore, A. Seimon, A. Tait, et al. 2020. Going to extremes: Installing the world’s highest weather stations on Mount Everest. Bulletin of the American Meteorological Society 101:E1870–E1890. doi:10.1175/BAMS-D-19-0198.1.
  • Merino, N., H. S. Aronson, D. P. Bojanova, J. Feyhl-Buska, M. L. Wong, S. Zhang, and D. Giovannelli. 2019. Living at the extremes: Extremophiles and the limits of life in a planetary context. Frontiers in Microbiology 10:780. doi:10.3389/fmicb.2019.00780.
  • Mevs, U., E. Stackebrandt, P. Schumann, C. A. Gallikowski, and P. Hirsch. 2000. Modestobacter multiseptatus gen. nov., sp. nov., a budding Actinomycete from soils of the Asgard Range (Transantarctic Mountains). International Journal of Systematic and Evolutionary Microbiology 50:337–46. doi:10.1099/00207713-50-1-337.
  • Montero-Calasanz, M. C., M. Göker, G. Pötter, M. Rohde, C. Spröer, P. Schumann, A. A. Gorbushina, and H. P. Klenk. 2012. Geodermatophilus arenarius sp. Nov., a xerophilic Actinomycete isolated from Saharan Desert sand in Chad. Extremophiles 16:903–09. doi:10.1007/s00792-012-0486-4.
  • Montero-Calasanz, M. C., M. Göker, G. Pötter, M. Rohde, C. Spröer, P. Schumann, A. A. Gorbushina, and H. Klenk. 2013a. Geodermatophilus africanus sp. nov., a halotolerant Actinomycete isolated from Saharan Desert sand. Antonie van Leeuwenhoek 104:207–16. doi:10.1007/s10482-013-9939-8.
  • Montero-Calasanz, M. C., M. Göker, G. Pötter, M. Rohde, C. Spröer, P. Schumann, A. A. Gorbushina, and H. P. Klenk. 2013b. Geodermatophilus arenarius sp. Nov., a xerophilic Actinomycete isolated from Saharan Desert sand in Chad. Archives of Microbiology 195:153–59. doi:10.1007/s00203-012-0860-8.
  • Montero-Calasanz, M. C., M. Göker, M. Rohde, P. Schumann, G. Pötter, C. Spröer, A. A. Gorbushina, and H. Klenk. 2013. Geodermatophilus siccatus sp. nov., isolated from arid sand of the Saharan Desert in Chad. Antonie van Leeuwenhoek 103:449–56. doi:10.1007/s10482-012-9824-x.
  • Montero-Calasanz, M. C., K. Hezbri, M. Göker, H. Sghaier, M. Rohde, C. Spröer, P. Schumann, and H. Klenk. 2015. Description of gamma radiation-resistant Geodermatophilus dictyosporus sp. nov. to accommodate the not validly named Geodermatophilus obscurus subsp. dictyosporus (Luedemann, 1968). Extremophiles 19:77–85. doi:10.1007/s00792-014-0708-z.
  • Montero-Calasanz, M. C., B. Hofner, M. Göker, M. Rohde, C. Spröer, K. Hezbri, M. Gtari, P. Schumann, and H. Klenk. 2014. Geodermatophilus poikilotrophi sp. nov.: A multitolerant Actinomycete isolated from dolomitic marble. BioMed Research International 2014:e914767. doi:10.1155/2014/914767.
  • Montero-Calasanz, M. C., J. P. Meier-Kolthoff, D. Zhang, A. Yaramis, M. Rohde, T. Woyke, N. C. Kyrpides, P. Schumann, W. Li, and M. Göker. 2017. Genome-scale data call for a taxonomic rearrangement of Geodermatophilaceae. Frontiers in Microbiology 8:2501. doi:10.3389/fmicb.2017.02501.
  • Montero-Calasanz, M. C., A. Yaramis, I. Nouioui, J. M. Igual, C. Spröer, J. F. Castro, P. Schumann, H. Klenk, and C. Urzì. 2019. Modestobacter italicus sp. nov., isolated from Carrara marble quarry and emended descriptions of the genus Modestobacter and the species Modestobacter marinus, Modestobacter multiseptatus, Modestobacter roseus and Modestobacter versicolor. International Journal of Systematic and Evolutionary Microbiology 69:1537–45. doi:10.1099/ijsem.0.003282.
  • Montes, M. J., E. Mercadé, N. Bozal, and J. Guinea. 2004. Paenibacillus antarcticus sp. nov., a novel psychrotolerant organism from the Antarctic environment. International Journal of Systematic and Evolutionary Microbiology 54:1521–26. doi:10.1099/ijs.0.63078-0.
  • Moore, G. W. K., and J. L. Semple. 2004. High Himalayan meteorology: Weather at the South Col of Mount Everest. Geophysical Research Letters 31:L18109. doi:10.1029/2004GL020621.
  • Nagase, N., A. Sasaki, K. Yamashita, A. Shimizu, Y. Wakita, S. Kitai, and J. Kawano. 2002. Isolation and species distribution of Staphylococci from animal and human skin. Journal of Veterinary Medical Science 64:245–50. doi:10.1292/jvms.64.245.
  • National Geographic Society. 2022. Weather data from Mt. Everest. Online Resource. https://www.nationalgeographic.org/projects/perpetual-planet/everest/weather-data/
  • Nemergut, D. R., E. K. Costello, A. F. Meyer, M. Y. Pescador, M. N. Weintraub, and S. K. Schmidt. 2005. Structure and function of alpine and Arctic soil microbial communities. Research in Microbiology 156:775–84. doi:10.1016/j.resmic.2005.03.004.
  • Nie, G., H. Ming, S. Li, E. Zhou, J. Cheng, T. Yu, J. Zhang, H. Feng, S. Tang, and W. Li. 2012. Geodermatophilus nigrescens sp. nov., isolated from a dry-hot valley. Antonie van Leeuwenhoek 101:811–17. doi:10.1007/s10482-012-9696-0.
  • Nilsson, R. H., K. Larsson, A. F. S. Taylor, J. Bengtsson-Palme, T. S. Jeppesen, D. Schigel, P. Kennedy, K. Picard, F. O. Glöckner, L. Tedersoo, et al. 2019. The UNITE database for molecular identification of fungi: Handling dark taxa and parallel taxonomic classifications. Nucleic Acids Research 47:D259–D264. doi:10.1093/nar/gky1022.
  • Nizovoy, P., N. Bellora, S. Haridas, H. Sun, C. Daum, K. Barry, I. V. Grigoriev, D. Libkind, L. B. Connell, and M. Moliné. 2021. Unique genomic traits for cold adaptation in Naganishia vishniacii, a polyextremophile yeast isolated from Antarctica. FEMS Yeast Research 21:foaa056. doi:10.1093/femsyr/foaa056.
  • Normand, P., J. Gury, P. Pujic, B. Chouaia, E. Crotti, L. Brusetti, D. Daffonchio, B. Vacherie, V. Barbe, C. Medigue, et al. 2012. Genome sequence of radiation-resistant Modestobacter marinus strain BC501, a representative Actinobacterium that thrives on calcareous stone surfaces. Journal of Bacteriology 2012:4773–74. https://journals.asm.org/doi/abs/10.1128/JB.01029-12
  • Otto, M. 2009. Staphylococcus epidermidis—the ‘accidental’ pathogen. Nature Reviews. Microbiology 7:555–67. doi:10.1038/nrmicro2182.
  • Otto, M. 2010. Staphylococcus colonization of the skin and antimicrobial peptides. Expert Review of Dermatology 5:183–95. doi:10.1586/edm.10.6.
  • Palmieri, C., P. Varaldo, and B. Facinelli. 2011. Streptococcus suis, an emerging drug-resistant animal and human pathogen. Frontiers in Microbiology 2:235. doi:10.3389/fmicb.2011.00235.
  • Petrovič, U., N. Gunde-Cimerman, and P. Zalar. 2000. Xerotolerant mycobiota from high altitude Annapurna soil, Nepal. FEMS Microbiology Letters 182:339–42. doi:10.1111/j.1574-6968.2000.tb08918.x.
  • Potocki, M., P. A. Mayewski, T. Matthews, L. B. Perry, M. Schwikowski, A. M. Tait, E. Korotkikh, H. Clifford, S. Kang, T. C. Sherpa, et al. 2022. Mt. Everest’s highest glacier is a sentinel for accelerating ice loss. njp Climate and Atmospheric Science 5:1–8. doi:10.1038/s41612-022-00230-0.
  • Pulschen, A. A., A. G. Bendia, A. D. Fricker, V. H. Pellizari, D. Galante, and F. Rodrigues. 2017. Isolation of uncultured bacteria from Antarctica using long incubation periods and low nutritional media. Frontiers in Microbiology 8:1346. doi:10.3389/fmicb.2017.01346.
  • Pulschen, A. A., F. Rodrigues, R. T. D. Duarte, G. G. Araujo, I. F. Santiago, I. G. Paulino-Lima, C. A. Rosa, M. J. Kato, V. H. Pellizari, and D. Galante. 2015. UV-resistant yeasts isolated from a high-altitude volcanic area on the Atacama Desert as eukaryotic models for astrobiology. MicrobiologyOpen 4:574–488. doi:10.1002/mbo3.262.
  • Qin, S., G. Bian, Y. Zhang, K. Xing, C. Cao, C. Liu, C. Dai, W. Li, and J. Jiang. 2013. Modestobacter roseus sp. nov., an endophytic Actinomycete isolated from the coastal halophyte Salicornia europaea linn., and emended description of the genus Modestobacter. International Journal of Systematic and Evolutionary Microbiology 63:2197–202. doi:10.1099/ijs.0.044412-0.
  • Quast, C., E. Pruesse, P. Yilmaz, J. Gerken, T. Schweer, P. Yarza, J. Peplies, and F. O. Glöckner. 2013. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Research 41:D590–D596. doi:10.1093/nar/gks1219.
  • Rashid, I., and S. A. Romshoo. 2013. Impact of anthropogenic activities on water quality of Lidder River in Kashmir Himalayas. Environmental Monitoring and Assessment 185:4705–19. doi:10.1007/s10661-012-2898-0.
  • Rather, R. A., H. Bano, S. A. Padder, T. R. Baba, S. Ara, F. A. Lone, and S. Nazir. 2022. Impact of anthropogenic pressure on physico-chemical characteristics of forest soils of Kashmir Himalaya. Bulletin of Environmental Contamination and Toxicology 2022:1–10. doi:10.1007/s00128-022-03458-x.
  • R Core Team. 2017. R: A language and environment for statistical computing. Vienna, AT: R Foundation for Statistical Computing. https://www.R-project.org/
  • Reasoner, D. J., and E. E. Geldreich. 1985. A new medium for the enumeration and subculture of bacteria from potable water. Applied and Environmental Microbiology 49:1–7. doi:10.1128/AEM.49.1.1-7.1985.
  • Reina-Bueno, M., M. Argandoña, J. J. Nieto, A. Hidalgo-García, F. Iglesias-Guerra, M. J. Delgado, and C. Vargas. 2012. Role of trehalose in heat and desiccation tolerance in the soil Bacterium rhizobium etli. BMC Microbiology 12:207. doi:10.1186/1471-2180-12-207.
  • Ruiz-Gil, T., J. J. Acuña, S. Fujiyoshi, D. Tanaka, J. Noda, F. Maruyama, and M. A. Jorquera. 2020. Airborne bacterial communities of outdoor environments and their associated influencing factors. Environment International 145:106156. doi:10.1016/j.envint.2020.106156.
  • Saygin, H., H. Ay, K. Guven, and N. Sahin. 2019. Kribbella turkmenica sp. nov., isolated from the Karakum Desert. International Journal of Systematic and Evolutionary Microbiology 69:2533–40. doi:10.1099/ijsem.0.003538.
  • Schmidt, D. 1999. Das Extremklima Der Nordchilenischen Hochatacama Unter Besonderer Berücksichtigung Der Höhengradienten. Dresdener Geographische Beiträge 4:1–122.
  • Schmidt, S. K., E. M. S. Gendron, K. Vincent, A. J. Solon, P. Sommers, Z. R. Schubert, L. Vimercati, D. L. Porazinska, J. L. Darcy, and P. Sowell. 2018. Life at extreme elevations on Atacama volcanoes: The closest thing to Mars on Earth? Antonie van Leeuwenhoek 111:1389–401. doi:10.1007/s10482-018-1066-0.
  • Schmidt, S. K., R. C. Lynch, A. J. King, D. Karki, M. S. Robeson, L. Nagy, M. W. Williams, M. S. Mitter, and K. R. Freeman. 2011. Phylogeography of microbial phototrophs in the dry valleys of the high Himalayas and Antarctica. Proceedings of the Royal Society B: Biological Sciences 278:702–08. doi:10.1098/rspb.2010.1254.
  • Schmidt, S. K., L. Vimercati, J. L. Darcy, P. Arán, E. M. S. Gendron, A. J. Solon, D. Porazinska, and C. Dorador. 2017. A Naganishia in high places: Functioning populations or dormant cells from the atmosphere?. Mycology 8:153–63. doi:10.1080/21501203.2017.1344154.
  • Schnell, I. B., K. Bohmann, and M. T. P. Gilbert. 2015. Tag jumps illuminated – Reducing sequence-to-sample misidentifications in metabarcoding studies. Molecular Ecology Resources 15:1289–303. doi:10.1111/1755-0998.12402.
  • Schubert, Z. R. 2014. Dew formation and water availability at high elevation in the Atacama Desert, Chile. Undergraduate Honors Thesis. Paper 192. University of Colorado, Boulder
  • Searle, M. P. 1999. Extensional and compressional faults in the Everest–Lhotse massif, Khumbu Himalaya, Nepal. Journal of the Geological Society 156 (2): 227–240. doi:10.1144/gsjgs.156.2.0227.
  • Singh, P., S. M. Singh, and U. Roy. 2016. Taxonomic characterization and the bio-potential of bacteria isolated from glacier ice cores in the High Arctic. Journal of Basic Microbiology 56:275–85. doi:10.1002/jobm.201500298.
  • Singh, D., K. Takahashi, M. Kim, J. Chun, and J. M. Adams. 2012. A hump-backed trend in bacterial diversity with elevation on Mount Fuji, Japan. Microbial Ecology 63:429–37. doi:10.1007/s00248-011-9900-1.
  • Sinton, L. W., R. K. Finlay, and D. J. Hannah. 1998. Distinguishing human from animal faecal contamination in water: A review. New Zealand Journal of Marine and Freshwater Research 32:323–48. doi:10.1080/00288330.1998.9516828.
  • Smith, D. J., D. A. Jaffe, M. N. Birmele, D. W. Griffin, A. C. Schuerger, J. Hee, and M. S. Roberts. 2012. Free tropospheric transport of microorganisms from Asia to North America. Microbial Ecology 64:973–85. doi:10.1007/s00248-012-0088-9.
  • Smith, J. J., L. A. Tow, W. Stafford, C. Cary, and D. A. Cowan. 2006. Bacterial diversity in three different Antarctic cold desert mineral soils. Microbial Ecology 51:413–21. doi:10.1007/s00248-006-9022-3.
  • Solon, A. J., L. Vimercati, J. L. Darcy, P. Arán, D. Porazinska, C. Dorador, M. E. Farías, and S. K. Schmidt. 2018. Microbial communities of high-elevation fumaroles, penitentes, and dry tephra ‘soils’ of the Puna de Atacama volcanic zone. Microbial Ecology 76:340–51. doi:10.1007/s00248-017-1129-1.
  • Sommers, P., J. L. Darcy, E. M. S. Gendron, L. F. Stanish, E. A. Bagshaw, D. L. Porazinska, and S. K. Schmidt. 2018. Diversity patterns of microbial eukaryotes mirror those of bacteria in Antarctic cryoconite holes. FEMS Microbiology Ecology 94:fix167. doi:10.1093/femsec/fix167.
  • Souza, F. F. C., D. V. Rissi, F. O. Pedrosa, E. M. Souza, V. A. Baura, R. A. Monteiro, E. Balsanelli, L. M. Cruz, R. A. F. Souza, M. O. Andreae, et al. 2019. Uncovering prokaryotic biodiversity within aerosols of the pristine Amazon Forest. Science of the Total Environment 688:83–86. doi:10.1016/j.scitotenv.2019.06.218.
  • Stamatakis, A. 2014. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–13. doi:10.1093/bioinformatics/btu033.
  • Stucky, B. J. 2012. SeqTrace: A graphical tool for rapidly processing DNA sequencing chromatograms. Journal of Biomolecular Techniques 23:90–93. doi:10.7171/jbt.12-2303-004.
  • Tarlachkov, S. V., T. V. Shevchuk, M. C. Montero-Calasanz, and I. P. Starodumova. 2020. Diversity of rhodopsins in cultivated bacteria of the family Geodermatophilaceae associated with non-aquatic environments. Bioinformatics 36:1668–72. doi:10.1093/bioinformatics/btz840.
  • Thomas-Hall, S. R., B. Turchetti, P. Buzzini, E. Branda, T. Boekhout, B. Theelen, and K. Watson. 2010. Cold-adapted yeasts from Antarctica and the Italian Alps—description of three novel species: Mrakia robertii sp. nov., Mrakia blollopis sp. nov. and Mrakiella niccombsii sp. nov. Extremophiles 14:47–59. doi:10.1007/s00792-009-0286-7.
  • Trujillo, M. E., M. Goodfellow, K. Busarakam, and R. Riesco. 2015. Modestobacter lapidis sp. nov. and Modestobacter muralis sp. nov., isolated from a deteriorated sandstone historic building in Salamanca, Spain. Antonie van Leeuwenhoek 108:311–20. doi:10.1007/s10482-015-0482-7.
  • Turchetti, B., S. R. Thomas-Hall, L. B. Connell, E. Branda, P. Buzzini, B. Theelen, W. H. Müller, and T. Boekhout. 2011. Psychrophilic yeasts from Antarctica and European glaciers: Description of Glaciozyma gen. nov., Glaciozyma martinii sp. nov. and Glaciozyma watsonii sp. nov. Extremophiles 15:573. doi:10.1007/s00792-011-0388-x.
  • Ursell, L. K., W. Van Treuren, J. L. Metcalf, M. Pirrung, A. Gewirtz, and R. Knight. 2013. Replenishing our defensive microbes. BioEssays 35:810–17. doi:10.1002/bies.201300018.
  • Vimercati, L., J. L. Darcy, and S. K. Schmidt. 2019. The disappearing periglacial ecosystem atop Mt. Kilimanjaro supports both cosmopolitan and endemic microbial communities. Scientific Reports 9:10676. doi:10.1038/s41598-019-46521-0.
  • Vimercati, L., S. Hamsher, Z. Schubert, and S. K. Schmidt. 2016. Growth of a high-elevation Cryptococcus sp. during extreme freeze-thaw cycles. Extremophiles 20:579–88. doi:10.1007/s00792-016-0844-8.
  • Wade, W. G. 2013. Characterisation of the human oral microbiome. Journal of Oral Biosciences 55:143–48. doi:10.1016/j.job.2013.06.001.
  • Walters, W., E. R. Hyde, D. Berg-Lyons, G. Ackermann, G. Humphrey, A. Parada, J. A. Gilbert, J. K. Jansson, J. G. Caporaso, J. A. Fuhrman, A. Apprill, and R. Knight. 2016. Improved bacterial 16S rRNA gene (V4 and V4-5) and fungal internal transcribed spacer marker gene primers for microbial community surveys. mSystems 1:e00009-15. doi:10.1128/mSystems.00009-15.
  • Wang, Q., G. M. Garrity, J. M. Tiedje, and J. R. Cole. 2007. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology 73:5261–67. doi:10.1128/AEM.00062-07.
  • Xiao, J., Y. Luo, J. Xu, S. Xie, and J. Xu. 2011. Modestobacter marinus sp. nov., a psychrotolerant Actinobacterium from deep-sea sediment, and emended description of the genus Modestobacter. International Journal of Systematic and Evolutionary Microbiology 61:1710–14. doi:10.1099/ijs.0.023085-0.
  • Yilmaz, P., L. W. Parfrey, P. Yarza, J. Gerken, E. Pruesse, C. Quast, T. Schweer, J. Peplies, W. Ludwig, and F. O. Glöckner. 2014. The SILVA and ‘all-species living tree project (LTP)’ taxonomic frameworks. Nucleic Acids Research 42:D643–D648. doi:10.1093/nar/gkt1209.
  • Yuan, Y., G. Si, J. Wang, T. Luo, and G. Zhang. 2014. Bacterial community in alpine grasslands along an altitudinal gradient on the Tibetan Plateau. FEMS Microbiology Ecology 87:121–32. doi:10.1111/1574-6941.12197.
  • Zanne, A. E., K. Abarenkov, M. E. Afkhami, C. A. Aguilar-Trigueros, S. Bates, J. M. Bhatnagar, P. E. Busby, N. Christian, W. K. Cornwell, T. W. Crowther, et al. 2020. Fungal functional ecology: Bringing a trait-based approach to plant-associated fungi. Biological Reviews 95:409–33. doi:10.1111/brv.12570.
  • Zhang, Y., J. Chen, H. Liu, Y. Zhang, W. Li, and L. Yu. 2011. Geodermatophilus ruber sp. nov., isolated from rhizosphere soil of a medicinal plant. International Journal of Systematic and Evolutionary Microbiology 61:190–93. doi:10.1099/ijs.0.020610-0.
  • Zhang, L., M. Wang, J. I. Prosser, Y. Zheng, and J. He. 2009. Altitude ammonia-oxidizing bacteria and archaea in soils of Mount Everest. FEMS Microbiology Ecology 70:208–17. doi:10.1111/j.1574-6941.2009.00775.x.
  • Zhao, W., X. Liu, Q. Huang, and P. Cai. 2015. Streptococcus suis sorption on agricultural soils: Role of soil physico-chemical properties. Chemosphere 119:52–58. doi:10.1016/j.chemosphere.2014.05.060.