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Zawierucha, K. & Shain, D. H. Disappearing Kilimanjaro snow—are we the last generation to explore equatorial glacier biodiversity? Ecol. Evol. 9, 8911–8918 (2019).
Google Scholar
Hodson, A. et al. Glacial ecosystems. Ecol. Monogr. 78, 41–67 (2008).
Anesio, A. M., Lutz, S., Chrismas, N. A. M. & Benning, L. G. The microbiome of glaciers and ice sheets. NPJ Biofilms Microbiomes 3, 10 (2017).
Google Scholar
Stibal, M., Sabacka, M. & Zarsky, J. Biological processes on glacier and ice sheet surfaces. Nat. Geosci. 5, 771–774 (2012).
Google Scholar
Pittino, F. et al. Bacterial communities of cryoconite holes of a temperate alpine glacier show both seasonal trends and year-to-year variability. Ann. Glaciol. 59, 1–9 (2018).
Boetius, A., Anesio, A. M., Deming, J. W., Mikucki, J. A. & Rapp, J. Z. Microbial ecology of the cryosphere: sea ice and glacial habitats. Nat. Rev. Microbiol. 13, 677–690 (2015).
Google Scholar
Yarzábal, L. A., Salazar, L. M. B. & Batista-García, R. A. Climate change, melting cryosphere and frozen pathogens: should we worry…? Environ. Sustain. 4, 489–501 (2021).
Knowlton, C., Veerapaneni, R., D’Elia, T. & Rogers, S. O. Microbial analyses of ancient ice core sections from greenland and antarctica. Biology 2, 206–232 (2013).
Google Scholar
Miteva, V. I. & Brenchley, J. E. Detection and isolation of ultrasmall microorganisms from a 120,000-year-old Greenland glacier ice core. Appl. Environ. Microbiol. 71, 7806–7818 (2005).
Google Scholar
Ma, L.-J., Rogers, S. O., Catranis, C. M. & Starmer, W. T. Detection and characterization of ancient fungi entrapped in glacial ice. Mycologia 92, 286–295 (2000).
Christner, B. C., Mosley-Thompson, E., Thompson, L. G. & Reeve, J. N. Bacterial recovery from ancient glacial ice. Environ. Microbiol. 5, 433–436 (2003).
Google Scholar
Santibanez, P. A. et al. Prokaryotes in the WAIS Divide ice core reflect source and transport changes between Last Glacial Maximum and the early Holocene. Glob. Chang. Biol. 24, 2182–2197 (2018).
Google Scholar
Yao, T. et al. Different glacier status with atmospheric circulations in Tibetan Plateau and surroundings. Nat. Clim. Chang. 2, 663–667 (2012).
Bibi, S. et al. Climatic and associated cryospheric, biospheric, and hydrological changes on the Tibetan Plateau: a review. Int. J. Climatol. 38, e1–e17 (2018).
Cauvy-Fraunié, S. & Dangles, O. A global synthesis of biodiversity responses to glacier retreat. Nat. Ecol. Evol. 3, 1675–1685 (2019).
Google Scholar
Stibal, M. et al. Glacial ecosystems are essential to understanding biodiversity responses to glacier retreat. Nat. Ecol. Evol. 4, 686–687 (2020).
Google Scholar
Souney, J. M. et al. Core handling, transportation and processing for the South Pole ice core (SPICEcore) project. Ann. Glaciol. 62, 118–130 (2021).
Nayfach, S. et al. A genomic catalog of Earth’s microbiomes. Nat. Biotechnol. 39, 499–509 (2021).
Google Scholar
Mogrovejo-Arias, D. C., Brill, F. H. H. & Wagner, D. Potentially pathogenic bacteria isolated from diverse habitats in Spitsbergen, Svalbard. Environ. Earth Sci. 79, 109 (2020).
Abedon, S. T. & Lejeune, J. T. Why bacteriophage encode exotoxins and other virulence factors. Evol. Bioinform. Online 1, 97–110 (2007).
Google Scholar
Casacuberta, E. & Gonzalez, J. The impact of transposable elements in environmental adaptation. Mol. Ecol. 22, 1503–1517 (2013).
Google Scholar
Soucy, S. M., Huang, J. & Gogarten, J. P. Horizontal gene transfer: building the web of life. Nat. Rev. Genet. 16, 472–482 (2015).
Google Scholar
Bowers, R. M. et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat. Biotechnol. 35, 725–731 (2017).
Google Scholar
Cao, S. et al. Structure and function of the Arctic and Antarctic marine microbiota as revealed by metagenomics. Microbiome 8, 47 (2020).
Google Scholar
Royo-Llonch, M. et al. Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean. Nat. Microbiol. 6, 1561–1574 (2021).
Google Scholar
Chaumeil, P. A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36, 1925–1927 (2019).
Google Scholar
Benaud, N. et al. Harnessing long-read amplicon sequencing to uncover NRPS and type I PKS gene sequence diversity in polar desert soils. FEMS Microbiol. Ecol. 95, fiz031 (2019).
Google Scholar
Kautsar, S. A. et al. MIBiG 2.0: a repository for biosynthetic gene clusters of known function. Nucleic Acids Res. 48, D454–D458 (2019).
Google Scholar
Vila, E., Hornero-Méndez, D., Azziz, G., Lareo, C. & Saravia, V. Carotenoids from heterotrophic bacteria isolated from Fildes Peninsula, King George Island, Antarctica. Biotechnol. Rep. (Amst). 21, e00306 (2019).
Google Scholar
Moeller, R., Horneck, G., Facius, R. & Stackebrandt, E. Role of pigmentation in protecting Bacillus sp. endospores against environmental UV radiation. FEMS Microbiol. Ecol. 51, 231–236 (2005).
Google Scholar
Nupur, L. N. U. et al. ProCarDB: a database of bacterial carotenoids. BMC Microbiol. 16, 96–96 (2016).
Google Scholar
Anesio, A. M. & Laybourn-Parry, J. Glaciers and ice sheets as a biome. Trends Ecol. Evol. 27, 219–225 (2012).
Google Scholar
Feller, G. Life at low temperatures: is disorder the driving force? Extremophiles 11, 211–216 (2007).
Google Scholar
Houwenhuyse, S., Macke, E., Reyserhove, L., Bulteel, L. & Decaestecker, E. Back to the future in a petri dish: origin and impact of resurrected microbes in natural populations. Evol. Appl. 11, 29–41 (2017).
Google Scholar
Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012).
Google Scholar
Li, D., Liu, C. M., Luo, R., Sadakane, K. & Lam, T. W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674–1676 (2015).
Google Scholar
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Google Scholar
Buchfink, B., Reuter, K. & Drost, H. G. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat. Methods 18, 366–368 (2021).
Google Scholar
Kang, D. D. et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7, e7359 (2019).
Google Scholar
Wu, Y. W., Simmons, B. A. & Singer, S. W. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics 32, 605–607 (2016).
Google Scholar
Nissen, J. N. et al. Improved metagenome binning and assembly using deep variational autoencoders. Nat. Biotechnol. 39, 555–560 (2021).
Google Scholar
Parks, D. H. et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat. Microbiol. 2, 1533–1542 (2017).
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 (2015).
Google Scholar
Lowe, T. M. & Eddy, S. R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964 (1997).
Google Scholar
Nawrocki, E. P., Kolbe, D. L. & Eddy, S. R. Infernal 1.0: inference of RNA alignments. Bioinformatics 25, 1335–1337 (2009).
Google Scholar
Kalvari, I. et al. Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. Nucleic Acids Res. 46, D335–d342 (2018).
Google Scholar
Olm, M. R., Brown, C. T., Brooks, B. & Banfield, J. F. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 11, 2864–2868 (2017).
Google Scholar
Almeida, A. et al. A unified catalog of 204,938 reference genomes from the human gut microbiome. Nat. Biotechnol. 39, 105–114 (2021).
Google Scholar
Parks, D. H. et al. A complete domain-to-species taxonomy for Bacteria and Archaea. Nat. Biotechnol. 38, 1079–1086 (2020).
Google Scholar
Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 47, W256–w259 (2019).
Google Scholar
Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010).
Google Scholar
Steinegger, M. & Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026–1028 (2017).
Google Scholar
Li, J. et al. An integrated catalog of reference genes in the human gut microbiome. Nat. Biotechnol. 32, 834–841 (2014).
Google Scholar
Patro, R., Duggal, G., Love, M. I., Irizarry, R. A. & Kingsford, C. Salmon provides fast and bias-aware quantification of transcript expression. Nat. Methods 14, 417–419 (2017).
Google Scholar
Boeckmann, B. et al. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31, 365–370 (2003).
Google Scholar
Suzek, B. E., Wang, Y., Huang, H., McGarvey, P. B. & Wu, C. H. UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. Bioinformatics 31, 926–932 (2015).
Google Scholar
Huerta-Cepas, J. et al. Fast genome-wide functional annotation through orthology assignment by eggNOG-Mapper. Mol. Biol. Evol. 34, 2115–2122 (2017).
Google Scholar
Huerta-Cepas, J. et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 47, D309–D314 (2019).
Google Scholar
Kanehisa, M., Furumichi, M., Tanabe, M., Sato, Y. & Morishima, K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 45, D353–d361 (2017).
Google Scholar
Levasseur, A., Drula, E., Lombard, V., Coutinho, P. M. & Henrissat, B. Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes. Biotechnol. Biofuels 6, 41 (2013).
Google Scholar
Tatusov, R. L. et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4, 41 (2003).
Google Scholar
Jia, B. et al. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res. 45, D566–D573 (2017).
Google Scholar
Alcock, B. P. et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. 48, D517–D525 (2020).
Google Scholar
Liu, B., Zheng, D., Jin, Q., Chen, L. & Yang, J. VFDB 2019: a comparative pathogenomic platform with an interactive web interface. Nucleic Acids Res. 47, D687–D692 (2019).
Google Scholar
Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014).
Google Scholar
de Nies, L. et al. PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data. Microbiome 9, 49 (2021).
Google Scholar
Blin, K. et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res. 47, W81–w87 (2019).
Google Scholar
Navarro-Muñoz, J. C. et al. A computational framework to explore large-scale biosynthetic diversity. Nat. Chem. Biol. 16, 60–68 (2020).
Google Scholar
Tibetan Glacier Genome and Gene catalogue Raw sequence reads. Tibetan Glacier Genome and Gene catalogue. National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB12327 (2022).
