IPCC. IPCC Special Report on the Ocean and Cryosphere in a Changing Climate (in the press).
Cavicchioli, R. et al. Scientists’ warning to humanity: microorganisms and climate change. Nat. Rev. Microbiol. 17, 569–586 (2019).
Google Scholar
Meltofte, H. (ed.) Arctic Biodiversity Assessment: Status and Trends in Arctic Biodiversity (CAFF International Secretariat, 2013).
Wassmann, P. & Reigstad, M. Future Arctic Ocean seasonal ice zones and implications for pelagic-benthic coupling. Oceanography 24, 220–231 (2011).
Bunse, C. & Pinhassi, J. Marine bacterioplankton seasonal succession dynamics. Trends Microbiol. 25, 494–505 (2017).
Google Scholar
Olli, K. et al. Seasonal variation in vertical flux of biogenic matter in the marginal ice zone and the central Barents Sea. J. Mar. Syst. 38, 189–204 (2002).
Riedel, A., Michel, C., Gosselin, M. & LeBlanc, B. Winter–spring dynamics in sea-ice carbon cycling in the coastal Arctic Ocean. J. Mar. Syst. 74, 918–932 (2008).
Joli, N., Monier, A., Logares, R. & Lovejoy, C. Seasonal patterns in Arctic prasinophytes and inferred ecology of Bathycoccus unveiled in an Arctic winter metagenome. ISME J. 11, 1372–1385 (2017).
Google Scholar
Alonso-Sáez, L., Sánchez, O., Gasol, J. M., Balagué, V. & Pedrós-Alio, C. Winter-to-summer changes in the composition and single-cell activity of near-surface Arctic prokaryotes. Environ. Microbiol. 10, 2444–2454 (2008).
Google Scholar
Alonso-Sáez, L. et al. Role for urea in nitrification by polar marine Archaea. Proc. Natl Acad. Sci. USA 109, 17989–17994 (2012).
Google Scholar
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
Circumpolar Biodiversity Monitoring Program, Conservation of Arctic Flora and Fauna. State of the Arctic Marine Biodiversity Report (Conservation of Arctic Flora and Fauna International Secretariat, 2017).
Kirchman, D. L., Cottrell, M. T. & Lovejoy, C. The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes. Environ. Microbiol. 12, 1132–1143 (2010).
Google Scholar
Galand, P. E., Casamayor, E. O., Kirchman, D. L., Potvin, M. & Lovejoy, C. Unique archaeal assemblages in the Arctic Ocean unveiled by massively parallel tag sequencing. ISME J. 3, 860–869 (2009).
Google Scholar
Pedrós-Alió, C., Potvin, M. & Lovejoy, C. Diversity of planktonic microorganisms in the Arctic Ocean. Prog. Oceanogr. 139, 233–243 (2015).
Amaral-Zettler, L. et al. in Life in the World’s Oceans: Diversity, Distribution, and Abundance (ed. McIntyre, A. D.) 221–245 (Blackwell Publishing Ltd, 2010).
Christman, G. D., Cottrell, M. T., Popp, B. N., Gier, E. & Kirchman, D. L. Abundance, diversity, and activity of ammonia-oxidizing prokaryotes in the coastal Arctic Ocean in summer and winter. Appl. Environ. Microbiol. 77, 2026–2034 (2011).
Google Scholar
Alonso-Sáez, L., Galand, P. E., Casamayor, E. O., Pedrós-Alió, C. & Bertilsson, S. High bicarbonate assimilation in the dark by Arctic bacteria. ISME J. 4, 1581–1590 (2010).
Google Scholar
Galand, P. E., Lovejoy, C., Pouliot, J., Garneau, M.-È. & Vincent, W. F. Microbial community diversity and heterotrophic production in a coastal Arctic ecosystem: a stamukhi lake and its source waters. Limnol. Oceanogr. 53, 813–823 (2008).
Nguyen, D. et al. Winter diversity and expression of proteorhodopsin genes in a polar ocean. ISME J. 9, 1835–1845 (2015).
Google Scholar
Cifuentes-Anticevic, J. et al. Proteorhodopsin phototrophy in Antarctic coastal waters. mSphere 6, e00525–21 (2021).
Google Scholar
Ghiglione, J.-F. et al. Pole-to-pole biogeography of surface and deep marine bacterial communities. Proc. Natl Acad. Sci. USA 109, 17633–17638 (2012).
Google Scholar
Salazar, G. et al. Gene expression changes and community turnover differentially shape the global ocean metatranscriptome. Cell 179, 1068–1083.e21 (2019).
Google Scholar
Kraemer, S., Ramachandran, A., Colatriano, D., Lovejoy, C. & Walsh, D. A. Diversity and biogeography of SAR11 bacteria from the Arctic Ocean. ISME J. 14, 79–90 (2020).
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
Sunagawa, S. et al. Tara Oceans: towards global ocean ecosystems biology. Nat. Rev. Microbiol. 18, 428–445 (2020).
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
Parks, D. H. et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat. Biotechnol. 36, 996–1004 (2018).
Google Scholar
Delmont, T. O. et al. Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. Nat. Microbiol. 3, 804–813 (2018).
Google Scholar
Ibarbalz, F. M. et al. Global trends in marine plankton diversity across kingdoms of life. Cell 179, 1084–1097.e21 (2019).
Google Scholar
Aagaard, K., Swift, J. H. & Carmack, E. C. Thermohaline circulation in the Arctic Mediterranean Seas. J. Geophys. Res. Oceans 90, 4833–4846 (1985).
Dupont, C. L. et al. Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities. ISME J. 9, 1076–1092 (2015).
Google Scholar
Franzosa, E. A. et al. Relating the metatranscriptome and metagenome of the human gut. Proc. Natl Acad. Sci. USA 111, E2329–E2338 (2014).
Google Scholar
Jones, S. E. & Lennon, J. T. Dormancy contributes to the maintenance of microbial diversity. Proc. Natl Acad. Sci. USA 107, 5881–5886 (2010).
Google Scholar
Mestre, M. & Höfer, J. The microbial conveyor belt: connecting the globe through dispersion and dormancy. Trends Microbiol. 29, 482–492 (2021).
Google Scholar
Ciufo, S. et al. Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI. Int. J. Syst. Evol. Microbiol. 68, 2386–2392 (2018).
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
Nelson, W. C., Tully, B. J. & Mobberley, J. M. Biases in genome reconstruction from metagenomic data. PeerJ 8, e10119 (2020).
Google Scholar
Alneberg, J. et al. Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes. Commun. Biol. 3, 119 (2020).
Google Scholar
Tully, B. J., Graham, E. D. & Heidelberg, J. F. The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans. Sci. Data 5, 170203 (2018).
Google Scholar
Christensen, M. & Nilsson, A. E. Arctic sea ice and the communication of climate change. Pop. Commun. 15, 249–268 (2017).
Jaffe, A. L., Castelle, C. J., Dupont, C. L. & Banfield, J. F. Lateral gene transfer shapes the distribution of RuBisCO among candidate phyla radiation bacteria and DPANN Archaea. Mol. Biol. Evol. 36, 435–446 (2019).
Google Scholar
Kono, T. et al. A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea. Nat. Commun. 8, 14007 (2017).
Google Scholar
Sato, T., Atomi, H. & Imanaka, T. Archaeal type III RuBisCOs function in a pathway for AMP metabolism. Science 315, 1003–1006 (2007).
Google Scholar
Tabita, F. R., Satagopan, S., Hanson, T. E., Kreel, N. E. & Scott, S. S. Distinct form I, II, III, and IV Rubisco proteins from the three kingdoms of life provide clues about Rubisco evolution and structure/function relationships. J. Exp. Bot. 59, 1515–1524 (2008).
Google Scholar
Yelton, A. P. et al. Global genetic capacity for mixotrophy in marine picocyanobacteria. ISME J. 10, 2946–2957 (2016).
Google Scholar
Cordero, P. R. F. et al. Atmospheric carbon monoxide oxidation is a widespread mechanism supporting microbial survival. ISME J. 13, 2868–2881 (2019).
Google Scholar
King, G. M. & Weber, C. F. Distribution, diversity and ecology of aerobic CO-oxidizing bacteria. Nat. Rev. Microbiol. 5, 107–118 (2007).
Google Scholar
Sunagawa, S. et al. Ocean plankton. Structure and function of the global ocean microbiome. Science 348, 1261359 (2015).
Google Scholar
Sul, W. J., Oliver, T. A., Ducklow, H. W., Amaral-Zettler, L. A. & Sogin, M. L. Marine bacteria exhibit a bipolar distribution. Proc. Natl Acad. Sci. USA 110, 2342–2347 (2013).
Google Scholar
Roller, B. R. K., Stoddard, S. F. & Schmidt, T. M. Exploiting rRNA operon copy number to investigate bacterial reproductive strategies. Nat. Microbiol. 1, 16160 (2016).
Google Scholar
Levins, R. Evolution in Changing Environments: Some Theoretical Explorations (Princeton Univ. Press, 1968).
Colwell, R. K. & Futuyma, D. J. On the measurement of niche breadth and overlap. Ecology 52, 567–576 (1971).
Google Scholar
Massana, R. & Logares, R. Eukaryotic versus prokaryotic marine picoplankton ecology. Environ. Microbiol. 15, 1254–1261 (2013).
Google Scholar
Székely, A. J., Berga, M. & Langenheder, S. Mechanisms determining the fate of dispersed bacterial communities in new environments. ISME J. 7, 61–71 (2013).
Google Scholar
Brooks, J. P. et al. The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies. BMC Microbiol. 15, 66 (2015).
Google Scholar
Logares, R. et al. Biogeography of bacterial communities exposed to progressive long-term environmental change. ISME J. 7, 937–948 (2013).
Google Scholar
Ruiz-González, C. et al. Higher contribution of globally rare bacterial taxa reflects environmental transitions across the surface ocean. Mol. Ecol. 28, 1930–1945 (2019).
Google Scholar
Staley, J. T. & Gosink, J. J. Poles apart: biodiversity and biogeography of sea ice bacteria. Annu. Rev. Microbiol. 53, 189–215 (1999).
Google Scholar
Chaffron, S. et al. Environmental vulnerability of the global ocean epipelagic plankton community interactome. Sci. Adv. 7, eabg1921 (2021).
Google Scholar
Estrada, E. Characterization of topological keystone species: local, global and “meso-scale” centralities in food webs. Ecol. Complex. 4, 48–57 (2007).
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
Tully, B. J., Sachdeva, R., Graham, E. D. & Heidelberg, J. F. 290 metagenome-assembled genomes from the Mediterranean Sea: a resource for marine microbiology. PeerJ 2017, e3558 (2017).
Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. Commun. Biol. 4, 604 (2021).
Pesant, S. et al. Open science resources for the discovery and analysis of Tara Oceans data. Sci. Data 2, 150023 (2015).
Google Scholar
Alberti, A. et al. Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition. Sci. Data 4, 170093 (2017).
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
Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659 (2006).
Google Scholar
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Google Scholar
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Google Scholar
Kang, D. D., Froula, J., Egan, R. & Wang, Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 3, e1165 (2015).
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
Huang, X. & Madan, A. CAP3: a DNA sequence assembly program. Genome Res. 9, 868–877 (1999).
Google Scholar
Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014).
Google Scholar
Kanehisa, M. & Goto, S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27–30 (2000).
Google Scholar
Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).
Google Scholar
Wheeler, T. J. & Eddy, S. R. nhmmer: DNA homology search with profile HMMs. Bioinformatics 29, 2487–2489 (2013).
Google Scholar
Jain, C., Rodriguez-R, L. M., Phillipy, A. M., Konstantinidis, K. T. & Aluru, S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat. Commun. 9, 5114 (2018).
Google Scholar
Lawrence, M. et al. Software for computing and annotating genomic ranges. PLoS Comput. Biol. 9, e1003118 (2013).
Google Scholar
Vieira-Silva, S. & Rocha, E. P. C. The systemic imprint of growth and its uses in ecological (meta)genomics. PLoS Genet. 6, e1000808 (2010).
Google Scholar
Pertea, G. & Pertea, M. GFF utilities: GffRead and GffCompare. F1000Res. 9, ISCB Comm J-304 (2020).
Google Scholar
Aylward, F. O. & Santoro, A. E. Heterotrophic Thaumarchaeota with ultrasmall genomes are widespread in the ocean. mSystems 5, e00415–20 (2020).
Google Scholar
Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539 (2011).
Google Scholar
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2––approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).
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
Louca, S., Doebeli, M. & Parfrey, L. W. Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem. Microbiome 6, 41 (2018).
Google Scholar
