Cavicchioli, R. et al. Scientists’ warning to humanity: Microorganisms and climate change. Nat. Rev. Microbiol. 17, 569–586 (2019).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Azam, F. & Malfatti, F. Microbial structuring of marine ecosystems. Nat. Rev. Microbiol 5, 782–791 (2007).

CAS 
PubMed 

Google Scholar
 

Hutchins, D. A. & Fu, F. Microorganisms and ocean global change. Nat. Microbiol 2, 17058 (2017).

CAS 
PubMed 

Google Scholar
 

Falkowski, P. G., Fenchel, T. & Delong, E. F. The microbial engines that drive earth’s biogeochemical cycles. Science 320, 1034–1039 (2008).

CAS 
PubMed 

Google Scholar
 

Grossart, H. P. et al. Fungi in aquatic ecosystems. Nat. Rev. Microbiol 17, 339–354 (2019).

CAS 
PubMed 

Google Scholar
 

Worden, A. Z. et al. Environmental science. Rethinking the marine carbon cycle: factoring in the multifarious lifestyles of microbes. Science 347, 1257594 (2015).

PubMed 

Google Scholar
 

Richards, T. A., Jones, M. D., Leonard, G. & Bass, D. Marine fungi: Their ecology and molecular diversity. Ann. Rev. Mar. Sci. 4, 495–522 (2012).

PubMed 

Google Scholar
 

Baltar, F., Zhao, Z. & Herndl, G. J. Potential and expression of carbohydrate utilization by marine fungi in the global ocean. Microbiome 9, 106 (2021).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Breyer, E., Zhao, Z., Herndl, G. J. & Baltar, F. Global contribution of pelagic fungi to protein degradation in the ocean. Microbiome 10, 143 (2022).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Breyer, E. & Baltar, F. The largely neglected ecological role of oceanic pelagic fungi. Trends Ecol. Evol. 38, 870–888 (2023).

PubMed 

Google Scholar
 

Debeljak, P. & Baltar, F. Fungal diversity and community composition across ecosystems. J. Fungi 9, 510 (2023).

Orsi, W., Biddle, J. F. & Edgcomb, V. Deep sequencing of subseafloor eukaryotic rRNA reveals active fungi across marine subsurface provinces. PLOS ONE 8, e56335 (2013).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Orsi, W. D., Edgcomb, V. P., Christman, G. D. & Biddle, J. F. Gene expression in the deep biosphere. Nature 499, 205–208 (2013).

CAS 
PubMed 

Google Scholar
 

Orsi, W. D. et al. Carbon assimilating fungi from surface ocean to subseafloor revealed by coupled phylogenetic and stable isotope analysis. ISME J. 16, 1245–1261 (2022).

CAS 
PubMed 

Google Scholar
 

Solanki, V. et al. Glycoside hydrolase from the GH76 family indicates that marine Salegentibacter sp. Hel_I_6 consumes alpha-mannan from fungi. ISME J. 16, 1818–1830 (2022).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Lima-Mendez, G. et al. Determinants of community structure in the global plankton interactome. Science 348, 1262073 (2015).

PubMed 

Google Scholar
 

Stein, A., Gerstner, K. & Kreft, H. Environmental heterogeneity as a universal driver of species richness across taxa, biomes and spatial scales. Ecol. Lett. 17, 866–880 (2014).

PubMed 

Google Scholar
 

Stegen, J. C., Lin, X., Konopka, A. E. & Fredrickson, J. K. Stochastic and deterministic assembly processes in subsurface microbial communities. ISME J. 6, 1653–1664 (2012).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Sen, K., Bai, M., Sen, B. & Wang, G. Disentangling the structure and function of mycoplankton communities in the context of marine environmental heterogeneity. Sci. Total Environ. 766, 142635 (2021).

CAS 
PubMed 

Google Scholar
 

Carradec, Q. et al. A global ocean atlas of eukaryotic genes. Nat. Commun. 9, 373 (2018).

PubMed 
PubMed Central 

Google Scholar
 

Salazar, G. et al. Gene expression changes and community turnover differentially shape the global ocean metatranscriptome. Cell 179, 1068–1083e1021. (2019).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Endo, H. et al. Biogeography of marine giant viruses reveals their interplay with eukaryotes and ecological functions. Nat. Ecol. Evol. 4, 1639–1649 (2020).

PubMed 

Google Scholar
 

Kharbush, J. J. et al. Particulate organic carbon deconstructed: Molecular and chemical composition of particulate organic carbon in the ocean. Front. Mar. Sci. 7, 518 (2020).

Cerro-Gálvez, E. et al. Microbial responses to anthropogenic dissolved organic carbon in the Arctic and Antarctic coastal seawaters. Environ. Microbiol 21, 1466–1481 (2019).

PubMed 

Google Scholar
 

Zhao, Z., Amano, C., Reinthaler, T., Orellana, M. V. & Herndl, G. J. Substrate uptake patterns shape niche separation in marine prokaryotic microbiome. Sci. Adv. 10, eadn5143 (2024).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Zhao, Z., Baltar, F. & Herndl, G. J. Linking extracellular enzymes to phylogeny indicates a predominantly particle-associated lifestyle of deep-sea prokaryotes. Sci. Adv. 6, eaaz4354 (2020).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Wang, F.-Q. et al. Particle-attached bacteria act as gatekeepers in the decomposition of complex phytoplankton polysaccharides. Microbiome 12, 32 (2024).

PubMed 
PubMed Central 

Google Scholar
 

Comstock, J. et al. Marine particle size-fractionation indicates organic matter is processed by differing microbial communities on depth-specific particles. ISME Commun. 4, 1 (2024).

Mestre, M., Borrull, E., Sala, M. & Gasol, J. M. Patterns of bacterial diversity in the marine planktonic particulate matter continuum. ISME J. 11, 999–1010 (2017).

PubMed 
PubMed Central 

Google Scholar
 

Kellogg, C. T. E. & Deming, J. W. Particle-associated extracellular enzyme activity and bacterial community composition across the Canadian Arctic Ocean. FEMS Microbiol. Ecol. 89, 360–375 (2014).

CAS 
PubMed 

Google Scholar
 

Yin, Q., He, K., Collins, G., De Vrieze, J. & Wu, G. Microbial strategies driving low concentration substrate degradation for sustainable remediation solutions. npj Clean. Water 7, 52 (2024).


Google Scholar
 

Giovannoni, S. J., Cameron Thrash, J. & Temperton, B. Implications of streamlining theory for microbial ecology. ISME J. 8, 1553–1565 (2014).

PubMed 
PubMed Central 

Google Scholar
 

Chen, P. et al. Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep. Genome Biol. 22, 207 (2021).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Hassett, B. T. & Gradinger, R. Chytrids dominate arctic marine fungal communities. Environ. Microbiol 18, 2001–2009 (2016).

CAS 
PubMed 

Google Scholar
 

Hassett, B. T. et al. Arctic marine fungi: biomass, functional genes, and putative ecological roles. ISME J. 13, 1484–1496 (2019).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Terrado, R. et al. Protist community composition during spring in an Arctic flaw lead polynya. Polar Biol. 34, 1901–1914 (2011).


Google Scholar
 

Kilias, E. S. et al. Chytrid fungi distribution and co-occurrence with diatoms correlate with sea ice melt in the Arctic Ocean. Commun. Biol. 3, 183 (2020).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Zhao, Z., Baltar, F. & Herndl Gerhard, J. Decoupling between the genetic potential and the metabolic regulation and expression in microbial organic matter cleavage across microbiomes. Microbiol Spectr. 0, e03036–03023 (2024).


Google Scholar
 

Arnosti, C. Microbial extracellular enzymes and the marine carbon cycle. Ann. Rev. Mar. Sci. 3, 401–425 (2011).

PubMed 

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).

CAS 
PubMed 

Google Scholar
 

Bochdansky, A. B., Clouse, M. A. & Herndl, G. J. Eukaryotic microbes, principally fungi and labyrinthulomycetes, dominate biomass on bathypelagic marine snow. ISME J. 11, 362–373 (2016).

PubMed 
PubMed Central 

Google Scholar
 

Orsi, W. D., Richards, T. A. & Francis, W. R. Predicted microbial secretomes and their target substrates in marine sediment. Nat. Microbiol 3, 32–37 (2018).

CAS 
PubMed 

Google Scholar
 

Sen, K. Sen, B. & Wang, G. Diversity, abundance, and ecological roles of planktonic fungi in marine environments. J. Fungi (Basel) 8, 491 (2022).

Teufel, F. et al. SignalP 6.0 predicts all five types of signal peptides using protein language models. Nat. Biotechnol. 40, 1023–1025 (2022).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Salazar-Alekseyeva, K., Herndl, G. J. & Baltar, F. Release of cell-free enzymes by marine pelagic fungal strains. Front Fungal Biol. 4, 1209265 (2023).

PubMed 
PubMed Central 

Google Scholar
 

Barrett, K., Jensen, K., Meyer, A. S., Frisvad, J. C. & Lange, L. Fungal secretome profile categorization of CAZymes by function and family corresponds to fungal phylogeny and taxonomy: Example Aspergillus and Penicillium. Sci. Rep. 10, 5158 (2020).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Chrismas, N. & Cunliffe, M. Depth-dependent mycoplankton glycoside hydrolase gene activity in the open ocean—evidence from the Tara Oceans eukaryote metatranscriptomes. ISME J. 14, 2361–2365 (2020).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Kasana, R. C. Proteases from psychrotrophs: An overview. Crit. Rev. Microbiol. 36, 134–145 (2010).

CAS 
PubMed 

Google Scholar
 

Bruno, S., Coppola, D., di Prisco, G., Giordano, D. & Verde, C. Enzymes from marine polar regions and their biotechnological applications. Mar. Drugs 17, 544 (2019).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Sturluson, M., Gissel Nielsen, T. & Wassmann, P. Bacterial abundance, biomass and production during spring blooms in the northern Barents Sea. Deep Sea Res. Part II: Top. Stud. Oceanogr. 55, 2186–2198 (2008).

CAS 

Google Scholar
 

Fuhrman, J. A. et al. A latitudinal diversity gradient in planktonic marine bacteria. PNAS 105, 7774–7778 (2008).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Sul, W. J., Oliver, T. A., Ducklow, H. W., Amaral-Zettler, L. A. & Sogin, M. L. Marine bacteria exhibit a bipolar distribution. PNAS 110, 2342–2347 (2013).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Abdel-Sater, F., El Bakkoury, M., Urrestarazu, A., Vissers, S. & André, B. Amino acid signaling in yeast: Casein kinase I and the Ssy5 endoprotease are key determinants of endoproteolytic activation of the membrane-bound Stp1 transcription factor. Mol. Cell. Biol. 24, 9771–9785 (2004).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Ibarbalz, F. M. et al. Global trends in marine plankton diversity across kingdoms of life. Cell 179, 1084–1097 e1021 (2019).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Morales, S. E., Biswas, A., Herndl, G. J. & Baltar, F. Global structuring of phylogenetic and functional diversity of pelagic fungi by depth and temperature. Front Mar. Sci. 6, 131 (2019).

Cunliffe, M., Hollingsworth, A., Bain, C., Sharma, V. & Taylor, J. D. Algal polysaccharide utilisation by saprotrophic planktonic marine fungi. Fungal Ecol. 30, 135–138 (2017).


Google Scholar
 

Alekseyeva, K. S., Herndl, G. J. & Baltar F. Extracellular enzymatic activities of oceanic pelagic fungal strains and the influence of temperature. J. Fungi (Basel) 8, 571 (2022).

Trejos-Espeleta, J. C. et al. Principal role of fungi in soil carbon stabilization during early pedogenesis in the high Arctic. Proc. Natl. Acad. Sci. 121, e2402689121 (2024).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Wang, Y., Sen, K., He, Y., Xie, Y. & Wang, G. Impact of environmental gradients on the abundance and diversity of planktonic fungi across coastal habitats of contrasting trophic status. Sci. Total Environ. 683, 822–833 (2019).

CAS 
PubMed 

Google Scholar
 

Gow Neil AR, Latge J-P, Munro Carol A. The fungal cell wall: StrUcture, Biosynthesis, And Function. Microbiol. Spectrum 5, https://doi.org/10.1128/microbiolspec.funk-0035-2016 (2017).

Raghukumar, S. Fungi in Coastal and Oceanic Marine Ecosystems, (2017).

Amend, A. et al. Fungi in the Marine Environment: Open Questions and Unsolved Problems. mBio. 10, https://doi.org/10.1128/mbio.01189-01118 (2019).

Gutiérrez, M. H., Jara, A. M. & Pantoja, S. Fungal parasites infect marine diatoms in the upwelling ecosystem of the Humboldt current system off central Chile. Environ. Microbiol 18, 1646–1653 (2016).

PubMed 

Google Scholar
 

Marchetta, A. et al. A deep insight into the diversity of microfungal communities in Arctic and Antarctic Lakes. J. Fungi 9, 1095 (2023).

CAS 

Google Scholar
 

Freeman, K. R. et al. Evidence that chytrids dominate fungal communities in high-elevation soils. PNAS 106, 18315–18320 (2009).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Schmidt, S. K., Naff, C. S. & Lynch, R. C. Fungal communities at the edge: Ecological lessons from high alpine fungi. Fungal Ecol. 5, 443–452 (2012).


Google Scholar
 

Triadó-Margarit, X. & Casamayor, E. O. Genetic diversity of planktonic eukaryotes in high mountain lakes (Central Pyrenees, Spain). Environ. Microbiol 14, 2445–2456 (2012).

PubMed 

Google Scholar
 

Kagami, M., Miki, T. & Takimoto, G. Mycoloop: chytrids in aquatic food webs. Front microbiol 5, 166 (2014).

Proceedings of 3rd International Conference on Document Analysis and Recognition. In: Proceedings of 3rd International Conference on Document Analysis and Recognition) (1995).

Muszewska, A. et al. Fungal lifestyle reflected in serine protease repertoire. Sci. Rep. 7, 9147 (2017).

PubMed 
PubMed Central 

Google Scholar
 

Zhou, J., Zhang, Y.-Y., Li, Q.-Y. & Cai, Z.-H. Evolutionary History of Cathepsin L (L-like) Family Genes in Vertebrates. Int. J. Biol. Sci. 11, 1016–1025 (2015).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Chitkara, C. et al. Seasonality in phytoplankton communities and production in three Arctic fjords across a climate gradient. Prog. Oceanogr. 227, 103317 (2024).


Google Scholar
 

Rawlings, N. & Barrett, A. J. Introduction: Serine Peptidases and Their Clans. Handb. Proteolytic Enzymes 3, 1417–1439 (2013).


Google Scholar
 

Irwin, J. A., Alfredsson, G. A., Lanzetti, A. J., Gudmundsson, H. M. & Engel, P. C. Purification and characterisation of a serine peptidase from the marine psychrophile strain PA-43. FEMS Microbiol. Lett. 201, 285–290 (2001).

CAS 
PubMed 

Google Scholar
 

Wang, Y., Zhang, Y. & Ha, Y. Crystal structure of a rhomboid family intramembrane protease. Nature 444, 179–180 (2006).

CAS 
PubMed 

Google Scholar
 

Bourne, Y. & Henrissat, B. Glycoside hydrolases and glycosyltransferases: families and functional modules. Curr. Opin. Struct. Biol. 11, 593–600 (2001).

CAS 
PubMed 

Google Scholar
 

Lairson, L. L., Henrissat, B., Davies, G. J. & Withers, S. G. Glycosyltransferases: Structures, Functions, and Mechanisms. Annu Rev. Biochem 77, 521–555 (2008).

CAS 
PubMed 

Google Scholar
 

Fujimoto, Z. Structure and Function of Carbohydrate-Binding Module Families 13 and 42 of Glycoside Hydrolases, Comprising a β-Trefoil Fold. Biosci. Biotechnol. 77, 1363–1371 (2013).

CAS 

Google Scholar
 

van Aalten, D. M. F. et al. Structure of a two-domain chitotriosidase from Serratia marcescens at 1.9-Å resolution. PNAS 97, 5842–5847 (2000).

PubMed 
PubMed Central 

Google Scholar
 

Dutschei, T. et al. Marine Bacteroidetes enzymatically digest xylans from terrestrial plants. Environ. Microbiol 25, 1713–1727 (2023).

CAS 
PubMed 

Google Scholar
 

Breton, C., Šnajdrová, L., Jeanneau, C., Koča, J. & Imberty, A. Structures and mechanisms of glycosyltransferases. Glycobiology 16, 29R–37R (2005).

PubMed 

Google Scholar
 

Treseder, K. K. & Lennon, J. T. Fungal traits that drive ecosystem dynamics on land. Microbiol. Mol. Biol. Rev. 79, 243–262 (2015).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Lombard, V., Golaconda Ramulu, H., Drula, E., Coutinho, P. M. & Henrissat, B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 42, D490–D495 (2014).

CAS 
PubMed 

Google Scholar
 

Bowman, S. M. & Free, S. J. The structure and synthesis of the fungal cell wall. Bioessays 28, 799–808 (2006).

PubMed 

Google Scholar
 

Moremen, K. W. & Haltiwanger, R. S. Emerging structural insights into glycosyltransferase-mediated synthesis of glycans. Nat. Chem. Biol. 15, 853–864 (2019).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Miksch, S. et al. Taxonomic and functional stability overrules seasonality in polar benthic microbiomes. ISME J. 18, wrad005 (2024).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Cheng, H., Shao, Z., Lu, C. & Duan, D. Genome-wide identification of chitinase genes in Thalassiosira pseudonana and analysis of their expression under abiotic stresses. BMC Plant Biol. 21, 87 (2021).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Souza, C. P., Almeida, B. C., Colwell, R. R. & Rivera, I. N. G. The Importance of Chitin in the Marine Environment. Mar. Biotechnol. 13, 823–830 (2011).

CAS 

Google Scholar
 

Feller, G. & Gerday, C. Psychrophilic enzymes: Hot topics in cold adaptation. Nat. Rev. Microbiol. 1, 200–208 (2003).

CAS 
PubMed 

Google Scholar
 

Cuskin, F. et al. How nature can exploit nonspecific catalytic and carbohydrate binding modules to create enzymatic specificity. PNAS 109, 20889–20894 (2012).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Nguyen, S. T. C., Freund, H. L., Kasanjian, J. & Berlemont, R. Function, distribution, and annotation of characterized cellulases, xylanases, and chitinases from CAZy. Appl Microbiol Biotechnol. 102, 1629–1637 (2018).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Talamantes, D., Biabini, N., Dang, H., Abdoun, K. & Berlemont, R. Natural diversity of cellulases, xylanases, and chitinases in bacteria. Biotechnol. Biofuels 9, 133 (2016).

PubMed 
PubMed Central 

Google Scholar
 

Fong, M., Berrin, J.-G. & Paës, G. Investigation of the binding properties of a multi-modular GH45 cellulase using bioinspired model assemblies. Biotechnol. Biofuels 9, 12 (2016).

PubMed 
PubMed Central 

Google Scholar
 

Pasari, N., Gupta, M., Sinha, T., Ogunmolu, F. E. & Yazdani, S. S. Systematic identification of CAZymes and transcription factors in the hypercellulolytic fungus Penicillium funiculosum NCIM1228 involved in lignocellulosic biomass degradation. Biotechnol. Biofuels Bioprod. 16, 150 (2023).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Quinlan, R. J. et al. Insights into the oxidative degradation of cellulose by a copper metalloenzyme that exploits biomass components. PNAS 108, 15079–15084 (2011).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Lo Leggio, L. et al. Structure and boosting activity of a starch-degrading lytic polysaccharide monooxygenase. Nat. Commun. 6, 5961 (2015).

CAS 
PubMed 

Google Scholar
 

Willis, M. D. et al. Polar oceans and sea ice in a changing climate. Elementa: Sci. Anthropocene 11, 1 (2023).

Grau, O. et al. Abrupt changes in the composition and function of fungal communities along an environmental gradient in the high Arctic. Mol. Ecol. 26, 4798–4810 (2017).

PubMed 

Google Scholar
 

Pickup RW, Rhodes G, Saunders JR. Extraction of microbial DNA from aquatic sources: Freshwater. In: Molecular Microbial Ecology Manual (eds Akkermans ADL, Van Elsas JD, De Bruijn FJ). Springer Netherlands (1995).

Rio DC, Ares M, Jr., Hannon GJ, Nilsen TW. Purification of RNA using TRIzol (TRI reagent). Cold Spring Harb Protoc 2010, pdb prot5439 (2010).

Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Kopylova, E., Noe, L. & Touzet, H. SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics 28, 3211–3217 (2012).

CAS 
PubMed 

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).

CAS 
PubMed 

Google Scholar
 

Levy Karin, E., Mirdita, M. & Söding, J. MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics. Microbiome 8, 48 (2020).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Zhang, H. et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 46, W95–W101 (2018).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).

CAS 
PubMed 

Google Scholar
 

Rawlings, N. D. et al. The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database. Nucleic Acids Res. 46, D624–D632 (2018).

CAS 
PubMed 

Google Scholar
 

Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinforma. 11, 119 (2010).


Google Scholar
 

Tang, S., Lomsadze, A. & Borodovsky, M. Identification of protein coding regions in RNA transcripts. Nucleic Acids Res. 43, e78 (2015).

PubMed 
PubMed Central 

Google Scholar
 

Zhao, Z. et al. Metaproteomic analysis decodes trophic interactions of microorganisms in the dark ocean. Nat. Commun. 15, 6411 (2024).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Belliardo, C. et al. Improvement of eukaryotic protein predictions from soil metagenomes. Sci. Data 9, 311 (2022).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Liaw, A. & Wiener, M. Classification and regression by randomForest. R. N. 2, 18–22 (2002).


Google Scholar
 

Liao, H. et al. Prophage-encoded antibiotic resistance genes are enriched in human-impacted environments. Nat. Commun. 15, 8315 (2024).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Jiao, S. et al. Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems. Microbiome 6, 146 (2018).

PubMed 
PubMed Central 

Google Scholar
 

Brownrigg, M. R. Package ‘maps’. R package, (2013).

Huang, H. LinkET: Everything is linkable. R package version 00 3, (2021).

Oksanen, J. et al. Vegan: Community Ecology Package. R. Package Version 2, 1–2 (2015). 22-1.


Google Scholar
 

Wickham, H., Chang, W. & Wickham, M. H. Package ‘ggplot2’. Creat. Elegant Data Visualisations Using Gramm. Graph. Version 2, 1–189 (2016).


Google Scholar