Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, et al. Structure and function of the global ocean microbiome. Science. 2015;348:1261359.
Article
PubMed
CAS
Google Scholar
Vargas C d, Audic S, Henry N, Decelle J, Mahé F, Logares R, et al. Eukaryotic plankton diversity in the sunlit ocean. Science. 2015;348:1261605.
Article
PubMed
CAS
Google Scholar
Biard T, Stemmann L, Picheral M, Mayot N, Vandromme P, Hauss H, et al. In situ imaging reveals the biomass of giant protists in the global ocean. Nature. 2016;532:504–7 Nature Publishing Group.
Article
CAS
PubMed
Google Scholar
Decelle J, Romac S, Stern RF, Bendif EM, Zingone A, Audic S, et al. PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy. Mol Ecol Resour. 2015;15:1435–45.
Article
CAS
PubMed
Google Scholar
Mordret S, Romac S, Henry N, Colin S, Carmichael M, Berney C, et al. The symbiotic life of Symbiodinium in the open ocean within a new species of calcifying ciliate (Tiarina sp.). ISME J. 2016;10:1424–36 Nature Publishing Group.
Article
CAS
PubMed
Google Scholar
Carradec Q, Pelletier E, Da Silva C, Alberti A, Seeleuthner Y, Blanc-Mathieu R, et al. A global ocean atlas of eukaryotic genes. Nat Commun. 2018;9:373 Nature Publishing Group.
Article
PubMed
PubMed Central
CAS
Google Scholar
Toseland A, Daines SJ, Clark JR, Kirkham A, Strauss J, Uhlig C, et al. The impact of temperature on marine phytoplankton resource allocation and metabolism. Nat Climate Change. 2013;3:979–84.
Article
CAS
Google Scholar
Salazar G, Paoli L, Alberti A, Huerta-Cepas J, Ruscheweyh H-J, Cuenca M, et al. Gene expression changes and community turnover differentially shape the global ocean metatranscriptome. Cell. 2019;179:1068–1083.e21.
Article
CAS
PubMed
PubMed Central
Google Scholar
Novichkov PS, Wolf YI, Dubchak I, Koonin EV. Trends in prokaryotic evolution revealed by comparison of closely related bacterial and archaeal genomes. J Bacteriol. 2009;191:65–73 American Society for Microbiology Journals.
Article
CAS
PubMed
Google Scholar
Bobay L-M, Ochman H. Factors driving effective population size and pan-genome evolution in bacteria. BMC Evol Biol. 2018;18:153.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2017;35:725–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
West PT, Probst AJ, Grigoriev IV, Thomas BC, Banfield JF. Genome-reconstruction for eukaryotes from complex natural microbial communities. Genome Res. 2018;28:569–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Parks DH, Rinke C, Chuvochina M, Chaumeil P-A, Woodcroft BJ, Evans PN, et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat Microbiol. 2017;2:1533–42 Nature Publishing Group.
Article
CAS
PubMed
Google Scholar
Tully BJ, Graham ED, Heidelberg JF. The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans. Scientific Data. 2018;5:170203.
Article
CAS
PubMed
PubMed Central
Google Scholar
Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol. 2013;31:533–8.
Article
CAS
PubMed
Google Scholar
Fu H, Smith CB, Sharma S, Moran MA. Genome sequences and metagenome-assembled genome sequences of microbial communities enriched on phytoplankton exometabolites. Microbiol Resourc Announcements. 2020;9:30.
Google Scholar
Zhou Z, Tran PQ, Kieft K, Anantharaman K. Genome diversification in globally distributed novel marine Proteobacteria is linked to environmental adaptation. ISME J. 2020;14:2060–77 Nature Publishing Group.
Article
CAS
PubMed
PubMed Central
Google Scholar
Marques M, Borges N, Silva SG, Rocha UN d, Lago-Lestón A, Keller-Costa T, et al. Metagenome-assembled genome sequences of three uncultured Planktomarina sp. strains from the Northeast Atlantic Ocean. Microbiol Resourc Announcements. 2020;9:12.
Google Scholar
Delmont TO, Gaia M, Hinsinger DD, Fremont P, Guerra AF, Eren AM, et al. Functional repertoire convergence of distantly related eukaryotic plankton lineages revealed by genome-resolved metagenomics. bioRxiv. 2020;2020(10):15.341214 Cold Spring Harbor Laboratory.
Google Scholar
Sibbald SJ, Archibald JM. More protist genomes needed. Nat Ecol Evol. 2017;1:0145.
Article
Google Scholar
Zhang W, Cao S, Ding W, Wang M, Fan S, Yang B, et al. Structure and function of the Arctic and Antarctic marine microbiota as revealed by metagenomics. Microbiome. 2020;8:1–12 Springer.
Google Scholar
Kang S, Ahn D-H, Lee JH, Lee SG, Shin SC, Lee J, et al. The genome of the Antarctic-endemic copepod, Tigriopus kingsejongensis. Gigascience. 2017;6:1–9.
CAS
PubMed
PubMed Central
Google Scholar
Jørgensen TS, Petersen B, Petersen HCB, Browne PD, Prost S, Stillman JH, et al. The genome and mRNA transcriptome of the cosmopolitan calanoid copepod Acartia tonsa Dana improve the understanding of copepod genome size evolution. Genome Biol Evol. 2019;11:1440–50.
Article
PubMed
PubMed Central
CAS
Google Scholar
Li WKW. Primary production of prochlorophytes, cyanobacteria, and eucaryotic ultraphytoplankton: measurements from flow cytometric sorting. Limnol Oceanogr. 1994;39:169–75.
Article
CAS
Google Scholar
Detmer AE, Bathmann UV. Distribution patterns of autotrophic pico- and nanoplankton and their relative contribution to algal biomass during spring in the Atlantic sector of the Southern Ocean. Deep-Sea Res II Top Stud Oceanogr. 1997;44:299–320.
Article
CAS
Google Scholar
Balzano S, Marie D, Gourvil P, Vaulot D. Composition of the summer photosynthetic pico and nanoplankton communities in the Beaufort Sea assessed by T-RFLP and sequences of the 18S rRNA gene from flow cytometry sorted samples. ISME J. 2012;6:1480–98.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li WKW, Carmack EC, McLaughlin FA, Nelson RJ, Williams WJ. Space-for-time substitution in predicting the state of picoplankton and nanoplankton in a changing Arctic Ocean. J Geophys Res Oceans. 2013;118:5750–9.
Article
Google Scholar
Metfies K, Appen W-JV, Kilias E, Nicolaus A, Nöthig E-M. Biogeography and photosynthetic biomass of Arctic marine pico-eukaroytes during summer of the record sea ice minimum 2012. PLoS One. 2016;11:e0148512 Public Library of Science.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ardyna M, Mundy CJ, Mayot N, Matthes LC, Oziel L, Horvat C, et al. Under-ice phytoplankton blooms: shedding light on the “invisible” part of Arctic primary production. Front Mar Sci. 2020;7:985.
Article
Google Scholar
Assmy P, Fernández-Méndez M, Duarte P, Meyer A, Randelhoff A, Mundy CJ, et al. Leads in Arctic pack ice enable early phytoplankton blooms below snow-covered sea ice. Sci Rep. 2017;7:40850 Nature Publishing Group.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lovejoy C, Vincent WF, Bonilla S, Roy S, Martineau M-J, Terrado R, et al. Distribution, phylogeny, and growth of cold-adapted picoprasinophytes in Arctic seas. J Phycol. 2007;43:78–89.
Article
CAS
Google Scholar
Crampton JS, Cody RD, Levy R, Harwood D, McKay R, Naish TR. Southern Ocean phytoplankton turnover in response to stepwise Antarctic cooling over the past 15 million years. PNAS. 2016;113:6868–73 National Academy of Sciences.
Article
CAS
PubMed
PubMed Central
Google Scholar
Amin SA, Parker MS, Armbrust EV. Interactions between diatoms and bacteria. Microbiol Mol Biol Rev. 2012;76:667–84 American Society for Microbiology.
Article
CAS
PubMed
PubMed Central
Google Scholar
Seymour JR, Amin SA, Raina J-B, Stocker R. Zooming in on the phycosphere: the ecological interface for phytoplankton–bacteria relationships. Nat Microbiol. 2017;2:1–12 Nature Publishing Group.
Article
CAS
Google Scholar
Mock T, Otillar RP, Strauss J, McMullan M, Paajanen P, Schmutz J, et al. Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. Nature. 2017;541:536–40.
Article
CAS
PubMed
Google Scholar
Stephens TG, González-Pech RA, Cheng Y, Mohamed AR, Burt DW, Bhattacharya D, et al. Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions. BMC Biol. 2020;18:56.
Article
CAS
PubMed
PubMed Central
Google Scholar
Keeling PJ, Campo J d. Marine protists are not just big bacteria. Curr Biol. 2017;27:R541–9.
Article
CAS
PubMed
Google Scholar
Frioux C, Singh D, Korcsmaros T, Hildebrand F. From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes. Comput Struct Biotechnol J. 2020;18:1722–34.
Article
CAS
PubMed
PubMed Central
Google Scholar
Martin K, Schmidt K, Toseland A, Boulton CA, Barry K, Beszteri B, et al. The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole. Nat Commun. 2021;12:5483.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mukherjee S, Stamatis D, Bertsch J, Ovchinnikova G, Katta HY, Mojica A, et al. Genomes OnLine database (GOLD) v.7: updates and new features. Nucleic Acids Res. 2019;47:D649–59.
Article
CAS
PubMed
Google Scholar
Chen I-MA, Chu K, Palaniappan K, Pillay M, Ratner A, Huang J, et al. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res. 2019;47:D666–77.
Article
CAS
PubMed
Google Scholar
Huntemann M, Ivanova NN, Mavromatis K, Tripp HJ, Paez-Espino D, Tennessen K, et al. The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4). Stand Genomic Sci. 2016;11:17.
Article
PubMed
PubMed Central
CAS
Google Scholar
Bushnell B. BBTools software package. 2014. URL http://sourceforge net/projects/bbmap
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. 2015;31:1674–6.
Article
CAS
PubMed
Google Scholar
Pireddu L, Leo S, Zanetti G. SEAL: a distributed short read mapping and duplicate removal tool. Bioinformatics. 2011;27:2159–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lukashin AV, Borodovsky M. GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res. 1998;26:1107–15.
Article
CAS
PubMed
PubMed Central
Google Scholar
Noguchi H, Taniguchi T, Itoh T. MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA Res. 2008;15:387–96.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119.
Article
PubMed
PubMed Central
CAS
Google Scholar
Rho M, Tang H, Ye Y. FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res. 2010;38:e191.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kang DD, Froula J, Egan R, Wang Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ. 2015;3:e1165.
Article
PubMed
PubMed Central
CAS
Google Scholar
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics. 2020;36:1925–7.
CAS
Google Scholar
Bray NL, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol. 2016;34:525–7.
Article
CAS
PubMed
Google Scholar
Steinegger M, Söding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat Biotechnol. 2017;35:1026–8 Nature Publishing Group.
Article
CAS
PubMed
Google Scholar
Keeling PJ, Burki F, Wilcox HM, Allam B, Allen EE, Amaral-Zettler LA, et al. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol. 2014;12:e1001889.
Article
PubMed
PubMed Central
CAS
Google Scholar
Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31:3210–2.
Article
PubMed
CAS
Google Scholar
Saary P, Mitchell AL, Finn RD. Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC. Genome Biol. 2020;21:244.
Article
PubMed
PubMed Central
Google Scholar
Darling AE, Jospin G, Lowe E, Iv FAM, Bik HM, Eisen JA. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ. 2014;2:e243.
Article
PubMed
PubMed Central
Google Scholar
Klemetsen T, Raknes IA, Fu J, Agafonov A, Balasundaram SV, Tartari G, et al. The MAR databases: development and implementation of databases specific for marine metagenomics. Nucleic Acids Res. 2018;46:D692–9.
Article
CAS
PubMed
Google Scholar
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Letunic I, Bork P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2019;47:W256–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25:1972–3.
Article
PubMed
PubMed Central
CAS
Google Scholar
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–402.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huson DH, Albrecht B, Bağcı C, Bessarab I, Górska A, Jolic D, et al. MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs. Biol Direct. 2018;13:6.
Article
PubMed
PubMed Central
CAS
Google Scholar
Pritchard L, Glover RH, Humphris S, Elphinstone JG, Toth IK. Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal Methods. 2015;8:12–24.
Article
Google Scholar
Parks D. CompareM. 2016. Available from: https://github.com/dparks1134/CompareM
Google Scholar
Grigoriev IV, Hayes RD, Calhoun S, Kamel B, Wang A, Ahrendt S, et al. PhycoCosm, a comparative algal genomics resource. Nucleic Acids Res. 2021;49:D1004–11.
Article
CAS
PubMed
Google Scholar
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25:25–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gene Ontology Consortium. The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Res. 2021;49:D325–34.
Article
CAS
Google Scholar
Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, et al. InterPro: the integrative protein signature database. Nucleic Acids Res. 2009;37:D211–5.
Article
CAS
PubMed
Google Scholar
Ter-Hovhannisyan V, Lomsadze A, Chernoff YO, Borodovsky M. Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Res. 2008;18:1979–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Holt C, Yandell M. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics. 2011;12:491.
Article
PubMed
PubMed Central
Google Scholar
Levy Karin E, Mirdita M, Söding J. MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics. Microbiome. 2020;8:48.
Article
CAS
PubMed
PubMed Central
Google Scholar
O’Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D, McVeigh R, et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 2016;44:D733–45.
Article
PubMed
CAS
Google Scholar
Jones P, Binns D, Chang H-Y, Fraser M, Li W, McAnulla C, et al. InterProScan 5: genome-scale protein function classification. Bioinformatics. 2014;30:1236–40.
Article
CAS
PubMed
PubMed Central
Google Scholar
Haft DH, Selengut JD, White O. The TIGRFAMs database of protein families. Nucleic Acids Res. 2003;31:371–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pegg SC-H, Brown SD, Ojha S, Seffernick J, Meng EC, Morris JH, et al. Leveraging enzyme structure−function relationships for functional inference and experimental design: the Structure−Function Linkage Database. Biochemistry. 2006;45:2545–55 American Chemical Society.
Article
CAS
PubMed
Google Scholar
de Lima Morais DA, Fang H, Rackham OJL, Wilson D, Pethica R, Chothia C, et al. SUPERFAMILY 1.75 including a domain-centric gene ontology method. Nucleic Acids Res. 2011;39:D427–34.
Article
PubMed
CAS
Google Scholar
Lees J, Yeats C, Perkins J, Sillitoe I, Rentzsch R, Dessailly BH, et al. Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis. Nucleic Acids Res. 2012;40:D465–71.
Article
CAS
PubMed
Google Scholar
Pedruzzi I, Rivoire C, Auchincloss AH, Coudert E, Keller G, de Castro E, et al. HAMAP in 2013, new developments in the protein family classification and annotation system. Nucleic Acids Res. 2013;41:D584–9.
Article
CAS
PubMed
Google Scholar
Sigrist CJA, de Castro E, Cerutti L, Cuche BA, Hulo N, Bridge A, et al. New and continuing developments at PROSITE. Nucleic Acids Res. 2013;41:D344–7.
Article
CAS
PubMed
Google Scholar
El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, et al. The Pfam protein families database in 2019. Nucleic Acids Res. 2019;47:D427–32 Oxford Academic.
Article
CAS
PubMed
Google Scholar
Necci M, Piovesan D, Dosztányi Z, Tosatto SCE. MobiDB-lite: fast and highly specific consensus prediction of intrinsic disorder in proteins. Bioinformatics. 2017;33:1402–4.
CAS
PubMed
Google Scholar
Wu CH, Nikolskaya A, Huang H, Yeh LL, Natale DA, Vinayaka CR, et al. PIRSF: family classification system at the Protein Information Resource. Nucleic Acids Res. 2004;32:D112–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25.
Article
PubMed
PubMed Central
CAS
Google Scholar
Quinlan AR. BEDTools: The Swiss-Army Tool for genome feature analysis. Curr Protoc Bioinformatics. 2014;47:11.12.1–11.12.34.
Article
Google Scholar
Olm MR, West PT, Brooks B, Firek BA, Baker R, Morowitz MJ, et al. Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms. Microbiome. 2019;7:26.
Article
PubMed
PubMed Central
Google Scholar
Ivars-Martínez E, D’auria G, Rodríguez-Valera F, Sánchez-Porro C, Ventosa A, Joint I, et al. Biogeography of the ubiquitous marine bacterium Alteromonas macleodii determined by multilocus sequence analysis. Mol Ecol. 2008;17:4092–106.
Article
PubMed
CAS
Google Scholar
Delmont TO, Quince C, Shaiber A, Esen ÖC, Lee ST, Rappé MS, et al. Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. Nat Microbiol. 2018;3:804.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bar Dolev M, Braslavsky I, Davies PL. Ice-binding proteins and their function. Annu Rev Biochem. 2016;85:515–42.
Article
CAS
PubMed
Google Scholar
Raymond JA, Janech MG, Fritsen CH. Novel ice-binding proteins from a psychrophilic Antarctic alga (Chlamydomonadaceae, Chlorophyceae). J Phycol. 2009;45:130–6.
Article
CAS
PubMed
Google Scholar
Cloutier J, Prévost D, Nadeau P, Antoun H. Heat and cold shock protein synthesis in arctic and temperate strains of rhizobia. Appl Environ Microbiol. 1992;58:2846–53 American Society for Microbiology.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jiao L, Ran J, Xu X, Wang J. Heat, acid and cold stresses enhance the expression of DnaK gene in Alicyclobacillus acidoterrestris. Food Res Int. 2015;67:183–92.
Article
CAS
Google Scholar
Cirri E, Pohnert G. Algae−bacteria interactions that balance the planktonic microbiome. New Phytol. 2019;223:100–6.
Article
PubMed
Google Scholar
Flombaum P, Gallegos JL, Gordillo RA, Rincón J, Zabala LL, Jiao N, et al. Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus. PNAS National Academy of Sciences. 2013;110:9824–9.
Article
CAS
Google Scholar
Falciatore A, Jaubert M, Bouly J-P, Bailleul B, Mock T. Diatom molecular research comes of age: model species for studying phytoplankton biology and diversity. Plant Cell. 2020;32:547–72.
Article
CAS
PubMed
Google Scholar
Luque I, Riera-Alberola ML, Andújar A, Ochoa de Alda JAG. Intraphylum diversity and complex evolution of cyanobacterial aminoacyl-tRNA synthetases. Mol Biol Evol. 2008;25:2369–89 Oxford Academic.
Article
CAS
PubMed
Google Scholar
Papudeshi B, Haggerty JM, Doane M, Morris MM, Walsh K, Beattie DT, et al. Optimizing and evaluating the reconstruction of metagenome-assembled microbial genomes. BMC Genomics. 2017;18:915.
Article
PubMed
PubMed Central
CAS
Google Scholar
Worden AZ, Lee J-H, Mock T, Rouzé P, Simmons MP, Aerts AL, et al. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science. 2009;324:268–72 American Association for the Advancement of Science.
Article
CAS
PubMed
Google Scholar
Behrenfeld MJ, O’Malley RT, Siegel DA, McClain CR, Sarmiento JL, Feldman GC, et al. Climate-driven trends in contemporary ocean productivity. Nature. 2006;444:752–5 Nature Publishing Group.
Article
CAS
PubMed
Google Scholar
Pires APF, Guariento RD, Laque T, Esteves FA, Farjalla VF. The negative effects of temperature increase on bacterial respiration are independent of changes in community composition. Environ Microbiol Rep. 2014;6:131–5.
Article
PubMed
Google Scholar
Lomas MW, Bonachela JA, Levin SA, Martiny AC. Impact of ocean phytoplankton diversity on phosphate uptake. PNAS. 2014;111:17540–5 National Academy of Sciences.
Article
CAS
PubMed
PubMed Central
Google Scholar
Browning TJ, Achterberg EP, Yong JC, Rapp I, Utermann C, Engel A, et al. Iron limitation of microbial phosphorus acquisition in the tropical North Atlantic. Nat Commun. 2017;8:15465 Nature Publishing Group.
Article
CAS
PubMed
PubMed Central
Google Scholar
Duncan A. Metagenome-assembled genomes of phytoplankton communities across the Arctic Circle. figshare; 2020. Available from: https://doi.org/10.6084/m9.figshare.c.5017517
Google Scholar
Grigoriev IV, Nordberg H, Shabalov I, Aerts A, Cantor M, Goodstein D, et al. The Genome Portal of the Department of Energy Joint Genome Institute. Nucleic Acids Res; 2012;40:D26–D32. Oxford Academic
Nordberg H, Cantor M, Dusheyko S, Hua S, Poliakov A, Shabalov I, et al. The genome portal of the Department of Energy Joint Genome Institute: 2014 updates. Nucleic Acids Res. 2014;42:D26–31.
Article
CAS
PubMed
Google Scholar
Moderate-resolution Imaging Spectroradiometer (MODIS) Aqua 11μm Day/Night Sea Surface Temperature Data; 2014 Reprocessing. [Internet]. NASA Goddard Space Flight Center, Ocean Ecology Laboratory, Ocean Biology Processing Group; [cited 2020 Jan 9]. Available from: doi: data/https://doi.org/10.5067/AQUA/MODIS/L3B/SST/2014