Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans

Duncan, Anthony; Barry, Kerrie; Daum, Chris; Eloe-Fadrosh, Emiley; Roux, Simon; Schmidt, Katrin; Tringe, Susannah G.; Valentin, Klaus U.; Varghese, Neha; Salamov, Asaf; Grigoriev, Igor V.; Leggett, Richard M.; Moulton, Vincent; Mock, Thomas

doi:10.1186/s40168-022-01254-7

Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans

Journal Article · Thu Apr 28 00:00:00 EDT 2022 · Microbiome

DOI:https://doi.org/10.1186/s40168-022-01254-7· OSTI ID:1865498

Duncan, Anthony; ; Daum, Chris; Eloe-Fadrosh, Emiley; Roux, Simon; Schmidt, Katrin; Tringe, Susannah G.; Valentin, Klaus U.; Varghese, Neha; ; ; Leggett, Richard M.; Moulton, Vincent;

Abstract Background

Phytoplankton communities significantly contribute to global biogeochemical cycles of elements and underpin marine food webs. Although their uncultured genomic diversity has been estimated by planetary-scale metagenome sequencing and subsequent reconstruction of metagenome-assembled genomes (MAGs), this approach has yet to be applied for complex phytoplankton microbiomes from polar and non-polar oceans consisting of microbial eukaryotes and their associated prokaryotes.

Results

Here, we have assembled MAGs from chlorophyll a maximum layers in the surface of the Arctic and Atlantic Oceans enriched for species associations (microbiomes) with a focus on pico- and nanophytoplankton and their associated heterotrophic prokaryotes. From 679 Gbp and estimated 50 million genes in total, we recovered 143 MAGs of medium to high quality. Although there was a strict demarcation between Arctic and Atlantic MAGs, adjacent sampling stations in each ocean had 51–88% MAGs in common with most species associations between Prasinophytes and Proteobacteria . Phylogenetic placement revealed eukaryotic MAGs to be more diverse in the Arctic whereas prokaryotic MAGs were more diverse in the Atlantic Ocean. Approximately 70% of protein families were shared between Arctic and Atlantic MAGs for both prokaryotes and eukaryotes. However, eukaryotic MAGs had more protein families unique to the Arctic whereas prokaryotic MAGs had more families unique to the Atlantic.

Conclusion

Our study provides a genomic context to complex phytoplankton microbiomes to reveal that their community structure was likely driven by significant differences in environmental conditions between the polar Arctic and warm surface waters of the tropical and subtropical Atlantic Ocean.

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Research Organization:: USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)

Sponsoring Organization:: Natural Environmental Research Council; USDOE; USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1865498

Alternate ID(s):: OSTI ID: 1904123

Journal Information:: Microbiome, Journal Name: Microbiome Journal Issue: 1 Vol. 10; ISSN 2049-2618

Publisher:: Springer Science + Business MediaCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (99)

BEDTools: The Swiss-Army Tool for Genome Feature Analysis: BEDTools: the Swiss-Army Tool for Genome Feature Analysis Quinlan, Aaron R. Current Protocols in Bioinformatics, Vol. 47, Issue 1 https://doi.org/10.1002/0471250953.bi1112s47	journal	September 2014
Space-for-time substitution in predicting the state of picoplankton and nanoplankton in a changing Arctic Ocean: Arctic Picoplankton and Nanoplankton Li, William K. W.; Carmack, Eddy C.; McLaughlin, Fiona A. Journal of Geophysical Research: Oceans, Vol. 118, Issue 10 https://doi.org/10.1002/jgrc.20417	journal	October 2013
Distribution patterns of autotrophic pico- and nanoplankton and their relative contribution to algal biomass during spring in the Atlantic sector of the Southern Ocean Detmer, A. E.; Bathmann, U. V. Deep Sea Research Part II: Topical Studies in Oceanography, Vol. 44, Issue 1-2 https://doi.org/10.1016/S0967-0645(96)00068-9	journal	January 1997
Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome Salazar, Guillem; Paoli, Lucas; Alberti, Adriana Cell, Vol. 179, Issue 5 https://doi.org/10.1016/j.cell.2019.10.014	journal	November 2019
From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes Frioux, Clémence; Singh, Dipali; Korcsmaros, Tamas Computational and Structural Biotechnology Journal, Vol. 18 https://doi.org/10.1016/j.csbj.2020.06.028	journal	January 2020
Marine Protists Are Not Just Big Bacteria Keeling, Patrick J.; Campo, Javier del Current Biology, Vol. 27, Issue 11 https://doi.org/10.1016/j.cub.2017.03.075	journal	June 2017
Heat, acid and cold stresses enhance the expression of DnaK gene in Alicyclobacillus acidoterrestris Jiao, Lingxia; Ran, Junjian; Xu, Xixi Food Research International, Vol. 67 https://doi.org/10.1016/j.foodres.2014.11.023	journal	January 2015
Leveraging Enzyme Structure−Function Relationships for Functional Inference and Experimental Design: The Structure−Function Linkage Database ^† Pegg, Scott C. -H.; Brown, Shoshana D.; Ojha, Sunil Biochemistry, Vol. 45, Issue 8 https://doi.org/10.1021/bi052101l	journal	February 2006
Gene Ontology: tool for the unification of biology Ashburner, Michael; Ball, Catherine A.; Blake, Judith A. Nature Genetics, Vol. 25, Issue 1 https://doi.org/10.1038/75556	journal	May 2000
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 Balzano, Sergio; Marie, Dominique; Gourvil, Priscillia The ISME Journal, Vol. 6, Issue 8 https://doi.org/10.1038/ismej.2011.213	journal	January 2012
The symbiotic life of Symbiodinium in the open ocean within a new species of calcifying ciliate (Tiarina sp.) Mordret, Solenn; Romac, Sarah; Henry, Nicolas The ISME Journal, Vol. 10, Issue 6 https://doi.org/10.1038/ismej.2015.211	journal	December 2015
Climate-driven trends in contemporary ocean productivity Behrenfeld, Michael J.; O’Malley, Robert T.; Siegel, David A. Nature, Vol. 444, Issue 7120 https://doi.org/10.1038/nature05317	journal	December 2006
In situ imaging reveals the biomass of giant protists in the global ocean Biard, Tristan; Stemmann, Lars; Picheral, Marc Nature, Vol. 532, Issue 7600 https://doi.org/10.1038/nature17652	journal	April 2016
Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus Mock, Thomas; Otillar, Robert P.; Strauss, Jan Nature, Vol. 541, Issue 7638 https://doi.org/10.1038/nature20803	journal	January 2017
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes Albertsen, Mads; Hugenholtz, Philip; Skarshewski, Adam Nature Biotechnology, Vol. 31, Issue 6 https://doi.org/10.1038/nbt.2579	journal	May 2013
Near-optimal probabilistic RNA-seq quantification Bray, Nicolas L.; Pimentel, Harold; Melsted, Páll Nature Biotechnology, Vol. 34, Issue 5 https://doi.org/10.1038/nbt.3519	journal	April 2016
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas Nature Biotechnology, Vol. 35, Issue 8 https://doi.org/10.1038/nbt.3893	journal	August 2017
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets Steinegger, Martin; Söding, Johannes Nature Biotechnology, Vol. 35, Issue 11 https://doi.org/10.1038/nbt.3988	journal	October 2017
The impact of temperature on marine phytoplankton resource allocation and metabolism Toseland, A.; Daines, S. J.; Clark, J. R. Nature Climate Change, Vol. 3, Issue 11 https://doi.org/10.1038/nclimate1989	journal	September 2013
Iron limitation of microbial phosphorus acquisition in the tropical North Atlantic Browning, T. J.; Achterberg, E. P.; Yong, J. C. Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms15465	journal	May 2017
Zooming in on the phycosphere: the ecological interface for phytoplankton–bacteria relationships Seymour, Justin R.; Amin, Shady A.; Raina, Jean-Baptiste Nature Microbiology, Vol. 2, Issue 7 https://doi.org/10.1038/nmicrobiol.2017.65	journal	May 2017
Genome diversification in globally distributed novel marine Proteobacteria is linked to environmental adaptation Zhou, Zhichao; Tran, Patricia Q.; Kieft, Kristopher The ISME Journal, Vol. 14, Issue 8 https://doi.org/10.1038/s41396-020-0669-4	journal	May 2020
A global ocean atlas of eukaryotic genes Carradec, Quentin; Pelletier, Eric; Da Silva, Corinne Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-017-02342-1	journal	January 2018
The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole Martin, Kara; Schmidt, Katrin; Toseland, Andrew Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-25646-9	journal	September 2021
More protist genomes needed Sibbald, Shannon J.; Archibald, John M. Nature Ecology & Evolution, Vol. 1, Issue 5 https://doi.org/10.1038/s41559-017-0145	journal	April 2017
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life Parks, Donovan H.; Rinke, Christian; Chuvochina, Maria Nature Microbiology, Vol. 2, Issue 11 https://doi.org/10.1038/s41564-017-0012-7	journal	September 2017
Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes Delmont, Tom O.; Quince, Christopher; Shaiber, Alon Nature Microbiology, Vol. 3, Issue 7 https://doi.org/10.1038/s41564-018-0176-9	journal	June 2018
The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans Tully, Benjamin J.; Graham, Elaina D.; Heidelberg, John F. Scientific Data, Vol. 5, Issue 1 https://doi.org/10.1038/sdata.2017.203	journal	January 2018
Leads in Arctic pack ice enable early phytoplankton blooms below snow-covered sea ice Assmy, Philipp; Fernández-Méndez, Mar; Duarte, Pedro Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/srep40850	journal	January 2017
Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens Pritchard, Leighton; Glover, Rachel H.; Humphris, Sonia Analytical Methods, Vol. 8, Issue 1 https://doi.org/10.1039/C5AY02550H	journal	January 2016
Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus Flombaum, P.; Gallegos, J. L.; Gordillo, R. A. Proceedings of the National Academy of Sciences, Vol. 110, Issue 24 https://doi.org/10.1073/pnas.1307701110	journal	May 2013
Impact of ocean phytoplankton diversity on phosphate uptake Lomas, Michael W.; Bonachela, Juan A.; Levin, Simon A. Proceedings of the National Academy of Sciences, Vol. 111, Issue 49 https://doi.org/10.1073/pnas.1420760111	journal	November 2014
Southern Ocean phytoplankton turnover in response to stepwise Antarctic cooling over the past 15 million years Crampton, James S.; Cody, Rosie D.; Levy, Richard Proceedings of the National Academy of Sciences, Vol. 113, Issue 25 https://doi.org/10.1073/pnas.1600318113	journal	June 2016
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing Bankevich, Anton; Nurk, Sergey; Antipov, Dmitry Journal of Computational Biology, Vol. 19, Issue 5 https://doi.org/10.1089/cmb.2012.0021	journal	May 2012
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses Capella-Gutierrez, S.; Silla-Martinez, J. M.; Gabaldon, T. Bioinformatics, Vol. 25, Issue 15 https://doi.org/10.1093/bioinformatics/btp348	journal	June 2009
SEAL: a distributed short read mapping and duplicate removal tool Pireddu, L.; Leo, S.; Zanetti, G. Bioinformatics, Vol. 27, Issue 15 https://doi.org/10.1093/bioinformatics/btr325	journal	June 2011
InterProScan 5: genome-scale protein function classification Jones, P.; Binns, D.; Chang, H. -Y. Bioinformatics, Vol. 30, Issue 9 https://doi.org/10.1093/bioinformatics/btu031	journal	January 2014
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies Stamatakis, Alexandros Bioinformatics, Vol. 30, Issue 9 https://doi.org/10.1093/bioinformatics/btu033	journal	January 2014
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph Li, Dinghua; Liu, Chi-Man; Luo, Ruibang Bioinformatics, Vol. 31, Issue 10 https://doi.org/10.1093/bioinformatics/btv033	journal	January 2015
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs Simão, Felipe A.; Waterhouse, Robert M.; Ioannidis, Panagiotis Bioinformatics, Vol. 31, Issue 19 https://doi.org/10.1093/bioinformatics/btv351	journal	June 2015
MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes Noguchi, H.; Taniguchi, T.; Itoh, T. DNA Research, Vol. 15, Issue 6 https://doi.org/10.1093/dnares/dsn027	journal	October 2008
The Genome and mRNA Transcriptome of the Cosmopolitan Calanoid Copepod Acartia tonsa Dana Improve the Understanding of Copepod Genome Size Evolution Jørgensen, Tue Sparholt; Petersen, Bent; Petersen, H. Cecilie B. Genome Biology and Evolution, Vol. 11, Issue 5 https://doi.org/10.1093/gbe/evz067	journal	March 2019
Intraphylum Diversity and Complex Evolution of Cyanobacterial Aminoacyl-tRNA Synthetases Luque, I.; Riera-Alberola, M. L.; Andujar, A. Molecular Biology and Evolution, Vol. 25, Issue 11 https://doi.org/10.1093/molbev/msn197	journal	August 2008
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A. Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402 https://doi.org/10.1093/nar/25.17.3389	journal	September 1997
GeneMark.hmm: new solutions for gene finding Lukashin, A. Nucleic Acids Research, Vol. 26, Issue 4 https://doi.org/10.1093/nar/26.4.1107	journal	February 1998
The Gene Ontology resource: enriching a GOld mine Carbon, Seth; Douglass, Eric; Good, Benjamin M. Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa1113	journal	December 2020
PhycoCosm, a comparative algal genomics resource Grigoriev, Igor V.; Hayes, Richard D.; Calhoun, Sara Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa898	journal	October 2020
The TIGRFAMs database of protein families Haft, D. H. Nucleic Acids Research, Vol. 31, Issue 1 https://doi.org/10.1093/nar/gkg128	journal	January 2003
PIRSF: family classification system at the Protein Information Resource Wu, C. H. Nucleic Acids Research, Vol. 32, Issue 90001 https://doi.org/10.1093/nar/gkh097	journal	January 2004
MUSCLE: multiple sequence alignment with high accuracy and high throughput Edgar, R. C. Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797 https://doi.org/10.1093/nar/gkh340	journal	March 2004
InterPro: the integrative protein signature database Hunter, S.; Apweiler, R.; Attwood, T. K. Nucleic Acids Research, Vol. 37, Issue Database https://doi.org/10.1093/nar/gkn785	journal	January 2009
SUPERFAMILY 1.75 including a domain-centric gene ontology method de Lima Morais, D. A.; Fang, H.; Rackham, O. J. L. Nucleic Acids Research, Vol. 39, Issue Database https://doi.org/10.1093/nar/gkq1130	journal	November 2010
FragGeneScan: predicting genes in short and error-prone reads Rho, Mina; Tang, Haixu; Ye, Yuzhen Nucleic Acids Research, Vol. 38, Issue 20 https://doi.org/10.1093/nar/gkq747	journal	August 2010
Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis Lees, J.; Yeats, C.; Perkins, J. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1181	journal	December 2011
New and continuing developments at PROSITE Sigrist, Christian J. A.; de Castro, Edouard; Cerutti, Lorenzo Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1067	journal	November 2012
HAMAP in 2013, new developments in the protein family classification and annotation system Pedruzzi, I.; Rivoire, C.; Auchincloss, A. H. Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1157	journal	November 2012
The genome portal of the Department of Energy Joint Genome Institute: 2014 updates Nordberg, Henrik; Cantor, Michael; Dusheyko, Serge Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1069	journal	November 2013
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation O'Leary, Nuala A.; Wright, Mathew W.; Brister, J. Rodney Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1189	journal	November 2015
The MAR databases: development and implementation of databases specific for marine metagenomics Klemetsen, Terje; Raknes, Inge A.; Fu, Juan Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx1036	journal	November 2017
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes Chen, I-Min A.; Chu, Ken; Palaniappan, Krishna Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky901	journal	October 2018
Genomes OnLine database (GOLD) v.7: updates and new features Mukherjee, Supratim; Stamatis, Dimitri; Bertsch, Jon Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky977	journal	October 2018
The Pfam protein families database in 2019 El-Gebali, Sara; Mistry, Jaina; Bateman, Alex Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky995	journal	October 2018
Interactive Tree Of Life (iTOL) v4: recent updates and new developments Letunic, Ivica; Bork, Peer Nucleic Acids Research, Vol. 47, Issue W1 https://doi.org/10.1093/nar/gkz239	journal	April 2019
Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training Ter-Hovhannisyan, V.; Lomsadze, A.; Chernoff, Y. O. Genome Research, Vol. 18, Issue 12 https://doi.org/10.1101/gr.081612.108	journal	October 2008
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T. Genome Research, Vol. 25, Issue 7 https://doi.org/10.1101/gr.186072.114	journal	May 2015
Genome-reconstruction for eukaryotes from complex natural microbial communities West, Patrick T.; Probst, Alexander J.; Grigoriev, Igor V. Genome Research, Vol. 28, Issue 4 https://doi.org/10.1101/gr.228429.117	journal	March 2018
Diatom Molecular Research Comes of Age: Model Species for Studying Phytoplankton Biology and Diversity Falciatore, Angela; Jaubert, Marianne; Bouly, Jean-Pierre The Plant Cell, Vol. 32, Issue 3 https://doi.org/10.1105/tpc.19.00158	journal	December 2019
PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy Decelle, Johan; Romac, Sarah; Stern, Rowena F. Molecular Ecology Resources, Vol. 15, Issue 6 https://doi.org/10.1111/1755-0998.12401	journal	April 2015
The negative effects of temperature increase on bacterial respiration are independent of changes in community composition: Bacterial community and temperature changes Pires, Aliny P. F.; Guariento, Rafael D.; Laque, Thais Environmental Microbiology Reports, Vol. 6, Issue 2 https://doi.org/10.1111/1758-2229.12143	journal	January 2014
Biogeography of the ubiquitous marine bacterium Alteromonas macleodii determined by multilocus sequence analysis Ivars-MartÍNez, Elena; D’Auria, Giuseppe; RodrÍGuez-Valera, Francisco Molecular Ecology, Vol. 17, Issue 18 https://doi.org/10.1111/j.1365-294X.2008.03883.x	journal	September 2008
Distribution, Phylogeny, and Growth of Cold-Adapted Picoprasinophytes in Arctic seas Lovejoy, Connie; Vincent, Warwick F.; Bonilla, Sylvia Journal of Phycology, Vol. 43, Issue 1 https://doi.org/10.1111/j.1529-8817.2006.00310.x	journal	February 2007
Novel Ice-Binding Proteins from a Psychrophilic Antarctic alga (Chlamydomonadaceae, Chlorophyceae) Raymond, James A.; Janech, Michael G.; Fritsen, Christian H. Journal of Phycology, Vol. 45, Issue 1 https://doi.org/10.1111/j.1529-8817.2008.00623.x	journal	February 2009
Algae−bacteria interactions that balance the planktonic microbiome Cirri, Emilio; Pohnert, Georg New Phytologist, Vol. 223, Issue 1 https://doi.org/10.1111/nph.15765	journal	March 2019
Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas Worden, A. Z.; Lee, J. -H.; Mock, T. Science, Vol. 324, Issue 5924 https://doi.org/10.1126/science.1167222	journal	April 2009
Structure and function of the global ocean microbiome Sunagawa, S.; Coelho, L. P.; Chaffron, S. Science, Vol. 348, Issue 6237 https://doi.org/10.1126/science.1261359	journal	May 2015
Eukaryotic plankton diversity in the sunlit ocean de Vargas, C.; Audic, S.; Henry, N. Science, Vol. 348, Issue 6237 https://doi.org/10.1126/science.1261605	journal	May 2015
Trends in Prokaryotic Evolution Revealed by Comparison of Closely Related Bacterial and Archaeal Genomes Novichkov, Pavel S.; Wolf, Yuri I.; Dubchak, Inna Journal of Bacteriology, Vol. 191, Issue 1 https://doi.org/10.1128/JB.01237-08	journal	October 2008
Interactions between Diatoms and Bacteria Amin, S. A.; Parker, M. S.; Armbrust, E. V. Microbiology and Molecular Biology Reviews, Vol. 76, Issue 3 https://doi.org/10.1128/MMBR.00007-12	journal	August 2012
Heat and cold shock protein synthesis in arctic and temperate strains of rhizobia Cloutier, J.; Prévost, D.; Nadeau, P. Applied and Environmental Microbiology, Vol. 58, Issue 9 https://doi.org/10.1128/aem.58.9.2846-2853.1992	journal	September 1992
Ice-Binding Proteins and Their Function Bar Dolev, Maya; Braslavsky, Ido; Davies, Peter L. Annual Review of Biochemistry, Vol. 85, Issue 1 https://doi.org/10.1146/annurev-biochem-060815-014546	journal	June 2016
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects Holt, Carson; Yandell, Mark BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-491	journal	December 2011
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Langmead, Ben; Trapnell, Cole; Pop, Mihai Genome Biology, Vol. 10, Issue 3 https://doi.org/10.1186/gb-2009-10-3-r25	journal	January 2009
Factors driving effective population size and pan-genome evolution in bacteria Bobay, Louis-Marie; Ochman, Howard BMC Evolutionary Biology, Vol. 18, Issue 1 https://doi.org/10.1186/s12862-018-1272-4	journal	October 2018
Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes Papudeshi, Bhavya; Haggerty, J. Matthew; Doane, Michael BMC Genomics, Vol. 18, Issue 1 https://doi.org/10.1186/s12864-017-4294-1	journal	November 2017
Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions Stephens, Timothy G.; González-Pech, Raúl A.; Cheng, Yuanyuan BMC Biology, Vol. 18, Issue 1 https://doi.org/10.1186/s12915-020-00782-8	journal	May 2020
Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC Saary, Paul; Mitchell, Alex L.; Finn, Robert D. Genome Biology, Vol. 21, Issue 1 https://doi.org/10.1186/s13059-020-02155-4	journal	September 2020
MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs Huson, Daniel H.; Albrecht, Benjamin; Bağcı, Caner Biology Direct, Vol. 13, Issue 1 https://doi.org/10.1186/s13062-018-0208-7	journal	January 2018
Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms Olm, Matthew R.; West, Patrick T.; Brooks, Brandon Microbiome, Vol. 7, Issue 1 https://doi.org/10.1186/s40168-019-0638-1	journal	February 2019
Viruses in the Built Environment (VIBE) meeting report Prussin, Aaron J.; Belser, Jessica A.; Bischoff, Werner Microbiome, Vol. 8, Issue 1 https://doi.org/10.1186/s40168-019-0777-4	journal	January 2020
MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics Levy Karin, Eli; Mirdita, Milot; Söding, Johannes Microbiome, Vol. 8, Issue 1 https://doi.org/10.1186/s40168-020-00808-x	journal	April 2020
The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4) Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos Standards in Genomic Sciences, Vol. 11, Issue 1 https://doi.org/10.1186/s40793-016-0138-x	journal	February 2016
The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing Keeling, Patrick J.; Burki, Fabien; Wilcox, Heather M. PLoS Biology, Vol. 12, Issue 6 https://doi.org/10.1371/journal.pbio.1001889	journal	June 2014
Biogeography and Photosynthetic Biomass of Arctic Marine Pico-Eukaroytes during Summer of the Record Sea Ice Minimum 2012 Metfies, Katja; von Appen, Wilken-Jon; Kilias, Estelle PLOS ONE, Vol. 11, Issue 2 https://doi.org/10.1371/journal.pone.0148512	journal	February 2016
Under-Ice Phytoplankton Blooms: Shedding Light on the “Invisible” Part of Arctic Primary Production Ardyna, Mathieu; Mundy, C. J.; Mayot, Nicolas Frontiers in Marine Science, Vol. 7 https://doi.org/10.3389/fmars.2020.608032	journal	November 2020
Primary production of prochlorophytes, cyanobacteria, and eucaryotic ultraphytoplankton: Measurements from flow cytometric sorting Li, William K. W. Limnology and Oceanography, Vol. 39, Issue 1 https://doi.org/10.4319/lo.1994.39.1.0169	journal	January 1994
Metagenome-assembled genomes of phytoplankton microbiomes from Arctic and Atlantic Oceans repository Duncan, Anthony figshare https://doi.org/10.6084/m9.figshare.c.5017517	collection	January 2021
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities Kang, Dongwan D.; Froula, Jeff; Egan, Rob PeerJ, Vol. 3 https://doi.org/10.7717/peerj.1165	journal	January 2015
PhyloSift: phylogenetic analysis of genomes and metagenomes Darling, Aaron E.; Jospin, Guillaume; Lowe, Eric PeerJ, Vol. 2 https://doi.org/10.7717/peerj.243	journal	January 2014

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