Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods
This article is contribution number 118 of Tara Oceans.-- 18 pages, 10 figures, supplementary information https://doi.org/10.1038/s41467-021-24299-y.-- Data availability: The authors declare that all the data supporting the findings of this study are publicly available in the following repositories and in the supplementary information files of this paper. The contextual data are available in Pangaea (www.pangaea.de)21 with the identifier https://doi.org/10.1594/PANGAEA.875582. Flow cytometry data23,108 are available in Mendeley Data (https://data.mendeley.com) with the identifier https://doi.org/10.17632/p9r9wttjkm.2. The confocal microscopy30 and UVP533 images annotated as diazotrophs in the current work and their corresponding metadata were submitted to the EMBL-EBI repository BioStudies (www.ebi.ac.uk/biostudies) under accession S-BSST529; while the whole image databases and their metadata are available at Ecotaxa (confocal microscopy of 5–20 µm sized-fractionated samples: https://ecotaxa.obs-vlfr.fr/prj/3365; confocal microscopy of 20–180 μm sized-fractionated samples: https://ecotaxa.obs-vlfr.fr/prj/2274; UVP5: https://ecotaxa.obs-vlfr.fr/prj/579). Tara Oceans metagenomes22,24,25 are archived at ENA under the accession numbers: PRJEB1787, PRJEB1788, PRJEB4352, PRJEB4419, PRJEB9691, PRJEB9740, and PRJEB9742. The nifH and recA catalogs were compiled from Integrated Microbial Genomes (IMG, https://img.jgi.doe.gov/); Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP; https://github.com/dib-lab/dib-MMETSP); OM-Reference Gene Catalog version 2 (OM-RGC-v2, https://www.ocean-microbiome.org/); Tara Oceans assemblies (Supplementary Table 8 from ref. 16); and the nifH database (version April 2014) curated and hosted at Zehr Lab, University of California, Santa Cruz, CA, USA (https://www.jzehrlab.com/nifh). The 10 nifH sequences generated in the clone libraries of the current work were submitted to ENA under the accession numbers: MW590317–MW590326. Source data are provided with this paper ; Nitrogen fixation has a critical role in marine primary production, yet our understanding of marine nitrogen-fixers (diazotrophs) is hindered by limited observations. Here, we report a quantitative image analysis pipeline combined with mapping of molecular markers for mining >2,000,000 images and >1300 metagenomes from surface, deep chlorophyll maximum and mesopelagic seawater samples across 6 size fractions (20 µm). Using imaging and molecular data, we estimate that polyploidy can substantially affect gene abundances of symbiotic versus colony-forming diazotrophs. Our results support the canonical view that larger diazotrophs (>10 μm) dominate the tropical belts, while unicellular cyanobacterial and non-cyanobacterial diazotrophs are globally distributed in surface and mesopelagic layers. We describe co-occurring diazotrophic lineages of different lifestyles and identify high-density regions of diazotrophs in the global ocean. Overall, we provide an update of marine diazotroph biogeographical diversity and present a new bioimaging-bioinformatic workflow ; This work has been supported by the FFEM - French Facility for Global Environment, French Government 'Investissements d'Avenir' programs OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08), MEMO LIFE (ANR-10-LABX-54), and PSL Research University (ANR-11-IDEX-0001-02). R.A.F. acknowledges funding from Knut and Alice Wallenberg foundation. C.B. acknowledges funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Diatomic; grant agreement No. 835067) and Agence Nationale de la Recherche "Phytomet" (ANR-16-CE01-0008) projects. F.M.C.-C. acknowledges funding from the European Union's Horizon 2020 research program under the Marie Sklodowska-Curie grant agreement No. 749380 (UCYN2PLAST). S.G.A. acknowledges funding from the project "MAGGY" (CTM2017-87736-R) from the Spanish Ministry of Economy and Competitiveness and the 'Severo Ochoa Centre of Excellence' accreditation (CEX2019-000928-S). J.J.P.K. acknowledges postdoctoral funding from the Fonds Français pour l'Environnement Mondial ; Peer reviewed