Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods

Abstract

Biological nitrogen fixation sustains ~50% of ocean primary production. However, our understanding of marine N2-fixers (diazotrophs) is hindered by limited observations. Here, we developed a quantitative image analysis pipeline in concert with mapping of molecular markers for mining >2,000,000 images and >1,300 metagenomes from Tara Oceans, covering surface, deep chlorophyll maximum and mesopelagic layers across 6 organismal size fractions (0-2000 μm). Imaging and molecular data were remarkably congruent. Diazotrophs were detected from ultrasmall bacterioplankton (<0.2 μm) to mesoplankton (180 to 2000 μm). We identified several new high density regions of diazotrophs. Distributional and abundance patterns support the previous canonical view that larger sized diazotrophs (>10 μm) dominate the tropical belts, while unicellular diazotrophs were found in surface and mesopelagic samples. Multiple co-occurring diazotrophic lineages were frequently encountered, suggesting that complex overlapping niches are common. Overall, this work provides an updated global snapshot of marine diazotroph biogeographical diversity and highlights new sources and sinks of diazotroph-fueled new production.

Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean

“…It is worth mentioning that within cyanobacterial diazotrophs, the two populations of Trichodesmium thiebautii , highly abundant in some of the large size fractions, were mostly detected in the Indian Ocean (Figure 1). Trichodesmium might prevail in this region, but the overall geographic distribution of diazotrophs indicates that the Pacific Ocean is especially dominated by HBDs, corroborating previously observed trends 17,34,39 with an extended set of diazotrophs and considering a wide size fraction for planktonic cells.…”

“…The 47 nifH genes identified in the MAGs were considered novel if their sequence identity scores never exceeded 98% identity over an alignment of al least 200 nucleotides, when compared to a recently built nifH gene catalog by Pierella Karlusich et a. 17 using blast 81 . Briefly, the nifH gene catalog consists of sequences from Zehr laboratory (mostly diazotroph isolates and environmental clone libraries; https://www.jzehrlab.com), sequenced genomes, and additional sequences retrieved from Tara Oceans metagenomic assemblies (co-assemblies 39 and the OM-Reference Gene Catalog version 2 40 ).…”

“…Cyanobacterial diazotrophs are abundant in the surface of the open ocean and contribute to a substantial portion of nitrogen input [13][14][15] . They include populations within the genus Trichodesmium [16][17][18] and other lineages that enter symbiotic associations with eukaryotes (e.g., Richelia 19,20 , the Candidatus Atelocyanobacterium also labeled UCYN-A 21,22 ) or exist under the form of free living cells (some of the Crocosphaera watsonii cells also labeled UCYN-B 23,24 ). A wide range of noncyanobacterial diazotrophs has also been detected using amplicon surveys of the nifH gene required for nitrogen fixation.…”

Environmental genomics points to non-diazotrophicTrichodesmiumspecies abundant and widespread in the open ocean

“…Insights from culture representatives and oceanic expeditions have provided a wealth of information regarding their biogeography, functional life styles and nitrogen fixation regulation mechanisms 14,19 . Most notably, Trichodesmium cells are capable of forming large blooms of filaments and colonies in the sunlit ocean 13,[20][21][22] , regulate nitrogen fixation rates on a daily basis using a dedicated circadian rhythm 23,24 as well as an associated microbiome [25][26][27] , and possess genes linked to the recycling of hydrogen, a by-product of nitrogen fixation [28][29][30] . Decades of scientific insights have shaped a dogma depicting the numerous Trichodesmium cells as carbon and nitrogen fixers with a highly beneficial role for plankton productivity.…”

“…Recent large-scale single cell and genome-resolved metagenomic surveys have dramatically expanded the genomic characterization of free-living marine microbes [31][32][33][34] and lead to new insights into primary processes in the surface of the open ocean, including nitrogen fixation 34 . However, a major focus on small planktonic size fractions typically excluded organisms such as Trichodesmium that form filaments and colonies and occur in larger size fractions 21 . This gap is partially filled by a recent metagenomic survey that reconstructed and manually curated more than one thousand bacterial genomes abundant in large size fractions of the Tara Oceans expeditions 35 , which included five near-complete environmental Trichodesmium genomes.…”