Intriguing size distribution of the uncultured and globally widespread marine non-cyanobacterial diazotroph Gamma-A

Abstract

Non-cyanobacterial diazotrophs (NCDs) have recently emerged as potentially important contributors to marine nitrogen fixation. One of the most widely distributed NCDs is Gamma-A, yet information about its autecology is still scarce and solely relies on the PCR-based detection of its nitrogenase (nifH) gene in seawater, since previous metagenomic surveys targeting free-living planktonic size fractions (<3 μm) have not detected it. Here, we explore the diversity, biogeography, size-distribution, and nitrogenase gene expression of Gamma-A across four larger planktonic size-fractions (0.8-5, 5-20, 20-180, and 180-2000 μm) using metagenomes and metatranscriptomes from the Tara Oceans. We detected a single variant of a complete Gamma-A nifH gene along with other nitrogenase-related genes (nifKDT) within a metatranscriptomic-based contig of the Marine Atlas of Tara Ocean Unigenes. Gamma-A was detected in tropical and subtropical oceanic regions across all the size-fractions. However, the highest gene and transcript abundances were found in the 0.8-5 and 5-20 μm size-fractions at the surface, whereas abundances at the deep chlorophyll maximum were lower and similar across all size-fractions. The ubiquitous presence of active Gamma-A in large planktonic size-fractions suggests a filamentous or particle-attached lifestyle and places its potential to fix nitrogen in larger planktonic compartments.

Fig. 1. Distribution of Gamma-A-MATOU in the surface ocean.

Abundance (metagenome-based; left panel) and expression (metatranscriptome-based; right panel) of Gamma-A-MATOU across size fractions are shown. The area of the bubble is proportional to the abundance of metagenomic reads (blue) or transcripts (red) of Gamma-A-MATOU for each sample. Abundances of metagenomic and metatranscriptomic reads are expressed as RPKM (Reads Per Kilobase covered per Million of mapped reads).

Fig. 2. Abundance and expression of the Gamma-A-MATOU nitrogenase gene cluster across size fractions and depths.

Boxplots representing the abundance (blue) and expression (red) of Gamma-A-MATOU. The number of samples used for the calculation of each boxplot is indicated between parentheses. Abundances of metagenomic and metatranscriptomic reads are expressed as RPKM (Reads Per Kilobase covered per Million of mapped reads).