Facets of diazotrophy in the OMZ off Peru revisited- what we couldn’t see from a single marker gene approach

Abstract

Correspondence to cloescher@biology.sdu.dk Significance statementThis study addresses the important process of N 2 fixation, based on a whole-metagenome and -transcriptome screening, reports an increased diversity of N 2 fixing microbes in the sulfidic shelf water off Peru, as compared to previous target-gene based studies from the same waters. In addition to a generally higher diversity, genes encoding for alternative nitrogenases, which were previously not subject of any study on N 2 fixation in oxygen minimum zones, were detected. The ecological meaning and evolutionary history of those alternative nitrogenases is subject of ongoing debates, however, their presence in OMZ waters would allow for N 2 fixation at extreme anoxia, which may become important in a future ocean challenged by progressive deoxygenation. AbstractBiological dinitrogen (N 2 ) fixation is the pathway making the large pool of atmospheric N 2 available to marine life. Besides direct rate measurements, a common approach to explore the potential for N 2 fixation in the ocean is a mining based on molecular genetic methods targeting the key functional gene nifH, coding for a subunit of the nitrogenase reductase. As novel sequencing and single cell techniques improved, our knowledge on the diversity of marine N 2 fixers grew exponentially. However, to date one aspect of N 2 fixation in the ocean is commonly left aside. This is the existence of two alternative types of nitrogenases, which are besides the Mo-Fe nitrogenase Nif, the Fe-Fe nitrogenase Anf, and the V-Fe nitrogenase Vnf, which differ with regard to their metal co-enzymes, as well as regarding their operon structure and composition. nifH-based studies may thus be biased, and alternative nitrogenases could not be recovered. Here, we screened a set of 6 metagenomes and -transcriptomes from a sulfidic water patch from the oxygen minimum zone off Peru for genes involved in N 2 fixation. We identified genes related to all three nitrogenases, and generally increased diversity as compared to our previous nifH-based study from the same waters. While we could not confirm gene expression of the alternative nitrogenases from our transcriptomes, we detected additional diazotrophs involved in N 2 fixation. We suggest that alternative nitrogenases may not be used under conditions present in those waters, however, depending on trace metal limitation in the future they may become active.

Biological nitrogen fixation by alternative nitrogenases in terrestrial ecosystems: a review

“…These findings are consistent with previous reports on alternative nitrogenase genes in N 2 -fixing isolates from mangrove sediments in Puerto Rico and North Carolina creek sediment (Betancourt et al 2008). The presence of alternative nitrogenase genes was also recently reported in anoxic coastal waters off the coast of Peru (Christiansen and Loscher 2019), again suggesting that alternative nitrogen fixation in marine and coastal ecosystems may be more prevalent than usually recognized.…”

The bacterial sulfur cycle in expanding dysoxic and euxinic marine waters

“…These genes are also encoded by Nitrospirae NIOZ‐UU55 (73% complete, 1% contaminated). This supports a growing body of evidence for nitrogen fixation by putative SRB in DMW (Jayakumar et al ., 2012 ; Bonnet et al ., 2013 ; Loescher et al ., 2014 ; Christiansen and Loescher, 2019 ).…”

No nitrogen fixation in the Bay of Bengal?

“…Their quantitative importance for global N 2 fixation, however, is not yet clear. In oxy-gen minimum zones (OMZs) of the eastern tropical North and South Pacific Ocean, hypoxic basins in the San Pedro Ocean Time-series and the Santa Monica Bay Observatory in the Southern California Bight, and the Arabian Sea, those N 2 fixers form a unique community consisting of different clades of proteobacteria, clostridia, spirochaetes, chlorobia, and methanogenic archaea (Christiansen and Loescher, 2019;Dekaezemacker et al, 2013;Fernandez et al, 2011;Gaby et al, 2018;Gier et al, 2017;Goebel et al, 2010;Halm et al, 2012;Hamersley et al, 2011;Jayakumar et al, 2012Jayakumar et al, , 2017Löscher et al, 2014). In contrast, cyanobacterial N 2 fixers and diatom-diazotroph associations (DDAs), which are commonly considered the most important N 2 fixers in the surface ocean, were either absent or were detected only in low abundances in OMZs (Turk-Kubo et al, 2014;White et al, 2013;Jayakumar et al, 2012).…”