Geographic Distribution of Archaeal Ammonia Oxidizing Ecotypes in the Atlantic Ocean

Abstract

In marine ecosystems, Thaumarchaeota are most likely the major ammonia oxidizers. While ammonia concentrations vary by about two orders of magnitude in the oceanic water column, archaeal ammonia oxidizers (AOA) vary by only one order of magnitude from surface to bathypelagic waters. Thus, the question arises whether the key enzyme responsible for ammonia oxidation, ammonia monooxygenase (amo), exhibits different affinities to ammonia along the oceanic water column and consequently, whether there are different ecotypes of AOA present in the oceanic water column. We determined the abundance and phylogeny of AOA based on their amoA gene. Two ecotypes of AOA exhibited a distribution pattern reflecting the reported availability of ammonia and the physico-chemical conditions throughout the Atlantic, and from epi- to bathypelagic waters. The distinction between these two ecotypes was not only detectable at the nucleotide level. Consistent changes were also detected at the amino acid level. These changes include substitutions of polar to hydrophobic amino acid, and glycine substitutions that could have an effect on the configuration of the amo protein and thus, on its activity. Although we cannot identify the specific effect, the ratio of non-synonymous to synonymous substitutions (dN/dS) between the two ecotypes indicates a strong positive selection between them. Consequently, our results point to a certain degree of environmental selection on these two ecotypes that have led to their niche specialization.

Thaumarchaeal ecotype distributions across the equatorial Pacific Ocean and their potential roles in nitrification and sinking flux attenuation

“…We did, however, observe a relatively sharp transition at approximately the r t 5 26 kg m 22 isopycnal, just below the euphotic zone and at the maximum NO3 : Si, suggesting that niche differentiation between the WCA and WCB ecotypes may be driven by substrate (ammonium) flux. These data support the observations of Sintes et al (2013Sintes et al ( , 2015Sintes et al ( , 2016 and Smith et al (2015), who suggested that the shallow and deep ecotypes are adapted to "high" and "low" ammonium concentrations, respectively. We posit, however, it is not ammonium concentration, but rather ammonium flux, through these depths that is more likely a driver of niche differentiation, as [NH 1 4 ] in our dataset is below 120 nM at all depths.…”

Molecular Systematics of the Genus Acidithiobacillus: Insights into the Phylogenetic Structure and Diversification of the Taxon

“…albertensis clade had values > 1, indicating that positive selection is ongoing in this branch. This statement is also supported by clearly distinguishable oligotypes between the two lineages at the level of the 16S rRNA gene, implying probable ecotype level differentiation (e.g., Sintes et al, 2016). Some obvious phenotypic features between the two lineages support this view.…”

Influence of ammonia oxidation rate on thaumarchaeal lipid composition and the TEX 86 temperature proxy

“…>200-500 m), whereas high-ammonia adapted ecotypes dominate more productive sites such as subpolar and equatorial upwelling regions (11,12). Differences in the TEX 86 -ammonia oxidation rate responses of these ecotypes potentially offer an explanation for regional TEX 86 -temperature correlations.…”

“…Based on the phylogeny of their ammonia monooxygenase gene, the planktonic Thaumarchaeota are divided into two distinct clusters, the Water Column Cluster A that is most abundant in the epi-and upper mesopelagic (above ∼200 to ∼500 m, depending on location) and the Water Column Cluster B that dominates thaumarchaeal assemblages in the deeper mesopelagic and bathypelagic (7-10). These clusters putatively represent thaumarchaeal ecotypes adapted to high and low ammonium flux, respectively (11,12).Thaumarchaeota produce GDGTs containing from zero to four cyclopentane rings (GDGT-0 to GDGT-4) or four cyclopentane rings and one additional cyclohexane ring (e.g., in crenarchaeol; see SI Appendix, Fig. S1).…”