Depth distributions of nitrite reductase (nirK) gene variants reveal spatial dynamics of thaumarchaeal ecotype populations in coastal Monterey Bay

Abstract

Summary Ammonia‐oxidizing archaea (AOA) of the phylum Thaumarchaeota are key players in nutrient cycling, yet large gaps remain in our understanding of their ecology and metabolism. Despite multiple lines of evidence pointing to a central role for copper‐containing nitrite reductase (NirK) in AOA metabolism, the thaumarchaeal nirK gene is rarely studied in the environment. In this study, we examine the diversity of nirK in the marine pelagic environment, in light of previously described ecological patterns of pelagic thaumarchaeal populations. Phylogenetic analyses show that nirK better resolves diversification patterns of marine Thaumarchaeota, compared to the conventionally used marker gene amoA. Specifically, we demonstrate that the three major phylogenetic clusters of marine nirK correspond to the three ‘ecotype’ populations of pelagic Thaumarchaeota. In this context, we further examine the relative distributions of the three variant groups in metagenomes and metatranscriptomes representing two depth profiles in coastal Monterey Bay. Our results reveal that nirK effectively tracks the dynamics of thaumarchaeal ecotype populations, particularly finer‐scale diversification patterns within major lineages. We also find evidence for multiple copies of nirK per genome in a fraction of thaumarchaeal cells in the water column, which must be taken into account when using it as a molecular marker.

Time series assessment of Thaumarchaeota ecotypes in Monterey Bay reveals the importance of water column position in predicting distribution–environment relationships

“…We found equivalent abundances of nirK genes as amoA genes (NP‐ nirK : 4.5 × 10 3 to 1.1 × 10 8 copies L −1 ; WCG‐ nirK : 1.2 × 10 4 to 1.7 × 10 8 copies L −1 ). Similar depth trends were observed before in Monterey Bay (Lund et al ) and match analysis of metagenome‐derived nirK genes sequenced from these depths (Reji et al ).…”

“…WCB ecotype abundance only showed a weak correlation to WCG‐ nirK with qPCR ( R 2 = 0.08, p < 0.001). This improved when adding WCA and WCB qPCR abundance together ( R 2 = 0.28, p < 0.001), matching the expected phylogenetic affiliation of WCG‐ nirK (Reji et al ).…”

“…Estimates of ecotype abundance agreed between sequencing (total reads) and qPCR (copies L −1 ) for WCA ( R 2 = 0.29, p < 0.001) and WCB ( R 2 = 0.45, p < 0.001). Additional correlations were observed with NP‐ nirK (AnirKa) qPCR abundance and 16S rRNA reads affiliated with the NP ecotype ( R 2 = 0.22, p < 0.001) as would be predicted based on phylogenetic analysis (Reji et al ). WCA ecotype showed a correlation with WCG‐ nirK (AnirKb, WCA and WCB; R 2 = 0.22; p < 0.001) as expected; these correlations were stronger with WCA qPCR abundance ( R 2 = 0.22 or 0.27, respectively; p < 0.001).…”

“…Following work with archaeal nirK in Monterey Bay, we used assays targeting the two major marine clades—termed AnirKa and AnirKb (Lund et al )—to investigate how their abundance changed over time. Recent work found that these clades are actually related to the major Thaumarchaeota ecotypes discussed here (Reji et al ), with AnirKa representing the NP ecotype, while AnirKb contains both WCA and WCB as subgroups within (AnirKb‐I and AnirKb‐II in Lund et al ). Henceforth, we will refer to AnirKa as NP‐ nirK and AnirKb as WCG‐ nirK (water column group).…”

Aerobic heterotrophy and RuBisCO-mediated CO2metabolism in marineThaumarchaeota

“…As part of the time-series microbiome survey in Monterey Bay, we previously obtained a depth-108 resolved dataset of 16S rRNA V4-V5 amplicon sequences, as well as metagenomes and 109 metatranscriptomes (43,44). We were able to match one of the MAG-derived 16S rRNA sequences to an operational taxonomic unit (OTU) obtained in a time-series molecular survey 111 targeting the V4-V5 region of the 16S rRNA genes.…”