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

Reji, Linta; Tolar, Bradley B.; Smith, Jason M.; Chavez, Francisco P.; Francis, Christopher A.

doi:10.1111/1462-2920.14753

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

Journal Article · 09 August 2019 · Environmental Microbiology

DOI: https://doi.org/10.1111/1462-2920.14753 · OSTI ID:1549194

Reji, Linta ^[1]; Tolar, Bradley B. ^[1]; Smith, Jason M. ^[2]; Chavez, Francisco P. ^[3];

^[1]

Department of Earth System Science Stanford University Stanford CA
Monterey Bay Aquarium Research Institute Moss Landing CA, Marine Science Institute University of California Santa Barbara Santa Barbara CA
Monterey Bay Aquarium Research Institute Moss Landing CA

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.

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Sponsoring Organization:: USDOE

OSTI ID:: 1549194

Journal Information:: Environmental Microbiology, Journal Name: Environmental Microbiology Journal Issue: 11 Vol. 21; ISSN 1462-2912

Publisher:: Wiley-BlackwellCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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