Biogeographical distributions of nitrogen‐cycling functional genes in a subtropical estuary

Abstract Microbial biogeography has predominantly been studied through a taxonomic lens. However, functional properties of microbial communities are often decoupled from their taxonomic compositions, emphasizing the need to study the biogeography of microbial functional genes directly. Here, using the Pearl River Estuary (PRE) sediments as a study system, we characterized the biogeographical patterns of the diversities and abundances of key microbial nitrogen‐cycling genes using metagenomic techniques. We found that functional genes involved in denitrification and dissimilatory nitrate reduction to ammonium pathways were more diverse and abundant than genes involved in other processes (i.e. nitrogen fixation, nitrification, assimilatory nitrite reduction). The diversities and abundances of certain nitrogen‐cycling genes were, to some extent, spatially decoupled. Specifically, the diversities of narG , napA , nirK and nrfA were greater adjacent to the river outlet, whereas the abundances of narG , napA and norB were greater in the downstream of the PRE. These spatial variations were mainly driven by water depth, C/N and . Moreover, nitrogen‐cycling genes involved in the same pathways (e.g. denitrification) showed no consistent responses to environmental changes and the main taxa involved in different nitrogen‐cycling steps were diverse, providing important clues for explaining why the abundance of single functional gene often seems not to be a reliable proxy for the specific process rate. Overall, our results demonstrate that studying the biogeography of microbial functional genes can help expand our knowledge of the nitrogen cycle from a biogeographical perspective. A free Plain Language Summary can be found within the Supporting Information of this article.