Activity, Abundance, and Diversity of Nitrifying Archaea and Denitrifying Bacteria in Sediments of a Subtropical Estuary: Bahía del Tóbari, Mexico

Abstract

Fixed nitrogen (N) removal from estuaries via coupled nitrification–denitrification plays a significant role in the global N cycle and the biogeochemistry of individual estuaries. Much of our understanding of these processes is drawn from temperate estuaries, yet tropical and subtropical estuaries may respond differently to N inputs. I tested the hypothesis that nitrification is limited within subtropical estuaries by comparing nitrification and denitrification potentials, and the abundance of archaeal ammonia monooxygenase (amoA) and bacterial nitrite reductase (nirS) genes, across five sites in Bahia del Tobari, Mexico. Sampling was conducted when agricultural runoff supplied substantial quantities of N (ca. 20–80 μM ammonium), yet nitrification was detected at a single site. Denitrification was measured at four sites, and three displayed nitrate uptake rather than net nitrification—indicating a N sink within these sediments. Bacterial nirS genes uniformly outnumbered archaeal amoA genes (3- to 49-fold) and were more abundant in the northern part of the estuary. Patterns of community similarity among different sites were also different for nirS and archaeal amoA: similarities between sites based on nirS were often greater than for amoA, and sites were more rarely statistically different from each other. While amoA abundance was inversely related to temperature, neither amoA nor nirS was correlated with nitrification or denitrification potentials. My results are broadly consistent with known and proposed patterns of nitrification and denitrification in subtropical estuarine sediments, including the idea that nitrification is limited within subtropical estuarine sediments.