Small-scale variation of ammonia oxidisers within intertidal sediments dominated by ammonia-oxidising bacteria Nitrosomonas sp. amoA genes and transcripts

Aoife M Duff,Cindy J Smith,Li-Mei Zhang

doi:10.1038/s41598-017-13583-x

Abstract

While numerous studies have investigated the abundance of ammonia oxidising bacteria and archaea (AOB/AOA) via the ammonia monooxygenase gene amoA, less is known about their small-scale variation and if amoA gene abundance equates to activity. Here we present a spatial and temporal study of ammonia oxidation in two small intertidal bays, Rusheen and Clew bay, Ireland. Potential Nitrification Rate (PNR) was ten-fold higher in Rusheen bay (Clew: 0.27 ± SD 0.55; Rusheen: 2.46 ± SD 3.4 NO2− µg−1 g−1 day−1, P < 0.001) than in Clew bay but amoA gene abundances were similar between bays, and comparable to those in other coastal ecosystems. Within bays AOB genes increased towards the muddy sediments and were positively correlated with PNR and pH. Less spatial variation was observed in AOA abundances which nevertheless positively correlated with pH and temperature and negatively with salinity and ammonia. Transcriptionally active AOB and AOA were quantified from all sites in Rusheen bay, February 2014, following the general trends observed at DNA level. AOB phylotypes predominantly from the known Nitrosomonas group were distributed across the bay, while Nitrosomonas group B phylotypes were absent from low salinity sites. AOA genes and transcripts were primarily affiliated with Thaumarchaeota group I.1a.

Highlights

Nitrogen is a limited element for primary productivity
We postulated that ammonia oxidising bacteria (AOB) would be more abundant than AOA due to elevated ammonia concentrations; and that AOA and AOB diversity would vary with changing environmental parameters within intertidal bays
Within Clew bay Potential Nitrification Rate (PNR) did not vary spatially with the exception of the low salinity site (CSed_6) which was significantly higher than all other sites in August (0.54 μg−1 g−1 d−1) and November (0.97 μg−1 g−1 d−1; One-way analysis of variance (ANOVA) P < 0.05)

Summary

Introduction

Nitrogen is a limited element for primary productivity. While nitrate-limited environments suffer from low primary productivity, excess nitrate in the environment is problematic as it leads to eutrophication and hypoxia. We hypothesise that such small-scale variation in environmental parameters is likely to drive differences in nitrification activity, diversity and abundances. To this end, we investigated nitrification across a range of sediment types and salinities within and between two small intertidal bays (~1 km2) on the west coast of Ireland over an annual period. The objectives of the study were to monitor nitrification potential in addition to AOA and AOB amoA gene abundances within and between bays over an annual cycle. Intertidal bays are highly complex and dynamic ecosystems; we hypothesised that nitrifier activity and amoA gene abundances would vary spatially and temporally within and between bays due to fluctuating environmental parameters. We postulated that AOB would be more abundant than AOA due to elevated ammonia concentrations; and that AOA and AOB diversity would vary with changing environmental parameters within intertidal bays

Objectives

Methods

Results

Conclusion