Intentional summer flooding of an Avicennia germinans mangrove forest has a more direct effect on ammonia-oxidizing Betaproteobacteria than on Thaumarchaea

Abstract

Aims

Rotational Impoundment Management (RIM) involves summer inundation of impounded mangrove forests for mosquito management. The goal of this study was to investigate the impact of RIM on communities of aerobic ammonia-oxidizing microorganisms in Avicennia germinans dominated mangrove forest soils.

Methods

Soil samples were collected annually in a managed and an adjacent, non-managed impoundment before and after the start of RIM at three elevation levels with their characteristic mangrove habitats, i.e., dwarf (highest elevation), sparse and dense (lowest elevation). The ammonia-oxidizing communities were studied by qPCR and amplicon analyses based on thaumarchaeal and betaproteobacterial amoA genes.

Results

Temporal variations in copy numbers and assemblies of amoA gene amplicons were limited. Thaumarchaeal amoA genes increased in the dwarf and sparse habitat in the non-managed impoundment, and betaproteobacterial amoA genes increased in the dwarf habitat in the RIM impoundment. No copies of the amoA gene of Nitrospirota (comammox bacteria) were detected in either impoundment. Whereas there were no significant effects of RIM on the composition of thaumarchaeal communities, RIM affected the composition of betaproteobacterial amoA assemblies in all habitats in the RIM impoundment.

Conclusions

Direct consequences of RIM were reflected in changes in the composition of assemblies of amplicon sequence variants (ASVs) of ammonia-oxidizing Betaproteobacteria in all mangrove habitats of the RIM impoundment. Significant temporal changes at higher elevations in the non-managed impoundment were likely due to groundwater exchange between the impoundments.