NIOO-KNAWSep 6, 2024
New publication: Intentional summer flooding of an Avicennia germinans #mangrove forest has a more direct effect on ammonia-oxidizing #Betaproteobacteria than on #Thaumarchaea. #ammoniaoxidation
https://doi.org/10.1007/s11104-024-06935-w
Intentional summer flooding of an Avicennia germinans mangrove forest has a more direct effect on ammonia-oxidizing Betaproteobacteria than on Thaumarchaea - Plant and Soil

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.

SpringerLink
Professor Mark OsbornJan 31, 2023

The identification of the role of #Archaea in carrying out ammonia oxidation in #nitrification in both aquatic and soil #ecosystems was a game changer in our understanding of (microbial) #nitrogencycling

This new research reveals hitherto unknown complexity in the enzyme that catalyses #ammoniaoxidation in Archaea and the involvement of additional Amo protein subunits.

Learn more in the ISME Journal on:

https://www.nature.com/articles/s41396-023-01367-3

#microbiology #ecology #MicrobialEcology

Unexpected complexity of the ammonia monooxygenase in archaea - The ISME Journal

Ammonia oxidation, as the first step of nitrification, constitutes a critical process in the global nitrogen cycle. However, fundamental knowledge of its key enzyme, the copper-dependent ammonia monooxygenase, is lacking, in particular for the environmentally abundant ammonia-oxidizing archaea (AOA). Here the structure of the enzyme is investigated by blue-native gel electrophoresis and proteomics from native membrane complexes of two AOA. Besides the known AmoABC subunits and the earlier predicted AmoX, two new protein subunits, AmoY and AmoZ, were identified. They are unique to AOA, highly conserved and co-regulated, and their genes are linked to other AMO subunit genes in streamlined AOA genomes. Modeling and in-gel cross-link approaches support an overall protomer structure similar to the distantly related bacterial particulate methane monooxygenase but also reveals clear differences in extracellular domains of the enzyme. These data open avenues for further structure-function studies of this ecologically important nitrification complex.

Nature