Composition, diversity, and activity of aerobic ammonia‐oxidizing Bacteria and Archaea in the intertidal sands of a grand strand South Carolina beach

Abstract

Aerobic ammonia oxidation to nitrite has been established as an important ecosystem process in regulating the level of nitrogen in marine ecosystems. This process is carried out by ammonia‐oxidizing bacteria (AOB) within the classes Betaproteobacteria and Gammaproteobacteria and ammonia‐oxidizing Archaea (AOA) from the phylum Thaumarchaeota, and the latter of which has been established as more prevalent in marine systems. This study investigated the presence, abundance, and activity of these groups of microbes at a beach near Springmaid Pier in Myrtle Beach, South Carolina, through the implementation of next generation sequencing, quantitative PCR (qPCR), and microcosm experiments to monitor activity. Sequencing analysis revealed a diverse community of ammonia‐oxidizing microbes dominated by AOA classified within the family Nitrosopumilaceae, and qPCR revealed the abundance of AOA amoA genes over AOB by at least an order of magnitude in most samples. Microcosm studies indicate that the rates of potential ammonia oxidation in these communities satisfy Michaelis–Menten substrate kinetics and this process is more active at temperatures corresponding to summer months than winter. Potential rates in AOA medium were higher than that of AOB medium, indicating a potentially greater contribution of AOA to this process in this environment. In conclusion, this study provides further evidence of the dominance of AOA in these environments compared with AOB and highlights the overall efficiency of this process at turning over excess ammonium that may be present in these environments.

Carbon dioxide sink in the Arctic Ocean from cross-shelf transport of dense Barents Sea water

“…Results of the 16S and 18S amplicon sequencing are deposited in the European Nucleotide Archive at EMBL-EBI under accession number PRJEB53455. Sequence data submission was done using the data brokerage service of the German Federation for Biological Data 81 in compliance with the Minimal Information about any (X) Sequence (MIxS) standard [82][83][84][85][86][87][88][89][90][91][92][93][94][95][96][97] . Results of the FESOM ocean current model and particle backtracking calculations are publicly available on Zenodo (https://doi.org/10.5281/zenodo.7085120).…”

Diversity of nitrifying bacteria in microbial communities from water and epilithic biofilms of the Lake Baikal littoral zone

“…microbial community (area of the Posolsk Bank cold methane seep, Lake Baikal), the water of Lake Maggiore, the bottom sediments of an oligotrophic lake of the Andes, etc. Previously, the members of Thaumarchaeota were found in the bottom sediments of Southern Baikal; in different layers, their proportion varied from 1 to 100% (Zemskaya et al, 2018). In the surface sedimentary layer of the Posolsk Bank methane seep, the sequences of the phylum Thaumarchaeota were numerically dominant in the microbial community (Chernitsyna et al, 2016).…”

“…The genera Nitrosomonas, Nitrosospira, Nitrosovibrio (Betaproteobacteria), and Nitrosococcus (Gammaproteobacteria) represent the phylogenetic diversity of AOB; the genera Nitrobacter (Alphaproteobacteria), Nitrococcus (Gammaproteobacteria), Nitrospina (Nitrospinae), Nitrospira (Nitrospirae), Nitrotoga (Betaproteobacteria), Nitrolancea (Chloroflexi), and "Candidatus Nitromaritima" (Nitrospinae) -NOB (Daims et al, 2016). All known AOA are the members of the phylum Thaumarchaeota (Taylor and Kurtz, 2020).…”

Sediment microbial community structure associated to different ecological types of mangroves in Celestún, a coastal lagoon in the Yucatan Peninsula, Mexico

“…All ecological types of mangroves, except for FRm, had Nitrosopumilaceae as their indicator taxa. Members of this family are capable of aerobic ammonium oxidation, an important process that regulates the level of nitrogen in marine ecosystems, however the mechanisms by which this process is accomplished, are not completely understood ( Taylor & Kurtz Jr, 2020 ). Nevertheless, their high abundances in these mangroves highlights the importance of nitrogen cycling.…”