Surface ammonia-oxidizer abundance during the late summer in the West Antarctic coastal system

ABSTRACT Marine ammonia oxidizers that oxidize ammonium to nitrite are abundant in polar waters, especially during the winter in the deeper mixed-layer of West Antarctic Peninsula (WAP) waters. However, the activity and abundance of ammonia-oxidizers during the summer in surface coastal Antarctic waters remain unclear. In this study, the ammonia-oxidation rates, abundance, and identity of ammonia-oxidizing bacteria (AOB) and archaea (AOA) were evaluated in the marine surface layer (to 30 m depth) in Chile Bay (Greenwich Island, WAP) over three consecutive late-summer periods (2017, 2018 and 2019). Ammonia-oxidation rates of 68.31 nmol N L-1 d-1 (2018) and 37.28 nmol N L-1 d-1 (2019) were detected from illuminated 2 m seawater incubations. However, high ammonia-oxidation rates between 267.75 and 109.38 nmol N L-1 d-1 were obtained under the dark condition at 30 m in 2018 and 2019, respectively. During the late-summer sampling periods both stratifying and mixing events occurring in the water column over short timescales (February-March). Metagenomic analysis of seven nitrogen cycle modules revealed the presence of ammonia-oxidizers, such as the Archaea Nitrosopumilus and the Bacteria Nitrosomonas and Nitrosospira, with AOA often being more abundant than AOB. However, quantification of specific amoA gene transcripts showed number of AOB being two orders of magnitude higher than AOA, with Nitrosomonas representing the most transcriptionally active AOB in the surface waters. Additionally, Candidatus Nitrosopelagicus and Nitrosopumilus, phylogenetically related to surface members of the NP-ε and NP-γ clades respectively, were the predominant AOA. Our findings expand the known distribution of ammonium-oxidizers to the marine surface layer, exposing their potential ecological role in supporting the marine Antarctic system during the productive summer periods. Material and Methods Genomic identification of nitrification pathway. Proteins related to nitrification (amoCA, hao) and nitrite/nitrate reduction (nirBD, nasA) were searched in the protein catalog from Chile Bay metagenomes using hmmsearch (hmmer.org) using the hidden Markov models (HMM) profiles detailed in supplementary Table S3. Nitrification enzyme orthologues were identified with Diamond (diamond blastp -e 1e-5 --id 80 --query-cover 70). The identified proteins were curated against the KEGG database using Blast-KOALA. The file contigs_enzymes_nit_cyc.fna contains the contigs in which we identified the p