Activity, abundance and diversity of nitrifying archaea and bacteria in the central California Current

• Published in: Environmental microbiology Vol. 12; no. 7; pp. 1989 - 2006
• Main Authors: Santoro, Alyson E, Casciotti, Karen L, Francis, Christopher A
• Format: Journal Article
• Language: English
• Published: Oxford, UK Oxford, UK : Blackwell Publishing Ltd 01.07.2010; Blackwell Publishing Ltd
• Subjects: ammonia; Ammonia - metabolism; Archaea; Archaea - classification; Archaea - isolation & purification; Archaea - metabolism; Archaeal Proteins; Archaeal Proteins - genetics; bacteria; Bacteria - classification; Bacteria - isolation & purification; Bacteria - metabolism; Bacterial Proteins; Bacterial Proteins - genetics; Biodiversity; California; chemistry; classification; Cluster Analysis; Crenarchaeota; DNA, Archaeal; DNA, Archaeal - chemistry; DNA, Archaeal - genetics; DNA, Bacterial; DNA, Bacterial - chemistry; DNA, Bacterial - genetics; DNA, Ribosomal; DNA, Ribosomal - chemistry; DNA, Ribosomal - genetics; euphotic zone; genes; Genes, rRNA; genetics; isolation & purification; metabolism; microbiology; Molecular Sequence Data; nitrates; Nitrates - metabolism; nitrification; Nitrites; Nitrites - metabolism; Nitrogen; Nitrogen - metabolism; Nitrospina; nitrous oxide; nucleotide sequences; oxidation; Oxidoreductases; Oxidoreductases - genetics; Phylogeny; polymerase chain reaction; ribosomal RNA; RNA, Archaeal; RNA, Archaeal - genetics; RNA, Bacterial; RNA, Bacterial - genetics; RNA, Ribosomal, 16S; RNA, Ribosomal, 16S - genetics; Seawater; Seawater - microbiology; Sequence Analysis, DNA; Sequence Homology, Nucleic Acid; species diversity; stable isotopes; surface water; California
• ISSN: 1462-2912; 1462-2920; 1462-2920
• DOI: 10.1111/j.1462-2920.2010.02205.x

A combination of stable isotope and molecular biological approaches was used to determine the activity, abundance and diversity of nitrifying organisms in the central California Current. Using ¹⁵NH₄⁺ incubations, nitrification was detectable in the upper water column down to 500 m; maximal rates were observed just below the euphotic zone. Crenarchaeal and betaproteobacterial ammonia monooxygenase subunit A genes (amoA), and 16S ribosomal RNA (rRNA) genes of Marine Group I Crenarchaeota and a putative nitrite-oxidizing genus, Nitrospina, were quantified using quantitative PCR. Crenarchaeal amoA abundance ranged from three to six genes ml⁻¹ in oligotrophic surface waters to > 8.7 x 10⁴ genes ml⁻¹ just below the core of the California Current at 200 m depth. Bacterial amoA abundance was lower than archaeal amoA and ranged from below detection levels to 400 genes ml⁻¹. Nitrification rates were not directly correlated to bacterial or archaeal amoA abundance. Archaeal amoA and Marine Group I crenarchaeal 16S rRNA gene abundances were correlated with Nitrospina 16S rRNA gene abundance at all stations, indicating that similar factors may control the distribution of these two groups. Putatively shallow water-associated archaeal amoA types ('Cluster A') decreased in relative abundance with depth, while a deep water-associated amoA type ('Cluster B') increased with depth. Although some Cluster B amoA sequences were found in surface waters, expressed amoA gene sequences were predominantly from Cluster A. Cluster B amoA transcripts were detected between 100 and 500 m depths, suggesting an active role in ammonia oxidation in the mesopelagic. Expression of marine Nitrosospira-like bacterial amoA genes was detected throughout the euphotic zone down to 200 m. Natural abundance stable isotope ratios (δ¹⁵N and δ¹⁸O) in nitrate (NO₃⁻) and nitrous oxide (N₂O) were used to evaluate the importance of nitrification over longer time scales. Using an isotope mass balance model, we calculate that nitrification could produce between 0.45 and 2.93 μmol m⁻² day⁻¹ N₂O in the central California Current, or approximately 1.5-4 times the local N₂O flux from deep water.