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

Abstract

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 (15)NH(4)(+) 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 10(4) 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 (delta(15)N and delta(18)O) in nitrate (NO(3)(-)) and nitrous oxide (N(2)O) 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 micromol m(-2) day(-1) N(2)O in the central California Current, or approximately 1.5-4 times the local N(2)O flux from deep water.

Enrichment and characterization of ammonia-oxidizing archaea from the open ocean: phylogeny, physiology and stable isotope fractionation

“…Isotope fractionation by ammonia-oxidizing archaea AE Santoro and KL Casciotti CN25 and CN75 are 97% identical to amoA sequences obtained in DNA-based clone libraries from the environment from which they were enriched (GU360825, (Santoro et al, 2010)) and CN150 is 100% identical to an amoA actively expressed in the environment (GU364088). The CN strains are also highly similar on the 16S and amoA level to abundant groups of open ocean archaea from a range of oceanic provinces including the Sargasso Sea, Fernandina Island and the coast of Africa as indicated by BLAST searches of the Global Ocean Survey dataset (Rusch et al, 2007).…”

“…The enrichments lack 16S rRNA and amoA genes associated with known g-or b-proteobacterial ammonia oxidizers. Though no NO 2 À or NO 3 À production was observed in the enrichment from 500 m, this cannot be used to infer a lack of NH 3 -oxidizing ability in field populations at this depth, as active NH 3 oxidation was measured in situ (Santoro et al, 2010).…”

“…The CN strains are also highly similar on the 16S and amoA level to abundant groups of open ocean archaea from a range of oceanic provinces including the Sargasso Sea, Fernandina Island and the coast of Africa as indicated by BLAST searches of the Global Ocean Survey dataset (Rusch et al, 2007). Previous amoAbased phylogenies of AOA have shown that water column-derived sequences fall into two clusters termed 'A' and 'B' (Francis et al, 2005) thought to represent a depth-dependent partitioning of AOA (Hallam et al, 2006;Mincer et al, 2007;Beman et al, 2008 (Wuchter et al, 2006), and estimates of in situ per-cell activity rates in the California Current (0.2-15 fmol cell À1 day À1 ) (Santoro et al, 2010).…”

“…Mesophilic archaea are ubiquitous and abundant members of diverse marine environments including coastal waters (Mincer et al, 2007;Beman et al, 2010), marine sediments, estuaries (Mosier and Francis, 2008;Bernhard et al, 2010;Urakawa et al, 2010), stratified basins (Coolen et al, 2007;Lam et al, 2007) and open ocean water columns (Beman et al, 2008;Church et al, 2010;Santoro et al, 2010). The recent cultivation of the first mesophilic marine archaeon, Nitrosopumilus maritimus, (Konneke et al, 2005;Martens-Habbena et al, 2009), two thermophilic archaea, Nitrosocaldus yellowstonii and Nitrosophaera gargensis (Hatzenpichler et al, 2008;de la Torre et al, 2008) and a freshwater archaeon, Nitrosoarchaeum limnia (Blainey et al, 2011) established that at least some of these organisms are chemolithoautotrophic ammonia oxidizers.…”

“…The recent cultivation of the first mesophilic marine archaeon, Nitrosopumilus maritimus, (Konneke et al, 2005;Martens-Habbena et al, 2009), two thermophilic archaea, Nitrosocaldus yellowstonii and Nitrosophaera gargensis (Hatzenpichler et al, 2008;de la Torre et al, 2008) and a freshwater archaeon, Nitrosoarchaeum limnia (Blainey et al, 2011) established that at least some of these organisms are chemolithoautotrophic ammonia oxidizers. Several studies coupling geneand cell-based quantification of putative ammoniaoxidizing archaea (AOA) to rate measurements (Wuchter et al, 2006;Beman et al, 2008;Santoro et al, 2010) suggest that nitrification by AOA in the ocean is significant. However, direct demonstration of ammonia-oxidizing activity by the AOA genotypes encountered in the open ocean has not yet been demonstrated.…”