Ammonia oxidation kinetics and temperature sensitivity of a natural marine community dominated by Archaea

Abstract

Archaeal ammonia oxidizers (AOAs) are increasingly recognized as prominent members of natural microbial assemblages. Evidence that links the presence of AOA with in situ ammonia oxidation activity is limited, and the abiotic factors that regulate the distribution of AOA natural assemblages are not well defined. We used quantitative PCR to enumerate amoA (encodes α-subunit of ammonia monooxygenase) abundances; AOA amoA gene copies greatly outnumbered ammonia-oxidizing bacteria and amoA transcripts were derived primarily from AOA throughout the water column of Hood Canal, Puget Sound, WA, USA. We generated a Michaelis-Menten kinetics curve for ammonia oxidation by the natural community and found that the measured Km of 98±14 nmol l(-1) was close to that for cultivated AOA representative Nitrosopumilus maritimus SCM1. Temperature did not have a significant effect on ammonia oxidation rates for incubation temperatures ranging from 8 to 20 °C, which is within the temperature range for depths of measurable ammonia oxidation at the site. This study provides substantial evidence, through both amoA gene copies and transcript abundances and the kinetics response, that AOA are the dominant active ammonia oxidizers in this marine environment. We propose that future ammonia oxidation experiments use a Km for the natural community to better constrain ammonia oxidation rates determined with the commonly used (15)NH4(+) dilution technique.

Figure 1

Representative CTD data and inorganic N vertical profiles for Hoodsport study site (CB974, May 2012, data are shown). (a) Temperature and salinity; (b) fluorescence and oxygen; (c) NO₃⁻, NO₂⁻ and NH₄⁺. (d) q-PCR amoA abundance profile. Dotted horizontal line is 1% surface PAR (approximately 11 m). Data are the mean of replicate q-PCR measurements for AOA amoA gene copies, AOA amoA transcripts and β-AOB amoA gene copies.

Figure 2

The effect of temperature amendment on ¹⁵NH₄ oxidation rate for water collected at 50 m. Data are presented for four cruises (inset legend). Data are mean±1 s.d. (n=3 or 4). Letters (a, b) indicate treatments which had significantly different rates than the in situ temperature treatment.

Figure 3

Kinetics of ammonia oxidation. (a) The increase in the δ¹⁵N of the NO₂⁻+NO₃⁻ pool is linear for ¹⁵NH₄⁺ oxidation rate incubations. Data points are individual bottle incubations. Legend indicates ¹⁵NH₄⁺ added (nmol l⁻¹). (b) Regression fit for Michaelis–Menten kinetics model. The mean and 95% confidence interval for the rate are indicated for the substrate concentration.

Figure 4

Ammonia oxidation rate profile and a kinetics correction for cruise CB974 (May 2012). (a) A comparison of the raw ¹⁵NH₄⁺ oxidation rate (raw rate; hidden by closed circles for depths 0–15 m) and a rate corrected for kinetic effects in the bottle incubation (corrected rate). Ambient NH₄⁺ is indicated with the solid line. Each data point is the rate from an individual bottle. (b) Percent decrease in ammonia oxidation rate resulting from a correction for the addition of substrate.