Quantification of ammonia oxidation rates and the distribution of ammonia-oxidizing Archaea and Bacteria in marine sediment depth profiles from Catalina Island, California

Abstract

Microbial communities present in marine sediments play a central role in nitrogen biogeochemistry at local to global scales. Along the oxidation-reduction gradients present in sediment profiles, multiple nitrogen cycling processes (such as nitrification, denitrification, nitrogen fixation, and anaerobic ammonium oxidation) are active and actively coupled to one another - yet the microbial communities responsible for these transformations and the rates at which they occur are still poorly understood. We report pore water geochemical (O(2), [Formula: see text], and [Formula: see text]) profiles, quantitative profiles of archaeal and bacterial amoA genes, and ammonia oxidation rate measurements, from bioturbated marine sediments of Catalina Island, California. Across triplicate sediment cores collected offshore at Bird Rock (BR) and within Catalina Harbor (CH), oxygen penetration (0.24-0.5 cm depth) and the abundance of amoA genes (up to 9.30 × 10(7) genes g(-) (1)) varied with depth and between cores. Bacterial amoA genes were consistently present at depths of up to 10 cm, and archaeal amoA was readily detected in BR cores, and CH cores from 2008, but not 2007. Although detection of DNA is not necessarily indicative of active growth and metabolism, ammonia oxidation rate measurements made in 2008 (using isotope tracer) demonstrated the production of oxidized nitrogen at depths where amoA was present. Rates varied with depth and between cores, but indicate that active ammonia oxidation occurs at up to 10 cm depth in bioturbated CH sediments, where it may be carried out by either or both ammonia-oxidizing archaea and bacteria.

Keywords: amoA; archaea; bioturbation; nitrification; sediments.

FIGURE 1

Location of Catalina Island along the coast of California (B), and of Catalina Harbor and Bird Rock sampling locations (A). Catalina Harbor sediment sampling location is shown in (C) with scale bar at lower left, and collection of Bird Rock sediments is shown in (D). Burrow density at Catalina Harbor in 2008 was ~120 burrow opening per square meter.

FIGURE 2

Microsensor profiles of oxygen in sediment cores. Data from Bird Rock cores from (A–C), and Catalina Harbor cores from 2007 (D–F) and 2008 (G–I) are shown; vertical axis depicts depth in sediment (0 μm depth represents the sediment surface and negative values represent overlying water) and the horizontal axis displays oxygen concentrations in micromolar. Error bars denote one standard deviation of triplicate microsensor profiles taken for each core.

FIGURE 3

Sediment profiles of dissolved inorganic nitrogen and ammonia oxidizers. Average pore water $\left[\mathrm{N}{\mathrm{H}}_4^{+}\right]$ is shown for Bird Rock in 2007 (A), Catalina Harbor in 2007 (E), and Catalina Harbor in 2008 (I), and pore water $[\mathrm{N}{\mathrm{O}}_3^{\mathrm{-}}\mathrm{+}\mathrm{N}{\mathrm{O}}_2^{\mathrm{-}}]$ is shown for Bird Rock (B), Catalina Harbor in 2007 (F), and Catalina Harbor in 2008 (J). Archaeal amoA genes (g-sediment^–1) are shown for individual cores collected at Bird Rock (C), Catalina Harbor in 2007 (G), and Catalina Harbor in 2008 (K). Bacterial amoA genes (g-sediment^–1) are shown for individual cores collected at Bird Rock (D), Catalina Harbor in 2007 (H), and Catalina Harbor in 2008 (L). In (C–L), dashed lines denote depths were data values are omitted due to qPCR inhibition of samples, and color shading denotes different cores. Light green/light blue denotes BR1 (C,D), CH1 (G,H), and CH4 (K,L); “mid” green/“mid” blue denotes BR2 (C,D), CH2 (G,H), and CH5 (K,L); dark green/dark blue denotes BR3 (C,D), CH3 (G,H), and CH6 (K,L). In (G), archaeal amoA was only detectable in one core.

FIGURE 4

Measured δ¹⁵N of pore water $\mathrm{N}{\mathrm{O}}_3^{\mathrm{-}}\mathrm{+}\mathrm{N}{\mathrm{O}}_2^{\mathrm{-}}$ following incubation with added ${}^{15}\mathrm{N}{\mathrm{H}}_{\mathrm{4}}^{\mathrm{+}}$ label (A–C), and ${}^{15}\mathrm{N}{\mathrm{H}}_{\mathrm{4}}^{\mathrm{+}}$ oxidation rates (D,E) in Catalina Harbor in 2008. Note differences in scales in (A–C); oxidation rates were not calculated in Catalina Harbor core 5 owing to the lack of clear isotopic enrichment.