Abundances of crenarchaeal amoA genes and transcripts in the Pacific Ocean

Abstract

Planktonic Crenarchaea are thought to play a key role in chemolithotrophic ammonia oxidation, a critical step of the marine nitrogen (N) cycle. In this study, we examined the spatial distributions of ammonia-oxidizing Crenarchaea across a large (approximately 5200 km) region of the central Pacific Ocean. Examination of crenarchaeal 16S rRNA, ammonia monooxygenase subunit A (amoA) genes, and amoA transcript abundances provided insight into their spatial distributions and activities. Crenarchaeal gene abundances increased three to four orders of magnitude with depth between the upper ocean waters and dimly lit waters of the mesopelagic zone. The resulting median value of the crenarchaeal amoA: 16S rRNA gene ratio was 1.3, suggesting the majority of Crenarchaea in the epi- and mesopelagic regions of the Pacific Ocean have the metabolic machinery for ammonia oxidation. Crenarchaeal amoA transcript abundances typically increased one to two orders of magnitude in the transitional zone separating the epipelagic waters from the mesopelagic (100-200 m), before decreasing into the interior of the mesopelagic zone. The resulting gene copy normalized transcript abundances revealed elevated amoA expression in the upper ocean waters (0-100 m) where crenarchaeal abundances were low, with transcripts decreasing into the mesopelagic zone as crenarchaeal gene abundances increased. These results suggest ammonia-oxidizing Crenarchaea are active contributors to the N cycle throughout the epi- and mesopelagic waters of the Pacific Ocean.

Fig. 1

Contour plots depicting vertical and meridional distributions in ocean temperature (upper panel), nitrate + nitrite (N+N; middle panel), and dissolved O₂ (bottom panel). Stations and depths sampled as part of this study depicted by filled symbols.

Fig. 3

(A) Vertical profiles of crenarchaeal amoA, (B) MGI 16S rRNA, (C) psL12-related phylotype 16S rRNA gene abundances for all stations sampled, and (D) ratio of crenarchaeal amoA to total Crenarchaea 16S rRNA (MGI + psL12) gene copies; dotted line depicts 1:1 ratio.

Fig. 2

Depth-dependent variations in biogeochemical properties and crenarchaeal amoA gene abundance and gene transcripts at selected stations in the subtropical South Pacific (7.5°S; A, B), near-equatorial (1.7°N; C, D), northern equatorial (8.6°N; E, F), and subtropical North Pacific Ocean (16.86°N; G, H). (Top panels) Chloropigment concentrations based on in vivo fluorescence (green circles), N+N (open diamonds), and dissolved O₂ (cyan circles). (Bottom panels) log₁₀ crenarchaeal amoA genes (red circles) and amoA transcripts (blue triangles).

Fig. 4

A. Vertical profiles of crenarchaeal amoA gene transcripts. B. Ratio of amoA transcripts per gene copy. Dotted line depicts 1:1 ratio.