Novel genes for nitrite reductase and Amo‐related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling

TLDR

Mesophilic crenarchaeota are abundant in terrestrial and marine habitats, yet their physiology remains largely unknown. A 43‑kb fosmid fragment isolated from a 1.2‑Gb environmental library of calcareous grassland soil encoded a copper‑containing nitrite reductase with an amicyanin‑like domain and AmoAB/PmoAB‑related proteins, and expression of nirK and an amoA‑like gene was confirmed by RT‑PCR, upregulated by ammonia, with additional variants detected in soil and marine samples. These findings indicate that mesophilic crenarchaeota may be capable of ammonia oxidation under aerobic and potentially anaerobic conditions.

Abstract

Summary Mesophilic crenarchaeota are frequently found in terrestrial and marine habitats worldwide, but despite their considerable abundance the physiology of these as yet uncultivated archaea has remained unknown. From a 1.2 Gb large‐insert environmental fosmid library of a calcareous grassland soil, a 43 kb genomic fragment was isolated with a ribosomal RNA that shows its affiliation to group 1.1b of crenarchaeota repeatedly found in soils. The insert encoded a homologue of a copper‐containing nitrite reductase with an unusual C‐terminus that encoded a potential amicyanin‐like electron transfer domain as well as two proteins related to subunits of ammonia monooxygenases or particulate methane monooxygenases (AmoAB/PmoAB) respectively. Expression of nirK and the amo A‐like gene was shown by reverse transcription polymerase chain reaction (PCR) analyses in soil samples, the latter being found at higher levels when the soil was incubated with ammonia (measured by quantitative PCR). Further variants of both genes were amplified from soil samples and were found in the environmental database from the Sargasso Sea plankton. Taken together, our findings suggest that mesophilic terrestrial and marine crenarchaeota might be capable of ammonia oxidation under aerobic and potentially also under anaerobic conditions.