Environmental controls on estuarine nitrifying communities along a salinity gradient

ABSTRACT: Estuaries are transitional zones between marine and freshwater environments and are ideal systems to study the influence of environmental gradients on microbial biodiversity and activity. In this study, we investigated the effect of a salinity gradient on the structure of prokaryotic communities from intertidal sediments of the Douro estuary, and on the nitrification process. Four locations were chosen with distinct salinities and characterized for a range of environmental parameters including measurements of potential nitrification rates. The structure of prokaryotic communities and ammonia-oxidizing bacteria and archaea were described and identified using the 16S rRNA gene. Potential nitrification rates ranged from 1.3 to 7.4 µmol cm-2 h–1, with the highest rate at mesohaline sites; however, the relative abundance of nitrifying taxa was higher at locations with higher salinity. Ammonia-oxidizing bacteria could not be detected in oligohaline sites, in contrast to ammonia-oxidizing archaea, which showed a ubiquitous distribution. Nitrite-oxidizing bacteria were more abundant than ammonia-oxidizing groups across meso-oligohaline sites, showing increased relative abundance at less saline sites. One operational taxonomic unit closely related to Nitrospira moscoviensis showed a positive correlation with potential nitrification rates, suggesting a possible association of N. moscoviensis with ammonia-oxidizing organisms in a natural ecosystem. Such results point out the need to re-assess the relative roles of different nitrifying groups in the nitrification process.

KEYWORDS: Estuaries · Salinity · 16S rRNA gene · Nitrification · Nitrifying communities