The response of nitrifying microbial assemblages to ammonium (NH₄⁺) enrichment from salmon farm activities in a northern Chilean Fjord

The consequences of aquaculture include alterations in nitrogen cycling in aquatic environments that may lead to ecosystem degradation. Herein salmon aquaculture release of ammonium (NH₄⁺) to the water column and its effects on natural archaea and bacteria ammonia-oxidizers (AOA and AOB) and nitrite-oxidizing bacteria (NOB) community structure were studied in the Comau fjord using molecular approaches, such as: cloning (AOA and AOB richness), qPCR for C. Nitrosopumilus maritimus (AOA) and Nitrospina sp. (NOB) abundance (DNA) and RT-qPCR only for Nitrospina sp activity (RNA). Sampling was carried out in brackish (0.7-25 salinity, <5 m depth) and marine (>30 salinity, 25 m depth) waters during contrasting salmon production periods: rest (winter 2012), growth and harvest (summer and winter 2013). During the rest period, the highest NH₄⁺ concentration was observed at Vodudahue River, whereas during productive periods NH₄⁺ accumulated in the brackish layer inside salmon cages and in the vicinty (up to 700 m distance from the cages). The nitrifier community from the fjord reference station (Stn-C) was characterized by C. N. maritimus (AOA) and Nitrosomonas sp. (AOB) sequences affiliated with cosmopolitan ecotypes (e.g., marine, freshwater, hydrothermal), maxima abundances of C. N. maritimus (AOA) and Nitrospina sp. and extreme ranges of Nitrospina sp. activity occurred in the brackish layer. During productive periods, abundances of C. N. maritimus were co-varied with NH₄⁺ concentrations inside salmon cages (summer) and the adjacent areas (winter). Productive periods were characterized by lower abundances but more homogeneity between brackish and marine areas than for the Stn-C nitrifiers. The physiological state of Nitrospina sp. estimated from cDNA:DNA ratios indicated higher growth during winter 2013 associated with NH₄⁺ enrichment derived from production and river input. Our results suggest that in Comau Fjord, NH₄⁺ enrichment events occur during salmon production and also naturally by river inputs, supporting an abundant and active nitrifying community potentially processing only part of the extra NH₄⁺ that occurs, predominantly outside the salmon cages. Our work highlights the abundance and activities of nitrifying communities and identifies these communities as being sensitive to increased loads of NH₄⁺.