High abundances of ammonia-oxidizing archaea in nitrifying biofilters of brackish recirculating aquaculture systems (RAS) with tolerance for abrupt salinity changes
Year: 2025
Type: article
Abstract: While bacterial diversity is heavily studied in recirculating aquaculture systems (RAS), little is known about how nitrifying communities differ across commercial biofilters operated at varying salinities. This particularly applies to ammonia-oxidizing microbes, as most studies have not been designed to target archaea and comammox Nitrospira . Furthermore, the relationship between the composition of these nitrifying communities and their tolerance to salinity changes remains understudied. The overall aim of this study was to clarify the relationship between the composition of the nitrifying communities and the salinity tolerance of nitrifying biofilters in commercial RAS. The objectives were to (i) assess the immediate tolerance of brackish and seawater biofilters subjected to abrupt and large salinity changes, (ii) evaluate the temporal dynamics of microbial communities in the biofilter-biofilm during operational changes, and (iii) determine the relative abundances of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and complete ammonia oxidizers (comammox Nitrospira ) in RAS biofilters operated at different salinities. Microbial communities were characterized using 16S rRNA gene amplicon and shotgun sequencing. We found that the brackish biofilter was relatively tolerant to abrupt and large salinity changes, with reductions in nitrification capacity of around 16 % and 22 % after exposure to freshwater (0 ppt) and seawater (31 ppt), respectively, and the seawater biofilter declined by around 50 % when exposed to freshwater (0 ppt). We observed an increasing similarity in microbial community composition between the donor and recipient biofilters, suggesting that biofilter seeding can foster the establishment of robust nitrifying consortia. This may help accelerate biofilter start-up in RAS. The RAS operated at high salinity had a higher relative abundance of AOA than the freshwater RAS. Furthermore, the relative abundance of comammox Nitrospira was high in the freshwater RAS but undetectable in the brackish and seawater systems. Stable and ammonia-poor conditions in RAS appeared to select microbes physiologically adapted with high affinities to ammonia, such as AOA and comammox Nitrospira . • A biofilter from a commercial brackish RAS with tolerance to abrupt and large salinity changes (0 to 31 ppt). • Shotgun sequencing revealed high abundances of ammonia-oxidizing archaea and comammox Nitrospira in biofilters operated at high and low salinity, respectively. • Low diversity of archaea in the biofilter communities despite high sequencing depth, with dominance by the ammonia oxidizers Nitrosopumilus and Nitrosarchaeum.
Source: Aquaculture
Authors: Fernando Fernando, Simen Fredriksen, Eirik Degré Lorentsen, Line Moen, Ingrid Bakke
Institution: Norwegian University of Science and Technology
Language: English
Subfield: Pollution
Field: Environmental Science
Domain: Physical Sciences
Open Access status: hybrid
Estimated APC paid: $3,910
OpenAlex ID: W4414939155