Adapting monitoring tools for bacterial load detection in closed marine fish farms: for improved fish health and reduced mortalities.

In this project we use modern methods for microbial analyses and sequencing technology to identify all microbes in the fish farm rearing units. We have developed strategies for sampling and adapted these tools to be applied in regular monitoring. Weekly samplings and analyses from a flow through farm for lumpfish and a RAS farm for salmon smolt have resulted in millions of sequenc reads, providing information about microorganisms present and their relative abundance in a community. The results reveal the dynamics within different microbial communities and how these are affected by changing water parameters over time. The methods used had not been applied for this type of biological material, but the results obtained after testing were good and have consequently been used throughout the performed work. Mainly, the analyses describe the dynamics in the microbial community structures and how it is affected by water quality over time. By microbial monitoring one can observe potential harmful bacteria and thereby non-favorable conditions in the rearing conditions. The initial complex analyses performed in this project provides a good overview of microbial communities present and this provide information on where to collect samples and the frequency of sampling for microbial surveillance. So far, production water and fish skin has been identified as potential valuable samples, but this must be further verified using more bacterial specific probes. Particularly this project has provided important information on startup period of a biofilter when water quality and the efficiency of the biofilter might not be optimal. This includes describing the establishment of the nitrogen cycle. We looked for the time required for establishing the nitrification process by the biofilm on the biofilter carriers using a commercial starter bacterial inoculum and compared this with bacteria on established biofilter carriers. The inoculation by the farms own biofilter carriers proved to be most efficient, likely because the inoculum bacteria was adapted to water and temperature in the RAS farm. In another study, we compared the establishment of the nitrification process in two new RAS biofilters, when fish production tanks contained few or many fish. The fastest development of the nitrification process took place when the fish population was small giving with less amount of ammonium produced, which provided better development of the biofilter. The microbial composition is also studied for a flow through system with successful lumpfish production. The results showed a relatively stable bacterial community in the rearing facilities. Moritella and Tenacibaculum genera are natural parts of the environment and were generally frequent at low levels, but at were sometimes more dominating in samples from water, biofilm and fish skin and on eggs. In a RAS unit different incidents occur. The studies included microbial colonization, taxa stability, taxaflux and taxa shifts at changes caused by different conditions antimicrobial treatment of fish, washing of biofilters with oxidative agents, reinoculations og biofilters and after sudden changes in physiochemical water parameters. The findings demonstrated the complex composition and shifts in diversity and abundance of the microbes that might be present in a RAS.

Oppdrettere og forskere har fått bedre innsikt i mikrobielle prosesser i RAS og gjennomstrømmingsanlegg. Resultatene har gitt viktig bidrag til oppstart av RAS biofilter om bruk og effektiviet av inokulum materiale.Type bakterier og forekomster er kartlagt ulike steder i RAS anlegg, under produksjonsyklus og over flere produksjonsyklyser og egnet type materiale for videre detaljerte monitoreringsforsøk er indikert. Kompetanse er generert og videreført gjennom prosjektansattes videre ansettelser/arbeid der også opplæring og formidling inngår både for næringsakrører og studenter. Prosjetmedarbeider som ble tilsatt i fast stilling ved instituttet har valgt dette område som forskningssatsing og har oppnådd eget prosjekt med nordisk samfinansiering samt deltakelse i et nytt nasjonalt prosjekt. Innen forskning er metoder og analyse verktøy utprøvd og videre brukt i analysene. Dette har stor overførigsverdi både for forskning og praktisk mikrobiell monitorering av anlegg.

Stable water quality is one of the main benefits of closed fish farms by providing a more controllable living environment for farmed fish. Closed systems are also potential incubators for bacterial selection. Compared to open systems, the enhanced water stability allows more representative and valid data upon bacteria composition and load. Thus, knowledge based surveillance programs can be implemented to predict bacterial risk of infection caused by both opportunistic and obligate pathogens. The aim of this project is to implement and streamline bacterial load monitoring tools of closed marine farms to monitor risk factors for impaired fish health. Regular use of high resolution tools upon community member's 16S identification, allows pathogens detection to genera and species level. Further, molecular tools allow detection even to subspecies level that is needed to determine virulence of the classic pathogens. The project has a third monitoring tool for detection of the virulence "on" switch in opportunistic bacteria by GC/LC-MS quantification, biosensors and RT-QPCR of expressed regulatory genes. Tenacibaculum is the model organism, frequently observed and documented to cause infections in closed systems. The streamlined protocols for microbial monitoring in closed fish farms will be basis for design of rational preventive routines and measures to meet the risk of infections and reduced water quality. The three closed rearing concepts are; a marine RAS for enhanced growth of salmon smolt and two with direct flow through system -being "Egget" and a lump fish farm- with regular removal or no of biofilm removal respectively. The project embraces national and international co-operation, and institutional knowledge transfer. This interdisciplinary project use cutting edge methodology and expertise from environmental microbiology to be implemented for bacterial monitoring of closed fish farming systems. Several masters will be posted and the project has female leader.