Profiling of bacterial assemblages in the marine cage farm environment, with implications on fish, human and ecosystem health

Kolda, Anamarija; Gavrilović, Ana; Jug–Dujaković, Jurica; Ljubešić, Zrinka; El‐Matbouli, Mansour; Lillehaug, Atle; Lončarević, Semir; Perić, Lorena; Knežević, Dražen; Lušić, Darija Vukić; Kapetanović, Damir

doi:10.1016/j.ecolind.2020.106785

Cited by 21 publications

(26 citation statements)

References 49 publications

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“…For example, environmental microorganisms can form the initial inocula for fish eggs or larvae, and pathogens can be transferred through the water, especially when fish biomass/density is very high. Therefore, significant effort has been invested in studying the aquatic microbiome in some aquaculture types, with the aim of using these measurements to understand fish health, to identify biomarkers/early markers of emerging diseases, or to explore the use of probiotics ( Dawood et al, 2019 ; Kuebutornye et al, 2019 ; Kolda et al, 2020 ; Zhang et al, 2020 ). In our dataset, we identify several bacterial lineages known as fish pathogens, including the genera Aeromonas , Vibrio , and Enterobacter , in agreement with previous studies from DARU ( Patil et al, 2016 , 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Seasonal Dynamics Are the Major Driver of Microbial Diversity and Composition in Intensive Freshwater Aquaculture

et al. 2021

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Aquaculture facilities such as fishponds are one of the most anthropogenically impacted freshwater ecosystems. The high fish biomass reared in aquaculture is associated with an intensive input into the water of fish-feed and fish excrements. This nutrients load may affect the microbial community in the water, which in turn can impact the fish health. To determine to what extent aquaculture practices and natural seasonal cycles affect the microbial populations, we characterized the microbiome of an inter-connected aquaculture system at monthly resolution, over 3 years. The system comprised two fishponds, where fish are grown, and an operational water reservoir in which fish are not actively stocked. Clear natural seasonal cycles of temperature and inorganic nutrients concentration, as well as recurring cyanobacterial blooms during summer, were observed in both the fishponds and the reservoir. The structure of the aquatic bacterial communities in the system, characterized using 16S rRNA sequencing, was explained primarily by the natural seasonality, whereas aquaculture-related parameters had only a minor explanatory power. However, the cyanobacterial blooms were characterized by different cyanobacterial clades dominating at each fishpond, possibly in response to distinct nitrogen and phosphate ratios. In turn, nutrient ratios may have been affected by the magnitude of fish feed input. Taken together, our results show that, even in strongly anthropogenically impacted aquatic ecosystems, the structure of bacterial communities is mainly driven by the natural seasonality, with more subtle effects of aquaculture-related factors.

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Section: Discussionmentioning

confidence: 99%

Seasonal Dynamics Are the Major Driver of Microbial Diversity and Composition in Intensive Freshwater Aquaculture

et al. 2021

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show abstract

“…For example, environmental microorganisms can form the initial inocula for fish eggs or larvae, and pathogens can be transferred through the water, especially when fish biomass/density is very high. Therefore, significant effort has been invested in studying the aquatic microbiome in some aquaculture types, with the aim of using these measurements to understand fish health, to identify biomarkers/early markers of emerging diseases, or to explore the use of probiotics (Dawood et al, 2019; Kolda et al, 2020; Kuebutornye et al, 2019; Zhang et al, 2020b). In our dataset, we identify several bacterial lineages known as fish pathogens, including the genera Aeromonas , Vibrio and Enterobacter , in agreement with previous studies from DARU (Patil et al, 2016; Patil et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

Seasonal dynamics are the major driver of microbial diversity and composition in intensive freshwater aquaculture

Marmen

Fadeev

Al-Ashhab

et al. 2021

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Aquaculture facilities such as fishponds are one of the most anthropogenically impacted freshwater ecosystems. The high fish biomass reared in aquaculture is associated with an intensive input into the water of fish-feed and fish excrements. This nutrients load may affect the microbial community in the water, which in turn can impact the fish health. To determine to what extent aquaculture practices and natural seasonal cycles affect the microbial populations, we characterized the microbiome of an inter-connected aquaculture system at monthly resolution, over three years. The system comprised two fishponds, where fish are grown, and a "control" operational water reservoir in which fish are not actively stocked. Clear natural seasonal cycles of temperature and inorganic nutrients concentration, as well as recurring cyanobacterial blooms during summer, were observed in both the fishponds and the reservoir. The structure of the aquatic bacterial communities in the system, characterized using 16S rRNA sequencing, was explained primarily by the natural seasonality, whereas aquaculture-related parameters had only a minor explanatory power. However, the cyanobacterial blooms were characterized by different cyanobacterial clades dominating at each fishpond, possibly in response to distinct nitrogen and phosphate ratios. In turn, nutrient ratios may have been by the magnitude of fish feed input. Taken together, our results show that, even in strongly anthropogenically impacted aquatic ecosystems, the structure of bacterial communities is mainly driven by the natural seasonality, with more subtle effects if aquaculture-related factors.

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“…This genus could be a common bacterial group found in the waters around the studied farm (shallow area, five meters deep) considering its high organic content and the fact that the farm location has experienced previous algal bloom events (personal communication, farm owner). Uncultured Coraliomargarita genus apparently grows preferentially on high organic compounds which are important indicators of increased phytoplankton concentration and algal blooms, for which this genus was reported to account for 1.15-5.51% of the bacterial communities in marine cage farms [60,61]. The association of Coraliomargarita with algal blooms which are usually triggered by physical-chemical and environmental parameters should be further studied as it may clarify any link of this bacterial group and the abundance of C. irritans in marine environments.…”

Section: Discussionmentioning

confidence: 99%

“…Higher C. irritans was also associated with relative high levels of NS4 marine group in water. NS4 marine group is another indicator of increased phytoplankton concentration and algal blooms aforementioned [61]. The intensive aquaculture in coastal marine cages caused the dominance of NS4 marine group in Vietnam due to its strong correlations with inorganic nutrients such as ammonium and phosphate (good predictor of algae proliferation) [62].…”

Section: Discussionmentioning

confidence: 99%

Digital Droplet PCR-Based Environmental DNA Tool for Monitoring Cryptocaryon irritans in a Marine Fish Farm from Hong Kong

et al. 2021

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The adoption of new investigative strategies based on environmental DNA (eDNA) can be used to monitor parasites, associated bacterial microbiomes, and physical-chemical parameters in fish farms. In this study, we used the economically important and globally distributed fish ciliate parasite Cryptocaryon irritans as a model to understand the parasite abundance and potential drivers of its presence in marine fish farms. Environmental (rainfall) and physical-chemical (temperature, oxygen, salinity, pH) data collected from a marine fish farm in Hong Kong were analyzed together with the eDNA approach targeting C. irritans abundance based on digital droplet PCR and 16S metagenomics to determine associations and triggers between parasites and specific bacterial groups. Rainfall and temperature demonstrated positive associations with high abundance of C. irritans (eDNA) at the studied marine fish cage farm. However, rainfall was the only parameter tested that demonstrated a significant association with parasite eDNA, indicating that the raining season is a risky period for fish farmers in Hong Kong. Coraliomargarita was the bacterial genus with the most significant relationship with low abundance of C. irritans in water. Understanding the environmental triggers of ciliate parasites propagation and associated bacterial microbiome could elucidate new insights into environmental control, microbial management, and promote the reduction of chemical use in marine fish farms.

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Profiling of bacterial assemblages in the marine cage farm environment, with implications on fish, human and ecosystem health

Cited by 21 publications

References 49 publications

Seasonal Dynamics Are the Major Driver of Microbial Diversity and Composition in Intensive Freshwater Aquaculture

Seasonal Dynamics Are the Major Driver of Microbial Diversity and Composition in Intensive Freshwater Aquaculture

Seasonal dynamics are the major driver of microbial diversity and composition in intensive freshwater aquaculture

Digital Droplet PCR-Based Environmental DNA Tool for Monitoring Cryptocaryon irritans in a Marine Fish Farm from Hong Kong

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