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

Abstract

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.

Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades

“…In our study we found that such seasonal effects overpowered any potential effect of the intervention in shifting community dynamics of downstream river sites. Similar examples have been noted in aquaculture systems (Marmen et al 2021, Zeng et al 2019), indicating the pervasiveness of seasonality as a major contributor to microbial community structure. We also found that there was relatively minimal overlap in the specific ASVs most affected by seasonality when comparing between effluent and water samples, suggesting that microbial populations most significantly affected by seasonality are community and environment specific.…”

Relationships between pond water and tilapia skin microbiomes in aquaculture ponds in Malawi

“…At most pond sites, one photoautotroph ( Cyanobium or Synechocystis ) was dominant, at up to 20% relative abundance. While Synechocystis is well studied as a model organism, little is known of Cyanobium and its large contribution to primary production despite being among the most abundant taxa in carp aquaculture ponds (Marmen et al, 2021) and freshwater lakes (Rogers et al, 2021). Additionally, the harmful algal bloom agent Microcystis was detected at very high abundance in pond sites 5, 6 and 7, which is concurrent with observations of rich blue-green algae during sampling.…”

“…Additionally, the harmful algal bloom agent Microcystis was detected at very high abundance in pond sites 5, 6 and 7, which is concurrent with observations of rich blue-green algae during sampling. Microcystis (see Marmen et al, 2021, 2016; Zimba and Grimm, 2003), and its toxin microcystin, are frequently detected in aquaculture ponds and can have toxic effects in tilapia (Abdel-Latif and Khashaba, 2017). Conversely, eukaryotic microalgae, in particular diatoms, contribute positively to the freshwater ecosystem as key primary producers and stabilisers of water quality (Guedes and Malcata, 2012; Li et al, 2017).…”