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-connec… Show more
“…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.…”
Section: Clr Abundancesupporting
confidence: 57%
“…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, 2021Marmen et al, , 2016Zimba 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).…”
“…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.…”
Section: Clr Abundancesupporting
confidence: 57%
“…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, 2021Marmen et al, , 2016Zimba 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).…”
“…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, 2021Marmen et al, , 2016Zimba 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).…”
Intensification of fish farming practices is being driven by the demand for increased food production to support a rapidly growing global human population, particularly in lower-middle income countries. Intensification of production, however, increases the risk of disease outbreaks and thus likelihood for crop losses. The microbial communities that colonise the skin mucosal surface of fish are poorly understood, but are important in maintaining fish health and resistance against disease. This skin microbial community is susceptible to disruption through stressors associated with transport, handling and the environment of intensive practices, and this risks the propagation of disease-causing pathogens. In this study, we characterised the microbial assemblages found on tilapia skin - the most widely farmed finfish globally - and in the surrounding water of seven earthen aquaculture ponds from two pond systems in distinct geographic regions in Malawi. Metabarcoding approaches were used to sequence the prokaryotic and microeukaryotic communities. We found 92% of prokaryotic amplicon sequence variants were common to both skin and water samples. Differentially enriched and core taxa, however, differed between the skin and water samples. In tilapia skin, Cetobacterium, Paucibacter, Pseudomonas and Comamonadaceae were enriched, whereas, the cyanobacteria Cyanobium, Microcystis and/or Synechocystis, and the diatom Cyclotella, were most prevalent in pond water. Ponds that clustered together according to their water prokaryotic communities also had similar microeukaryotic communities indicating strong environmental influences on prokaryotic and microeukaryotic community structures. While strong site-specific clustering was observed in pond water, the grouping of tilapia skin prokaryotes by pond site was less distinct, suggesting fish microbiota have a greater buffering capacity against environmental influences. The characterised diversity, structure and variance of microbial communities associated with tilapia culture in Malawi provides the baseline for studies on how future intensification practices may lead to microbial dysbiosis and disease onset.
“…2 ). Dataset 1 has not been presented elsewhere, datasets 2 and 3 include metagenomics data for samples analyzed previously in the context of community structure (16 S rRNA gene amplicon sequencing 9 , 10 ). Fig.…”
Section: Background Informationmentioning
confidence: 99%
“…The Dor Aquaculture Research Unit is a research facility used for both aquaculture research and intensive 33 – 55 , semi-commercial outgrowth 9 , 56 , 57 . We followed the microbial populations from several ponds at this site over a three-year period at monthly intervals, showing that seasonality is the main driver of planktonic microbial populations in this system despite it being highly impacted by the aquaculture activity 9 . Here we present the metagenomes sequenced from 23 monthly samples over two consecutive years (2013–2014, Table 2 ).…”
Freshwater bodies are critical components of terrestrial ecosystems. The microbial communities of freshwater ecosystems are intimately linked water quality. These microbes interact with, utilize and recycle inorganic elements and organic matter. Here, we present three metagenomic sequence datasets (total of 182.9 Gbp) from different freshwater environments in Israel. The first dataset is from diverse freshwater bodies intended for different usages – a nature reserve, irrigation and aquaculture facilities, a tertiary wastewater treatment plant and a desert rainfall reservoir. The second represents a two-year time-series, collected during 2013–2014 at roughly monthly intervals, from a water reservoir connected to an aquaculture facility. The third is from several time-points during the winter and spring of 2015 in Lake Kinneret, including a bloom of the cyanobacterium Microcystis sp. These datasets are accompanied by physical, chemical, and biological measurements at each sampling point. We expect that these metagenomes will facilitate a wide range of comparative studies that seek to illuminate new aspects of freshwater microbial ecosystems and inform future water quality management approaches.
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