Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus)

Abstract

The majority of seafood is farmed, with most finfish coming from freshwater ponds. Ponds are often fertilized to promote microbial productivity as a natural feed source to fish. To understand if pond fertilization with livestock manure induces a probiotic or prebiotic effect, we communally reared tilapia (Oreochromis shiranus), and North African catfish (Clarias gariepinus), for 4 weeks under seven manure treatments including layer chicken, broiler chicken, guinea fowl, quail, pig, cow, vs. commercial feed to evaluate microbial community dynamics of the manure, pond water, and fish feces using 16S and 18S rRNA marker genes along with metagenome sequencing. Catfish growth, but not tilapia, was positively associated with plankton abundance (p = 0.0006, R = 0.4887) and greatest in ponds fertilized with quail manure (ANOVA, p < 0.05). Manure was unique and influenced the 16S microbiome in pond water, tilapia gut, and catfish gut and 18S community in pond water and catfish guts (PERMANOVA, p = 0.001). On average, 18.5%, 18.6%, and 45.3% of manure bacteria sOTUs, (sub-operational taxonomic units), were present in the water column, catfish feces, and tilapia feces which comprised 3.7%, 12.8%, and 10.9% of the total microbial richness of the communities, respectively. Antibiotic resistance genes were highest in the manure and water samples followed by tilapia feces and lowest in catfish feces (p < 0.0001). In this study, we demonstrate how the bacterial and eukaryotic microbial composition of fish ponds are influenced by specific livestock manure inputs and that the gut microbiome of tilapia is more sensitive and responsive than catfish to these changes. We conclude that animal manure used as fertilizer induces a primarily prebiotic effect on the pond ecosystem rather than a direct probiotic effect on fish.

Comparison of Two Commercial Recirculated Aquacultural Systems and Their Microbial Potential in Plant Disease Suppression

“…Fish species in the system also had significant effect in the water tank environment, which, with Tilapia, was richer with bacteria ( Figure 2), while with Clarias it hosted more fungi than bacteria (Figure 4). These findings are in line with other studies [32,33] indicating how fish species develop their own characteristic microbial communities. The results also agree with [33], who found higher fungal diversity in a Clarias than in a Tilapia system.…”

“…These findings are in line with other studies [32,33] indicating how fish species develop their own characteristic microbial communities. The results also agree with [33], who found higher fungal diversity in a Clarias than in a Tilapia system. By contrast, sampling site had a significant effect on the evenness and richness of bacterial communities in the Clarias RAS ( Figure 2), and of fungal communities in the Tilapia system ( Figure 4).…”

Comparison of Two Commercial Recirculated Aquacultural Systems and Their Microbial Potential in Plant Disease Suppression

“…Fish species in the system also had significant effect in the water tank environment, which with Tilapia was richer with bacteria ( Figure 2), while with Clarias it hosted more fungi than bacteria (Figure 4). These findings are in line with other studies [25,26] indicating how fish species develop their own characteristic microbial communities. The results also agree with [26], who found higher fungal diversity in a Clarias than in a Tilapia system.…”

“…These findings are in line with other studies [25,26] indicating how fish species develop their own characteristic microbial communities. The results also agree with [26], who found higher fungal diversity in a Clarias than in a Tilapia system.…”

A high amylase‐producing bacterial strain exhibiting the phosphorus‐dissolving ability, isolated from freshwater aquaculture pond

“…is beneficial to the self‐purification of the shrimp pond environment and plays a key role in constructing and stabilizing the balanced ecosystems in shrimp ponds (Doroteo, Pedroso, Lopez, & Apines‐Amar, 2018). But those exogenous strains from a non‐aqueous environment are not ideal for water purification due to their poor enzyme stability and activity; therefore, they are not conducive to the application and promotion in aquaculture (Minich et al., 2018; Prieto et al., 2014).…”