Longitudinal study (16S and 18S rRNA metabarcoding) of tilapia and pangasius aquaculture pond water in Bangladesh

The pondwater microbiome is believed to play a key role in fish health, including shaping mucosal surface microbiomes that help to protect against disease. Tilapia and pangasius are some of the most widely farmed fish species, and disease is a significant impediment to the expansion of their production. We used a 16S/18S rRNA metabarcoding approach to investigate how season, various features of pond water physico-chemistry, geographical location, crop species, and reported disease and algal blooms affected the water microbiome in pangasius and tilapia aquaculture earthen ponds in the Mymensingh division, Bangladesh. Sixteen fish farms were sampled monthly across six different villages and three Upazilas (subdistricts) over a period of 21 months (2016-2018). Pangasius (Pangasianodon hypophthalmus) was the main crop in eight ponds while Nile tilapia (Oreochromis niloticus) was the main crop in the other eight ponds. This work was carried out as part of the UKRI-Newton Fund Global Research Partnership project entitled 'Prediction and mitigation of diseases outbreaks in aquaculture through large scale community engagement'.