Microbial metacommunity dynamics associated with the cyclopoid copepod Mesocyclops hyalinus (Rehberg, 1880) in freshwater mesocosm using low-cost organic media.

This mesocosm study evaluated the impact of various organic manure treatments on the growth performance of the copepod M. hyalinus and its associated microbial communities. Laboratory reared copepod, M. hyalinus was fed with six different types of filtrate of organic manure comprising of CM (cow manure), PM (poultry manure) and combinations CMC* (Cow dung, groundnut cake, mustard oil cake, rice bran, fish waste and single super phosphate), PMC** (Poultry manure, groundnut cake, mustard oil cake, rice bran, fish waste and single super phosphate), PMB*** (PMC + Bacillus clausii), CMB**** (CMC + B. clausii). Results indicated that CMC, PMC, and CMB at a concentration of 8.00 mL/L produced the highest population densities. CMC achieved a peak of 650.00 ± 11.55 Individuals/L by Day 6, while PMC and CMB peaked later on Day 9 (463.33 ± 6.67 Individuals/L) and Day 15 (563.33 ± 6.67 Individuals/L), respectively. 16S rRNA amplicon sequencing analysis of the high performing media (CMC and PMC) identified Actinobacteriota, Proteobacteria, Firmicutes, and Bacteroidota as the dominant bacterial phyla. In CMC, Actinobacteriota (54%) and Proteobacteria (20%-47%) predominated at peak growth. In contrast, PMC was dominated by Firmicutes (20%-39%) and Campylobacterota (26%-28%). These findings suggest that manure composition significantly dictates microbial structure and subsequent copepod productivity; cow manure based media promote rapid early growth, whereas poultry manure supports sustained population stability. The identified bacterial consortia offer a framework for developing targeted bioinoculants to optimize Mesocyclops hyalinus culture systems. By harnessing these microbiome driven insights, producers can enhance copepod yields and population stability. This research provides a scalable, sustainable strategy for mass producing live feed, addressing a critical bottleneck in global freshwater aquaculture.