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.

The Southeast Arm of Lake Malawi catchment has a wide range of natural resources that require prudent management for sustainability and maximisation of benefits. The current management practice is government sector based, with individual Departments and Ministries using their own policies, legislations and management approaches, yet dealing with the same composite resource and user communities. This has resulted in fragmentation of management leading to the lack of alignment between formal and informal institutions, and competition for power and authority for management. Fragmentation is also leading to loss of resource rent. This paper analyses how and why management is fragmented in the Southeast Arm of Lake Malawi catchment and suggests how management could be defragmented, with special interest on fisheries. Activities with high negative impacts on fisheries include: overfishing; soil erosion resulting in siltation and turbidity of the lake; chemical and organic pollution; loss of access to land and beaches; and habitat loss. There is need for a better and more holistic understanding of how human activities represent both livelihood benefits and a threat to sustainability of natural resources in order to find ways for balancing these two aspects. We suggest that to increase the efficacy of management of Lake Malawi's Southeast Arm will require 'defragmented decentralization', an approach whereby devolution of authority and responsibility are ceded to the district and local levels, respectively.

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