Climate–Microbiome Dynamics in Aquaculture Systems and Their Implications for Fish Production Stability, Food Availability and SDG Attainment in Sub-Saharan Africa

Abstract

Climate variability is emerging as a major limiting factor in aquaculture production, but its indirect impacts via microbial ecology are poorly understood, especially in Sub-Saharan Africa. This research proposes and tests a climate-microbiome-production pathway to understand the effects of environmental variability on aquaculture production and food security. A panel design was implemented across 42 aquaculture farms in southern Nigeria, combining climate data, water quality, 16S rRNA microbiome sequencing and production metrics over two production cycles. Structural equation modeling (SEM) reveals that temperature variability has a significant negative effect on microbial diversity (β = −0.41, p < 0.01), impairs nutrient cycling, and promotes pathogen growth. Microbiome dynamics play a key role in fish survival (β = 0.36, p < 0.01) and yield (β = 0.29, p < 0.05), and mediate climate variability impacts on production. These impacts flow through to food security, as production stability declines reduce food availability. The research reveals microbiome-mediated pathways are essential for aquaculture resilience in the face of climate change and that microbiome-informed aquaculture management strategies are needed to support food security and sustainable development in Sub-Saharan Africa.

Keywords: Climate variability; Aquaculture microbiome; Fish production stability; Food availability; Sub-Saharan Africa