Comparative analysis of bacterial communities in healthy and ice-ice diseased seaweeds farmed at the southern Kenyan coastline

Seaweed aquaculture is increasingly recognized as a sustainable livelihood option and a key contributor to Kenyan coastal resilience. However, ice-ice disease (IID) a non-infectious algal condition poses significant challenges, particularly to commercially valuable red algae species such as Kappaphycus alvarezii and Eucheuma denticulatum. This disease leads to tissue bleaching, reduced biomass, and lower carrageenan yield, making the study of seaweed associated bacterial communities crucial for sustainable cultivation. Healthy and diseased samples of seaweed thalli were collected from commercial farming sites in Mkwiro and Kibuyuni including recording of physicochemical parameters. Phenotypic contrasts between healthy and diseased seaweeds were assessed, total genomic DNA was extracted and subjected to full-length 16S rRNA gene sequencing using PacBio technology, sequences were processed using the DADA2 pipeline in R. Microbial community analysis included alpha and beta-diversity metrics, differential abundance testing (DESeq2), and distance-based redundancy analysis (dbRDA) to link community structure to environmental parameters and functional potential was inferred using PICRUSt2.The results revealed a severe and environmentally-mediated disruption (dysbiosis) associated with Ice-ice disease in the seaweed. The overall microbial community was co-dominated by the phyla Pseudomonadota and Bacteroidota.Diseased samples exhibited a clear structural shift, characterized by a massive enrichment of opportunistic pathogenic genera, primarily Alteromonas and Tenacibaculum

By identifying key pathogens and potential beneficial bacteria, this study provides a solid foundation for targeted disease management, supporting healthier and more sustainable seaweed farming in Kenya.