Microbial community structure and niche differentiation in healthy and infected samples of Kappaphycus alvarezii in the commercial farming sites of Tamil Nadu coastal, India

Seaweed cultivation, particularly of Kappaphycus alvarezii , plays a significant role in the coastal economy of Tamil Nadu, India. K. alvarezii is frequently affected by ice-ice disease caused by microbial imbalances. This disease leads to tissue bleaching, reduced biomass, and lower carrageenan yield, making the study of seaweed-associated bacterial communities crucial for sustainable cultivation. In this study, healthy and diseased samples of K. alvarezii were collected from five commercial farming sites. High-throughput Illumina sequencing of the V3–V4 region of the 16S rRNA gene was performed to analyze microbial diversity. Bioinformatics tools such as OTU clustering, alpha diversity indices, heat tree visualization, and functional prediction were applied to characterize differences between healthy and diseased samples across locations. The results revealed Proteobacteria as the dominant phylum, with Gammaproteobacteria being prevalent in all samples. Diseased seaweed samples exhibited greater microbial diversity, with genera including Pseudoalteromonas and Vibrio frequently associated with disease, while Cobetia was more abundant in healthy samples. Variations in microbial community structure were closely linked to environmental factors, including temperature, salinity, dissolved oxygen, and nutrient levels. Functional prediction showed that diseased samples had elevated pathways related to fermentation, nitrate reduction, and nitrogen respiration. Whereas healthy samples were enriched in aerobic chemoheterotrophy and hydrocarbon degradation. The study demonstrates that site-specific environmental conditions significantly influence microbial dynamics and disease progression in seaweed farms. Identifying potential pathogens and beneficial bacteria provides a foundation for developing targeted probiotics and disease management strategies that can support sustainable cultivation and improve seaweed health.