Ocean Acidification

Highlights

• Stomopneustes variolaris gut microbiota shows clear seasonal structuring in response to monsoon-driven biogeochemical variability.
• The gut microbiota of Stomopneustes variolaris is dominated by Bacteroidota, and most diverse during winter and spring inter-monsoon.
• Gut microbial composition covaries with seasonal oxygen, pH, temperature, and nutrient gradients.
• The sea urchin gut microbiome shows seasonal plasticity under monsoon-linked stress.

Abstract

Tropical coastal ecosystems of the Eastern Arabian Sea (EAS) experience pronounced monsoon-driven shifts in water-column biogeochemistry, yet their influence on the gut-associated microbiomes of benthic invertebrates remains poorly understood. Sea urchins are ecologically important grazers in reef-associated habitats, and their gut microbiota may reflect both environmental and dietary variability. Here, we provide an exploratory characterisation of the gut-associated microbiome of the sea urchin Stomopneustes variolaris from the Grande Island archipelago (Goa, India) across four monsoon-associated periods: Winter monsoon (WM), Spring-inter monsoon (SIM), Summer monsoon (SM), and Fall-inter monsoon (FIM). Using 16S rRNA gene sequencing, we analysed gut tissue and gut digesta from S. variolaris alongside environmental samples (seawater, sediment, and seaweed). Bacteroidota dominated the urchin gut microbiome, whereas Proteobacteria were more abundant in environmental samples. Gut microbial diversity was highest in WM and SIM and lowest during SM and FIM. Exploratory analyses indicated that gut microbial composition varied temporally, with taxa affiliated with sulphur-cycling lineages more prevalent during sampling points associated with low-oxygen monsoon phases (SM and FIM) and Firmicutes and organic matter-associated taxa more prominent during comparatively oxygenated periods (WM and SIM). Ordination analyses suggested an association between gut and environmental microbial assemblages and gradients in dissolved oxygen, temperature, pH, nutrients, and pCO₂. This study provides baseline insights into the gut microbiome of a tropical echinoid from an understudied region and highlights monsoon-associated patterns in microbial community composition, forming a foundation for future functional and experimental investigations.

Graphical abstract

Lakshmi S., Shetye S., Damare S. & Kuniyil N., 2026. Monsoon-linked gut microbiome variation in a tropical sea urchin: a single-reef case study from the Arabian Sea. Estuarine, Coastal and Shelf Science 343: 110272. doi: 10.1016/j.ecss.2026.110272. Article (subscription required).