Light limitation enhances microbiome competitiveness and reduces microbial network stability in coastal waters

Abstract Light plays a crucial role in microbiomes, maintaining the amount and transfer of primary productivity and directing ecosystem functioning. Coastal microbiomes are frequently exposed to light-limited conditions, but how their community organization is affected remains unclear. This study aimed to investigate the assembly, association and functional activity of coastal microbiomes (both prokaryotes and eukaryotes) in response to low light. Results presented here show that light limitation reduces the diversity, phylogenetic distance and niche breadth of microbiomes and increases dispersal limitation, especially for microeukaryotes. A reduced proportion of photosynthetic microbes under light-limited conditions, suggests that decreased primary production and carbon input would further alter microbial composition and physiology. Reduced microeukaryotic diversity could enhance the influence of deterministic processes on the community assembly of microbiomes under light-limited conditions. Under light-limited conditions, deterministic processes structure the assembly of microeukaryotes, whereas the assembly of prokaryotes is mostly driven by stochastic processes. Light limitation weakens prokaryotic relations and intensifies microeukaryotic relations. Compositional and functional inefficiency and inefficient element cycling across microbial loops ultimately destabilize the light-limited ecosystems. The metatranscriptomic analysis identified that light deprivation reduces the expressions of genes involved in photosynthesis, nutrient utilization, oxidative phosphorylation, and biosynthesis of antibiotics, but enhances the expressions of genes related to the secretion system, purine metabolism and the citrate cycle. These results provide important insights into how microbiomes alter their composition and co-occurrences in light-limited environments.