The community diversity and metabolic function of symbiont bacteria associated with soil amoebae (dictyostelids) in free-living habitats

Abstract

Dictyostelids, soil protists with stable bacterial symbiosis, are significant in microbial ecology. Beyond the model organism Dictyostelium discoideum, other amoebae-bacteria relationships are understudied. We isolated pure cultures of symbionts from 13 Chinese soil localities. Using 16S rRNA, we identified 125 strains (40 species) across four phyla, seven classes, 10 orders, 16 families, 21 genera. Notably, five potentially novel strains were discovered. Pseudomonadota and Gammaproteobacteria were dominated. Interestingly, Gansu's alkaline soil exhibited the highest bacterial diversity, suggesting a unique ecological niche fostering diverse symbiotic interactions. Moreover, preferential predatory response by dictyostelids towards Gram (−) bacteria was observed, providing insights into their symbiotic selectivity, which may be influenced by environmental factors such as soil pH, moisture, and nutrient availability. Furthermore, Redundancy and Spearman analysis showed that elevation and temperature significantly affected the symbiont communities. FAPROTAX predicted that symbionts were mainly chemoheterotrophs involved in the nitrogen cycle or pathogenic forms. Collectively, our findings highlight the potential application of amoeba-bacteria symbiosis in modulating soil ecological functions, serving as a foundation for exploring their intricate interaction mechanisms. In addition, the ecological implications of these symbiotic relationships could have significant impacts on public health, given the role of soil microorganisms in disease transmission and environmental resilience. The data obtained from this study offers a rich context for exploring bacterial colonization of eukaryotes, the origins of symbiosis, and foundational microbiomes.