Free-living Bacterial Communities Are Mostly Dominated by Oligotrophs

Abstract

In response to resource availability, bacteria have evolved two distinct ecological strategies. Copiotrophic bacteria grow fast and are heavily favored by selection where the resource is abundant. In contrast, oligotrophic bacteria grow slowly but more efficiently and are highly adaptive in nutrient-poor environments (Koch, 2001). Although oligotrophs and copiotrophs are ubiquitous, except for a few well-characterized environments like the open ocean and animal gut, the relative abundance of oligotrophic and copiotrophic bacteria and their importance in the global ecosystem are still unclear. In addition, although several studies have demonstrated the impact of nutrient availability on the bacterial community structure under experimental conditions (Klappenbach et al., 2000, Nemergut et al., 2016), the role of nutrients in shaping the structures of bacterial communities in their natural habitats remains largely unknown. Using the ribosomal RNA operon (rrn) copy number to capture the bacterial ecological strategy, we analyzed 44,045 samples from two large bacterial community repositories that cover 78 environmental types. Here we show that animal-associated microbiota are dominated by copiotrophs while plant-associated and free-living bacterial communities are mostly dominated by oligotrophs. Our results suggest that nutrient availability plays an important role in determining the structure and ecological strategy of bacterial communities in nature. We demonstrate that the average and distribution of rrn copy number are simple yet robust predictors of the ecological strategy of bacterial communities that can be applied to all sequence-based microbial surveys to link the community structure and function.