Taxonomic variability and functional stability in microbial communities infected by phages

Abstract

Microbial communities can display large variation in taxonomic composition, yet this variation can coincide with stable metabolic functional structure and performance. The mechanisms driving the taxonomic variation within functional groups remain largely unknown. Biotic interactions, such as predation by phages, have been suggested as potential cause of taxonomic turnover, but the conditions for this scenario have not been rigorously examined. Further, it is unknown how predation by phages affects community function, and how these effects are modulated by functional redundancy in the communities. Here, we address these questions using a model for a methanogenic microbial community that includes several interacting metabolic functional groups. Each functional group comprises multiple competing clades, and each clade is attacked by a specialist lytic phage. Our model predicts that phages induce intense taxonomic turnover, resembling the variability observed in previous experiments. The functional structure and performance of the community are also disturbed by phage predation, but they become more stable as the functional redundancy in the community increases. The extent of this stabilization depends on the particular functions considered. Our model suggests mechanisms by which functional redundancy stabilizes community function and supports the interpretation that biotic interactions promote taxonomic turnover within microbial functional groups.

Function and functional redundancy in microbial systems

“…For example, models for methanogenic bioreactors fed continuously with glucose suggest that the relative flux rates through "alternative" catabolic pathways (e.g., the various alternative routes from glucose to volatile fatty acids and eventually to methane; Fig. 3A) may be less stable in the face of taxonomic shifts, than the overall methane production rate 40 .…”

Rumen Virus Populations: Technological Advances Enhancing Current Understanding

“…Advances in sequencing and proteomics provide vast quantities of data that enable us to characterize, understand and model the role of rumen viruses. Basic knowledge of the rumen microbiome as a whole, including viruses, is essential to allow us to explore the rumen microbiome through modeling (Louca and Doebeli, 2017). Modeling of whole microbial communities opens the possibility to understand community functionality and dynamics (Widder et al, 2016).…”

“…Phage therapy using intact viruses is highly host specific and presents regulatory issues, the use of virus-derived products or "enzybiotics" could directly replace conventional antimicrobials (O'Mahony et al, 2011;Shen et al, 2012;Louca and Doebeli, 2017). Mechanisms for the delivery and release of viral material from the host often involves enzymes (lysins/holins, peptidases, depolymerases, tail spike proteins), which can be repurposed as enzybiotics (Murphy et al, 1995;Andres et al, 2012;São-José, 2018).…”

Bacterial Diversification in the Light of the Interactions with Phages: The Genetic Symbionts and Their Role in Ecological Speciation

“…It has been recently predicted that the more violent the perturbations by phage predation (i.e., lytic interactions), the more diverse the community is (Maslov and Sneppen, 2017). Phages contribute to taxonomic variability and functional stability in microbial communities (Louca and Doebeli, 2017).…”