Long-term genomic coevolution of host-parasite interaction in the natural environment

Abstract

The antagonistic coevolution of parasite infectivity and host resistance alters the biological functionality of species, with effects spanning to communities and ecosystems. Still, studies describing long-term host-parasite coevolutionary dynamics in nature are largely missing.Furthermore, the role of host resistance mechanisms for parasite evolution is poorly understood, necessitating for the molecular and phenotypic characterization of both coevolving parasites and their hosts. We combined long-term field sampling (2007)(2008)(2009)(2010)(2011)(2012)(2013)(2014), in vitro cross-infections and timeshift experiments with bacteriophage whole genome sequencing and bacterial (Flavobacterium columnare) CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) profiling to show the molecular details of the phage-bacterium arms race in the environment. Bacteria were generally resistant to phages from the past and susceptible to phages in the future. The bacterial resistance selected for increased phage infectivity and host range, correlating directly with the expansion of phage genome size by 2656 bp. In the bacterial host, two CRISPR loci were identified: a type II-C locus and an RNA-targeting type VI-B locus. While maintaining a core set of conserved spacers, phage-matching spacers appeared in the variable end of both CRISPR loci over time. The appearance of these CRISPR spacers in the bacterial host often corresponded with arms race -manner molecular changes in the protospacers of the coevolving phage population. However, the phenotypic data indicated that the relative role of constitutive defence may be more important in high phage pressure, highlighting the importance of our findings for understanding microbial community ecology and in the development of phage therapy applications.

Phage resistance evolution in vitro is not reflective of in vivo outcome in a plant‐bacteria‐phage system*

“…In light of the growing interest in understanding the role phages play in host-associated microbiomes, it is imperative that we study the impact of phages on bacterial ecology and evolution within their natural environments. There is reason to predict that knowledge gained from laboratory studies will not clearly translate to natural patterns, as in vitro studies that aim to incorporate more ecological realism consistently find that increasing complexity critically changes bacteria-phage interactions (Gómez and Buckling 2011;Jończyk et al 2011;Gómez et al 2015;De Sordi et al 2017;Laanto et al 2017;Wang et al 2017). We set out to test the impact of phages on evolution of an agriculturally relevant bacterial pathogen, P. syringae, based in part on ex-panding industry interest in using phages as biocontrol in this system.…”

“…Few studies have examined bacteria-phage (co)evolution in vivo (Capparelli et al 2006;Meaden and Koskella 2017;Wang et al 2017;De Sordi et al 2018), and none have directly compared the outcome of serially passaged bacteria and phage in vitro and in vivo. However, a growing body of work has focused on understanding bacteria and phage dynamics in ecologi-cally relevant conditions (Gómez and Buckling 2011;Laanto et al 2017;Scanlan et al 2019). For example, recent work investigating Vibrio cholerae phage replication in aquatic environments found that two of three clinically isolated phages had some level of replication in estuarine water, but none were able to replicate in fresh water (Silva-Valenzuela and Camilli 2019).…”

Neutral mechanisms and niche differentiation in steady‐state insular microbial communities revealed by single cell analysis

“…Synthetic co-cultures are well known to also mutually benefit from the cross-feeding of organic acids and nutrients (e.g., McCully et al, 2017) and various individualbased modelling approaches are developed to predict the individuals' competition for process control (Friedman et al, 2017;Daly et al, 2018). Additionally, predator-prey relationships contribute to microbial assembly dynamics, such as the bacterial predator Bdellovibrio spp., which feeds on gram-negative bacterial species (Johnke et al, 2014), or host-parasite relationships in which genotypespecific phages change community structures (Laanto et al, 2017). All these deterministic niche differentiation mechanisms ultimately lead to equilibria, corresponding to a steady-state climax community (Morris and Blackwood, 2007;Nemergut et al, 2013).…”

Expansion of CRISPR loci with multiple memories of infection enables the survival of structured bacterial communities

“…To test these hypotheses, we performed a time-shift experiment that evaluates the resistance of bacterial samples over time against phage from past, concurrent, and future time points [29,30]. We repeated the experimental setup used in Figures 1F (mono-spacer founder F) and 1G (multi-spacer founder C), collecting 12 surviving colonies at 24h, 36h, and 48h post-infection and isolating and amplifying phage from each of them Finally, each colony and their founders were grown in liquid cultures and used to seed top agar media, on which 2 µl of stock phage (which has not co-evolved with CRISPR-resistant staphylococci and was used to obtain the "time zero" datapoint) or phage isolated from each colony was spotted.…”