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bioRxiv · 10.1101/2020.04.21.053553

Long-run bacteria-phage coexistence dynamics under natural habitat conditions in an environmental biotechnology system

Guerrero, L. D.·Perez, M. V.·Orellana, E.·Piuri, M.·Quiroga, C.·Erijman, L.
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Abstract

Bacterial viruses are widespread and abundant across natural and engineered habitats. They influence ecosystem functioning through interactions with their hosts. Laboratory studies of phage-host pairs have advanced our understanding of phenotypic and genetic diversification in bacteria and phages. However, the dynamics of phage-host interactions has been seldom recorded in complex natural environments. We conducted an observational metagenomic study of the dynamics of interaction between Gordonia and their phages using a three-year data series of samples collected from a full-scale wastewater treatment plant. The aim was to obtain a comprehensive picture of the coevolution dynamics in naturally evolving populations at relatively high time resolution. Co-evolution was followed by monitoring changes over time in the CRISPR loci of Gordonia metagenome-assembled genome, and reciprocal changes in the viral genome. Genome-wide analysis indicated low strain variability of Gordonia, and almost clonal conservation of the trailer-end of the CRISPR loci. Incorporation of newer spacers gave rise to multiple coexisting bacterial populations. A host population containing a CRISPR array variant, which did not contain spacers against the coexisting phages, accounted for more than half of the total host abundance in the majority of samples. Phages genome co-evolved by introducing directional changes, with no preference for mutations within the protospacer and PAM regions. Metagenomic reconstruction of time-resolved variants of host and virus genomes revealed how selection operates at the population level. In activated sludge, it differed from the arms-race observed in nutrient rich media and resembled the fluctuating selection dynamics observed in natural environments.

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Guerrero, L. D., Perez, M. V., Orellana, E., Piuri, M., Quiroga, C., Erijman, L.. 2020-04-22. Long-run bacteria-phage coexistence dynamics under natural habitat conditions in an environmental biotechnology system. https://doi.org/10.1101/2020.04.21.053553

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