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Adaptation to sub-optimal hosts is a driver of viral diversification in the ocean.

ABSTRACT: Cyanophages of the Myoviridae family include generalist viruses capable of infecting a wide range of hosts including those from different cyanobacterial genera. While the influence of phages on host evolution has been studied previously, it is not known how the infection of distinct hosts influences the evolution of cyanophage populations. Here, using an experimental evolution approach, we investigated the adaptation of multiple cyanophage populations to distinct cyanobacterial hosts. We show that when infecting an "optimal" host, whose infection is the most efficient, phage populations accumulated only a few mutations. However, when infecting "sub-optimal" hosts, different mutations spread in the phage populations, leading to rapid diversification into distinct subpopulations. Based on our results, we propose a model demonstrating how shifts in microbial abundance, which lead to infection of "sub-optimal" hosts, act as a driver for rapid diversification of viral populations.

SUBMITTER: Enav H

PROVIDER: S-EPMC6224464 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

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Adaptation to sub-optimal hosts is a driver of viral diversification in the ocean.

Enav Hagay H Kirzner Shay S Lindell Debbie D Mandel-Gutfreund Yael Y Béjà Oded O

Nature communications 20181108 1

Cyanophages of the Myoviridae family include generalist viruses capable of infecting a wide range of hosts including those from different cyanobacterial genera. While the influence of phages on host evolution has been studied previously, it is not known how the infection of distinct hosts influences the evolution of cyanophage populations. Here, using an experimental evolution approach, we investigated the adaptation of multiple cyanophage populations to distinct cyanobacterial hosts. We show th ...[more]

PMID: 30409965

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Project description:The Southern Ocean (SO) represents up to one-fifth of the total carbon drawdown worldwide. Intense selective pressures (low temperature, high UV radiation, and strong seasonality) and physical isolation characterize the SO, serving as a "natural" laboratory for the study of ecogenomics and unique adaptations of endemic viral populations. Here, we report 2,416 novel viral genomes from the SO, obtained from newly sequenced viral metagenomes in combination with mining of publicly available data sets, which represents a 25% increase in the SO viral genomes reported to date. They comprised 567 viral clusters (defined as approximately genus-level groups), with 186 genera endemic to the SO, demonstrating that the SO viral community is predominantly constituted by a large pool of genetically divergent viral species from widespread viral families. The predicted proteome from SO viruses revealed that several protein clusters related to cold-shock-event responses and quorum-sensing mechanisms involved in the lysogenic-lytic cycle shift decision were under positive selection, which is ultimately important for fine adaptation of viral populations in response to the strong selective pressures of the SO. Finally, changes in the hydrophobicity patterns and amino acid frequencies suggested marked temperature-driven genetic selection of the SO viral proteome. Our data provide valuable insights into how viruses adapt and remain successful in this extreme polar marine environment. IMPORTANCE Viruses are the most abundant biologic entities in marine systems and strongly influence the microbial community composition and diversity. However, little is known about viral communities' adaptation and diversification in the ocean. In this work, we take advantage of the geographical isolation and the intense selective pressures of the SO, to which viruses are exposed, to identify potential viral adaptations due to positive environmental selection and dispersal limitation. To that end, we recovered more than two thousand novel viral genomes, revealing a high degree of divergence in these SO endemic communities. Furthermore, we describe remarkable viral adaptations in amino acid frequencies and accessory proteins related to cold shock response and quorum sensing that allow them to thrive at lower temperatures. Consequently, our work greatly expands the understanding of the diversification of the viral communities of the SO and their particular adaptations to low temperatures.

Project description:BackgroundGrowth traits can be used as indicators of adaptation to sub-optimal conditions. The current study aimed at identifying quantitative trait loci (QTL) that control performance under variable temperature conditions in chickens.MethodsAn F2 population was produced by crossing the Taiwan Country chicken L2 line (selected for body weight, comb area, and egg production) with an experimental line of Rhode Island Red layer R- (selected for low residual feed consumption). A total of 844 animals were genotyped with the 60 K Illumina single nucleotide polymorphism (SNP) chip. Whole-genome interval linkage mapping and a genome-wide association study (GWAS) were performed for body weight at 0, 4, 8, 12, and 16 weeks of age, shank length at 8 weeks of age, size of comb area at 16 weeks of age, and antibody response to sheep red blood cells at 11 weeks of age (7 and 14 days after primary immunization). Relevant genes were identified based on functional annotation of candidate genes and potentially relevant SNPs were detected by comparing whole-genome sequences of several birds between the parental lines.ResultsWhole-genome QTL analysis revealed 47 QTL and 714 effects associated with 178 SNPs were identified by GWAS with 5% Bonferroni genome-wide significance. Little overlap was observed between the QTL and GWAS results, with only two chromosomal regions detected by both approaches, i.e. one on GGA24 (GGA for Gallus gallus chromosome) for BW04 and one on GGAZ for six growth-related traits. Based on whole-genome sequence, differences between the parental lines based on several birds were screened in the genome-wide QTL regions and in a region detected by both methods, resulting in the identification of 106 putative candidate genes with a total of 15,443 SNPs, of which 41 were missense and 1698 were not described in the dbSNP archive.ConclusionsThe QTL detected in this study for growth and morphological traits likely influence adaptation of chickens to sub-tropical climate. Using whole-genome sequence data, we identified candidate SNPs for further confirmation of QTL in the F2 design. A strong QTL effect found on GGAZ underlines the importance of sex-linked inheritance for growth traits in chickens.

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Adaptation to sub-optimal hosts is a driver of viral diversification in the ocean.

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Adaptation to sub-optimal hosts is a driver of viral diversification in the ocean.

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