Published January 13, 2021 | Version v1

Multi-year time shift study of bacteria and phage dynamics in the phyllosphere

  • 1. University of California, Berkeley
  • 2. University of Exeter
  • 3. Imperial College London

Description

Coevolutionary dynamics shape diversity within and among populations but are difficult to study directly. Time shift experiments, where populations of species A from one point in time are experimentally challenged against populations of species B from past, contemporary, and/or future time points, and vice versa, are a particularly powerful tool to measure coevolution. This approach has been primarily applied to study host-parasite interactions and proven useful in directly measuring coevolutionary change and distinguishing among coevolutionary models. However, these data are only as informative as the time window over which they were collected, and data from shorter coevolutionary windows might conflict with data collected over longer time periods. Previous work on natural microbial communities from horse chestnut tree leaves used time shifts to uncover an apparent asymmetry, whereby hosts tended to be resistant to phages from all earlier points in the growing season while phages tended to be most infective on hosts from the recent past. Here we extend the time window over which these infectivity and resistance ranges are observed from within a growing season to across years and confirm that the previously observed asymmetry holds over longer timescales.

Notes

Note that when grouping was chosen based on Geneious grades and ability to call to a given taxonomic resoluation, the class Gammaproteobacteria was recorded as Genus = "Gamma" and Species = "Gamma proteobacterium". This grouping was not removed from the data, but it is important to be aware that this is not a genus- nor species-level identification, and is actually a class of bacteria that contains many genera, including Erwinia, Pantoea, and Pseudomonas.

Metadata for datasheets:

Column Description
Tree Tree from which phage and bacteria samples were collected
Host.year Year in which bacteria sample was collected
Host Randomized name given to individual hosts in each set of 96 hosts from a given tree in a given year (A1-H12)
Genus Genus assigned to successfully to individual hosts from NCBI blast
Species Species assigned to successfully sequenced individual hosts from NCBI blast
E.value The Expect value from NCBI blast
Geneious.Grade Geneious grade given to individual hosts when identifying via sequencing
Phage.inoculum (All phage/bacteria dataset only) Year in which phage sample was collected
Phage.clone (Phage clones dataset only) Identifier of the isolated phage clone used in the second set of time shift crosses. Identifiers assigned based on collection data: [Tree# (1-8)] [Year (2011-2014)] [Initial susceptible host (A1-H12)].
Infected 0 = Not infected; 1 = Successful infection
Unique.Host Identifier of individual bacterial isolates used in both sets of time shift crosses, to allow for cross-reference to sequencing data. Identifiers assigned based on collection data: [Host (A1-H12)]_[Tree# (1-8)]_[Year (2011-2014)].

Funding provided by: Natural Environment Research Council
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100000270
Award Number: NERC: NE/K00879X/1

Files

Data_for_submission_Time_Shift_All_phage_All_bacteria.csv

Files (1.6 MB)

Additional details

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