Data analysis for the project hambiDoubleEvo

Authors

Affiliations

Shane L Hogle

University of Turku

Julius Hoffmann

University of Konstanz

Published

October 31, 2024

Keywords

Microbiology, Ecology, Evolution, Predator-prey

1 Manuscript:

‡ equal contribution, ◇ Corresponding author and equal contribution

1.1 Published record

Temporal changes in the role of species sorting and evolution determine community dynamics
Hoffman J^‡, Hogle SL^‡, Hiltunen T^◇, Becks L^◇ XYZ (2024/5) doi:

1.2 Preprint

Temporal changes in the role of species sorting and evolution determine community dynamics
Hoffman J^‡, Hogle SL^‡, Hiltunen T^◇, Becks L^◇ Research Square(2024) doi: 10.21203/rs.3.rs-4647074/v1

2 Experiment overview

This project is a collaboration between teams at University of Turku in Finland and the University of Konstanz in Germany. The repo contains data from an experiment investigating the relative roles of ecology and evolution in an multitrophic synthetic microbial ecosystem. 24 HAMBI bacterial species were individually grown and coevolved for 100 days (3% vol transfer every 4 days) with the generalist bacterivore Tetrahymena thermophila to generate 6 (replicates A-F) x 24 (species) coevolved bacterial and ciliate populations. Bacteria and ciliates were separated from the coevolution cocultures and bacteria made axenic via freeze-thaw. The 24 predator-coevolved bacterial species were pooled in equal proportions into a “coevolved” prey inoculum. Evolved phenotypically variable ciliates were taken from a 3 year long coevolution experiment (see Cairns 2018, Hogle 2022 Ecol Lett, Hogle 2022 ISME J) and were combined in equal proportions into a “Evolved” predator inoculum. Finally, the 24 clonal/ancestral bacterial species were pooled in equal proportions into a “ancestral” prey incolum and the ancestral Tetrahymena was used as the “ancestral” predator incolum. The inocula were used to start a serial transfer experiment in a full factorial design in six biological replicates (anc prey + anc pred, anc prey + evo pred, evo prey + anc pred, evo prey + evo pred). A no-predator treatment was also used (anc prey + no pred, evo prey + no pred). These evolutionary treatments were serially passaged every 48 hours (30% transfer - 1800 μl to 4.2mL fresh 5% KB medium). The serial transfer microcosms were grown for 60 days after which the experiment was terminated.

3 Measurements and data types

There are many different types of data collected. However, not all data types were collected for all treatment combinations.

Bacterial density (OD600) measured from replicates A-F in all treatment combinations at days 4, 8, 12, 16, 20, 24, 28, 32, 36, 40, 44, 48, 52, 56, 60
Ciliate density (cells/ml) measured from replicates A-F in all treatment combinations at days 4, 8, 12, 16, 20, 24, 28, 32, 36, 40, 44, 48, 52, 56, 60
Bacterial species frequencies (amplicon counts) were measured from replicates A, C, and E at days 4, 8, 12, 16, 20, 24, 28, 32, 36, 40, 44, 48, 52, 56, 60
Bacterial species frequencies (amplicon counts) were measured from the “ancestral” and “evolved” inocula used to start the experiment (called “init”). Note this is not measurement from the actual experiment at T0, but a measurement of the inocula.
Whole genome sequencing data (wgs) for all ancestral/clonal bacterial species (24 total)
Whole genome sequencing data (wgs) for each coevolved bacterial species population used to inoculate replicates A,C, E (3 x 24 = 72 total).
Metagenome sequencing data from all evolution treatment combinations, excluding the no predator control conditions (anc prey + no pred, evo prey + no pred) from replicates A, C, E and on days 8, 28, and 60.
Initial defense traits (resistance to ciliate grazing) were measured by XYZ for:
- All 24 ancestral bacterial species
- All 24 co-evolved bacterial populations
Evolved defense traits (resistance to ciliate grazing) for:
- 16 Random clones isolated from 8, 28, and 60 days for each prey/predator/dilution combination
- Measure OD600 after 48 and 96 hours of growth with and without consumer

4 Availability

Data and code in this GitHub repository (https://github.com/slhogle/hambiDoubleEvo) is provided under GNU AGPL3. Feel free to use or remix as you see fit. The rendered project site is available at https://slhogle.github.io/hambiDoubleEvo/, which has been produced using Quarto notebooks. The content on the rendered site is released under the CC BY 4.0. This repository hosts all code and data for this project including the code necessary to fully recreate the rendered webpage.

An archived release of the code here is available from Zenodo:

Raw sequencing data using in the project is available from NCBI Bioproject PRJNA1179357.

5 Reproducibility

The project uses renv to create reproducible environment to execute the code in this project. See here for a brief overview on collaboration and reproduction of the entire project. To get up and running you can do:

install.packages("renv")
renv::restore()

Reuse

CC BY 4.0

--- title: "Data analysis for the project hambiDoubleEvo" date: today author: - name: Shane L Hogle orcid: 0000-0003-2595-3863 affiliation: - name: University of Turku city: Turku state: Finland url: https://www.utu.fi/en - name: Julius Hoffmann affiliation: - name: University of Konstanz city: Konstanz state: Germany url: https://www.uni-konstanz.de/en/ #abstract: > # The abstract text can go here # and also here ... keywords: - Microbiology - Ecology - Evolution - Predator-prey license: "CC BY" copyright: holder: Shane L Hogle year: 2024 # citation: # container-title: BioRxiv # volume: # issue: # doi: funding: "The author received no specific funding for this work." --- ## Manuscript: ‡ equal contribution, ◇ Corresponding author and equal contribution ### Published record **Temporal changes in the role of species sorting and evolution determine community dynamics**\ Hoffman J^‡^, Hogle SL^‡^, Hiltunen T^◇^, Becks L^◇^ *XYZ* (2024/5) [doi:]() ### Preprint **Temporal changes in the role of species sorting and evolution determine community dynamics**\ Hoffman J^‡^, Hogle SL^‡^, Hiltunen T^◇^, Becks L^◇^ *Research Square*(2024) [doi: 10.21203/rs.3.rs-4647074/v1](https://doi.org/10.21203/rs.3.rs-4647074/v1) ## Experiment overview This project is a collaboration between teams at University of Turku in Finland and the University of Konstanz in Germany. The repo contains data from an experiment investigating the relative roles of ecology and evolution in an multitrophic synthetic microbial ecosystem. 24 HAMBI bacterial species were individually grown and coevolved for 100 days (3% vol transfer every 4 days) with the generalist bacterivore *Tetrahymena thermophila* to generate 6 (replicates A-F) x 24 (species) coevolved bacterial and ciliate populations. Bacteria and ciliates were separated from the coevolution cocultures and bacteria made axenic via freeze-thaw. The 24 predator-coevolved bacterial species were pooled in equal proportions into a "coevolved" prey inoculum. Evolved phenotypically variable ciliates were taken from a 3 year long coevolution experiment (see Cairns 2018, Hogle 2022 Ecol Lett, Hogle 2022 ISME J) and were combined in equal proportions into a "Evolved" predator inoculum. Finally, the 24 clonal/ancestral bacterial species were pooled in equal proportions into a "ancestral" prey incolum and the ancestral *Tetrahymena* was used as the "ancestral" predator incolum. The inocula were used to start a serial transfer experiment in a full factorial design in six biological replicates (anc prey + anc pred, anc prey + evo pred, evo prey + anc pred, evo prey + evo pred). A no-predator treatment was also used (anc prey + no pred, evo prey + no pred). These evolutionary treatments were serially passaged every 48 hours (30% transfer - 1800 μl to 4.2mL fresh 5% KB medium). The serial transfer microcosms were grown for 60 days after which the experiment was terminated. ## Measurements and data types There are many different types of data collected. However, not all data types were collected for all treatment combinations. - Bacterial density (OD600) measured from replicates A-F in all treatment combinations at days 4, 8, 12, 16, 20, 24, 28, 32, 36, 40, 44, 48, 52, 56, 60 - Ciliate density (cells/ml) measured from replicates A-F in all treatment combinations at days 4, 8, 12, 16, 20, 24, 28, 32, 36, 40, 44, 48, 52, 56, 60 - Bacterial species frequencies (amplicon counts) were measured from replicates A, C, and E at days 4, 8, 12, 16, 20, 24, 28, 32, 36, 40, 44, 48, 52, 56, 60 - Bacterial species frequencies (amplicon counts) were measured from the "ancestral" and "evolved" inocula used to start the experiment (called "init"). Note this is not measurement from the actual experiment at T0, but a measurement of the inocula. - Whole genome sequencing data (wgs) for all ancestral/clonal bacterial species (24 total) - Whole genome sequencing data (wgs) for each coevolved bacterial species population used to inoculate replicates A,C, E (3 x 24 = 72 total). - Metagenome sequencing data from all evolution treatment combinations, excluding the no predator control conditions (anc prey + no pred, evo prey + no pred) from replicates A, C, E and on days 8, 28, and 60. - Initial defense traits (resistance to ciliate grazing) were measured by *XYZ* for: - All 24 ancestral bacterial species - All 24 co-evolved bacterial populations - Evolved defense traits (resistance to ciliate grazing) for: - 16 Random clones isolated from 8, 28, and 60 days for each prey/predator/dilution combination - Measure OD600 after 48 and 96 hours of growth with and without consumer ## Availability Data and code in this GitHub repository (<https://github.com/slhogle/hambiDoubleEvo>) is provided under [GNU AGPL3](https://www.gnu.org/licenses/agpl-3.0.html). Feel free to use or remix as you see fit. The rendered project site is available at <https://slhogle.github.io/hambiDoubleEvo/>, which has been produced using [Quarto notebooks](https://quarto.org/). The content on the rendered site is released under the [CC BY 4.0.](https://creativecommons.org/licenses/by/4.0/) This repository hosts all code and data for this project including the code necessary to fully recreate the rendered webpage. An archived release of the code here is available from Zenodo: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14017296.svg)](https://doi.org/10.5281/zenodo.14017296) Raw sequencing data using in the project is available from NCBI Bioproject [PRJNA1179357](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1179357). ## Reproducibility The project uses [`renv`](https://rstudio.github.io/renv/index.html) to create reproducible environment to execute the code in this project. [See here](https://rstudio.github.io/renv/articles/renv.html#collaboration) for a brief overview on collaboration and reproduction of the entire project. To get up and running you can do: ``` r install.packages("renv") renv::restore() ```