Disruption of host-associated and benthic microbiota affects reproductive output and settlement of a habitat-forming macroalga
Data files
May 16, 2025 version files 6.92 GB
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ASV_16S_EXP3.rds
7.71 MB
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dada2.R
2.42 KB
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dadaFs_EXP3.rds
216.96 MB
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dadaRs_EXP3.rds
193.92 MB
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Disruption_of_host-associated_and_benthic_microbial_communities_plot_and_stats_code.R
10.61 KB
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Experiment_3_Response_Variables_200.xlsx
19.81 KB
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Fastas.zip
6.46 GB
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mergers_EXP3.rds
43.45 MB
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README.md
3.59 KB
Abstract
Host-associated microbial communities have been widely acknowledged as being fundamentally important for normal host function and performance. Whilst there is evidence that microbial communities associated with habitat-forming macroalgae can strongly influence various aspects of host performance, to have a deeper understanding of these effects we need to understand the role of host-associated microbiota on the fitness of the host, throughout its entire life cycle. We addressed these issues using a dominant habitat-forming macroalga on Australian rocky-shores, Hormosira banksii. We manipulated host- and benthic-associated microbiota to determine the relative importance of microorganisms to reproductive output (number of viable eggs released) and settlement of the host. Disruption of the host microbiota using antibiotics decreased reproductive output after two weeks, with the effect dependent on the type of antibiotic used. Disruption of host- and benthic-associated microbiota, independently and in combination, caused a significant decrease in settlement of Hormosira-zygotes, with the combined disruption having the greatest impact on settlement success. Our results demonstrate the importance of host-associated microbiota in macroalgal reproduction and an interactive effect of host- and benthic-associated microbiota on settlement for a dominant habitat forming alga. Thus microbiota affect key ecological processes with important implications for host fitness and potentially ecosystem persistence.
https://doi.org/10.5061/dryad.1rn8pk13s
Description of the data and file structure
Data collected from an experiment run at Cape Banks Aquatic Reserve on algal reproductive output and settlement in response to microbial disruption. Data are Microbial community responses (16S Phyloseq) and host responses (Response variables). The various steps within the DADA2 pipeline are also included here as well as the code to generate the plots and analyses.
Design was as follows - Host treatments 4 (Antibiotics 2; Antibiotics 3; Control and Procedural control) and tile treatments 5 (AB2; AB3; Control; Procedural control and Autoclaving).
Files and variables
File: Experiment_3_Response_Variables_200.xlsx
Description: Host Response data for an experiment run at Cape Banks Aquatic Reserve on algal reproductive output and settlement in response to microbial disruption. Design was as follows - Host treatments 4 (Antibiotics 2; Antibiotics 3; Control and Procedural control) and tile treatments 5 (AB2; AB3; Control; Procedural control and Autoclaving).
Variables
- Plate treatment - Treatment applied to benthic biofilm - AB2 (Antibiotic 2), AB3 (Antibiotic mix 3), Control, AFSW (Procedural Control - Autoclaved filtered seawater), Autoclaved.
- Host Treatment -Treatment applied to host - AB2 (Antibiotic 2), AB3 (Antibiotic mix 3), Control, AFSW (Procedural Control - Autoclaved filtered
- Number of Eggs/50ml - number of eggs per 50ml AFSW
- Number of eggs settled/200 - number of eggs per treatment settled after 4hrs
- Percentage settled eggs calculated from the total released/settled
- PS - predicted settled eggs - Percentage settled/total released
- MT - Merged treatment codes for both host and tile treatments
File: dada2.R
Description: Pipeline for bioinformatics
File: ASV_16S_EXP3.rds
Description: ASV table generated by pipeline
File: mergers_EXP3.rds
Description: mergers step in pipeline
File: dadaRs_EXP3.rds
Description: Reverse sequences prior to merging
File: dadaFs_EXP3.rds
Description: Forwardsequences prior to merging
File: Fasta.zip
Description: Raw sequences from the experiment in raw fasta format each file within the zip corresponds with the forward and reverse reads of each sample. The file naming convention follow the standard illumina protocol with the addition of each sample name (treatment x replicate)
File: Disruption_of_host-associated_and_benthic_microbial_communities_plot_and_stats_code code
Description: R version 4.3.2 code required to analyse the data associated with this study and produce the plots within the manuscript.
Code/software
R version 4.3.2 (2023-10-31 ucrt) -- "Eye Holes"
library(performance)
library(car)
library(MASS)
library(tidyverse)
library(dplyr)
library(patchwork)
library(glmmTMB)
library(see)
library(readxl)
library(vegan)
library(ade4)
library(reshape2)
library(ggplot2)
library(ggforce)
library(PNWColors)
library(MetBrewer)
library(emmeans)
library(multcomp)
library(multcompView)
library(ggsignif)
library(ggpubr)
library(RColorBrewer)
library(MetBrewer)
Access information
Other publicly accessible locations of the data:
- NCBI - Raw sequence data
Data was derived from the following sources:
- Hormosira banksii (macroalgae) microbiome and host responses, and benthic biofilm microbiome
Data collected from an experiment run at Cape Banks Aquatic Reserve on algal reproductive output and settlement in response to microbial disruption. Data are Microbial community responses (16S Phyloseq) and host responses (Response variables). The various steps within the DADA2 pipeline are also included here, as well as the code to generate the plots and analyses.
Design was as follows - Host treatments 4 (Antibiotics 2; Antibiotics 3; Control and Procedural control) and tile treatments 5 (AB2; AB3; Control; Procedural control and Autoclaving).