DOI: 10.5061/dryad.1rn8pk13s
title: Disruption of host-associated and benthic microbiota affects reproductive output and settlement of a habitat-forming macroalga

description: 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.
description: 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).
description: # Disruption of host-associated and benthic microbiota affects
 reproductive output and settlement of a habitat-forming macroalga
 [https://doi.org/10.5061/dryad.1rn8pk13s](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