DOI: 10.5061/dryad.2z34tmps9
title: Functional changes across marine habitats due to ocean acidification

description: Global environmental change drives diversity loss and shifts in community
 structure. A key challenge is to better understand the impacts on
 ecosystem function and to connect species and trait diversity of
 assemblages with the possible consequences for ecosystem function. Here we
 quantify shifts in species composition and trait diversity associated with
 ocean acidification (OA) by using field measurements at marine CO2 vent
 systems spanning four reef habitats across different depths in a temperate
 coastal ecosystem. We find that both species and trait diversity decreased
 and that ecosystem properties (understood as the interplay between
 species, traits, and ecosystem function) shifted with acidification.
 Furthermore, shifts in trait categories such as autotrophs, filter
 feeders, herbivores, and habitat-forming species were habitat-specific,
 indicating that OA may produce divergent responses across habitats and
 depths. Combined, these findings reveal the importance of connecting
 species and trait diversity of marine benthic habitats with key ecosystem
 properties to anticipate the impacts of global environmental change. Our
 results also generate new insights into the predicted general and
 habitat-specific ecological consequences of OA.
description: <strong>Sampling design of benthic surveys</strong>.
 Percent cover of 215 benthic species was quantified using two approaches
 with scuba diving: i) visual census techniques in Shallow Reef (benthic
 surveys were performed from 0.5 to 3 m depth) and Reef habitats (benthic
 surveys at ~10 m depth) dominated by algae and ii) photographic surveys in
 Caves (benthic surveys at ~3 m depth) and Deep Reef habitats (benthic
 surveys at ~ 40 m depth) dominated by sessile invertebrate animals. For
 visual censuses, 12 quadrats (25x25 cm) were haphazardly placed at Vent 1
 and Vent 3 and the two corresponding ambient pH sites (n = 3 sites per
 habitat, n = 36 quadrats for Shallow Reefs and Reefs, respectively). For
 photographic surveys, 48–54 and 24 photoquadrats (25x25 cm) were taken at
 Vent 2 and Vent 4 and the two corresponding reference sites with ambient
 pH for each habitat (n = 3 sites per habitat, n = 144 photographic
 quadrats for Caves and n = 72 photographic quadrats for Deep Reefs,
 respectively). Both types of quadrats (visual censuses in the field and
 photographs in the lab) were divided into a grid of 25 squares (5 cm x 5
 cm each). Percentage cover was quantified by counting the number of
 squares filled in the grid by the species and expressing the final values
 as relative percentages. <strong>Trait
 characterization of benthic species. </strong>The trait diversity of
 benthic assemblages was assessed using seven traits, which were chosen to
 provide an overview of each species’ ecological strategy. The traits were:
 1) morphological form, 4 categories: a) encrusting, b) filaments, c)
 massive, and d) tree-like; 2) feeding, 6 categories: a) autotroph, b)
 filter feeders, c) herbivores/grazers, d) carnivores, e) detritivores, and
 f) parasites; 3) growth rates, 3 categories: 1) extreme low (&lt;1
 cm/year), 2) moderate (1–5 cm/year), 3) high (&gt;5–10 cm/year; 4)
 calcification, 2 categories: a) without and b) with calcareous structures;
 5) mobility, 2 categories: a) sessile and b) vagile; 6) age at
 reproductive maturity, 2 categories: 1) &lt; than 1 year, 2) &gt;
 than 1 year; and 7) chemical defenses, 2 categories: 1) no and 2) yes (see
 Table S5 for a detailed description of the seven traits and
 categories). <strong><br></strong>
 <strong>Bayesian Dirichlet-Multinomial
 Model. </strong>We used Bayesian models to predict the probability
 of a species’ cover belonging to a specific trait category across habitats
 and between pH conditions. We applied a Bayesian Dirichlet-Multinomial
 model (DMM) to analyze benthic cover for the four functional traits
 (morphological form, feeding activity, growth rate, and
 calcification).
description: # Functional changes across marine habitats due to ocean acidification
 This repository contains
 the ecological data files used to analyze the data and generate the
 results for this study ## Description of the data and file structure Data
 S1 is the raw data of percent cover of benthic species obtained from field
 surveys. Each quadrat measures 25x25 cm. It includes: Quadrats (label of
 the quadrat), species (species name), cover (percentage), and
 description.condition (description of the habitat and pH condition). Data
 S2 is the code of 7 traits (and categories) for the 215 species identified
 in this study. It includes: Species (species name), FE (combination of the
 7 Functional Entities), and the 7 traits with their categories. The traits
 are: 1) morphological form, 4 categories: a) encrusting, b) filaments, c)
 massive, and d) tree-like; 2) feeding, 6 categories: a) autotroph, b)
 filter feeders, c) herbivores/grazers, d) carnivores, e) detritivores, and
 f) parasites; 3) growth rates, 3 categories, 1) extreme low (&lt;1
 cm/year), 2) moderate (1-5cm/year), 3) high (&gt;5-10 cm/year; 4)
 calcification, 2 categories, a) without and b) with calcareous structures;
 5) mobility, 2 categories, a) sessile and b) vagile; 6) age at
 reproductive maturity, 2 categories, 1) &lt; than 1 year, 2) &gt; than 1
 year; and 7) chemical defences, 2 categories, 1) no and 2) yes Data S3
 contains the outputs from the Bayesian model of the likelihood of benthic
 cover belonging to a trait category across habitats and between pH zones.
 The file contains the description of the type of habitat (Habitat), pH (pH
 conditions), trait category (Condition), Trait (ecological trait), Cover
 (estimate mean cover), std.error (standard variation), and Q2.5 and Q97.5
 ( the two-side intervals). ## Sharing/Access information ## Code/Software
 The R codes used for data analysis and generate the results will be
 available upon publication approval.