Data files pertaining to Recommendations to maintain functioning on the GBR 2018-2019 (NESP TWQ 4.6, UQ)

The majority of data integrated in NESP 4.6 was based on either a) expert elicitation and surveys, or b) literature reviews. Two case studies used data from additional sources:
Case study 2: carbonate budget data was calculated for the GBR from AIMS LTMP data between 2014-2018.
Case study 5: included experiments of CoTS juvenile feeding preferences between three algal types (biofilm, CCA and Ampiroa), and so data in this spreadsheet is unique.

Methods:
Elicitation scores and ranks: Main modes expert elicitation and literature review

In a two-day workshop that convened our panel of GBR experts, we identified 70 functionally and taxonomically distinct groups of marine species common on the GBR. A methodology to assess functionally important species was developed by our scientific panel during the workshop. Outcomes were used to construct annotated online surveys that operated under three main criteria: (1) Functional importance: a process-based assessment of species’ contributions to ecosystem processes and functions; (2) Vulnerability: an assessment of the sensitivity and exposure of species to current and near-future stressors, and their likely recoverability; and (3) Manageability: an assessment of the probable effectiveness and feasibility of a management intervention in context of biological functioning. 

Surveys to address these criteria were developed online using the Surveymonkey platform, which were open for several weeks (July–August 2018). Surveys were targeted at our expert panel, but responses remained anonymous. A low-range scoring system (e.g. none/low/high) was employed to reduce ambiguity in responses, as qualitative words and broad scoring ranges are prone to subjectivity and uncertainty. Space for comments and feedback was provided throughout the surveys, which are available as an Appendix of the NESP 4.6 report. A total of 16 survey responses were completed across our taxonomic and functional groups, with equal-weighted averages taken across expert responses. Group averages are simple but can be effective in producing estimates of elicitation. Scores were checked and calibrated against the literature and empirical data (where possible) to reduce subjectivity and bias. Scoring criteria are explicitly outlined for each assessment in the NESP 4.6 report.

CS1 data file: Main modes literature review

A systematic literature review was conducted to identify the fish predators of mobile benthic
invertebrates on the GBR. The literature was searched using the ISI Web of Science database. Searches used combinations of the terms “invertivore”, “Great Barrier Reef”, “invertebrate”, “predator”, “predation”, “diet”, “crustacea”, “molluscs”, “cephalopods”, “echinoderms”, “polychaetes”, “annelids”, “worms”, “fishes” and “fish”. The search was further supplemented by examining the reference lists of papers that were found, and subsequent searches on Google Scholar. Fish species were only included when invertebrates contributed &gt;10% to their diet. Data were provided by the authors or extracted from digital publications using the measuring tool in Adobe Acrobat XI. For prey species and groups, information recorded included taxonomy and size, if available. Information on the abundance of invertebrate fauna, and densities of macroinvertebrates and fishes on the GBR, were obtained from papers that measured this directly, and from the Reef Life Survey database.

CS2 data file: Main modes literature review and AIMS LTMP datasets

Calculations of carbonate production and bioerosion rates and carbonate budget followed a modified census-based method described in Perry et al. (2012), as well as further detailed methodologies and spreadsheets for the Indo-Pacific in ReefBudget website (http://www.exeter.ac.uk/ geography/reefbudget). In our study, the estimated total carbonate budget for the GBR is calculated only from the biological processes by marine organisms included in the AIMS LTMP data. To accomplish these aims we used data of % cover of major carbonate producers (i.e. hard corals and calcareous algae) from the AIMS LTMP data collected along reefs in the northern, central and southern sections of the GBR between 2014-2018, and published data on growth rates to calculate carbonate production. Data on the abundance of bioeroders such as parrotfish, sponges and urchins were also obtained from the LTMP while rates of bioerosion from these organisms were gathered from the literature. Rates of carbonate production and bioerosion were then used to estimate carbonate budgets for the GBR. The data used for the study was collected before, during and after the 2016–2017 coral bleaching events in the GBR, and a total of 672 transects in 92 locations were examined.

CS3 data file: Main modes literature review 

To deliver putative taxonomic and functional groups of reef microbes across known abiotic gradients for the GBR, we undertook an assessment of the available literature. Studies establishing robust links between physical-chemical conditions and the microbial communities inhabiting the reef water column are scarce, particularly for regions of the GBR. In assessing the relevant information available for the study, we took advantage of the few existing detailed microbial datasets for the GBR as case studies to characterize the pelagic microbiome in response to: a) input of riverine floodwaters and plumes on inshore reefs; b) changes in benthic composition (macroalgal versus coral cover) and health of the reef, and; c) increasing distance from shore along an inshore to offshore gradient.  All microbial data has been transformed into relative abundance data and figures in this report summarize the most abundant microbial taxa in each case. For all data generated by BioPlatforms Australia (BPA) (Burdekin, Yongala and Coral Sea datasets), further documentation outlining the standard operating procedures for generating and processing sequencing amplicons is available at https://data.bioplatforms.com/organization/pages/bpa-marine-microbes/methods. Otherwise, all pre-processing data analyses steps are detailed in the respective publications for each of the GBR regions: Tully (Angly et al. 2016), Burdekin (Glasl et al. in review), Mackay (Alongi et al. 2015) and Heron Island (Epstein et al. in review). The microbial data here summarized originates from 256 samples collected from shallow pelagic habitats across 25 locations that fall into 5 different groups within our meta-analysis.
Environmental parameters and nutrient concentrations were acquired from the BPA website (https://data.bioplatforms.com/) for the Burdekin, Yongala and Coral Sea regions, from the NCBI SRA website (accession nr PRJNA276058) for the Tully region, and from the Water Quality Particulate and Dissolved Nutrient Data repository (Australian Institute of Marine Science (AIMS) 2017) for the Mackay region. No metadata was available for the Heron Island study. All environmental parameters are reported as averages ± SD.

CS4 data file: Main modes survey and elicitation data

An online survey (Surveymonkey) was constructed based on preliminary assessments of spearfishers from the foremost Queensland spearfishing online noticeboard; the “Northern Freediver” spearfishing forum, and an interview with the Queensland Spearfishing Commissioner. The anonymous survey was approved by the University of Queensland Institutional Human Research Ethics Approval board and participants gave written consent before partaking. A total of 149 surveys were completed between November 2016 and February 2017, of which 141 contained sufficient information to be used in analyses. Spearfishers were approached to complete the survey using the “Northern Freediver” forum. All surveys were completed online to ensure anonymity of participants. Spearfishers were surveyed from Bundaberg to Cooktown, and twenty-two common coral reef fish species were selected to examine spearfishing catches. Primary questions within the survey were developed to quantify (1) the proportion of time spearfishers spent in different regions of the Reef and Marine Park, (2) the contribution of functionally important coral reef fish species to spearfisher’s catches, annually, and (3) the perceived changes in catch dynamics of three target species (representing each functional guild) on the GBR. Further details on these primary aims are outlined below. 

CS5 data file: Main modes laboratory experiment

In November 2017, COTS were collected near Cairns, North Queensland (16°550’S, 145°460’E) and transported to the Southern Cross National Marine Science Centre (NMSC) in Coffs Harbour, NSW where they were maintained in flow through aquaria at 26-27°C. Within days of arrival, two male and two female starfish were spawned and raised. When the juveniles were ~7-8 mm in diameter they were randomly distributed into individual pots (~4 cm diameter). Pots were haphazardly distributed in a flow through system that was designed to deliver 1 µm-UV filtered fresh sea water through an individual dripper into each pot to maintain ~26°C.
The juveniles were fed three diets: biofilm, CCA and Amphiroa sp. Food was replaced every two weeks or as necessary to ensure that the starfish were fed ad libitum. The starfish were photographed using Cellsens imaging program after two weeks and then at monthly intervals using an Olympus camera mounted to a dissecting microscope. The number of any visually distinguishable arms were counted and the 2D-area of the juvenile was measured using ImageJ, and growth rate calculated over 0.5, 1.5, 2.5, 3.5 and 4.5 months. After ~3.5 months (105 days) in treatment, each individual starfish was placed in the centre of a Petri-dish and offered a ~1 x 1.5 cm sample of each diet (Amphiroa sp, biofilm, CCA) that were spaced ~2 cm apart. The starfish was then left to select a food source. A “choice” was recorded if the starfish arrived on the sample and stopped moving for &gt;5 minutes.

Format:

This dataset consists of six Excel files that contribute to NESP 4.6 with values extracted from (a) survey and elicitation processes, (b) literature reviews, (c) AIMS LTMP data, and/or (d) novel experimental data. The data is not georeferenced or modelled. Generally, means were calculated across scores within spreadsheets, with explicit methods described in the NESP 4.6 report.
1)  Datasheet on results from expert elicitation process aiming to rate 70 groups of species on their functional importance, vulnerability and manageability on the GBR. 
2)  Case study 1: Invertivory on the GBR
3)  Case study 2: Carbonate budget of the GBR
4)  Case study 3: Microbial assemblages on the GBR
5)  Case study 4: Recreational spearfishing on the GBR
6)  Case study 5: CoTS juveniles: early diet and growth 

References:
Wolfe, K. et al. (2019) Recommendations to maintain functioning of the Great Barrier Reef. Report to the National Environmental Science Program. Reef and Rainforest Research Centre Limited, Cairns (330 pp.).
http://bit.ly/330aGoe

Data Location:

This dataset is filed in the eAtlas enduring data repository at: data\nesp4\4.6_Recommendations-maintain-GBR

Organization: Australian Ocean Data Network