'Australian National Moorings Network' (ANMN) is a facility of the Australian 'Integrated Marine Observing System' (IMOS) project. This data set was collected by the ANMN sub-facility 'National Reference Systems' (NRS).

'Australian National Moorings Network' (ANMN) is a facility of the Australian 'Integrated Marine Observing System' (IMOS) project. This data set was collected by the ANMN sub-facility 'National Reference Systems' (NRS).

'Australian National Moorings Network' (ANMN) is a facility of the Australian 'Integrated Marine Observing System' (IMOS) project. This data set was collected by the ANMN sub-facility 'National Reference Systems' (NRS).

R scripts and data files used to process, analyse and visualise eReefs catchment counter-factual scenario model data for the paper, "Kroon, Frederieke J., Joseph R. Crosswell, and Barbara J. Robson. The effect of catchment load reductions on water quality in the crown-of-thorn starfish outbreak initiation zone. Marine Pollution Bulletin 195 (2023): 115255." Four R scripts are included: cots1.R extracts all data from the eReefs model scenario outputs and produces an R data file for each scenario. These intermediate data files are not provided but can be re-created using this script and the original eReefs model data. cots_reprocess.R puts all six scenarios into one combined dataframe and produces daily_values_all_scenarios3.rda or daily_values_all_scenarios3_large.rda, depending on settings. These intermediate data files are not provided. ccip_salinity.R extracts salinity from the baseline scenario and adds it to the dataframe for all scenarios, producing daily_values_all_scenarios4.rda or daily_values_all_scenarios4_large.rda, depending on settings. These final data files are provided. cots_analysis.R produces the figures and tables used in the manuscript. Data used come from eReefs model counter-factual scenarios produced by CSIRO and available from https://dapds00.nci.org.au/thredds/catalogs/fx3/catalog.html

This metadata record describes chlorophyll fluorescence and turbidity time-series data collected through in situ monitoring by the Great Barrier Reef Marine Monitoring Program for Inshore Water Quality (MMP WQ). A full description of the MMP WQ and its associated datasets can be found in the parent metadata record linked above. Continuous in situ chlorophyll fluorescence and turbidity were measured using WET Labs ECO FLNTUSB Combination Fluorometer and Turbidity Sensors. The MMP WQ currently has instruments deployed at 19 sites summarised by Natural Resource Management (NRM) region below. The date ranges of instrument deployments are also shown; some sites were discontinued in 2014 but data are still available for download. Cape York NRM: Annan-Endeavour focus region: Forrester Reef (2020-present), Dawson Reef (2020-present) Wet Tropics NRM: Barron-Daintree focus region: Snapper Island North (2007-2014) Russell-Mulgrave focus region: Fitzroy Island West (2007-present), High Island West (2007-present), Russell-Mulgrave River mooring (2015-present), Frankland West (2007-present) Tully focus region: Dunk Island North (2007-present), Tully River mooring (2015-present) Burdekin NRM: Pelorus (2007-present), Pandora (2007-present), Geoffrey Bay (2007-present), Burdekin River mooring (2015-present) Mackay Whitsunday NRM: Double Cone Island (2007-present), Daydream Island (2007-2014), Pine Island (2007-present), Seaforth Island (2015-present), Repulse Island dive mooring (2015-2021), O'Connell River mooring (2021-present) Fitzroy NRM (monitored 2005-2014 under MMP WQ, 2020-present under Fitzroy Basin program): Pelican Island (2007-2015), Humpy Island (2007-2015, 2021-present), Barren Island (2007-2015, 2021-present), Fitzroy River mouth (2021-present). Instruments are deployed for approximately 4 months at a time at 5 m below the water's surface. They collect one sample every 10 minutes, where each data point is calculated as the mean of 50 instantaneous burst readings. Pre- and post-deployment checks of each instrument include measurements of the maximum fluorescence response and the dark count (instrument response with no external fluorescence, essentially the ‘zero’ point). Factory servicing and calibration checks are performed at the WET Labs facility in the USA after 12-18 months of in-water deployment time. After retrieval, the instruments are cleaned and data downloaded and converted from raw instrumental records into measurement units (µg L-1 for chlorophyll fluorescence and NTU for turbidity) according to the standard procedures of the manufacturer. Deployment information and all raw and converted instrumental records are stored in an Oracle-based data management system developed by AIMS. Detailed procedures for data handling can be found the MMP WQ's QA/QC Reports (see link below in Related Information). Instrument data are validated against concurrently-collected water samples. Water samples for analyses of chlorophyll a and total suspended solids are collected three times per year to calibrate logger fluorescence and turbidity to in situ conditions. Diver-operated Niskin bottles are used to sample close to the moored loggers and samples are preserved and analysed in the same manner as ship-based water samples (see link below in Related Information). Instruments in the Cape York region are deployed at 3 m below the surface and have different processing and servicing procedures than other regions. These procedures are detailed in the files containing instrument data, linked below. Instrument data can be downloaded in hourly or daily averaged formats (see links below in Data Downloads).

The chlorophyll monitoring under the Reef Plan Marine Monitoring Programme (Reef Plan MMP) is an extension from the Long-term Chlorophyll Monitoring Program, which was initiated by the Great Barrier Reef Marine Park Authority (GBRMPA) in December 1992 as a long-term water quality monitoring program. The chlorophyll monitoring has been managed by the Australian Institute of Marine Science since 1999 and is an important part of the AIMS water quality research and monitoring activities. Since 2005, the Chlorophyll Monitoring is a component of the Reef Plan Marine Monitoring Program, a responsibility of the GBRMPA under the Reef Water Quality Protection Plan. Sample analysis and data management has been undertaken by AIMS. The Great Barrier Reef (GBR) is the largest contiguous coral reef ecosystem in the world. The biological productivity of the GBR is supported by nutrients (e.g. nitrogen, phosphorus, silicate, iron) supplied from a number of sources, including upwelling from the Coral Sea, rainwater, nitrogen fixation by cyanobacteria and runoff from the adjacent catchment. Freshwater runoff is the largest source of new nitrogen to the GBR, however, the nutrients used by GBR marine primary producers (phytoplankton, benthic algae, seagrasses and mangroves) come predominantly from recycling of nutrients already in the system. Water quality is one of the most important factors determining the long-term health of the Great Barrier Reef (GBR). Increased nutrient availability, for example from human activity (e.g. agricultural runoff, soil erosion, discharges of sewage and aquaculture waste) usually leads to an increase in chlorophyll concentrations in coastal waters because of increased phytoplankton biomass. Phytoplankton can rapidly deplete nutrients to levels which would be difficult to sample and analyse directly. Concentrations of the plant pigment chlorophyll a (occurs in all marine phytoplankton) are a useful proxy indicator of the amount of nutrients incorporated into phytoplankton biomass. Chlorophyll a is today the most commonly used parameter for the monitoring of phytoplankton biomass and nutrient status, as an index of water quality. The data can be downloaded Data have been used for the e-Atlas: http://e-atlas.org.au/content/water-column-chlorophyll

This research monitored inshore island fringing reef communities, including fish and benthos, for over 20 years in the Palm, Magnetic, Whitsunday and Keppel Island groups, to better understand the effects of marine park zoning on these reefs. It is the only large-scale, long-term dataset on the inshore Great Barrier Reef that includes fish assemblages as well as benthic communities. The data were initially collected to inform the Great Barrier Reef Marine Park Authority about the effects of no-take (green) zones on fisheries target species, along with other fish species and benthic assemblages. The monitoring began in 1999 in the Whitsundays, subsequent years in other island groups, and ended in 2019. Elements were added as the surveys progressed, and the entire fish assemblage captured in this analysis was surveyed from 2007 onwards. The surveys were conducted by SCUBA divers using underwater visual survey for fish and point intercept transects for benthos, with five 50m transects at each site. We are analysing this dataset using boosted regression tree models that test the influence of different predictor variables on the fish assemblage.

The activity of aminoacyl-tRNA synthetase (AARS), an index of growth rate, and of the electron transport system (ETS), an index of respiration, was measured in three size fractions (73-150 µm, >150 µm and >350 µm) of zooplankton during five cruises to tropical coastal waters of the Kimberley coast (North West Australia) and four cruises to waters of the Great Barrier Reef (GBR, North East Australia). Temperature, salinity and chlorophyll a data was also recorded. Data enables comparison of growth and secondary production of tropical zooplankton from waters of NW and NE Australia based on both AARS and ETS measurements, and also facilitates comparison of zooplankton respiration derived from ETS measurements. These estimates of growth and respiration enable calculation of grazing rates to better understand the fate of primary production in Australian tropical waters and the nature of pelagic food chains in these regions.

This dataset comprises of microbial metagenomics sequencing reads of seawater collected across 48 reef sites across the Great Barrier Reef. Samples were collected across four Long Term Monitoring Program (LTMP) field trips between November 2019-July 2020, combining water chemistry data, LTMP field surveys and microbial metagenomics data. This data collection was a major part of the QRCIF IMOS GBR microbial genomic database project, which aims to generate a comprehensive open access repositor of microbial genomic data from across the region. Seawater was collected in quadruplicate either by SCUBA or using Niskin Bottles at each reef site, 5L of seawater was pre-filtered using a 5µm filter and applied to a 0.22µm sterivex filter, snap frozen and stored at -20°C in preparation of DNA extraction. DNA was extracted from sterivex filters using phenol:chloroform:Iso-amyl alcolol extraction, ethanol precipitation and cleanup using the Zymo Clean and Concentrator® kit before submission for sequencing at the Australian Centre for Ecogenomics sequencing facility, Illumina. The data presented as illumina paired-end shotgun metagenomics sequencing runs, in fastq format, generated by Microba Life Sciences, Brisbane, QLD, Australia. Each downloadable archive contains forward and reverse reads for all replicate sampling performed at that particular site. Water quality particulate and dissolved nutrient data was generated as previously described (https://doi.org/10.25845/5c09b551f315b) from water samples collected simultaneously at each reef site. Zip files are available through the spatial layer under each site's 'illumina.seawater.zip' - please note these are large downloads (between 6 - 14 GB).

This metadata record describes vertical profile data from Conductivity Temperature and Depth (CTD) profilers collected through in situ monitoring by the Great Barrier Reef Marine Monitoring Program for Inshore Water Quality (MMP WQ). A full description of the MMP WQ and its associated datasets can be found in the parent metadata record linked above. Sea-Bird Electronics CTD profilers are used for vertical casts and are typically fitted with additional sensors to measure parameters such as fluorescence (a proxy for chlorophyll a concentration), turbidity, beam attenuation, dissolved oxygen concentration, and photosynthetically active radiation (downwelling light) sensors. Instrument models SBE 19plus and SBE 19plusV2 are used currently, while older records include data from SBE 25, SBE 25plus, and SBE 9plus instrument models. Annual calibrations of profilers are carried out in Sea-Bird Electronics laboratories in the USA. These calibration values are included within the instrument configuration file. Pre-trip CTD checks are carried out before each field trip, which include checking the physical status of the sensors and cables and battery voltage. Prior to conducting a cast, the CTD is secured to the hydrographic wire, tubing is removed to allow flush water to drain from the conductivity-temperature cell, and any protective caps are removed from the other sensors. The CTD is lowered into the water sitting ~3 m below the surface, and a three minute "soak" allows sensors to equilibrate and air bubbles to be flushed by the pump. The CTD is then raised to ~0.2 below the surface and the profile is commenced at a rate of 0.5 – 1 m s-1. The CTD is sent to near-bottom, ensuring it does not touch the seafloor, and retrieved to the surface. Casts are done on the sunny side of the boat to avoid the boat's shadow interfering with the measured light profiles. Data processing is conducted using Sea-Bird proprietary software and includes: conversion of raw instrumental records to measurement units, alignment, removal of ship roll, outlier removal, and bin averaging the down-cast at 1 m increments. Detailed procedures for data handling can be found in the MMP WQ's QA/QC Reports (see link below under Related Information). CTD data can be downloaded from the Australian Ocean Data Network THREDDS Data Server in netCDF or csv format (see link below under Data Downloads). Water chemistry measurements taken at the time of each CTD cast can be retrieved from the MMP WQ physico-chemical and nutrient database (see parent metadata record above). Water quality data are collected in conjunction with the Great Barrier Reef Marine Monitoring Program for Inshore Coral Reefs (see link below under Related Information). AIMS' full database of CTD profiles from all around northern Australia can be found attached to a separate metadata record (see link below under Related Information).