'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).

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).

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

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.

Data from two missions of the Liquid Robotics SV3 Wave Glider, the first mission in the central GBR from the 19th to the 26th of September 2017 and the second around Browse Island in Western Australia from the 30th of November to the 5th of December 2017. Both missions had the same sensors on the Wave Glider including: Seabird CTD + DO sensor (temp + salinity + DO) Teledyne Workhorse Monitor 600kHz ADCP (currents, waves) Turner C3 Fluorometer (algae, hydro-carbons) AirMar 200WX weather Station without humidity (weather) Datawell MOSE-G1000 GPS motion sensor (waves) The GBR deployment was from the R.V. Cape Ferguson and completed transects in the central GBR matrix including observatons beside the DISITI Wave Rider Buoy off Cape Cleveland and the Yongala NRS. The objective of the mission was to test teh glider in shelf applications near reefs and to test the ability of the platform to collect data equivalent to the Wave-Ride and Yongala moorings. The WA deployment was from the R.V. Solander and did surveys around Browse Island then undertook a transect to Echuca Shoals where it did a number of transects across the shoals before returning to Browse Island. The main objective was to test the utility of the platform in conditions on the North-West shelf including a period with tides over 5m in range. Wave data from the Prelude platform was also obtained for comparison.

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).