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AIMS-LTMP and MMP Coral Reef Monitoring Modelled Output
The Australian Institute of Marine Science (AIMS) has been running coral reef monitoring programs since the 1980s, including both the Long-Term Monitoring Program (LTMP) and Marine Monitoring Program (MMP). These monitoring programs are designed to detect changes in coral reef communities at a sub-regional scale. Within this context, a subregion consists of inshore, mid-shelf, and outer shelf reefs across the continental shelf within one band of latitude (considered a sector). Data are modelled for presentation on the AIMS Reef Reporting Dashboard https://apps.aims.gov.au/reef-monitoring/reefs. The Reef Monitoring Reporting (MonRep) platform displays modelled data collected by AIMS' Long-Term Monitoring Program and Marine Monitoring Program at reef level, latitudinal Sector or Natural Resource Management (NRM)-region level in the Reef Monitoring Tool. How the data has been modelled for each graph is explained below for each data type. Benthic community cover Reef-level photo transect data. Bayesian hierarchical models (INLA) to model the benthos over time. Specifically, for each major benthic group (live hard coral, algae and soft corals) a model containing the population-level effects of year crossed with major taxonomic groups and the varying effects of transects nested within sites were fit to binomial photo point counts. NRM-region/Sector photo transect data. Bayesian hierarchical models (INLA) to model the benthos over time. Specifically, for each NRM region/Sector and major benthic group (live hard coral, macroalgae and soft corals) a model containing the population-level effects of year and the varying effects of depth and transects nested within sites nested within reefs were fit to binomial photo point counts. Manta tow surveys Reef-level manta-tow data. Bayesian hierarchical models (INLA) to model the benthos over time. Specifically, for each major benthic group (live hard coral and soft corals) a model containing the population-level effects of year and the varying effects of tows were fit against a beta distribution to percentage cover data. For NRM region//Sector level manta-tow data. Bayesian hierarchical models (INLA) to model the benthos over time. Specifically, for each NRM region/Sector major benthic group (live hard coral and soft corals) a model containing the population-level effects of year and the varying effects of tows nested within reef were fit against a beta distribution to percentage cover data. Juvenile hard corals Reef-level data Bayesian hierarchical models (INLA) were used to model the juvenile coral abundances (counts) over time. Specifically, a model containing the population-level effects of year and the varying effects of sites were fit against a zero-inflated negative binomial and also included a (log-transformed) offset for available substrate. NRM region/Sector level data Bayesian hierarchical models (INLA) were used to model the juvenile coral abundances (counts) over time. Specifically, for each NRM region/Sector a model containing the population-level effects of year and the varying effects of sites nested within reefs were fit against a zero-inflated negative binomial and also included a (log-transformed) offset for available substrate. Reef fish Reef-level data Bayesian hierarchical models (INLA) to model the fish abundances (counts) over time. Specifically, for each major fish group (Harvested, Herbivores, Coral Trout, Large fishes and Small fishes) a model containing the population-level effects of year and the varying effects of transects nested within sites were fit against zero-inflated negative binomials. NRM region/Sector level data Bayesian hierarchical models (INLA) to model the fish abundances (counts) over time. Specifically, for each NRM region/Sector and for each major fish group (Harvested, Herbivores, Coral Trout, Large fishes and Small fishes) a model containing the population-level effects of year and the varying effects of transects nested within sites nested
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AIMS Long-term Monitoring Program
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The AIMS Long-term Monitoring Program (LTMP) is designed to detect changes in reef communities at a subregional scale. In this context, a subregion encompasses inshore, mid-shelf and outer shelf reefs across the continental shelf within one band of latitude (a sector).Reef surveys involve three approaches:1. broadscale manta tow surveys of crown-of-thorns starfish populations and reef-wide coral cover2. Intensive photographic surveys of stationary seafloor (benthic) organisms on fixed transects3. intensive visual counts of reef fish, juvenile corals, crown-of-thorns starfish, coral-eating snails and coral disease and bleaching.
AIMS Long-term Monitoring Program Reef Aesthetics
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Data on the general appearance and condition of coral reefs which have been manta towed in the Long Term Monitoring Project (LTMP). The data from 4 reef zones - front (seaward) and back (leeward), and north and south (flanks 1 and 2) - are used to create a web page on each zone for each reef (http://apps.aims.gov.au/reef-monitoring/). The general condition of the reef is recorded, along with its structural complexity (1 and 2), the percentage of live and bleached coral, the dominant benthic lifeform, and dominant hard coral cover and genus. The general abundance of reef fish and giant clams (Tridacna gigas) is also recorded. To provide a broad overview of the reef environment. Coral Reef - Zone, Lifeform - Benthic, Relative Frequency, Genus. May include some information on coral disease.
Scott Reef, Seringapatam and Rowley Shoals LTM 2017, WESTERN AUSTRALIA (WEL)
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The coral and communities at the AIMS Long Term Monitoring (LTM) sites at Scott Reef, Seringapatam and Rowley Shoals were re-surveyed, following periodic surveys since 1994. In addition to the Proposed Field Program, the following work was completed: Benthic LTM surveys at three additional sites at Scott Reef. Coral species diversity surveys at four additional sites at Scott Reef. Benthic LTM surveys of coral communities at 13 sites in the deep lagoon (20-60m) at South Reef using ROV. Colony size-frequency surveys at six sites at Scott Reef. Genetic samples of surviving Seriatopora hystrix from 7 sites at Scott Reef. Additional temperature loggers and current metres deployed at Rowley Shoals. Video and photographic documentation of the Rowley Shoals, in water and from air using drones This project is a co-investment between Woodside Energy Ltd (WEL) and AIMS, in order to build scientific knowledge at Scott Reef, Seringapatam and Rowley Shoals and was undertaken between 4th – 25th November 2017.
AIMS Long-term Monitoring Program Water Quality Data 1990-1996 (Great Barrier Reef)
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Water Quality Data from the AIMS Long Term Monitoring Program. Water and sediments (another dataset) were sampled at the same sites adjacent to all 52 reefs where fish and benthic transects are conducted. Sampling occurs in open water within 500 metres of the reef, on both sides (north and south flanks) of the reef. Sampled reefs occur throughout the Great Barrier Reef, and the reefs of the North West coast of Australia. To track change. Data recorded includes temperature, salinity, Secchi depth, suspended solids, silicates, ammonium, nitrite, dissolved nitrogen (organic, inorganic and total), dissolved phosphorus (organic, inorganic and total), chlorophyll-a and phaetophytin pigments. Observations commenced in August 1990 and ceased in 1996.
Commonwealth of the Northern Mariana Islands (CNMI) long-term coral reef monitoring from 2011-10-01 to 2014-09-30 (NCEI Accession 0129268)
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Currently, the LTMMP has ~50 long-term monitoring sites across Saipan, Tinian, and Rota that are surveyed on a rotating biennial basis. Three main habitat types are covered: Fore reef, reef flat (lagoon), and seagrass beds (lagoon). Most sites have been selected based on their association with management concerns (runoff, sewage outfalls, urban development, etc.) and/or management actions (watershed restorations efforts, marine protected areas, etc.) and include impacted sites and relatively non-impacted reference sites. In general, monitoring surveys are conducted using standard and proven ecological field survey methods. All surveys are conducted along 3-5, 50 m transect lines laid out along the depth contour (~9m depth) on the fore reef, or along consistent habitat in the lagoon (back reef and seagrass). While benthic cover analysis provides the foundation of the CNMI monitoring program, the current protocol uses several survey types per site to provide ecological depth beyond percent cover. Fore Reef Photos are taken every meter along each transect line using a 0.25m2 quadrat frame, for a total of 250 photos at each site. In the office, the computer program CPCe is used to place five random points on each photo and the biota or substrate type under each point is identified. Organisms are identified to the genus level. This analysis provides benthic percent cover and community diversity. Twelve, 3 minute, 5 m radius stationary point counts (SPC) are conducted at each site to evaluate fish assemblages. Each SPC is systematically positioned throughout the length of a site (250 m). The species and size (fork length) of all food fishes within the 5 meter radius are recorded. This provides relative diversity, abundances, species compositions, size class distribution, and biomass of the fish community. Sixteen 0.25m2 quadrats are haphazardly tossed along the length of the site and every coral colony within the quadrats is identified to the species level and measured. This method provides relative diversity, abundances, species composition, and size class of the coral community. Within these same quadrats, all algae species present are identified to the species level to provide a measure of algae community composition and species richness. Finally, non-coral macro-invertebrates including sea cucumbers, urchins, crown-of-thorns starfish, giant clams, among others, are identified and counted within 1 m of each side of the transect lines (i.e., 5, 2mx50m belt transects). This provides invertebrate abundances, species composition, and diversity. Saipan Lagoon Saipan Lagoon habitats that are monitored include Halodule uninervis beds, staghorn Acropora thickets, and mixed coral back reefs. At lagoon sites, benthic cover is quantified using a 0.25 m2 string quadrat with six intersections, placed every meter along the transect line. The biota or substrate under each intersection is recorded to the genus level, in situ. Additionally, 10, 1 m2 quads are haphazardly placed across the length of the site (250 m) and all seagrass, algae, coral, and macro-invertebrates are identified to the species level and recorded. This method captures the relative diversity, abundance, and species compositions of lagoon communities. Finally, non-coral macro-invertebrate abundances and diversity are quantified as described above for reef slope sites.
AIMS Long-term Monitoring Program: Visual Census Fish Data (Great Barrier Reef)
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70 selected reefs throughout the Great Barrier Reef (GBR) are sampled in the AIMS Long-term Monitoring Project (LTMP). Underwater visual census is used to survey reef fishes on fixed transects (3 sites per reef, 5 x 50 m transects per site). The abundance and length of all diurnally active, non-cryptic fishes are recorded. A full list of species observed each year can be obtained on request. The overarching goal of LTMP fish surveys are to detect changes in reef fish communities over time at a regional scale, but also to examine the effectiveness of Marine Protected Areas. All fish species counted are largely non-cryptic, easily identified underwater and include both commercial and non-commercial taxa. Because surveys span the annual recruitment season, 0+ individuals are excluded from counts: these are distinguished from adults by their small size and often distinctive colouration. Abundance data for each fish species is subsequently summed over the five transects at each site on each reef to provide reasonable sample sizes for analysis and interpretation. Updated results of surveys can be found at: https://apps.aims.gov.au/reef-monitoring/reefs A subset of the data has been provided to the Ocean Biogeographic Information System (OBIS, http://www.iobis.org/explore/#/dataset/3936). Data have been used for the e-Atlas: http://eatlas.org.au/data/uuid/05bde62a-70ec-407b-b999-30cf369498af
Rowley Shoals Environmental Survey 2013, WESTERN AUSTRALIA (WEL)
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The coral and fish communities at the AIMS Long Term Monitoring (LTM) sites at Mermaid, Clerke and Imperiuse reefs were re-surveyed, following periodic surveys since 1994. To inform the design of future monitoring programs, communities at different habitats at the Rowley Shoals were surveyed at Clerke and Mermaid Reefs. In particular, coral and fish communities were surveyed at the reef slope in 9m, 6m, 3m and reef flat habitats, and at the base and top of three replicate bombies within the lagoon and false lagoon (Clerke Reef only). Additionally, Baited Remote Underwater Videos (BRUVS - single)) were deployed at the reef slope at 9m and 3m, and at the bombie habitats within the lagoon, to investigate their use as a remote monitoring method for certain fish and shark populations. Several coral species were also sampled opportunistically to investigate whether their participation in the predicted mass spawning at the end of October differs from that documented previously at Scott Reef, and samples of the dominant brooding coral Isopora brueggemanni were collected to add existing samples of several species from Scott Reef and the Rowley Shoals for genetic analyses, when funding becomes available. This project is a co-investment between Woodside Petroleum Limited (WEL) and AIMS, in order to build scientific knowledge at the Rowley Shoals and was undertaken between 11th October - 2 December 2013.
AIMS Sea Water Temperature Observing System (AIMS Temperature Logger Program)
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The data provided here are from a number of sea water temperature monitoring programs conducted in tropical and subtropical coral reefs environments around Australia. Data are available from approximately 80 GBR sites, 16 Coral Sea sites, 7 sites in North West Western Australia (WA), 8 Queensland regional ports, 13 sites in the Solitary Islands, 4 sites in PNG and 10 sites in the Cocos (Keeling) Islands. Data are obtained from in-situ data loggers deployed on the reef. Temperature instruments sample water temperatures every 5-10 minutes (typically) and are exchanged and downloaded approximately every 12 months. Temperature loggers on the reef-flat are generally placed just below Lowest Astronomical Tide level. Reef-slope (or where specified as Upper reef-slope) generally refers to depths 5 - 9 m while Deep reef-slope refers to depths of ~20 m. Reefs are under threat from climate change. Elevated sea temperature is a major stress to reefs, capable of causing widespread coral bleaching and mortality. Small excursions of temperature outside normal summer levels can cause stress and bleaching in corals, especially sensitive species. Temperature data from this program are used to correlate with bleaching events and derive local bleaching thresholds. Data are also used in a wide variety of other marine research programs, including fisheries, balast water, turtles, sea birds, seagrass, coral disease, oceanography, process studies, validation of proxy climate records etc. Download via the AODN Portal is currently unavailable, access through programming links below or the AIMS Time Series Explorer - https://apps.aims.gov.au/ts-explorer/
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