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.

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.

Two trips were made to the north-western Australian shelf atolls to identify the hermatypic corals occurring on these reefs. In July, 1982 the Rowley Shoals were were visited and sites on two of the three main reefs (Mermaid Reef and Clerke Reef) were surveyed. In September 1984, the three main reefs of the Scott Reef complex (North Reef, South Reef and Sandy Islet) and nearby Seringapatam Reef were surveyed.Sites were selected to encompass the range of habitats available. Habitats included reef flat zones, lagoonal habitats (pinnacles and soft substrates) and outer slopes with differing exposures to wave action. The number of sites visited at each reef were: Mermaid Reef (2), Clerke Reef (16), North Reef (11), South Reef (5), Sandy Islet (5) and Seringapatam Reef (2). Surveys were primarily undertaken using SCUBA, which was supplemented by snorkelling and reef walking. Corals were initially identified in situ. If further investigation was required, samples were collected and sent to the Australian Institute of Marine Science. The purpose of this research was to compile an accumulative species inventory, with the aim of reaching a complete list for each reef. The hermatypic coral surveys were a component of a survey of the fauna of the north-western Australian shelf atolls conducted by the Western Australian Museum.

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

In 6 sectors of the Great Barrier Reef (Cooktown/Lizard island, Cairns, Townsville, Whitsunday, Swain and Capricorn Bunker) 49 of the key manta tow reefs are designated 'core' survey reefs and are also surveyed using the scuba search technique. Where possible, three or more reefs in each sector have been selected in each of three positions across the continental shelf: inshore, mid-shelf and outer shelf. Results of scuba searches for juvenile Crown-of-Thorns Starfish (COTS), Acanthaster cf. solaris, and the mollusc Drupella. Observations have been obtained since October 1989 and are ongoing. Data includes counts of COTS and Drupella, coral feeding scars caused by COTS and Drupella, and the outbreaking status of COTS and Drupella. Also recorded are the percentage of bleached coral and the number of corals affected by disease. Diseases identified are: white syndrome, black band, skeletal eroding band and brown band. Any scar of unknown origin is also recorded. Information is also recorded about the reef environment of each survey (e.g. reef slope, substratum at reef base) and its benthic community (dominant benthic group, dominant hard coral, dominant coral life form). To facilitate causes of coral mortality including juvenile and adult Crown-of-Thorns Starfish (COTS), Acanthaster cf. solaris, and the mollusc Drupella. To assess the amount of coral bleaching and disease. Bleaching is recorded as a percentage of the total hard coral cover: 0=absent, 0+ = individual colonies, -1= 1-5%, +1= 6-10%, 2=11-30%, 3=31-50%, 4 =51-75%, 5=76-100%

The Rowley Shoals, Scott Reef and nearby Seringapatam Reef form a series of large emergent shelf atolls arising from depth of between 300 and 700m along the edge of the broad continental shelf about 260km from mainland north-western Australia. The Rowley Shoals have been described as morphologically the most perfect examples of shelf atolls in Australian waters and appear to represent three distinct stages of atoll formation. Experiencing oceanic water conditions, but with a semi-diurnal tidal range of at least 4.5m, these atolls exhibit an unusual, If not unique, combination of physical environmental and geomorphological characteristics. These are described as a background to the faunal inventories presented in subsequent parts of this publication

Diver Based Sampling (LTM) ROV BRUVS Grab Samples A biological survey expedition to Scott Reef in December 1999 providing information on the benthic and demersal fish communities found in the deeper areas of South Scott Reef lagoon and benthic communities in North Scott Reef lagoon.

Long-term changes in benthic communities and habitat conditions were studied at Rowley Shoals and Scott reef systems. This collection includes data from surveys from the Long-Term Monitoring (LTM) programs at Scott Reef (from 1994) and Rowley shoals (from 1995) which are conducted usually every 1–2 years (<4 years), in addition to heat stress habitat surveys in 2016. Each LTM location contains three replicate sites, separated by 300 m, consisting of five permanently marked 50-m transects, laid end to end and separated by 10 m. Images of the benthic community were captured at a distance of 30–50 cm from the substratum, along 1m intervals. Each image was analysed by identifying the benthic group under each of five fixed points to the lowest taxonomic resolution (Jonker et al., 2008). Additional monitoring locations were established in 2016 to assess the effects of predicted heat stress. Sites were established at the reef crest and lagoon at each location, consisting of six permanently marked 20-m transects, laid end to end and separated by 10 m. Surveys were conducted before (January) and during (April) the time of peak heat stress in 2016, and in October 2016 at Scott Reef and October 2017 at Rowley Shoals to quantify associated reductions in coral cover. Spatial and temporal variation in reef slope communities were compared using multivariate analyses, as well as analysis of environmental parameters. For full details see Gilmour et al., (2022).

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.

Annual Benthic monitoring of six reefs within Southern Inshore Reporting Zone for the Mackay Whitsunday Isaac Regional Report Card Data utilise the same sampling methods as the Marine Monitoring Program: Photopoint intercept for benthic cover, counts of juvenile corals in belt transects and scuba searchs in belt transects for vectors of coral mortality. At each Pine Peak Island, Pine Islets, Connor Island and Henderson Island, five 20m long transects are monitored at each of two sites and at 2m and 5m depth below lowest astronomic tide. At Aquila Island and Temple Island transects are at 1 to 2m depth only. Note: Monitoring of Connor Island ceased in 2021 due to visibility and logistic constraints.