To support a long-term NOAA Coral Reef Conservation Program (CRCP) for sustainable management and conservation of coral reef ecosystems, from 20110407 to 20110509, reef fish assessment surveys were conducted, as a part of Rapid Ecological Assessments (REA), during the Pacific Reef Assessment and Monitoring Program (RAMP) Cruise HA1101 in the Marianas region by the Coral Reef Ecosystem Division (CRED) at the NOAA Pacific Islands Fisheries Science Center (PIFSC). During the cruise, 5 REA sites were surveyed at Alamagan in the Marianas region. At each REA site, fish biologists entered the water and conducted a fine-scale (~700 m^2) and high degree of taxonomic resolution REA survey to assess and monitor species diversity, size distribution, and abundance of fish in shallow-water hard-bottom (less than 30 m) habitats. Reef fish assessment surveys were focused on cataloging the diversity (species richness), abundance (numeric density) and biomass (fish mass per unit area) of diurnally active reef fish assemblages. The stationary point count (SPC) method was used to quantify reef fish species. Two divers lay out a 30 m transect line, and position themselves at the 7.5 and 22.5 meter marks. The SPC biologist then records estimated size and abundance of all fish within a visually estimated 15-m diameter cylinder centered on the stationary diver (7.5-m radius, total area ~ 177m^2 per cylinder). The diver first spends 5 minutes identifying all fish species in the cylindrical area, then proceeds to count and estimate size (total length) for each in a series of "instantaneous" point counts or sweeps of the cylinder. Fish were identified at the species level, wherever possible. All reef-associated fish, including those in the water column, were surveyed. The survey time for each stationary point count survey was approximately 20 min and generally four stationary point count surveys (two per diver) were conducted at each fish REA site. After completing REA surveys, divers noted the presence, at the survey site, of any unusual fish species not counted during SPC counts, in order to facilitate species lists per location.

The distribution and abundance of soft coral genera on 14 reefs of the central Great Barrier Reef was investigated in relation to reef position, recent history of disturbance, wave exposure, substratum slope and depth. Eighty-five 25 m long transects were surveyed at 10 m depth on the windward sides of these mid- and outer-shelf reefs. At Davies Reef a further 75 transects in different zones were censused along contours at 5 m depth increments: windward side 5-30 m; leeward 5-25 m; north and south flanks 5-20 m; lagoon 5-15 m (deepest depths were at the base of the reef at each site). Transects were standardised by subtracting the proportion of sand and unconsolidated coral rubble.Percentage cover (of total consolidated reef substratum); abundance (number per linear meter); size frequency distribution of 11 benthos categories (massive, encrusting and branching forms of scleractinian corals; soft corals; turf and coralline algae; sponges; zoanthids; tunicates; macroalgae; Halimeda and 'other'); and 'space' were estimated. (Space was defined as the proportion of consolidated hard substrata covered by filamentous or coralline algae but not occupied by macro-invertebrates or macro-algae). Identity and size of 12,603 soft coral colonies growing in a 0.5 m wide strip along the transects was also recorded. Chord length (indicating colony or patch diameter) of turf algae (TA), coralline algae (CA), massive corals (CM), encrusting corals (CE), branching corals (CB), and soft corals (SC) was measured.Soft corals were identified to genus, and the longest and shortest diameters of each colony recorded. The two genera Nephthea/Stereonephthya, and Xenia/Heteroxenia, were each treated as one category, as not all colonies could be distinguished with certainty.Whether high densities of the crown-of-thorns starfish, Acanthaster planci, had been active (8 reefs) on each reef 5-10 years prior to the study, or not (6 reefs), was also recorded. To determine if there were differences in area cover and abundance of specific soft coral taxa between reefs that were and were not recently affected by Acanthaster planci.Differences in cover, abundance and colony sizes of the relatively fast-growing branching stony corals and the slower-growing massive and encrusting stony coral taxa, and in cover and abundance of several other common macro-benthos groups (sponges, zoanthidae, tunicates, macroalgae, and Halimeda) were also assessed.To assess the potential effect of some abiotic parameters (current and wave exposure, substratum angle, and water depth), as well as of space competition with hard corals, on cover and abundance of common soft coral taxa. Soft coral species: Alcyoniidae (Alcyonium, Cladiella, Lobophytum, Parerythropodium, Sarcophyton, Sinularia); Xeniidae (Anthelia, Cespitularia, Efflatounaria, Heteroxenia, Sympodium, Xenia); Nephtheidae (Capnella, Dendronephthya, Lemnalia, Nephthea, Paralemnalia, Stereonephthya); Asterospiculariidae (Asterospicularia); Briareidae (Briareum); Isididae (Isis); Gorgoniidae (Rumphella, Pinnigorgia flava); Clavulariidae (Clavularia); Other genera.Reefs were: Outer-shelf (18-025, Bowl, Chicken, Coil, Dip, Fork, Needle); Mid-shelf (Brewer, Centipede, Davies, Faraday, Grub, Rib, Yankee); affected by Acanthaster planci (18-025, Brewer, Dip, Fork, Grub, Needle, Rib, Yankee).

Acropora cervicornis fragments of each genotype were evenly and haphazardly assigned to two nutrient treatments: ambient nutrients (Ambient) or elevated ammonium (NH4). Each nutrient treatment was replicated in four independent tanks (n = 3 fragments per genotype per tank). For ~1.5 months (47 d), Ambient tanks were maintained under nutrient levels consistent with the values in Virginia Key, FL, while elevated NH4 tanks were dosed with NH4Cl [3 mM] every 15 minutes using peristaltic pumps. The initial NH4 dose volume was 10 mL of the stock solution, targeting a ~10 μM increase in NH4 concentration. These values were calculated to account for the dilution of the nutrients resulting from adding new ambient seawater to the tanks (200 mL/min in a total tank volume of 180 L). After detecting higher than normal NH4 concentrations in the incoming seawater from Biscayne Bay, the NH4 dose volume was lowered to 5 mL of the stock solution, targeting ~5 μM NH4 increase above ambient values. The fragments were also assigned to disease vs. placebo treatments, the disease treatments involving exposure to homogenates of corals showing signs of white band disease following the protocol found in Rosales & Palacio-Castro (2024). Water samples (~40 mL) were collected to monitor NH4 levels in the treatments and immediately refrigerated at 4C. The elevated NH4 tanks were sampled daily, but the Ambient tanks were sampled less frequently (~2-3 days and no samples were collected during weeks 1 and 3 of the experiment). Nutrient concentrations were measured at NOAA-AOML using an AA3 nutrient analyzer (Seal Analytical, Southampton, UK). The instrument was calibrated before each run using standard solutions and procedures. Initially, only NH4 was monitored, but after high NH4 concentrations in the source seawater were detected, additional measurements of PO4 were included.

To support a long-term NOAA Coral Reef Conservation Program (CRCP) for sustainable management and conservation of coral reef ecosystems, from 20110407 to 20110509, reef fish assessment surveys were conducted, as a part of Rapid Ecological Assessments (REA), during the Pacific Reef Assessment and Monitoring Program (RAMP) Cruise HA1101 in the Marianas region by the Coral Reef Ecosystem Division (CRED) at the NOAA Pacific Islands Fisheries Science Center (PIFSC). During the cruise, 20 REA sites were surveyed at Asuncion in the Marianas region. At each REA site, fish biologists entered the water and conducted a fine-scale (~700 m^2) and high degree of taxonomic resolution REA survey to assess and monitor species diversity, size distribution, and abundance of fish in shallow-water hard-bottom (less than 30 m) habitats. Reef fish assessment surveys were focused on cataloging the diversity (species richness), abundance (numeric density) and biomass (fish mass per unit area) of diurnally active reef fish assemblages. The stationary point count (SPC) method was used to quantify reef fish species. Two divers lay out a 30 m transect line, and position themselves at the 7.5 and 22.5 meter marks. The SPC biologist then records estimated size and abundance of all fish within a visually estimated 15-m diameter cylinder centered on the stationary diver (7.5-m radius, total area ~ 177m^2 per cylinder). The diver first spends 5 minutes identifying all fish species in the cylindrical area, then proceeds to count and estimate size (total length) for each in a series of "instantaneous" point counts or sweeps of the cylinder. Fish were identified at the species level, wherever possible. All reef-associated fish, including those in the water column, were surveyed. The survey time for each stationary point count survey was approximately 20 min and generally four stationary point count surveys (two per diver) were conducted at each fish REA site. After completing REA surveys, divers noted the presence, at the survey site, of any unusual fish species not counted during SPC counts, in order to facilitate species lists per location.

To support a long-term NOAA Coral Reef Conservation Program (CRCP) for sustainable management and conservation of coral reef ecosystems, from 15 April - 7 May 2009, reef fish assessment surveys were conducted, as a part of Rapid Ecological Assessments (REA), during the Pacific Reef Assessment and Monitoring Program (RAMP) Cruise HI0903 in the Marianas Archipelago at biennial intervals by the Coral Reef Ecosystem Division (CRED) at the NOAA Pacific Islands Fisheries Science Center (PIFSC). During the cruise, 6 REA sites were surveyed at Alamagan Island in the Marianas Archipelago. At the specific REA sites, fish biologists along with coral biologists, algal biologists and marine invertebrate zoologist entered the water and conducted a fine-scale (~300 m2) and high degree of taxonomic resolution REA survey to assess and monitor species composition, abundance, percent cover, size distribution, diversity, and general health of fish, corals, macro-invertebrates, and algae in shallow-water (< 35 m) habitats. Reef fish assessment surveys were focused on cataloging the diversity (species richness), abundance (numeric density [# fish 100 m-2] and biomass density [kg 100 m-2]) of diurnally active reef fish assemblages. Three complementary noninvasive underwater survey methods were used, including belt-transect, stationary point count, and roving-diver surveys. For all methods, fish were identified at the species level, when possible, and assigned to a size bin ranging from 1 to 200 cm based on a visual estimate of total fish length. Belt-transect (BLT) surveys were used to quantify the entire diurnal fish community (all size classes). In belt-transect surveys, two fish biologists swam side-by-side along three consecutively-placed, 25m transect lines. The BLT team swam each transect two times. During the initial swim-out, each fish diver recorded all fish larger than 20 cm observed within a 4-m wide belt perpendicular to their respective side of the transect (200 m2 area per line, 100 m2 per diver). On the return swim, each fish diver recorded all fish less than 20 cm observed within a 2-m wide belt (100 m2 area per line, 50 m2 per diver). The survey of large fish took approximately 5 min to complete while the survey of smaller fish took about 10 min to complete. All reef-associated fish, including those in the water column (including planktivores), were counted. Any coastal pelagic species (e.g., clupeids [sardines], belonids [beakfish], antherinids [silversides]) seen near the surface were not recorded. The stationary point count (SPC) method were used to quantify larger, more mobile reef fish species that can be missed on belt-transect surveys. In stationary point count survey, a fish biologist swam approximately 15 m away from a transect line concurrently being surveyed by the other two BLT fish biologists. The SPC biologist then recorded all fish greater than 25 cm in length that passed within a visually estimated 20-m diameter cylinder centered on the diver's fixed position (10-m radius, total area = 314 m2). The survey time for each stationary point count survey was 5 min and a total of four stationary point count surveys were conducted at each REA site. Roving-diver surveys were followed belt-transect and stationary point count surveys. As diver bottom time permitted, the fish assessment team conducted random swim surveys throughout the REA site area, recording, to the species level or the lowest recognizable taxon, the presence of reef fish not encountered during previous methods.

One, 25-m line transect was surveyed at 50-cm intervals as part of the Rapid Ecological Assessment conducted at 3 sites at Laysan Island in the Northwestern Hawaiian Islands in September, 2004 from the NOAA vessel Hi'ialakai (HI04-01). Raw survey data included percent live coral cover. Following the line-interspect survey, a 6m-wide transect, placed along the previously laid 25-m line was examined for the prevalence of coral disease.

This research targets the Hawaii Coral Reef Initiative (HCRI) Priority Area A: Kahekili, Maui: Herbivore Fisheries Management Area (KHFMA). The project goal was to evaluate the efficacy of this new management action by developing a detailed algal production/herbivore consumption budget. The KHFMA was established in an effort to promote herbivore grazing and thus reverse the decline in coral cover on the reef through increased algal consumption. Because it may take several years for monitoring programs of fish and benthic communities to detect changes associated with the recent protection from fishing at KHFMA, additional data are needed to identify benchmarks of success. By developing a growth/consumption budget for the algal and herbivore communities at KHFMA, this will enable the determination how much algae is currently being grazed and how many more herbivores would be needed to actually begin controlling algal abundance at Kahekili. Observations of fish and urchin consumption of algae were made during 2010-2011 at KHFMA. Additional observations were made at Lanai Lighthouse, which is the SW corner of the island of Lanai and Canoe Beach, which is just south of KHFMA, in 2009. Laboratory experiments were conducted at the Maui Ocean Center in 2010-2011.

Coral health and disease assessments were conducted along 2 consecutively placed 25-m transects, as part of Rapid Ecological Assessments conducted at 5 sites at Tinian Island in the Marianas Archipelago during 12 May to 9 June 2007, aboard the NOAA Hi'ialakai Reef Assessment and Monitoring Program (RAMP) Cruise HI0702 and HI0703. Within an area of 1-3m on each side of both transect lines, each colony was inspected and every diseased/afflicted coral enumerated and identified to the lowest taxonomic level. For each affected coral the following information was recorded: colony size, type of affliction, area affected, percent live/dead, and severity of the affliction (mild = 1-10%, moderate = 11-25%, marked = 26-50%, severe = 51-75%, acute = 76-100%). Coral afflictions were classified into one of six general categories (following Willis et al., 2004) including: bleaching, tissue loss, black band disease, skeletal growth anomaly, predation, and other lesions. This latter category included algal overgrowth, as well as unidentified syndromes causing deterioration of scleractinian corals. Tissue samples of selected cases were procured for histopathological analyses. These data provide the basis for computing quantitative estimates of disease incidence and prevalence. Samples and photographs provide aid in further disease characterization and description. Histological tissue samples are traditionally fixed in a formaldehyde solution prior to preparation for processing and analysis.

To support a long-term NOAA Coral Reef Conservation Program (CRCP) for sustainable management and conservation of coral reef ecosystems, from 20110407 to 20110509, reef fish assessment surveys were conducted, as a part of Rapid Ecological Assessments (REA), during the Pacific Reef Assessment and Monitoring Program (RAMP) Cruise HA1101 in the Marianas region by the Coral Reef Ecosystem Division (CRED) at the NOAA Pacific Islands Fisheries Science Center (PIFSC). During the cruise, 19 REA sites were surveyed at Tinian in the Marianas region. At each REA site, fish biologists entered the water and conducted a fine-scale (~700 m^2) and high degree of taxonomic resolution REA survey to assess and monitor species diversity, size distribution, and abundance of fish in shallow-water hard-bottom (less than 30 m) habitats. Reef fish assessment surveys were focused on cataloging the diversity (species richness), abundance (numeric density) and biomass (fish mass per unit area) of diurnally active reef fish assemblages. The stationary point count (SPC) method was used to quantify reef fish species. Two divers lay out a 30 m transect line, and position themselves at the 7.5 and 22.5 meter marks. The SPC biologist then records estimated size and abundance of all fish within a visually estimated 15-m diameter cylinder centered on the stationary diver (7.5-m radius, total area ~ 177m^2 per cylinder). The diver first spends 5 minutes identifying all fish species in the cylindrical area, then proceeds to count and estimate size (total length) for each in a series of "instantaneous" point counts or sweeps of the cylinder. Fish were identified at the species level, wherever possible. All reef-associated fish, including those in the water column, were surveyed. The survey time for each stationary point count survey was approximately 20 min and generally two stationary point count surveys (one per diver) were conducted at each fish REA site. After completing REA surveys, divers noted the presence, at the survey site, of any unusual fish species not counted during SPC counts, in order to facilitate species lists per location.