GPS linked photos of benthic cover transect surveys in Heron Reef

Underwater photo-transect surveys were conducted on September 23-27, 2007 at different sections of the reef flat, reef crest and reef slope in Heron Reef. This survey was done by swimming along pre-defined transect sites and taking a picture of the bottom substrate parallel to the bottom at constant vertical distance (30cm) every two to three metres. A total of 3,586 benthic photos were taken. A floating GPS setup connected to the swimmer/diver by a line enabled recording of coordinates of transect surveys. Approximation of the coordinates for each benthic photo was based on the photo timestamp and GPS coordinate time stamp, using GPS Photo Link Software. Coordinates of each photo were interpolated by finding the the gps coordinates that were logged at a set time before and after the photo was captured. The output of this process was an ArcMap point shapefile, a Google Earth KML file and a thumbnail of each benthic photo taken. The data in the ArcMap shapefile and in the Google Earth KML file consisted of the approximated coordinate of each benthic photo taken during the survey. Using the GPS Photo Link extension within the ArcMap environment, opening the ArcMap shapefile will enable thumbnail to be displayed on the associated benthic cover photo whenever hovering with the mouse over a point on the transect. By downloading the GPSPhotoLink software from the www.geospatialexperts.com, and installing it as a trial version the ArcMap exstension will be installed in the ArcMap environment.

Benthic and substrate cover data derived from photo-transect surveys in Lizard Island Reef conducted on December 10-15, 2011

Underwater georeferenced photo-transect surveys were conducted on December 10-15, 2011 at various sections of the reef at Lizard Island, Great Barrier Reef. For this survey a snorkeler or diver swam over the bottom while taking photos of the benthos at a set height using a standard digital camera and towing a GPS in a surface float which logged the track every five seconds. A standard digital compact camera was placed in an underwater housing and fitted with a 16 mm lens which provided a 1.0 m x 1.0 m footprint, at 0.5 m height above the benthos. Horizontal distance between photos was estimated by three fin kicks of the survey diver/snorkeler, which corresponded to a surface distance of approximately 2.0 - 4.0 m. The GPS was placed in a dry-bag and logged the position as it floated at the surface while being towed by the photographer. A total of 5,735 benthic photos were taken. A floating GPS setup connected to the swimmer/diver by a line enabled recording of coordinates of each benthic photo (Roelfsema 2009). Approximation of coordinates of each benthic photo was conducted based on the photo timestamp and GPS coordinate time stamp, using GPS Photo Link Software (www.geospatialexperts.com). Coordinates of each photo were interpolated by finding the GPS coordinates that were logged at a set time before and after the photo was captured. Benthic or substrate cover data was derived from each photo by randomly placing 24 points over each image using the Coral Point Count for Microsoft Excel program (Kohler and Gill, 2006). Each point was then assigned to 1 of 78 cover types, which represented the benthic feature beneath it. Benthic cover composition summary of each photo scores was generated automatically using CPCE program. The resulting benthic cover data of each photo was linked to GPS coordinates, saved as an ArcMap point shapefile, and projected to Universal Transverse Mercator WGS84 Zone 55 South.

Benthic and substrate cover data derived from photo-transect surveys in Lizard Island, Great Barrier Reef conducted on October 3-7, 2012

Underwater georeferenced photo-transect surveys were conducted on October 3-7, 2012 at various sections of the reef and lagoon at Lizard Island, Great Barrier Reef. For this survey a snorkeler swam while taking photos of the benthos at a set distance from the benthos using a standard digital camera and towing a GPS in a surface float which logged the track every five seconds. A Canon G12 digital camera was placed in a Canon underwater housing and photos were taken at 1 m height above the benthos. Horizontal distance between photos was estimated by three fin kicks of the survey snorkeler, which corresponded to a surface distance of approximately 2.0 - 4.0 m. The GPS was placed in a dry bag and logged the position at the surface while being towed by the photographer (Roelfsema, 2009). A total of 1,265 benthic photos were taken. Approximation of coordinates of each benthic photo was conducted based on the photo timestamp and GPS coordinate time stamp, using GPS Photo Link Software (www.geospatialexperts.com). Coordinates of each photo were interpolated by finding the GPS coordinates that were logged at a set time before and after the photo was captured. Benthic or substrate cover data was derived from each photo by randomly placing 24 points over each image using the Coral Point Count for Microsoft Excel program (Kohler and Gill, 2006). Each point was then assigned to 1 of 79 cover types, which represented the benthic feature beneath it. Benthic cover composition summary of each photo scores was generated automatically using CPCE program. The resulting benthic cover data of each photo was linked to GPS coordinates, saved as an ArcMap point shapefile, and projected to Universal Transverse Mercator WGS84 Zone 55 South.

Habitat Map for Lizard Island reef, Australia derived from a photo-transect survey field data collected in December 2011 and September/October 2012

An object based image analysis approach (OBIA) was used to create a habitat map of the Lizard Reef. Briefly, georeferenced dive and snorkel photo-transect surveys were conducted at different locations surrounding Lizard Island, Australia. For the surveys, a snorkeler or diver swam over the bottom at a depth of 1-2m in the lagoon, One Tree Beach and Research Station areas, and 7m depth in Watson's Bay, while taking photos of the benthos at a set height using a standard digital camera and towing a surface float GPS which was logging its track every five seconds. The camera lens provided a 1.0 m x 1.0 m footprint, at 0.5 m height above the benthos. Horizontal distance between photos was estimated by fin kicks, and corresponded to a surface distance of approximately 2.0 - 4.0 m. Approximation of coordinates of each benthic photo was done based on the photo timestamp and GPS coordinate time stamp, using GPS Photo Link Software (www.geospatialexperts.com). Coordinates of each photo were interpolated by finding the gps coordinates that were logged at a set time before and after the photo was captured. Dominant benthic or substrate cover type was assigned to each photo by placing 24 points random over each image using the Coral Point Count excel program (Kohler and Gill, 2006). Each point was then assigned a dominant cover type using a benthic cover type classification scheme containing nine first-level categories - seagrass high (>=70%), seagrass moderate (40-70%), seagrass low (<= 30%), coral, reef matrix, algae, rubble, rock and sand. Benthic cover composition summaries of each photo were generated automatically in CPCe. The resulting benthic cover data for each photo was linked to GPS coordinates, saved as an ArcMap point shapefile, and projected to Universal Transverse Mercator WGS84 Zone 56 South. The OBIA class assignment followed a hierarchical assignment based on membership rules with levels for "reef", "geomorphic zone" and "benthic community" (above).

Seawater carbonate chemistry and processes during experiments with a coral community, 2008

Ocean acidification represents a key threat to coral reefs by reducing the calcification rate of framework builders. In addition, acidification is likely to affect the relationship between corals and their symbiotic dinoflagellates and the productivity of this association. However, little is known about how acidification impacts on the physiology of reef builders and how acidification interacts with warming. Here, we report on an 8-week study that compared bleaching, productivity, and calcification responses of crustose coralline algae (CCA) and branching (Acropora) and massive (Porites) coral species in response to acidification and warming. Using a 30-tank experimental system, we manipulated CO2 levels to simulate doubling and three- to fourfold increases [Intergovernmental Panel on Climate Change (IPCC) projection categories IV and VI] relative to present-day levels under cool and warm scenarios. Results indicated that high CO2 is a bleaching agent for corals and CCA under high irradiance, acting synergistically with warming to lower thermal bleaching thresholds. We propose that CO2 induces bleaching via its impact on photoprotective mechanisms of the photosystems. Overall, acidification impacted more strongly on bleaching and productivity than on calcification. Interestingly, the intermediate, warm CO2 scenario led to a 30% increase in productivity in Acropora, whereas high CO2 lead to zero productivity in both corals. CCA were most sensitive to acidification, with high CO2 leading to negative productivity and high rates of net dissolution. Our findings suggest that sensitive reef-building species such as CCA may be pushed beyond their thresholds for growth and survival within the next few decades whereas corals will show delayed and mixed responses.

Seawater carbonate chemistry and calcification during experiments with coral communities, 2002

The effect of increased CO2 partial pressure (pCO2) on the community metabolism (primary production, respiration, and calcification) of a coral community was investigated over periods ranging from 9 to 30 d. The community was set up in an open-top mesocosm within which pCO2 was manipulated (411, 647, and 918 µatm). The effect of increased pCO2 on the rate of calcification of the sand area of the mesocosm was also investigated. The net community primary production (NCP) did not change significantly with respect to pCO2 and was 5.1 ± 0.9 mmol O2 m-2 h-1, Dark respiration (R) increased slightly during the experiment at high pCO2, but this did not affect significantly the NCP:R ratio (1.0 ± 0.2). The rate of calcification exhibited the trend previously reported; it decreased as a function of increasing pCO2 and decreasing aragonite saturation state. This re-emphasizes the predictions that reef calcification is likely to decrease during the next century. The dissolution process of calcareous sand does not seem to be affected by open seawater carbonate chemistry; rather, it seems to be controlled by the biogeochemistry of sediment pore water.

Seawater carbonate chemistry and net calcification during experiments with coral communities, 2009

Acidification of seawater owing to oceanic uptake of atmospheric CO2 originating from human activities such as burning of fossil fuels and land-use changes has raised serious concerns regarding its adverse effects on corals and calcifying communities. Here we demonstrate a net loss of calcium carbonate (CaCO3) material as a result of decreased calcification and increased carbonate dissolution from replicated subtropical coral reef communities (n=3) incubated in continuous-flow mesocosms subject to future seawater conditions. The calcifying community was dominated by the coral Montipora capitata. Daily average community calcification or Net Ecosystem Calcification (NEC=CaCO3 production - dissolution) was positive at 3.3 mmol CaCO3 m-2 h-1 under ambient seawater pCO2 conditions as opposed to negative at -0.04 mmol CaCO3 m-2 h-1 under seawater conditions of double the ambient pCO2. These experimental results provide support for the conclusion that some net calcifying communities could become subject to net dissolution in response to anthropogenic ocean acidification within this century. Nevertheless, individual corals remained healthy, actively calcified (albeit slower than at present rates), and deposited significant amounts of CaCO3 under the prevailing experimental seawater conditions of elevated pCO2.

Seawater carbonate chemistry in Hog reef, Bermuda reef community, 2010

Despite the potential impact of ocean acidification on ecosystems such as coral reefs, surprisingly, there is very limited field data on the relationships between calcification and seawater carbonate chemistry. In this study, contemporaneous in situ datasets of seawater carbonate chemistry and calcification rates from the high-latitude coral reef of Bermuda over annual timescales provide a framework for investigating the present and future potential impact of rising carbon dioxide (CO2) levels and ocean acidification on coral reef ecosystems in their natural environment. A strong correlation was found between the in situ rates of calcification for the major framework building coral species Diploria labyrinthiformis and the seasonal variability of [CO32-] and aragonite saturation state omega aragonite, rather than other environmental factors such as light and temperature. These field observations provide sufficient data to hypothesize that there is a seasonal "Carbonate Chemistry Coral Reef Ecosystem Feedback" (CREF hypothesis) between the primary components of the reef ecosystem (i.e., scleractinian hard corals and macroalgae) and seawater carbonate chemistry. In early summer, strong net autotrophy from benthic components of the reef system enhance [CO32-] and omega aragonite conditions, and rates of coral calcification due to the photosynthetic uptake of CO2. In late summer, rates of coral calcification are suppressed by release of CO2 from reef metabolism during a period of strong net heterotrophy. It is likely that this seasonal CREF mechanism is present in other tropical reefs although attenuated compared to high-latitude reefs such as Bermuda. Due to lower annual mean surface seawater [CO32-] and omega aragonite in Bermuda compared to tropical regions, we anticipate that Bermuda corals will experience seasonal periods of zero net calcification within the next decade at [CO32-] and omega aragonite thresholds of ~184 micro moles kg-1 and 2.65. However, net autotrophy of the reef during winter and spring (as part of the CREF hypothesis) may delay the onset of zero NEC or decalcification going forward by enhancing [CO32-] and omega aragonite. The Bermuda coral reef is one of the first responders to the negative impacts of ocean acidification, and we estimate that calcification rates for D. labyrinthiformis have declined by >50% compared to pre-industrial times.

Seawater carbonate chemistry and net ecosystem calcification and production in a coral community Kaneohe Bay, Oahu, Hawaii, 2011

Net ecosystem calcification rates (NEC) and net photosynthesis (NP) were determined from CO2 seawater parameters on the barrier coral reef of Kaneohe Bay, Oahu, Hawaii. Autosamplers were deployed to collect samples on the barrier reef every 2 hours for six 48-hour deployments, two each in June 2008, August 2009, and January/February 2010. NEC on the Kaneohe Bay barrier reef increased throughout the day and decreased at night. Net calcification continued at low rates at night except for six time periods when net dissolution was measured. The barrier reef was generally net photosynthetic (positive NP) during the day and net respiring (negative NP) at night. NP controlled the diel cycles of the partial pressure of CO2 (pCO2) and aragonite saturation state resulting in high daytime aragonite saturation state levels when calcification rates were at their peak. However, the NEC and NP diel cycles can become decoupled for short periods of time (several hours) without affecting calcification rates. On a net daily basis, net ecosystem production (NEP) of the barrier reef was found to be sometimes net photosynthetic and sometimes net respiring and ranged from -378 to 80 mmol m-2 d-1 when calculated using simple box models. Daily NEC of the barrier reef was positive (net calcification) for all deployments and ranged from 174 to 331 mmol CaCO3 m-2 d-1. Daily NEC was strongly negatively correlated with average daily pCO2 (R2 = 0.76) which ranged from 431 to 622 µatm. Daily NEC of the Kaneohe Bay barrier reef is similar to or higher than daily NEC measured on other coral reefs even though aragonite saturation state levels (mean aragonite saturation state = 2.85) are some of the lowest measured in coral reef ecosystems. It appears that while calcification rate and ?arag are correlated within a single coral reef ecosystem, this relationship does not necessarily hold between different coral reef systems. It can be expected that ocean acidification will not affect coral reefs uniformly and that some may be more sensitive to increasing pCO2 levels than others.

Madrepora oculata and Lophelia pertusa mass and 210Pb-226Ra chronology, Røst Reef, Norway, 2011

Here we show the use of the 210Pb-226Ra excess method to determine the growth rate of corals from one of the world's largest known cold-water coral reef, the Røst Reef off Norway. Two large branching framework-forming cold-water coral specimens, one Lophelia pertusa and one Madrepora oculata were collected alive at 350 m water depth from the Røst Reef at ~67° N and ~9° E. Pb and Ra isotopes were measured along the major growth axis of both specimens using low level alpha and gamma spectrometry and the corals trace element compositions were studied using ICP-QMS. Due to the different chemical behaviors of Pb and Ra in the marine environment, 210Pb and 226Ra were not incorporated the same way into the aragonite skeleton of those two cold-water corals. Thus to assess of the growth rates of both specimens we have here taken in consideration the exponential decrease of initially incorporated 210Pb as well as the ingrowth of 210Pb from the decay of 226Ra. Moreover a~post-depositional 210Pb incorporation is found in relation to the Mn-Fe coatings that could not be entirely removed from the oldest parts of the skeletons. The 226Ra activities in both corals were fairly constant, then assuming constant uptake of 210Pb through time the 210Pb-226Ra chronology can be applied to calculate linear growth rate. The 45.5 cm long branch of M. oculata reveals an age of 31 yr and a~linear growth rate of 14.4 ± 1.1 mm yr-1, i.e. 2.6 polyps per year. However, a correction regarding a remaining post-depositional Mn-Fe oxide coating is needed for the base of the specimen. The corrected age tend to confirm the radiocarbon derived basal age of 40 yr (using 14C bomb peak) with a mean growth rate of 2 polyps yr-1. This rate is similar to the one obtained in Aquaria experiments under optimal growth conditions. For the 80 cm-long specimen of L. pertusa a remaining contamination of metal-oxides is observed for the middle and basal part of the coral skeleton, inhibiting similar accurate age and growth rate estimates. However, the youngest branch was free of Mn enrichment and this 15 cm section reveals a growth rate of 8 mm yr-1 (~1 polyp every two to three years). However, the 210Pb growth rate estimate is within the lowermost ranges of previous growth rate estimates and may thus reflect that the coral was not developing at optimal growth conditions. Overall, 210Pb-226Ra dating can be successfully applied to determine the age and growth rate of framework-forming cold-water corals, however, removal of post-depositional Mn-Fe oxide deposits is a prerequisite. If successful, large branching M. oculata and L. pertusa coral skeletons provide unique oceanographic archive for studies of intermediate water environmentals with an up to annual time resolution and spanning over many decades.

Seawater carbonate chemistry and calcification rate during mesocosm experiments with coral Montipora capitata, 2008

A long-term (10 months) controlled experiment was conducted to test the impact of increased partial pressure of carbon dioxide (pCO2) on common calcifying coral reef organisms. The experiment was conducted in replicate continuous flow coral reef mesocosms flushed with unfiltered sea water from Kaneohe Bay, Oahu, Hawaii. Mesocosms were located in full sunlight and experienced diurnal and seasonal fluctuations in temperature and sea water chemistry characteristic of the adjacent reef flat. Treatment mesocosms were manipulated to simulate an increase in pCO2 to levels expected in this century [midday pCO2 levels exceeding control mesocosms by 365 ± 130 µatm (mean ± sd)]. Acidification had a profound impact on the development and growth of crustose coralline algae (CCA) populations. During the experiment, CCA developed 25% cover in the control mesocosms and only 4% in the acidified mesocosms, representing an 86% relative reduction. Free-living associations of CCA known as rhodoliths living in the control mesocosms grew at a rate of 0.6 g buoyant weight per year while those in the acidified experimental treatment decreased in weight at a rate of 0.9 g buoyant weight per year, representing a 250% difference. CCA play an important role in the growth and stabilization of carbonate reefs, so future changes of this magnitude could greatly impact coral reefs throughout the world. Coral calcification decreased between 15% and 20% under acidified conditions. Linear extension decreased by 14% under acidified conditions in one experiment. Larvae of the coral Pocillopora damicornis were able to recruit under the acidified conditions. In addition, there was no significant difference in production of gametes by the coral Montipora capitata after 6 months of exposure to the treatments.

Les Millepora (Hydrozoaires) de la Baie de Nhatrang

The importance of the variation of Millepora in connection with their habitat is so well known. Boschma (1948) describes some relationships between those variations and some ecological factors. The present paper establishes the taxonomy of Millepora living in the Nhatrang Bay and describes their distribution on the different parts of the coral reef of this bay. Some observations on the variations of some species in relationship with their habitat seem to agree with Boschma's opinion about the action of some ecological factors.

Identification, diversity and distribution patterns of fish larvae in Khark & Kharko Coralline Islands ecosystem – Persian Gulf, by GIS method

Khark & Kharko Islands are the last Northern point for fringing coral reefs in Iranian side of the Persian Gulf. These Coralline habitats are the Protected Area and Wildlife Refugees with the total area of 2400 ha which located in the territory of Bushehr Province. This research carried out during 2006-2007 with monthly sampling from 12 stations, which selected around Islands and inshore waters with maximum depth of 20 meter. Sampling was conducted using by Bongo-Net plankton sampler with 500μ of mesh size. Totally, 1808 specimen from 45 family fish larvae was identified in studied area, including: 21 coralline fish larva families and 24 shore fish larvae such as pelagic and demersal fishes which some of them known as indicator, sentinel or endemic species for coral reef ecosystems. The results was shown that coral reef diversity in coral reefs (Khark & Kharko Islands) is more than other habitats such as estuary and river mouth, creeks, mangrove forest sites, and off shore water of the Persian Gulf and Oman Sea Iranian side. Among Identified families, Clupeidae, Blenniidae, Sillaginidae, Atherinidae and Tripterygiidae; with more abundance were dominant families in studied area. The pick of fish larvae abundance family were estimated in spring. There were significant differences between seasonally abundance and sub areas, but there were not significant differences in diversity indexes between Khark and Kharko stations with coastal stations (p< 0.05). The mean abundance of fish larvae were estimated 18.7083 larvae under 10m² of sea surface, and the mean diversity indexes and evenness were estimated 0.7135 and 0.565342 consequently, that was showed the area is under ecological stress for fish larvae, and wasn’t stable. Therefore, from the ecological point of view, only some of the fish larvae groups as like Clupeidae were dominant. Thus, they were the main cause of the fish larvae abundance change in studied area. Due to geographical location of Khark and Kharko Islands and among the environmental parameters, Its seems that the condition of sea current is the main cause for present or absent and distribution patterns of fish larvae in area. Abundance of fish larvae in west of Islands was higher than eastern parts in the spring. But this condition will be reversed in eastern part of Island and several coastal stations, so that the Islands surrounding clock wise current to cause fish larvae distribution patterns.

Survey of Amphiprion clarki & Amphiprion sebae populations in Persian Gulf by molecular genetics

Anemone fishes are a group of 28 species of coral reef fishes belonging to the family Pomacentridae, subfamily Amphiprioninae and all have an obligate symbiotic relationship with sea anemones. Two species of these small ornamental fishes have been identified in the Persian Gulf including Amphiprion clarkii and A. sebae. The phylogenetic relationship between Amphiprion species of the Persian Gulf was studied by collecting 15 samples from three Iranian islands, Larak, Farur and Kish. DNA was extracted from each sample and a part of mtDNA was amplified. Two pairs of primers were designed to amplify a final target of 400 by nested-PCR. Each amplicon was sequenced, aligned and genetic diversity among samples was investigated by phylogenetic analysis. Results show that there is no significant genetic variation among A. clarkii individuals; however, A. sebae individuals from Larak were different from other fishes of the same species. Most probably this is due to the ability of A. clarkii to be symbiotant with all 10 species of host sea anemones which enables it to spread its own population in the 3 islands. However, A. sebae is observed to be symbiotant only with one host in the sea, therefore, has one option that reduces its distribution.