acropora

Genomic sequence data for non-model organisms are increasingly available requiring the development of efficient and reproducible workflows. Here, we develop the first genomic resources and reproducible workflows for two threatened members of the reef-building coral genus Acropora We generated genomic sequence data from multiple samples of the Caribbean A. cervicornis (staghorn coral) and A. palmata (elkhorn coral), and predicted millions of nucleotide variants among these two species and the Pacific A. digitifera A subset of predicted nucleotide variants were verified using restriction length polymorphism assays and proved useful in distinguishing the two Caribbean acroporids and the hybrid they form ("A. prolifera"). Nucleotide variants are freely available from the Galaxy server (usegalaxy.org), and can be analyzed there with computational tools and stored workflows that require only an internet browser. We describe these data and some of the analysis tools, concentrating on fixed differences between A. cervicornis and A. palmata In particular, we found that fixed amino acid differences between these two species were enriched in proteins associated with development, cellular stress response, and the host's interactions with associated microbes, for instance in the ABC transporters and superoxide dismutase. Identified candidate genes may underlie functional differences in how these threatened species respond to changing environments. Users can expand the presented analyses easily by adding genomic data from additional species, as they become available

Since the severe decline of the Acropora populations in Bonaire in the 1980s, no assessment has characterized the distribution of remnant colonies. Because of their patchy distribution, a large sampling effort is necessary to adequately describe their occurrence. However, the spatial scale at which this assessment needs to be carried out makes this prohibitive with approaches such as transects using SCUBA gear and photogrammetry. This internship project aimed to optimize and apply a simple methodology trialed by relevant stakeholders on the island to obtain coarse but spatially explicit data with relatively low time-investment. Snorkelers utilizing a waterproof GPS and a slate to record coarse categorical data outlined patches of Acropora cervicornis and Acropora palmata in-situ. These were processed with an ArcGIS workflow to create shapefiles of coral patches as polygons joined to their corresponding data. The resulting polygons were used to describe the distribution of Acropora spp. along the leeward coast of Bonaire. Furthermore, these were used as ground-truthing data to test whether remote sensing imagery can be used to detect A. cervicornis remotely. 466 polygons along 14.5km of the coast were created, showing a patchy distribution of both species, more frequent occurrence of A. palmata in the northern leeward coast compared to the southern, and vice-versa for A. cervicornis. A multinomial logistic regression, maximum likelihood classification, and forest-based classification all showed a high accuracy in labelling A. cervicornis correctly in remote sensing data, but all showed frequent misclassification of other reef structures as A. cervicornis. The mapping approach presented in this internship could be applied to investigate fragmentation effects in Acropora populations and to gather in-situ ground-truthing data for other benthic habitats.

Abstract
Since the severe decline of the Acropora populations in Bonaire in the 1980s, no assessment has characterized the distribution of remnant colonies. Because of their patchy distribution, a large sampling effort is necessary to adequately describe their occurrence. However, the spatial scale at which this assessment needs to be carried out makes this prohibitive with approaches such as transects using SCUBA gear and photogrammetry. This internship project aimed to optimize and apply a simple methodology trialed by relevant stakeholders on the island to obtain coarse but spatially explicit data with relatively low time-investment. Snorkelers utilizing a waterproof GPS and a slate to record coarse categorical data outlined patches of Acropora cervicornis and Acropora palmata in-situ. These were processed with an ArcGIS workflow to create shapefiles of coral patches as polygons joined to their corresponding data. The resulting polygons were used to describe the distribution of Acropora spp. along the leeward coast of Bonaire. Furthermore, these were used as ground-truthing data to test whether remote sensing imagery can be used to detect A. cervicornis remotely. 466 polygons along 14.5km of the coast were created, showing a patchy distribution of both species, more frequent occurrence of A. palmata in the northern leeward coast compared to the southern, and vice-versa for A. cervicornis. A multinomial logistic regression, maximum likelihood classification, and forest-based classification all showed a high accuracy in labelling A. cervicornis correctly in remote sensing data, but all showed frequent misclassification of other reef structures as A. cervicornis. The mapping approach presented in this internship could be applied to investigate fragmentation effects in Acropora populations and to gather in-situ ground-truthing data for other benthic habitats.

For full report or more information,  please contact erik.meesters@wur.nl or gulsah.dogruer@wur.nl

Abstract

Coral-dwelling crabs form a diverse community on coral reefs, and various families independently colonised scleractinian corals. Species of Domecia have a circumtropical distribution, with two known species in the Indo-Pacific, one in the West Atlantic and one in the East Atlantic. New host records for the West Atlantic species D. acanthophora are recorded from Guadeloupe, as well as the first dwellings in Acropora prolifera from Curaçao. Here we provide an overview of all known hosts of Domecia species and, based on COI mtDNA, the first phylogeny of the genus. The coral Orbicella faveolata and the sponge Callyspongia sp. are recorded as new hosts for D. acanthophora. Host records for this species now include eight scleractinian hosts, Millepora fire corals and records on sponges. Our phylogenetic reconstruction shows that D. acanthophora is closest to the wide-ranging Indo-Pacific species D. hispida, and more distantly related to D. glabra. Domecia acanthophora appears to be less host specific than its congeners D. hispida and D. glabra that predominantly associate with Pocillopora and Acropora corals, respectively. Differences in host-specificity between Indo-Pacific and Atlantic species are briefly discussed in the light of similar observations on other coral-dwelling crab species.

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Abstract: Coral reefs in the Caribbean are known to be affected by many coral diseases, yet the ecology and etiology of most diseases remain understudied. The Caribbean ciliate infection (CCI) caused by ciliates belonging to the genus Halofolliculina is a common disease on Caribbean reefs, with direct contact considered the most likely way through which the ciliates can be transmitted between infected and healthy colonies. Here we report an observation regarding a Coralliophila sp. snail feeding in proximity to a cluster of ciliates forming the typical disease band of CCI. The result of this observation is twofold. The feeding behavior of the snail may allow the passive attachment of ciliates on the body or shell of the snail resulting in indirect transport of the ciliates among colonies, which makes it eligible as a possible disease vector. Alternatively, the lesions created from snail feeding may enhance the progression of the ciliates already present on the coral as well as promoting additional infections allowing pathogens to enter through the feeding scar

Reef restoration activities have proliferated in response to the need to mitigate coral declines and recover lost reef structure, function, and ecosystem services. Here, we describe the recent shift from costly and complex engineering solutions to recover degraded reef structure to more economical and efficient ecological approaches that focus on recovering the living components of reef communities. We review the adoption and expansion of the coral gardening framework in the Caribbean and Western Atlantic where practitioners now grow and outplant 10,000’s of corals onto degraded reefs each year. We detail the steps for establishing a gardening program as well as long-term goals and direct and indirect benefits of this approach in our region. With a strong scientific basis, coral gardening activities now contribute significantly to reef and species recovery, provide important scientific, education, and outreach opportunities, and offer alternate livelihoods to local stakeholders. While challenges still remain, the transition from engineering to ecological solutions for reef degradation has opened the field of coral reef restoration to a wider audience poised to contribute to reef conservation and recovery in regions where coral losses and recruitment bottlenecks hinder natural recovery.