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Lim Y.W.,San Diego State University | Cuevas D.A.,San Diego State University | Silva G.G.Z.,San Diego State University | Aguinaldo K.,San Diego State University | And 21 more authors.
PeerJ | Year: 2014

Genomics and metagenomics have revolutionized our understanding of marine microbial ecology and the importance of microbes in global geochemical cycles. However, the process of DNA sequencing has always been an abstract extension of the research expedition, completed once the samples were returned to the laboratory. During the 2013 Southern Line Islands Research Expedition, we started the first effort to bring next generation sequencing to some of the most remote locations on our planet. We successfully sequenced twenty six marine microbial genomes, and two marine microbial metagenomes using the Ion Torrent PGM platform on the Merchant Yacht Hanse Explorer. Onboard sequence assembly, annotation, and analysis enabled us to investigate the role of the microbes in the coral reef ecology of these islands and atolls. This analysis identified phosphonate as an important phosphorous source for microbes growing in the Line Islands and reinforced the importance of Lserine in marine microbial ecosystems. Sequencing in the field allowed us to propose hypotheses and conduct experiments and further sampling based on the sequences generated. By eliminating the delay between sampling and sequencing, we enhanced the productivity of the research expedition. By overcoming the hurdles associated with sequencing on a boat in the middle of the Pacific Ocean we proved the flexibility of the sequencing, annotation, and analysis pipelines. © 2014 Lim et al. Source

Haas A.F.,San Diego State University | Guibert M.,ENSTA ParisTech | Foerschner A.,Getty Research Institute | Co T.,San Diego State University | And 12 more authors.
PeerJ | Year: 2015

The natural beauty of coral reefs attracts millions of tourists worldwide resulting in substantial revenues for the adjoining economies. Although their visual appearance is a pivotal factor attracting humans to coral reefs current monitoring protocols exclusively target biogeochemical parameters, neglecting changes in their aesthetic appearance. Here we introduce a standardized computational approach to assess coral reef environments based on 109 visual features designed to evaluate the aesthetic appearance of art. The main feature groups include color intensity and diversity of the image, relative size, color, and distribution of discernable objects within the image, and texture. Specific coral reef aesthetic values combining all 109 features were calibrated against an established biogeochemical assessment (NCEAS) using machine learning algorithms. These values were generated for ~2,100 random photographic images collected from 9 coral reef locations exposed to varying levels of anthropogenic influence across 2 ocean systems. Aesthetic values proved accurate predictors of the NCEAS scores (root mean square error < 5 for N ≥ 3) and significantly correlated to microbial abundance at each site. This shows that mathematical approaches designed to assess the aesthetic appearance of photographic images can be used as an inexpensive monitoring tool for coral reef ecosystems. It further suggests that human perception of aesthetics is not purely subjective but influenced by inherent reactions towards measurable visual cues. By quantifying aesthetic features of coral reef systems this method provides a cost efficient monitoring tool that targets one of the most important socioeconomic values of coral reefs directly tied to revenue for its local population. © 2015 Haas et al. Source

Barott K.L.,San Diego State University | Williams G.J.,University of California at San Diego | Vermeij M.J.A.,Caribbean Research and Management of Biodiversity CARMABI | Vermeij M.J.A.,University of Amsterdam | And 4 more authors.
Marine Ecology Progress Series | Year: 2012

Competition between corals and benthic algae is prevalent on coral reefs worldwide and has the potential to influence the structure of the reef benthos. Human activities may influence the outcome of these interactions by favoring algae to become the superior competitor, and this type of change in competitive dynamics is a potential mechanism driving coral-algal phase shifts. Here we surveyed the types and outcomes of coral interactions with benthic algae in the Line Islands of the Central Pacific. Islands ranged from nearly pristine to heavily fished. We observed major differences in the dominant groups of algae interacting with corals between sites, and the outcomes of coral-algal interactions varied across reefs on the different islands. Corals were generally better competitors against crustose coralline algae regardless of location, and were superior competitors against turf algae on reefs surrounding uninhabited islands. On reefs surrounding inhabited islands, however, turf algae were generally the superior competitors. When corals were broken down by size class, we found that the smallest and the largest coral colonies were the best competitors against algae; the former successfully fought off algae while being completely surrounded, and the latter generally avoided algal overgrowth by growing up above the benthos. Our data suggest that human disruption of the reef ecosystem may lead to a building pattern of competitive disadvantage for corals against encroaching algae, particularly turf algae, potentially initiating a transition towards algal dominance. © Inter-Research 2012. Source

Wolf A.T.,Leibniz Center for Tropical Marine Ecology | Nugues M.M.,Leibniz Center for Tropical Marine Ecology | Nugues M.M.,CNRS Insular Research Center and Environment Observatory | Nugues M.M.,Caribbean Research and Management of Biodiversity CARMABI
Ecology | Year: 2013

Indirect biotic interactions play a crucial role in structuring ecological communities, but many of these interactions have not been explored. Algal competition and corallivory are two major stressors contributing to the decline of coral reefs. Here, we provide the first evidence of algal-induced corallivory and synergistic effects between the two stressors on corals. When corals (Montastraea faveolata) were placed in contact with algae (Halimeda opuntia) together with corallivorous fireworms (Hermodice carunculata) in aquaria, corals suffered high tissue mortality. This mortality was reduced in the presence of algae only, and no mortality occurred in the presence of fireworms only or when excluding both algae and fireworms. These findings were supported by field observations showing a predominance of fireworms inside algae contacting live corals, and by an in situ experiment demonstrating higher coral mortality in contact with algae left undisturbed than with algae from which all mobile epifauna were periodically removed. Among the main contributing mechanisms, we suggest that algal contact produces decaying coral tissue that attracts the corallivore and enhances its aggregation behavior. Our study demonstrates an indirect effect pathway by which algae can impact corals, which shares similarities with the classic models of apparent competition and habitat facilitation. © 2013 by the Ecological Society of America. Source

Wolf A.T.,Leibniz Center for Tropical Marine Ecology | Nugues M.M.,Leibniz Center for Tropical Marine Ecology | Nugues M.M.,CNRS Insular Research Center and Environment Observatory | Nugues M.M.,Caribbean Research and Management of Biodiversity CARMABI | And 2 more authors.
Coral Reefs | Year: 2014

The fireworm Hermodice carunculata is a facultative corallivore on coral reefs. It can interact with algal overgrowth to cause coral mortality. However, because of its cryptic nature, little is known about its ecology. We used micropredator attracting devices (MADs) and stable isotope analyses to provide insights into the distribution and diet of H. carunculata in a coral reef on Curaçao, southern Caribbean. MADs consisted of algal clumps inside accessible mesh nets which H. carunculata could use as refuge. To obtain indications on its distribution pattern, MADs filled with Halimeda opuntia were deployed in different reef habitats ranging from 0 to 16 m water depth. Fireworms were found inside MADs in all reef habitats, indicating that they have a widespread horizontal and vertical distribution, ranging from the shoreline to the deeper reef slope. On the reef crest, MADs were filled using different algal species and deployed on dead or live scleractinian corals. MADs hosted more fireworms when placed on live corals, regardless of algal species used, suggesting that algal-induced corallivory may be widespread. To test for food preferences, different food sources were added inside the MADs. Fireworms detected potential prey within 6 h and were significantly more attracted by decaying corals and raw fish than by live corals, hydrozoans, or gorgonians. Stable isotope analyses indicated detritus, macroalgae, and scleractinian corals as potential food sources and revealed an ontogenetic dietary shift toward enriched δ13C and δ15N values with increasing fireworm size, suggesting that large-sized individuals feed on food sources of higher trophic levels. Our findings highlight H. carunculata as a widespread, and omnivorous scavenger that has the potential to switch feeding toward weakened or stressed corals, thereby likely acting as a harmful corallivore on degraded reefs. © 2014, Springer-Verlag Berlin Heidelberg. Source

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