Click
here to close Hello! We notice that
you are using Internet Explorer, which is not supported by Echinobase
and may cause the site to display incorrectly. We suggest using a
current version of Chrome,
FireFox,
or Safari.
Front Microbiol
2018 Jan 01;9:2203. doi: 10.3389/fmicb.2018.02203.
Show Gene links
Show Anatomy links
Metagenomics of Coral Reefs Under Phase Shift and High Hydrodynamics.
Meirelles PM
,
Soares AC
,
Oliveira L
,
Leomil L
,
Appolinario LR
,
Francini-Filho RB
,
de Moura RL
,
de Barros Almeida RT
,
Salomon PS
,
Amado-Filho GM
,
Kruger R
,
Siegle E
,
Tschoeke DA
,
Kudo I
,
Mino S
,
Sawabe T
,
Thompson CC
,
Thompson FL
.
???displayArticle.abstract???
Local and global stressors have affected coral reef ecosystems worldwide. Switches from coral to algal dominance states and microbialization are the major processes underlying the global decline of coral reefs. However, most of the knowledge concerning microbialization has not considered physical disturbances (e.g., typhoons, waves, and currents). Southern Japan reef systems have developed under extreme physical disturbances. Here, we present analyses of a three-year investigation on the coral reefs of Ishigaki Island that comprised benthic and fish surveys, water quality analyses, metagenomics and microbial abundance data. At the four studied sites, inorganic nutrient concentrations were high and exceeded eutrophication thresholds. The dissolved organic carbon (DOC) concentration (up to 233.3 μM) and microbial abundance (up to 2.5 × 105 cell/mL) values were relatively high. The highest vibrio counts coincided with the highest turf cover (∼55-85%) and the lowest coral cover (∼4.4-10.2%) and fish biomass (0.06 individuals/m2). Microbiome compositions were similar among all sites and were dominated by heterotrophs. Our data suggest that a synergic effect among several regional stressors are driving coral decline. In a high hydrodynamics reef environment, high algal/turf cover, stimulated by eutrophication and low fish abundance due to overfishing, promote microbialization. Together with crown-of-thorns starfish (COTS) outbreaks and possible of climate changes impacts, theses coral reefs are likely to collapse.
FIGURE 1. Modeled wave generated near bottom orbital velocity (m/s) in the area of interest. Example for calm (A) and typhoon (B) wave conditions. Note difference in color bar scales.
FIGURE 2. Coral reefs from Ishigaki Island are impacted at different levels. Yellow and green lines represent coral and algal cover in percentages for the reef sites and years, respectively (A). The first two axes of non-metric multidimensional scaling (nMDS) based on benthic cover (B) and fish abundance (C) show each benthic sample replicate using different colors for sites and different shapes for years. The taxonomic compositions of water metagenomes, heterotrophic bacteria, potential coral pathogenic bacteria, and highly abundant bacteria in turf algae are represented by different colors (D). The asterisk in Cyanobacteria represents the bacterial genera Anabaena, Nostoc, and Trichodesmium (cyanobacteria genera commonly found in turf algae). CFB complex, Cytophaga–Flavobacterium–Bacteroides complex.
FIGURE 3. Ishigaki coral reef and fish community composition structure. (A) Relative coral cover. (B) Relative abundance of fish families. (C) Canonical correspondence analysis (CCA) biplot of benthic cover and fish assemblages of Ishigaki coral reefs. Each replicate is represented by dots in different colors (for sites) and different shapes (for years). Species abbreviations are: CTESTR, Ctenochaetus striatus; STEALT, Stegastes altus; CHLSOR, Chlorurus sordidus; POMLEP, Pomacentrus lepidogenys; CHRMAR, Chromis margaritifer; CHRREX, Chrysiptera rex; CHRATR, Chromis atripectoralis; ABUSEX, Abudefduf sexfasciatus; THALUT, Thalassoma lutescens; THAHAR, Thalassoma hardwicke; GOMVAR, Gomphosus varius; LABDIM, Labroides dimidiatus; ZEBSCO, Zebrasoma scopas.
FIGURE 4. The microbial communities of Ishigaki coral reef seawater have similar genetic compositions. Cladograms representing the fraction of cross-contigs (i.e., shared contigs that contain reads from two or more metagenomes) after cross-assembly.
Amin,
The First Temporal and Spatial Assessment of Vibrio Diversity of the Surrounding Seawater of Coral Reefs in Ishigaki, Japan.
2016, Pubmed
Amin,
The First Temporal and Spatial Assessment of Vibrio Diversity of the Surrounding Seawater of Coral Reefs in Ishigaki, Japan.
2016,
Pubmed
Andrade,
Flow cytometry assessment of bacterioplankton in tropical marine environments.
2003,
Pubmed
Barott,
Unseen players shape benthic competition on coral reefs.
2012,
Pubmed
Bell,
Reevaluation of ENCORE: support for the eutrophication threshold model for coral reefs.
2007,
Pubmed
Blanco,
Planktonic and benthic microalgal community composition as indicators of terrestrial influence on a fringing reef in Ishigaki Island, Southwest Japan.
2008,
Pubmed
Bruce,
Abrolhos bank reef health evaluated by means of water quality, microbial diversity, benthic cover, and fish biomass data.
2012,
Pubmed
Casey,
Farming behaviour of reef fishes increases the prevalence of coral disease associated microbes and black band disease.
2014,
Pubmed
Casey,
Coral transplantation triggers shift in microbiome and promotion of coral disease associated potential pathogens.
2015,
Pubmed
Chevreux,
Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs.
2004,
Pubmed
Colgan,
Coral Reef Recovery on Guam (Micronesia) After Catastrophic Predation by Acanthaster Planci.
1987,
Pubmed
,
Echinobase
De'ath,
The 27-year decline of coral cover on the Great Barrier Reef and its causes.
2012,
Pubmed
,
Echinobase
Dinsdale,
Microbial ecology of four coral atolls in the Northern Line Islands.
2008,
Pubmed
Dutilh,
The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise.
2004,
Pubmed
Dutilh,
Reference-independent comparative metagenomics using cross-assembly: crAss.
2012,
Pubmed
Dutilh,
Assessment of phylogenomic and orthology approaches for phylogenetic inference.
2007,
Pubmed
Edwards,
Global assessment of the status of coral reef herbivorous fishes: evidence for fishing effects.
2014,
Pubmed
Francini-Filho,
Dynamics of coral reef benthic assemblages of the Abrolhos Bank, eastern Brazil: inferences on natural and anthropogenic drivers.
2013,
Pubmed
Garcia,
Metagenomic analysis of healthy and white plague-affected Mussismilia braziliensis corals.
2013,
Pubmed
Garren,
New directions in coral reef microbial ecology.
2012,
Pubmed
Gascuel,
BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
1997,
Pubmed
Gregg,
Biological oxygen demand optode analysis of coral reef-associated microbial communities exposed to algal exudates.
2013,
Pubmed
Haas,
Global microbialization of coral reefs.
2016,
Pubmed
Haas,
Effects of coral reef benthic primary producers on dissolved organic carbon and microbial activity.
2011,
Pubmed
Hata,
Coral larvae are poor swimmers and require fine-scale reef structure to settle.
2017,
Pubmed
Hoegh-Guldberg,
Coral reefs under rapid climate change and ocean acidification.
2007,
Pubmed
Hughes,
Catastrophes, phase shifts, and large-scale degradation of a Caribbean coral reef.
1994,
Pubmed
Jackson,
Historical overfishing and the recent collapse of coastal ecosystems.
2001,
Pubmed
Jessen,
In-Situ Effects of Simulated Overfishing and Eutrophication on Benthic Coral Reef Algae Growth, Succession, and Composition in the Central Red Sea.
2013,
Pubmed
Jorissen,
Evidence for water-mediated mechanisms in coral-algal interactions.
2016,
Pubmed
Kelly,
Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors.
2014,
Pubmed
Kepner,
Use of fluorochromes for direct enumeration of total bacteria in environmental samples: past and present.
1994,
Pubmed
Kitada,
Distribution of pesticides and bisphenol A in sediments collected from rivers adjacent to coral reefs.
2008,
Pubmed
Knowlton,
Shifting baselines, local impacts, and global change on coral reefs.
2008,
Pubmed
Korbel,
SHOT: a web server for the construction of genome phylogenies.
2002,
Pubmed
Liu,
A trophic model of fringing coral reefs in Nanwan Bay, southern Taiwan suggests overfishing.
2009,
Pubmed
McDole,
Assessing coral reefs on a Pacific-wide scale using the microbialization score.
2012,
Pubmed
McDole Somera,
Energetic differences between bacterioplankton trophic groups and coral reef resistance.
2016,
Pubmed
Meirelles,
Baseline Assessment of Mesophotic Reefs of the Vitória-Trindade Seamount Chain Based on Water Quality, Microbial Diversity, Benthic Cover and Fish Biomass Data.
2015,
Pubmed
Meirelles,
BaMBa: towards the integrated management of Brazilian marine environmental data.
2015,
Pubmed
Meirelles,
Metagenomics of Coral Reefs Under Phase Shift and High Hydrodynamics.
2018,
Pubmed
Meyer,
The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes.
2008,
Pubmed
Nelson,
Coral and macroalgal exudates vary in neutral sugar composition and differentially enrich reef bacterioplankton lineages.
2013,
Pubmed
Roach,
Microbial bioenergetics of coral-algal interactions.
2017,
Pubmed
Roberts,
Marine biodiversity hotspots and conservation priorities for tropical reefs.
2002,
Pubmed
Roff,
Global disparity in the resilience of coral reefs.
2012,
Pubmed
Sandin,
Baselines and degradation of coral reefs in the Northern Line Islands.
2008,
Pubmed
Schmieder,
Quality control and preprocessing of metagenomic datasets.
2011,
Pubmed
Smith,
Indirect effects of algae on coral: algae-mediated, microbe-induced coral mortality.
2006,
Pubmed
Smith,
Re-evaluating the health of coral reef communities: baselines and evidence for human impacts across the central Pacific.
2016,
Pubmed
Sowa,
Influence of land development on Holocene Porites coral calcification at Nagura Bay, Ishigaki Island, Japan.
2014,
Pubmed
Stone,
Mass Coral Reef Bleaching: A Recent Outcome of Increased El Niño Activity?
1999,
Pubmed
West,
Spatial and temporal variance of river discharge on Okinawa (Japan): inferring the temporal impact on adjacent coral reefs.
2001,
Pubmed
White,
Shifting communities after-- typhoon damage on an upper mesophotic reef in Okinawa, Japan.
2017,
Pubmed
Willner,
Metagenomic signatures of 86 microbial and viral metagenomes.
2009,
Pubmed