MERMAID - Metagenomic Examinations of Reefs; Microbial Assessments Including Disease
MERMAID - Metagenomic Examinations of Reefs; Microbial Assessments Including Disease
This project aims to understand the microbial processes, including disease, that influence the health of coral reef communities. We use microbiology and molecular biology techniques to better understand the role of microorganisms in shaping reef structure and function.
![Illustration of a mermaid on a coral reef with a double helix (DNA strand) tail.](https://d9-wret.s3.us-west-2.amazonaws.com/assets/palladium/production/s3fs-public/styles/side_image/public/media/images/mermaid3.png?itok=kknWr3_B)
Why Does the USGS Study the Microbes Found on Coral Reefs?
The loss and degradation of coral-reef ecosystems are occurring at increasing rates worldwide, in no small part due to coral diseases and die-offs of important herbivores like Diadema sea urchins. This decline negatively impacts society via removal of the ecosystem services provided by reefs, including storm protection, food supply through fish habitat, and tourism. Microbes play critical roles in the health of coral reefs, yet are generally underappreciated despite their ubiquity, abundance, complexity, and formative roles in the metabolic and chemical processes on reefs, including as agents of disease or as markers of land-based pollution.
![A SCUBA diver beside a Massive starlet coral on the sea floor at Dry Tortugas National Park](https://d9-wret.s3.us-west-2.amazonaws.com/assets/palladium/production/s3fs-public/styles/half_width/public/thumbnails/image/DRTO_Coral%20Gardens_Ssid_Drilled_CG2_2012%20%283%29.jpg?itok=IF07vX74)
Project MERMAID
MERMAID aims to increase our understanding of the critical and complex relationships between corals and microbes and their importance in reef health. This project employs a variety of metagenomic tools and methods to identify and track disease-causing agents that are negatively affecting coral reef ecosystems, establish biomarkers of stress or land-based pollution in coral reef ecosystems, and uncover new connections between abiotic conditions (e.g., measurement of sedimentation, nutrients, water circulation) and their biological effects on corals.
![Photo taken as SPMSC scientist Lauren Toth conducts a photographic survey of Porter Patch reef off Key Largo](https://d9-wret.s3.us-west-2.amazonaws.com/assets/palladium/production/s3fs-public/styles/half_width/public/thumbnails/image/Transect%20for%20reef%20complexity_Porter%20Patch_0.jpg?itok=YkMg0YR8)
For more details, please see our topical pages on:
- Characterizing microbial communities of healthy and degraded reefs to determine if there are microbial species or functional genes that can serve as indicators that correlate with reef processes such as calcification and submarine groundwater discharge.
Stony Coral Tissue Loss Disease:
- Investigating the unknown causative agent(s) of stony coral tissue loss disease (SCTLD) and determining possible modes of disease transmission.
Antibiotic-Resistance Gene (ARG) Baselines:
- Generating benchmark datasets on the presence/absence and diversity of antibiotic-resistance genes in coral tissue and reef sediments.
Coral Reef Project
Microbial Processes on Reefs
Coral Microbial Ecology
Coral Reef Ecosystem Studies (CREST)
Coral Disease
Prokaryotic Communities Shed by Diseased and Healthy Coral (Diploria labyrinthiformis, Pseudodiploria strigosa, Montastraea cavernosa, Colpophyllia natans, and Orbicella faveolata) into Filtered Seawater Mesocosms - Raw and Processed Data
The files in this data release are those referenced in the journal article by Evans and others (2023) entitled 'Investigating microbial size classes associated with the transmission of stony coral tissue loss disease (SCTLD)'. The files contain an amplicon sequence variant (ASV) table and the raw 16S rRNA gene amplicon files from fifty-six 0.22-micrometer (µm) pore size filters, as well as six rea
Prokaryotic Communities From Marine Biofilms Formed on Stainless Steel Plates in Coral Mesocosms - Raw and Processed Data
The files in this data release are those referenced in the journal article by Evans and others (2022) entitled "Ship Biofilms as Potential Reservoirs of Stony Coral Tissue Loss Disease." They contain an amplicon sequence variant (ASV) table and the raw 16S ribosomal ribonucleic acid (rRNA) gene amplicon deoxyribonucleic acid (DNA) sequence files from 15 microbial communities (sample names: CnD16B,
Bacterial Communities Shed by Montastraea cavernosa Coral Fragments into Filtered Seawater Mesocosms-Raw Data
Coral Microbiome Preservation and Extraction Method Comparison-Raw Data
Investigating microbial size classes associated with the transmission of stony coral tissue loss disease (SCTLD)
Effective treatment and prevention of any disease necessitates knowledge of the causative agent, yet the causative agents of most coral diseases remain unknown, in part due to the difficulty of distinguishing the pathogenic microbe(s) among the complex microbial backdrop of coral hosts. Stony coral tissue loss disease (SCTLD) is a particularly destructive disease of unknown etiology, capable of tr
Rapid prototyping for quantifying belief weights of competing hypotheses about emergent diseases
A meta-analysis of the stony coral tissue loss disease microbiome finds key bacteria in unaffected and lesion tissue in diseased colonies
Stony coral tissue loss disease (SCTLD) has been causing significant whole colony mortality on reefs in Florida and the Caribbean. The cause of SCTLD remains unknown, with the limited concurrence of SCTLD-associated bacteria among studies. We conducted a meta-analysis of 16S ribosomal RNA gene datasets generated by 16 field and laboratory SCTLD studies to find consistent bacteria associated with S
Biofilms as potential reservoirs of stony coral tissue loss disease
Since 2014, corals throughout Florida’s Coral Reef have been plagued by an epizootic of unknown etiology, colloquially termed stony coral tissue loss disease (SCTLD). Although in Florida the movement of this waterborne coral disease has been consistent with natural transport via water currents, outbreaks in the Caribbean have been more sporadic, with infections occurring in locations inconsistent
Combining tangential flow filtration and size fractionation of mesocosm water as a method for the investigation of waterborne coral diseases
Comparison of preservation and extraction methods on five taxonomically disparate coral microbiomes
Physicochemical controls on zones of higher coral stress where Black Band Disease occurs at Mākua Reef, Kauaʻi, Hawaiʻi
This project aims to understand the microbial processes, including disease, that influence the health of coral reef communities. We use microbiology and molecular biology techniques to better understand the role of microorganisms in shaping reef structure and function.
![Illustration of a mermaid on a coral reef with a double helix (DNA strand) tail.](https://d9-wret.s3.us-west-2.amazonaws.com/assets/palladium/production/s3fs-public/styles/side_image/public/media/images/mermaid3.png?itok=kknWr3_B)
Why Does the USGS Study the Microbes Found on Coral Reefs?
The loss and degradation of coral-reef ecosystems are occurring at increasing rates worldwide, in no small part due to coral diseases and die-offs of important herbivores like Diadema sea urchins. This decline negatively impacts society via removal of the ecosystem services provided by reefs, including storm protection, food supply through fish habitat, and tourism. Microbes play critical roles in the health of coral reefs, yet are generally underappreciated despite their ubiquity, abundance, complexity, and formative roles in the metabolic and chemical processes on reefs, including as agents of disease or as markers of land-based pollution.
![A SCUBA diver beside a Massive starlet coral on the sea floor at Dry Tortugas National Park](https://d9-wret.s3.us-west-2.amazonaws.com/assets/palladium/production/s3fs-public/styles/half_width/public/thumbnails/image/DRTO_Coral%20Gardens_Ssid_Drilled_CG2_2012%20%283%29.jpg?itok=IF07vX74)
Project MERMAID
MERMAID aims to increase our understanding of the critical and complex relationships between corals and microbes and their importance in reef health. This project employs a variety of metagenomic tools and methods to identify and track disease-causing agents that are negatively affecting coral reef ecosystems, establish biomarkers of stress or land-based pollution in coral reef ecosystems, and uncover new connections between abiotic conditions (e.g., measurement of sedimentation, nutrients, water circulation) and their biological effects on corals.
![Photo taken as SPMSC scientist Lauren Toth conducts a photographic survey of Porter Patch reef off Key Largo](https://d9-wret.s3.us-west-2.amazonaws.com/assets/palladium/production/s3fs-public/styles/half_width/public/thumbnails/image/Transect%20for%20reef%20complexity_Porter%20Patch_0.jpg?itok=YkMg0YR8)
For more details, please see our topical pages on:
- Characterizing microbial communities of healthy and degraded reefs to determine if there are microbial species or functional genes that can serve as indicators that correlate with reef processes such as calcification and submarine groundwater discharge.
Stony Coral Tissue Loss Disease:
- Investigating the unknown causative agent(s) of stony coral tissue loss disease (SCTLD) and determining possible modes of disease transmission.
Antibiotic-Resistance Gene (ARG) Baselines:
- Generating benchmark datasets on the presence/absence and diversity of antibiotic-resistance genes in coral tissue and reef sediments.
Coral Reef Project
Microbial Processes on Reefs
Coral Microbial Ecology
Coral Reef Ecosystem Studies (CREST)
Coral Disease
Prokaryotic Communities Shed by Diseased and Healthy Coral (Diploria labyrinthiformis, Pseudodiploria strigosa, Montastraea cavernosa, Colpophyllia natans, and Orbicella faveolata) into Filtered Seawater Mesocosms - Raw and Processed Data
The files in this data release are those referenced in the journal article by Evans and others (2023) entitled 'Investigating microbial size classes associated with the transmission of stony coral tissue loss disease (SCTLD)'. The files contain an amplicon sequence variant (ASV) table and the raw 16S rRNA gene amplicon files from fifty-six 0.22-micrometer (µm) pore size filters, as well as six rea
Prokaryotic Communities From Marine Biofilms Formed on Stainless Steel Plates in Coral Mesocosms - Raw and Processed Data
The files in this data release are those referenced in the journal article by Evans and others (2022) entitled "Ship Biofilms as Potential Reservoirs of Stony Coral Tissue Loss Disease." They contain an amplicon sequence variant (ASV) table and the raw 16S ribosomal ribonucleic acid (rRNA) gene amplicon deoxyribonucleic acid (DNA) sequence files from 15 microbial communities (sample names: CnD16B,
Bacterial Communities Shed by Montastraea cavernosa Coral Fragments into Filtered Seawater Mesocosms-Raw Data
Coral Microbiome Preservation and Extraction Method Comparison-Raw Data
Investigating microbial size classes associated with the transmission of stony coral tissue loss disease (SCTLD)
Effective treatment and prevention of any disease necessitates knowledge of the causative agent, yet the causative agents of most coral diseases remain unknown, in part due to the difficulty of distinguishing the pathogenic microbe(s) among the complex microbial backdrop of coral hosts. Stony coral tissue loss disease (SCTLD) is a particularly destructive disease of unknown etiology, capable of tr
Rapid prototyping for quantifying belief weights of competing hypotheses about emergent diseases
A meta-analysis of the stony coral tissue loss disease microbiome finds key bacteria in unaffected and lesion tissue in diseased colonies
Stony coral tissue loss disease (SCTLD) has been causing significant whole colony mortality on reefs in Florida and the Caribbean. The cause of SCTLD remains unknown, with the limited concurrence of SCTLD-associated bacteria among studies. We conducted a meta-analysis of 16S ribosomal RNA gene datasets generated by 16 field and laboratory SCTLD studies to find consistent bacteria associated with S
Biofilms as potential reservoirs of stony coral tissue loss disease
Since 2014, corals throughout Florida’s Coral Reef have been plagued by an epizootic of unknown etiology, colloquially termed stony coral tissue loss disease (SCTLD). Although in Florida the movement of this waterborne coral disease has been consistent with natural transport via water currents, outbreaks in the Caribbean have been more sporadic, with infections occurring in locations inconsistent