Ethan C. Cissell

Cyanobacterial mats as benthic reservoirs and vectors for coral black band disease pathogens

The concurrent rise in the prevalence of conspicuous benthic cyanobacterial mats and the incidence of coral diseases independently markmajor axes of degradation of coral reefs globally. Recent advances have uncovered the potential for the existence of interactions between the expanding cover of cyanobacterial mats and coral disease, especially black band disease (BBD), and this intersection represents both an urgent conservation concern and a critical challenge for future research. Here, we propose links between the transmission of BBD and benthic cyanobacterial mats. We provide molecular and ecophysiological evidence suggesting that cyanobacterial mats may create and maintain physically favorable benthic refugia for BBD pathogens while directly harboring BBD precursor assemblages, and discuss how mats may serve as direct (mediated via contact) and indirect (mediated via predator–prey–pathogen relationships) vectors for BBD pathogens. Finally, we identify and outline future priority research directions that are aligned with actionable management practices and priorities to support evidence-based coral conservation practices.

Data type
Scientific article
Research and monitoring
Geographic location

Exploring species and functional diversity of coral reef benthic cyanobacterial mats

Benthic cyanobacterial mats, at low cover, are an important benthic component of coral reefs, but have recently drastically proliferated on reefs worldwide. To better understand the factors that are driving this proliferation, we first must understand the identity of, and the interactions between, the microorganisms that build these mats. In a recent study published in Science of the Total Environment, researchers from Florida State University used next-generation DNA sequencing to explore the total species diversity of a benthic cyanobacterial mat sampled from the island of Bonaire. They found that coral reef cyanobacterial mats are cooperatively built by multiple species of microorganisms spanning all domains of life, and likely rely on this diversity to exploit environmental changes and proliferate. These data can be used to develop mechanistic hypotheses about what factors are most important in controlling the growth of coral reef benthic cyanobacterial mats.

A benthic cyanobacterial mat bloom (yellow) at Salt Pier, Bonaire, reaching near 100% cover of the benthos. This sequencing data will help scientists better understand how environmental factors interactively drive massive bloom events, such as the one pictured here. © Ethan Cissell

The rise of cyanobacterial mats

Cyanobacterial mats are naturally present at low abundance on coral reefs (~1% cover), and are thought to be critical in supplying bioavailable nitrogen to the reef environment that supports the growth of other benthic taxa such as coral. Recently, however, the abundance of cyanobacterial mats has expanded to cover ~20% of many Caribbean reefs, with massive blooms sometimes reaching close to 100% cover of the benthos. The increase in cover of benthic cyanobacterial mats poses numerous threats to overall reef health. To understand how different environmental factors are driving the rise of cyanobacterial mats, it is important to characterize the identity of the species that build these mats, and to understand the unique functional role of each mat community member.

DNA sequencing

To characterize the total diversity of benthic cyanobacterial mats, the team utilized a type of genetic sequencing known as shotgun metagenomic sequencing for its first ever application on a coral reef benthic cyanobacterial mat sample. In contrast to other sequencing methods that specifically target the DNA of only certain target species in a sample, this method instead sequences all of the DNA from a sample, and allows scientists to characterize all organisms in a sample, including viruses. The team sequenced 2 samples in this way – 1 taken from the growing edge of a cyanobacterial mat and 1 taken from the interior of that same cyanobacterial mat.

Species diversity

Shotgun metagenomic sequencing revealed that representative species from all domains of life can be found in coral reef benthic cyanobacterial mats, including members of domain Archaea, Bacteria, and Eukarya. The Florida State University team found that cyanobacteria were present at only 47.57% relative abundance in the mat samples, alongside other bacteria present at a relative abundance of 45.78%. Viruses, including viruses that can infect and kill bacteria called bacteriophages, were also present in the sampled mat at a relative abundance of 0.08%.

A benthic cyanobacterial mat (red) overgrowing an Orbicella annularis colony at Oil Slick Leap, Bonaire. Overgrowth interactions, such as the one pictured here, are detrimental to coral health, and will become more common as benthic cyanobacterial mats proliferate. © Ethan Cissell

Functional diversity

The team also found that the sampled mat possessed a diverse set of metabolic functions, including numerous cooperative functions for living as a coordinated community. The sampled mat community possessed numerous functions for the efficient utilization and storage of environmental phosphorous and nitrogen, both potentially limiting to the growth of cyanobacterial mats. Interestingly, the team also found evidence for multiple different pathways of nitrogen cycling, including the removal of bioavailable nitrogen in a process termed denitrification, that suggests the paradigm of cyanobacterial mats as an important nitrogen source to coral reefs should be revisited.

Future directions

Ongoing work by Cissell and McCoy seeks to characterize the dynamics of benthic cyanobacterial mats across multiple spatiotemporal scales using novel map-based tracking performed from May – July 2019 at Angel City, Bonaire. Additionally, Cissell and McCoy are using shotgun sequencing of both the DNA and RNA of multiple cyanobacterial mats to better understand daily cycles of mat community members, and their expressed functions. Combining an understanding of spatiotemporal variability in mat functions with a robust characterization of the persistence and volatility of cyanobacterial mats across multiple scales will facilitate rigorous tests of factors controlling mat abundance on Caribbean reefs.

More information

Cissell, E.C., McCoy, S.J. 2021. Shotgun metagenomic sequencing reveals the full taxonomic, trophic, and functional diversity of a coral reef benthic cyanobacterial mat from Bonaire, Caribbean Netherlands. Science of the Total Environment 755: 142719.


Article published in BioNews 42


Data type
Geographic location