Active Research Projects
Our research projects and interest are always evolving. This page provides a brief overview of our current research.
Genomics of Coral Disease Resistance
Ever since we identified that ~20% of staghorn coral genotypes are highly resistant to White Band Disease infection (Vollmer and Kline 2008), we have been trying to understand the genetic basis of this disease resistance. We started using RNA sequencing to profile coral immune genes and then characterize gene expression patterns associated with disease resistance. First, we showed that staghorn corals display strong immune response across 4% of their transcriptome, but don’t use “classic” innate immune pathways – Toll-like receptors (TLR), Complement, and Prophenoloxydase pathways – and instead use genes associated with phagocytosis, apoptosis, and the arachodonic acid pathway.
Next, we next asked if highly disease resistant staghorn corals responded differently to infection compared to susceptible corals. We identified 35 constitutively expressed genes underlying staghorn coral disease resistance whose expression was independent from the immune response due to disease exposure. Genes involved in RNA interference-mediated gene silencing, including Argonaute, were up-regulated in resistant corals, whereas heat shock proteins (HSPs) were down-regulated. Up-regulation of Argonaute proteins indicates that post-transcriptional gene silencing plays a key, but previously unsuspected role in coral disease resistance. Constitutive expression of HSPs has been linked to thermal resilience in other Acropora corals, suggesting that the down-regulation of HSPs in disease resistant staghorn corals may confer a dual benefit of thermal resilience. We hypothesize that miRNA gene regulation is playing a key role in coral immunity and disease resistance.
We then moved to the genome to identify gene variants associated with disease resistance using whole genome sequencing and a genome-wide association study of disease resistance. The good news is that disease resistance is genetic with numerous genome regions strongly associated with disease resistance in staghorn corals.
Etiology and Ecology of Coral Disease
Coral diseases represent one of the biggest threats to tropical coral reefs worldwide, and yet we often lack even basic information about the etiology and ecology of many coral diseases such as White Band Disease (WBD), which caused unprecedented die-offs in the Caribbean Acropora and placed them on the US Endangered Species List. Our research has closed significant gaps in our knowledge about the nature and transmission of the coral pathogens and helped developed WBD on staghorn coral as a model for coral-pathogen research.
First, we tested whether White Band Disease was transmissible and caused by bacterial or viral pathogens. In Kline and Vollmer 2011, we used filtrates and antibiotics to demonstrate that WBD is caused by a bacterial pathogen (and not a virus) whose transmission can be suppressed using broad spectrum antibiotics. Experimental use of antibiotics to study and suppress coral diseases has since become an important experimental and management tool.
Our research on coral disease transmission dynamics demonstrated that WBD can be transmitted via direct contact (Vollmer and Kline 2008), in the water column to injured corals or via a host-specific corallivorous snail vector (Gignoux-Wolfsohn et al. 2012), and even zooplankton (Certner et al. 2017). We developed reliable ways to experimentally transmit coral diseases using tank-based methods (Gignoux-Wolfsohn and Vollmer 2015b, Gignoux-Wolfsohn et al. 2017), which has help facilitate the identification on the WBD pathogen and our research on coral immunogenomics. Experimental evidence for waterborne transmission helped reconcile how the disease spread rapidly across the Caribbean in the 1980s.
Our tank-based transmission methods has allowed us to identifying resistant corals, characterize the microbes associated with disease, and experimentally manipulate bacterial transmission. Our initial focus was to identify microbes associated with WBD on staghorn corals by comparing the bacterial communities between healthy versus WBD-infected corals in the field and in tank-based infection experiments. We have used 16s bacterial rDNA sequencing to identify numerous candidate WBD pathogens within the bacterial families Vibrionaceae, Flavobacteriaceae, Campylobacteraceae, and Francisellaceae. We also documented the rapid loss of the symbiotic bacteria Endozoicomonas in immune compromised corals.
To advance beyond ASV-based disease associations, our research has become more manipulative and mechanistic. We initiated a series of experiments to manipulate (i.e. turn off and turn on) bacterial quorum sensing, which is a key pathway to initiate bacterial virulence. In Certner and Vollmer 2015, we demonstrated that a quorum sensing autoinducer – N-Hexanoyl-DL-homoserine lactone (AHL) – could cause a healthy staghorn coral microbiome to become pathogenic and illicit WBD signs. In the follow-up experiment by Certner and Vollmer 2018, we demonstrated that the addition of a quorum-sensing inhibitor (QSI) to a diseased coral microbiome halts WBD transmission, and that QSI-supplemented microbial communities contained lower abundances of disease-causing Vibrionaceae and Flavobacteriaceae bacteria. Given that quorum sensing is well-established in Vibrios, but not well-characterized in Flavobacteria, these results suggest that Vibrios are likely primary WBD pathogens.
We are actively engaged in narrowing down our list of likely pathogens through broad-scale metagenomic sequencing and bacterial focused microbiome manipulations.
Coral-Microbe Interactions
Corals possess hyper-diverse microbiomes filled with potentially beneficial bacteria as well as pathogens. Different coral species on the same reef possess very different microbial communities and these species specific differences are stable across time and space. Our research aims to understand how diverse coral microbiomes structure themselves across evolutionary lineages and in space and time because understanding how coral microbiomes assemble naturally is key to identifying beneficial and mutualistic bacteria within and across coral species and unlocking how these relationships break down under stress and pathogen infection.
While our primary focus has been on coral pathogens, our initial forays into comparing the variation in coral microbiomes across pairs of related coral species in Panama over time and space (Chu and Vollmer 2016) showed that microbe community structure mirrors coral phylogenetic relationships (Chu and Vollmer 2106) and that microbial communities sort first by species, then by space and less by time suggesting strong regulation of microbial community structure. We explored how this could be in the Dunphy et al. papers and it theoretical modeling.