Projects

Coral Disease Ecology and Etiology

The rise of coral diseases represents one of the biggest threats to tropical coral reefs worldwide, yet we often lack even basic information about the etiology and ecology of most coral diseases. A large part of my research program focuses on identifying coral pathogens, understanding how coral pathogens infect and impact the coral host, and understanding how the coral host responds and resists pathogen infection.

In Vollmer and Kline (2008), we used in situ transmission assays to identify that more than 6% of staghorn corals are naturally resistant to WBD infection1. This first evidence of coral disease resistance demonstrated that corals may be more resilient than thought to the disease epidemics. Our pioneering method of identifying resistant corals using in situ and tank-based transmission has since been adopted by numerous other researchers and conservation groups – such as my collaborators at the Coral Restoration Foundation – to identify disease resistant corals for large-scale coral restoration efforts across the Florida Keys and elsewhere. In our second paper2, we used a combination of 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.

My laboratory has continued to improve our understanding of WBD transmission dynamics demonstrating that WBD can be transmitted via direct contact 1, in the water column to injured corals 3, via a host-specific corallivorous snail vector 3, and even zooplankton 4 . This has helped us model the impact and spread of WBD in these endangered coral populations. Experimental evidence for waterborne transmission helped reconcile how the disease spread rapidly across the Caribbean in the 1980s, whereas the removal of the snail vector offers a means to mitigate local WBD outbreaks.

Publications

  1. Vollmer, S. V. & Kline, D. I. Natural disease resistance in threatened staghorn corals. PLoS One 3, e3718 (2008).
  2. Kline, D. I. & Vollmer, S. V. White Band Disease (type I) of endangered caribbean acroporid corals is caused by pathogenic bacteria. Sci. Rep. 1, 7 (2011).
  3. Gignoux-Wolfsohn, S. A., Marks, C. J. & Vollmer, S. V. White Band Disease transmission in the threatened coral, Acropora cervicornis. Sci. Rep. 2, 804 (2012).
  4. Certner, R. H., Dwyer, A. M., Patterson, M. R. & Vollmer, S. V. Zooplankton as a potential vector for white band disease transmission in the endangered coral, Acropora cervicornis. PeerJ 5, e3502 (2017).
Coral-Microbe Interactions and Metagenomics

Reef-building corals are a holobiont comprised of the coral animal, its symbiotic dinoflagellates Symbiodinium (or zooxanthellae), and a diverse set of associated bacteria and viruses. Viewing corals as a holobiont has greatly improved our understanding of the interactions between the coral host, its algae and microbes, including when these interactions breakdown as in the case of coral bleaching and coral disease. While significant gains have been made towards understanding the coral-algal symbioses, the nature of most coral-microbial interactions are still being teased apart.

My lab uses metagenomic approaches to characterize the structure and function of coral microbial communities in conjunction with manipulative experiments and classical microbiology techniques. Our primary focus has been disease coral microbiomes, specifically WBD-associated microbes. We have used 16s metagenomic sequencing to determine which bacteria are most strongly associated with WBD. We began by comparing the bacterial communities between healthy (asymptomatic) versus WBD-infected corals in the field (across multiple reefs and years) as well as in controlled, tank-based infection experiments5. Using Illumina 16s metagenomics sequencing, we identified strong community-level differences between diseased and healthy staghorn corals sampled in the field across sites and time as well as within the tank-based experiments. By comparing abundance differences at individual operational taxonomic units (OTUs), we identified 106 bacterial OTUs that were strongly and consistently associated with disease, which are good candidates for putative WBD pathogens. These putative pathogens including members of the orders Vibrionales and Rickettsiales, which had previously been suggested as WBD pathogens, as well as large numbers of Flavobacteriales.

In Gignoux-Wolfsohn et al. (2017), we used tank-based infection experiments coupled with 16s metagenomics to identify changes in the composition of the coral microbial community early (10 hrs post-inoculation) and late (22 – 60 hrs post-inoculation) into disease exposure6; this allowed us to identify primary (early) and secondary (late) colonizers. We identified 265 likely pathogens including Vibrionaceae (one OTU) and Rickettsiaceae (five OTUs), Flavobacteriaceae (22 OTUs), Campylobacteraceae (25 OTUs), Francisellaceae (38 OTUs) and Pasteurellaceae (26 OTUs). One of the strongest patterns in this study was that the rapid loss of Endozoicomonas, putative bacterial symbionts in corals, is a key indicators of compromised health in corals; this corroborates growing evidence the Endozoicomonas may be highly-specific coral bacterial symbionts much like the algal symbiont Symbiodinium.

To advance beyond these important OTU-based disease associations, our coral microbial research has become more manipulative and mechanistic. Because Vibrios are likely WBD pathogens, 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 coral microbiome to become pathogenic and cause WBD7. In Certner and Vollmer (in review), we demonstrate that the addition of a quorum sensing inhibitor (QSI) to a diseased coral microbiome halts 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 yet established for Flavobacteria, these results indicate that  Vibrios are likely primary WBD pathogens. We have experiments underway to confirm this hypothesis using infection experiments with specific Vibrio strains.

In 2015, I received $664k from NSF_Biological Oceanography (with Tarik Gouhier at Northeastern U) to investigate coral microbial competition, dispersal and disease dynamics using tank-based experiments, field surveys, metagenomics and mathematical modeling approaches. To manipulate coral microbiomes, we are using broad spectrum antibiotics to create “simplified” coral microbiomes that, when coupled with disease transmission experiments, allow us to study microbial resource and interference competition within the coral microbial community. By simplifying coral microbial diversity with antibiotics, we are essentially asking whether there is a “probiotic” effect of a healthy coral microbiome (i.e. not treated with antibiotics) that helps ward off pathogenic bacteria during disease infection. To determine how our tank-based experiments scale-up to coral communities on reefs, we are using a coral-microbial metacommunity model with two years of spatially-explicit and temporally-replicated, field-based 16s metagenomic and disease incidence data to model how microbial competition, dispersal and seasonal temperature variation jointly influence coral disease outbreaks and the structure of coral-microbial communities across spatial scales.

Publications

  1. Gignoux-Wolfsohn, S. A. & Vollmer, S. V. Identification of Candidate Coral Pathogens on White Band Disease-Infected Staghorn Coral. PLoS One 10, e0134416 (2015).
  2. Gignoux-Wolfsohn, S. A., Aronson, F. M. & Vollmer, S. V. Complex interactions between potentially pathogenic, opportunistic, and resident bacteria emerge during infection on a reef-building coral. FEMS Microbiol. Ecol. 93, (2017).
  3. Certner, R. H. & Vollmer, S. V. Evidence for Autoinduction and Quorum Sensing in White Band Disease-Causing Microbes on Acropora cervicornis. Sci. Rep. 5, 11134 (2015).
The Genetic Basis of Coral Immunity and Disease Resistance

In 2009, I received NSF funding to identify the genetic bases of coral innate immunity and disease resistance using RNA-sequencing of staghorn corals infected with White Band Disease (WBD). At the time, little was known about coral (or cnidarian) immunity, nothing was known about the genetics of coral disease resistance, and RNAseq was an emerging technology.

In Libro et al. (2013) we sequenced, assembled and annotated the transcriptome of A. cervicornis and produced the first transcriptome-wide, RNAseq gene expression profiles of a coral innate immune response8. RNAseq profiles comparing healthy (asymptomatic) versus diseased staghorn corals demonstrated that infected corals exhibited a strong immune response across 4% (1,805 out of 47,748 transcripts) of the transcriptome. However, rather than using the three “classic” innate immune pathways – Toll-like receptors (TLR), Complement, and Prophenoloxydase pathways – the primary immune response in staghorn corals involved genes associated with macrophage-mediated phagocytosis and apoptosis. We also observed strong up-regulation of the enzyme allene oxide synthase-lipoxygenase (ALOX) in infected corals suggesting a key (and potentially novel) role of the allene oxide pathway in coral immunity; we are now following up on the possibility that the ALOX pathway produces potent antimicrobials.

This led us to ask how disease resistant corals might respond differently to disease infection by comparing transcriptome-wide gene expression between disease resistant and susceptible staghorn corals exposed to WBD using in situ transmission assays9. We identified 35 constitutively expressed genes that differed significantly due to disease resistance and 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. Understanding how miRNA gene regulation influences coral gene regulation – as it relates to immunity, disease resistance, and beyond – is an active area of research in my lab; the role of small, non-coding RNAs in general is one of the hottest fields in molecular genetics.

Publications

  1. Libro, S., Kaluziak, S. T. & Vollmer, S. V. RNA-seq profiles of immune related genes in the staghorn coral Acropora cervicornis infected with white band disease. PLoS One 8, e81821 (2013).
  2. Libro, S. & Vollmer, S. V. Genetic Signature of Resistance to White Band Disease in the Caribbean Staghorn Coral Acropora cervicornis. PLoS One 11, e0146636 (2016).
Coral Speciation and Hybridization

My research established that the three Caribbean Acropora coral species constituted a natural hybridization system 9–12 where A. prolifera was actually a hybrid that acts as a conduit to pass genes (differentially) from the elkhorn coral A. palmata to the staghorn coral A. cervicornis. While my work on the Caribbean Acropora corals has shifted to include coral immunity and disease research, I continue to work and publish speciation and population genetic research on corals and other taxa.

With the Caribbean Acropora, I published two additional papers on the population genetics of staghorn corals 12,13, which reconstruct the history of gene flow , population size changes, and geographic patterns of introgression within these threatened coral populations. My paper with my former PhD student Liz Hemond (now an Assistant Professor at xxx in Turkey) was notable because it provided conservation managers with the first data on the genetic diversity and connectivity in Florida’s staghorn coral populations. My collaborators and I have also published further on the Caribbean Acropora hybridization system. Fogarty et al. (2012) focused the strength and direction of pre-zygotic isolation barriers in the system establishing that egg choice is an important barrier to hybridization 14. Palumbi et al. (2011) used coalescent analyses to estimate rates differential introgression between A. cervicornis and A. palmata the greater Caribbean 15.

In addition, my former PhD student David Combosch (now an Assistant Professor at University of Guam) and I identified a new hybridization system in Eastern Pacific Pocillopora corals, where introgressive hybridization corresponded with a reproductive shift from brooding to broadcast spawning in the Tropical Eastern Pacific (TEP) populations of these corals16,17. In 2015, we published trans-Pacific genetic comparison of Pocillopora damicornis and its hybrid partners using RAD and RNAseq, which confirmed the pattern of one-way introgression in TEP Pocillopora, but also demonstrated the poor correspondence between genetics (i.e. monophyly) and morphological species designations in the group18. Moreover, it is not yet known if the shift to hybridization in the TEP started before or after the 2500 year hiatus in reef growth observed in our Science paper19.

A lingering question about coral speciation relates to how coral species maintain their genetic distinctiveness despite hybridization potential. In the Caribbean Acropora hybridization system, I demonstrated that coral species are maintained by differential selection against introgressed genes crossing coral species boundaries 10,12. This argues for a gene-based or genic view of corals species 10,15, which predicts that key “speciation” genes define the genetic distinctiveness of hybridizing coral species.

It is still not known how permeable hybridizing coral genomes are to introgressing genes, primarily because we did not have enough genetic markers to survey patterns across coral genomes. Next-generation sequencing solves this problem and we are now examining genome-wide patterns of introgression between elkhorn and staghorn corals with our newly assembled staghorn coral genome, wealth of RNAseq expression data, and newly acquired RADseq data from Panama and Florida.

Publications

  1. Vollmer, S. V. & Palumbi, S. R. Testing the utility of internally transcribed spacer sequences in coral phylogenetics. Mol. Ecol. 13, 2763–2772 (2004).
  2. Vollmer, S. V. & Palumbi, S. R. Restricted gene flow in the Caribbean staghorn coral Acropora cervicornis: implications for the recovery of endangered reefs. J. Hered. 98, 40–50 (2007).
  3. Hemond, E. M. & Vollmer, S. V. Genetic diversity and connectivity in the threatened staghorn coral (Acropora cervicornis) in Florida. PLoS One 5, e8652 (2010).
  4. Fogarty, N. D., Vollmer, S. V. & Levitan, D. R. Weak prezygotic isolating mechanisms in threatened Caribbean Acropora corals. PLoS One 7, e30486 (2012).
  5. Palumbi, S. R., Vollmer, S., Romano, S., Oliver, T. & Ladner, J. The role of genes in understanding the evolutionary ecology of reef building corals. Evol. Ecol. 26, 317–335 (2011).
  6. Combosch, D. J., Guzman, H. M., Schuhmacher, H. & Vollmer, S. V. Interspecific hybridization and restricted trans-Pacific gene flow in the Tropical Eastern Pacific Pocillopora. Mol. Ecol. 17, 1304–1312 (2008).
  7. Combosch, D. J. & Vollmer, S. V. Population genetics of an ecosystem-defining reef coral Pocillopora damicornis in the Tropical Eastern Pacific. PLoS One 6, e21200 (2011).
  8. Combosch, D. J. & Vollmer, S. V. Trans-Pacific RAD-Seq population genomics confirms introgressive hybridization in Eastern Pacific Pocillopora corals. Mol. Phylogenet. Evol. 88, 154–162 (2015).
  9. Toth, L. T. et al. ENSO drove 2500-year collapse of eastern Pacific coral reefs. Science 337, 81–84 (2012).
Phylogenomics of North Atlantic Marine Taxa

In addition to my interest in coral genomics, I also have a strong interest in the evolutionary history of North Atlantic marine taxa. One of my first N. Atlantic projects examined patterns of evolution in the periwinkle snail Littorina saxatilis, which inhabits both N. Atlantic shores and is believed to be one of the few marine examples of incipient sympatric speciation. This species has multiple distinct morphotypes in multiple locations in the NE Atlantic due to differences in the intensity of crab predation. Essentially, high crab predation led to the emergence of thick shelled “ecotypes” multiple times across NE Atlantic shores. Our paper 20 raised new questions about this classic model of sympatric speciation by demonstrating that L. saxatilis and its periwinkle relatives have a much more complex evolutionary history than previously thought. By analyzing mtDNA sequences from snails on both sides of the Atlantic, we demonstrated that L. saxatilis types, which give live birth, originated twice in the past 640,000 years from their egg-laying relatives L. arcana and L. compressa. Both L. saxatilis mtDNA lineages now co-exist on both sides of the Atlantic in a patchwork influenced by different colonization histories. We even show that live-bearing L. saxatilis may be hybridizing with their egg-laying species.

My lab has also examined the phylogenomics and transcriptomics of the predatory dogwhelk Nucella lapillus in the NW Atlantic. Chu et al. (2014a) used RAD-seq and a transcriptome assembled from RNA-seq data to analyse the genetic structure of this low-dispersal intertidal snail 21. Our phylogenomic approach identified a phylogenetic break between northern and southern latitudinal clades. By mapping our RAD-seq data on our transcriptome assembly, we identified thousands of fixed single-nucleotide polymorphisms (SNPs) between these latitudinal clades that map to protein-coding genes, including genes associated with heat tolerance. In Chu et al. (2014b), we use RNA-seq to examine the transcriptomic  response of N. lapillus to thermal stress and crab predation risk. N. lapillus displayed a pronounced genetic response to thermal stress by upregulating many heat-shock proteins and other molecular chaperones 22. In contrast, crab exposure triggered few significant changes in gene expression, and showed no significant overlap with the snail’s response to thermal stress, suggesting that thermal stress and predation risk pose distinct challenges for N. lapillus.

My labs most recent NW Atlantic project focused on the population genetics of the sea scallop Placopecten magellanicus. Using $456k in NOAA_RSA funding, my collaborators and I used a RADseq-based, phylogenomic approach to examine source-sink dynamics in this important commercial fishery. We identified fine-scale population structure in sea scallop populations along the NW Atlantic, as well as strong regional structure between Nova Scotia, the Gulf of Maine, and populations south of Cape Cod down to North Carolina. The existence of regional population structure overlaid on fine-scale population subdivision within regions supports existing management strategies aimed at protecting local scallop stocks using no-take or limited-take fishing zones.

Publications

  1. Doellman, M. M., Trussell, G. C., Grahame, J. W. & Vollmer, S. V. Phylogeographic analysis reveals a deep lineage split within North Atlantic Littorina saxatilis. Proc. Biol. Sci. 278, 3175–3183 (2011).
  2. Chu, N. D., Kaluziak, S. T., Trussell, G. C. & Vollmer, S. V. Phylogenomic analyses reveal latitudinal population structure and polymorphisms in heat stress genes in the North Atlantic snail Nucella lapillus. Mol. Ecol. 23, 1863–1873 (2014).
  3. 22. Chu, N. D., Miller, L. P., Kaluziak, S. T., Trussell, G. C. & Vollmer, S. V. Thermal stress and predation risk trigger distinct transcriptomic responses in the intertidal snail Nucella lapillus. Mol. Ecol. 23, 6104–6113 (2014).