Discussion
Strong transcriptional responses to SCTLD exposure in both coral species
Exposure to stony coral tissue loss disease in these experiments caused
evident transcriptional responses in both coral species. In general, we
observed a depression of host metabolic pathways and a corresponding
increase in expression of stress response genes and nuclear processes
(Figure S2). This is unsurprising given consistency in transcriptomic
responses to myriad stressors, a phenomenon characterized as a conserved
stress response among diverse coral taxa
(G. Dixon et al.,
2020; Wang et al., 2009). While there was evidence of a strong
transcriptional response to disease exposure in host corals, there was
little variation in the transcriptional response of symbionts in both
experiments. This may be due to lower alignment rates to the symbiont
transcriptomes relative to the coral hosts (6.5 ± 0.3% forCladocopium and 15.6 ± 0.8% for Durusdinium versus 61.2 ±
0.7% for M. cavernosa and 60.3 ± 1.6% for O. faveolata ,
respectively), or comparatively poor annotations in symbiont references.
Therefore, we have focused primarily on interpretation of the coral host
datasets to minimize speculation with the symbiont datasets.
Through comparative analyses between coral species in the transmission
experiment, we found consistent overlap in transcriptional responses
following exposure to SCTLD. There were 681 DEGs and 21 GO terms shared
between disease-exposed M. cavernosa and O. faveolata(Figures 2; 3), which may be an underestimation of orthologous genes
between species, since some orthogroups had different gene-level
annotations. The majority of DEGs (~64%) and all GO
terms were expressed or enriched in the same direction in response to
SCTLD exposure, suggesting that there are many conserved pathways among
coral species functioning in the same roles. This relationship has been
corroborated in a recent study by MacKnight and colleagues
(2022), which
examined transcriptional responses of seven coral species (including our
study species) to white plague disease. They reported expression of
immunity and cytoskeletal arrangement gene pathways across all species
following disease exposure, with variation in intracellular protein
trafficking pathways related to differences between disease
susceptibility among and within species. Similarly, we observed higher
enrichment of protein trafficking GO and KOG terms in M.
cavernosa , which is less susceptible to SCTLD than O. faveolata(Figure 3; Figure S2)
(Meiling et al., 2021;
NOAA, 2018).
Conversely, a minority of DEGs showed inverse relationships between
species following exposure to SCTLD (Figure 2). Despite this, functional
enrichment of GO and KOG terms were largely similar between species
(Figure 3; Figure S2), potentially indicating modulation of conserved
gene pathways between M. cavernosa and O. faveolata (i.e.,
different species using the same gene pathways in different ways). This
modulation may be indicative of plasticity related to disease
susceptibility (e.g.,
MacKnight et al., 2022), and warrants additional investigation with
other species affected by SCTLD.
Traylor-Knowles and colleagues
(2021) identified
differentially expressed gene processes implicated in coral immunity
following exposure to SCTLD. In this study, we observed 26 DEGs in
SCTLD-exposed M. cavernosa associated with these same immune
processes, and 19 DEGs in O. faveolata . These included two
apoptosis regulation pathways that were differentially expressed inM. cavernosa only, which are implicated in cell death and
necrosis (D’Arcy,
2019; Fuess et al., 2017). Extracellular matrix genes (four forM. cavernosa and three for O. faveolata ) were generally
downregulated in both species, and are hypothesized to be related to
wound healing and the prevention of lesion progression
(Traylor-Knowles et
al., 2021; Young et al., 2020). Four transforming growth factor-beta
(TGF-β) DEGs were downregulated in M. cavernosa only, which are
likely part of the coral’s immune response
(Fuess et al., 2020;
Traylor-Knowles et al., 2021). Two NF-𝜅B activation genes for each
species were upregulated (though one M. cavernosa DEG was
downregulated), where this transcription factor is well-known for its
role in immune activation and potentially in regulation of the
coral-algal symbiosis
(Voolstra et al.,
2009; Williams et al., 2018). This is perhaps related to the hypothesis
that SCTLD may be a virus targeting Symbiodiniaceae
(Veglia et al., 2022;
Work et al., 2021), but this observation requires further study.
Four peroxidases were upregulated in M. cavernosa , but ten DEGs
had variable expression levels in O. faveolata . Peroxidases have
been shown to be a component of the innate immune response to disease
and thermal stress
(Mydlarz & Harvell,
2007; Palmer, 2018). Protein tyrosine kinase (PTK) genes, which promote
inflammatory responses to pathogens in corals
(Fuess et al., 2016),
had variable expression levels (nine in M. cavernosa and three inO. faveolata ), corroborating that cytokine production may play a
role in the response to SCTLD exposure
(Traylor-Knowles et
al., 2021). Finally, one WD-repeat gene per species was downregulated,
which is likely involved in apoptotic and immune responses
(Aranda et al.,
2011). While these genes do not provide the complete picture of coral’s
transcriptomic responses to SCTLD, their differential expression in both
studies provides evidence of their importance in the immune response to
this disease and may be useful in the identification of biomarkers of
disease exposure in wild corals.
Effects of antibiotic treatments on coral transcriptional patterns
Treatment of corals with amoxicillin appears to result in a
‘normalization’ of transcriptional pathways associated with the response
to SCTLD. When comparing expression profiles across all genes, treated
corals appeared more similar to apparently-healthy controls than they
did their original diseased state (Figure 4). Comparisons of diseased
versus healthy samples in both transmission and intervention experiments
revealed mostly similar patterns, with downregulation of metabolic
pathways and upregulation of stress response, immune, and nuclear
processes (Figure S4). The majority of shared DEGs between diseased
individuals in both experiments were expressed in the same direction
(~64%), however, examination of treated versus diseased
colonies showed an inverse relationship of expression patterns across
the majority of shared DEGs (~76%, Figure 5). This
implies a reversal of the same transcriptomic mechanisms involved in the
immune response to SCTLD following treatment with amoxicillin, and
provides evidence that disease intervention may be beneficial to the
coral beyond removal of potential pathogens and co-occurring
opportunistic microbes that may be affecting host transcription. As
studies evaluating the effectiveness of antibiotic treatments on
diseased corals often focus on visible observations (i.e., lesion
progression and/or quiescence; Forrester et al., 2022; Neely et al.,
2020; Shilling et al., 2021; Walker et al., 2021) or shifts in microbial
communities (Sweet et
al., 2011, 2014) as a means of assessing treatment success, this
hypothesis requires further testing to elucidate the impacts of
antibiotic treatment on other members of the holobiont including the
coral host. For example, antibiotics have additional immune-modulating
and anti-inflammatory impacts on humans beyond alteration of associated
microbial communities
(Pradhan et al.,
2016), which may prove beneficial to corals affected by SCTLD.
Examination of the SCTLD-associated immune responses described by
Traylor-Knowles and colleagues
(2021) in our
datasets also corroborated the reversal of transcriptional patterns
following amoxicillin treatment. Eleven immune-related pathways were
differentially expressed in diseased versus healthy corals, with
fourteen in treated versus diseased corals. While overlap was minimal
between treatment comparisons (four identical DEGs), expression patterns
were often inversely related among immune classes. Four extracellular
matrix genes were upregulated in treated colonies compared to
downregulated in diseased samples from the transmission experiment (no
DEGs were observed for diseased versus healthy colonies in the
intervention experiment). Two NF-𝜅B activation DEGs were found for each
treatment comparison and were upregulated in diseased versus
downregulated in treated colonies. Three PTK genes were upregulated in
diseased colonies while two matching genes (and one additional) were
downregulated following treatment. TGF-β and WD-repeat DEGs were also
inversely-expressed between diseased and treated colonies, indicative of
a shift in immune responses following antibiotic treatment.
Evaluation of antibiotic treatment as an SCTLD intervention
Amoxicillin is effective at slowing or halting SCTLD lesion progression
on individual colonies, including in a field setting
(Forrester et al.,
2022; Neely et al., 2020; Shilling et al., 2021; Walker et al., 2021).
There are multiple limitations of antibiotic effectiveness on
broad-scale disease intervention efforts, including that this approach
often requires multiple re-treatments, continuous monitoring, and is
labor-intensive (Neely
et al., 2020; Walker et al., 2021). The time investment is especially
important when considering reef systems with substantially more corals
than southeast Florida, such as the Flower Garden Banks that recently
experienced its first potential signs of a SCTLD outbreak
(Johnston et al.,
2023). While application of amoxicillin shows a high rate of success
(~95%) in halting individual lesions, it does not
necessarily prevent the formation of new lesions on a treated colony
through time (e.g.,
Shilling et al., 2021). Finally, it is currently unknown what impacts
antibiotic application may have on diverse coral reef ecosystems,
notably potential antibiotic resistance in microbial communities
(Griffin et al., 2020;
Liu et al., 2020). Antibiotic treatment may additionally have negative
impacts on healthy coral microbiomes, potentially increasing
susceptibility of corals to other stressors such as elevated
temperatures (Connelly
et al., 2022).
Alternative treatment approaches are therefore warranted for further
investigation in the mitigation of SCTLD, as well as future coral
disease outbreaks. In particular, probiotic treatments are gaining
research interest due to their potential benefits to coral survival
following disease exposure
(Peixoto et al.,
2021), thermal stress
(Doering et al., 2021;
Santoro et al., 2021), and exposure to pollutants
(Silva et al., 2021).
Probiotic treatments are in development for SCTLD
(Deutsch et al.,
2022), and field trials are necessary to assess treatment effectiveness
in a reef environment
(Peixoto et al.,
2021). Phage therapy also shows promise for the treatment of bacterial
pathogens that affect corals
(Jacquemot et al.,
2018; Teplitski & Ritchie, 2009; Thurber et al., 2020), but many of
these approaches are not yet fully operational.
While treatment of individual coral colonies with antibiotics is not
intended to be a long-term solution to curbing the spread of SCTLD, it
may represent a feasible method of mitigating impacts on high-value
conservation and restoration targets, particularly
ecologically-important, rare, and reproductively-viable members of the
population. This is of particular importance while disease diagnostics
are still being developed for SCTLD and other diseases. Disease
diagnostics, when operational and scalable, may instead allow broad
mitigation of pathogen transport via disease vectors and sources,
potentially eliminating the need for colony-level disease intervention.
Continued examination of gene mechanisms and functions will also improve
understanding of coral immune responses
(Traylor-Knowles et
al., 2022), facilitating targeted treatment approaches in future
disease outbreaks. Disease response efforts focusing on identification
and diagnosis, mitigation of spread, and treatment of affected
individuals require a holistic understanding of coral immunity and
resilience at the individual level in order to maximize conservation and
restoration success at the population level.