Identifying corals displaying aberrant behavior in Fiji’s Lau Archipelago

Mayfield, Anderson B.; Chen, Chii-Shiarng; Dempsey, Alexandra C.

doi:10.1371/journal.pone.0177267

Cited by 16 publications

(21 citation statements)

References 35 publications

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“…Please see Table 3 for hypotheses regarding gene expression behavior for each of the eight mRNAs targeted. Real-time PCR (qPCR)-based gene expression quantification of these eight targets was carried out as described previously [ 31 ].…”

Section: Methodsmentioning

confidence: 99%

Biomarker profiling in reef corals of Tonga’s Ha’apai and Vava’u archipelagos

2017

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Given the significant threats towards Earth’s coral reefs, there is an urgent need to document the current physiological condition of the resident organisms, particularly the reef-building scleractinians themselves. Unfortunately, most of the planet’s reefs are understudied, and some have yet to be seen. For instance, the Kingdom of Tonga possesses an extensive reef system, with thousands of hectares of unobserved reefs; little is known about their ecology, nor is there any information on the health of the resident corals. Given such knowledge deficiencies, 59 reefs across three Tongan archipelagos were surveyed herein, and pocilloporid corals were sampled from approximately half of these surveyed sites; 10 molecular-scale response variable were assessed in 88 of the sampled colonies, and 12 colonies were found to be outliers based on employment of a multivariate statistics-based aberrancy detection system. These outliers differed from the statistically normally behaving colonies in having not only higher RNA/DNA ratios but also elevated expression levels of three genes: 1) Symbiodinium zinc-induced facilitator-like 1-like, 2) host coral copper-zinc superoxide dismutase, and 3) host green fluorescent protein-like chromoprotein. Outliers were also characterized by significantly higher variation amongst the molecular response variables assessed, and the response variables that contributed most significantly to colonies being delineated as outliers differed between the two predominant reef coral species sampled, Pocillopora damicornis and P. acuta. These closely related species also displayed dissimilar temporal fluctuation patterns in their molecular physiologies, an observation that may have been driven by differences in their feeding strategies. Future works should attempt to determine whether corals displaying statistically aberrant molecular physiology, such as the 12 Tongan outliers identified herein, are indeed characterized by a diminished capacity for acclimating to the rapid changes in their abiotic milieu occurring as a result of global climate change.

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Section: Methodsmentioning

confidence: 99%

Biomarker profiling in reef corals of Tonga’s Ha’apai and Vava’u archipelagos

2017

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“…Although the potential utility of molecular biomarkers in diagnosing and predicting health outcomes has long been recognized in the coral restoration science community (Downs et al 2005b; Evans and Hofmann 2012; Traylor-Knowles and Palumbi 2014), research in this area has yet to produce any management-ready tools. As is evidenced by numerous studies reporting on putative biomarkers (Downs et al 2000(Downs et al , 2005aKenkel et al 2011Kenkel et al , 2014Lundgren et al 2013;Palumbi 2014, 2017;Jin et al 2016;Mayfield et al 2016Mayfield et al , 2017aMayfield et al , 2017bParkinson et al 2018), the problem lies not in the discovery phase, but in the subsequent phases of validation, field trials, and implementation (Traylor-Knowles and Palumbi 2014). There are many steps between identifying a potential biomarker and refining it for standard use, and the inherent difficulties involved in downstream biomarker development and validation are often overlooked.…”

Section: Box 1 Defining Biomarkersmentioning

confidence: 99%

“…Coral molecular biomarker discovery is not currently a bottleneck: many putative markers have already been proposed (Downs et al 2000(Downs et al , 2005aKenkel et al 2011Kenkel et al , 2014Lundgren et al 2013;Palumbi 2014, 2017;Jin et al 2016;Mayfield et al 2016Mayfield et al , 2017aMayfield et al , 2017bParkinson et al 2018). Furthermore, given the substantial progress being made in the field of coral ecological genomics, additional candidates could be identified through a larger meta-analysis of currently published studies which quantify both '-omics' markers and phenotypes of interest.…”

Section: Molecular Biomarker Discoverymentioning

confidence: 99%

“…More recently, a broader multivariate approach to validation was trialed in a survey of a few pocilloporid colonies from each of ~50 sites in Fiji and Tonga (Mayfield et al 2017a(Mayfield et al , 2017b. RNA/DNA ratios and the expression levels of several host and symbiont genes were used to determine the biomarker profile of an "average" coral at these locations, and statistical outliers were identified as "aberrant" (Mayfield et al 2017a(Mayfield et al , 2017b. In total, 23 of the 136 colonies (17%) were considered aberrant, but the lack of additional phenotypic trait data precluded linking the differences in assay values to health outcomes.…”

Section: Molecular Biomarker Validation and Field Trialsmentioning

confidence: 99%

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Molecular tools for coral reef restoration: beyond biomarker discovery

Parkinson¹,

Baker²,

Baums³

et al. 2018

Preprint

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As coral reefs continue to decline due to climate change and other stressors, scientists have proposed adopting genomic tools, such as biomarkers, to aid in the conservation and restoration of these threatened ecosystems. Biomarkers are easily measured indicators of higher-order biological processes that can be used to predict or diagnose health, resilience, and other key performance metrics. The ultimate goal of developing biomarkers is to determine the conservation value and utility of a given coral colony, including the host animal, its algal symbionts, and their microbial partners. However, we remain far from achieving this goal because most efforts have not yet moved beyond the initial discovery phase. Here, we review recent progress in the development of coral molecular biomarkers from a practical standpoint and consider the many challenges that remain as roadblocks to large-scale implementation. We caution practitioners that, while biomarkers are a promising technology, they are unlikely to be available for field application in the near future barring a rapid shift in research focus from discovery to subsequent validation and field trials. To facilitate such a shift, we propose a stepwise framework to guide additional study in this area, with the aim of accelerating practical molecular biomarker development to enhance coral restoration practice.

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“…Since molecular biology-driven approaches have revolutionized our understanding of the fundamental biology of anthozoan-dinoflagellate endosymbioses (e.g., Peng et al, 2011;Mayfield et al, 2012b;Wang et al, 2013;Mayfield et al, 2014b;Chen et al, 2015Chen et al, , 2016Chen et al, , 2017, as well as how these environmentally sensitive mutualisms respond to environmental change (e.g., Putnam et al, 2012;Mayfield et al, 2013;Putnam et al, 2013;Mayfield, Fan & Chen 2013b;Mayfield, Chen & Liu, 2014;Mayfield et al, 2014a;Mayfield, 2016;Mayfield et al, 2016a;Mayfield, Chen & Dempsey, 2017), a next generation sequencing (NGS)-based transcriptome profiling approach (RNA-Seq) was previously taken to attempt to uncover how the aforementioned pocilloporid corals from upwelling reefs of Southern Taiwan acclimated to such dramatic and prolonged increases in temperature (Mayfield et al, 2014c). Numerous mRNAs in both compartments (coral host and dinoflagellate endosymbionts of the genus Symbiodinium) were found to be affected by both short-(2-week) and long-term (36-week) elevated temperature exposure.…”

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confidence: 99%

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Supplemental Information 3: Peptide Sequences for the Differentially Expressed Proteins (DEPs) Identified at the Eight-Week Sam

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Although most reef-building corals live near the upper threshold of their thermotolerance, some scleractinians are resilient to temperature increases. For instance, Pocillopora acuta specimens from an upwelling habitat in Southern Taiwan survived a 9-month experimental exposure to 30°C, a temperature hypothesized to induce stress. To gain a greater understanding of the molecular pathways underlying such high-temperature acclimation, the protein profiles of experimental controls incubated at 27°C were compared to those of conspecific P. acuta specimens exposed to 30°C for two, four, or eight weeks, and differentially expressed proteins (DEPs) were removed from the protein gels and sequenced with mass spectrometry. Sixty unique DEPs were uncovered across both eukaryotic compartments of the P. acuta-dinoflagellate (genus Symbiodinium) mutualism, and Symbiodinium were more likely to up-regulate protein expression in response to high temperature exposure than the coral hosts in which they resided at the 2-week sampling time. Furthermore, different cellular pathways were affected by elevated temperature exposure in each compartment; Symbiodinium tended to up-regulate the expression of proteins involved in the cellular stress response, whereas the differentially expressed host coral proteome featured numerous proteins involved in cytoskeletal structure, immunity, and metabolism. These proteome-scale data suggest that the coral host and its intracellular dinoflagellates have differing cellular strategies for acclimating to elevated temperatures. AbstractAlthough most reef-building corals live near the upper threshold of their thermotolerance, some scleractinians are resilient to temperature increases. For instance, Pocillopora acuta specimens from an upwelling habitat in Southern Taiwan survived a nine-month experimental exposure to 30°C, a temperature hypothesized to induce stress. To gain a greater understanding of the molecular pathways underlying such high-temperature acclimation, the protein profiles of experimental controls incubated at 27°C were compared to those of conspecific P. acuta specimens exposed to 30°C for two, four, or eight weeks, and differentially expressed proteins (DEPs) were removed from the protein gels and sequenced with mass spectrometry. Sixty unique DEPs were uncovered across both eukaryotic compartments of the P. acuta-dinoflagellate (genus Symbiodinium) mutualism, and Symbiodinium were more likely to up-regulate protein expression in response to high temperature exposure than the coral hosts in which they resided at the twoweek sampling time. Furthermore, different cellular pathways were affected by elevated temperature exposure in each compartment; Symbiodinium tended to up-regulate the expression of proteins involved in the cellular stress response, whereas the differentially expressed host coral proteome featured numerous proteins involved in cytoskeletal structure, immunity, and metabolism. These proteome-scale data suggest that the coral host and its intracellular dinoflagellates hav...

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Identifying corals displaying aberrant behavior in Fiji’s Lau Archipelago

Cited by 16 publications

References 35 publications

Biomarker profiling in reef corals of Tonga’s Ha’apai and Vava’u archipelagos

Biomarker profiling in reef corals of Tonga’s Ha’apai and Vava’u archipelagos

Molecular tools for coral reef restoration: beyond biomarker discovery

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