Novel Mitochondrial DNA Markers for Scleractinian Corals and Generic-Level Environmental DNA Metabarcoding

Shinzato, Chuya; Narisoko, Haruhi; Nishitsuji, Koki; Nagata, Takuya; Satoh, Noriyuki; Inoue, Jun

doi:10.3389/fmars.2021.758207

Cited by 13 publications

(43 citation statements)

References 24 publications

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“…Therefore, our results reflect the need for optimization or a new primer design for COI, as is already being pursued for stony corals (Shinzato et al, 2021).…”

Section: Specific Methodical Limitationsmentioning

confidence: 99%

“…Therefore, in addition to designing new primer pairs for the taxon under study, combining different primer pairs in a multi-assay approach seems to be a promising strategy to achieve a better resolution of the actual species diversity. In this context, combinations of Nevertheless, our study and others (Nichols & Marko, 2019;Shinzato et al, 2021) show that genus-level monitoring of stony corals using mt genes is quite feasible and useful. However, future studies should favor multi-assay approaches that include nuclear markers to combine the advantages of marker systems and obtain the best possible combination of species detection and assignment.…”

Section: Specific Methodical Limitationsmentioning

confidence: 99%

“…Furthermore, studies are needed to expand our knowledge of eDNA replenishment, transport, and degradation in aquatic environments (Andruszkiewicz et al, 2021; Jeunen et al, 2019, 2020; Koziol et al, 2019; Nichols & Marko, 2019; Rourke et al, 2022). Although eDNA metabarcoding has been widely used to survey biodiversity in different taxonomic groups (Mariani et al, 2021; Rourke et al, 2022; Ruppert et al, 2019; West et al, 2020), its use for monitoring coral biodiversity is just beginning (e.g., Alexander et al, 2020; Dugal et al, 2022; Ip et al, 2022; Nichols & Marko, 2019; Shinzato et al, 2021; West et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

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An environmental DNA metabarcoding approach versus a visual survey for reefs of Koh Pha‐ngan in Thailand

et al. 2022

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Information on diversity indices and abundance of individual species is crucial for the assessment of ecosystem health, especially for endangered ecosystems as coral reefs. The application of environmental DNA (eDNA) to monitor coral biodiversity is, however, just beginning to come into focus for marine biologists. In this study, an eDNA metabarcoding approach of seawater samples in three different reefs on Koh Pha‐ngan, Thailand, was compared with simultaneously collected visual census data. In addition, differences in read abundance and number of genera detected between daytime and nighttime eDNA samples were examined, and a local coral barcode reference database (n = 23 genera; COI gene) was constructed to improve assignment of eDNA reads to the genus level. As a technical extension of existing assays, two methods for library construction were compared: a commercial kit and in‐house developed fusion primers. Combining eDNA metabarcoding and visual data, 29 different genera of scleractinian corals from 14 families were detected. In addition, a log‐linear correlation was found between the abundance of eDNA reads and visually determined relative coral cover at the genus level, suggesting a predictive relationship between eDNA reads and coral cover. Results also showed diurnal variation between day and night samples in the number of eDNA reads, purported to relate to the activity phases of corals. The use of uniquely labeled fusion primers, gave comparable results to a commercially available library preparation kit. Especially with frequent use, fusion primers can be very cost‐effective, and therefore a consideration for large‐scale studies. Using a custom reference database of 89 sequences from coral tissue samples of 23 different coral genera produced better results than querying against NCBI GenBank, highlighting the importance of locally optimized databases. We consider these results important for establishing eDNA as a complementary tool to visual surveys to track changes in coral diversity and cover.

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“…Therefore, our results reflect the need for optimization or a new primer design for COI, as is already being pursued for stony corals (Shinzato et al, 2021).…”

Section: Specific Methodical Limitationsmentioning

confidence: 99%

Section: Specific Methodical Limitationsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

An environmental DNA metabarcoding approach versus a visual survey for reefs of Koh Pha‐ngan in Thailand

et al. 2022

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“…Such studies are likely to be hampered by difficulties in defining coral species based on visual surveys (Postaire et al, 2016;Forsman et al, 2020;Oury et al, 2020;Prada and Hellberg, 2021;Rippe et al, 2021). This could be overcome by using molecular surveying techniques such as environmental DNA, which could make it possible to establish objective molecular boundaries to distinguish between surveyed species (Shinzato et al, 2018;Shinzato et al, 2021;Dugal et al, 2022).…”

Section: Perspectivesmentioning

confidence: 99%

Worldwide analysis of reef surveys sorts coral taxa by associations with recent and past heat stress

et al. 2022

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Coral reefs around the world are under threat from anomalous heat waves that are causing the widespread decline of hard corals. Different coral taxa are known to have different sensitivities to heat, although variation in susceptibilities have also been observed within the same species living in different environments. Characterizing such taxa-specific variations is key to enforcing efficient reef conservation strategies. Here, we combine worldwide-reef-survey data with remote sensed environmental variables to evaluate how local differences in taxa-specific coral cover are associated with past trends of thermal anomalies, as well as of non-heat related conditions. While the association with non-heat related environmental variation was seldom significant, we found that heat stress trends matched local differences in coral cover. Coral taxa were sorted based on the different patterns of associations with recent heat stress (measured the year before the survey) and past heat stress (measured since 1985). For branching, tabular and corymbose Acroporidae, reefs exposed to recent heat stress had lower coral cover than locally expected. Among such reefs, those previously exposed to frequent past heat stress displayed relatively higher coral cover, compared to those less frequently exposed. For massive and encrusting Poritidae, and for meandroid Favidae and Mussidae, we observed a negative association of coral cover with recent heat stress. However, unlike with Acroporidae, these associations were weaker and did not vary with past heat exposure. For Pocilloporidae, we found a positive association between coral cover and recent heat stress for reefs frequently exposed to past heat, while we found a negative association at reefs less frequently exposed to past heat. A similar pattern was observed for the branching Poritidae, although the associations were weaker and not statistically significant. Overall, these results show taxa-specific heat association patterns that might correspond to taxa-specific responses to past heat exposure, such as shifts in the assembly of coral communities, evolutionary adaptation or physiological acclimation.

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Section: Perspectivesmentioning

confidence: 99%

Worldwide analysis of reef surveys sorts coral taxa by associations with recent and past heat stress

Selmoni

Lecellier

Berteaux‐Lecellier

et al. 2021

Preprint

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Coral reefs around the world are under threat due to widespread decline of hard corals caused by anomalous heat waves. Coral taxa of different morphologies are known to have different sensitivities to heat stress. However, little is known about how long-term effects of heat exposure differ between coral taxa, nor in particular how such effects might drive adaptive processes.Here, we combined worldwide reef survey data with remotely sensed thermal anomalies to evaluate how local rates of taxa-specific coral cover were associated with heat stress. We found a negative association between coral cover and heat stress, where associations were weaker for corals with boulder-like morphology (massive corals), intermediate for corals with arborescent morphology (branching corals) and stronger for corals with encrusting or laminar morphology (plating corals). Additionally, we found that the negative association between branching coral cover and recent exposure to heat stress (measured as the year before a survey) was mitigated by the effect of long-term heat stress (measured since 1985), suggesting that adaptive processes occurred. In contrast, this “mitigating effect” of past heat-stress was not observed for either massive or plating corals.We hypothesize that these different responses to recent and past heat stress mirror different life history traits of coral taxa. For instance, branching corals are known to show higher sensitivities to heat stress and faster growth rates, two characteristics that might boost adaptive rates via evolutionary processes, when compared with other taxa.The results of this work suggest that all coral taxa, regardless of their morphology, will be “losers” of coral bleaching, and that conservation strategies should be adjusted to match taxa-specific responses to heat stress.

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Novel Mitochondrial DNA Markers for Scleractinian Corals and Generic-Level Environmental DNA Metabarcoding

Cited by 13 publications

References 24 publications

An environmental DNA metabarcoding approach versus a visual survey for reefs of Koh Pha‐ngan in Thailand

An environmental DNA metabarcoding approach versus a visual survey for reefs of Koh Pha‐ngan in Thailand

Worldwide analysis of reef surveys sorts coral taxa by associations with recent and past heat stress

Worldwide analysis of reef surveys sorts coral taxa by associations with recent and past heat stress

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