Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding

Increasing speed and magnitude of global change threaten the world's biodiversity and particularly coral reef fishes. A better understanding of large-scale patterns and processes on coral reefs is essential to prevent fish biodiversity decline but it requires new monitoring approaches. Here, we use environmental DNA metabarcoding to reconstruct well-known patterns of fish biodiversity on coral reefs and uncover hidden patterns on these highly diverse and threatened ecosystems. We analysed 226 environmental DNA (eDNA) seawater samples from 100 stations in five tropical regions (Caribbean, Central and Southwest Pacific, Coral Triangle and Western Indian Ocean) and compared those to 2047 underwater visual censuses from the Reef Life Survey in 1224 stations. Environmental DNA reveals a higher (16%) fish biodiversity, with 2650 taxa, and 25% more families than underwater visual surveys. By identifying more pelagic, reef-associated and crypto-benthic species, eDNA offers a fresh view on assembly rules across spatial scales. Nevertheless, the reef life survey identified more species than eDNA in 47 shared families, which can be due to incomplete sequence assignment, possibly combined with incomplete detection in the environment, for some species. Combining eDNA metabarcoding and extensive visual census offers novel insights on the spatial organization of the richest marine ecosystems

Benchmarking fish biodiversity of seaports with eDNA and nearby marine reserves

\ₑprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/conl.13001International audienceCoastal areas offer a diversity of habitats providing refugia and nursery for fish, promoting their biodiversity and associated contributions to people. Yet, natural coastlines are replaced by artificial infrastructures such as seaports and the influence of this artificialization on fish biodiversity remains poorly known. Here, we assessed fish biodiversity indicators using environmental DNA metabarcoding inside seaports and adjacent natural habitats including no-take marine reserves. We found that species assemblages within seaports were primarily influenced by their area and habitat. We detected a similar species richness in seaports and reserves during lockdown, but seaports host more threatened species than natural habitats. Yet, species turnover between seaports was lower than between natural areas, reflecting biotic homogenization. Seaport managers should consider that complexifying artificial infrastructures could increase habitat diversity and coastal fish biodiversity. Our study illustrates that eDNA-based indicators can be integrated in management and policy applications toward greener marine artificial infrastructures

Benchmarking bioinformatic tools for fast and accurate eDNA metabarcoding species identification

Bioinformatic analysis of eDNA metabarcoding data is crucial toward rigorously assessing biodiversity. Many programs are now available for each step of the required analyses, but their relative abilities at providing fast and accurate species lists have seldom been evaluated. We used simulated mock communities and real fish eDNA metabarcoding data to evaluate the performance of 13 bioinformatic programs and pipelines to retrieve fish occurrence and read abundance using the 12S mt rRNA gene marker. We used four indices to compare the outputs of each program with the simulated samples: sensitivity, F-measure, root-mean-square error (RMSE) on read relative abundances, and execution time. We found marked differences among programs only for the taxonomic assignment step, both in terms of sensitivity, F-measure and RMSE. Running time was highly different between programs for each step. The fastest programs with best indices for each step were assembled into a pipeline. We compare this pipeline to pipelines constructed from existing toolboxes (OBITools, Barque, and QIIME 2). Our pipeline and Barque obtained the best performance for all indices and appear to be better alternatives to highly used pipelines for analyzing fish eDNA metabarcoding data with a complete reference database. Real eDNA metabarcoding data also indicated differences for taxonomic assignment and execution time only. This study reveals major differences between programs during the taxonomic assignment step. The choice of algorithm for the taxonomic assignment can have a significant impact on diversity estimates and should be made according to the objectives of the study

Three‐dimensional conservation planning of fish biodiversity metrics to achieve the deep‐sea 30×30 conservation target

International audienceAccelerating rate of human impact and environmental change severely affects marine biodiversity and increases the urgency to implement the Convention on Biological Diversity (CBD) 30×30 plan for conserving 30% of sea areas by 2030. However, area‐based conservation targets are complex to identify in a 3‐dimensional (3D) ocean where deep‐sea features such as seamounts have been seldom studied mostly due to challenging methodologies to implement at great depths. Yet, the use of emerging technologies, such as environmental DNA combined with modern modeling frameworks, could help address the problem. We collected environmental DNA, echosounder acoustic, and video data at 15 seamounts and deep island slopes across the Coral Sea. We modeled 7 fish community metrics and the abundances of 45 individual species and molecular operational taxonomic units (MOTUs) in benthic and pelagic waters (down to 600‐m deep) with boosted regression trees and generalized joint attribute models to describe biodiversity on seamounts and deep slopes and identify 3D protection solutions for achieving the CBD area target in New Caledonia (1.4 million km 2 ). We prioritized the identified conservation units in a 3D space, based on various biodiversity targets, to meet the goal of protecting at least 30% of the spatial domain, with a focus on areas with high biodiversity. The relationship between biodiversity protection targets and the spatial area protected by the solution was linear. The scenario protecting 30% of each biodiversity metric preserved almost 30% of the considered spatial domain and accounted for the 3D distribution of biodiversity. Our study paves the way for the use of combined data collection methodologies to improve biodiversity estimates in 3D structured marine environments for the selection of conservation areas and for the use of biodiversity targets to achieve area‐based international targets.Planeación tridimensional de la conservación de las medidas de biodiversidad de peces para lograr el objetivo de conservación 30x30 de mar profundo Resumen El impacto antropogénico y el cambio ambiental acelerados afectan gravemente a la biodiversidad marina y aumentan la urgencia de aplicar el plan 30x30 del Convenio sobre la Diversidad Biológica (CDB) para conservar el 30% de las zonas marinas para el 2030. Sin embargo, la identificación de objetivos de conservación basados en zonas es compleja en un océano tridimensional (3D) en el que rara vez se han estudiado las características de las profundidades marinas, como los montes marinos, sobre todo por la dificultad de aplicar metodologías a grandes profundidades. No obstante, el uso de tecnologías emergentes, como el ADN ambiental combinado con marcos actuales de modelación, podría ayudar a resolver el problema. Recopilamos datos de ADN ambiental, acústica de ecosonda y video en 15 montes marinos y taludes de islas profundas del mar del Coral. Modelamos siete medidas de comunidades de peces y 45 abundancias de especies individuales y unidades taxonómicas moleculares (UTOM) en aguas bentónicas y pelágicas (hasta 600 m de profundidad) con árboles de regresión reforzada (ARR) y modelos de atributos conjuntos generalizados (MACJ) para describir la biodiversidad en los montes marinos y taludes profundos e identificar soluciones de protección en 3D para alcanzar el objetivo de área del CDB en Nueva Caledonia (1.4 millones de km 2 ). Priorizamos las unidades de conservación identificadas en un espacio 3D con base en varios objetivos de biodiversidad para cumplir el objetivo de proteger al menos el 30% del dominio espacial con un enfoque en las zonas con una gran biodiversidad. La relación entre los objetivos de protección de la biodiversidad y el área espacial protegida por la solución fue lineal. El escenario que protegía el 30% de cada medida de biodiversidad preservó casi el 30% del dominio espacial considerado y consideró la distribución tridimensional de la biodiversidad. Nuestro estudio prepara el camino para el uso de metodologías combinadas de recopilación de datos con el fin de mejorar las estimaciones de biodiversidad en entornos marinos estructurados en 3D para la selección de áreas de conservación y para el uso de objetivos de biodiversidad con el fin de alcanzar objetivos internacionales basados en áreas

The distribution of coastal fish eDNA sequences in the Anthropocene

Aim: Coastal fishes have a fundamental role in marine ecosystem functioning and contributions to people, but face increasing threats due to climate change, habitat degradation and overexploitation. The extent to which human pressures are impacting coastal fish biodiversity in comparison with geographic and environmental factors at large spatial scale is still under scrutiny. Here, we took advantage of environmental DNA (eDNA) metabarcoding to investigate the relationship between fish biodiversity, including taxonomic and genetic components, and environmental but also socio-economic factors. Location: Tropical, temperate and polar coastal areas. Time period: Present day. Major taxa studied: Marine fishes. Methods: We analysed fish eDNA in 263 stations (samples) in 68 sites distributed across polar, temperate and tropical regions. We modelled the effect of environmental, geographic and socio-economic factors on alpha-and beta-diversity. We then computed the partial effect of each factor on several fish biodiversity components using taxonomic molecular units (MOTU) and genetic sequences. We also investigated the relationship between fish genetic alpha-and beta-diversity measured from our barcodes, and phylogenetic but also functional diversity. Results: We show that fish eDNA MOTU and sequence alpha-and beta-diversity have the strongest correlation with environmental factors on coastal ecosystems worldwide. However, our models also reveal a negative correlation between biodiversity and human dependence on marine ecosystems. In areas with high dependence, diversity of all fish, cryptobenthic fish and large fish MOTUs declined steeply. Finally, we show that a sequence diversity index, accounting for genetic distance between pairs of MOTUs, within and between communities, is a reliable proxy of phylogenetic and functional diversity. Main conclusions: Together, our results demonstrate that short eDNA sequences can be used to assess climate and direct human impacts on marine biodiversity at large scale in the Anthropocene and can further be extended to investigate biodiversity in its phylogenetic and functional dimensions.ISSN:1466-822XISSN:1466-823

Circumglobal distribution of fish environmental DNA in coral reefs

DNAQUA International Conference : international Conference on the Use of DNA for Water Biomonitoring , [En ligne], , -Coral reefs host the highest fish diversity on Earth despite covering less than 0.1% of theocean’s seafloor. At the same time they are also extremely threatened. Data synthesesover decades of surveys estimate the total number of coral reef fishes to vary from 2,400 to8,000 species distributed among roughly 100 families. But this diversity remains largelyunknown

The distribution of coastal fish eDNA sequences in the Anthropocene

Aim: Coastal fishes have a fundamental role in marine ecosystem functioning and contributions to people, but face increasing threats due to climate change, habitat degradation and overexploitation. The extent to which human pressures are impacting coastal fish biodiversity in comparison with geographic and environmental factors at large spatial scale is still under scrutiny. Here, we took advantage of environmental DNA (eDNA) metabarcoding to investigate the relationship between fish biodiversity, including taxonomic and genetic components, and environmental but also socio‐economic factors. Location: Tropical, temperate and polar coastal areas. Time period: Present day. Major taxa studied: Marine fishes. Methods: We analysed fish eDNA in 263 stations (samples) in 68 sites distributed across polar, temperate and tropical regions. We modelled the effect of environmental, geographic and socio‐economic factors on α‐ and β‐diversity. We then computed the partial effect of each factor on several fish biodiversity components using taxonomic molecular units (MOTU) and genetic sequences. We also investigated the relationship between fish genetic α‐ and β‐diversity measured from our barcodes, and phylogenetic but also functional diversity. Results: We show that fish eDNA MOTU and sequence α‐ and β‐diversity have the strongest correlation with environmental factors on coastal ecosystems worldwide. However, our models also reveal a negative correlation between biodiversity and human dependence on marine ecosystems. In areas with high dependence, diversity of all fish, cryptobenthic fish and large fish MOTUs declined steeply. Finally, we show that a sequence diversity index, accounting for genetic distance between pairs of MOTUs, within and between communities, is a reliable proxy of phylogenetic and functional diversity. Main conclusions: Together, our results demonstrate that short eDNA sequences can be used to assess climate and direct human impacts on marine biodiversity at large scale in the Anthropocene and can further be extended to investigate biodiversity in its phylogenetic and functional dimensions