Matthieu Leray

• PhD https://www.matthieuleray.website
• PostDoc Position at Smithsonian Tropical Research Institute

Bacterial symbionts, with their shorter generation times and capacity for horizontal gene transfer (HGT), play a critical role in allowing marine organisms to cope with environmental change. The closure of the Isthmus of Panama created distinct environmental conditions in the Tropical Eastern Pacific (TEP) and Caribbean, offering a “natural experim...

The ability of consumers to adjust their diet in response to resource shifts is a key mechanism allowing the persistence of populations and underlying species adaptive capacity. Yet on coral reefs, one of the marine habitats most vulnerable to global change, the extent to which species alter their diet remains poorly understood. Here, we integrated...

Phages (viruses of bacteria and archaea) are a ubiquitous top-down control on microbial communities by selectively infecting and killing cells. As obligate parasites, phages are inherently linked to processes that impact their hosts’ distribution and physiology, but phages can also be impacted by external, environmental factors, such as UV radiatio...

Phages, or viruses that infect bacteria and archaea, are ubiquitous and abundant members of Earth′s ecosystems that impact the flow of nutrients, evolution of microbes, and food web dynamics by selectively infecting and killing their prokaryotic hosts. Because phages can only replicate through their hosts, they are inherently linked to processes im...

Environmental degradation has the potential to alter key mutualisms that underlie the structure and function of ecological communities. How microbial communities associated with fishes vary across populations and in relation to habitat characteristics remains largely unknown despite their fundamental roles in host nutrition and immunity. We find si...

Analysis of environmental DNA is increasingly used to characterize ecological communities, but the effectiveness of this approach depends on the accuracy of taxonomic reference databases. The MIDORI databases, first released in 2017, were built to improve accuracy for mitochondrial metazoan (animal) sequences. MIDORI has now been significantly impr...

Marine multicellular organisms host a diverse collection of bacteria, archaea, microbial eukaryotes, and viruses that form their microbiome. Such host-associated microbes can significantly influence the host’s physiological capacities; however, the identity and functional role(s) of key members of the microbiome (“core microbiome”) in most marine h...

Loss of oxygen in the global ocean is accelerating due to climate change and eutrophication, but how acute deoxygenation events affect tropical marine ecosystems remains poorly understood. Here we integrate analyses of coral reef benthic communities with microbial community sequencing to show how a deoxygenation event rapidly altered benthic commun...

Significance Knowledge of host–symbiont biogeography is critical to understanding fundamental aspects of symbiosis such as host–symbiont specificity. Marine animals typically acquire their symbionts from the environment, a strategy that enables the host to associate with symbionts that are well-suited to local conditions. In contrast, we discovered...

Benthic suspension feeders have significant impacts on plankton communities by depleting plankton or modifying the composition of the plankton through prey selectivity. Quantifying diets of planktivorous animals can be difficult because plankton are frequently microscopic, may lack diagnostic characters, and are digested at variable rates. With DNA...

In a recent paper, “Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring,” Pawlowski et al. argue that the term eDNA should be used to refer to the pool of DNA isolated from environmental samples, as opposed to only extra‐organismal DNA from macro‐organisms. We agree with this...

Two new species of the palaemonid shrimp genus Typton Costa, 1844 are described based on material from Panama and Mexico. Both species are closely related to T. tortugae McClendon, 1911, a species originally described from the Dry Tortugas, off southern Florida, USA, and later scarcely recorded from other western Atlantic localities, from Bermuda t...

Alpheus viserion sp. n. is described based on the material from Bocas del Toro archipelago on the Caribbean coast of Panama. The new species is morphologically closest to three members of the speciose A. armillatus H. Milne-Edwards, 1837 species complex, viz. A. carlae Anker, 2012, A. angulosus McClure, 2002, and A. tenuis Kim & Abele, 1988, differ...

In a recent paper, “Environmental DNA: What’s behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring”, Pawlowski et al. argue that the term eDNA should be used to refer to the pool of DNA isolated from environmental samples, as opposed to only extra-organismal DNA from macro-organisms. We agree with this...

In a recent paper, “Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring”, Pawlowski et al. argue that the term eDNA should be used to refer to the pool of DNA isolated from environmental samples, as opposed to only extra-organismal DNA from macro-organisms. We agree with this...

Benthic suspension feeders have significant impacts on plankton communities by depleting plankton or modifying composition of the plankton through prey selectivity. Quantifying diets of planktivorous animals can be difficult because plankton are frequently microscopic, may lack diagnostic characters, and are digested at variable rates. With DNA met...

The deep seafloor is teeming with life, most of which remains poorly known to science. It also constitutes an important reserve of natural resources, particularly minerals, that mining companies will start harvesting in the next few years (Nat Rev Earth Environ, 1, 2020, 158). In this context, broad biodiversity assessments of deep‐sea ecosystems a...

Environmental degradation has the potential to alter key mutualisms that underline the structure and function of ecological communities. While it is well recognized that the global loss of coral reefs alters fish communities, the effects of habitat degradation on microbial communities associated with fishes remain largely unknown despite their fund...

Accurate, rapid, and comprehensive biodiversity assessments are critical for investigating ecological processes and supporting conservation efforts. Environmental DNA (eDNA) surveys show promise as a way to effectively characterize fine-scale patterns of community composition. We tested whether a single PCR survey of eDNA in seawater using a broad...

The spongicolid genus Microprosthema Stimpson, 1860 is currently composed of 16 species inhabiting tropical and subtropical marine shallow waters worldwide, with six species found in the western Atlantic (one of them also present in the central and eastern Atlantic), one species in the eastern Pacific, and nine species in the Indo-West Pacific (Sai...

The significance of symbioses between eukaryotic hosts and microbes extends from the organismal to the ecosystem level and underpins the health of Earth’s most threatened marine ecosystems. Despite rapid growth in research on host-associated microbes, from individual microbial symbionts to host-associated consortia of significantly relevant taxa, l...

Traditional methods of characterizing biodiversity are increasingly being supplemented and replaced by approaches based on DNA sequencing alone. These approaches commonly involve extraction and high-throughput sequencing of bulk samples from biologically complex communities or samples of environmental DNA (eDNA). In such cases, vouchers for individ...

Accurate, rapid, and comprehensive biodiversity assessments are critical for investigating ecological processes and supporting conservation efforts. Environmental DNA (eDNA) surveys show promise as a way to effectively characterize fine-scale patterns of community composition, but most studies to date have evaluated its effectiveness in single habi...

Internal Transcribed Spacer structures are important in preserving accessibility to specific enzymes for the maturation of rRNAs. ITS1 sequences reported in the literature in Crustaceans range between 182 and 820 bp and are characterized by the absence of repeats or the presence of only a limited number of microsatellites. Here, we sequenced ITS1 f...

The significance of mutualisms between eukaryotic hosts and microbes extends from the organismal to the ecosystem level, and mutualistic symbioses underpin the health of Earth’s most threatened marine ecosystems. Despite rapid growth in research on host-associated microbes (microbiomes), very little is known about their interactions for the vast ma...

Theories involving niche diversification to explain high levels of tropical diversity propose that species are more likely to co‐occur if they partition at least one dimension of their ecological niche space. Yet, numerous species appear to have widely overlapping niches based upon broad categorizations of resource use or functional traits. In part...

Sponges act as important microhabitats in the marine environment and promote biodiversity by harboring a wide variety of macrofauna, but little is known about the magnitude and patterns of diversity of sponge-associated communities. This study uses DNA barcoding to examine the macrofaunal communities associated with Stylissa carteri in the central...

Corals and humans represent two extremely disparate metazoan lineages and are therefore useful for comparative evolutionary studies. Two lipid-based molecules that are central to human immunity, platelet-activating factor (PAF) and Lyso-PAF were recently identified in scleractinian corals. To identify processes in corals that involve these molecule...

Five species of shrimps, four carideans and one stenopodidean, are recorded for the first time from the Caribbean coast of Panama: Lysmata vittata (Stimpson, 1860) [Lysmatidae Dana, 1852], Periclimenaeus ascidiarum Holthuis, 1951, P. bredini Chace, 1972, P. maxillulidens (Schmitt, 1936) [Palaemonidae Rafinesque, 1815], and Odontozona edyli Criales...

We present MIDORI server, a user-friendly web platform that uses a curated reference dataset, MIDORI, for high throughput taxonomic classification of unknown metazoan mitochondrial-encoded gene sequences. Currently three methods of taxonomic assignments: RDP Classifier, SPINGO and SINTAX, are implemented. Availability: The web server is freely av...

Coral reefs harbor diverse assemblages of organisms yet the majority of this diversity is hidden within the three dimensional structure of the reef and neglected using standard visual surveys. This study uses Autonomous Reef Monitoring Structures (ARMS) and amplicon sequencing methodologies, targeting mitochondrial cytochrome oxidase I and 18S rRNA...

Scientific Reports 7 : Article number: 44923 10.1038/srep44923 ; published online: 30 March 2017 ; updated: 16 May 2017 This Article contains typographical errors in Table 2. For Gene ‘COI’, species ‘ T. guttata ’ under ‘Present study’, the location ‘RI’ should read ‘RI, NC’.

The advancement of metabarcoding techniques, declining costs of high-throughput sequencing and development of systematic sampling devices, such as autonomous reef monitoring structures (ARMS), have provided the means to gather a vast amount of diversity data from cryptic marine communities. However, such increased capability could also lead to anal...

Detailed methodologies. (PDF)

PERMANOVA and ANOSIMs for motile preservation experiment OTU data (Table A and C, respectively), and data merged by phylum (Table B and D, respectively). (PDF)

One-Way ANOSIMs and Tukey tests showing differences in community composition retrieved by processing method (Table A) and preservation method (Table B). (PDF)

Accuracy of relaxed parameters (≥85% sequence similarity) when assigning to higher-level taxonomic ranks with Blastn. Data shown represent phyla distribution among queries. (PDF)

Raw data (top tables) and overall summary (bottom table) of the quantity of DNA and the percentage of that DNA that is > 1000 bp (as determined by ImageJ analysis) recovered from DNA extractions of sessile and motile ARMS samples across different processing and preservation methods. Bold values indicate low DNA quantity (<100 ng/ul) or quality (<20...

One-Way ANOSIMs and Tukey Tests showing differences in community composition retrieved by processing method (OTU data; Table A), preservation method (OTU data; Table B) and differences in community richness retrieved by preservation and preservation method (OTU data; Table C). (PDF)

One-Way ANOSIMs and Tukey tests showing differences in community composition retrieved by processing and preservation method, void of Rhodophyta, for OTU data (Table A) and data merged by phylum (Table B). (PDF)

SIMPER analysis showing phylum level differences in community composition across all data from the sessile processing experiment, as retrieved by processing method (Table A; top table) and preservation technique (Table A; bottom table) and partitioned by preservation method (Table B; top two tables) and processing method (Table B; bottom two tables...

Conflicting and altered taxonomies in database searches. (PDF)

PERMANOVA for sessile processing experiment (OTU data). (PDF)

Phylum level identifications of OTUs and their relative abundance by ARMS fraction. Bold text represents most abundant phyla in each fraction. (PDF)

Several obligate associate crabs and shrimps species may co-occur and interact within a single coral host, leading to patterns of associations that can provide essential ecological services. However, knowledge of the dynamics of interactions in this system is limited, partly because identifying species involved in the network remains challenging. I...

DNA metabarcoding, the PCR-based profiling of natural communities, is becoming the method of choice for biodiversity monitoring because it circumvents some of the limitations inherent to traditional ecological surveys. However, potential sources of bias that can affect the reproducibility of this method remain to be quantified. The interpretation o...

List of specimens, including taxonomy and GenBank accession numbers, that were tissue subsampled to make up the mock sample Specimens are ranked based on the proportion of sequences recovered in the metabarcoding dataset.

Sample by observation contingency table displaying the number of reads per OTU and per sample

Phylogenetic relationships between representative COI sequences (313 bp) of 120 OTUs detected in the mock sample estimated using a Maximum Likelihood approach We used a general time reversible nucleotide model with a proportion of invariant sites and among site rate heterogeneity modeled with a discrete gamma distribution (GTR +I +G) together with...

COI amplicon data analysis script

Effect of rarefaction subsampling on the reproducibility of beta diversity The OTU table was rarefied five times down to the lowest number of sequences that a sample contained (45,609). See Table 2 for a summary of pairwise dissimilarity calculations.

Mitochondrial-encoded genes are increasingly targeted in studies using high-throughput sequencing approaches for characterizing metazoan communities from environmental samples (e.g., plankton, meiofauna, filtered water). Yet, unlike nuclear ribosomal RNA markers, there is to date no high-quality reference dataset available for taxonomic assignments...

The ocean constitutes one of the vastest and richest biomes on our planet. Most recent estimations, all based on indirect approaches, suggest that there are millions of marine eukaryotic species. Moreover, a large majority of these are small (less than 1 mm), cryptic and still unknown to science. However, this knowledge gap, caused by the lack of d...

A study led by researchers from the University of Jordan and the Smithsonian Institution reports the first survey of the typically overlooked cryptic organisms found on reefs of the Jordanian coast of the Gulf of Aqaba (Northern Red Sea) using a standardized sampling protocol and high-throughput DNA barcoding (metabarcoding).

High-Throughput Sequencing (HTS) of DNA barcodes (metabarcoding), particularly when combined with standardized sampling protocols, is one of the most promising approaches for censusing overlooked cryptic invertebrate communities. We present biodiversity estimates based on sequencing of the cytochrome c oxidase subunit 1 (COI) gene for coral reefs o...

This protocol details the preparation of multiplexed amplicon libraries for metabarcoding (amplicon-based) studies of microscopic marine eukaryotes. Metabarcoding studies, based on the amplification of a taxonomically informative marker from a collection of organisms or an environmental sample, can be performed to analyze biodiversity patterns or p...

PCR amplification followed by deep sequencing of homologous gene regions is increasingly used to characterize the diversity and taxonomic composition of marine eukaryotic communities. This approach may generate millions of sequences for hundreds of samples simultaneously. Therefore, tools that researchers can use to visualize complex patterns of di...

Amplicon-based studies of marine microscopic eukaryotes, also referred to as metabarcoding studies, can be performed to analyze patterns of biodiversity or predator–prey interactions targeting the mitochondrial cytochrome oxidase 1 (CO1) or the small ribosomal subunit (SSU) markers. Because high-throughput sequencing (HTS) Illumina platforms provid...

Understanding the role of predators in food webs can be challenging in highly diverse predator/prey systems composed of small cryptic species. DNA based dietary analysis can supplement predator removal experiments and provide high resolution for prey identification. Here we use a metabarcoding approach to provide initial insights into the diet and...

Significance High-throughput DNA sequencing methods are revolutionizing our ability to census communities, but most analyses have focused on microbes. Using an environmental DNA sequencing approach based on cytochrome c oxidase subunit 1 primers, we document the enormous diversity and fine-scale geographic structuring of the cryptic animals living...

The tools of molecular genetics have been transformed over the last decades and have in turn transformed our understanding of coral reefs. Initially limited to information on single genes, we are now capable of analyzing entire genomes. These developments make it possible to do many things that were either impossible or extremely difficult before:...

Coral reefs are the most diverse marine systems in the world, yet our understanding of the processes that maintain such extraordinary diversity remains limited and taxonomically biased toward the most conspicuous species. Cryptofauna that live deeply embedded within the interstitial spaces of coral reefs make up the majority of reef diversity, and...

Introduction The PCR-based analysis of homologous genes has become one of the most powerful approaches for species detection and identification, particularly with the recent availability of Next Generation Sequencing platforms (NGS) making it possible to identify species composition from a broad range of environmental samples. Identifying species f...

Characterization of predator-prey interactions is challenging as researchers have to rely on indirect methods that can be costly, biased and too imprecise to elucidate the complexity of food webs. DNA amplification and sequencing techniques of gut and fecal contents are promising approaches, but their success largely depends on the ability to ampli...

Identifying species involved in consumer–resource interactions is one of the main limitations in the construction of food webs. DNA barcoding of prey items in predator guts provides a valuable tool for characterizing trophic interactions, but the method relies on the availability of reference sequences to which prey sequences can be matched. In thi...

Although benthic motile invertebrate communities encompass the vast majority of coral reef diversity, their response to habitat modification has been poorly studied. A variety of benthic species, particularly decapods, provide benefits to their coral host enabling them to cope with environmental stressors, and as a result benefit the overall divers...

Mutualisms often involve one host supporting multiple symbionts, whose identity, density and intraguild interactions can influence the nature of the mutualism and performance of the host. However, the implications of multiple co-occurring symbionts on services to a host have rarely been quantified. In this study, we quantified effects of decapod sy...

Long pelagic larval phases and the absence of physical barriers impede rapid speciation and contrast the high diversity observed in marine ecosystems such as coral reefs. In this study, we used the three-spot dascyllus (Dascyllus trimaculatus) species complex to evaluate speciation modes at the spatial scale of the Indo-Pacific. The complex include...

Here the population genetic structure of an ecologically and economically important coral reef fish, the coral trout Plectropomus leopardus, is investigated in the context of contemporary and historical events. Coral trout were sampled from four regions (six locations) and partial mtDNA D-loop sequences identified six populations (Fst=0.89209, P<0....

A set of 13 simple sequence repeat markers was developed from D. trimaculatus genomic DNA, tested for D. auripinnis and characterized using 40 individuals per species. All the loci were polymorphic with a number of alleles ranging from three to 30. Observed heterozygosities varied from 0.23 to 0.89 for D. trimaculatus and from 0.11 to 0.85 for D. a...