Biodiversity assessment of marine benthic communities with COI metabarcoding: methods and applications

Abstract

[eng] Ecosystem biomonitoring is crucial for proper management of natural communities during the Anthropocene era. With the advent of new sequencing technologies, DNA metabarcoding has been proposed as a game-changing tool for biomonitoring. In this Thesis we plead for the use of metabarcoding of a highly variable marker to infer not only the interspecies but also the intraspecies variability to assess both biogeographic, at the species level, and metaphylogeographic patterns, at the haplotype level. We focused on highly complex hard-substratum benthic littoral communities. The term "Metaphylogeography", coined in this Thesis, refers to the study of phylogeographic patterns of many species at the same time using metabarcoding data. However, as of the start of this Thesis, only a few studies had tested the metabarcoding method to directly characterize the whole eukaryotic community in highly diverse benthic ecosystems. This required to set up and calibrate methods for these communities as a prior step. We first evaluated both the sampling methods and the bioinformatic pipelines. We assessed the viability of detecting the environmental DNA released from the benthic community into the adjacent water layer using metabarcoding of COI with highly degenerated primers targeting the whole eukaryotic community. We sampled water from 0 to 20m from shallow rocky benthic communities and compared the DNA signal with the results obtained from metabarcoding directly the benthic communities by traditional quadrat sampling. We also designed a pipeline combining clustering and denoising methods to treat metabarcoding data of COI. We considered the entropy of each codon position of this coding fragment both to improve the detection of spurious sequences and to calibrate the best performing parameters of the software used. In addition, we created our own denoising program, DnoisE, to incorporate information on the codon position. This new code and parameter calibration were required as the commonly used bioinformatic pipelines had been designed and tested mostly for less variable ribosomal

fragments and, particularly, in prokaryotes. Results showed that the DNA signal from the benthos decreased with the distance but was too weak for a correct assessment of benthic biodiversity. The proportion of eukaryotic DNA sequenced was also very low in water samples due to the amplification of prokaryotic DNA. We thus concluded that the benthos must be sampled directly to properly assess its biodiversity composition. The new bioinformatic developments allowed us to propose new methods for processing metabarcoding reads, combining clustering and denoising steps, and to set optimal values for the parameters used at each step. These contributions effectively expanded the field to the novel analysis of inter- and intraspecies genetic variability with metabarcoding data. Finally, we applied this methodology to 12 localities of the Western Iberian Coast along two well studied fronts, the Almeria-Oran Front (AOF) and the Ibiza Channel (IC). We analysed the species and haplotypes using the COI barcode. From a biogeographical perspective, the AOF had a strong effect in separating regions, while IC effect was less marked, but still half of the MOTUs were found in only one side of this divide. For the metaphylogeographic analysis, only 10% of the MOTUs could be used. However, they showed a good separation between populations of the three regions with a strong effect of the AOF break. The IC, on the other hand, seemed to be more a transitional zone than a fixed break. This Thesis laid the ground for the efficient use of metabarcoding in the biomonitoring of benthic reef habitats, allowing community composition, β-diversity, and biogeographic patterns to be analysed in a fast, repeatable, and cost-efficient way. We also developed the metaphylogeography approach as a new tool to assess population genetic structure at the community-wide level.