eDNA Reveals the Associated Metazoan Diversity of Mediterranean Seagrass Sediments

Abstract

Anthropogenic impacts on marine ecosystems have led to a decline of biodiversity across the oceans, threatening invaluable ecosystem services on which we depend. Ecological temporal data to track changes in diversity are relatively rare, and the few long-term datasets that exist often only date back a few decades or less. Here, we use eDNA taken from dated sediment cores to investigate changes over approximately the last 100 years of metazoan communities in native (Cymodocea nodosa and Posidonia oceanica) and exotic (Halophila stipulacea) seagrass meadows within the eastern Mediterranean Sea, at two locations in Greece and two in Cyprus. Overall, metazoan communities showed a high turnover of taxa during the past century, where losses of individual taxa in a seagrass meadow were compensated by the arrival of new taxa, probably due to the arrival of exotic species introduced in the Mediterranean Sea from the Suez Canal or the Gibraltar Strait. Specifically, bony fishes (Class Actinopteri) and soft corals (Class Anthozoa) presented significantly higher richness in the past (before the 1980s) than in the most recent time periods (from 1980–2017) and some Cnidarian orders were solely found in the past, whereas sponges and Calanoids (Class Hexanauplia), an order of copepods, showed an increase in richness since the 1980s. Moreover, the Phyla Porifera, Nematoda and the Classes Staurozoa, Hydrozoa and Ophiuroidea were detected in P. oceanica meadows but not in C. nodosa and H. stipulacea, which led to P. oceanica meadows having twice the richness of other seagrasses. The greater richness resulted from the more complex habitat provided by P. oceanica. The combination of eDNA and sediment cores allowed us to reconstruct temporal patterns of metazoan community diversity and provides a novel approach to follow natural communities back in time in the absence of time series and baseline data. The ongoing loss of P. oceanica meadows, likely to be compounded with future warming, might lead to a major loss of biodiversity and the replacement by other seagrass species, whether native or exotic, does not compensate for the loss.

Metabarcoding the eukaryotic community of a threatened, iconic Mediterranean habitat: Posidonia oceanica seagrass meadows

“…The latter can be analysed by paleoecological methods, including metabarcoding of ancient DNA currently applied to other environments, such as lake sediments (Domaizon et al, 2017). In seagrass beds, Wesselmann et al, 2022 analysed sediments in Mediterranean meadows (Cymodocea nodosa and P. oceanica) to determine decadal changes (over the last century) in metazoan composition. Piñeiro-Juncal et al (2021), analysed the prokaryote composition of corers (1.5 m long) of soil under P. oceanica meadows at different degradation states.…”

A review of fish diversity in Mediterranean seagrass habitats, with a focus on functional traits

“…Conversely, a comparison of juveniles’ distribution across 14 different vegetated and unvegetated habitats highlighted a higher fish species richness and abundance in P. oceanica with respect to C. nodosa, although comparable to soft and rocky substrates (Chemineé et al 2021). A recent pioneering study investigating metazoan communities in P. oceanica , C. nodosa and the invasive Halophila stipulacea across the last century by using eDNA showed a higher diversity in P. oceanica for all examined phyla, including fish (Wesselmann et al 2022). The Authors linked such diversity with the structural complexity of seagrass beds, known to be higher for the large P. oceanica than for the smaller C. nodosa and H. stipulacea (Buia et al 2000; Hemminga and Duarte 2000).…”

“…sediments, rocks, coralligenous, seaweeds. Recent works have been able to provide a direct confrontation of fish communities associated with different seagrasses taking advantage of the emerging eDNA techniques, so paving the way for the use of a quick and reliable approach allowing to overcome this scarcity of relevant data (He et al 2022; Wesselmann et al 2022).…”

Enumeration potential of environmental DNA for Pacific salmon stock assessments

“…Environmental DNA (eDNA) methods have been rapidly evolving and developing over the last 10 years. Indeed, several approaches to utilizing eDNA to detect the presence of a target species are available, including a variety of sampling methods and DNA detection methods (e.g., Métris & Métris, 2023;Ruppert et al, 2019;Sansom & Sassoubre, 2017;Wesselmann et al, 2022;Zhu et al, 2023). In general, eDNA detection may be targeted, such as species-specific quantitative real-time polymerase chain reaction (qPCR)-based methods, metagenomic, or metabarcoding, which use combinations of PCR and next-generation sequencing (Acharya-Patel et al, 2023).…”