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The abyssal seafloor is a mosaic of highly diverse habitats that represent the least known marine ecosystems on Earth. Some regions enriched in natural resources, such as polymetallic nodules in the Clarion-Clipperton Zone (CCZ), attract much interest because of their huge commercial potential. Since nodule mining will be destructive, baseline data are necessary to measure its impact on benthic communities. Hence, we conducted an environmental DNA and RNA metabarcoding survey of CCZ biodiversity targeting microbial and meiofaunal eukaryotes that are the least known component of the deep-sea benthos. We analyzed two 18S rRNA gene regions targeting eukaryotes with a focus on Foraminifera (37F) and metazoans (V1V2), sequenced from 310 surface-sediment samples from the CCZ and other abyssal regions. Our results confirm huge unknown deep-sea biodiversity. Over 60% of benthic foraminiferal and almost a third of eukaryotic operational taxonomic units (OTUs) could not be assigned to a known taxon. Benthic Foraminifera are more common in CCZ samples than metazoans and dominated by clades that are only known from environmental surveys. The most striking results are the uniqueness of CCZ areas, both datasets being characterized by a high number of OTUs exclusive to the CCZ, as well as greater beta diversity compared to other abyssal regions. The alpha diversity in the CCZ is high and correlated with water depth and terrain complexity. Topography was important at a local scale, with communities at CCZ stations located in depressions more diverse and heterogeneous than those located on slopes. This could result from eDNA accumulation, justifying the interim use of eRNA for more accurate biomonitoring surveys. Our descriptions not only support previous findings and consolidate our general understanding of deep-sea ecosystems, but also provide a data resource inviting further taxon-specific and large-scale modeling studies. We foresee that metabarcoding will be useful for deep-sea biomonitoring efforts to consider the diversity of small taxa, but it must be validated based on ground truthing data or experimental studies.
The endozoic ciliates of the family Clevelandellidae Kidder, 1938 typically inhabit the hindgut of wood-feeding panesthiine cockroaches. To assess the consistency of species delimitation in clevelandellids, we tested the utility of three sources of taxonomic data: morphometric measurements, cell geometrical information, and 18S rRNA gene sequences. The morphometric and geometrical data delimited the clevelandellid morphospecies consistently and unambiguously. However, only Paraclevelandia brevis Kidder, 1937 represented a homogenous taxon in both morphological and molecular analyses; the morphospecies Clevelandella constricta (Kidder, 1937) and C. hastula (Kidder, 1937) contained two or three distinct, more or less closely related genotypes each; and the genetic homogeneity of the morphospecies C. panesthiae (Kidder, 1937) and C. parapanesthiae (Kidder, 1937) was not corroborated by the 18S rRNA gene sequences at all. Moreover, the 18S rRNA gene phylogenies suggested the C. panesthiae-like morphotype to be the ancestral phenotype from which all other clevelandellid morphotypes arose. The only exception was the C. constricta-like morphotype, which very likely branched off before the diversification of the C. panesthiae-like progenitor. The present molecular analyses also suggested that a huge proportion of the clevelandellid diversity still waits to be discovered, since examination of only four panesthiine populations revealed 10 distinct clevelandellid genotypes/molecular species.
Four earthworm species, the endogeic Octolasion tyrtaeum (Savigny, 1826), the anecic Lumbricus terrestris Linnaeus, 1758 as well as the epigeic Eisenia fetida (Savigny, 1826) and Dendrobaena veneta (Rosa, 1886), were examined for the presence of astome ciliates. Based on the integrative taxonomic approach, five ciliate species were recognized in their gastrointestinal tracts: Metaradiophrya lumbrici (Dujardin, 1841), M. varians (de Puytorac, 1954), Anoplophrya lumbrici (Schrank, 1803), A. vulgaris de Puytorac, 1954 and A. nodulata (Dujardin, 1841). Their distinctness was assessed using the multivariate morphometric approach and molecular phylogenetic analyses. Although the two species of Metaradiophrya Jankowski, 2007 on the one hand and the two former species of Anoplophrya Stein, 1860 on the other, were not distinctly separated by the multivariate morphometric analyses, they were clearly delimited by the 18S rRNA gene sequences. Species within each genus also differed by their hosts, M. lumbrici and A. lumbrici occurred only in anecic earthworms while M. varians and A. vulgaris occured exclusively in epigeic earthworms. Only a single species, A. nodulata, was detected in endogeic earthworms. It was morphologically distinct from and did not cluster with the two other species of Anoplophrya but was nested within the paraphyletic assemblage containing other astomes from endogeic earthworms. This indicates that the evolution of endosymbiotic ciliates from earthworms has very likely proceeded through a specialization to various ecological groups of their host organisms.