Although animals are among the best studied organisms, we still lack a full description of their diversity, especially for microscopic taxa. This is partly due to the time-consuming and costly nature of surveying animal diversity through morphological and molecular studies of individual taxa. A powerful alternative is the use of high-throughput environmental sequencing, providing molecular data from all organisms sampled. We here address the unknown diversity of animal phyla in marine environments using an extensive dataset designed to assess eukaryotic ribosomal diversity among European coastal locations. A multi-phylum assessment of marine animal diversity that includes water column and sediments, oxic and anoxic environments, and both DNA and RNA templates, revealed a high percentage of novel 18S rRNA sequences in most phyla, suggesting that marine environments have not yet been fully sampled at a molecular level. This novelty is especially high among Platyhelminthes, Acoelomorpha, and Nematoda, which are well studied from a morphological perspective and abundant in benthic environments. We also identified, based on molecular data, a potentially novel group of widespread tunicates. Moreover, we recovered a high number of reads for Ctenophora and Cnidaria in the smaller fractions suggesting their gametes might play a greater ecological role than previously suspected.

This work was supported by an Institució Catalana de Recerca i Estudis Avançats contract, two grants (BFU-2011-23434 and BFU2014-57779-P) from the Ministerio de Economia y Competitividad (MINECO), one of which (BFU2014-57779-P) was co-funded by the European Regional Development Fund (FEDER), and a European Research Council Consolidator Grant (ERC-2012-Co -616960) to I.R.-T. We also acknowledge financial support from the Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya (Project 2014 SGR 619). J.d.C. was supported by a Marie Curie International Outgoing Fellowship grant (FP7-PEOPLE-2012-IOF - 331450 CAARL). J.P. acknowledges support from the European Research Council under the European Union’s Seventh Framework Program (FP7/2007–2013)/ERC grant [268513]. The work is part of the EU ERA-Net program BiodivERsA, under the project BioMarKs (Biodiversity of Marine euKaryotes)