Species Delimitation of Hexacorallia and Octocorallia Around Iceland Using Nuclear and Mitochondrial DNA and Proteome Fingerprinting

Abstract

Cold-water corals build up reef structures or coral gardens and play an important role for many organisms in the deep sea. Climate change, deep-sea mining, and bottom trawling are severely compromising these ecosystems, making it all the more important to document the diversity, distribution, and impacts on corals. This goes hand in hand with species identification, which is morphologically and genetically challenging for Hexa- and Octocorallia. Morphological variation and slowly evolving molecular markers both contribute to the difficulty of species identification. In this study, a fast and cheap species delimitation tool for Octocorallia and Scleractinia, an order of the Hexacorallia, of the Northeast Atlantic was tested based on 49 specimens. Two nuclear markers (ITS2 and 28S rDNA) and two mitochondrial markers (COI and mtMutS) were sequenced. The sequences formed the basis of a reference library for comparison to the results of species delimitation based on proteomic fingerprinting using MALDI-TOF MS. The genetic methods were able to distinguish 17 of 18 presumed species. Due to a lack of replicates, using proteome fingerprinting only 7 species were distinguishable. Species that could not be distinguished from one another still achieved good signals of spectra but were not represented by enough specimens for comparison. Therefore, it is predicted that with an extensive reference library of proteome spectra for Scleractinia and Octocorallia, MALDI-TOF MS may provide a rapid and cost-effective alternative for species discrimination in corals.

Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean

“…However, in metazoan identification it is still in its infancy. Nevertheless, successful species identification of specimens has been achieved from a large variety of taxonomic groups such as different crustaceans (Bode et al, 2017; Hynek et al, 2018; Kaiser et al, 2018; Kürzel et al, 2022; Laakmann et al, 2013; Paulus et al, 2022; Rossel et al, 2019; Rossel & Martínez Arbizu, 2018b, 2019), fish (Maász et al, 2017; Mazzeo et al, 2008; Rossel et al, 2020; Volta et al, 2012), cnidarians (Holst et al, 2019; Korfhage et al, 2022), molluscs (Hamlili, Thiam, et al, 2021; Wilke et al, 2020) and a large variety of insects, preferentially those which are potential disease vectors (Dieme et al, 2014; Hasnaoui et al, 2022; Loaiza et al, 2019; Mathis et al, 2015; Nabet et al, 2021; Nebbak et al, 2017; Yssouf et al, 2014).…”

Potential of MALDI‐TOF MS‐based proteomic fingerprinting for species identification of Cnidaria across classes, species, regions and developmental stages

“…The general applicability of MALDI-TOF MS for differentiation of cnidarian species was shown before on three staurozoans from the North Sea (Holst et al, 2019) and on nine siphonophores of the family Diphyidae (Park et al, 2021). It was furthermore used in an integrative approach for the differentiation of notoriously difficult to identify hexa-and octocorallian species showing tendencies to delimit a species complex that could not be resolved using the investigated molecular genetic markers (Korfhage et al, 2022). In the present study, we confirmed that MALDI-TOF MS is also applicable for the fragile gelatinous tissues of hydrozoan and scyphozoan medusae with water contents of >95% (Arai, 1997).…”

“…In some taxa, a combination of several molecular genetic markers achieves a satisfying resolution (McFadden et al, 2011, 2014, 2021; Quattrini et al, 2018). As an alternative to the expensive and time‐consuming molecular genetic analyses, proteomic fingerprinting was successfully used for species identification in Cnidaria (Holst et al, 2019; Korfhage et al, 2022; Park et al, 2021). Using matrix‐assisted laser desorption/ionization–time of flight (MALDI‐TOF) mass spectrometry, a subset of the specimen's peptides and proteins are measured resulting in a mass spectrum that can be used for differentiation of species.…”

“…MALDI‐TOF MS is a promising tool for species identification in Cnidaria but it has only been applied on selected cnidarian taxa so far including benthic stalked jellyfish (Staurozoa) (Holst et al, 2019), siphonophores (colonial pelagic Hydrozoa) (Park et al, 2021), and cold water corals (Anthozoa) (Korfhage et al, 2022). However, MALDI‐TOF MS has never been tested for species identification by using the gelatinous tissues of scyphozoan and hydrozoan medusae before.…”

A universal tool for marine metazoan species identification: towards best practices in proteomic fingerprinting

“…It was also used for food fraud detection 8 , 9 or to check food adulteration 10 . In pilot studies, it was successfully applied for identification of metazoans such as copepods 11 – 17 , isopods 18 , 19 , different groups of Cnidaria 20 – 22 , molluscs 23 , fish 8 , 24 and especially disease vectors such as ticks, sandflies or mosquitoes 25 – 29 . Most studies only analyzed a few species or were limited to a certain taxonomic group while studies across different classes and phyla are still missing.…”