Proteomic fingerprinting facilitates biodiversity assessments in understudied ecosystems: A case study on integrated taxonomy of deep sea copepods

Renz, Jasmin; Markhaseva, Elena L.; Laakmann, Silke; Rossel, Sven; Arbizu, Pedro Martínez; Peters, Janna

doi:10.1111/1755-0998.13405

Cited by 11 publications

(33 citation statements)

References 70 publications

(125 reference statements)

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“…In a classification test, all specimens were classified correctly, showing the use of mass spectra for specimen identification. These results are in concordance with previous studies showing the high success of proteome fingerprinting in metazoan specimen identification on taxa such as fish (Mazzeo and Siciliano, 2016;Rossel et al, 2021), insects (Dieme et al, 2014;Raharimalala et al, 2017) or other crustaceans (Bode et al, 2017;Rossel et al, 2019;Renz et al, 2021). Overall, MALDI-TOF MS seems to be a promising fast and low-cost tool for the identification of deep-sea isopods.…”

Section: Discussionsupporting

confidence: 92%

Correct Species Identification and Its Implications for Conservation Using Haploniscidae (Crustacea, Isopoda) in Icelandic Waters as a Proxy

et al. 2022

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Correct identification of species is required to assess and understand the biodiversity of an ecosystem. In the deep sea, however, this is only possible to a limited extent, as a large part of the fauna is undescribed and the identification keys for most taxa are inadequate or missing. With the progressive impact of climate change and anthropogenic activities on deep-sea ecosystems, it is imperative to define reliable methods for robust species identification. In this study, different techniques for the identification of deep-sea species are tested, including a combination of morphological, molecular (DNA barcoding, and proteomic fingerprinting), biogeographical and ecological modeling approaches. These are applied to a family of isopods, the Haploniscidae, from deep waters around Iceland. The construction of interactive identification keys based on the DELTA format (DEscription Language for TAxonomy) were a major pillar of this study, the evaluation of which was underpinned by the application of the supplementary methods. Overall, interactive keys have been very reliable in identifying species within the Haploniscidae. Especially in a deep-sea context, these types of keys could become established because they are easy to adapt and flexible enough to accommodate newly described species. Remarkably, in this study, the interactive key enabled identification of a supposedly new species within the Haploniscidae that was later verified using both molecular genetic – and proteomic methods. However, these keys are limited given that they are based on purely morphological characteristics, including where species with strong ontogenetic or sexual dimorphism occur as both genders are not always described. In this case, integrative taxonomy is the method of choice and the combination presented here has been shown to be very promising for correct identification of deep-sea isopods.

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Section: Discussionsupporting

confidence: 92%

Correct Species Identification and Its Implications for Conservation Using Haploniscidae (Crustacea, Isopoda) in Icelandic Waters as a Proxy

et al. 2022

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“…In line with previous studies on marine copepods (Riccardi et al, 2012, Laakmann et al, 2013, Bode et al, 2017, Kaiser et al, 2018, Rossel & Martinez Arbizu, 2018a, Renz et al, 2021, Yeom et al, 2021, our results clearly support the high discriminatory power of proteomic fingerprinting on species level in this taxonomic group. All specimens were correctly assigned to the different 27 species by a RF model for classification with only low sensitivity to data processing indicating high robustness of the method.…”

Section: Species Identification and Species-specific Markerssupporting

confidence: 92%

“…Proteomic fingerprinting as a fast, efficient, and low-cost method for species identification , Renz et al, 2021 has a large potential to evolve to a valuable add-on to the current classical and molecular toolbox in zooplankton identification. In short, sample tissue is extracted in a matrix-solution, which is then applied onto a target plate.…”

Section: Introductionmentioning

confidence: 99%

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Perspectives of species identification by MALDI-TOF MS in monitoring - stability of proteomic fingerprints in marine epipelagic copepods

Peters

Laakmann

Rossel

et al. 2022

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We analyzed robustness of species identification based on proteomic composition to data processing and intraspecific variability, specificity and sensitivity of species-markers as well as discriminatory power of proteomic fingerprinting and its sensitivity to phylogenetic distance. Our analysis is based on MALDI-TOF MS data from 32 marine copepod species coming from 13 regions (North and Central Atlantic and adjacent seas). A random forest (RF) model correctly classified all specimens to species level with only small sensitivity to data processing, demonstrating the strong robustness of the method. Compounds with high specificity showed low sensitivity i.e., identification was rather based on complex pattern-differences than on presence of single markers. Proteomic distance was not consistently related to phylogenetic distance. A species-gap in proteome composition appeared at 0.8 Euclidean distance when using only specimens from the same sample. When other regions or seasons were included, intra-specific variability increased, resulting in overlaps of intra- and inter-specific distance. Highest intra-specific distances (> 0.8) were observed between specimens from brackish and marine habitats i.e., salinity likely affects proteomic patterns. When testing library sensitivity of the RF model to regionality, strong misidentification was only detected between two congener pairs. Still, choice of reference library may have an impact on identification of closely related species and should be tested before routine application. We envision high relevance of this time- and cost-efficient method for future zooplankton monitoring as it provides not only in-depth taxonomic resolution for counted specimens but also add-on information e.g., on developmental stage or environmental conditions.

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“…resedaeformis and D. pertusum were found in distinct clusters. Thus, a library with a sufficient number of spectra for all species, respectively, would probably also allow the supervised identification of unknown specimens using either reference library based approaches such as RF or factory delivered software such as the Bruker Biotyper as was shown in previous studies on metazoans with high success rates (Bode et al, 2017;Kaiser et al, 2018;Rossel et al, , 2021Wilke et al, 2020;Paulus et al, 2021;Renz et al, 2021). Unfortunately, some species in our analysis were represented with an insufficient number of specimens, resulting in a mixed cluster of species that lacked conspecifics for comparison (Figure 4, cluster CX).…”

Section: Proteome Fingerprintingmentioning

confidence: 99%

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

et al. 2022

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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.

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Proteomic fingerprinting facilitates biodiversity assessments in understudied ecosystems: A case study on integrated taxonomy of deep sea copepods

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 11 publications

References 70 publications

Correct Species Identification and Its Implications for Conservation Using Haploniscidae (Crustacea, Isopoda) in Icelandic Waters as a Proxy

Correct Species Identification and Its Implications for Conservation Using Haploniscidae (Crustacea, Isopoda) in Icelandic Waters as a Proxy

Perspectives of species identification by MALDI-TOF MS in monitoring - stability of proteomic fingerprints in marine epipelagic copepods

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

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