Identification of freshwater zooplankton species using protein profiling and principal component analysis

Abstract

Crustaceans are vital components of the freshwater zooplankton that link various trophic levels. Because crustaceans, particularly cladocerans of the Daphnia genus, are sensitive to environmental changes, they can serve as indicators of environmental fluctuations. Therefore, it is highly desirable to have a fast and reliable method for the identification of individual Daphnia species. In this study, we demonstrated the ability of protein profiling to distinguish between freshwater zooplankton species. Individual specimens were morphologically identified before being analyzed by proteomic fingerprinting using matrix-assisted laser desorption/ ionization time of flight mass spectrometry (MALDI-TOF MS). The obtained mass spectra were used to create a reference library. Subsequently, the individual species were successfully identified using Biotyper software. The variability between the spectra of individual Daphnia species was verified by principal component analysis (PCA). Our results suggest that the combination of proteome fingerprinting using MALDI-TOF MS and PCA has considerable potential as a rapid tool for the unambiguous identification of individual species of freshwater zooplankton without the need for expert morphological analysis.

Revealing higher than expected diversity of Harpacticoida (Crustacea:Copepoda) in the North Sea using MALDI-TOF MS and molecular barcoding

“…It is an interesting method for taxa with difficult morphological identifications such as small copepods or important disease vectors such as mosquitos 67 and fleas 68 . Especially in biodiversity assessments, traditionally favoring quantitative data over qualitative data, this technique can be used as a cost-effective, yet fast alternative to genetic barcoding to identify animal groups occurring in high abundances or taxa which are difficult and time-consuming to identify due to their small size 29–32,64,69,70 .…”

Comparison of Rapid Biodiversity Assessment of Meiobenthos Using MALDI-TOF MS and Metabarcoding

“…Our results further align with low identification errors from other field studies of Bode et al (2017) and Kaiser et al (2018) on calanoid copepods or by Kaufmann et al (2012) on biting midges (Diptera). However, most studies about metazoans using MALDI-TOF MS for species identification were pilot studies which did not provide biodiversity assessments (Kaufmann et al, 2012;Volta et al, 2012;Laakmann et al, 2013;Müller et al, 2013;Steinmann et al, 2013;Yssouf et al, 2013Yssouf et al, , 2014aDieme et al, 2014;Mathis et al, 2015;Hynek et al, 2018), making it difficult to compare results to existing literature. Nevertheless, all studies carried out so far provide high identification success making MALDI-TOF MS a promising tool for biodiversity assessments.…”

Toward a reliable assessment of potential ecological impacts of deep‐sea polymetallic nodule mining on abyssal infauna

“…Often factory delivered software is used, returning identifications and identification probabilities based on provided or self‐generated libraries (Yssouf et al 2014). These are sometimes accompanied by cluster analyses (Dieme et al 2014), principal component analysis (PCA) (Hynek et al 2018), or solely based on cluster analyses (Bode et al 2017; Kaiser et al 2018). However, it is arguable if employing clustering or ordination methods alone makes it possible to recognize singletons or species boundaries in general (Collins and Cruickshank 2013; Rossel and Martínez Arbizu 2018).…”