Abstract
Nowadays, most biodiversity assessments involving meiofauna are mainly carried out specimen by specimen based on morphological identifications, which is very time-consuming and demands comprehensive taxonomic knowledge. Specimens have to be examined for minor differences of setae compositions, mouthpart morphology or number of segments for various extremities. DNA-based methods such as metabarcoding as well as recently emerged rapid analyses using MALDI-TOF mass spectrometry to identify specimens based on a proteome fingerprint could vastly accelerate the process of specimen identification in biodiversity assessments. However, these techniques depend on reference libraries to connect assessed data to morphologically described species. In this study the success rate of both approaches have been tested based on reference libraries constructed using part of the samples from a new study area to identify unknown samples. Using MALDI-TOF MS we found, that species not contained in an incomplete mass spectra reference library only have minor impact on the results, when employing a post hoc test for Random Forest classifications. This test reveals specimens that demand morphological re-examination for the final species assignment. Metabarcoding however strongly demands a rich reference library to provide correct MOTU assessments in congruence with morphological determination. Nevertheless, with a complete library and a suitable data transformation (herein log(x+1)), the number or reads per MOTU reflects relative species abundances in metabarcoding inference. Furthermore, a single gene barcoding approach on selected specimens was performed here in order to provide a cost comparison among the three techniques. The results of this study facilitate specimen identification by using MALDI-TOF MS, which is incomparably cheap for specimen-by-specimen identification, but when it comes to sample wise analyses, metabarcoding outperforms other techniques by far.
Highlights
Assessing species’ diversity, distribution, and community structure is crucial to understand the relationship of species to the surrounding environment
One E. gariene and three P. littoralis specimens were misclassified as Laophonte spec., and a fourth P. littoralis specimen was classified as Microarthridion fallax Perkins, 1956
All specimens were classified correctly by Random Forest, including those species for which only one specimen was contained in the reference library (Laophonte sp., Ectinosomatidae sp. 38, and D. palustris)
Summary
Assessing species’ diversity, distribution, and community structure is crucial to understand the relationship of species to the surrounding environment. Monitoring of communities is necessary to detect the influence of environmental changes on species compositions. Accurate species identification is necessary for biodiversity research. Morphological identification in particular for the tiny meiofauna organisms is very challenging and time-consuming (e.g., Brannock et al, 2014; Morad et al, 2017; RzeznikOrignac et al, 2017). An exact determination often demands dissection of the smallest appendages (Huys et al, 1996) and a comprehensive taxonomic knowledge. Taxonomic identification using morphology only has shown to underestimate the true diversity compared to DNA-based methods (Tang et al, 2012), mainly because of cryptic diversity for many species (Knowlton, 1993)
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