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

Abstract

Nowadays, most biodiversity assessments involving meiofauna are mainly carried out using very time-consuming, specimen-wise morphological identifications, which demands comprehensive taxonomic knowledge. Animals 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 collected 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 which do not exist 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 of reads per MOTU reflects relative species abundances in metabarcoding inference. 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.

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

“…A fast and reliable provision of comprehensive baselines for biodiversity is an urgent need for ecosystem management, yet still a strong challenge specifically in understudied marine ecosystems, such as the deep sea. Next to morphological identification, DNA based methods such as barcoding/metabarcoding, as well as the recently emerged rapid analyses using MALDI‐TOF mass spectrometry to identify specimens using proteomic fingerprinting, were shown to accelerate the process of specimen identification in biodiversity assessments (Rossel et al, 2019). A crucial step in using these methods is to build reference libraries that connect morphological data to species‐specific COI barcodes and proteome fingerprints.…”

“…While optical identification of morphospecies is cheap in terms of consumables, this method requires, in absence of keys or species descriptions, the most personal costs, as the process is long lasting and can only be performed by highly experienced taxonomists. Barcoding also requires experienced staff (at least well‐trained technician level) and the cost of consumables are generally high, more than 5 Euro per specimen (Rossel et al, 2019). MALDI‐TOF, on the other hand, is a fast and low‐cost (0.1 Euro consumables) method (Rossel et al, 2019), which can be accomplished easily after very short training, resulting in relatively low personal costs.…”

“…Barcoding also requires experienced staff (at least well‐trained technician level) and the cost of consumables are generally high, more than 5 Euro per specimen (Rossel et al, 2019). MALDI‐TOF, on the other hand, is a fast and low‐cost (0.1 Euro consumables) method (Rossel et al, 2019), which can be accomplished easily after very short training, resulting in relatively low personal costs.…”

“…Of these 97 genera only six were reported for abyssal depths. The most detailed information is given in the database by Razouls et al (2005‐2020, accessed 061219), reporting approximately 300 pelagic calanoid copepod species for the Central South Atlantic. This database includes 15 obligate benthopelagic species described in recent years from abyssal depth.…”

Biases in bulk: DNA metabarcoding of marine communities and the methodology involved

“…A weak correlation was found between read abundance and biomass, but not with number of individuals (Lamb et al, 2019). This may explain why studies with low differences in size/biomass between sampled specimens do show a correlation between species abundance and read abundance (Rossel et al, 2019). Likely even more important than biomass, are the biases introduced during PCR and primer bias (Nichols et al, 2018).…”