The use of metabarcoding for meiofauna ecological patterns assessment

Faria, Laiza Cabral de; Domênico, Maikon Di; Andrade, Sónia C. S.; Santos, Monique Cristina dos; Fonseca, Gustavo; Zanol, Joana; Amaral, A. Cecília Z.

doi:10.1016/j.marenvres.2018.06.013

Cited by 33 publications

(25 citation statements)

References 48 publications

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“…Concerning the result of this study, the reads of D. palustris, the species missing from the reference library during the initial analyses, were clustered into a discrete MOTU, which further confirms the ability of metabarcoding using V1 and V2 hypervariable region of 18S in 97% pairwise similarity to discriminate the sequences into species. In congruence with previous metabarcoding studies (Guardiola et al, 2015;De Faria et al, 2018;Günther et al, 2018), we further suggest the successful use of 18S gene especially in case of metabarcoding of meiofauna communities in which amplification of COI barcode region has shown to be less successful for some organisms such as nematodes (Haenel et al, 2017). Laophonte sp.…”

Section: Metabarcodingsupporting

confidence: 88%

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

2019

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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.

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Section: Metabarcodingsupporting

confidence: 88%

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

2019

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“…In addition, it is known that the 18S rDNA marker we selected may underestimate diversity for some taxa 32 , potentially explaining the low number of ZOTUs for some groups such as Rotifera and Kinorhyncha. Regardless of potential problems and differences between different approaches, one of the main messages of our study is that we confirm the use of metabarcoding on meiofauna as a tool for biodiversity monitoring 19,21,22,25 .…”

Section: Discussionsupporting

confidence: 58%

Human access impacts biodiversity of microscopic animals in sandy beaches

et al. 2020

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Whereas most work to understand impacts of humans on biodiversity on coastal areas has focused on large, conspicuous organisms, we highlight effects of tourist access on the diversity of microscopic marine animals (meiofauna). We used a DNA metabarcoding approach with an iterative and phylogeny-based approach for the taxonomic assignment of meiofauna and relate diversity patterns to the numbers of tourists accessing sandy beaches on an otherwise un-impacted island National Park. Tourist frequentation, independently of differences in sediment granulometry, beach length, and other potential confounding factors, affected meiofaunal diversity in the shallow "swash" zone right at the mean water mark; the impacts declined with water depth (up to 2 m). The indicated negative effect on meiofauna may have a consequence on all the biota including the higher trophic levels. Thus, we claim that it is important to consider restricting access to beaches in touristic areas, in order to preserve biodiversity.

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“…There is now strong evidence supporting that eDNA techniques can detect complex spatial variability in estuarine and coastal marine ecosystems (Chariton et al, 2015;Faria et al, 2018); and our data additionally supports its use to biodiversity assessment in a heavily impacted estuary.…”

Section: Discussionsupporting

confidence: 75%

“…The Rio Doce eDNA composition was similar to other estuarine and marine sediments assessed by metabarcoding methods (Fonseca et al, 2010;Faria et al, 2018). Nematoda, Gastrotricha and Crustaceans were highly dominant in the estuary with local changes in relative abundance across PeerJ reviewing PDF | (2019:08:40630:1:1:NEW 1 Oct 2019)…”

Section: Discussionmentioning

confidence: 58%

“…Our data suggest that benthic assemblages were highly sensitive to chronic metal contamination in polluted estuaries, and partially explains a lower effect of sediment grain size and organic matter on local meiofauna (e.g. Faria et al, 2018;Menegotto et al, 2019). This could indicate that the Rio Doce estuarine assemblages were strongly impacted after the disaster through the exclusion of intolerant species, although we lack baseline eDNA to fully support that hypothesis.…”

Section: Discussionmentioning

confidence: 72%

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Peer Review #1 of "Chronic trace metals effects of mine tailings on estuarine assemblages revealed by environmental DNA (v0.1)"

2019

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Mine tailing disasters have occurred worldwide and contemporary release of tailings of large proportions raise concerns of the chronic impacts that trace metals may have on the aquatic biodiversity. Environmental metabarcoding (eDNA) offers an yet poorly explored opportunity for biological monitoring of impacted aquatic ecosystems from mine tailings and contaminated sediments. eDNA has been increasingly recognized to be an effective method to detect previously unrecognized small-sized Metazoan taxa, but their ecological responses to environmental pollution has not been assessed by metabarcoding. Here we evaluated chronic effects of trace metal contamination from sediment eDNA of the Rio Doce estuary, 1.7 years after the Samarco mine tailing disaster, which released over 40 million m 3 of iron tailings in the Rio Doce river basin. We identified 123 new sequence variants (eOTUs) of benthic taxa and an assemblage composition dominated by Nematoda, Crustacea and Platyhelminthes; typical of other estuarine ecosystems. We detected environmental filtering on the meiofaunal assemblages and multivariate analysis revealed strong influence of Fe contamination, supporting chronic impacts from mine tailing deposition in the estuary. This was in contrast to environmental filtering of meiofaunal assemblages of non-polluted estuaries. Here we suggest that the eDNA metabarcoding technique provides an opportunity to fill up biodiversity gaps in coastal marine ecology and may become a valid method for long term monitoring studies in mine tailing disasters and estuarine ecosystems with high trace metals content.

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The use of metabarcoding for meiofauna ecological patterns assessment

Cited by 33 publications

References 48 publications

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

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

Human access impacts biodiversity of microscopic animals in sandy beaches

Peer Review #1 of "Chronic trace metals effects of mine tailings on estuarine assemblages revealed by environmental DNA (v0.1)"

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