Biodiversity estimates and ecological interpretations of meiofaunal communities are biased by the taxonomic approach

Abstract

Accurate assessments of biodiversity are crucial to advising ecosystem-monitoring programs and understanding ecosystem function. Nevertheless, a standard operating procedure to assess biodiversity accurately and consistently has not been established. This is especially true for meiofauna, a diverse community (>20 phyla) of small benthic invertebrates that have fundamental ecological roles. Recent studies show that metabarcoding is a cost-effective and time-effective method to estimate meiofauna biodiversity, in contrast to morphological-based taxonomy. Here, we compare biodiversity assessments of a diverse meiofaunal community derived by applying multiple taxonomic methods based on comparative morphology, molecular phylogenetic analysis, DNA barcoding of individual specimens, and metabarcoding of environmental DNA. We show that biodiversity estimates are strongly biased across taxonomic methods and phyla. Such biases affect understanding of community structures and ecological interpretations. This study supports the urgency of improving aspects of environmental high-throughput sequencing and the value of taxonomists in correctly understanding biodiversity estimates.

Human access impacts biodiversity of microscopic animals in sandy beaches

“…We thus found a stronger effect of tourists at the swash level, but we cannot disentangle whether this could be due only to a higher presence of tourists in the swash level than in the other two water levels or if this habitat is indeed more sensitive to human presence. Changes in the taxonomic composition of meiofauna, as expected from previous studies 15,[17][18][19] , were due mostly to differences between beaches and sediment granulometry, but also to the presence of tourists and not so much to the differences between depths. We suggest that the effect of presence of people could be assigned mostly to trampling, since walking on the beach at the swash level is the major disturbance activity of humans in the sampled areas, where other more impacting recreational activities (e.g.…”

“…In contrast, microscopic animals, collectively called meiofauna 15 , are rich in species consisting of members of almost all animal phyla with a wide range of ecological features, differentially responding to human stresses, with a short generation time, allowing for a rapid detection of different types of impacts at different time scales [16][17][18] . Although these features make meiofauna a candidate to test the impact of human-driven changes in marine coastal areas 17 , very few studies on the effect of tourists on meiofauna of sandy beaches are available 5 , mostly because it is difficult to obtain reliable estimates of diversity on meiofauna dealing with morphological approaches in species identification 19 . The main problems are due to the vast diversity of meiofaunal organisms, with different extraction methods for each group to obtain animals for morphological identification 18 , and to the lack of taxonomic expertise for several taxa making it almost impossible to identify meiofauna in biodiversity inventories 20 .…”

Comparison of morphological, DNA barcoding, and metabarcoding characterizations of freshwater nematode communities

“…As the true species richness could not be determined using barcoding and metabarcoding approaches, the validity of the comparison with the morphological sample was limited. A more reliable comparison would have been possible if the specimens had been identified prior to Sanger sequencing or metabarcoding, as was the case in other studies (Leasi et al, 2018;Macheriotou et al, 2019).…”

“…Metabarcoding has facilitated studies of small multicellular organisms, either whole communities or specific groups, with marine eukaryotes being a frequent focus (Brannock & Halanych, ; Dell'Anno, Carugati, Corinaldesi, Riccioni, & Danovaro, ; Haenel, Holovachov, Jondelius, Sundberg, & Bourlat, ). It can also be used in combination with morphological analyses, as demonstrated in studies of estuarine plankton (Abad et al, ; Harvey, Johnson, Fisher, Peterson, & Vrijenhoek, ; Leasi et al, ) and nematodes (Holovachov, ; Macheriotou et al, ) in marine habitats but also diatoms and other small organisms in freshwater habitats (Keck, Vasselon, Rimet, Bouchez, & Kahlert, ; Rimet, Vasselon, A.‐Keszte, & Bouchez, ). For nematodes in soil and marine habitats, however, combined microscopy and metabarcoding investigations have been carried out only at the family level (Darby, Todd, & Herman, ; Griffiths, Groot, Laros, Stone, & Geisen, ; Holovachov, Haenel, Bourlat, & Jondelius, ; Treonis et al, ), and direct comparisons of the performances of morphological identification, barcoding, and metabarcoding at the species level are still scarce (Leasi et al, ).…”

“…It can also be used in combination with morphological analyses, as demonstrated in studies of estuarine plankton (Abad et al, 2016;Harvey, Johnson, Fisher, Peterson, & Vrijenhoek, 2017;Leasi et al, 2018) and nematodes (Holovachov, 2016;Macheriotou et al, 2019) in marine habitats but also diatoms and other small organisms in freshwater habitats (Keck, Vasselon, Rimet, Bouchez, & Kahlert, 2018;Rimet, Vasselon, A.-Keszte, & Bouchez, 2018). For nematodes in soil and marine habitats, however, combined microscopy and metabarcoding investigations have been carried out only at the family level (Darby, Todd, & Herman, 2013;Griffiths, Groot, Laros, Stone, & Geisen, 2018;Treonis et al, 2018), and direct comparisons of the performances of morphological identification, barcoding, and metabarcoding at the species level are still scarce (Leasi et al, 2018). Therefore, in this study, we compared the results of a morphological analysis with those from single-specimen barcoding and metabarcoding to determine the most accurate approach to specimen identification.…”