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Molecular and morphological identification methods show contrasting trends in soil fauna diversity along land-use intensity gradients

Köninger, Julia ; Beule, Lukas ; Tsiafouli, Maria ; Seeber, Julia ; Blasbichler, Helene ; Sousa, Jose Paul ; Martins da Silva, Pedro ; Frouz, Jan ; Hedlund, Katarina LU orcid and Orgiazzi, Alberto , et al. (2025) In Applied Soil Ecology 216.
Abstract

Current advancements in molecular techniques for identifying multiple species from bulked soil samples have expanded our capacity for large-scale soil biodiversity assessments. However, these methods often lack validation and contextualization. Recent cross-European studies based on environmental DNA (eDNA) have reported unexpectedly high biodiversity in intensively managed agricultural soils compared to woodlands and grasslands, challenging previous findings based on morphological assessments. Here, we analyze these discrepancies by comparing standardized soil faunal diversity data from the LUCAS Soil 2018 survey (eDNA) with morphological assessments from the EU-funded projects EcoFINDERS (2012) and SOILSERVICE (2015). We found that... (More)

Current advancements in molecular techniques for identifying multiple species from bulked soil samples have expanded our capacity for large-scale soil biodiversity assessments. However, these methods often lack validation and contextualization. Recent cross-European studies based on environmental DNA (eDNA) have reported unexpectedly high biodiversity in intensively managed agricultural soils compared to woodlands and grasslands, challenging previous findings based on morphological assessments. Here, we analyze these discrepancies by comparing standardized soil faunal diversity data from the LUCAS Soil 2018 survey (eDNA) with morphological assessments from the EU-funded projects EcoFINDERS (2012) and SOILSERVICE (2015). We found that molecular methods indicate higher soil biodiversity in croplands, whereas morphological methods suggest the opposite trend. A significant variability in diversity metrics across ecosystem types emphasizes the need to compare and validate molecular results with complementary morphological approaches. The increasing need for biodiversity indicators and thresholds in monitoring frameworks demands robust methods, yet widely used molecular techniques remain insufficiently standardized. We call for more systematic assessments to clarify the interpretation of eDNA signals (e.g., primer bias, relict DNA), and to enable a better integration of molecular and morphological data in conservation policies and large-scale monitoring efforts.

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type
Contribution to journal
publication status
published
subject
keywords
Biodiversity assessment, DNA barcoding, Methodological comparison, Molecular methods, Morphological identification, soil monitoring, Soil organisms
in
Applied Soil Ecology
volume
216
article number
106499
publisher
Elsevier
external identifiers
  • scopus:105020412598
ISSN
0929-1393
DOI
10.1016/j.apsoil.2025.106499
language
English
LU publication?
yes
additional info
Publisher Copyright: © 2025 The Authors.
id
25b43850-5490-431e-82dc-bdc9b18f6f53
date added to LUP
2025-12-04 09:53:56
date last changed
2025-12-05 09:08:16
@article{25b43850-5490-431e-82dc-bdc9b18f6f53,
  abstract     = {{<p>Current advancements in molecular techniques for identifying multiple species from bulked soil samples have expanded our capacity for large-scale soil biodiversity assessments. However, these methods often lack validation and contextualization. Recent cross-European studies based on environmental DNA (eDNA) have reported unexpectedly high biodiversity in intensively managed agricultural soils compared to woodlands and grasslands, challenging previous findings based on morphological assessments. Here, we analyze these discrepancies by comparing standardized soil faunal diversity data from the LUCAS Soil 2018 survey (eDNA) with morphological assessments from the EU-funded projects EcoFINDERS (2012) and SOILSERVICE (2015). We found that molecular methods indicate higher soil biodiversity in croplands, whereas morphological methods suggest the opposite trend. A significant variability in diversity metrics across ecosystem types emphasizes the need to compare and validate molecular results with complementary morphological approaches. The increasing need for biodiversity indicators and thresholds in monitoring frameworks demands robust methods, yet widely used molecular techniques remain insufficiently standardized. We call for more systematic assessments to clarify the interpretation of eDNA signals (e.g., primer bias, relict DNA), and to enable a better integration of molecular and morphological data in conservation policies and large-scale monitoring efforts.</p>}},
  author       = {{Köninger, Julia and Beule, Lukas and Tsiafouli, Maria and Seeber, Julia and Blasbichler, Helene and Sousa, Jose Paul and Martins da Silva, Pedro and Frouz, Jan and Hedlund, Katarina and Orgiazzi, Alberto and Briones, Maria Jesús Iglesias and Potapov, Anton}},
  issn         = {{0929-1393}},
  keywords     = {{Biodiversity assessment; DNA barcoding; Methodological comparison; Molecular methods; Morphological identification; soil monitoring; Soil organisms}},
  language     = {{eng}},
  publisher    = {{Elsevier}},
  series       = {{Applied Soil Ecology}},
  title        = {{Molecular and morphological identification methods show contrasting trends in soil fauna diversity along land-use intensity gradients}},
  url          = {{http://dx.doi.org/10.1016/j.apsoil.2025.106499}},
  doi          = {{10.1016/j.apsoil.2025.106499}},
  volume       = {{216}},
  year         = {{2025}},
}