Extracting DNA from soil or directly from isolated nematodes indicate dissimilar community structure for Europe-wide forest soils

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  • Maria J.I. Briones
  • Juha Mikola
  • Davey L. Jones
  • Reinhard Eder
  • Juliane Filser
  • Aline Frossard
  • Paul Henning Krogh
  • José Paulo Sousa
  • Jérome Cortet
  • Ellen Desie
  • Xavier Domene
  • Simoneda Djuric
  • Davorka Hackenberger
  • Juan J. Jimenez
  • Maria Iamandei
  • Cornelia Rissmann
  • Olaf Schmidt
  • Merrit Shanskiy
  • Tarja Silfver
  • Karen Vancampenhout
  • Martina Vasutova
  • Emiliya Velizarova
  • Beat Frey
Nematodes are numerous in soils and play a crucial role in soil food-webs. DNA metabarcoding offers a time-effective alternative to morphology-based assessments of nematode diversity. However, it is unclear how different DNA extraction methods prior to metabarcoding could affect community analysis. We used soils with woody vegetation from a European latitudinal gradient (29 sites, 39 to 79°N, ∼4500 km, covering six biomes) to systematically evaluate the effect of two sources of nematode DNA either directly extracted from soils vs. extracted from nematodes previously isolated from soils hypothesizing that the DNA source material may produce different diversities, community structures and abundances of feeding types. Nematode-sample DNA exhibited a higher richness, while no difference in Shannon diversity was found between the approaches. The DNA sources also created significantly different community structures, with greater differences observed across soil-extracted DNA than nematode-sample DNA. The most overrepresented species in nematode-sample DNA were Heterocephalobus elongatus, Eucephalobus striatus and Hexatylus sp., whereas Phasmarhabditis sp. and Eumonhystera filiformis were overrepresented in soil-extracted DNA. Read abundances of feeding types significantly differed between the DNA sources and across sites, with a significant effect of biome on both ecto- and endoparasitic herbivores in soil-extracted DNA and for ectoparasitic herbivores only in nematode-sample DNA. Collectively, our data suggest that choice of the DNA source material may lead to different patterns of nematode community composition across space and environmental conditions. Improving the sensitivity of the soil-extracted DNA method by developing protocols using larger amounts of soil and designing nematode-specific primers will make this approach an efficient screening tool to analyse nematode diversity and community structure complementing the labour-intensive isolation of intact nematodes from soils (nematode-sample DNA).
OriginalsprogEngelsk
Artikelnummer109154
TidsskriftSoil Biology and Biochemistry
Vol/bind185
Antal sider16
ISSN0038-0717
DOI
StatusUdgivet - 2023

Bibliografisk note

Funding Information:
This work was conducted within the COST Action KEYSOM (ES 1406: Soil fauna – Key to soil organic matter dynamics and modelling). We thank Simon Dummermuth and Samuel Gunz for their support in the laboratory. We are grateful to Irma Roth (Research Group Phytopathology and Zoology in Fruit and Vegetable Production, Agroscope, Wädenswil, Switzerland) for helping with the nematode extraction, counting and determination. We acknowledge the contribution of the staff at the McGill University and Génome Québec Innovation Centre, Montréal, Canada, for their sequencing service. We thank Oliver Schramm from the Swiss Long-term Forest Ecosystem Research programme LWF ( www.lwf.ch ), which is part of the UNECE Co-operative Programme on Assessment and Monitoring of Air Pollution Effects on Forests (ICP Forests, www.icp-forests.net ) for helping with sampling in the Swiss LWF sites. We also thank Melissa Dawes for her valuable contribution to the editing of this article. BF acknowledges funding of the Swiss National Science Foundation (SNSF) (grant IZCNZ0-174585 ).

Funding Information:
This work was conducted within the COST Action KEYSOM (ES 1406: Soil fauna – Key to soil organic matter dynamics and modelling). We thank Simon Dummermuth and Samuel Gunz for their support in the laboratory. We are grateful to Irma Roth (Research Group Phytopathology and Zoology in Fruit and Vegetable Production, Agroscope, Wädenswil, Switzerland) for helping with the nematode extraction, counting and determination. We acknowledge the contribution of the staff at the McGill University and Génome Québec Innovation Centre, Montréal, Canada, for their sequencing service. We thank Oliver Schramm from the Swiss Long-term Forest Ecosystem Research programme LWF (www.lwf.ch), which is part of the UNECE Co-operative Programme on Assessment and Monitoring of Air Pollution Effects on Forests (ICP Forests, www.icp-forests.net) for helping with sampling in the Swiss LWF sites. We also thank Melissa Dawes for her valuable contribution to the editing of this article. BF acknowledges funding of the Swiss National Science Foundation (SNSF) (grant IZCNZ0-174585).

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