Tullgren extracts of soil mesofauna are proving challenging to identify using trained volunteers. Could metabarcoding be a rapid, cost-effective approach for monitoring soil mesofauna and characterising their communities

Andujar, Carmelo

Griffiths, Robert I.

Gweon, Hyun Soon

Keith, Aidan

Read, Daniel A.

Shepherd, Matthew J.

Spurgeon, David A.

Vogler, Alfried

NERC Open Research Archive

Monitoring soil biodiversity in nature reserves in England – a role for metabarcoding Matthew J. Shepherd, Natural England, Renslade House, Bonhay Road, Exeter, EX4 3AW, U.K. David. A. Spurgeon, Robert I. Griffiths, Daniel A. Read, Hyun Soon Gweon,  Centre for Ecology and Hydrology, Benson Lane, Wallingford, OX10 8BB, U.K. Aidan Keith, Centre for Ecology & Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, LA1 4AP, U.K. Alfried Vogler, Carmelo Andújar Imperial College London, South Kensington Campus, London, SW7 2AZ, U.K. Rationale:  Natural England assesses soil biodiversity as part of our monitoring across 40 National Nature Reserves to detect long-term environmental trends. Tullgren extracts of soil mesofauna are proving challenging to identify using trained volunteers.  Could metabarcoding be a rapid, cost-effective approach for monitoring soil mesofauna and characterising their communities? Compare ability to: • distinguish different communities • identify realistic community composition   Conclusions: • Metabarcoding shows good potential for rapid characterisation and monitoring of soil mesofauna communities, but better COi primers are needed for some groups and for bulk soil approaches. • More effort to generate barcodes for more soil species will help identify realistic soil communities. Two sets of six samples were taken from  three chalk grasslands: ancient species-rich, agriculturally improved and naturally reverting grassland. Metabarcoded for 18S rRNA and COi Broad morphological identification Method: Tullgren extraction of mesofauna Bulk soil sub-sample DNA extracted  ~200 individuals of most common species Soil mesofauna community DNA extracted  Identified to species / genus / family Barcoded 18S rRNA &COi Training volunteers Site-specific barcode reference database 12cm  OTU’s compared to…. Compatibility: All approaches showed  distinct and congruent differences in soil communities between grassland types. Above: first and second axes from non-metric multidimensional scaling analysis. Methods: The minibarcode primers used for COi analysis of bulk soil resulted in poor amplification, and require more optimisation. Folmer primers worked well for collembola and oribatids in Tullgren extracts.  Results:  Community composition:  18S rRNA represented broad soil communities (mesofauna, plants, algae, fungi and protists) but gave a poor match to ecologically appropriate species in GenBank. There were more collembola OTUs in agriculturally improved grassland and more acari in the species-rich grassland soil in Tullgren extracts.   Remaining soil  OTU’s compared to GenBank barcode database 8cm  Imagery © 2014 DigitalGlobe, Getmapping PLC, Infoterra Ltd & Bluesky Map data © 2014 Google. Photo: R. Marris, Natural England Ancient Spp. Rich Naturally Reverting Agriculturally Improved ® Intensive Grassland Lepidocyrtus-cyaneus (Entomobryidae) (95% match) Isotoma-caerulea (Isotomidae) (94% match) Isotoma-anglicana (Isotomidae) (94% match) Unidentifiable  DNA Parisotoma-notabilis (Isotomidae) (94% match) Parasitidae (95% match) Achromobacter-xylosoxidans (Alcaligenaceae) (90% match) Pseudosinella-alba (Entomobryida) (94% match) Tectocepheus-sp-BOLD-AAM7998 (Tectocepheidae) (83% match) Sminthurinus-aureus (Katiannidae) (94% match) Achaeta-cf-bohemica-PDW-2010 (Enchytraeidae) (84% match) Pachylaealpidae (87% match) Bdellidae (83% match) Others (>1% of sample) Improved Grassland Folsomia-quadrioculata (Isotomidae) (87% match) Conosanus-obsoletus (Cicadellidae) (94% match) Scheloribatidae sp. 0 (92% match) Stenaphorura-denisi (Tullbergiidae) (95% match) Scheloribatidae sp.1 (94% match) Sminthurinus-aureus (Katiannidae) (94% match) Lepidocyrtus-cyaneus (Entomobryidae) (95% match) Unidentified DNA  (0% match) Oppiidae (96% match) Isotoma-caerulea (Isotomidae) (94% match) Anolis-sp-2-MDC-2011 (Iguanidae) (81% match) Carabus-huangi (Carabidae) (75% match) Lithobius-valesiacus (Lithobiidae) (84% match) Eueremaeus-oblongus (Eremaeidae) (80% match) Mycobates-sp-BOLD-AAZ5801 (Mycobatidae) (79% match) Tipula-paludosa (Tipulidae) (96% match) Others <1% of sample Ancient Semi-natural COi OTU abundance and matches in two samples  Morphological identification 18S rRNA Tullgren extracts 18S rRNA from bulk soil COi from Tullgren extracts Long-Term Monitoring Network (LTMN) Sites The de-novo site-specific database  significantly improved matching of COi metabarcode OTUs over GenBank alone, describing more ecologically realistic communities. OribatidaCollembolade novoGenBankde novoGenBank1009590858075Percent matchThis work was funded by Natural England, the government’s adviser on England’s natural environment, landscapes and wildlife.  N.E. is an executive non-departmental public body, sponsored by the Department for Environment, Food & Rural Affairs. 

Monitoring soil biodiversity in nature reserves in England - a role for metabarcoding

http://nora.nerc.ac.uk/509712/1/N509712PO.pdf

Monitoring soil biodiversity in nature reserves in England - a role for metabarcoding

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