Soil fungi

In an extensive program we study the diversity and community composition of fungi in the Arctic tundra, and the community composition, distribution patterns and altitudinal gradients of fungi in the forests of the Neotropics and Palaeotropics. We employ DNA metabarcoding to better understand how fungal community composition correlates to environmental variables. Furthermore, we study the interaction of fungi and bacteria with vascular plants, such as vanilla and the rare Spiranthes aestivalis orchids. Projects are funded by the municipality of Eindhoven, the Werkgroep Europese Orchideeën of the KNNV, the Topsector Tuinbouw en Uitgangsmaterialen and SIA.

American Bird Cherry

Funded by the Uyttenboogaart-Eliasen Stichting and Team Invasieve Exoten, we investigated the incorporation of invasive American bird cherry (Prunus serotina) into a native insect herbivore food web. A surprisingly diverse community of aphids, beetles, caterpillars, both specialists and generalists, adapted to American bird cherry in less than 200 years. Our results indicate that removing this invasive is not a good idea as this will slow down the process of adaptation of local herbivores.

Pond Bat

Co-financed by the Mammal Society Zuid Holland, we currently investigate the diet of the endangered pond bat (Myotis dasycneme). Females of this bat species are slightly larger than the males and combined DNA and morphological data generated from dung samples show that the diet between the sexes is different. With this knowledge, conservation of the species can be improved. During the past five years we also analysed feces of extant and extinct animal species such as goats, horses, bisons and mammoths, using our ancient DNA labs.

St. Eustatius Terrestrial Baseline

The Dutch volcanic islands of St. Eustatius and Saba provide a natural laboratory to study the effects of climate change on biodiversity. In 2015 we organized a first terrestrial baseline study at St. Eustatius, using a multi-taxon approach. For twelve vegetation types we set out a plot of 25 square metres and recorded or collected all possible species. Specimens were sorted to morphospecies and DNA barcoded. We deployed malaise traps to collect invertebrates and took soil samples for fungi, both analysed via metabarcoding techniques.  Preliminary results: several hundreds of species new to the island and many new to science. This study is a collaboration of Naturalis, the Dutch Mammal Society, RAVON, STENAPA and the Caribbean Netherlands Science Institute.

Key scientific publications

  • Veldman, S., Gravendeel, B., Otieno, J.N., Lammers, Y. Duijm, E., Nieman, A., van Andel, T., de Boer, H. In press. High-throughput sequencing of African orchid cake reveals species diversity and raises orchid conservation concerns. Biodiversity and Conservation.
  • Haarsma, A.J., Siepel, H., Gravendeel, B. 2016. Added value of metabarcoding combined with microscopy for evolutionary studies of mammals. Zoological Scripta 45: 47-49.
  • Staats M., Arulandu A.J., Gravendeel B., Holst-Jensen A., Scholtens I., Peelen T., Prins T.W., Kok E. 2016. Advances in DNA metabarcoding for food and wildlife forensic species identification. Analytical and Bioanalytical Chemistry 408: 4615-4630.
  • Yang C., Wang X., Miller J.A., Blécourt M. de, Ji Y., Yang C., Harrison R.D., Yu D.W. 2014. Using metabarcoding to ask if easily collected soil and leaf-litter samples can be used as a general biodiversity indicator. Ecological Indicators 46: 379-389.
  • Lammers Y., Peelen T., Vos R.A., Gravendeel B. 2014. The HTS barcode checker pipeline, a tool for automated detection of illegally traded species from high-throughput sequencing data. BMC Bioinformatics 15: 44.
  • Geel B. van, Protopopov A., Bull I., Duijm E., Gill F., Nieman A., Rudaya N., Trofimova S., Tikhonov A., Vos R.A., Zhilich S., Gravendeel B. 2014. Multiproxy diet analysis of the last meal of an early Holocene Yakutian Bison. Journal of Quaternary Science 29: 261-268.
  • Bellemain E., Davey M.L., Kauserud H., Epp L.S., Boessenkool S., Coissac E., Geml J., Edwards M., Willerslev E., Gussarova G., Taberlet P., Brochmann C. 2013. Fungal palaeodiversity revealed using high-throughput metabarcoding of ancient DNA from arctic permafrost. Environmental Microbiology 15: 1176-1189.
  • Welker F., Gravendeel B. 2013. Dung reveals goat’s last days. Nature 503: 440.