Environmental DNA

- eDNA: a research area in focus at the Department of Environmental Science (a "Strategic Growth Area", SGA)

Graphical representation of DNA sequences of mobile genetic elements from different environmental phyla

Microorganisms are present in practically all parts of the environment as well as in tissues of living organisms, where they may greatly influence the life of humans and the environment in multiple ways. DNA sequencing analysis of microbial DNA sampled from these environments constitutes a great opportunity to study the role and ecology of these organisms and get insight into their metabolism, function and evolutionary relationship. The Section of Microbiology and Biotechnology houses state-of-the-art sequencing facilities to support participation in all types of projects involving analysis of microbial eDNA. This includes identification of single microorganisms and entire microbial communities in various matrices, their expression of genes relevant for provision of important ecosystem services and health of humans, animals and plants. In addition, the eDNA SGA works with development of techniques for detection and monitoring of DNA from higher organisms.

Illumina MiSeq- and NextSeq-sequencing platforms for analysing eDNA

Main research areas

Study microbial eDNA from various environments (soil, water, atmosphere, the arctics, animal gut, food production) in order to understand their ecology and function in these settings.
Through DNA sequencing investigate genetic drivers of bacterial evolution by comparing metagenomic contents of between pristine and evolutionary challenged environments.
Characterization of bacterial communities by 16S rRNA gene analysis, whole genome sequencing of key microbial organisms (vira, bacteria, fungi and protozoans) and transcriptome analysis related with diseases in humans, animals and plants and degradation of pollutants.
Use eDNA analysis to understand the role of microbes in provision of ecosystem services like biogeochemical cycling of nutrients, degradation of organic micro pollutants, suppression of plant pests.
Detection and risk assessment of hazardous microorganism in air, soil, water and food in relation to human and environmental health.
Mobilomics: Sequence-based studies on mobile genetic elements such as plasmids, bacteriophages and IS elements.

Examples of recent and ongoing projects

MICROWINE (www.microwine.eu)
Phagemid (http://envs.au.dk/instituttet/sektioner/embi/emg/phagemid/)
Phytoprotect (http://envs.au.dk/instituttet/sektioner/embi/emg/phytoprotect/)
Food Spill - Strategies and technologies to reduce food waste in potatoes and vegetables (http://pure.au.dk/portal/en/projects/strategier-og-teknologier-til-at-begraense-madspild-i-spisekartofler-og-groensager(b9a10b29-e628-4221-b4f5-677656346147).html)
NUMEN (http://inano.au.dk/organization/research-groups/electrochemical-biosensors-and-bioelectrocatalysis-group-elena-ferapontova/numen/)
MEM2BIO - Innovative combination of MEMbrane technology and BIOlogical filtration for water purification http://envs.au.dk/instituttet/sektioner/embi/emg/mem2bio/
MIRESOWA - MICROBIAL REMEDIATION OF CONTAMINATED SOIL AND WATER RESOURCES http://miresowa.dk/

Testing a bacterial strain for resistance to antibiotics

Masters projects offered

http://envs.au.dk/instituttet/sektioner/embi/emg/apro/

Publications

Environmental DNA - publications within the research area.

Click to expand publications list

Jakszyn, P., Luján-Barroso, L., Agudo, A., Bueno-de-Mesquita, H. B., Molina, E., Sánchez, M. J., Fonseca-Nunes, A., Siersema, P. D., Matiello, A., Tumino, R., Saieva, C., Pala, V., Vineis, P., Boutron-Ruault, M.-C., Racine, A., Bastide, N., Travis, R. C., Khaw, K.-T., Riboli, E. ... González, C. A. (2013). Meat and heme iron intake and esophageal adenocarcinoma the European Prospective investigation into Cancer and Nutrition study. International Journal of Cancer, 133(11), 2744-50. https://doi.org/10.1002/ijc.28291

Ellegaard-Jensen, L., Knudsen, B. E., Johansen, A., Albers, C. N., Aamand, J. & Rosendahl, S. (2014). Fungal-bacterial consortia increase diuron degradation in water-unsaturated systems. Science of the Total Environment, 466-467, 699-705. https://doi.org/10.1016/j.scitotenv.2013.07.095

Imparato, V., Santos, S., Hansen, V., Johansen, A., Giagnoni, L., Renella, G., Nielsen, H. H. & Winding, A. (2014). How do soil biota react to gasification biochar?. Poster session præsenteret på ISME Symposium , Seoul, Sydkorea.

Santos, S. S., Nielsen, T. K., Hansen, L. H. & Winding, A. (2015). Comparison of three DNA extraction methods for recovery of soil protist DNA. Journal of Microbiological Methods, 115, 13-19. https://doi.org/10.1016/j.mimet.2015.05.011

Albers, C. N., Ellegaard-Jensen, L., Harder, C. B., Rosendahl, S., Knudsen, B. E., Ekelund, F. & Aamand, J. (2015). Groundwater chemistry determines the prokaryotic community structure of waterworks sand filters. Environmental Science & Technology (Washington), 49, 839-846. https://doi.org/10.1021/es5046452

Nunes, I., Jacquiod, S., Brejnrod, A., Holm, P. E., Johansen, A., Brandt, K. K., Prieme, A. & Sorensen, S. J. (2016). Coping with copper: legacy effect of copper on potential activity of soil bacteria following a century of exposure. F E M S Microbiology Reviews, 92(11), Artikel 175. https://doi.org/10.1093/femsec/fiw175

Frková, Z., Johansen, A., de Jonge, L. W., Olsen, P., Gosewinkel, U. & Bester, K. (2016). Degradation and enantiomeric fractionation of mecoprop in soil previously exposed to phenoxy acid herbicides - New insights for bioremediation. Science of the Total Environment, 569-570, 1457-65. https://doi.org/10.1016/j.scitotenv.2016.06.236

Imparato, V., Hansen, V., Santos, S., Nielsen, T. K., Giagnoni, L., Hauggaard-Nielsen, H., Johansen, A., Renella, G. & Winding, A. (2016). Gasification biochar has limited effects on functional and structural diversity of soil microbial communities in a temperate agroecosystem. Soil Biology & Biochemistry, 99, 128-136. https://doi.org/10.1016/j.soilbio.2016.05.004

Wang, Y., Qin, Y., Kot, W., Zhang, F., Zheng, S., Wang, G., Hansen, L. H. & Rensing, C. (2016). Genome Sequence of Selenium-Solubilizing Bacterium Caulobacter vibrioides T5M6. Genome Announcements, 4(1), Artikel e01721-15. https://doi.org/10.1128/genomeA.01721-15

Jacquiod, S. J. A., Stenbæk, J., Santos, S., Winding, A., Sørensen, S. J. & Priemé, A. (2016). Metagenomes provide valuable comparative information on soil microeukaryotes. Research in Microbiology, 167(5), 436-450. Artikel 167. https://doi.org/10.1016/j.resmic.2016.03.003

Winding, A., Santos, S., Browne, P. D., Hansen, L. H., Johansen, A. & Krogh, P. H. (2016). Metagenomics of bacteria, fungi and protists affected by biochar and earthworms in soil. Poster session præsenteret på Danmarks Mikrobiologiske Selskab, København, Danmark.

Imparato, V., Santos, S., Johansen, A., Geisen, S. & Winding, A. (2016). Stimulation of bacteria and protists in rhizosphere of glyphosate-treated barley. Applied Soil Ecology, 98, 47-55. https://doi.org/10.1016/j.apsoil.2015.09.007

Stæhr, P. A., Santos, S., Hansen, L. H., Lundsteen, S., Haraguchi, L., Dahl, K., Ávila, M. & Winding, A. (2017). Comparison of eDNA and conventional techniques for monitoring species diversity of boulder reefs in Danish waters. Poster session præsenteret på DNAqua-Net Kick-off, Essen, Tyskland. http://dnaqua.net/wp-content/uploads/2017/03/Poster_Winding.pdf

Eckholdt, A., Winding, A. & Krogh, P. H. (2017, nov. 15). Dine marker har DNA. FBG Medier A/S.

Santos, S. S., Hendriksen, N. B., Jakobsen, H. H. & Winding, A. (2017). Effects of Bacillus cereus Endospores on Free-Living Protist Growth. Microbial Ecology, 73(3), 699-709. https://doi.org/10.1007/s00248-016-0905-7

Hylling, O., Fini, M. N., Muff, J., Madsen, H. T., Aamand, J., Hansen, L. H. & Ellegaard-Jensen, L. (2017). Aminobacter sp. biodegradation of 2,6-dichlorobenzamide (BAM) is stimulated in membrane treated residual water. Poster session præsenteret på Danish Microbiological Society (DMS) congress 2017, Copenhagen, Danmark.

Hylling, O., Fini, M. N., Muff, J., Madsen, H. T., Aamand, J., Hansen, L. H. & Ellegaard-Jensen, L. (2017). MEM2BIO - Membrane residual water as a feed for bioaugmented waterworks sand filters. Poster session præsenteret på the second international congress on microbial resource management (MRM2), Ghent, Belgien.

Santos, S. S., Nunes, I., Nielsen, T. K., Jacquiod, S., Hansen, L. H. & Winding, A. (2017). Soil DNA Extraction Procedure Influences Protist 18S rRNA Gene Community Profiling Outcome. Protist, 168(3), 283-293. https://doi.org/10.1016/j.protis.2017.03.002

Albers, C. N., Ellegaard-Jensen, L., Hansen, L. H. & Sørensen, S. R. (2018). Bioaugmentation of rapid sand filters by microbiome priming with a nitrifying consortium will optimize production of drinking water from groundwater. Water Research, 129, 1-10. https://doi.org/10.1016/j.watres.2017.11.009

Winding, A., Bang-Andreasen, T., Hansen, L. H., Panitz, F., Krogh, P. H., Krause-Jensen, D., Stæhr, P., Nicolaisen, M., Hendriksen, N. B., Sapkota, R., Santos, S. & Andersen, L. W. (2019). eDNA in environmental monitoring. Aarhus University, DCE - Danish Centre for Environment and Energy. DCE Technical reports Nr. 133 https://dce2.au.dk/pub/TR133.pdf

Gobbi, A., Santini, R. G., Filippi, E., Ellegaard-Jensen, L., Jacobsen, C. S. & Hansen, L. H. (2019). Quantitative and qualitative evaluation of the impact of the G2 enhancer, bead sizes and lysing tubes on the bacterial community composition during DNA extraction from recalcitrant soil core samples based on community sequencing and qPCR. PLOS ONE, 14(4), Artikel e0200979. https://doi.org/10.1371/journal.pone.0200979

Sapkota, R., Santos, S., Farias, P. D. G., Krogh, P. H. & Winding, A. (2020). Insights into the earthworm gut multi-kingdom microbial communities. Science of the Total Environment, 727, Artikel 138301. https://doi.org/10.1016/j.scitotenv.2020.138301

Santos, S., Schöler, A., Nielsen, T. K., Hansen, L. H., Schloter, M. & Winding, A. (2020). Land use as a driver for protist community structure in soils under agricultural use across Europe. Science of the Total Environment, 717, Artikel 137228. https://doi.org/10.1016/j.scitotenv.2020.137228

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Environmental DNA - persons involved

Lea Ellegaard-Jensen , Lektor , Institut for Miljøvidenskab - Mikrobiel Økologi
Ulrich Bay Gosewinkel , Seniorforsker , Institut for Miljøvidenskab - Mikrobiel Økologi
Niels Bohse Hendriksen , Seniorforsker , Institut for Miljøvidenskab - Mikrobiel Økologi
Carsten Suhr Jacobsen , Institutleder, Professor , Institut for Miljøvidenskab
Anders Johansen , Seniorforsker - sektionsleder , Institut for Miljøvidenskab - Mikrobiel Økologi
Anne Winding , Professor , Institut for Miljøvidenskab - Mikrobiel Økologi

Revideret 14.02.2024

Institut for Miljøvidenskab

Environmental DNA

Main research areas

Examples of recent and ongoing projects

Masters projects offered

Publications

Click to expand publications list

Environmental DNA - persons involved

Environmental DNA - contact

Coordinator (lead)

Anne Winding

Coordinator (co-lead)

Rumakanta Sapkota