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Scientific peer-reviewed articles

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Peer-reviewed publications:


Girlanda, M., Orgiazzi, A., Vizzini, A., Roggero, P.P., Bagella, S., Lai, R., Rossetti, I., Seddau, G., Bioanciotto, V., Lumini, E. 2011. EcoFINDERS: increasing the understanding of the role of soil fungal diversity in ecosystem functioning. Boll. Mus. Ist. Biol. Univ. Genova, 73: 199. 106° Congresso Società Botanica Italiana – Genova 21-23 September 2011 See more here

Mulder, C., Helder, J., Vervoort, M.T.W., Vonk, J.A. 2011.Trait-mediated diversification in nematode predator-prey systems. Ecology and Evolution doi: 10.1002/ece3.36, 386-391. Read the abstract

Mulder, C., Boit, A., Bonkowski, M., De Ruiter, P.C., Mancinelli, G., Van der Heijden, M.G.A., Van Wijnen, H.J., Vonk, J.A., Rutgers, M. 2011. A Belowground Perspective on Dutch Agroecosystems: How Soil Organisms Interact to Support Ecosystem Services, In: Guy Woodward, Editor(s), Advances in Ecological Research, Academic Press, 2011, Volume 44, Pages 277-357, ISSN 0065-2504, ISBN 9780123747945, DOI: 10.1016/B978-0-12-374794-5.00005-5. Read the article

Mulder, C., Vonk, A.J. 2011. Nematode traits and environmental constraints in 200 soil systems: scaling within the 60–6000 μm body size range. Ecology, 92:10. Read the article 


Brussaard, L.; Aanen, D.K.; Briones, M.J.I.; Decaëns, T.; Deyn, G.B. de; Fayle, T.M.; James, S.W.; Nobre, T. (2012). Biogeography and phylogenetic community structure of soil invertebrate ecosystem engineers, Global to Local Patterns, Implications for Ecosystem, Functioning and Services and Global, Environmental Change Impacts. In: Soil Ecology Ecosystems Services / Wall, D.H., . - Oxford UK : Oxford University Press, - p. 201 - 232. Find book here

Brussaard, L. 2012. Ecosystem Services Provided by the Soil Biota.  In: Wall, D.H., Bardgett, R.D., Behan-Pelletier, V., Herrick, J.E., Jones, H., Ritz, K., Six, J., Strong, D.R., and van der Putten, W.H. (eds). Soil Ecology and Ecosystem Services. Oxford University Press, UK, 45-58. Read abstract

Hallin S., Welsh A., Stenström J., Hallet S., Enwall K., Bru D.,  Philippot L. 2012. Soil functional operating range linked to microbial biodiversity and community composition using denitrifiers as model guild. PLoS ONE 7(12): e51962. doi:10.1371/journal.pone.0051962. Read article here (Pdf here)

Philippot, L., Ritz, K., Pandard, P., Hallin, S. and Martin-Laurent, F. (2012), Standardisation of methods in soil microbiology: progress and challenges. FEMS Microbiology Ecology, 82: 1–10. doi: 10.1111/j.1574-6941.2012.01436.x Read the article

Plassart, P., Terrat, S.., Thomson, B., Griffiths, R., Dequiedt, S., Lelievre, M., Regnier, T., Nowak, V., Bailey, M., Lemanceau, P., Bispo, A., Chabbi, A., Maron, P.-A., Mougel,C., Ranjard, L. (2012), Evaluation of the ISO Standard 11063 DNA Extraction Procedure for Assessing Soil Microbial Abundance and Community Structure.PLOSOne,7: e44279. DOI: 10.1371/journal.pone.0044279. Read the article (Pdf here)


Andriuzzi, W.S., Bolger, T, Schmidt, O. 2013 The drilosphere concept: Fine-scale incorporation of surface residue-derived N and C around natural Lumbricus terrestris burrows. Soil Biology & Biochemistry. 64:136–138. DOIRead the article

Bardgett R.D., Manning P., Morriën E., de Vries F.T. Hierarchical responses of plant-soil interactions to climate change: consequences for the global carbon cycle. Journal of Ecology, volume 101(2), pp. 334-343. Read the abstract

Baus, P., Kováč, U., Pauditšová, E., Kohutková, I., Komorník, J. 2013. Identification of interconnections between landscape pattern and urban dynamics—Case study Bratislava, Slovakia. Ecological Indicators, in press. Read the article

Chobotová, V. (2013) The Role of Market–Based Instruments for Biodiversity Conservation in Central and Eastern Europe. Ecological Economics 95:41-50. Read the article

Kemmers, RH, Bloem, J, Faber, JH. 2013. Nitrogen retention by soil biota; A key role in the rehabilitation of natural grasslands? Restoration Ecology. 21:431-438. Read the article

Kluvánková-Oravská, T., Chobotová, V., Smolková, E.: The Challenges of Policy Convergence: The Europeanization of Biodiversity Governance in an Enlarging EU. Environment and Planning C: Government and Policy 2013, volume 31 (3), pp. 401-413, doi:10.1068/c1034j. Read the article

Mulder, C., Arestani, F.S., Bahn, M., Bohan, D.A., Bonkowski, M., Griffiths, B.S., Guicharnaud, R.A., Kattge, J., Krogh, P.H., Lavorel, S., Lewis, O.T., Mancinelli, G., Naeem, S., Peñuelas, J., Poorter, H., Reich, P.B., Rossi, L., Rusch, G.M., Sardans, J. and Wright, I.J. (2013) Connecting the green and brown worlds: allometric and stoichiometric predictability of above- and below-ground networks. Advances in Ecological Research 49, Ecological Networks in an Agricultural World. Eds Woodward G and Bohan D.A. Elsevier, Amsterdam. Pp. 69-175. Read the chapter

Orgiazzi A., Bianciotto V., Bonfante P., Daghino S., Ghignone S., Lazzari A., Lumini E., A. Mello, Napoli C., Perotto S., Vizzini A., Bagella S., Murat C., Girlanda M. (2013) 454 Pyrosequencing Analysis of Fungal Assemblages from Geographically Distant, Disparate Soils Reveals Spatial Patterning and a Core Mycobiome. Diversity 2013, 5(1), 73-98, doi:10.3390/d5010073. Read the article

Faber J.H, Creamer R.E., Mulder C., Römbke J., Rutgers M., Sousa J.P., Stone D., Griffiths B.S. The practicalities and pitfalls of establishing a policy-relevant and cost-effective soil biological monitoring scheme. Integrated Environmental Assessment and Management - Volume 9, Number 2 - pp. 276-284. Read the article

Griffiths, B.S, Philippot, L. Insights into the resistance and resilience of the soil microbial community. FEMS Microbiology Reviews. DOI: 10.1111/j.1574-6976.2012.00343. Read the article

Jones, C.M., Graf, D., Bru, D., Philippot, L., Hallin, S. The unaccounted yet abundant nitrous oxide reducing microbial community - a potential nitrous oxide sink. ISME J. (2013), volume 7, pp. 417–426.  doi: 10.1038/ismej.2012.125. Read the article

Philippot, L, Spor, A, Hénault, C, Bru, D, Bizouard, Jones, CM, Sarr A, Maron, P-A. Loss in microbial diversity affects nitrogen cycling in soil. The ISME Journal advance online publication, 7 March 2013; doi:10.1038/ismej.2013.34. Read the article

Philippot, L., Raaijmakers, J.M., Lemanceau, P.,  van der Putten, WH. 2013. Going back to the roots: the microbial ecology of the rhizosphere. Nature Reviews Microbiology (11)789–799. doi:10.1038/nrmicro3109. Published online23 September 2013. Read the article

David J. Spurgeon, Aidan M. Keith, Olaf Schmidt, Dennis R. Lammertsma and Jack H. Faber, 2013. Land-use and land-management change: relationships with earthworm and fungi communities and soil structural properties. BMC Ecology 2013, 13:46 doi:10.1186/1472-6785-13-46 Read the article

Thomson, BC, Ostle, NJ, McNamara, NP, Oakley, S, Whiteley, AS, Bailey, M. Griffiths, RI. 2013. Plant soil interactions alter carbon cycling in an upland grassland soil. Front. Microbiol., 10 September 2013 | Read the article

Uroz, S, Ioannidis, P., Lengelle, J., Cébron, A., Morin, E., Buée, M., Martin, F. 2013. Functional Assays and Metagenomic Analyses Reveals Differences between the Microbial Communities Inhabiting the Soil Horizons of a Norway Spruce Plantation. PLOS One 8: e55929 doi: 10.1371/journal.pone.0055929 Read the article here and here


Yuan, Y., Krogh, P.H., Bai, X., Roelofs, D., Chen, F., Zhu-Salzman, K., Liang, Y., Sun, Y., Ge, F., 2014. Microarray detection and qPCR screening of potential biomarkers of Folsomia candida Collembola: Isotomidae) exposed to Bt proteins (Cry1Ab and Cry1Ac). Environmental Pollution 184, 170-178. Read the article

Sechi, V., D'Annibale, A., Maraldo, K., Johansen, A., Bossi, R., Jensen, J., Krogh, P.H., 2014. Species composition of a soil invertebrate multi-species test system determines the level of ecotoxicity. Environmental Pollution 184, 586-596. Read article here

Tardy, V., Mathieu, O., Lévêque, J., Terrat, S., Chabbi, A., Lemanceau, P., Ranjard, L. and Maron, P.-A. (2014), Stability of soil microbial structure and activity depends on microbial diversity. Environmental Microbiology Reports, 6: 173–183. doi: 10.1111/1758-2229.12126. Read the article

Terrat, S., Plassart, P., Bourgeois, E., Ferreira, S., Dequiedt, S., Adele-Dit-De-Renseville, N., Lemanceau, P., Bispo, A., Chabbi, A., Maron, P.-A., Ranjard, L.  2014. Meta-barcoded evaluation of the ISO standard 11063 DNA extraction procedure to characterize soil bacterial and fungal community diversity and composition. Microbial Biotechnology. DOI: 10.1111/1751-7915.12162. Read the article

Jones, C.M., Spor, A., Brennan, F.P., Breuil, M.-C., Bru, D., Lemanceau, P., Griffiths, B., Hallin, S., Philippot, L. 2014. Recently identified microbial guild mediates soil N2O sink capacity. Nature Climate Change. 4:801-805. doi:10.1038/nclimate2301. Read the article

Andriuzzi, W., Schmidt, O., 2014. Production of rabbit dung triple-labelled with C, N and S stable isotopes. Pedobiologia 57, 155–160, DOI: 10.1016/j.pedobi.2014.02.001. Read the abstract here.

Bragalini, C., Ribière., Parisot, N., Vallon, L., Prudent, E., Peyretaillade, E., Girlanda, M., Peyret, P., Marmeisse, R., and Luis, P. 2014. Solution Hybrid Selection Capture for the Recovery of Functional Full-Length Eukaryotic cDNAs From Complex Environmental Samples. DNA Research. doi:10.1093/dnares/dsu030. LinkRead full paper.

Geisen S, Fiore-Donno A, Walochnik J, Bonkowski M. 2014. Acanthamoeba everywhere: high diversity of Acanthamoeba in soils. Parasitol Res 113: 3151-3158. Read abstract here.

Geisen S, Kudryavtsev A, Bonkowski M, Smirnov A. 2014. Discrepancy between species borders at morphological and molecular levels in the genus Cochliopodium (Amoebozoa, Himatismenida), with the description of Cochliopodium plurinucleolum n. sp. Protist 165: 364-383. Read abstract here.

Geisen S, Weinert J, Kudryavtsev A, Glotova A, Bonkowski M, Smirnov A. 2014. Two new species of the genus Stenamoeba (Discosea, Longamoebia): cytoplasmic MTOC is present in one more amoebae lineage. J Eukaryot Microbiol 50: 153-165. Read abstract here.

Thion, C. and Prosser, J.I. 2014. Differential response of nonadapted ammonia-oxidising archaea and bacteria to drying–rewetting stress. FEMS Microbio. Ecol. DOI: 10.1111/1574-6941.12395. Read abstract here.

Crittenden, S.J., Eswaramurthy, T, Goede, R.G.M de, Brussaard, L., Pulleman, M.M. 2014. Effect of tillage on earthworms over short- and medium-term in conventional and organic farming. Appl. Soil Ecol. 83: 140-148. DOI: 10.1016/j.apsoil.2014.03.001. Read abstract here.

Bagella, S., Filigheddu, R., Caria, M.C., Girlanda, M., & Roggero, P.P. 2014. Contrasting land uses in Mediterranean agro-silvo-pastoral systems generated patchy diversity patterns of vascular plants and below-ground microorganisms. Comptes Rendus Biologies. Read full paper here 


Geisen S, Bandow C, Römbke J, Bonkowski M. 2014. Soil water availability strongly alters the community composition of soil protists. Pedobiologia 57: 205–213. Read more here 

Henrys, P.A., Bee, E.J., Watkins, J.W., Smith, N.A. and Griffiths, R.I. 2014. Mapping natural capital: optimising the use of national scale datasets. Ecography. Read more here 

Orgiazzi, A., Dunbar, M.B., Panagos, P., Groot, G.E. de, Lemanceau, P. 2015. Soil biodiversity and DNA barcodes: opportunities and challenges. Soil Biology and Biochemistry, 80: 244–250. Read more here

In prep / in review

Thomson, B.C., Tisserant, E., Plassart, P., Uroz, S., Griffiths, r.I., Hannula, S. E., Buée, M., Mougel, C., Ranjard, L., van Veen, J.A., Martin, F., Bailey, M. J., Lemanceau, P. In review. Soil conditions and land use intensification effects on soil microbial communities across a range of European field sites. Molecular Ecology.

Andriuzzi, W.S., Ngoc, P-T. , Geisen, S., Keith, A.M., Dumack, K., Bolger, T., Bonkowski, M., Brussaard, L., Faber, J., Chabbi, A., Rumpel, C., Schmidt, O. In review. Two similar earthworm species produce dissimilar soil biochemical hotspots in temperate grassland.

Siegel K., Chapelle E., Edel-Hermann V., Jack A., Raaijmakers J., Lemanceau P., Steinberg C. In press. Are soils suppressive to fungal diseases the sources of biocontrol agents? IOBC Bulletin.

Siegel K., Daguerre Y., Edel-Hermann V., Steinberg C. Fungal proteins and genes associated with biocontrol mechanisms of soil-borne pathogens: a review. Submitted for publication in Fungal Biology Reviews

Chapelle E., Mendes R., Bakker P.A.H.M., Raaijmakers J.M. 2014. In prep. Fungal invasion of the rhizosphere microbiome.

Siegel et al. Comparative metagenomic of fungal communities of soils suppressive to Fusarium wilt and Rhizoctonia solani damping off. In prep.

Geisen, S., Hünninghaus, M., Dumack, K., Koller, R., Urich, T., Bonkowski, M. In prep. Protists as mycophages:  a neglected, but important link in soil food webs.

Geisen, S., Rosengarten, J., Koller, R., Mulder, C., Urich, T., Bonkowski, M. In prep. Dealing with large size prey like piranhas: multitasking soil amoebae attacking nematodes.

Albizua, A., Williams, A., Hedlund, K., Pascual, U. Submitted. Crop rotation promotes win-win effects among ecosystem services. Applied Soil Ecology.

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Revised 07.01.2015