Different molecular approaches reveal how arbuscular mycorrhizal fungal communities thrive in a winter-wheat rotation management system.

In the frame of EU project PURE (Pesticide Use-and-risk Reduction in European farming systems with Integrated Pest Management) our research group is involved with EU researchers in the topic "Pathogen suppression by soil microbial communities" (Task 10.1), which objective is the exploration of soil microbial communities' response to existing management actions, and considers their role in suppressing pathogens. The first aim of the research task is the investigation of soil microbiome associated with a rotation based management system typical of arable farming. In particular, a wheat based rotation provides the experimental platform where soil and winter wheat, grown under different management systems (including crop rotation, tillage and fertilization), are sampled twice in the winter wheat cropping seasons. In order to study and design new strategies to promote microbial mediated soil suppressiveness toward soil-borne pathogens and measure changes is soil biota due to different management strategies, some important groups of soil organisms have been selected (fungi, Arbuscular Mycorrhizal Fungi (AMF), bacteria, Lysobacter spp., nematodes). Among the microbial targets that could provide complementary measures of soil quality as well as indication on general and specific diseases suppressive capacity of soil, our research group analyzes Arbuscular Mycorrhizal Fungi (AMF), obligatory mutualistic symbionts that supply plants with inorganic nutrients and protect them against diverse abiotic and biotic stresses. The complexity of AMF community was estimated by morphological and molecular analysis in five different experimental sub-plots characterized by different crop rotations and managements (ploughed, or no-tilled). Since recent development of molecular tools and Next-Generation Sequencing (NGS) techniques have revolutionized the study of microbial ecology, providing insights into complex systems, we applied either Sanger sequencing or tag-encoded 454 pyrosequencing to investigate AM fungal communities (Davison et al., 2012; Lumini et al. 2010). Raw sequencing data plus metadata describing the samples were processed using the Quantitative Insights Into Microbial Ecology (QIIME) software pipeline (Caporaso et al. 2010). In brief, sequences below quality score of 30 and 200 bp in length were trimmed, and then assigned to different samples based on unique 5-bp barcodes. Sequences were clustered into OTUs using a 97% identity threshold. Taxonomy was assigned to representative sequence for each OTU. AM Fungal OTUs were identified using a customized reference repository, derived from the web-based MaarjAM database (Opik et al. 2010), and specially developed to overcome the limitations and biases of currently used fungal AMF databases. These approaches allowed us to describe wheat based rotation field AMF biodiversity and to highlight the differences between AMF communities associated to the different management systems. References Caporaso, J.G.; Kuczynski, J.; Stombaugh, J.; Bittinger, K.; Bushman, F.D.; Costello, E.K.; Fierer, N.; Gonzalez Pena, A.; Goodrich, J.K.; Gordon, J.I.; et al. (2010). Nature Methods 7, 335-336. Davison J, Öpik M, Zobel M, Vasar M, Metsis M, Moora M. (2012). PLoS One. 7(8):e41938. doi: 10.1371/journal.pone.00419382012. Lumini, E., Orgiazzi, A., Borriello, R., Bonfante, P., Bianciotto, V. (2010). Environmental Microbiology 12(8) 2165-2179. Öpik, M., Vanatoa, A., Vanatoa, E., Moora, M., Davison, J., Kalwij, J.M., Reier, Ü., Zobel, M. (2010). New Phytologist 188: 223-241.