Inferences from inventories of microbes in ecological vineyard settings


  • Hans-Josef Schroers Agricultural Institute of Slovenia Hacquetova ulica 17 1000 Ljubljana Slovenia
  • Maurizio Castaldini Council for Agricultural Research and Economics Research Center for Agriculture and Environment Via di Lanciola 12/A 50125 Cascine del Riccio (FI) Italy
  • Anna Mårtensson Swedish University of Agricultural Sciences, Uppsala, Sweden



microbial community structure, DGGE, fungi, bacteria, Actinobacteria, Streptomyces


The effect of degraded soil conditions on microbial communities associating the rhizosphere and roots of grapevines was investigated within the frame of project CORE Organic Plus ReSolVe. Several relationships based on Dice cluster analyses of DGGE gel profiles suggest that fungal and bacterial communities from degraded and non-degraded areas differ. Results also suggest that composted organic amendments had an effect on community structures. However, the comparison of diversity indexes did not show differences between degraded and non-degraded plots. They suggested rich and even diversity of bacteria and fungi in any of the tested samples. Culture dependent analysis emphasized that a high diversity of Streptomyces spp. associates grapevine roots in degraded and non-degraded areas. Streptomyces species, best known for their potential to produce antibiotics, are increasingly depicted as beneficial plant associated bacteria.


AISLABIE J., DESLIPPE J.R. (2013). Soil microbes and their contribution to soil services. In DYMOND J.R., ed. Ecosystem services in New Zealand – conditions and trends. Manaaki Whenua Press, Lincoln, New Zealand, 143-161.

ÁLVAREZ-PÉREZ J.M., GONZÁLEZ-GARCÍA S., COBOS R., OLEGO M.Á., IBAÑEZ A., DÍEZ-GALÁN A., GARZÓN-JIMENO E., COQUE J.J.R. (2017). Use of endophytic and rhizosphere actinobacteria from grapevine plants to reduce nursery fungal graft infections that lead to young grapevine decline. Applied and Environmental Microbiology, 83(24), e01564-17.

ANDERSON I.C., CAMPBELL C.D., PROSSER J.I. (2003). Diversity of fungi in organic soils under a moorland – Scots pine (Pinus sylvestris L.) gradient. Environmental Microbiology 5(11), 1121-1132.

ARAÚJO A.S., BORGES C.D., TSAI S.M., CESARZ S., EISENHAUER N. (2014). Soil bacterial diversity in degraded and restored lands of Northeast Brazil. Antonie Van Leeuwenhoek, 106(5), 891-899.

BARKA E.A., VATSA P., SANCHEZ L., GAVEAU-VAILLANT N., JACQUARD C., KLENK H.-P., CLÉMENT C., OUHDOUCH Y., VAN WEZEL G.P. (2016). Taxonomy, physiology, and natural products of Actinobacteria. Microbiology and Molecular Biology Reviews, 80, 1-43.

BENSON D.A., KARSCH-MIZRACHI I., LIPMAN D.J., OSTELL J., SAYERS E.W. (2010). Genbank. Nucleic Acids Research 38, D46–D51.

CASTALDINI M., TURRINI A., SBRANA C., BENEDETTI A., MARCHIONNI M., MOCALI S., FABIANI A., LANDI S., SANTOMASSIMO F., PIETRANGELI B., NUTI M.P., MICLAUS N., GIOVANNETTI M. (2005). Impact of Bt corn on rhizospheric and soil eubacterial communities and on beneficial mycorrhizal symbiosis in experimental microcosms. Applied Environmental Microbiology, 71(11), 6719-6729.

COLLADO J., PLATAS G., PAULUS B., BILLS G.F. (2007). High-throughput culturing of fungi from plant litter by a dilution-to-extinction technique. FEMS Microbiology Ecology, 60(3), 521-533.

COSTANTINI E.A.C, PRIORI S., GIFFARD B., FULCHIN E., TARDAGUILA J., SCHROERS H.J., PELENGIC R., AKCA E., TANGOLAR S., VALBOA G. (this issue). Causes of soil malfunctioning in degraded areas of European and Turkish vineyards. EQA-International Journal of Environmental Quality.

D’AVINO L., PRIORI S., SCHROERS H.J., TANGOLAR S., TARDAGUILA J., GIFFARD B., FANTAPPIÈ M., COSTANTINI E.A.C. (this issue). Restoring soil functionality in degraded areas within vineyards by organic treatments: the experimental layout of the RESOLVE Core-organic+ project. EQA-International Journal of Environmental Quality.

GRANDY A.S., WIEDER W.R., WICKINGS K., KYKER-SNOWMAN E. (2016). Beyond microbes: Are fauna the next frontier in soil biogeochemical models? Soil Biology and Biochemistry 102, 40-44.

LANE D.J. (1991). 16S/23S rRNA sequencing. In STACKEBRANDT E., GOODFELLOW M., eds. Nucleic acid techniques in bacterial systematics. New York, NY, John Wiley and Sons, 115-175.

LOQMAN S., BOUIZGARNE B., BARKA E.A., CLÉMENT C., VON JAN M., SPRÖER C., KLENK H.P., OUHDOUCH Y. (2009). Streptomyces thinghirensis sp. nov., isolated from rhizosphere soil of Vitis vinifera. International Journal of Systematic and Evolutionary Microbiology, 59, 3063-3067.

ROESCH L.F., FULTHORPE R.R., RIVA A., CASELLA G., HADWIN A.K., KENT A.D., DAROUB S.H., CAMARGO F.A., FARMERIE W.G., TRIPLETT E.W. (2007). Pyrosequencing enumerates and contrasts soil microbial diversity. International Society for Microbial Ecology, 1(4), 283-290.

SINGH S.S., SCHLOTER M., TIWARI S.C., DKHAR M.S. (2011). Diversity of community soil DNA and bacteria in degraded and undegraded tropical forest soils of north-eastern India as measured by ERIC–PCR fingerprints and 16S rDNA-DGGE profiles. Journal of Biological and Environmental Sciences, 5(15), 183-194.

TAMURA K., STECHER G., PETERSON D., FILIPSKI A., KUMAR S. (2013). MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution, 30, 2725-2729.

TIAN Q., TANIGUCHI T., SHI W.-Y., LI G., YAMANAKA N., DUA S. (2017). Land-use types and soil chemical properties influence soil microbial communities in the semiarid Loess Plateau region in China. Scientific reports, 7, 45289.

TROUVELOT A., KOUGH J.L., GIANINAZZI-PEARSON V. (1986). Mesure du taux de mycorhization VA d’un systeme radiculaire ayant une signification fonctionnelle. In GIANINAZZI-PEARSON V., GIANINAZZI S., eds. Physiological and genetical aspects of mycorrhizae. INRA, Paris, pp 217-221.

TROUVELOT S., BONNEAU L., REDECKER D., VAN TUINEN D., ADRIAN M., WIPF D. (2016). Arbuscular mycorrhiza symbiosis in viticulture: a review. Agronomy for Sustainable Development 35, 1449-1467.

VIAENE T., LANGENDRIES S., BEIRINCKX S., MAES M., GOORMACHTIG S. (2016). Streptomyces as a plant's best friend? FEMS Microbiology Ecology, 92, fiw119.




How to Cite

Schroers, H.-J., Castaldini, M., & Mårtensson, A. (2018). Inferences from inventories of microbes in ecological vineyard settings. EQA - International Journal of Environmental Quality, 31, 47–56.