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Abstract
Healthy soil microbiomes are crucial for achieving high productivity in combination with crop quality, but our understanding of microbial diversity is still limited. In a large-scale study including 116 composite samples from vineyards, orchards and other crops from all over Styria (south-east Austria), agricultural management as well as distinct soil parameters were identified as drivers of the indigenous microbial communities in agricultural soils. The analysis of the soil microbiota based on microbial profiling of prokaryotic 16S rRNA gene fragments and fungal ITS regions revealed high bacterial and fungal diversity within Styrian agricultural soils; 206,596 prokaryotic and 53,710 fungal OTUs. Vineyards revealed a significantly higher diversity and distinct composition of soil fungi over orchards and other agricultural soils, whereas the prokaryotic diversity was unaffected. Soil pH was identified as one of the most important edaphic modulators of microbial community structure in both, vineyard and orchard soils. In general, the acid-base balance, disorders in the soil sorption complex, content and quality of organic substance as well as individual nutrients were identified as important drivers of the microbial community structure of Styrian vineyard and orchard soils. However, responses to distinct parameters differed in orchards and vineyards, and prokaryotic and fungal community responded differently to the same abiotic factor. In comparison to orchards, the microbiome of vineyard soils maintained a higher stability when herbicides were applied. Orchard soils exhibited drastic shifts within community composition; herbicides seem to have a substantial impact on the bacterial order Chthoniobacterales as well as potential plant growth promoters and antagonists of phytopathogens (Flavobacterium, Monographella), with a decreased abundance in herbicide-treated soils. Moreover, soils of herbicide-treated orchards revealed a significantly higher presence of potential apple pathogenic fungi (Nectria, Thelonectria). These findings provide the basis to adapt soil management practices in the future in order to maintain a healthy microbiome in agricultural soils.
Highlights
Soil is a non-renewable natural bio-resource involved in important ecosystem functions and biogeochemical cycles on earth
116 composite soil samples consisting of five sub-samples each were collected in a horizon of 10–30 cm depth, which are assigned to three general sample groups: vineyards (73 samples), orchards (32; 28 apple orchards, 3 pear orchards, and 1 quince orchard), and other agricultural soils (11) of diverse usage
Agricultural management as well as distinct soil parameters were identified as drivers of the indigenous microbial communities of Styrian soils, whereby the prokaryotic and fungal community responded differently, and responses differed in orchard and vineyard soils
Summary
Soil is a non-renewable natural bio-resource involved in important ecosystem functions and biogeochemical cycles on earth. One of the most important characteristics of a soil ecosystem is soil health, which is the result of biotic as well as abiotic processes and connected to various interactions within the system These interactions have strong impact on the microbial activity, supporting many central processes in soil (Frac et al, 2018). It has been suggested that soils are the ecosystems with the most diverse composition of microbiota on earth as a consequence of so many different niches being present at small spatial scales (Jansson, 2011; Prosser, 2015). This microbial biodiversity is largely understudied, and regional or global overviews are rare. The first global atlas of soil bacterial taxa revealed a region-specific composition (DelgadoBaquerizo et al, 2018), but regional studies are barely available, e.g., for Austria
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