Hartmann Martin, Frey Beat, Mayer Jochen, Mäder Paul, Widmer Franco
1] Molecular Ecology, Institute for Sustainability Sciences, Agroscope, Zurich, Switzerland [2] Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.
Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.
ISME J. 2015 May;9(5):1177-94. doi: 10.1038/ismej.2014.210. Epub 2014 Oct 31.
Low-input agricultural systems aim at reducing the use of synthetic fertilizers and pesticides in order to improve sustainable production and ecosystem health. Despite the integral role of the soil microbiome in agricultural production, we still have a limited understanding of the complex response of microbial diversity to organic and conventional farming. Here we report on the structural response of the soil microbiome to more than two decades of different agricultural management in a long-term field experiment using a high-throughput pyrosequencing approach of bacterial and fungal ribosomal markers. Organic farming increased richness, decreased evenness, reduced dispersion and shifted the structure of the soil microbiota when compared with conventionally managed soils under exclusively mineral fertilization. This effect was largely attributed to the use and quality of organic fertilizers, as differences became smaller when conventionally managed soils under an integrated fertilization scheme were examined. The impact of the plant protection regime, characterized by moderate and targeted application of pesticides, was of subordinate importance. Systems not receiving manure harboured a dispersed and functionally versatile community characterized by presumably oligotrophic organisms adapted to nutrient-limited environments. Systems receiving organic fertilizer were characterized by specific microbial guilds known to be involved in degradation of complex organic compounds such as manure and compost. The throughput and resolution of the sequencing approach permitted to detect specific structural shifts at the level of individual microbial taxa that harbours a novel potential for managing the soil environment by means of promoting beneficial and suppressing detrimental organisms.
低投入农业系统旨在减少合成肥料和农药的使用，以提高可持续生产能力和生态系统健康水平。尽管土壤微生物群落在农业生产中起着不可或缺的作用，但我们对微生物多样性对有机农业和传统农业的复杂反应仍了解有限。在此，我们通过对细菌和真菌核糖体标记物采用高通量焦磷酸测序方法，在一项长期田间试验中报告了土壤微生物群对二十多年不同农业管理方式的结构反应。与仅施用矿物肥料的传统管理土壤相比，有机农业增加了土壤微生物的丰富度，降低了均匀度，减少了离散度，并改变了土壤微生物群的结构。这种影响很大程度上归因于有机肥料的使用和质量，因为在综合施肥方案下检查传统管理土壤时，差异变得较小。以适度和有针对性地施用农药为特征的植物保护措施的影响相对较小。不施用粪肥的系统中存在一个分散且功能多样的群落，其特征是可能有适应养分有限环境的贫营养生物。接受有机肥料的系统的特征是存在特定的微生物类群，这些类群已知参与复杂有机化合物（如粪肥和堆肥）的降解。测序方法的通量和分辨率能够检测到单个微生物分类单元水平上的特定结构变化，这为通过促进有益生物和抑制有害生物来管理土壤环境提供了新的潜力。
