Distinct soil microbial diversity under long-term organic and conventional farming

Abstract

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.

Microbial and biochemical basis of a Fusarium wilt-suppressive soil

“…These limitations, and the many still-unresolved questions about physical and biochemical interactions in the rhizosphere, await new tools to unravel ecological basis of the below-ground relationships that govern soil suppressiveness. Hartmann et al (2015) also have recently commented on the difficulty of inferring the ecological role of many microbial community members simply from phylogenetically based surveys.…”

Contribution of soil respiration to the global carbon equation

“…Major enzymes in soils include amylase, ␤-glucosidase, cellulase, chitinase, dehydrogenase, phosphatase, protease, and urease and are produced by various microbes (Dick and Tabatabai, 1984;Gupta et al, 1993;Makoi and Ndakidemi, 2008). Although new DNA sequencing technologies have made it possible to investigate microbial community composition (Torsvik and Øvreås, 2002;Cong et al, 2015;Hartmann et al, 2015;Pitombo et al, 2015), we have limited knowledge of the details of soil enzymes, such as their amounts, types, distribution, and efficiency, and little is known of individual microbial species and the corresponding enzyme(s) produced. The importance of soil enzymes to ecosystem functions, including soil respiration, has been reviewed by Makoi and Ndakidemi (2008).…”

Microbiome engineering: Current applications and its future

“…chemical fertilizers and herbicides. For example, compared to soil fertilized chemically, long-term use of organic fertilizers increases richness, decreases evenness, reduces dispersion and shifts the structure of the soil microbiome [41]. Another way to modify soil microbiome is to change land utilization.…”

“…Agricultural management Soil Organic farming, changing land usage, logging, tillage, cropping [7,[41][42][43][44][45][46] Improve soil fertility • Alter structure and function of soil microbiome;…”