Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming

Microbiome
Kyle HartmanKlaus Schlaeppi

Abstract

Harnessing beneficial microbes presents a promising strategy to optimize plant growth and agricultural sustainability. Little is known to which extent and how specifically soil and plant microbiomes can be manipulated through different cropping practices. Here, we investigated soil and wheat root microbial communities in a cropping system experiment consisting of conventional and organic managements, both with different tillage intensities. While microbial richness was marginally affected, we found pronounced cropping effects on community composition, which were specific for the respective microbiomes. Soil bacterial communities were primarily structured by tillage, whereas soil fungal communities responded mainly to management type with additional effects by tillage. In roots, management type was also the driving factor for bacteria but not for fungi, which were generally determined by changes in tillage intensity. To quantify an "effect size" for microbiota manipulation, we found that about 10% of variation in microbial communities was explained by the tested cropping practices. Cropping sensitive microbes were taxonomically diverse, and they responded in guilds of taxa to the specific practices. These microbes also included ...Continue Reading

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Citations

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Methods Mentioned

BETA
amplicon sequencing
Assay
PCR

Software Mentioned

QIIME
R package indicspecies
Cutadapt
PRINSEQ
NT
UPARSE
FLASH
vegan
R package TukeyC
IT

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