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

Kyle HartmanKlaus Schlaeppi


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


May 26, 1999·Proceedings of the National Academy of Sciences of the United States of America·K G Cassman
May 26, 1999·Proceedings of the National Academy of Sciences of the United States of America·D Tilman
Jun 8, 2001·Microbial Ecology·M.K. Chelius, E.W. Triplett
Feb 6, 2002·Journal of Environmental Management·C StoateP Eden
Jun 1, 2002·Science·Paul MäderUrs Niggli
Mar 10, 2004·Applied and Environmental Microbiology·Dave SeghersSteven D Siciliano
Feb 9, 2005·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Aaron ClausetCristopher Moore
Oct 17, 2006·Applied and Environmental Microbiology·Martin Hartmann, Franco Widmer
Aug 28, 2007·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Peter R HobbsRaj Gupta
Dec 1, 2007·Ecology Letters·Marcel G A van der HeijdenNico M van Straalen
Jan 30, 2010·Science·H Charles J GodfrayCamilla Toulmin
Apr 13, 2010·Nature Methods·J Gregory CaporasoRob Knight
Apr 23, 2010·The New Phytologist·Kessy AbarenkovUrmas Kõljalg
Nov 1, 2004·Molecular Plant Pathology·Rubella S Goswami, H Corby Kistler
Jul 25, 1997·Science·P A MatsonM J Swift
Feb 1, 2011·Bioinformatics·Robert Schmieder, Robert Edwards
Mar 8, 2011·Applied and Environmental Microbiology·Orin C ShanksMitchell L Sogin
Jun 28, 2011·Bioinformatics·Robert C EdgarRob Knight
Sep 9, 2011·The ISME Journal·Albert BarberánNoah Fierer
Sep 10, 2011·Bioinformatics·Tanja Magoč, Steven L Salzberg
May 9, 2012·Trends in Plant Science·Roeland L BerendsenPeter A H M Bakker
Jul 17, 2012·Nature Reviews. Microbiology·Karoline Faust, Jeroen Raes
Aug 4, 2012·Nature·Derek S LundbergJeffery L Dangl
Nov 17, 2012·Trends in Ecology & Evolution·Riccardo BommarcoSimon G Potts
Nov 30, 2012·Nucleic Acids Research·Christian QuastFrank Oliver Glöckner
Dec 26, 2012·Frontiers in Microbiology·Ashley ShadeJo Handelsman
Feb 5, 2013·Annual Review of Plant Biology·Davide BulgarelliPaul Schulze-Lefert
Apr 12, 2013·Proceedings of the National Academy of Sciences of the United States of America·Jason A PeifferRuth E Ley
Aug 27, 2013·Nature Biotechnology·Morgan G I LangilleCurtis Huttenhower
Nov 8, 2013·The ISME Journal·Jacqueline M ChaparroJorge M Vivanco
Jun 7, 2014·Frontiers in Microbiology·David Berry, Stefanie Widder
Oct 29, 2014·The ISME Journal·Martin HartmannFranco Widmer
Dec 17, 2014·Molecular Plant-microbe Interactions : MPMI·Klaus Schlaeppi, Davide Bulgarelli

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Methods Mentioned

amplicon sequencing

Software Mentioned

R package indicspecies
R package TukeyC

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