Impact of inoculation practices on microbiota assembly and community stability in a fabricated ecosystem
Impact of inoculation practices on microbiota assembly and community stability in a fabricated ecosystem
ABSTRACT Studying plant-microbe-soil interactions is challenging due to their high complexity and variability in natural ecosystems. While fabricated ecosystems provide opportunities to recapitulate aspects of these systems in reduced complexity and controlled environments, inoculation can be a significant source of variation. To tackle this, we evaluated how different bacteria inoculation practices and plant harvesting time points affect the reproducibility of a microbial synthetic community (SynCom) in association with the model grass Brachypodium distachyon. We tested three microbial inoculation practices: seed inoculation, transplant inoculation, and seedling inoculation; and two harvesting points: early (14-day-old plants) and late (21 days post-inoculation). We grew our plants and bacterial strains in sterile devices (EcoFABs) and characterized the microbial community from root, rhizosphere, and sand using 16S ribosomal RNA gene sequencing. The results showed that inoculation practices significantly affected the rhizosphere microbial community only when harvesting at an early time point but not at the late stage. As the SynCom showed a persistent association with B. distachyon at 21 days post-inoculation regardless of inoculation practices, we assessed the reproducibility of each inoculation method and found that transplant inoculation showed the highest reproducibility. Moreover, plant biomass was not adversely affected by transplant inoculation treatment. We concluded that bacteria inoculation while transplanting coupled with a later harvesting time point gives the most reproducible microbial community in the EcoFAB-B. distachyon-SynCom fabricated ecosystem and recommend this method as a standardized protocol for use with fabricated ecosystem experimental systems.
Glass N. Louise、Mortimer Jenny C.、Kuehl Jennifer V.、Lin Hsiao-Han、Owens Trenton K.、Andeer Peter F.、Torres Marta、Deutschbauer Adam M.、Jabusch Lauren K.、Carlson Hans K.、Zhalnina Kateryna、Adams Catharine A.、Northen Trent R.
Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory||Department of Plant & Microbial Biology, University of CaliforniaEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory||School of Agriculture , Food, and Wine, University of AdelaideEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National LaboratoryEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National LaboratoryEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National LaboratoryEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National LaboratoryEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National LaboratoryEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory||Department of Plant & Microbial Biology, University of CaliforniaEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National LaboratoryEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National LaboratoryEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National LaboratoryEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory||Department of Plant & Microbial Biology, University of CaliforniaEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory
环境生物学微生物学生物科学现状、生物科学发展
BrachypodiumEcoFABmicrobiomesynthetic communitySynCom
Glass N. Louise,Mortimer Jenny C.,Kuehl Jennifer V.,Lin Hsiao-Han,Owens Trenton K.,Andeer Peter F.,Torres Marta,Deutschbauer Adam M.,Jabusch Lauren K.,Carlson Hans K.,Zhalnina Kateryna,Adams Catharine A.,Northen Trent R..Impact of inoculation practices on microbiota assembly and community stability in a fabricated ecosystem[EB/OL].(2025-03-28)[2025-07-16].https://www.biorxiv.org/content/10.1101/2023.06.13.544848.点此复制
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