title: Live imaging of root-bacteria interactions in a microfluidics setup.
abstract: Plant roots play a dominant role in shaping the rhizosphere, the environment in which interaction with diverse microorganisms occurs. Tracking the dynamics of root-microbe interactions at high spatial resolution is currently limited because of methodological intricacy. Here, we describe a microfluidics-based approach enabling direct imaging of root-bacteria interactions in real time. The microfluidic device, which we termed tracking root interactions system (TRIS), consists of nine independent chambers that can be monitored in parallel. The principal assay reported here monitors behavior of fluorescently labeledBacillus subtilisas it colonizes the root ofArabidopsis thalianawithin the TRIS device. Our results show a distinct chemotactic behavior ofB. subtilistoward a particular root segment, which we identify as the root elongation zone, followed by rapid colonization of that same segment over the first 6 h of root-bacteria interaction. Using dual inoculation experiments, we further show active exclusion ofEscherichia colicells from the root surface afterB. subtiliscolonization, suggesting a possible protection mechanism against root pathogens. Furthermore, we assembled a double-channel TRIS device that allows simultaneous tracking of two root systems in one chamber and performed real-time monitoring of bacterial preference between WT and mutant root genotypes. Thus, the TRIS microfluidics device provides unique insights into the microscale microbial ecology of the complex root microenvironment and is, therefore, likely to enhance the current rate of discoveries in this momentous field of research.
authors.affiliation: Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
authors.forename: Hassan
authors.initials: H
authors.lastname: Massalha
authors.affiliation: Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
authors.forename: Elisa
authors.initials: E
authors.lastname: Korenblum
authors.affiliation: Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
authors.forename: Sergey
authors.initials: S
authors.lastname: Malitsky
authors.affiliation: Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel; orr@agri.gov.il asaph.aharoni@weizmann.ac.il.|Department of Food Quality and Safety, Institute for Postharvest and Food Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion 7528809, Israel.
authors.forename: Orr H
authors.initials: OH
authors.lastname: Shapiro
authors.affiliation: Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel; orr@agri.gov.il asaph.aharoni@weizmann.ac.il.
authors.forename: Asaph
authors.initials: A
authors.lastname: Aharoni
mesh_terms: D017360:Arabidopsis / Q000382:microbiology*; D001412:Bacillus subtilis / Q000502:physiology*; D044085:Microfluidics / Q000295:instrumentation* / Q000379:methods; D018613:Microscopy, Confocal / Q000295:instrumentation* / Q000379:methods; D018517:Plant Roots / Q000382:microbiology* / Q000502:physiology; D013559:Symbiosis
keywords: Bacillus subtilis; TRIS; live-imaging microscopy; microbial community dynamics; root–bacteria interaction