In recent years, our understanding of human, animal and plant microbiomes in a range of diverse environments has grown dramatically. However, one of the major challenges for generalized understanding of microbiomes in these complex ecosystems is extreme variation in microbiomes and environmental conditions. In many fields, simplified model systems have been developed and adopted by many researchers to accelerate the study various aspects of biology. In contrast, there is no agreed upon model system for studying plant microbiomes, and thus, nearly every researcher in the field is studying a different host plant with a different set of microbes in a different soil system. This heterogeneity of study systems and an inability to replicate experiments in different laboratories limits determination of causal mechanisms and the ability for scientists to build on each other’s work.
We are developing methods for ecosystem fabrication (EcoFAB) with the aim of constructing model soil ecosystems to allow for reproducible laboratory plant microbiomes that can be experimentally manipulated and disseminated between labs. Our approaches are based on recent workshop findings from a diverse cross-section of scientists (www.eco-fab.org). Broad scientific community acceptance of a few of these model ecosystems would no doubt exponentially increase our understanding of microbial communities as a whole by focusing diverse expertise and capabilities on the same systems.
Results/Conclusions
Each EcoFAB system is contained within a sterile plant-sized container with independent lighting. 3D printing is used to create root chambers (1.5-5 mL) attached to microscope slides, enabling the use of hydroponics, soil, or sand as substrate, as well as high-resolution rhizosphere imaging. The integrated fluidics system facilitates selective sampling and introduction of microbes, metabolites, etc. We have shown that these systems are suitable for growth of diverse plants, including Brachypodium distachyon, Arabidopsis thaliana, and bioenergy crop switchgrass for >1mo. Chemiluminescent imaging was used to examine localization and movement of labeled Pseudomonas fluorescens within the rhizosphere. Metabolomic analysis of EcoFAB culture was used for determination of the effects of microbiome composition on exudate plant exudate composition, and mass spectrometry imaging-based localization of root metabolites. Efforts are underway using individual bacterial mutants to investigate the biochemical ecology of specific exuded metabolites—a reductionistic approach typically not possible in natural ecosystems that enables determination of causal mechanisms of plant-microbe interactions. Future efforts are focused on extending EcoFABs to better reflect environmental processes e.g. to study soil nutrient cycling and plant growth promotion for low-input agriculture.