Microbiomes are understood to be important drivers of plant and soil health. However, the large variability inherent to these environments makes them particularly challenging to study in a reproducible manner, particularly under defined, yet environmentally relevant conditions. To address this need, we recently developed and published methods for making and using fabricated, single plant-scale ecosystems, or EcoFABs, designed for the research of plant and soil microbiomes (www.eco-fab.org; https://doi.org/10.3791/57170).
To assess the reproducibility plant and metabolite measurements within EcoFABs, a ring-trial was conducted between four laboratories growing the model plant Brachypodium distachyon within EcoFABs. To expand upon this research and to improve the capabilities of EcoFABs as well as examine methods for disseminating them for use by the larger scientific community. This includes the generation of stable microbiomes for use within EcoFABs and the development of an automated system for the incubation, sampling and imaging of EcoFABs at Lawrence Berkeley National Laboratory (LBNL).
Results/Conclusions
The ring-trial revealed that plant effects were statistically different between treatments but researchers both with respect to plant physiology and metabolic traits. Interestingly, the addition of a cell-free soil extract, affected root morphology, causing a significant increase in root hair growth along with indications that the plants took up a significant portion (~50%) of the compounds in the extract (https://doi.org/10.1111/nph.15662).
Our initial microbiome is composed of over 20 bacteria isolated from the rhizosphere of switchgrass. These bacteria, being sequenced and metabolically profiled, were selected from a set of > 300 isolates for a model microbiome based on several criteria, including: isolation source and media, relative abundance in field surveys, enrichment in the rhizosphere over bulk soil, in-situ activity and reproducible growth in communities.
The automated system being built at LBNL will engage with a new generation of EcoFABs and enable large ecological studies by allowing users to design experiments with a selectable microbial community, growth conditions and media/substrate concentration.