Specialized Plant Growth Chamber Designs to Study Complex Rhizosphere Interactions

Abstract

The rhizosphere is a dynamic ecosystem shaped by complex interactions between plant roots, soil, microbial communities and other micro- and macro-fauna. Although studied for decades, critical gaps exist in the study of plant roots, the rhizosphere microbiome and the soil system surrounding roots, partly due to the challenges associated with measuring and parsing these spatiotemporal interactions in complex heterogeneous systems such as soil. To overcome the challenges associated with in situ study of rhizosphere interactions, specialized plant growth chamber systems have been developed that mimic the natural growth environment. This review discusses the currently available lab-based systems ranging from widely known rhizotrons to other emerging devices designed to allow continuous monitoring and non-destructive sampling of the rhizosphere ecosystems in real-time throughout the developmental stages of a plant. We categorize them based on the major rhizosphere processes it addresses and identify their unique challenges as well as advantages. We find that while some design elements are shared among different systems (e.g., size exclusion membranes), most of the systems are bespoke and speaks to the intricacies and specialization involved in unraveling the details of rhizosphere processes. We also discuss what we describe as the next generation of growth chamber employing the latest technology as well as the current barriers they face. We conclude with a perspective on the current knowledge gaps in the rhizosphere which can be filled by innovative chamber designs.

Lessons Learned from the Studies of Roots Shaded from Direct Root Illumination

“…This demonstrates the importance of performing basic research under more natural conditions to allow a smoother transition of findings into applied science. Furthermore, Rhizotrons are commonly used to examine the interaction of roots with the rhizosphere, which is very sensitive to light, and most studies have been conducted on roots grown in soil [ 100 , 102 ]. Therefore, recent attempts to study biotic interactions with the root, which can be beneficial or threatening, include the use of transparent artificial soil for DGR, which in turn will allow a more detailed study of root growth adaptation at the cellular level under more natural conditions [ 103 , 104 ].…”

Maize root-associated microbes likely under adaptive selection by the host to enhance phenotypic performance

“…Paired-end 16S sequencing reads from a total of 3,313 samples were processed in R 3.5.2 using the workflow described by Callahan (Callahan et al, 2016a), which employs the package dada2 1.10.1 (Callahan et al, 2016b). Taxonomy was assigned to amplicon sequence variants (ASVs) using the SILVA database version 138 (Yilmaz et al, 2014) as the reference. Raw ASV reads were subjected to a series of filters to produce a final ASV table with biologically relevant and reproducible 16S sequences (Supplementary Dataset 1).…”

“…Microbial actors in the rhizosphere have been shown to promote plant growth (Saleem et al, 2019), improve nutrient use efficiency (Gomes et al, 2018;Zhu et al, 2016), and reduce abiotic stress response (Hussain et al, 2018). The promise of high throughput screens for plant growth promoting activity in isolated microbial strains or synthetic communities (Singer et al, 2021;Yee et al, 2021) is the potential discovery of microbial agents that can be used as seed or soil additives to improve crop performance under field conditions. Promising results have been observed in controlled environments (Van Gerrewey et al, 2020;Xi et al, 2020;Yu et al, 2021), but it remains a challenge to achieve similar outcomes in crops under agriculturally relevant field conditions (Eida et al, 2017;Sessitsch et al, 2019).…”

Translating CO$$_2$$ variability in a plant growth system into plant dynamics

“…Plant growth systems such as greenhouses and growth chambers contribute to increasing crop productivity and experimental capacities 7 , 8 . Contrary to the open field, protected cropping conditions such as greenhouses, indoor farms, and growth chambers may limit the impact of mass flow and turbulence on the air exchange between the air around a plant and the atmosphere.…”