Peat-based gnotobiotic plant growth systems for Arabidopsis microbiome research

Kremer, James M.; Sohrabi, Reza; Paasch, Bradley C.; Rhodes, David; Thireault, Caitlin A.; Schulze‐Lefert, Paul; Tiedje, James M.; He, Sheng Yang

doi:10.1038/s41596-021-00504-6

Cited by 34 publications

(39 citation statements)

References 31 publications

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“…We hypothesized that specific, host immune sectors might be necessary for beneficial, growth-promoting activities of microbial root commensals. In the gnotobiotic FlowPot system ( 39 , 41 ), we recolonized germ-free A. thaliana Columbia-0 (Col-0, referred to as wild type [WT]) as well as a wide range of immunocompromised mutants with a synthetic multikingdom microbial community representative of naturally occurring root microbiomes (183 bacteria [B], 25 fungi [F], and 6 oomycetes [O]; BFO synthetic microbial community [SynCom], SI Appendix , Fig. S1 and Dataset S1 ) ( 3 ).…”

Section: Resultsmentioning

confidence: 99%

“…FlowPots were prepared as described before ( 39 , 41 ) with six FlowPots per microbox (SacO2, TD3000 + TPD3000, 3 L volume). Each FlowPot was repopulated with 200 µL bacterial, 200 µL fungal, and 80 µL oomycete pools, and each sterile FlowPot was mock inoculated with 480 µL 10 mM MgCl 2 (to account for the solution used to resuspend microbial cultures) and placed in light cabinets (Versatile Environmental Test Chamber MLR-352, Panasonic) with 10 h light (luminous flux per unit area inside the growth chamber average 9627.929, inside Microboxes average 6992.714).…”

Section: Methodsmentioning

confidence: 99%

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Tryptophan metabolism and bacterial commensals prevent fungal dysbiosis in Arabidopsis roots

Wolinska

Vannier

Thiergart

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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In nature, roots of healthy plants are colonized by multikingdom microbial communities that include bacteria, fungi, and oomycetes. A key question is how plants control the assembly of these diverse microbes in roots to maintain host–microbe homeostasis and health. Using microbiota reconstitution experiments with a set of immunocompromised Arabidopsis thaliana mutants and a multikingdom synthetic microbial community (SynCom) representative of the natural A. thaliana root microbiota, we observed that microbiota-mediated plant growth promotion was abolished in most of the tested immunocompromised mutants. Notably, more than 40% of between-genotype variation in these microbiota-induced growth differences was explained by fungal but not bacterial or oomycete load in roots. Extensive fungal overgrowth in roots and altered plant growth was evident at both vegetative and reproductive stages for a mutant impaired in the production of tryptophan-derived, specialized metabolites (cyp79b2/b3). Microbiota manipulation experiments with single- and multikingdom microbial SynComs further demonstrated that 1) the presence of fungi in the multikingdom SynCom was the direct cause of the dysbiotic phenotype in the cyp79b2/b3 mutant and 2) bacterial commensals and host tryptophan metabolism are both necessary to control fungal load, thereby promoting A. thaliana growth and survival. Our results indicate that protective activities of bacterial root commensals are as critical as the host tryptophan metabolic pathway in preventing fungal dysbiosis in the A. thaliana root endosphere.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Tryptophan metabolism and bacterial commensals prevent fungal dysbiosis in Arabidopsis roots

Wolinska

Vannier

Thiergart

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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“…In recent years, a reductionist approach to the synthetic community (SynCom) has been developed to study the specific mechanisms that drive community assembly and the interactions among different members in a gnotobiotic system [42] , [43] . For instance, the consistent differences between the maize phenotypes of inbred lines and hybrids and the composition of rhizosphere bacterial and fungal communities [44] have been further confirmed by inoculation with a simple community of seven bacterial strains [45] .This reductionist approach would allow global research to replicate experiments easily through two standardized pipelines: high-throughput bacterial cultivation and identification [46] , [47] and the establishment of plant growth systems [48] .…”

Section: Plant-beneficial Functions Of the Rhizosphere Microbiomementioning

confidence: 99%

Rhizosphere microbiome: Functional compensatory assembly for plant fitness

Xun

Shao

Shen

et al. 2021

Computational and Structural Biotechnology Journal

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Environmental pressure to reduce our reliance on agrochemicals and the necessity to increase crop production in a sustainable way have made the rhizosphere microbiome an untapped resource for combating challenges to agricultural sustainability. In recent years, substantial efforts to characterize the structural and functional diversity of rhizosphere microbiomes of the model plant Arabidopsis thaliana and various crops have demonstrated their importance for plant fitness. However, the plant benefiting mechanisms of the rhizosphere microbiome as a whole community rather than as an individual rhizobacterium have only been revealed in recent years. The underlying principle dominating the assembly of the rhizosphere microbiome remains to be elucidated, and we are still struggling to harness the rhizosphere microbiome for agricultural sustainability. In this review, we summarize the recent progress of the driving factors shaping the rhizosphere microbiome and provide community-level mechanistic insights into the benefits that the rhizosphere microbiome has for plant fitness. We then propose the functional compensatory principle underlying rhizosphere microbiome assembly. Finally, we suggest future research efforts to explore the rhizosphere microbiome for agricultural sustainability.

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“…Associations between Arabidopsis and Pseudomonas species can serve as model systems to study plant-microbe interactions in the rhizosphere ( 9 – 11 ). Pseudomonas fluorescens and related species are widely plant-associated and are ubiquitously present in the rhizosphere microbiome.…”

Section: Introductionmentioning

confidence: 99%