Abstract
Plants are colonised by millions of microorganisms representing thousands of species with varying effects on plant growth and health. The microbial communities found on plants are compositionally consistent and their overall positive effect on the plant is well known. However, the effects of individual microbiota members on plant hosts and vice versa, as well as the underlying mechanisms, remain largely unknown. Here, we describe “Litterbox”, a highly controlled system to investigate plant–microbe interactions. Plants were grown gnotobiotically, otherwise sterile, on zeolite-clay, a soil replacement that retains enough moisture to avoid subsequent watering. Litterbox-grown plants resemble greenhouse-grown plants more closely than agar-grown plants and exhibit lower leaf epiphyte densities (106 cfu/g), reflecting natural conditions. A polydimethylsiloxane (PDMS) sheet was used to cover the zeolite, significantly lowering the bacterial load in the zeolite and rhizosphere. This reduced the likelihood of potential systemic responses in leaves induced by microbial rhizosphere colonisation. We present results of example experiments studying the transcriptional responses of leaves to defined microbiota members and the spatial distribution of bacteria on leaves. We anticipate that this versatile and affordable plant growth system will promote microbiota research and help in elucidating plant-microbe interactions and their underlying mechanisms.
Highlights
Plants offer three different habitats to microbes: the endosphere, the rhizosphere, and the phyllosphere
Arabidopsis plants were grown in tissue-culture boxes on either agar or zeolite, to compare the suitability of the substrates for gnotobiotic plant growth. Both substrates were covered by a PDMS sheet to reduce the cross-inoculation of phyllosphere and rhizosphere bacteria (Figure 1A,B)
Four-weeks-old plants grown on zeolite were slightly smaller (Figure 1C,D), had significantly fewer leaves (Figure 1L), and weighed significantly less than plants grown on agar (Figure 1K)
Summary
Plants offer three different habitats to microbes: the endosphere, the rhizosphere, and the phyllosphere. Owing to the diversity and complexity of the microbiota, it is not surprising that the traditional view of host–microbe interactions has tended to focus on important but discrete aspects of the whole, such as plant pathogens, nitrogen-fixing rhizobacteria, and phosphate-mobilizing mycorrhizal fungi. This view has recently shifted to a holistic one considering the plant and its associated microbiota as a metaorganism or holobiont [4,5,6]. The prospect of using synthetic microbial communities to promote sustainable agriculture is leading to a growing appreciation of plant microbiota research
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