An official website of the United States government
ABSTRACT Plant roots shape the rhizosphere community by secreting compounds that recruit diverse bacteria. Colonization of various plant roots by the motile alphaproteobacterium Azospirillum brasilens e causes increased plant growth, root volume, and crop yield. Bacterial chemotaxis in this and other motile soil bacteria is critical for competitive colonization of the root surfaces. The role of chemotaxis in root surface colonization has previously been established by endpoint analyses of bacterial colonization levels detected a few hours to days after inoculation. More recently, microfluidic devices have been used to study plant-microbe interactions, but these devices are size limited. Here, we use a novel slide-in chamber that allows real-time monitoring of plant-microbe interactions using agriculturally relevant seedlings to characterize how bacterial chemotaxis mediates plant root surface colonization during the association of A. brasilens e with Triticum aestivum (wheat) and Medicago sativa (alfalfa) seedlings. We track A. brasilense accumulation in the rhizosphere and on the root surfaces of wheat and alfalfa. A. brasilense motile cells display distinct chemotaxis behaviors in different regions of the roots, including attractant and repellent responses that ultimately drive surface colonization patterns. We also combine these observations with real-time analyses of behaviors of wild-type and mutant strains to link chemotaxis responses to distinct chemicals identified in root exudates to specific chemoreceptors that together explain the chemotactic response of motile cells in different regions of the roots. Furthermore, the bacterial second messenger c-di-GMP modulates these chemotaxis responses. Together, these findings illustrate dynamic bacterial chemotaxis responses to rhizosphere gradients that guide root surface colonization. IMPORTANCE Plant root exudates play critical roles in shaping rhizosphere microbial communities, and the ability of motile bacteria to respond to these gradients mediates competitive colonization of root surfaces. Root exudates are complex chemical mixtures that are spatially and temporally dynamic. Identifying the exact chemical(s) that mediates the recruitment of soil bacteria to specific regions of the roots is thus challenging. Here, we connect patterns of bacterial chemotaxis responses and sensing by chemoreceptors to chemicals found in root exudate gradients and identify key chemical signals that shape root surface colonization in different plants and regions of the roots.
more »
« less
Screening the maize rhizobiome for consortia that improve Azospirillum brasilense root colonization and plant growth outcomes
Plant growth-promoting bacteria (PGPB) are valuable for supporting sustainable food production and may alleviate the negative impacts of chemical fertilizers on human health and the environment. While single-strain inoculations have proven unreliable due to poor survival and colonization in the rhizosphere, application of PGPB in multispecies consortia has the potential to improve these outcomes. Here, we describe a new approach for screening and identifying bacterial consortia that improve the growth of corn relative to plants inoculated with a single strain. The method uses the microwell recovery array (MRA), a microfabricated high-throughput screening device, to rapidly explore the maize ( Zea mays L .) rhizobiome for higher-order combinations of bacteria that promote the growth and colonization of the nitrogen-fixing PGPB, Azospirillum brasilense . The device simultaneously generates thousands of random, unique combinations of bacteria that include A. brasilense and members of the maize rhizobiome, then tracks A. brasilense growth in each combination during co-culture. Bacteria that show the highest levels of A. brasilense growth promotion are then recovered from the device using a patterned light extraction technique and are identified. With this approach, the screen uncovered growth-promoting consortia consisting primarily of bacteria from the Acinetobacter - Enterobacter - Serratia genera, which were then co-inoculated with A. brasilense on axenic maize seedlings that were monitored inside a plant growth chamber. Compared to maize plants inoculated with A. brasilense alone, plants that were co-inoculated with these consortia showed accelerated growth after 15 days. Follow-up root colonization assays revealed that A. brasilense colonized at higher levels on roots from the co-inoculated seedlings. These findings demonstrate a new method for rapid bioprospecting of root and soil communities for complementary PGPB and for developing multispecies consortia with potential use as next-generation biofertilizers.
more »
« less
- PAR ID:
- 10423635
- Date Published:
- Journal Name:
- Frontiers in Sustainable Food Systems
- Volume:
- 7
- ISSN:
- 2571-581X
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
null (Ed.)Strategies to reduce crop losses due to drought are needed as climate variability affects agricultural productivity. Wheat (Triticum aestivum var. Juniper) growth in a nutrient-sufficient, solid growth matrix containing varied doses of CuO, ZnO, and SiO2 nanoparticles (NPs) was used to evaluate NP mitigation of drought stress. NP amendments were at fertilizer levels, with maxima of 30 Cu, 20 Zn, and 200 Si (mg metal/kg matrix). Seeds of this drought-tolerant cultivar were inoculated with Pseudomonas chlororaphis O6 (PcO6) to provide a protective root microbiome. An 8 day drought imposed on 14 day-old wheat seedlings decreased shoot and root mass, shoot water content, and the quantum yield of photosystem II when compared to watered plants. PcO6 root colonization was not impaired by drought or NPs. A dose-dependent increase in the Cu, Zn, and Si from the NPs was observed from analysis of the rhizosphere solution, and this process was not affected by drought. Consequently, fertilizer concentrations of the NPs did not further improve drought tolerance in wheat seedlings under the growth conditions of adequate mineral nutrition and the presence of a beneficial microbiome. These findings suggest that potential NP benefits in promoting plant drought tolerance occur only under certain environmental conditions.more » « less
-
Glass, Jennifer B (Ed.)ABSTRACT Azospirillum brasilenseis plant-growth promoting rhizobacteria that produces the phytohormone indole-3-acetic acid (IAA) to induce changes in plant root architecture. The major pathway for IAA biosynthesis inA. brasilenseconverts tryptophan into indole-3-pyruvic acid (I3P) and then, through the rate-limiting enzyme, indole-3-pyruvate decarboxylase (IpdC), into IAA. Here, we characterize the potential role for IAA biosynthesis in the physiology of these bacteria by characterizing the expression pattern of theipdCpromoter, analyzing anA. brasilense ipdCmutant using multiple physiological assays and characterizing the effect of I3P, which likely accumulates in the absence ofipdCand affects bacterial physiology. We found that theipdCmutant derivative has a reduced growth rate and an altered physiology, including reduced translation activity as well as a more depolarized membrane potential compared to the parent strain. Similar effects could be recapitulated in the parent strain by exposing these cells to increasing concentrations of I3P, as well as other indole intermediates of IAA biosynthesis. Our results also indicate a protective role for IAA against the harmful effects of indole derivatives, with exogenous IAA restoring the membrane potential of cells exposed to indole derivatives for prolonged periods. These protective effects appeared to restore cell physiology, including in the wheat rhizosphere. Together, our data suggest that the IAA biosynthesis pathway plays a major role inA. brasilensephysiology by maintaining membrane potential homeostasis and regulating translation, likely to mitigate the potential membrane-damaging effects of indoles that accumulate during growth under stressful conditions.IMPORTANCEIAA is widely synthesized in bacteria, particularly in soil and rhizosphere bacteria, where it functions as a phytohormone to modulate plant root architecture. IAA as a secondary metabolite has been shown to serve as a signaling molecule in several bacterial species, but the role of IAA biosynthesis in the physiology of the producing bacterium remains seldom explored. Results obtained here suggest that IAA serves to protectA. brasilensefrom the toxic effect of indoles, including metabolite biosynthetic precursors of IAA, on membrane potential homeostasis. Given the widespread production of IAA in soil bacteria, this protective effect of IAA may be conserved in diverse soil bacteria.more » « less
-
The root microbiome structure ensures optimal plant host health and fitness, and it is, at least in part, defined by the plant genotype. It is well documented that root-secreted amino acids promote microbial chemotaxis and growth in the rhizosphere. However, whether the plant-mediated re-uptake of amino acids contributes to maintaining optimal levels of amino acids in the root exudates, and, in turn, microbial growth and metabolism, remains to be established. Here, we show that Lysine-Histidine Transporter-1 (LHT1), an amino acid inward transporter expressed in Arabidopsis thaliana roots, limits the growth of the plant-growth-promoting bacteria Pseudomonas simiae WCS417r (Ps WCS417r). The amino acid profiling of the lht1 mutant root exudates showed increased levels of glutamine, among other amino acids. Interestingly, lht1 exudates or Gln-supplemented wild-type exudates enhance Ps WCS417r growth. However, despite promoting bacterial growth and robust root colonization, lht1 exudates and Gln-supplemented wild-type exudates inhibited plant growth in a Ps WCS417r-dependent manner. The transcriptional analysis of defense and growth marker genes revealed that plant growth inhibition was not linked to the elicitation of plant defense but likely to the impact of Ps WCS417r amino acids metabolism on auxin signaling. These data suggest that an excess of amino acids in the rhizosphere impacts Ps WCS417r metabolism, which, in turn, inhibits plant growth. Together, these results show that LHT1 regulates the amino-acid-mediated interaction between plants and Ps WCS417r and suggest a complex relationship between root-exuded amino acids, root colonization by beneficial bacteria, bacterial metabolism, and plant growth promotion.more » « less
-
null (Ed.)Understanding microbe-microbe interactions is critical to predict microbiome function and to construct communities for desired outcomes. Investigation of these interactions poses a significant challenge due to the lack of suitable experimental tools available. Here we present the microwell recovery array (MRA), a new technology platform that screens interactions across a microbiome to uncover higher-order strain combinations that inhibit or promote the function of a focal species. One experimental trial generates 10 4 microbial communities that contain the focal species and a distinct random sample of uncharacterized cells from plant rhizosphere. Cells are sequentially recovered from individual wells that display highest or lowest levels of focal species growth using a high-resolution photopolymer extraction system. Interacting species are then identified and putative interactions are validated. Using this approach, we screen the poplar rhizosphere for strains affecting the growth of Pantoea sp. YR343, a plant growth promoting bacteria isolated from Populus deltoides rhizosphere. In one screen, we montiored 3,600 microwells within the array to uncover multiple antagonistic Stenotrophomonas strains and a set of Enterobacter strains that promoted YR343 growth. The later demonstrates the unique ability of the platform to discover multi-membered consortia that generate emergent outcomes, thereby expanding the range of phenotypes that can be characterized from microbiomes. This knowledge will aid in the development of consortia for Populus production, while the platform offers a new approach for screening and discovery of microbial interactions, applicable to any microbiome.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.3389/fsufs.2023.1106528
