<i>Bacillus velezensis</i> stimulates resident rhizosphere <i>Pseudomonas stutzeri</i> for plant health through metabolic interactions

Sun, Xinli; Xu, Zhihui; Xie, Jiyu; Hesselberg-Thomsen, Viktor; Tan, Taimeng; Zheng, Daoyue; Strube, Mikael Lenz; Dragoš, Anna; Shen, Qirong; Zhang, Ruifu; Kovács, Ákos T.

doi:10.1038/s41396-021-01125-3

Cited by 220 publications

(162 citation statements)

References 82 publications

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“…In a previous study, we isolated 267 bacteria from the cucumber rhizosphere (Sun et al, 2021). Eleven isolates that co-exist in the natural environment were chosen to create a synthetic biofilm community.…”

Section: Resultsmentioning

confidence: 99%

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Keystone species determine the productivity of synthetic microbial biofilm communities

Sun

Xie

Zheng

et al. 2022

Preprint

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Microbes typically reside in multi-species communities, whose interactions have considerable impacts on the robustness and functionality of such communities. To manage microbial communities, it is essential to understand the factors driving their assemblage and maintenance. Even though the community composition could be easily assessed, interspecies interactions during community establishment remain poorly understood. Here, we combined co-occurrence network analysis with quantitative PCR to examine the importance of each species within synthetic communities (SynComs) of pellicle biofilms. Genome-scale metabolic models and in vivo experiments indicated that the biomass of SynComs was primarily affected by keystone species that are acting either as metabolic facilitators or as competitors. Our study suggests that a combination of co-occurrence network analysis and metabolic modeling could explain the importance of keystone species in SynComs.

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Section: Resultsmentioning

confidence: 99%

“…As shown in Table 1, eleven bacterial isolates were selected from the rhizosphere of cucumber plants by (Sun et al, 2021) were selected for this study.…”

Section: Methodsmentioning

confidence: 99%

Keystone species determine the productivity of synthetic microbial biofilm communities

Sun

Xie

Zheng

et al. 2022

Preprint

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“…Such a rearrangement activity is also found in transglycosylases from phytopathogenic fungi, as shown in Botrytis cinerea (Bi et al, 2021). Since P. stutzeri is a plant commensal (Pham et al, 2017;Sun et al, 2021), an additional role of transglycosylating GHs could be in the host-interaction mechanism.…”

Section: Discussionmentioning

confidence: 99%

Highlighting the factors governing transglycosylation in the GH5_5 endo-1,4-β-glucanase RBcel1

Collet¹,

Wauven²,

Oudjama³

et al. 2022

Acta Cryst Sect D Struct Biol

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Transglycosylating glycoside hydrolases (GHs) offer great potential for the enzymatic synthesis of oligosaccharides. Although knowledge is progressing, there is no unique strategy to improve the transglycosylation yield. Obtaining efficient enzymatic tools for glycan synthesis with GHs remains dependent on an improved understanding of the molecular factors governing the balance between hydrolysis and transglycosylation. This enzymatic and structural study of RBcel1, a transglycosylase from the GH5_5 subfamily isolated from an uncultured bacterium, aims to unravel such factors. The size of the acceptor and donor sugars was found to be critical since transglycosylation is efficient with oligosaccharides at least the size of cellotetraose as the donor and cellotriose as the acceptor. The reaction pH is important in driving the balance between hydrolysis and transglycosylation: hydrolysis is favored at pH values below 8, while transglycosylation becomes the major reaction at basic pH. Solving the structures of two RBcel1 variants, RBcel1_E135Q and RBcel1_Y201F, in complex with ligands has brought to light some of the molecular factors behind transglycosylation. The structure of RBcel1_E135Q in complex with cellotriose allowed a +3 subsite to be defined, in accordance with the requirement for cellotriose as a transglycosylation acceptor. The structure of RBcel1_Y201F has been obtained with several transglycosylation intermediates, providing crystallographic evidence of transglycosylation. The catalytic cleft is filled with (i) donors ranging from cellotriose to cellohexaose in the negative subsites and (ii) cellobiose and cellotriose in the positive subsites. Such a structure is particularly relevant since it is the first structure of a GH5 enzyme in complex with transglycosylation products that has been obtained with neither of the catalytic glutamate residues modified.

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“…Subsequently, seedlings were soaked on a P5_B1gfp bacterial solution (OD600 = 0.1) for 10 minutes and placed in LEGO brick boxes containing 50 g of beads (35). The root colonization was tracked by confocal laser scanning microscopy imaging (CLSM) as described previously (15,(36)(37)(38)(39). Colonized roots were washed twice with sterile ddH2O and placed onto microscope slides.…”

Section: Root Colonization Assaymentioning

confidence: 99%

Establishment of a transparent soil system to study Bacillus subtilis chemical ecology

Lozano-Andrade¹,

Nogueira²,

Wibowo

et al. 2022

Preprint

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Bacterial secondary metabolites are structurally diverse molecules that drive microbial interaction by altering growth, cell differentiation, and signaling. Bacillus subtilis, a Gram-positive soil-dwelling bacterium, produces a wealth of secondary metabolites, among them, lipopeptides have been vastly studied by their antimicrobial, antitumor, and surfactant activities. However, the natural functions of secondary metabolites in the lifestyles of the producing organism remain less explored under natural conditions, i.e. in soil. Here, we describe a hydrogel-based transparent soil system to investigate B. subtilis chemical ecology under controllable soil-like conditions. The transparent soil matrix allows the growth of B. subtilis and other isolates gnotobiotically and under nutrient-controlled conditions. Additionally, we show that transparent soil allows the detection of lipopeptides production and dynamics by HPLC-MS and MALDI-MS imaging, along with fluorescence imaging of 3-dimensional bacterial assemblages. We anticipate that this affordable and highly controllable system will promote bacterial chemical ecology research and help to elucidate microbial interactions driven by secondary metabolites.

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Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions

Cited by 220 publications

References 82 publications

Keystone species determine the productivity of synthetic microbial biofilm communities

Keystone species determine the productivity of synthetic microbial biofilm communities

Highlighting the factors governing transglycosylation in the GH5_5 endo-1,4-β-glucanase RBcel1

Establishment of a transparent soil system to study Bacillus subtilis chemical ecology

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