Bacterial Biosensors for in Vivo Spatiotemporal Mapping of Root Secretion

Pini, Francesco; East, Alison K.; Appia-Ayme, Corinne; Tomek, Jakub; Karunakaran, Ramakrishnan; Mendoza-Suárez, Marcela; Edwards, Anne; Terpolilli, Jason; Roworth, Joshua David; Downie, J. Allan; Poole, Philip S.

doi:10.1104/pp.16.01302

Cited by 79 publications

(119 citation statements)

References 45 publications

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“…This is consistent with a previous study on root exudates under similar conditions [92]. Previous studies reported that the amounts of secreted avonoids increased by inoculation with compatible symbionts or by treatment with Nod factors and were reduced by inoculation with nodC mutant rhizobium [35,36,93]. Accordingly, we found a signi cantly increased exudation of most avonoids when inoculating the WT strain.…”

Section: Discussionsupporting

confidence: 93%

The symbiotic capacity of rhizobium shapes root-associated microbiomes

Liu¹,

Ma²,

Chen³

et al. 2020

Preprint

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Background: Root-microbiome interactions are of central importance for plant performance and yield. A distinctive feature of legumes in this context is that they engage in symbiosis with rhizobia, which are abundant in soils and include both symbiotic and non-symbiotic bacterial strains. If and how the capacity of rhizobia to form symbiosis modulates root-associated microbiomes are not well understood. Results: We address this question by inoculating soybean (Glycine max) plants with wild type (WT) or a noeI mutant of Bradyrhizobium diazoefficiens. The noeI mutant produces a defective Nod factor and is thus compromised in its ability to establish functional symbiosis. Compared to soybean plants inoculated with WT rhizobia, plants inoculated with the noeI mutant showed a significant decrease in nodulation and root-flavonoid exudation, and exhibited strong changes in microbiome assembly in the rhizosphere and the rhizoplane. NoeI mutant-inoculated roots exhibited reduced diversity, co-occurrence interactions and a substantial depletion of beneficial microbes on the roots. The effects of the noeI mutation were absent in soils without plants, demonstrating that they are plant dependent. Complementation experiments showed that flavonoid supplementation is sufficient to restore recruitment of beneficial microbes. Conclusion: The results illustrate that the capacity of a rhizobium to form microbial symbiosis dramatically alters root-associated microbiomes, most likely by changing root exudation patterns. The results of this study have important implications for our understanding of the evolution of plant-microbiome interactions in the context of plant-bacterial symbioses.

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Section: Discussionsupporting

confidence: 93%

The symbiotic capacity of rhizobium shapes root-associated microbiomes

Liu¹,

Ma²,

Chen³

et al. 2020

Preprint

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“…Recent work has suggested that culturing rhizobia in the latter is correlated with an increase in mutations of symbiosis-associated genes 50 , raising questions about the utility of rich medium cultures in symbiosis work overall. A more detailed analysis of the host environment, including the full milieu of root exudates 51 , available carbon sources 52 and trace metals specific to each legume, will improve in vitro models of legume-bacteria interactions.…”

Section: Discussionmentioning

confidence: 99%

Extended hopanoid loss reduces bacterial motility and surface attachment and leads to heterogeneity in root nodule growth kinetics in a Bradyrhizobium-Aeschynomene symbiosis

Belin

Tookmanian

Anda

et al. 2018

Preprint

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Hopanoids are steroid-like bacterial lipids that enhance membrane rigidity and promote bacterial growth under diverse stresses. Hopanoid biosynthesis genes are conserved in nitrogen-fixing plant symbionts, and we previously found that the extended (C35) class of hopanoids in Bradyrhizobium diazoefficiens are required for efficient symbiotic nitrogen fixation in the tropical legume host Aeschynomene afraspera. Here we demonstrate that the nitrogen fixation defect conferred by extended loss can fully be explained by a reduction in root nodule sizes rather than per-bacteroid nitrogen fixation levels. Using a single-nodule tracking approach to track A. afraspera nodule development, we provide a quantitative model of root nodule development in this host, uncovering both the baseline growth parameters for wild-type nodules and a surprising heterogeneity of extended hopanoid mutant developmental phenotypes. These phenotypes include a delay in root nodule initiation and presence of a subpopulation of nodules with slow growth rates and low final volumes, which are correlated with reduced motility and surface attachment in vitro and lower bacteroid densities in planta, respectively. This work provides a quantitative reference point for understanding the phenotypic diversity of ineffective symbionts in A. afraspera and identifies specific developmental stages affected by extended hopanoid loss for future mechanistic work.

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“…viciae 3841 data contains gene expression information observed under 18 different growth conditions. These data come from n = 54 microarray channels with 3 independent samples per condition (Ramachandran et al, 2011;Pini et al, 2017;Karunakaran et al, 2009). The complete list of the conditions is in Sec.…”

Section: Datamentioning

confidence: 99%

Robust gene coexpression networks using signed distance correlation

Pardo-Diaz

Bozhilova

Beguerisse-Díaz

et al. 2020

Preprint

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Motivation: Even within well studied organisms, many genes lack useful functional annotations. One way to generate such functional information is to infer biological relationships between genes/proteins, using a network of gene coexpression data that includes functional annotations. However, the lack of trustworthy functional annotations can impede the validation of such networks. Hence, there is a need for a principled method to construct gene coexpression networks that capture biological information and are structurally stable even in the absence of functional information. Results: We introduce the concept of signed distance correlation as a measure of dependency between two variables, and apply it to generate gene coexpression networks. Distance correlation offers a more intuitive approach to network construction than commonly used methods such as Pearson correlation. We propose a framework to generate self-consistent networks using signed distance correlation purely from gene expression data, with no additional information. We analyse data from three different organisms to illustrate how networks generated with our method are more stable and capture more biological information compared to networks obtained from Pearson or Spearman correlations. Code availability: https://github.com/javier-pardodiaz/sdcorGCN.

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Bacterial Biosensors for in Vivo Spatiotemporal Mapping of Root Secretion

Cited by 79 publications

References 45 publications

The symbiotic capacity of rhizobium shapes root-associated microbiomes

The symbiotic capacity of rhizobium shapes root-associated microbiomes

Extended hopanoid loss reduces bacterial motility and surface attachment and leads to heterogeneity in root nodule growth kinetics in a Bradyrhizobium-Aeschynomene symbiosis

Robust gene coexpression networks using signed distance correlation

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