Biology subjects

Jacoby, R. P.

Publications and source records attributed to Jacoby, R. P..

3 recordsLinked to original sources

bioRxiv2026

Metabolic profiling and genome-scale modelling uncover mechanistic drivers of microbiome stability in synthetic maize root community

Stability is a desirable property for agricultural microbiomes, but there is a poor understanding of the mechanisms that mediate microbial community stability. A representative bacterial synthetic community from maize roots has been proposed by Niu et al. (2017, PNAS, 114:E2450) as a model system to study microbiome stability. This SynCom assembles stably when all seven members are present, but community diversity collapses without the keystone E. ludwigii strain. In this study, we used complementary in vitro experiments and in silico metabolic modelling to assess the role of metabolites for the stability of this SynCom, by defining the metabolic niches occupied by each strain, as well as their cross-feeding phenotypes and B-vitamin dependencies. We show that the individual member strains occupy complementary metabolic niches, measured by the depletion of distinct metabolites in exometabolomic experiments, as well as contrasting growth phenotypes on diverse carbon substrates, patterns which are largely recapitulated by computational simulations. Minimal medium experiments show that the established seven-member community comprises a mixture of prototrophic and auxotrophic strains. Correspondingly, experimental and in silico cross-feeding phenotypes showed that spent media harvested from the prototrophic strains can sustain growth of two auxotrophs and let to the identification of B-vitamin dependencies. Altogether, this study highlights the complementary power of in vitro and in silico approaches and suggests that the metabolic mechanisms of this SynCom can serve as design principles to inform the rational assembly of stable plant-associated microbial communities.

microbiology↗

bioRxiv2021

Metabolic analysis of a bacterial synthetic community from maize roots provides new mechanistic insights into microbiome stability

Stability is a desirable property for agricultural microbiomes, but there is a poor understanding of the mechanisms that mediate microbial community stability. Recently, a representative bacterial synthetic community from maize roots has been proposed as a model system to study microbiome stability (Niu 2017, PNAS, 114:E2450). This SynCom assembles stably when all seven members are present, but community diversity collapses without the keystone E. cloacae strain. The aim of this study was to assess the role of metabolites for the stability of this SynCom, by defining the metabolic niches occupied by each strain, as well as their cross-feeding phenotypes and B-vitamin dependencies. We show that the individual member strains occupy complementary metabolic niches, measured by the depletion of distinct metabolites in exometabolomic experiments, as well as contrasting growth phenotypes on diverse carbon substrates. Minimal medium experiments show that the established seven-member community comprises a mixture of prototrophic and auxotrophic strains. Correspondingly, experimental cross-feeding phenotypes showed that spent media harvested from the prototrophic strains can sustain growth of two auxotrophs. We suggest that the metabolic mechanisms exhibited by this SynCom could serve as design principles to inform the rational assembly of stable plant-associated microbial communities.

microbiology↗

bioRxiv2019

Metabolic mechanisms of nitrogen substrate utilisation in three rhizosphere bacterial strains investigated using quantitative proteomics

Nitrogen metabolism in the rhizosphere microbiome plays an important role in mediating plant nutrition, particularly under low inputs of mineral fertilisers. However, there is relatively little mechanistic information about which genes and metabolic pathways are induced by rhizosphere bacterial strains to utilise diverse nitrogen substrates. Here we investigate nitrogen substrate utilisation in three taxonomically diverse bacterial strains previously isolated from Arabidopsis roots. The three strains represent taxa that are consistently detected as core members of the plant microbiome: Pseudomonas, Streptomyces and Rhizobium. We use phenotype microarrays to determine the nitrogen substrate preferences of these strains, and compare the experimental results versus computational simulations of genome-scale metabolic network models obtained with EnsembleFBA. Results show that all three strains exhibit generalistic nitrogen substrate preferences, with substrate utilisation being well predicted by EnsembleFBA. Using label-free quantitative proteomics, we document hundreds of proteins in each strain that exhibit differential abundance values following cultivation on five different nitrogen sources: ammonium, glutamate, lysine, serine and urea. Proteomic data show that the three strains use different metabolic strategies to utilise specific nitrogen sources. One diverging trait appears to be their degree of proteomic flexibility, with Pseudomonas sp. Root9 utilising lysine nutrition via widespread protein-level alterations to its flexible metabolic network, whereas Rhizobium sp. Root491 shows relatively stable proteome composition across diverse nitrogen sources. Our results give new protein-level information about the specific transporters and enzymes induced by diverse rhizosphere bacterial strains to utilise organic nitrogen substrates.\n\nImportanceNitrogen is the primary macronutrient required for plant growth. In contemporary agriculture, the vast majority of nitrogen is delivered via mineral fertilisers, which have undesirable environmental consequences such as waterway eutrophication and greenhouse gas production. There is increasing research interest in designing agricultural systems that mimic natural ecosystems, where nitrogen compounds are cycled between plants and soil, with the mineralisation of recalcitrant soil organic-N molecules mediated via microbial metabolism. However, to date there is little mechanistic information about which genes and metabolic pathways are induced by rhizosphere bacterial strains to metabolise organic-N molecules. Here, we use quantitative proteomics to provide new information about the molecular mechanisms utilised by taxonomically diverse rhizosphere bacterial strains to utilise different nitrogen substrates. Furthermore, we generate computational models of bacterial metabolism from a minimal set of experimental information, providing a workflow that can be easily reused to predict nitrogen substrate utilisation in other strains.

microbiology↗