scholarly journals Investigating the role of root exudates in recruiting Streptomyces bacteria to the Arabidopsis thaliana root microbiome

2020 ◽  
Author(s):  
Sarah F. Worsley ◽  
Michael Macey ◽  
Sam Prudence ◽  
Barrie Wilkinson ◽  
J. Colin Murrell ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Stable Isotope ◽  
Plant Growth ◽  
Root Exudates ◽  
Soil Bacteria ◽  
Stable Isotope Probing ◽  
Plant Roots ◽  
Plant Metabolites ◽  
Complex Organic ◽  
Root Microbiome

AbstractStreptomyces species are saprophytic soil bacteria that produce a diverse array of specialised metabolites, including half of all known antibiotics. They are also rhizobacteria and plant endophytes that can promote plant growth and protect against disease. Several studies have shown that streptomycetes are enriched in the rhizosphere and endosphere of the model plant Arabidopsis thaliana. Here, we set out to test the hypothesis that they are attracted to plant roots by root exudates, and specifically by the plant phytohormone salicylate, which they might use as a nutrient source. We confirmed a previously published report that salicylate over-producing cpr5 plants are colonised more readily by streptomycetes but found that salicylate-deficient sid2-2 and pad4 plants had the same levels of root colonisation by Streptomyces bacteria as the wild-type plants. We then tested eight genome sequenced Streptomyces endophyte strains in vitro and found that none were attracted to or could grow on salicylate as a sole carbon source. We next used 13CO2 DNA stable isotope probing to test whether Streptomyces species can feed off a wider range of plant metabolites but found that Streptomyces bacteria were outcompeted by faster growing proteobacteria and did not incorporate photosynthetically fixed carbon into their DNA. We conclude that, given their saprotrophic nature and under conditions of high competition, streptomycetes most likely feed on more complex organic material shed by growing plant roots. Understanding the factors that impact the competitiveness of strains in the plant root microbiome could have consequences for the effective application of biocontrol strains.ImportanceStreptomyces bacteria are ubiquitous in soil but their role as rhizobacteria is less well studied. Our recent work demonstrated that streptomycetes isolated from A. thaliana roots can promote growth and protect against disease across plant species and that plant growth hormones can modulate the production of bioactive specialised metabolites by these strains. Here we used 13CO2 DNA stable isotope probing to identify which bacteria feed on plant metabolites in the A. thaliana rhizosphere and, for the first time, in the endosphere. We found that Streptomyces species are outcompeted for these metabolites by faster growing proteobacteria and instead likely subsist on more complex organic material such as cellulose derived from plant cell material that is shed from the roots. This work thus reveals the “winners and losers” in the battle between soil bacteria for plant metabolites and could inform the development of methods to apply streptomycetes as plant growth-promoting agents.

scholarly journals Investigating the Role of Root Exudates in Recruiting Streptomyces Bacteria to the Arabidopsis thaliana Microbiome

2021 ◽  
Vol 8 ◽  
Author(s):  
Sarah F. Worsley ◽  
Michael C. Macey ◽  
Samuel M. M. Prudence ◽  
Barrie Wilkinson ◽  
J. Colin Murrell ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Root Exudates ◽  
Plant Root ◽  
Stable Isotope Probing ◽  
Plant Roots ◽  
Plant Metabolites ◽  
Published Report ◽  
Promote Plant Growth

Streptomyces species are saprophytic soil bacteria that produce a diverse array of specialized metabolites, including half of all known antibiotics. They are also rhizobacteria and plant endophytes that can promote plant growth and protect against disease. Several studies have shown that streptomycetes are enriched in the rhizosphere and endosphere of the model plant Arabidopsis thaliana. Here, we set out to test the hypothesis that they are attracted to plant roots by root exudates, and specifically by the plant phytohormone salicylate, which they might use as a nutrient source. We confirmed a previously published report that salicylate over-producing cpr5 plants are colonized more readily by streptomycetes but found that salicylate-deficient sid2-2 and pad4 plants had the same levels of root colonization by Streptomyces bacteria as the wild-type plants. We then tested eight genome sequenced Streptomyces endophyte strains in vitro and found that none were attracted to or could grow on salicylate as a sole carbon source. We next used 13CO2 DNA stable isotope probing to test whether Streptomyces species can feed off a wider range of plant metabolites but found that Streptomyces bacteria were outcompeted by faster growing proteobacteria and did not incorporate photosynthetically fixed carbon into their DNA. We conclude that, given their saprotrophic nature and under conditions of high competition, streptomycetes most likely feed on more complex organic material shed by growing plant roots. Understanding the factors that impact the competitiveness of strains in the plant root microbiome could have consequences for the effective application of biocontrol strains.

scholarly journals Soil, senescence and exudate utilisation: characterisation of the Paragon var. spring bread wheat root microbiome

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Samuel MM. Prudence ◽  
Jake T. Newitt† ◽  
Sarah F. Worsley ◽  
Michael C. Macey ◽  
J. Colin Murrell ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Community Composition ◽  
Root Exudates ◽  
Crop Yields ◽  
Wheat Root ◽  
Stable Isotope Probing ◽  
Disease Suppression ◽  
Soil Conditions ◽  
Living Plant ◽  
Root Microbiome

Abstract Background Conventional methods of agricultural pest control and crop fertilisation are unsustainable. To meet growing demand, we must find ecologically responsible means to control disease and promote crop yields. The root-associated microbiome can aid plants with disease suppression, abiotic stress relief, and nutrient bioavailability. The aim of the present work was to profile the community of bacteria, fungi, and archaea associated with the wheat rhizosphere and root endosphere in different conditions. We also aimed to use 13CO2 stable isotope probing (SIP) to identify microbes within the root compartments that were capable of utilising host-derived carbon. Results Metabarcoding revealed that community composition shifted significantly for bacteria, fungi, and archaea across compartments. This shift was most pronounced for bacteria and fungi, while we observed weaker selection on the ammonia oxidising archaea-dominated archaeal community. Across multiple soil types we found that soil inoculum was a significant driver of endosphere community composition, however, several bacterial families were identified as core enriched taxa in all soil conditions. The most abundant of these were Streptomycetaceae and Burkholderiaceae. Moreover, as the plants senesce, both families were reduced in abundance, indicating that input from the living plant was required to maintain their abundance in the endosphere. Stable isotope probing showed that bacterial taxa within the Burkholderiaceae family, among other core enriched taxa such as Pseudomonadaceae, were able to use root exudates, but Streptomycetaceae were not. Conclusions The consistent enrichment of Streptomycetaceae and Burkholderiaceae within the endosphere, and their reduced abundance after developmental senescence, indicated a significant role for these families within the wheat root microbiome. While Streptomycetaceae did not utilise root exudates in the rhizosphere, we provide evidence that Pseudomonadaceae and Burkholderiaceae family taxa are recruited to the wheat root community via root exudates. This deeper understanding crop microbiome formation will enable researchers to characterise these interactions further, and possibly contribute to ecologically responsible methods for yield improvement and biocontrol in the future.

scholarly journals Bacterial Community Members Increase Bacillus subtilis Maintenance on the Roots of Arabidopsis thaliana

2020 ◽  
Vol 4 (4) ◽  
pp. 303-313
Author(s):  
Noam Eckshtain-Levi ◽  
Susanna Leigh Harris ◽  
Reizo Quilat Roscios ◽  
Elizabeth Anne Shank
Keyword(s):  
Arabidopsis Thaliana ◽  
Bacillus Subtilis ◽  
Crop Production ◽  
Crop Yields ◽  
Plant Root ◽  
Plant Roots ◽  
Plant Growth Promoting Bacteria ◽  
Bacterial Strains ◽  
Root Microbiome ◽  
Over Time

Plant-growth-promoting bacteria (PGPB) are used to improve plant health and promote crop production. However, because some PGPB (including Bacillus subtilis) do not maintain substantial colonization on plant roots over time, it is unclear how effective PGPB are throughout the plant growing cycle. A better understanding of the dynamics of plant root community assembly is needed to develop and harness the potential of PGPB. Although B. subtilis is often a member of the root microbiome, it does not efficiently monoassociate with plant roots. We hypothesized that B. subtilis may require other primary colonizers to efficiently associate with plant roots. We utilized a previously designed hydroponic system to add bacteria to Arabidopsis thaliana roots and monitor their attachment over time. We inoculated seedlings with B. subtilis and individual bacterial isolates from the native A. thaliana root microbiome either alone or together. We then measured how the coinoculum affected the ability of B. subtilis to colonize and maintain on A. thaliana roots. We screened 96 fully genome-sequenced strains and identified five bacterial strains that were able to significantly improve the maintenance of B. subtilis. Three of these rhizobacteria also increased the maintenance of two strains of B. amyloliquefaciens commonly used in commercially available bioadditives. These results not only illustrate the utility of this model system to address questions about plant–microbe interactions and how other bacteria affect the ability of PGPB to maintain their relationships with plant roots but also may help inform future agricultural interventions to increase crop yields. [Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

scholarly journals Stable-Isotope Probing Identifies Uncultured Planctomycetes as Primary Degraders of a Complex Heteropolysaccharide in Soil

2015 ◽  
Vol 81 (14) ◽  
pp. 4607-4615 ◽  
Author(s):  
Xiaoqing Wang ◽  
Christine E. Sharp ◽  
Gareth M. Jones ◽  
Stephen E. Grasby ◽  
Allyson L. Brady ◽  
...  
Keyword(s):  
Stable Isotope ◽  
16S Rrna ◽  
Soil Bacteria ◽  
Stable Isotope Probing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Content Type ◽  
Degrading Bacteria ◽  
Aerobic Soil

ABSTRACTThe exopolysaccharides (EPSs) produced by some bacteria are potential growth substrates for other bacteria in soil. We used stable-isotope probing (SIP) to identify aerobic soil bacteria that assimilated the cellulose produced byGluconacetobacter xylinusor the EPS produced byBeijerinckia indica. The latter is a heteropolysaccharide comprised primarily ofl-guluronic acid,d-glucose, andd-glycero-d-mannoheptose.13C-labeled EPS and13C-labeled cellulose were purified from bacterial cultures grown on [13C]glucose. Two soils were incubated with these substrates, and bacteria actively assimilating them were identified via pyrosequencing of 16S rRNA genes recovered from13C-labeled DNA. Cellulose C was assimilated primarily by soil bacteria closely related (93 to 100% 16S rRNA gene sequence identities) to known cellulose-degrading bacteria. However,B. indicaEPS was assimilated primarily by bacteria with low identities (80 to 95%) to known species, particularly by different members of the phylumPlanctomycetes. In one incubation, members of thePlanctomycetesmade up >60% of all reads in the labeled DNA and were only distantly related (<85% identity) to any described species. Although it is impossible with SIP to completely distinguish primary polysaccharide hydrolyzers from bacteria growing on produced oligo- or monosaccharides, the predominance ofPlanctomycetessuggested that they were primary degraders of EPS. Other bacteria assimilatingB. indicaEPS included members of theVerrucomicrobia, candidate division OD1, and theArmatimonadetes. The results indicate that some uncultured bacteria in soils may be adapted to using complex heteropolysaccharides for growth and suggest that the use of these substrates may provide a means for culturing new species.

scholarly journals Recent advances in the role of plant metabolites in shaping the root microbiome

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 151 ◽  
Author(s):  
Richard P. Jacoby ◽  
Li Chen ◽  
Melina Schwier ◽  
Anna Koprivova ◽  
Stanislav Kopriva
Keyword(s):  
Metabolic Networks ◽  
Plant Roots ◽  
Plant Metabolites ◽  
Plant Interaction ◽  
New Approaches ◽  
Recent Advances ◽  
Great Progress ◽  
Approaches To Study ◽  
Root Microbiome

The last decade brought great progress in describing the repertoire of microbes associated with plants and identifying principles of their interactions. Metabolites exuded by plant roots have been considered candidates for the mechanisms by which plants shape their root microbiome. Here, we review the evidence for several plant metabolites affecting plant interaction with microbes belowground. We also discuss the development of new approaches to study the mechanisms of such interaction that will help to elucidate the metabolic networks in the rhizosphere.

Compound‐specific13C stable isotope probing confirms synthesis of polyhydroxybutyrate by soil bacteria

2019 ◽  
Vol 33 (8) ◽  
pp. 795-802 ◽  
Author(s):  
Kyle Mason‐Jones ◽  
Callum C. Banfield ◽  
Michaela A. Dippold
Keyword(s):  
Stable Isotope ◽  
Soil Bacteria ◽  
Stable Isotope Probing

scholarly journals Impact of plants on the diversity and activity of methylotrophs in soil

Microbiome ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Michael C. Macey ◽  
Jennifer Pratscher ◽  
Andrew T. Crombie ◽  
J. Colin Murrell
Keyword(s):  
Stable Isotope ◽  
Plant Growth ◽  
Molecular Probes ◽  
Stable Isotope Probing ◽  
16S Rrna Genes ◽  
Bulk Soil ◽  
Rrna Genes ◽  
Methylotrophic Bacteria ◽  
Volatile Organic ◽  
Plant Exudates

Abstract Background Methanol is the second most abundant volatile organic compound in the atmosphere, with the majority produced as a metabolic by-product during plant growth. There is a large disparity between the estimated amount of methanol produced by plants and the amount which escapes to the atmosphere. This may be due to utilisation of methanol by plant-associated methanol-consuming bacteria (methylotrophs). The use of molecular probes has previously been effective in characterising the diversity of methylotrophs within the environment. Here, we developed and applied molecular probes in combination with stable isotope probing to identify the diversity, abundance and activity of methylotrophs in bulk and in plant-associated soils. Results Application of probes for methanol dehydrogenase genes (mxaF, xoxF, mdh2) in bulk and plant-associated soils revealed high levels of diversity of methylotrophic bacteria within the bulk soil, including Hyphomicrobium, Methylobacterium and members of the Comamonadaceae. The community of methylotrophic bacteria captured by this sequencing approach changed following plant growth. This shift in methylotrophic diversity was corroborated by identification of the active methylotrophs present in the soils by DNA stable isotope probing using 13C-labelled methanol. Sequencing of the 16S rRNA genes and construction of metagenomes from the 13C-labelled DNA revealed members of the Methylophilaceae as highly abundant and active in all soils examined. There was greater diversity of active members of the Methylophilaceae and Comamonadaceae and of the genus Methylobacterium in plant-associated soils compared to the bulk soil. Incubating growing pea plants in a 13CO2 atmosphere revealed that several genera of methylotrophs, as well as heterotrophic genera within the Actinomycetales, assimilated plant exudates in the pea rhizosphere. Conclusion In this study, we show that plant growth has a major impact on both the diversity and the activity of methanol-utilising methylotrophs in the soil environment, and thus, the study contributes significantly to efforts to balance the terrestrial methanol and carbon cycle.

scholarly journals Validation of Heavy-Water Stable Isotope Probing for the Characterization of Rapidly Responding Soil Bacteria

2011 ◽  
Vol 77 (13) ◽  
pp. 4589-4596 ◽  
Author(s):  
Zachary T. Aanderud ◽  
Jay T. Lennon
Keyword(s):  
Stable Isotope ◽  
Microbial Communities ◽  
Heavy Water ◽  
Soil Bacteria ◽  
Structure And Function ◽  
Stable Isotope Probing ◽  
Rrna Genes ◽  
Relative Recovery ◽  
Water Stable Isotope ◽  
And Function

ABSTRACTRapid responses of bacteria to sudden changes in their environment can have important implications for the structure and function of microbial communities. In this study, we used heavy-water stable isotope probing (H218O-SIP) to identify bacteria that respond to soil rewetting. First, we conducted experiments to address uncertainties regarding the H218O-SIP method. Using liquid chromatography-mass spectroscopy (LC-MS), we determined that oxygen from H218O was incorporated into all structural components of DNA. Although this incorporation was uneven, we could effectively separate18O-labeled and unlabeled DNAs derived from laboratory cultures and environmental samples that were incubated with H218O. We found no evidence forex vivoexchange of oxygen atoms between DNA and extracellular H2O, suggesting that18O incorporation into DNA is relatively stable. Furthermore, the rate of18O incorporation into bacterial DNA was high (within 48 to 72 h), coinciding with pulses of CO2generated from soil rewetting. Second, we examined shifts in the bacterial composition of grassland soils following rewetting, using H218O-SIP and bar-coded pyrosequencing of 16S rRNA genes. For some groups of soil bacteria, we observed coherent responses at a relatively course taxonomic resolution. Following rewetting, the relative recovery ofAlphaproteobacteria,Betaproteobacteria, andGammaproteobacteriaincreased, while the relative recovery ofChloroflexiandDeltaproteobacteriadecreased. Together, our results suggest that H218O-SIP is effective at identifying metabolically active bacteria that influence soil carbon dynamics. Our results contribute to the ecological classification of soil bacteria while providing insight into some of the functional traits that influence the structure and function of microbial communities under dynamic soil moisture regimes.

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