scholarly journals Plant-derived coumarins shape the composition of an Arabidopsis synthetic root microbiome

2019 ◽  
Vol 116 (25) ◽  
pp. 12558-12565 ◽  
Author(s):  
Mathias J. E. E. E. Voges ◽  
Yang Bai ◽  
Paul Schulze-Lefert ◽  
Elizabeth S. Sattely
Keyword(s):  
Microbial Community ◽  
Systematic Approach ◽  
Potential Role ◽  
Microbial Community Composition ◽  
Alkaline Soils ◽  
Arable Soils ◽  
Specialized Metabolites ◽  
Community Shifts ◽  
Root Microbiome

The factors that contribute to the composition of the root microbiome and, in turn, affect plant fitness are not well understood. Recent work has highlighted a major contribution of the soil inoculum in determining the composition of the root microbiome. However, plants are known to conditionally exude a diverse array of unique secondary metabolites, that vary among species and environmental conditions and can interact with the surrounding biota. Here, we explore the role of specialized metabolites in dictating which bacteria reside in the rhizosphere. We employed a reduced synthetic community (SynCom) of Arabidopsis thaliana root-isolated bacteria to detect community shifts that occur in the absence of the secreted small-molecule phytoalexins, flavonoids, and coumarins. We find that lack of coumarin biosynthesis in f6′h1 mutant plant lines causes a shift in the root microbial community specifically under iron deficiency. We demonstrate a potential role for iron-mobilizing coumarins in sculpting the A. thaliana root bacterial community by inhibiting the proliferation of a relatively abundant Pseudomonas species via a redox-mediated mechanism. This work establishes a systematic approach enabling elucidation of specific mechanisms by which plant-derived molecules mediate microbial community composition. Our findings expand on the function of conditionally exuded specialized metabolites and suggest avenues to effectively engineer the rhizosphere with the aim of improving crop growth in iron-limited alkaline soils, which make up a third of the world’s arable soils.

scholarly journals Plant-derived coumarins shape the composition of an Arabidopsis synthetic root microbiome

2018 ◽  
Author(s):  
Mathias J.E.E.E. Voges ◽  
Yang Bai ◽  
Paul Schulze-Lefert ◽  
Elizabeth S. Sattely
Keyword(s):  
Microbial Community ◽  
Iron Deficiency ◽  
Molecular Mechanisms ◽  
Microbial Community Composition ◽  
Alkaline Soils ◽  
Arable Soils ◽  
Specialized Metabolites ◽  
Soil Inoculum ◽  
The Impact ◽  
Root Microbiome

SignificanceThe root microbiome composition is largely determined by the soil inoculum, with a distinct contribution from the host. Yet, the molecular mechanisms with which the host influences its rhizobiome are only beginning to be discovered. Using a hydroponics-based synthetic community approach, we probe the impact of root-exuded specialized metabolites in shaping the root microbiome. We uncover a role for coumarins in structuring the rhizobiome, particularly by limiting the growth of a Pseudomonas strain, for which we propose a mechanism of action. Our findings support the exciting possibility that root-exuded coumarins form a part of the plant’s adaptive response to iron deficiency that goes beyond iron mobilization to modulate the rhizobiome, and highlights avenues towards engineering the rhizosphere for plant health.AbstractThe factors that dictate the composition of the root microbiome and its role in plant fitness has been a long-standing question. Recent work has highlighted a major contribution of the soil inoculum in determining the composition of the root microbiome. However, plants are known to conditionally exude a diverse array of unique secondary metabolites, largely varying between species and environmental conditions. Here, we explore the role of specialized metabolites in dictating which bacteria reside in the rhizosphere. We employed a reduced synthetic community (SynCom) of Arabidopsis thaliana root-isolated bacteria to detect community shifts that occur in the absence of the secreted small molecule phytoalexins, flavonoids, and coumarins. We find that lack of coumarin biosynthesis in f6’h1 mutant plant lines causes a shift in the root microbial community specifically under iron deficiency. We demonstrate a potential role for iron-mobilizing coumarins in sculpting the A. thaliana root bacterial community by inhibiting the proliferation of a relatively abundant Pseudomonas species via a redox-mediated mechanism. This work establishes a systematic approach enabling elucidation of specific mechanisms by which plant-derived molecules mediate microbial community composition. Our findings expand on the function of conditionally-exuded specialized metabolites and lead to new avenues to effectively engineer the rhizosphere for improving crop growth in alkaline soils, which make up a third of total arable soils.

scholarly journals The Role of the Microbiome of Truffles in Aroma Formation: a Meta-Analysis Approach

2015 ◽  
Vol 81 (20) ◽  
pp. 6946-6952 ◽  
Author(s):  
Maryam Vahdatzadeh ◽  
Aurélie Deveau ◽  
Richard Splivallo
Keyword(s):  
Microbial Community ◽  
Potential Role ◽  
Current Knowledge ◽  
Meta Analysis ◽  
Microbial Community Composition ◽  
Symbiotic Relationship ◽  
Fruiting Bodies ◽  
Dominant Group ◽  
Content Type

ABSTRACTTruffles (Tuberspp.) are ascomycete subterraneous fungi that form ectomycorrhizas in a symbiotic relationship with plant roots. Their fruiting bodies are appreciated for their distinctive aroma, which might be partially derived from microbes. Indeed, truffle fruiting bodies are colonized by a diverse microbial community made up of bacteria, yeasts, guest filamentous fungi, and viruses. The aim of this minireview is two-fold. First, the current knowledge on the microbial community composition of truffles has been synthesized to highlight similarities and differences among four truffle (Tuber) species (T. magnatum,T. melanosporum,T. aestivum, andT. borchii) at various stages of their life cycle. Second, the potential role of the microbiome in truffle aroma formation has been addressed for the same four species. Our results suggest that on one hand, odorants, which are common to many truffle species, might be of mixed truffle and microbial origin, while on the other hand, less common odorants might be derived from microbes only. They also highlight that bacteria, the dominant group in the microbiome of the truffle, might also be the most important contributors to truffle aroma not only inT. borchii, as already demonstrated, but also inT. magnatum,T. aestivum, andT. melanosporum.

Investigating Gut Microbial Taxa and Asparaginase Related Genes in Children Showing Different Direction of Change in Serum Asparaginase Activity Levels during Pegasparaginase Treatment for Acute Lymphoblastic Leukemia

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 40-41
Author(s):  
Ketan Kulkarni ◽  
Katherine A Dunn ◽  
Jessica Connors ◽  
Joseph Bielawski ◽  
Jacob Nearing ◽  
...  
Keyword(s):  
Microbial Community ◽  
Acute Lymphoblastic Leukemia ◽  
Stool Sample ◽  
Gut Microbiome ◽  
Lymphoblastic Leukemia ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Activity Levels ◽  
Dose Number

Background: L-asparaginase (ASNase) converts Asn to Asp and at sustained high levels depletes circulating Asn, leading to leukemic cell death. This dependency has led to the use of ASNase (in a peglyated form, PEGASNase) as an important therapy in the treatment of acute lymphoblastic leukemia (ALL) and has improved survival in patients with ALL. ASNase treatment efficacy relies on significant depletion of circulating Asn for sustained periods of time. Therapeutic monitoring is therefore critical to ensure sufficient levels of ASNase activity to maintain Asn depletion. Serum ASNase activity is monitored as a proxy for Asn levels, having an inverse relationship to Asn. The predictors of serum levels of ASNase activity are not clear however with variation in levels within the same patient between doses. The gut microbiome plays a role in human health and disease, producing metabolites that could impact ASNase therapy. To date, the role of the gut microbiome community in impacting serum ASNase activity levels has not been investigated. Methods: We investigated 12 paediatric ALL patients for which serum ASNase levels were measured (7 days post treatment) for two consecutive doses of PEGASNase and a stool sample was collected between these two doses (17 samples). Change in serum ASNase activity was determined by examining the difference in consecutive serum ASNase levels. Activity was considered to have decreased when change was negative (serum ASNase levels declined from previous measurement). Gut microbial community composition of the stool samples was determined from a portion of the 16S rRNA gene. In addition whole shotgun metagenome sequencing was used to investigate the relationship between microbial ASNase and ASNS genes and changes in serum ASNase levels during treatment. We utilized a Bayesian model to examine the microbial community structure in serum ASNase decreasing (SD) vs increasing (SI) samples. We used Mann-Whitney U test to examine differences in counts of bacterial ASNase and ASNS genes in SD and SI groups. Finally we investigated counts of bacterial ASNase and ASNS genes along with age, gender, disease risk, dose number, serum ASNase level at previous dose and time between stool sample and dose at predicting change in serum ASNase activity levels using regression models after applying lasso reduction. Results: Patients in this study were 50% male and had an average age of 5 years ranging from 1 month to 14.6 years. Among samples examined 35% had decreased serum activity compared to measurements from the previous dose. We identified differing assemblages of microbial taxa prior to PEGASNase treatment. The SD community was predominated by Escherichia prior to treatment while Bacteroides and Streptococcus predominated in the SI community (Fig 1). We found that counts of microbial ASNS were significantly (p=0.003) negatively correlated with change in serum ASNase activity levels (Fig 2), however neither bacterial ASNase gene (ansA or ansB) was significant. Including covariates and applying model reduction we find that ASNS (p=0.0005), dose number (p= 0.001), age at diagnosis (p= 0.001), serum ASNase levels at previous dose (p= 0.008), and counts of ansA (p=0.04) predict change in serum ASNase levels (adjusted R2=0.826, p= 0.0002). Only dose-number was positively correlated with change in serum ASNase level. Conclusions: We found differences in the microbial community prior to PEGASNase treatment possibly suggesting that modifying the microbiome (decreasing contribution of Escherichia) prior to treatment could result in increased serum ASNase activity. This data also suggests that increased amounts of bacterial ASNS genes present may be associated with a decrease in serum ASNase activity. Future work should focus on a larger and more diverse set of samples in order to further investigate SD and SI community-level properties and the role of covariates (e.g., age and dose number), and further exam the interplay between serum ASNase activity, and bacterial ASNS. Disclosures No relevant conflicts of interest to declare.

scholarly journals Cooperation, Competition, and Specialized Metabolism in a Simplified Root Nodule Microbiome

mBio ◽  
2020 ◽  
Vol 11 (4) ◽  
Author(s):  
Bridget L. Hansen ◽  
Rita de Cassia Pessotti ◽  
Monika S. Fischer ◽  
Alyssa Collins ◽  
Laila El-Hifnawi ◽  
...  
Keyword(s):  
Potential Role ◽  
Root Nodule ◽  
Root Nodules ◽  
Imaging Mass Spectrometry ◽  
In Planta ◽  
Content Type ◽  
Specialized Metabolites ◽  
Brevibacillus Brevis

ABSTRACT Microbiomes associated with various plant structures often contain members with the potential to make specialized metabolites, e.g., molecules with antibacterial, antifungal, or siderophore activities. However, when and where microbes associated with plants produce specialized metabolites, and the potential role of these molecules in mediating intramicrobiome interactions, is not well understood. Root nodules of legume plants are organs devoted to hosting symbiotic bacteria that fix atmospheric nitrogen and have recently been shown to harbor a relatively simple accessory microbiome containing members with the ability to produce specialized metabolites in vitro. On the basis of these observations, we sought to develop a model nodule microbiome system for evaluating specialized microbial metabolism in planta. Starting with an inoculum derived from field-grown Medicago sativa nodules, serial passaging through gnotobiotic nodules yielded a simplified accessory community composed of four members: Brevibacillus brevis, Paenibacillus sp., Pantoea agglomerans, and Pseudomonas sp. Some members of this community exhibited clear cooperation in planta, while others were antagonistic and capable of disrupting cooperation between other partners. Using matrix-assisted laser desorption ionization–imaging mass spectrometry, we found that metabolites associated with individual taxa had unique distributions, indicating that some members of the nodule community were spatially segregated. Finally, we identified two families of molecules produced by B. brevis in planta as the antibacterial tyrocidines and a novel set of gramicidin-type molecules, which we term the britacidins. Collectively, these results indicate that in addition to nitrogen fixation, legume root nodules are likely also sites of active antimicrobial production.

scholarly journals The Role of Microbial Community Composition in Controlling Soil Respiration Responses to Temperature

PLoS ONE ◽  
2016 ◽  
Vol 11 (10) ◽  
pp. e0165448 ◽  
Author(s):  
Marc D. Auffret ◽  
Kristiina Karhu ◽  
Amit Khachane ◽  
Jennifer A. J. Dungait ◽  
Fiona Fraser ◽  
...  
Keyword(s):  
Microbial Community ◽  
Soil Respiration ◽  
Community Composition ◽  
Microbial Community Composition

scholarly journals Emergence Shapes the Structure of the Seed Microbiota

2014 ◽  
Vol 81 (4) ◽  
pp. 1257-1266 ◽  
Author(s):  
Matthieu Barret ◽  
Martial Briand ◽  
Sophie Bonneau ◽  
Anne Préveaux ◽  
Sophie Valière ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Practical Applications ◽  
Bacterial Marker ◽  
Species Specific ◽  
Diversity Studies

ABSTRACTSeeds carry complex microbial communities, which may exert beneficial or deleterious effects on plant growth and plant health. To date, the composition of microbial communities associated with seeds has been explored mainly through culture-based diversity studies and therefore remains largely unknown. In this work, we analyzed the structures of the seed microbiotas of different plants from the family Brassicaceae and their dynamics during germination and emergence through sequencing of three molecular markers: the ITS1 region of the fungal internal transcribed spacer, the V4 region of 16S rRNA gene, and a species-specific bacterial marker based on a fragment ofgyrB. Sequence analyses revealed important variations in microbial community composition between seed samples. Moreover, we found that emergence strongly influences the structure of the microbiota, with a marked reduction of bacterial and fungal diversity. This shift in the microbial community composition is mostly due to an increase in the relative abundance of some bacterial and fungal taxa possessing fast-growing abilities. Altogether, our results provide an estimation of the role of the seed as a source of inoculum for the seedling, which is crucial for practical applications in developing new strategies of inoculation for disease prevention.

scholarly journals New insights into the role of microbial community composition in driving soil respiration rates

2018 ◽  
Vol 118 ◽  
pp. 35-41 ◽  
Author(s):  
Yu-Rong Liu ◽  
Manuel Delgado-Baquerizo ◽  
Jun-Tao Wang ◽  
Hang-Wei Hu ◽  
Ziming Yang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Soil Respiration ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Respiration Rates

scholarly journals Genomics of tailless bacteriophages in a complex lactic acid bacteria starter culture

2020 ◽  
Author(s):  
Svetlana Alexeeva ◽  
Yue Liu ◽  
Jingjie Zhu ◽  
Joanna Kaczorowska ◽  
Thijs R. H. M. Kouwen ◽  
...  
Keyword(s):  
Microbial Community ◽  
Selection Criteria ◽  
Potential Role ◽  
Starter Culture ◽  
Comparative Genome Analysis ◽  
Phage Group ◽  
Different Strains ◽  
Encoding Genes ◽  
Insight Into

Abstract Background Our previous study on a model microbial community originating from artisanal cheese fermentation starter revealed that bacteriophages not only co-exist with bacteria but also are highly abundant. To gain more insight into the potential role of prophages in the microbial community, we analysed the genomic content of 6 phage crops released by different strains in the starter culture, performed comparative genome analysis, and demonstrated their roles in phage defence of respective hosts. Results The identified prophages belong to three different subgroups of the Siphoviridae P335 phage group. Remarkably, most analysed prophages show disruptions in different tail encoding genes, resulting in a common tailless phenotype. Furthermore, a number of potentially beneficial features for the host carried by prophages were identified. The prophages carry up to 3 different phage defence systems per genome that are functional in protecting the host from foreign phage infection. Conclusion We suggest that the presumably defective prophages are a result of bacteria-phage coevolution and convey advantages to host bacteria; knowledge on the ecological role of such (defective) prophages may contribute to a refreshed look in strain selection criteria in (dairy) industry.

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