Diversifying Anaerobic Respiration Strategies to Compete in the Rhizosphere

The rhizosphere is the interface between plant roots and soil where intense, varied interactions between plants and microbes influence plants' health and growth through their influence on biochemical cycles, such as the carbon, nitrogen, and iron cycles. The rhizosphere is also a changing environment where oxygen can be rapidly limited and anaerobic zones can be established. Microorganisms successfully colonize the rhizosphere when they possess specific traits referred to as rhizosphere competence. Anaerobic respiration flexibility contributes to the rhizosphere competence of microbes. Indeed, a wide range of compounds that are available in the rhizosphere can serve as alternative terminal electron acceptors during anaerobic respiration such as nitrates, iron, carbon compounds, sulfur, metalloids, and radionuclides. In the presence of multiple terminal electron acceptors in a complex environment such as the rhizosphere and in the absence of O2, microorganisms will first use the most energetic option to sustain growth. Anaerobic respiration has been deeply studied, and the genes involved in anaerobic respiration have been identified. However, aqueous environment and paddy soils are the most studied environments for anaerobic respiration, even if we provide evidence in this review that anaerobic respiration also occurs in the plant rhizosphere. Indeed, we provide evidence by performing a BLAST analysis on metatranscriptomic data that genes involved in iron, sulfur, arsenate and selenate anaerobic respiration are expressed in the rhizosphere, underscoring that the rhizosphere environment is suitable for the establishment of anaerobic respiration. We thus focus this review on current research concerning the different types of anaerobic respiration that occur in the rhizosphere. We also discuss the flexibility of anaerobic respiration as a fundamental trait for the microbial colonization of roots, environmental and ecological adaptation, persistence and bioremediation in the rhizosphere. Anaerobic respiration appears to be a key process for the functioning of an ecosystem and interactions between plants and microbes

Assessing the effect of organic residue quality on active decomposing fungi in a tropical Vertisol using 15N-DNA stable isotope probing

15N-DNA stable isotope probing (15N-DNA-SIP) combined with 18S rRNA gene-based community analysis was used to identify active fungi involved in decomposition of 15N-labeled maize and soybean litter in a tropical Vertisol. Phylogenetic analysis of 15N-labeled DNA subjected to 18S rRNA gene-based community fingerprinting showed that organic residue quality promoted either slow (i.e. Penicillium sp., Aspergillus sp.) or fast growing (i.e. Fusarium sp., Mortierella sp.) fungal decomposers in soils treated with maize or soybean residues, respectively, whereas Chaetomium sp. were found as dominant decomposers in both residue treatments. Therefore, we have clear evidence that specific members of the fungal community used 15N derived from the two different organic resources for growth and stimulated early decomposition of maize or soybean decomposition. In conclusion, our study showed that 15N-DNA-SIP-based community analyses cannot only follow the flow of N from organic resources into bacteria, but also into the actively decomposing fungal communities of soils

Plant Nutrient Resource Use Strategies Shape Active Rhizosphere Microbiota Through Root Exudation

Plant strategies for soil nutrient uptake have the potential to strongly influence plant–microbiota interactions, due to the competition between plants and microorganisms for soil nutrient acquisition and/or conservation. In the present study, we investigate whether these plant strategies could influence rhizosphere microbial activities via root exudation, and contribute to the microbiota diversification of active bacterial communities colonizing the root-adhering soil (RAS) and inhabiting the root tissues. We applied a DNA-based stable isotope probing (DNA-SIP) approach to six grass species distributed along a gradient of plant nutrient resource strategies, from conservative species, characterized by low nitrogen (N) uptake, a long lifespans and low root exudation level, to exploitative species, characterized by high rates of photosynthesis, rapid rates of N uptake and high root exudation level. We analyzed their (i) associated microbiota composition involved in root exudate assimilation and soil organic matter (SOM) degradation by 16S-rRNA-based metabarcoding. (ii) We determine the impact of root exudation level on microbial activities (denitrification and respiration) by gas chromatography. Measurement of microbial activities revealed an increase in denitrification and respiration activities for microbial communities colonizing the RAS of exploitative species. This increase of microbial activities results probably from a higher exudation rate and more diverse metabolites by exploitative plant species. Furthermore, our results demonstrate that plant nutrient resource strategies have a role in shaping active microbiota. We present evidence demonstrating that plant nutrient use strategies shape active microbiota involved in root exudate assimilation and SOM degradation via root exudation

Long-term nutrient enrichment of an oligotroph-dominated wetland increases bacterial diversity in bulk soils and plant rhizospheres.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.In nutrient-limited conditions, plants rely on rhizosphere microbial members to facilitate nutrient acquisition, and in return, plants provide carbon resources to these root-associated microorganisms. However, atmospheric nutrient deposition can affect plant-microbe relationships by changing soil bacterial composition and by reducing cooperation between microbial taxa and plants. To examine how long-term nutrient addition shapes rhizosphere community composition, we compared traits associated with bacterial (fast-growing copiotrophs, slow-growing oligotrophs) and plant (C3 forb, C4 grass) communities residing in a nutrient-poor wetland ecosystem. Results revealed that oligotrophic taxa dominated soil bacterial communities and that fertilization increased the presence of oligotrophs in bulk and rhizosphere communities. Additionally, bacterial species diversity was greatest in fertilized soils, particularly in bulk soils. Nutrient enrichment (fertilized versus unfertilized) and plant association (bulk versus rhizosphere) determined bacterial community composition; bacterial community structure associated with plant functional group (grass versus forb) was similar within treatments but differed between fertilization treatments. The core forb microbiome consisted of 602 unique taxa, and the core grass microbiome consisted of 372 unique taxa. Forb rhizospheres were enriched in potentially disease-suppressive bacterial taxa, and grass rhizospheres were enriched in bacterial taxa associated with complex carbon decomposition. Results from this study demonstrate that fertilization serves as a strong environmental filter on the soil microbiome, which leads to distinct rhizosphere communities and can shift plant effects on the rhizosphere microbiome. These taxonomic shifts within plant rhizospheres could have implications for plant health and ecosystem functions associated with carbon and nitrogen cycling.ECU Open Access Publishing Support Fun

Feed Your Friends: Do Plant Exudates Shape the Root Microbiome?

Plant health in natural environments depends on interactions with complex and dynamic communities comprising macro- and microorganisms. While many studies have provided insights into the composition of rhizosphere microbiomes (rhizobiomes), little is known about whether plants shape their rhizobiomes. Here, we discuss physiological factors of plants that may govern plant-microbe interactions, focusing on root physiology and the role of root exudates. Given that only a few plant transport proteins are known to be involved in root metabolite export, we suggest novel families putatively involved in this process. Finally, building off of the features discussed in this review, and in analogy to well-known symbioses, we elaborate on a possible sequence of events governing rhizobiome assembly

Impact des exsudats racinaires dans la sélection des taxa et fonctions bactériens dans la rhizosphère

[...] Nous avons mis en oeuvre l approche ADN-SIP au laboratoire en utilisant une macromolécule (la cellulose), ce qui nous a permis d identifier les communautés bactériennes impliquées dans la cellulolyse dans le sol au cours du temps. Ensuite, nous avons étudié l impact des exsudats racinaires dans la structuration des communautés bactériennes au niveau de la rhizosphère. Nous avons déterminé la capacité de quatre espèces végétales à sélectionner des populations bactériennes à partir du même réservoir. Nous avons montré que la racine constituait l habitat le plus sélectif du fait que chacune des plantes : blé, maïs, colza et Medicago truncatula était colonisée spécifiquement par certaines rhizobactéries comparée au sol rhizosphérique où les communautés bactériennes ne sont pas très différentes entre plantes. Nous avons également mis en évidence un fort impact de la plante sur la dégradation de la matière organique du sol dans la rhizosphère. Nous avons également étudié la dynamique et l évolution de la structure des communautés bactériennes dans la rhizosphére d A. thaliana en combinant les deux approches ADN- et ARN-SIP. Nous avonss montré un shift des populations bactériennes au niveau du sol rhizosphérique pour des plantules âgées de six semaines probablement en relation avec une initiation de la floraison conduisant à une modification quantitative et qualitative des exsudats racinaires. Cependant, les bactéries colonisant les racines n ont pas été déplacées par de nouveaux colonisateurs. Nous avons mis au point l ARNm-SIP pour déterminer l impact des exsudats racinaires sur l expression de gènes : phlD (phytoprotection), gacA (régulateur de la production de métabolites secondaire), acdS (phytostimulation) et nosZ (cycle de l azote) dans la rhizosphère. [...][...] We first of all, performed DNA-SIP using a 13C labelled macromolecule, the cellulose in order to identify bacterial community involved in cellulose degradation in soil over time. We also examined the ability of different plant species to select different taxa and functions from the same reservoir. We determined which carbon source was used and by which bacterial group in the rhizosphere of four plant species using stable isotope probing technique. To do this, we growth wheat, maize, rape and Medicago truncatula, separately in the same soil under 13CO2 (99% of atom 13C). This study revealed that root compartment was the most selective habitat as the bacterial community inhabiting the roots of wheat, rape, maize and Medicago truncatula were specific for each plant compared to the rhizosphere soil, where bacterial community were not very different between plants. We also demonstrated that plant exert a high impact on soil organic matter turnover in the rhizosphere. The last study was devoted to the analysis of the structure and the dynamic of bacterial community using DNA- and RNA-SIP in the rhizosphere of Arabidopsis thaliana and to set up mRNA-SIP technic to analyse bacterial gene expression in the rhizosphere. The combination of rDNA- and rRNA-SIP in the rhizosphere of A. thaliana over time revealed an evolution of bacterial populations especially in the rhizosphere soil probably in relation to plant stage development leading to a modification of root exudates nature, whereas root colonizing bacteria seemed well established and were not delocalized by new colonizers. The development of mRNA-SIP allowed us to analyze the expression of certain genes in the rhizosphere of A. thaliana. [...]AIX-MARSEILLE2-BU Sci.Luminy (130552106) / SudocSudocFranceF

Application of stable isotope probing (DNA-SIP) in the identification of cellulolytic soil bacteria and fungi

International audienceCellulose is the most abundant organic polymer on the earth, and represents a huge source of energy for microorganisms. The ability to degrade cellulose is widespread among fungi and bacteria and can take place under aerobic and anaerobic conditions. Microbial degradation of cellulose is characterized by the biosynthesis of multicomponent enzymes, which can be divided into three classes: endoglucanases,exoglucanases and cellobiases. Traditionally, studies of cellulolytic microbes have focused on microorganisms that grow well under laboratory conditions, by using different media containing cellulose from divers origins. However, the major fraction of environmental microorganisms cannot yet be cultured. Recently, a worldwide scientific effort made available several cultivation-independent techniques to classify and understand microbial communities at the molecular level. Among these techniques, stable isotope probing (SIP) approach has been developed to identify functional groups of microbes directly within communities of uncultured microbes. SIP has especially been applied to identify cellulolytic bacteria through the amendment of bacterial 13C- cellulose in soil samples incubated under anaerobic and mesophilic conditions. This approach simultaneously yields information about which microbial populations are present and which members are degrading 13C- cellulose and assimilating derived compounds. Total DNA was extracted from the soil at different incubation periods, and the 13C-enriched DNA from cells that had incorporated 13C derived from labeled cellulose, was separated from unlabelled DNA, corresponding to microbial communities not involved in cellulose degradation, by ultracentrifugation. The identification of active bacterial communities was analyzed and characterized by denaturing gradient gel electrophoresis (DGGE) or by cloning sequencing. Cellulose degradation was associated with significant changes in bacterial community structure. These bacterial populations are closely related to soil bacteria known for their ability to degrade cellulose as well as uncultured bacteria and bacteria not previously known to degrade cellulose in soil. Recently, RNA-stable isotope probing (RNA-SIP) method was also applied in the identification of soil fungi involved in cellulose degradation in forest soil. In conclusion, stable isotope probing provides an important new tool for investigating members of microbial communities that are directly involved in biodegradation of cellulose in soils. The construction of metagenomic libraries from 13C-DNA or 13C-RNA fraction followed by the screening of the clones for cellulase activity will allow us to identify new cellulases having potential applications in industry

Host Plant Specific Control of 2,4-Diacetylphloroglucinol Production in the Rhizosphere

To shed light on phytobeneficial bacterial gene expression in situ, we investigated the expression of phlD gene involved in 2,4-diacetylphloroglucinol production. For that purpose, stable isotope probing (SIP) of DNA and mRNA approaches were used. Arabidopsis thaliana seedlings were grown under 13CO2 for 27 days, and the presence and expression of phlD gene was determined in the rhizosphere soil and on the roots of A. thaliana. Results showed that phlD was present and expressed by bacteria inhabiting rhizosphere soil and deriving nutrients from the breakdown of organic matter and from root exudates, whereas phlD gene expression seemed to be repressed on roots. These data were validated in vitro by inoculating four plant species by the phytobeneficial bacterium Pseudomonas brassicacearum. phlD gene expression was highly activated by root exudates of wheat and that of Medicago truncatula and to a lesser extent by that of Brassica napus while it was completely suppressed by root exudates of A. thaliana. Overall, these results lead us to the conclusion that the signals to down regulate phl gene expression may derive from A. thaliana root exudates

Couplages isotopes stables outils moléculaires en écologie microbienne

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Plant host habitat and root exudates shape fungal diversity

The rhizospheric microbiome is clearly affected by plant species and certain of their functional traits. These functional traits allow plants to adapt to their environmental conditions by acquiring or conserving nutrients, thus defining different ecological resource-use plant strategies. In the present study, we investigated whether plants with one of the two nutrient-use strategies (conservative versus exploitative) could influence fungal communities involved in soil organic matter degradation and root exudate assimilation, as well as those colonizing root tissues. We applied a DNA-based, stable-isotope probing (DNA-SIP) approach to four grass species distributed along a gradient of plant nutrient resource strategies, ranging from conservative to exploitative species, and analyzed their associated mycobiota composition using a fungal internal transcribed spacer (ITS) and Glomeromycotina 18S rRNA gene metabarcoding approach. Our results demonstrated that fungal taxa associated with exploitative and conservative plants could be separated into two general categories according to their location: generalists, which are broadly distributed among plants from each strategy and represent the core mycobiota of soil organic matter degraders, root exudate consumers in the root-adhering soil, and root colonizers; and specialists, which are locally abundant in one species and more specifically involved in soil organic matter degradation or root exudate assimilation on the root-adhering soil and the root tissues. Interestingly, for arbuscular mycorrhizal fungi analysis, all plant roots were mainly colonized by Glomus species, whereas an increased diversity of Glomeromycotina genera was observed for the exploitative plant species Dactylis glomerata