Plant-Microbe Symbiosis
197.2K views | +43 today
 
Scooped by Jean-Michel Ané
onto Plant-Microbe Symbiosis
Scoop.it!

Key microbial taxa in the rhizosphere of sorghum and sunflower grown in crop rotation

Key microbial taxa in the rhizosphere of sorghum and sunflower grown in crop rotation | Plant-Microbe Symbiosis | Scoop.it
Microbes are key determinants of plant health and productivity. Previous studies have characterized the rhizosphere microbiomes of numerous plant species, but little information is available on how rhizosphere microbial communities change over time under crop rotation systems. Here, we document microbial communities in the rhizosphere of sorghum and sunflower (at seedling, flowering and senescence stages) grown in crop rotation in four different soils under field conditions. A comprehensive 16S rRNA-based amplicon sequencing survey revealed that the differences in alpha-diversity between rhizosphere and bulk soils changed over time. Sorghum rhizosphere soil microbial diversity at flowering and senescence were more diverse than bulk soils, whereas the microbial diversity of sunflower rhizosphere soils at flowering were less diverse with respect to bulk soils. Sampling time was also important in explaining the variation in microbial community composition in soils grown with both crops. Temporal changes observed in the rhizosphere microbiome were both plant-driven and due to seasonal changes in the bulk soil biota. Several individual taxa were relatively more abundant in the rhizosphere and/or found to be important in maintaining rhizosphere microbial networks. Interestingly, some of these taxa showed similar patterns at different sampling times, suggesting that the same organisms may play the same functional/structural role at different plant growth stages and in different crops. Overall, we have identified prominent microbial taxa that might be used to develop microbiome-based strategies for improving the yield and productivity of sorghum and sunflower.

more...
No comment yet.
Plant-Microbe Symbiosis
Beneficial associations between plants and microbes
Your new post is loading...
Your new post is loading...
Rescooped by Jean-Michel Ané from Plant roots and rhizosphere
Scoop.it!

Genome-Wide Association Studies Reveal Genomic Regions Associated With the Response of Wheat (Triticum aestivum L.) to Mycorrhizae Under Drought Stress Conditions 

Genome-Wide Association Studies Reveal Genomic Regions Associated With the Response of Wheat (Triticum aestivum L.) to Mycorrhizae Under Drought Stress Conditions  | Plant-Microbe Symbiosis | Scoop.it
In the majority of wheat growing areas worldwide, the incidence of drought stress has increased significantly resulting in a negative impact on plant development and grain yield. Arbuscular mycorrhizal symbiosis is known to improve drought stress tolerance of wheat. However, quantitative trait loci (QTL) involved in the response to drought stress conditions in the presence of mycorrhizae are largely unknown. Therefore, a diverse set consisting of 94 bread wheat genotypes was phenotyped under drought stress and well watered conditions in the presence and absence of mycorrhizae. Grain yield and yield components, drought stress related traits as well as response to mycorrhizae were assessed. In parallel, wheat accessions were genotyped by using the 90k iSelect chip, resulting in a set of 15511 polymorphic and mapped SNP markers, which were used for genome-wide association studies (GWAS). In general, drought stress tolerance of wheat was significantly increased in the presence of mycorrhizae compared to drought stress tolerance in the absence of mycorrhizae. However, genotypes differed in their response to mycorrhizae under drought stress conditions. Several QTL regions on different chromosomes were detected associated with grain yield and yield components under drought stress conditions. Furthermore, two genome regions on chromosomes 3D and 7D were found to be significantly associated with the response to mycorrhizae under drought stress conditions. Overall, the results reveal that inoculation of wheat with mycorrhizal fungi significantly improves drought stress tolerance and that QTL regions associated with the response to mycorrhizae under drought stress conditions exist in wheat. Further research is necessary to validate detected QTL regions. However, this study may be the starting point for the identification of candidate genes associated with drought stress tolerance and response to mycorrhizae under drought stress conditions. Maybe in future, these initial results will help to contribute to use mycorrhizal fungi effectively in agriculture and combine new approaches i.e., use of genotypic variation in response to mycorrhizae under drought stress conditions with existing drought tolerance breeding programs to develop new drought stress tolerant genotypes.

Via Christophe Jacquet
more...
No comment yet.
Rescooped by Jean-Michel Ané from Plant immunity and legume symbiosis
Scoop.it!

Genes controlling legume nodule numbers affect phenotypic plasticity responses to nitrogen in the presence and absence of rhizobia 

Genes controlling legume nodule numbers affect phenotypic plasticity responses to nitrogen in the presence and absence of rhizobia  | Plant-Microbe Symbiosis | Scoop.it
We investigated the role of three autoregulation of nodulation (AON) genes in regulating of root and shoot phenotypes when responding to changing nitrogen availability in the model legume, Medicago truncatula. These genes, RDN1‐1 (ROOT DETERMINED NODULATION1‐1), SUNN (SUPER NUMERIC NODULES), and LSS (LIKE SUNN SUPERNODULAOR), act in a systemic signalling pathway that limits nodule numbers. This pathway is also influenced by nitrogen availability, but it is not well known if AON genes control root and shoot phenotypes other than nodule numbers in response to nitrogen. We conducted a controlled glasshouse experiment to compare root and shoot phenotypes of mutants and wild type plants treated with four nitrate concentrations. All AON mutants showed altered rhizobia‐independent phenotypes, including biomass allocation, lateral root length, lateral root density, and root length ratio. In response to nitrogen, uninoculated AON mutants were less plastic than the wild type in controlling root mass ratio, root length ratio, and lateral root length. This suggests that AON genes control nodulation‐independent root architecture phenotypes in response to nitrogen. The phenotypic differences between wild type and AON mutants were exacerbated by the presence of nodules, pointing to resource competition as an additional mechanism affecting root and shoot responses to nitrogen.

Via Christophe Jacquet
more...
No comment yet.
Rescooped by Jean-Michel Ané from LRSV Publications
Scoop.it!

Comparative genomics of Rhizophagus irregularis, R. cerebriforme, R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina2

Comparative genomics of Rhizophagus irregularis, R. cerebriforme, R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina2 | Plant-Microbe Symbiosis | Scoop.it

 Glomeromycotina is a lineage of early diverging Fungi establishing arbuscular mycorrhizal (AM) symbiosis with land plants. Despite their major ecological role, genetic bases of their obligate mutualism are largely unknown, hindering our understanding of their evolution and biology.

• We compared the genomes of Glomerales (Rhizophagus irregularis, Rhizophagus diaphanus, Rhizophagus cerebriforme) and Diversisporales (Gigaspora rosea)species, together with those of saprotrophic Mucoromycota, to identify gene families and processes associated with these lineages and to understand the molecular underpinning of their symbiotic lifestyle.

• Genomic features in Glomeromycotina appear to be very similar with a very high content in transposons and protein‐coding genes, extensive duplications of protein kinase genes, and loss of genes coding for lignocellulose degradation, thiamin biosynthesis and cytosolic fatty acid synthase. Most symbiosis‐related genes in R. irregularis and G. rosea are specific to Glomeromycotina. We also confirmed that the present species have a homokaryotic genome organization.

• The high interspecific diversity of Glomeromycotina gene repertoires, affecting all known protein domains, as well as symbiosis‐related orphan genes, may explain the known adaptation of Glomeromycotina to a wide range of environmental settings. Our findings contribute to an increasingly detailed portrait of genomic features defining the biology of AM fungi.


Via LRSV
more...
No comment yet.
Scooped by Jean-Michel Ané
Scoop.it!

Lotus Shaggy‐like Kinase 1 is required to suppress nodulation in Lotus japonicus

Glycogen Synthase Kinase/Shaggy‐like kinases (SKs) are a highly conserved family of signaling proteins that participate in many developmental, cell‐differentiation, and metabolic signaling pathways in plants and animals. Here, we investigate the involvement of SKs in legume nodulation, a process requiring integration of multiple signaling pathways. We describe a group of SKs in the model legume Lotus japonicus (LSKs), two of which respond to inoculation with the symbiotic nitrogen‐fixing bacterium Mesorhizobium loti. RNAi‐knockdown plants and an insertion‐mutant for one of these genes, LSK1, display increased nodulation. Ηairy root lines overexpressing LSK1 form only marginally fewer mature nodules compared to controls. The expression levels of genes involved in auto‐regulation of nodulation (AON) mechanism are affected in LSK1 knockdown plants, both at early and late stages of nodulation at low nitrate levels. At higher levels of nitrate, these same plants show the opposite expression pattern of AON‐related genes and lose the hypernodulation phenotype. Our findings reveal an additional role for the versatile Shaggy‐like kinase gene family in integrating the signaling pathways governing legume nodulation and pave the way for further study of their functions in legumes.

more...
No comment yet.
Scooped by Jean-Michel Ané
Scoop.it!

Contemporaneous radiations of fungi and plants linked to symbiosis

Contemporaneous radiations of fungi and plants linked to symbiosis | Plant-Microbe Symbiosis | Scoop.it
Interactions between fungi and plants, including parasitism, mutualism, and saprotrophy, have been invoked as key to their respective macroevolutionary success. Here we evaluate the origins of plant-fungal symbioses and saprotrophy using a time-calibrated phylogenetic framework that reveals linked and drastic shifts in diversification rates of each kingdom. Fungal colonization of land was associated with at least two origins of terrestrial green algae and preceded embryophytes (as evidenced by losses of fungal flagellum, ca. 720 Ma), likely facilitating terrestriality through endomycorrhizal and possibly endophytic symbioses. The largest radiation of fungi (Leotiomyceta), the origin of arbuscular mycorrhizae, and the diversification of extant embryophytes occurred ca. 480 Ma. This was followed by the origin of extant lichens. Saprotrophic mushrooms diversified in the Late Paleozoic as forests of seed plants started to dominate the landscape. The subsequent diversification and explosive radiation of Agaricomycetes, and eventually of ectomycorrhizal mushrooms, were associated with the evolution of Pinaceae in the Mesozoic, and establishment of angiosperm-dominated biomes in the Cretaceous.

more...
No comment yet.
Scooped by Jean-Michel Ané
Scoop.it!

A Bacterial Endophyte from Apoplast Fluids Protects Canola Plants from Different Phytopathogens via Antibiosis and Induction of Host Resistance

A Bacterial Endophyte from Apoplast Fluids Protects Canola Plants from Different Phytopathogens via Antibiosis and Induction of Host Resistance | Plant-Microbe Symbiosis | Scoop.it
Endophytic bacteria colonize inner plant tissues and thrive at the apoplast, which is considered its main reservoir. Because this niche is the place where the main molecular events take place between beneficial and pathogenic microorganisms, the aim of this work was to characterize culturable endophytic bacteria from apoplastic fluids obtained from field-grown canola leaves and analyze their potential for biological control of diseases caused by Xanthomonas campestris, Sclerotinia sclerotiorum, and Leptosphaeria maculans. Dual-culture analysis indicated that three isolates (Apo8, Apo11, and Apo12) were able to inhibit the growth of all three phytopathogens. Sequencing of the 16S ribosomal RNA and rpoD genes of these isolates revealed that they are closely related to Pseudomonas viridiflava. One of the isolates, Apo11, was able to diminish the propagation of X. campestris in whole-plant assays. At the same time, Apo11 inoculation reduced the necrotic lesions provoked by S. sclerotiorum on canola leaves. This protective effect might be due to the induction of resistance in the host mediated by salicylic and jasmonic acid signaling pathways or the production of compounds with antimicrobial activity. At the same time, Apo11 inoculation promoted canola plant growth. Thus, the isolate characterized in this work has several desirable characteristics, which make it a potential candidate for the formulation of biotechnological products to control plant diseases or promote plant growth.

more...
No comment yet.
Scooped by Jean-Michel Ané
Scoop.it!

Temperature‐mediated phylogenetic assemblage of fungal communities and local adaptation in mycorrhizal symbioses

Recent work demonstrates that habitat conditions exert striking effects on symbiont performance by mediating trade‐offs in plants, AM fungi and environmental interactions. However, how local temperature conditions influence the functional diversity of mycorrhizal symbioses and the genetics of coexisting AM fungi at the local scale remain unclear. In the present study, we conducted a reciprocal inoculation experiment to explore the performance of sympatric associations against allopatric associations under contrasting temperatures and the AM fungal community in colonized roots. No local adaptation of plant biomass was found under both temperature conditions investigated, but a consistent local versus foreign effect was found in AM fungal performance. The temperature and the origin of the inoculum relative to the plant origin were important in explaining symbiotic function. Correspondingly, the community structure and Nearest Relatedness Index of the AM fungal community of the root symbiont varied with inoculum source, and assemblages with more closely related taxa led to a decline in plant biomass and stronger disequilibrium among AM fungi in roots. Our findings suggest that functional divergence exists in naturally coexisting communities of AM fungi from contrasting climatic origins, and fungal relatedness is an important driver of plant growth.

more...
No comment yet.
Scooped by Jean-Michel Ané
Scoop.it!

Field efficacy of different combinations of Trichoderma harzianum, Pseudomonas fluorescens, and arbuscular mycorrhiza fungus against the major diseases of tomato in Uttarakhand (India)

Tomato is one of the major cash crops in the Golapar area of district Nainital in Uttarakhand (India), where farmers are facing the problem of diseases in tomato cultivation. In the present investigation, a survey of tomato fields in the Golapar area of Haldwani block was conducted. The survey revealed the occurrence of late blight, early blight, stem rot, and wilt diseases causing an average loss of 80% to tomato. To counter the above diseases, Trichoderma harzianum (Th43), Pseudomonas fluorescens (Pf173), Jas mycorrhiza (AMF), and the fungicide (Mancozeb) in different combinations applyed through soil application (SA), seedling treatment (ST), and foliar spray (FA) were evaluated for growth promotion and disease control in tomato at experimental and farmers’ fields. The results of the study revealed that in experimental field, the maximum plant height (43.67 cm), highest number of branches (7.33) per plant, highest weight of fruit (47 g), highest number of fruits (39) per plant, minimum plant mortality (4% at 30 DAT and 3.2% at 30–60 DAT), minimum plant disease index (6.85), maximum total yield (256.00 q/ha), and marketable yield (246.67 q/ha) were observed in Th+Pf+JM (SA) + Th+Pf (ST) + Mancozeb (FS). At farmer’s field, minimum plant mortality (7.31%) at 30 days after transplanting (DAT) (5.73%) in 30–60 DAT, minimum plant disease index (11.47), and maximum yield 249.91 q/ha were observed in Th+Pf+JM (SA) + Th+Pf (ST) + Mancozeb (FS) combination. So, it can be concluded that among all the treatments, integrated treatment comprising of soil application of T. harzianum, P. fluorescens, Jas mycorrhiza (AMF) + seedling treatment with T. harzianum and P. fluorescens + three foliar sprays of Mancozeb was found very effective in reducing the plant mortality, promoting the plant growth, and increasing the yield at experimental field as well as at farmers’ fields.

more...
No comment yet.
Scooped by Jean-Michel Ané
Scoop.it!

Interaction and Regulation of Carbon, Nitrogen, and Phosphorus Metabolisms in Root Nodules of Legumes

Interaction and Regulation of Carbon, Nitrogen, and Phosphorus Metabolisms in Root Nodules of Legumes | Plant-Microbe Symbiosis | Scoop.it
Members of the plant family Leguminosae (Fabaceae) are unique in that they have evolved a symbiotic relationship with rhizobia (a group of soil bacteria that can fix atmospheric nitrogen). Rhizobia infect and form root nodules on their specific host plants before differentiating into bacteroids, the symbiotic form of rhizobia. This complex relationship involves the supply of C4-dicarboxylate and phosphate by the host plants to the microsymbionts that utilize them in the energy-intensive process of fixing atmospheric nitrogen into ammonium, which is in turn made available to the host plants as a source of nitrogen, a macronutrient for growth. Although nitrogen-fixing bacteroids are no longer growing, they are metabolically active. The symbiotic process is complex and tightly regulated by both the host plants and the bacteroids. The metabolic pathways of carbon, nitrogen, and phosphate are heavily regulated in the host plants, as they need to strike a fine balance between satisfying their own needs as well as those of the microsymbionts. A network of transporters for the various metabolites are responsible for the trafficking of these essential molecules between the two partners through the symbiosome membrane (plant-derived membrane surrounding the bacteroid), and these are in turn regulated by various transcription factors that control their expressions under different environmental conditions. Understanding this complex process of symbiotic nitrogen fixation is vital in promoting sustainable agriculture and enhancing soil fertility.

more...
No comment yet.
Scooped by Jean-Michel Ané
Scoop.it!

Acclimatization of Rhizophagus irregularis Enhances Zn Tolerance of the Fungus and the Mycorrhizal Plant Partner

Acclimatization of Rhizophagus irregularis Enhances Zn Tolerance of the Fungus and the Mycorrhizal Plant Partner | Plant-Microbe Symbiosis | Scoop.it
Arbuscular mycorrhizal (AM) fungi confer heavy metal tolerance to plants, but this characteristic differs between different AM fungal strains. We tested the hypotheses if acclimatization of an AM fungus to Zn stress is possible and if this leads also to higher Zn tolerance of mycorrhizal plants. The AM fungus Rhizophagus irregularis was acclimatized in root organ cultures (Daucus carota L.) to Zn resulting in an acclimatized (Acc+) strain. The non-acclimatized (Acc-) strain remained untreated. Fungal development and RNA accumulation of a set of stress-related genes were analyzed in root organ cultures and the capacity of conferring Zn tolerance to maize plants was investigated in pot cultures. Development of Acc+ strain was significantly higher than Acc- strain, when strains were grown in Zn-enriched root organ cultures, whereas the growth of the Acc+ strain was reduced on normal medium probably due to a higher Zn demand compared to the Acc- strain. RNA accumulation analyses revealed different expression patterns of genes encoding glutathione S-transferase (RiGST), superoxide dismutase (RiSOD) and glutaredoxin (RiGRX) between the two strains. Plants inoculated with the Acc+ strain showed higher biomass and lower Zn content than those inoculated with the Acc- strain. The results showed that R. irregularis can be acclimatized to increased amounts of Zn. This acclimatization leads not only to improved fungal development in Zn-stress conditions, but also to an increase of mycorrhiza-induced Zn tolerance of colonized plants.

Jean-Michel Ané's insight:

Acclimatization of the fungus... interesting idea

more...
No comment yet.
Scooped by Jean-Michel Ané
Scoop.it!

Modeling the Role of the Microbiome in Evolution

Modeling the Role of the Microbiome in Evolution | Plant-Microbe Symbiosis | Scoop.it
There is undeniable evidence showing that bacteria have strongly influenced the evolution and biological functions of multicellular organisms. It has been hypothesized that many host-microbial interactions have emerged so as to increase the adaptive fitness of the holobiont (the host plus its microbiota). Although this association has been corroborated for many specific cases, general mechanisms explaining the role of the microbiota in the evolution of the host are yet to be understood. Here we present an evolutionary model in which a network representing the host adapts in order to perform a predefined function. During its adaptation, the host network (HN) can interact with other networks representing its microbiota. We show that this interaction greatly accelerates and improves the adaptability of the HN without decreasing the adaptation of the microbial networks. Furthermore, the adaptation of the HN to perform several functions is possible only when it interacts with many different bacterial networks in a specialized way (each bacterial network participating in the adaptation of one function). Disrupting these interactions often leads to non-adaptive states, reminiscent of dysbiosis, where none of the networks the holobiont consists of can perform their respective functions. By considering the holobiont as a unit of selection and focusing on the adaptation of the host to predefined but arbitrary functions, our model predicts the need for specialized diversity in the microbiota. This structural and dynamical complexity in the holobiont facilitates its adaptation, whereas a homogeneous (non-specialized) microbiota is inconsequential or even detrimental to the holobiont's evolution. To our knowledge, this is the first model in which symbiotic interactions, diversity, specialization and dysbiosis in an ecosystem emerge as a result of coevolution. It also helps us understand the emergence of complex organisms, as they adapt more easily to perform multiple tasks than non-complex ones.

more...
No comment yet.
Scooped by Jean-Michel Ané
Scoop.it!

The Role of Host Genetic Signatures on Root–Microbe Interactions in the Rhizosphere and Endosphere

Microbiomes inhabiting plants are crucial for plant productivity and well-being. A plethora of interactions between roots, microbiomes, and soil shapes the self-organization of the microbial community associated with the root system. The rhizosphere (i.e., the soil close to the root surface) and endosphere (i.e., all inner root tissues) are critical interfaces for the exchange of resources between roots and the soil environment. In recent years, next-generation sequencing technologies have enabled systemic studies of root-associated microbiomes in the endosphere and interactions between roots and microbes at the root-soil interfaces. Genetic factors such as species and genotype of host plants are the driving force of microbial community differentiation and composition. In this mini-review, we will survey the role of these factors on plant–microbe interactions by highlighting the results of next-generation genomic and transcriptomic studies in the rhizosphere and endosphere of land plants. Moreover, environmental factors such as geography and soil type shape the microbiome. Relationships between the root-associated microbiome, architectural variations and functional switches within the root system determine the health and fitness of the whole plant system. A detailed understanding of plant–microbe interactions is of fundamental agricultural importance and significance for crop improvement by plant breeding.

more...
No comment yet.
Scooped by Jean-Michel Ané
Scoop.it!

Diverse Sorghum bicolor accessions show marked variation in growth and transcriptional responses to arbuscular mycorrhizal fungi

Sorghum is an important crop grown world‐wide for feed and fibre. Like most plants, it has the capacity to benefit from symbioses with arbuscular mycorrhizal (AM) fungi and its diverse genotypes likely vary in their responses. Currently, the genetic basis of mycorrhiza‐responsiveness is largely unknown. Here we investigated transcriptional and physiological responses of sorghum accessions, founders of a bioenergy nested association mapping panel, for their responses to four species of AM fungi. Transcriptome comparisons across four accessions identified mycorrhiza‐inducible genes; stringent filtering criteria revealed 278 genes that show mycorrhiza‐inducible expression independent of genotype and 55 genes whose expression varies with genotype. The latter suggests variation in phosphate transport and defence across these accessions. The mycorrhiza growth and nutrient responses of eighteen sorghum accessions varied tremendously, ranging from mycorrhiza‐dependent to negatively mycorrhiza‐responsive. Additionally, accessions varied in the number of AM fungi to which they showed positive responses; from one to several fungal species. Mycorrhiza growth and phosphorus responses were positively correlated, while expression of two mycorrhiza‐inducible phosphate transporters, SbPT8 and SbPT9, correlated negatively with mycorrhizal growth responses. AM fungi improve growth and mineral nutrition of sorghum and the substantial variation between lines provides the potential to map loci influencing mycorrhiza responses.

more...
No comment yet.
Rescooped by Jean-Michel Ané from Plant roots and rhizosphere
Scoop.it!

Simultaneously maximizing root/mycorrhizal growth and phosphorus uptake by cotton plants by optimizing water and phosphorus management 

Simultaneously maximizing root/mycorrhizal growth and phosphorus uptake by cotton plants by optimizing water and phosphorus management  | Plant-Microbe Symbiosis | Scoop.it
Background

There are two plant phosphorus (P)-uptake pathways, namely the direct P uptake by roots and the indirect P uptake through arbuscular mycorrhizal fungi (AMF). Maximizing the efficiency of root and AMF processes associated with P acquisition by adjusting soil conditions is important for simultaneously ensuring high yields and the efficient use of available P.
Results

A root box experiment was conducted in 2015 and 2016. The aim was to investigate the effects of different P and soil water conditions on root/mycorrhizal growth and P uptake by cotton plants. Hyphal growth was induced in well-watered soil, but decreased with increasing P concentrations. Additionally, P fertilizers regulated root length only under well-watered conditions, with the longest roots observed in response to 0.2 g P2O5 kg− 1. In contrast, root elongation was essentially unaffected by P fertilizers under drought conditions. And soil water in general had more significant effects on root and hyphal growth than phosphorus levels. In well-watered soil, the application of P significantly increased the cotton plant P uptake, but there were no differences between the effects of 0.2 and 1 g P2O5 kg− 1. So optimizing phosphorus inputs and soil water can increase cotton growth and phosphorus uptake by maximizing the efficiency of phosphorus acquisition by roots/mycorrhizae.
Conclusions

Soil water and P contents of 19–24% and 20–25 mg kg− 1, respectively, simultaneously maximized root/mycorrhizal growth and P uptake by cotton plants.

Via Christophe Jacquet
more...
No comment yet.
Scooped by Jean-Michel Ané
Scoop.it!

FlowPot axenic plant growth system for microbiota research

The presence of resident microbiota on and inside plants is hypothesized to influence many phenotypic attributes of the host. Likewise, host factors and microbe-microbe interactions are believed to influence microbial community assembly. Rigorous testing of these hypotheses necessitates the ability to grow plants in the absence or presence of resident or defined microbiota. To enable such experiments, we developed the scalable and inexpensive FlowPot growth platform. FlowPots have a sterile peat substrate amenable to colonization by microbiota, and the platform supports growth of the model plant Arabidopsis thaliana in the absence or presence of soil-derived microbial communities. Mechanically, the FlowPot system is unique in that it allows for total-saturation of the sterile substrate by flushing with water and/or nutrient solution via an irrigation port. The irrigation port also facilitates passive drainage of the substrate, preventing root anoxia. Materials to construct an individual FlowPot total ~$2. A simple experiment with 12 FlowPots requires ~4.5 h of labor following peat and seed sterilization. Plants are grown on FlowPots within a standard tissue culture microbox after inoculation, thus the Flowpot system is modular and does not require a sterile growth chamber. Here, we provide a detailed assembly and microbiota inoculation protocol for the FlowPot system. Collectively, this standardized suite of tools and colonization protocols empowers the plant microbiome research community to conduct harmonized experiments to elucidate the rules microbial community assembly, the impact of microbiota on host phenotypes, and mechanisms by which host factors influence the structure and function of plant microbiota.

more...
No comment yet.
Scooped by Jean-Michel Ané
Scoop.it!

Legumes—The art and science of environmentally sustainable agriculture

Symbiotic nitrogen fixation, which is carried out by the legume‐rhizobia partnership, is a major source of nitrogen acquisition in natural ecosystems and in agriculture. The benefits to the plant gained through the rhizobial‐legume symbiosis can be further enhanced by associations of the legume with arbuscular mycorrhiza. The progressive engagement of the legume host with the rhizobial bacteria and mycorrhizal fungi requires an extensive exchange of signalling molecules. These signals alter the transcriptional profiles of the partners, guiding and enabling extensive microbial and fungal proliferation in the roots. Such interactions and associations are greatly influenced by environmental stresses, which also severely limit the productivity of legume crops. Part II of the Special Issue on Legumes provides new insights into the mechanisms that underpin sustainable symbiotic partnerships, as well as the effects of abiotic stresses, such as drought, waterlogging, and salinity on legume biology. The requirement for germplasm and new breeding methods is discussed as well as the future of legume production in the face of climate change.

more...
No comment yet.
Scooped by Jean-Michel Ané
Scoop.it!

InnB, a Novel Type III Effector of Bradyrhizobium elkanii USDA61, Controls Symbiosis With Vigna Species

InnB, a Novel Type III Effector of Bradyrhizobium elkanii USDA61, Controls Symbiosis With Vigna Species | Plant-Microbe Symbiosis | Scoop.it
Bradyrhizobium elkanii USDA61 is incompatible with mung bean (Vigna radiata cv. KPS1) and soybean (Glycine max cv. BARC2) and unable to nodulate either plant. This incompatibility is due to the presence of a functional type III secretion system (T3SS) that translocates effector protein into host cells. We previously identified five genes in B. elkanii that are responsible for its incompatibility with KPS1 plants. Among them, a novel gene designated as innB exhibited some characteristics associated with the T3SS and was found to be responsible for the restriction of nodulation on KPS1. In the present study, we further characterized innB by analysis of gene expression, protein secretion, and symbiotic phenotypes. The innB gene was found to encode a hypothetical protein that is highly conserved among T3SS-harboring rhizobia. Similar to other rhizobial T3SS-associated genes, the expression of innB was dependent on plant flavonoids and a transcriptional regulator TtsI. The InnB protein was secreted via the T3SS and was not essential for secretion of other nodulation outer proteins. In addition, T3SS-dependent translocation of InnB into nodule cells was confirmed by an adenylate cyclase assay. According to inoculation tests using several Vigna species, InnB promoted nodulation of at least one V. mungo cultivar. These results indicate that innB encodes a novel type III effector controlling symbiosis with Vigna species.
more...
No comment yet.
Scooped by Jean-Michel Ané
Scoop.it!

Plant health: feedback effect of root exudates-rhizobiome interactions

Plant health: feedback effect of root exudates-rhizobiome interactions | Plant-Microbe Symbiosis | Scoop.it
The well-being of the microbial community that densely populates the rhizosphere is aided by a plant’s root exudates. Maintaining a plant’s health is a key factor in its continued existence. As minute as rhizospheric microbes are, their importance in plant growth cannot be overemphasized. They depend on plants for nutrients and other necessary requirements. The relationship between the rhizosphere-microbiome (rhizobiome) and plant hosts can be beneficial, non-effectual, or pathogenic depending on the microbes and the plant involved. This relationship, to a large extent, determines the fate of the host plant’s survival. Modern molecular techniques have been used to unravel rhizobiome species’ composition, but the interplay between the rhizobiome root exudates and other factors in the maintenance of a healthy plant have not as yet been thoroughly investigated. Many functional proteins are activated in plants upon contact with external factors. These proteins may elicit growth promoting or growth suppressing responses from the plants. To optimize the growth and productivity of host plants, rhizobiome microbial diversity and modulatory techniques need to be clearly understood for improved plant health.

more...
No comment yet.
Scooped by Jean-Michel Ané
Scoop.it!

Evolution of substrate specificity and fungal symbiosis in filmy ferns (Hymenophyllaceae): a Bayesian approach for ambiguous character state reconstruction

Ferns, as landplants in general, originally form a symbiosis involving Arbuscular Mycorrhizal Fungi (AMF), which are prevalent in habitats directly connected to the soil, including low epiphytic sites, but are largely absent in the high epiphytic habitat. High probabilities of AMF should be expected in chiefly terrestrial lineages whereas truly, fully adapted epiphytic lineages should be lacking fungal endophytes or may have switched to other types of fungi; e.g. Dark Septate Endophytes (DSE), a morphological class of mostly unspecified fungi that is often found in epiphytic ferns and may include potentially symbiotic ascomycetes. We used a Bayesian approach for a comparison of the ambiguous character of preferred substrate with the incompletely known mycorrhization status for an ancient lineage of ferns, the Hymenophyllaceae or filmy ferns. The majority of the analysed 167 species prefers either the saxicolous, terrestrial or epiphytic habitat (differentiated into low and high epiphytic), but there are also many generalists without clear preference. For the whole family Hymenophyllaceae and one of the two main clades of the subfamily Trichomanoidae, the terrestrial habitat and AMF received the highest probability for representing the ancestral state. For the subfamily Hymenophylloidae, the low epiphytic habitat and DSE received the highest probability as ancestral state, whereas that for AMF was very low. The other main clade of the subfamily Trichomanoidae as well as the whole subfamily was found most likely to be originally terrestrial; but in both cases the probability values did not differ much from the values for low epiphytism, with all values around 50 ± 5%. The high epiphytic habitat, which in its present condition is thought to be possible only in angiosperm-dominated vegetation, did not receive high probability to be the ancestral state in any clade. This decouples the evolution of epiphytism in filmy ferns in time from the advent of the angiosperms, which is hypothesized to have triggered the radiation of all other major epiphytic fern lineages.

more...
No comment yet.
Scooped by Jean-Michel Ané
Scoop.it!

Agroecological coffee management increases arbuscular mycorrhizal fungi diversity

Agroecological coffee management increases arbuscular mycorrhizal fungi diversity | Plant-Microbe Symbiosis | Scoop.it
Agroecology aims to maintain ecosystem services by minimizing the impact of agriculture and promoting the use of biological potential. Arbuscular mycorrhizal fungi (AMF) are elements which are key to improving crop productivity and soil quality. It is pertinent to understand how agricultural management in the tropics affects the AMF spatio-temporal community composition, especially in crops of global importance, such as coffee (Coffea arabica L.). Soil and root samples were collected from three localities under three management systems (agroecological, conventional and forest fragment), during the phenological stages of coffee (flowering, grain filling, harvesting). Spores were extracted for morphological identification and molecular community analysis by PCR–DGGE. Dendrograms were prepared and the bands were sequenced and analyzed by bioinformatics. No differences were observed in the richness of morphospecies between management systems, localities and period, but little is known about tropical species. Molecular analysis showed that the agroecological management system was similar to natural forest and with a higher diversity indices than conventional management. Locality and period of sample affect AMF community composition. It is necessary to associate classical taxonomic evaluations with molecular biological techniques because different approaches can lead to different outcomes. This study contributes to the understanding of the impact of agriculture management systems on AMF and provides evidence that agroecology is a management system applicable to sustainable coffee production.

more...
No comment yet.
Scooped by Jean-Michel Ané
Scoop.it!

Plant-mediated partner discrimination in ectomycorrhizal mutualisms

Although ectomycorrhizal fungi have well-recognized effects on ecological processes ranging from plant community dynamics to carbon cycling rates, it is unclear if plants are able to actively influence the structure of these fungal communities. To address this knowledge gap, we performed two complementary experiments to determine (1) whether ectomycorrhizal plants can discriminate among potential fungal partners, and (2) to what extent the plants might reward better mutualists. In experiment 1, split-root Larix occidentalis seedlings were inoculated with spores from three Suillus species (S. clintonianus, S. grisellus, and S. spectabilis). In experiment 2, we manipulated the symbiotic quality of Suillus brevipes isolates on split-root Pinus muricata seedlings by changing the nitrogen resources available, and used carbon-13 labeling to track host investment in fungi. In experiment 1, we found that hosts can discriminate in multi-species settings. The split-root seedlings inhibited colonization by S. spectabilis whenever another fungus was available, despite similar benefits from all three fungi. In experiment 2, we found that roots and fungi with greater nitrogen supplies received more plant carbon. Our results suggest that plants may be able to regulate this symbiosis at a relatively fine scale, and that this regulation can be integrated across spatially separated portions of a root system.

more...
No comment yet.
Scooped by Jean-Michel Ané
Scoop.it!

Dynamic Phosphate Uptake in Arbuscular Mycorrhizal Roots Under Field Conditions

Dynamic Phosphate Uptake in Arbuscular Mycorrhizal Roots Under Field Conditions | Plant-Microbe Symbiosis | Scoop.it
Many crops are colonized with arbuscular mycorrhizal fungi (AMF), which can efficiently absorb nutrients such as phosphate from the soil. The utilization of mycorrhizal symbioses is one of the most promising options for developing resource-saving and sustainable agricultural systems. Most laboratory studies have illustrated the roles of AM symbiosis by inoculating plants with limited AMF isolates. In the field, however, the roots of crops are co-colonized with multiple AMF species, which are difficult to separate and identify and may have different abilities regarding phosphate uptake. In addition, it is difficult to understand which AMF are functional due to the dynamics of AMF colonization processes and the largely unknown genomic structure. This review summarizes key discoveries supporting the importance of the dynamics of AM colonization and genomic structure, which potentially influence the characteristics of AM phosphate uptake. Moreover, this review aims to identify the research direction necessary to obtain a better understanding of the phosphate uptake systems of crops in the field.

more...
No comment yet.
Scooped by Jean-Michel Ané
Scoop.it!

Editorial: Molecular and Cellular Mechanisms of the Legume-Rhizobia Symbiosis

Legume-rhizobia symbiosis is a remarkable and mutually beneficial association between higher plants and microbes, which is extremely important for sustainable agriculture and ecology. During this association, biological nitrogen fixation occurs in the nodule, which is a specialized accessory legume organ, generally formed on roots. In mature nodules, rhizobia convert inert atmospheric N2 into ammonia (NH3), essential for plant growth. In return, bacteria obtain photosynthetic carbon from the plant. The biologically fixed nitrogen during symbiosis accounts for approximately 65% of nitrogen use in agriculture (Burris and Roberts, 1993).

Due to its agricultural importance and interesting biological features, the legume-rhizobia symbiosis fascinated many researchers in the past decades. It has been discovered that the legume-rhizobia symbiosis is initiated through mutual chemical communication. The plant root releases flavonoids, which induce rhizobia to produce specific lipo-chitooligosaccharides (LCOs), called nodulation factors (Nod factors, or NFs) (Dénarié et al., 1996). These NFs are specifically recognized by the host plant and trigger a sophisticated symbiotic signaling cascade in the host root cells to coordinate rhizobial infection, nodule organogenesis and later on nitrogen fixation (Oldroyd et al., 2011). The main aim of this research topic was to assemble papers addressing and discussing the fundamental science of the molecular mechanisms of legume-rhizobia symbiosis. A total of nine articles were published under this research topic related to rhizobium characters (2), plant response to different type of bacteria (1), phytohormones (3), SYM pathway signals (2), and R genes determining specificity of rhizobia infection (1).
more...
No comment yet.
Scooped by Jean-Michel Ané
Scoop.it!

Nodule bacteria from the cultured legume Phaseolus dumosus (belonging to the Phaseolus vulgaris cross-inoculation group) with common tropici phenotypic characteristics and symbiovar but distinctive...

Nodule bacteria from the cultured legume Phaseolus dumosus (belonging to the Phaseolus vulgaris cross-inoculation group) with common tropici phenotypic characteristics and symbiovar but distinctive... | Plant-Microbe Symbiosis | Scoop.it
Phaseolus dumosus is an endemic species from mountain tops in Mexico that was found in traditional agriculture areas in Veracruz, Mexico. P. dumosus plants were identified by ITS sequences and their nodules were collected from agricultural fields or from trap plant experiments in the laboratory. Bacteria from P. dumosus nodules were identified as belonging to the phaseoli-etli-leguminosarum (PEL) or to the tropici group by 16S rRNA gene sequences. We obtained complete closed genomes from two P. dumosus isolates CCGE531 and CCGE532 that were phylogenetically placed within the tropici group but with a distinctive phylogenomic position and low average nucleotide identity (ANI). CCGE531 and CCGE532 had common phenotypic characteristics with tropici type B rhizobial symbionts. Genome synteny analysis and ANI showed that P. dumosus isolates had different chromids and our analysis suggests that chromids have independently evolved in different lineages of the Rhizobium genus. Finally, we considered that P. dumosus and Phaseolus vulgaris plants belong to the same cross-inoculation group since they have conserved symbiotic affinites for rhizobia.

more...
No comment yet.
Scooped by Jean-Michel Ané
Scoop.it!

The Inherent Conflicts in Developing Soil Microbial Inoculants

The Inherent Conflicts in Developing Soil Microbial Inoculants | Plant-Microbe Symbiosis | Scoop.it
Certain soil microorganisms can perform agriculturally valuable functions such as ethylene reduction, plant pathogen suppression, and soil nutrient solubilization.

Interest and investment in developing soil microbial inoculants to enhance these functions has recently surged, but in-field product success remains unpredictable and unreliable.

Microbial inoculants tend to be chosen based on their activity in controlled laboratory screenings and for ease of mass cultivation, with minimal regard for ecologically relevant traits that will both allow them to survive in the field during a target functional period and prevent excessive persistence.

We highlight the conflicting roles of microbial inoculant traits at each product stage, and how this may complicate selection for microorganisms that function as desired in the field.
more...
No comment yet.