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Root symbionts: Powerful drivers of plant above- and belowground indirect defenses - Rasmann - 2017 -

Root symbionts: Powerful drivers of plant above- and belowground indirect defenses - Rasmann - 2017 - | Crop yield | Scoop.it
Soil microbial mutualists of plants, including mycorrhizal fungi, non-mycorrhizal fungi and plant growth promoting rhizobacteria, have been typically characterized for increasing nutrient acquisition and plant growth. More recently, soil microbes have also been shown to increase direct plant defense against above- and belowground herbivores. Plants, however, do not only rely on direct defenses when attacked, but they can also recruit pest antagonists such as predators and parasitoids, both above and belowground, mainly via the release of volatile organic compounds (i.e., indirect defenses). In this review, we illustrate the main features and effects of soil microbial mutualists of plants on plant indirect defenses and discuss possible applications within the framework of sustainable crop protection against root- and shoot-feeding arthropod pests. We indicate the main knowledge gaps and the future challenges to be addressed in the study and application of these multifaceted interactions.
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The future of CRISPR technologies in agriculture - Nature Rev (2018) 

Conventional plant breeding is unlikely to meet increasing food demands and other environmental challenges. By contrast, CRISPR technology is erasing barriers to genome editing and could revolutionize plant breeding. However, to fully benefit from the CRISPR revolution, we should focus on resolving its technical and regulatory uncertainties... 


The biggest potential pitfall for the use of CRISPR technologies in agriculture is not scientific but public acceptance and government regulation. The majority of expected uses would produce ‘nature-identical’ traits... that could also be derived by conventional plant breeding... Such uses can easily be distinguished so that nature-identical CRISPR applications would not need to be equated with genetically modified organisms. 


Despite this, confidence in applying CRISPR tools in agriculture remains limited owing to the uncertain global regulatory environment. Overcoming this will require a political willingness to establish a clear position on CRISPR technologies and striving for some form of consistency among countries... 


Providing transparency to CRISPR breeding methods... would be crucial for gaining public trust and influencing regulatory policies that are evolving to govern the use of CRISPR technologies in agriculture. What has been achieved so far with CRISPR technologies is just the tip of the iceberg. 


A sustainable future for agriculture can now be imagined using this new powerful plant breeding tool. With that comes a responsibility to continue to resolve both the scientific and public concerns regarding its usage.


http://doi.org/10.1038/nrm.2018.2



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Suppression of the activity of arbuscular mycorrhizal fungi by the soil microbiota

Suppression of the activity of arbuscular mycorrhizal fungi by the soil microbiota | Crop yield | Scoop.it
Arbuscular mycorrhizal fungi (AMF) colonise roots of most plants; their extra-radical mycelium (ERM) extends into the soil and acquires nutrients for the plant. The ERM coexists with soil microbial communities and it is unresolved whether these communities stimulate or suppress the ERM activity. This work studied the prevalence of suppressed ERM activity and identified main components behind the suppression. ERM activity was determined by quantifying ERM-mediated P uptake from radioisotope-labelled unsterile soil into plants, and compared to soil physicochemical characteristics and soil microbiome composition. ERM activity varied considerably and was greatly suppressed in 4 of 21 soils. Suppression was mitigated by soil pasteurisation and had a dominating biotic component. AMF-suppressive soils had high abundances of Acidobacteria, and other bacterial taxa being putative fungal antagonists. Suppression was also associated with low soil pH, but this effect was likely indirect, as the relative abundance of, e.g., Acidobacteria decreased after liming. Suppression could not be transferred by adding small amounts of suppressive soil to conducive soil, and thus appeared to involve the common action of several taxa. The presence of AMF antagonists resembles the phenomenon of disease-suppressive soils and implies that ecosystem services of AMF will depend strongly on the specific soil microbiome.


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The Symbiosome: Legume and Rhizobia Co-evolution toward a Nitrogen-Fixing Organelle?

The Symbiosome: Legume and Rhizobia Co-evolution toward a Nitrogen-Fixing Organelle? | Crop yield | Scoop.it
In legume nodules, symbiosomes containing endosymbiotic rhizobial bacteria act as temporary plant organelles that are responsible for nitrogen fixation, these bacteria develop mutual metabolic dependence with the host legume. In most legumes, the rhizobia infect post-mitotic cells that have lost their ability to divide, although in some nodules cells do maintain their mitotic capacity after infection. Here, we review what is currently known about legume symbiosomes from an evolutionary and developmental perspective, and in the context of the different interactions between diazotroph bacteria and eukaryotes. As a result, it can be concluded that the symbiosome possesses organelle-like characteristics due to its metabolic behavior, the composite origin and differentiation of its membrane, the retargeting of host cell proteins, the control of microsymbiont proliferation and differentiation by the host legume, and the cytoskeletal dynamics and symbiosome segregation during the division of rhizobia-infected cells. Different degrees of symbiosome evolution can be defined, specifically in relation to rhizobial infection and to the different types of nodule. Thus, our current understanding of the symbiosome suggests that it might be considered a nitrogen-fixing link in organelle evolution and that the distinct types of legume symbiosomes could represent different evolutionary stages toward the generation of a nitrogen-fixing organelle.


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Microorganisms for Green Revolution | SpringerLink

Microorganisms for Green Revolution | SpringerLink | Crop yield | Scoop.it
This book explores basic and applied aspects of microorganisms, which have a unique ability to cope with abiotic stresses such as drought, salinity and changing climate, as well as biodegrader microor

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METHODS AND COMPOSITIONS FOR IMPROVING PLANT TRAITS - Pivot Bio, Inc.

Disclosed herein are methods of increasing nitrogen fixation in a non-leguminous plant. The methods can comprise exposing the plant to a plurality of bacteria. Each member of the plurality comprises one or more genetic variations introduced into one or more genes or non-coding polynucleotides of the bacteria's nitrogen fixation or assimilation genetic regulatory network, such that the bacteria are capable of fixing atmospheric nitrogen in the presence of exogenous nitrogen. The bacteria are not intergeneric microorganisms. Additionally, the bacteria, in planta, produce 1% or more of the fixed nitrogen in the plant.

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Genomics of microbial plasmids: classification and identification based on replication and transfer systems and host taxonomy

Plasmids are important “vehicles” for the communication of genetic information between bacteria. The exchange of plasmids transmits pathogenically and environmentally relevant traits to the host bacteria, promoting their rapid evolution and adaptation to various environments. Over the past six decades, a large number of plasmids have been identified and isolated from different microbes. With the revolution of sequencing technology, more than 4600 complete sequences of plasmids found in bacteria, archaea, and eukaryotes have been determined. The classification of a wide variety of plasmids is not only important to understand their features, host ranges, and microbial evolution but is also necessary to effectively use them as genetic tools for microbial engineering. This review summarizes the current situation of the classification of fully sequenced plasmids based on their host taxonomy and their features of replication and conjugative transfer. The majority of the fully sequenced plasmids are found in bacteria in the Proteobacteria, Firmicutes, Spirochaetes, Actinobacteria, Cyanobacteria and Euryarcheota phyla, and key features of each phylum are included. Recent advances in the identification of novel types of plasmids and plasmid transfer by culture-independent methods using samples from natural environments are also discussed.


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Beyond ICOM8: perspectives on advances in mycorrhizal research from 2015 to 2017

This report reviews important advances in mycorrhizal research that occurred during the past 2 years. We highlight major advancements both within and across levels of biological organization and describe areas where greater integration has led to unique insights. Particularly active areas of research include exploration of the mechanisms underpinning the development of the mycorrhizal symbiosis, the mycorrhizal microbiome, comparisons among types of mycorrhizas from molecular to ecosystem scales, the extent and function of mycorrhizal networks and enhanced understanding of the role of mycorrhizas in carbon dynamics from local to global scales. The top-tier scientific journals have acknowledged mycorrhizas to be complex adaptive systems that play key roles in the development of communities and ecosystem processes. Understanding the mechanisms driving these large-scale effects requires integration of knowledge across scales of biological organization.


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Microorganisms reveal what plants do not: wheat growth and rhizosphere microbial communities after Azospirillum brasilense inoculation and nitrogen fertilization under field conditions

Aims
Azospirillum brasilense is one of plant growth promoting bacteria used to improve plant growth and grain yield of cereal crops. The level of inoculation response is defined by complex plant-microorganism interactions, many of them still unknown. Thus, we evaluated both agronomic response and microbial ecology of wheat crop under A. brasilense inoculation and nitrogen fertilization at field conditions in order to improve inoculation efficiency.

Methods
Treatments were: control, nitrogen fertilization and inoculation with 40M and 42M strains. Functional and structural diversity of rhizosphere bacterial communities were evaluated by community-level physiological and terminal restriction fragment length polymorphism profiles. Besides, aerial biomass, grain yield and counts of microaerophilic diazotrophic rhizobacteria were determined.

Results
Plant ontogeny modified the number of culturable microaerophilic diazotrophic rhizobacteria. Although agronomic response did not show differences, plant ontogeny and the agricultural practices modified both physiology and genetic structure of rhizosphere microbial communities. Interestingly, these differences due to the treatments were observed at jointing stage but not at grain-filling stage of wheat.

Conclusions
Our results demonstrate how different management decisions can change plant- microorganism relationships. While wheat could not show differences between some agricultural treatments, under the soil surface microbial communities could show them.

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A mycorrhizal revolution

A mycorrhizal revolution | Crop yield | Scoop.it
It has long been postulated that symbiotic fungi facilitated plant migrations onto land through enhancing the scavenging of mineral nutrients and exchanging these for photosynthetically fixed organic carbon. Today, land plant–fungal symbioses are both widespread and diverse. Recent discoveries show that a variety of potential fungal associates were likely available to the earliest land plants, and that these early partnerships were probably affected by changing atmospheric CO2 concentrations. Here, we evaluate current hypotheses and knowledge gaps regarding early plant–fungal partnerships in the context of newly discovered fungal mutualists of early and more recently evolved land plants and the rapidly changing views on the roles of plant–fungal symbioses in the evolution and ecology of the terrestrial biosphere.


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Jean-Michel Ané's curator insight, January 4, 9:43 PM

Fantastic review!

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Impact of two arbuscular mycorrhizal fungi on Arundo donax L. response to salt stress

The mechanisms at the basis of the improved tolerance to abiotic stresses by arbuscular mycorrhizal (AM) fungi have been investigated mainly focusing on food crops. In this work, the potential impact of AM symbiosis on the performance of a bioenergy crop, Arundo donax, under saline conditions was considered. Specifically, we tried to understand whether AM symbiosis helps this fast-growing plant, often widespread in marginal soils, withstand salt. A combined approach, involving eco-physiological, morphometric and biochemical measurements, was used and the effects of two different AM fungal species (Funneliformis mosseae and Rhizophagus irregularis) were compared. Results indicate that potted A. donax plants do not suffer permanent damage induced by salt stress, but photosynthesis and growth are considerably reduced. Since A. donax is a high-yield biomass crop, reduction of biomass might be a serious agronomical problem in saline conditions. At least under the presently experienced growth conditions, and plant–AM combinations, the negative effect of salt on plant performance was not rescued by AM fungal colonization. However, some changes in plant metabolisms were observed following AM-inoculation, including a significant increase in proline accumulation and a trend toward higher isoprene emission and higher H2O2, especially in plants colonized by R. irregularis. This suggests that AM fungal symbiosis influences plant metabolism, and plant–AM fungus combination is an important factor for improving plant performance and productivity, in presence or absence of stress conditions.


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Functional traits in cover crop mixtures: Biological nitrogen fixation and multifunctionality

Cover crop mixtures with complementary plant functional traits including biological nitrogen fixation (BNF) may supply nitrogen (N) to farm fields while simultaneously providing other ecosystem functions such as N retention and weed suppression (i.e., multifunctionality). Understanding variation in these relationships across farms can help advance trait-based research in agroecology and ecological approaches to nutrient management.
This on-farm experiment explored the contributions of two- and three-species cover crop mixtures, which combined legumes, brassicas and cool season grasses, to ecosystem functions across a gradient of soil fertility levels driven by farm management history.
I evaluated the predictions that functional trait diversity of the cover crops would explain variation in multifunctionality, and that legume biomass and BNF within mixtures would be inversely correlated with indicators of soil N availability from organic matter across the farm gradient.
Ecosystem functions varied widely across farms. As expected, functional diversity was a significant predictor of multifunctionality, although the relationship was weak. Cover crop mixtures had significantly greater multifunctionality than a cereal rye monoculture, though not at the highest observed levels of each function, indicating trade-offs among functions. Linear regression models showed that legume biomass and BNF were negatively correlated with soil properties indicative of N availability from soil organic matter, whereas non-legume and weed biomass were positively correlated with other measures of soil fertility.
Synthesis and applications. Cover crop mixtures can increase functional diversity within crop rotations. Designing mixtures with complementary plant traits may be particularly effective for increasing multifunctionality and agroecosystem sustainability. On-farm research to understand variation in biological nitrogen fixation, which is both a plant trait and a key ecosystem function, across heterogeneous soil conditions, can inform management of soil fertility based on ecological principles.

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Nitrogen limitation impairs plant control over the arbuscular mycorrhizal symbiosis in response to phosphorus and shading in two European sand dune species

The symbiosis of plants with arbuscular mycorrhizal fungi (AMF) may become parasitic if the cost:benefit ratio (carbon:phosphorus ratio) increases. In case of mycorrhizal parasitism, a plant may prevent growth depression through the reduction of root colonization as a form of control over the symbiosis. In this greenhouse study, we attempted to manipulate the cost:benefit ratio of the arbuscular mycorrhizal symbiosis by shading and/or phosphorus (P) fertilization in the differentially mycotrophic plant species Hieracium pilosella and Corynephorus canescens. By repeated sampling of soil cores, we assessed the temporal progress of plant investment towards mycorrhizal structures as a measure of plant control over the AMF. Unexpectedly, we found no obvious treatment effects on mycorrhizal growth dependency (MGD), most likely caused by constant N-limitation in AM plants being enhanced by P-fertilization and shade probably not exacerbating plant C-budget for AMF. This highlights the importance of N:P:C stoichiometry for the outcome of the symbiosis. Nevertheless, we found possible control mechanisms in shaded H. pilosella, with considerably higher resource investments into root than into hyphal growth, while root colonization was only marginally suppressed. This control only manifested after 4 weeks of growth under potentially detrimental conditions, emphasizing the importance of time in plant control over the arbuscular mycorrhizal symbiosis. In contrast, the less mycotrophic C. canescens did not exhibit obvious changes in mycorrhizal investments in reaction to shading and P-fertilization, possibly because the low mycotrophy and AMF colonization already imposes a functioning control mechanism in this species. Our study suggests that highly mycotrophic plants may have a stronger need to keep AMF in check than less mycotrophic plants, which may have implications for the role of mycotrophy in the outcome of symbiotic interactions in natural situations.


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Native soils with their microbiotas elicit a state of alert in tomato plants

Native soils with their microbiotas elicit a state of alert in tomato plants | Crop yield | Scoop.it

Several studies have investigated soil microbial biodiversity, but understanding of the mechanisms underlying plant responses to soil microbiota remains in its infancy. Here, we focused on tomato (Solanum lycopersicum), testing the hypothesis that plants grown on native soils display different responses to soil microbiotas. Using transcriptomics, proteomics, and biochemistry, we describe the responses of two tomato genotypes (susceptible or resistant to Fusarium oxysporum f. sp. lycopersici) grown on an artificial growth substrate and two native soils (conducive and suppressive to Fusarium). Native soils affected tomato responses by modulating pathways involved in responses to oxidative stress, phenol biosynthesis, lignin deposition, and innate immunity, particularly in the suppressive soil. In tomato plants grown on steam-disinfected soils, total phenols and lignin decreased significantly. The inoculation of a mycorrhizal fungus partly rescued this response locally and systemically. Plants inoculated with the fungal pathogen showed reduced disease symptoms in the resistant genotype in both soils, but the susceptible genotype was partially protected from the pathogen only when grown on the suppressive soil. The ‘state of alert’ detected in tomatoes reveals novel mechanisms operating in plants in native soils and the soil microbiota appears to be one of the drivers of these plant responses.


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Nitrogen-Fixation by Endophytic Bacteria in Agricultural Crops: Recent Advances

Endophytic bacteria represents a unique class of bacteria that can colonize interior tissues of plant and provide a range of benefits to the plant similar to those provided by the rhizospheric bacteria. Certain endophytic bacteria can provide nitrogen to the plants through biological nitrogen fixation, which is an important source of nitrogen input in agriculture and represents a promising substitute for chemical fertilizers, and are known as endophytic diazotrophic bacteria. Besides fixing nitrogen, endophytic bacteria can produce plant growth hormones like auxin and gibberellin, help in nutrient uptake, and increase the plant’s tolerance to biotic and abiotic stresses. Various direct and indirect methods have been used to quantify the amount of nitrogen fixed by these bacteria, including the acetylene reduction assay, which is a quick but indirect method, and the 15N isotopic dilution assay, which is a robust and accurate method. Research on endophytic diazotrophic bacteria has come a long way, and in this chapter, we have briefly discussed the mechanisms of biological nitrogen fixation and methods to quantify the fixed nitrogen along with reviewing recent studies focused on evaluating the role of endophytic diazotrophic bacteria in promoting plant growth in both native and nonnative crop hosts.


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Nitrogen-Fixation by Endophytic Bacteria in Agricultural Crops: Recent Advances

Endophytic bacteria represents a unique class of bacteria that can colonize interior tissues of plant and provide a range of benefits to the plant similar to those provided by the rhizospheric bacteria. Certain endophytic bacteria can provide nitrogen to the plants through biological nitrogen fixation, which is an important source of nitrogen input in agriculture and represents a promising substitute for chemical fertilizers, and are known as endophytic diazotrophic bacteria. Besides fixing nitrogen, endophytic bacteria can produce plant growth hormones like auxin and gibberellin, help in nutrient uptake, and increase the plant’s tolerance to biotic and abiotic stresses. Various direct and indirect methods have been used to quantify the amount of nitrogen fixed by these bacteria, including the acetylene reduction assay, which is a quick but indirect method, and the 15N isotopic dilution assay, which is a robust and accurate method. Research on endophytic diazotrophic bacteria has come a long way, and in this chapter, we have briefly discussed the mechanisms of biological nitrogen fixation and methods to quantify the fixed nitrogen along with reviewing recent studies focused on evaluating the role of endophytic diazotrophic bacteria in promoting plant growth in both native and nonnative crop hosts.


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Trends in Genetics: Transposable Elements Direct The Coevolution between Plants and Microbes (2016)

Trends in Genetics: Transposable Elements Direct The Coevolution between Plants and Microbes (2016) | Crop yield | Scoop.it

Transposable elements are powerful drivers of genome evolution in many eukaryotes. Although they are mostly considered as ‘selfish’ genetic elements, increasing evidence suggests that they contribute to genetic variability; particularly under stress conditions. Over the past few years, the role of transposable elements during host–microbe interactions has been recognised. It has been proposed that many pathogenic microbes have evolved a ‘two-speed’ genome with regions that show increased variability and that are enriched in transposable elements and pathogenicity-related genes. Plants similarly display structured genomes with transposable-element-rich regions that mediate accelerated evolution. Immune receptor genes typically reside in such regions. Various mechanisms have recently been identified through which transposable elements contribute to the coevolution between plants and their associated microbes.


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Purple corn‐associated rhizobacteria with potential for plant growth promotion

Aims
Purple corn (Zea mays var. purple amylaceum) is a native variety of the Peruvian Andes, cultivated at 3000 m since pre-Inca times without N fertilization. We aimed to isolate and identify native plant growth promoting rhizobacteria (PGPR) for future microbial-based inoculants.

Methods and Results
Eighteen strains were isolated from the rhizosphere of purple corn plants grown without N-fertilization in Ayacucho (Peru). The 16S rRNA gene clustered the 18 strains into 9 groups that contained species of Bacillus, Stenotrophomonas, Achromobacter, Paenibacillus, Pseudomonas and Lysinibacillus. A representative strain from each group was selected and assayed for N2-fixation, phosphate solubilization, indol acetic (IAA) and siderophores production, ACC deaminase activity and biocontrol abilities. Inoculation of purple corn plants with single and combined strains selected after a principal component analysis (PCA) caused significant increases in root and shoot dry weight, total C and N contents of the plants.

Conclusions
PGPRs can support growth and crop production of purple corn in the Peruvian Andes and constitute the base for microbial-based inoculants.

Significance and Impact of the Study
This study enlarges our knowledge on plant-microbial interactions in high altitude mountains and provides new applications for PGPRs inoculation in purple amylaceum corn, which is part of the staple diet for the native Quechua communities.

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

Feed Your Friends: Do Plant Exudates Shape the Root Microbiome? | Crop yield | Scoop.it
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.
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Fenton reaction facilitates organic nitrogen acquisition by an ectomycorrhizal fungus 

Boreal trees rely on their ectomycorrhizal fungal symbionts to acquire growth-limiting nutrients, such as nitrogen (N), which mainly occurs as proteins complexed in soil organic matter (SOM). The mechanisms for liberating this N are unclear as ectomycorrhizal fungi have lost many genes encoding lignocellulose-degrading enzymes present in their saprotrophic ancestors. We hypothesized that hydroxyl radicals (˙OH), produced by the ectomycorrhizal fungus Paxillus involutus during growth on SOM, are involved in liberating organic N. Paxillus involutus was grown for 7 d on N-containing or N-free substrates that represent major organic compounds of SOM. ˙OH production, ammonium assimilation, and proteolytic activity were measured daily. ˙OH production was strongly induced when P. involutus switched from ammonium to protein as the main N source. Extracellular proteolytic activity was initiated shortly after the oxidation. Oxidized protein substrates induced higher proteolytic activity than unmodified proteins. Dynamic modeling predicted that ˙OH production occurs in a burst, regulated mainly by ammonium and ferric iron concentrations. We propose that the production of ˙OH and extracellular proteolytic enzymes are regulated by similar nutritional signals. Oxidation works in concert with proteolysis, improving N liberation from proteins in SOM. Organic N mining by ectomycorrhizal fungi has, until now, only been attributed to proteolysis.
 

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Biotechnological Advancements in Industrial Production of Arbuscular Mycorrhizal Fungi: Achievements, Challenges, and Future Prospects

The recent technological advancements in arbuscular mycorrhizal (AM)–plant symbiosis have helped improve the potential applications of mycorrhizal biotechnology in agriculture, horticulture, landscaping, phytoremediation, and other areas of plant market. The most common conventional methods used for large-scale production of AM fungi include cultivation in pots with sterilized soil, aeroponics, hydroponics, or greenhouse-based in vivo methods. However, these techniques suffer from severe problems of cross-contamination in the inoculum production; therefore, production of high-quality inoculum remains a major challenge. The most advanced method is transformed root organ culture (ROC) to produce AM propagules without adulterated microbial contaminants under strictly controlled sterilized conditions after pure AM fungi are inoculated into the transformed root organ. The scientific breakthroughs and advancements in the field of mycorrhizal research during past two-to-three decades have resulted in new technological developments with different types of products and diverse modes of their applications. For example, mycorrhizal formulations are available in the market for seed coating, liquid applications, or biostimulants. An established symbiosis in the plant roots confirms the adaptation even under unsuitable soil or unfavorable climatic conditions. These advantages have led to an increasing demand for mycorrhiza products in the last few years. There is a growing interest among the enterprises in the developed as well as developing world for the production of mycorrhizae-based inoculum given the fact presented by the emerging market trends in developing economies. However, even today it is not possible to trace out the absolute origin of the fungal species/strain used in commercial inoculum. Despite the regulatory challenges imposed by the regulatory bodies to maintain the highest quality standards, a significant number of commercialized products may still be found in the market which claims for extensive and effective mycorrhizal colonization even though they lack the necessary potential for this. This review provides an updated overview of the recent developments in the technology adoption and commercial production of mycorrhizae-based quality inoculum.


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A Community-Based Culture Collection for Targeting Novel Plant Growth-Promoting Bacteria from the Sugarcane Microbiome 

A Community-Based Culture Collection for Targeting Novel Plant Growth-Promoting Bacteria from the Sugarcane Microbiome  | Crop yield | Scoop.it
The soil-plant ecosystem harbors an immense microbial diversity that challenges investigative approaches to study traits underlying plant-microbe association. Studies solely based on culture-dependent techniques have overlooked most microbial diversity. Here we describe the concomitant use of culture-dependent and -independent techniques to target plant-beneficial microbial groups from the sugarcane microbiome. The community-based culture collection (CBC) approach was used to access microbes from roots and stalks. The CBC recovered 399 unique bacteria representing 15.9% of the rhizosphere core microbiome and 61.6–65.3% of the endophytic core microbiomes of stalks. By cross-referencing the CBC (culture-dependent) with the sugarcane microbiome profile (culture-independent), we designed a synthetic community comprised of naturally occurring highly abundant bacterial groups from roots and stalks, most of which has been poorly explored so far. We then used maize as a model to probe the abundance-based synthetic inoculant. We show that when inoculated in maize plants, members of the synthetic community efficiently colonize plant organs, displace the natural microbiota and dominate at 53.9% of the rhizosphere microbial abundance. As a result, inoculated plants increased biomass by 3.4-fold as compared to uninoculated plants. The results demonstrate that abundance-based synthetic inoculants can be successfully applied to recover beneficial plant microbes from plant microbiota.

Via Stéphane Hacquard, Jean-Michel Ané
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Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix N2 but may denitrify

Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix N2 but may denitrify | Crop yield | Scoop.it
Dinitrogen fixation by Nostoc azollae residing in specialized leaf pockets supports prolific growth of the floating fern Azolla filiculoides. To evaluate contributions by further microorganisms, the A. filiculoides microbiome and nitrogen metabolism in bacteria persistently associated with Azolla ferns were characterized.
A metagenomic approach was taken complemented by detection of N2O released and nitrogen isotope determinations of fern biomass. Ribosomal RNA genes in sequenced DNA of natural ferns, their enriched leaf pockets and water filtrate from the surrounding ditch established that bacteria of A. filiculoides differed entirely from surrounding water and revealed species of the order Rhizobiales. Analyses of seven cultivated Azolla species confirmed persistent association with Rhizobiales.
Two distinct nearly full-length Rhizobiales genomes were identified in leaf-pocket-enriched samples from ditch grown A. filiculoides. Their annotation revealed genes for denitrification but not N2-fixation. 15N2 incorporation was active in ferns with N. azollae but not in ferns without. N2O was not detectably released from surface-sterilized ferns with the Rhizobiales.
N2-fixing N. azollae, we conclude, dominated the microbiome of Azolla ferns. The persistent but less abundant heterotrophic Rhizobiales bacteria possibly contributed to lowering O2 levels in leaf pockets but did not release detectable amounts of the strong greenhouse gas N2O.

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Jean-Michel Ané's curator insight, November 16, 2017 11:37 AM

Wow... That's an awesome paper!

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New method for the identification of arbuscular mycorrhizal fungi by proteomic-based biotyping of spores using MALDI-TOF-MS

New method for the identification of arbuscular mycorrhizal fungi by proteomic-based biotyping of spores using MALDI-TOF-MS | Crop yield | Scoop.it
Arbuscular mycorrhizal fungi (AMF, Glomeromycota) are mutualistic symbionts associated with majority of land plants. These fungi play an important role in plant growth, but their taxonomic identification remains a challenge for academic research, culture collections and inoculum producers who need to certify their products. Identification of these fungi was traditionally performed based on their spore morphology. DNA sequence data have successfully been used to study the evolutionary relationships of AMF, develop molecular identification tools and assess their diversity in the environment. However, these methods require considerable expertise and are not well-adapted for “routine” quality control of culture collections and inoculum production. Here, we show that Matrix-Assisted Laser Desorption Ionisation Time of Flight Mass Spectrometry proteomic-based biotyping is a highly efficient approach for AMF identification. Nineteen isolates belonging to fourteen species, seven genera and five families were clearly differentiated by MALDI biotyping at the species level, and intraspecific differentiation was achieved for the majority. AMF identification by MALDI biotyping could be highly useful, not only for research but also in agricultural and environmental applications. Fast, accurate and inexpensive molecular mass determination and the possibility of automation make MALDI-TOF-MS a real alternative to conventional morphological and molecular methods for AMF identification.


Via Jean-Michel Ané
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Rescooped by Paul Laski from Plant-Microbe Symbiosis
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Isolation and molecular identification of endophytic diazotrophs from seeds and stems of three cereal crops

Isolation and molecular identification of endophytic diazotrophs from seeds and stems of three cereal crops | Crop yield | Scoop.it
Ten strains of endophytic diazotroph were isolated and identified from the plants collected from three different agricultural crop species, wheat, rice and maize, using the nitrogen-free selective isolation conditions. The nitrogen-fixing ability of endophytic diazotroph was verified by the nifH-PCR assay that showed positive nitrogen fixation ability. These identified strains were classified by 879F-RAPD and 16S rRNA sequence analysis. RAPD analyses revealed that the 10 strains were clustered into seven 879F-RAPD groups, suggesting a clonal origin. 16S rRNA sequencing analyses allowed the assignment of the 10 strains to known groups of nitrogen-fixing bacteria, including organisms from the genera Paenibacillus, Enterobacter, Klebsiella and Pantoea. These representative genus are not endophytic diazotrophs in the conventional sense. They may have obtained nitrogen fixation ability through lateral gene transfer, however, the evolutionary forces of lateral gene transfer are not well known. Molecular identification results from 16S rRNA analyses were also confirmed by morphological and biochemical data. The test strains SH6A and MZB showed positive effect on the growth of plants.


Via Jean-Michel Ané
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