Plant-Microbe Symbiosis
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Frontiers in Plant Proteomics: Leveraging Proteomics to Understand Plant–Microbe Interactions (2012)

Frontiers in Plant Proteomics: Leveraging Proteomics to Understand Plant–Microbe Interactions (2012) | Plant-Microbe Symbiosis | Scoop.it

Understanding the interactions of plants with beneficial and pathogenic microbes is a promising avenue to improve crop productivity and agriculture sustainability. Proteomic techniques provide a unique angle to describe these intricate interactions and test hypotheses. The various approaches for proteomic analysis generally include protein/peptide separation and identification, but can also provide quantification and the characterization of post-translational modifications. In this review, we discuss how these techniques have been applied to the study of plant-microbe interactions. We also present some areas where this field of study would benefit from the utilization of newly developed methods that overcome previous limitations. Finally, we reinforce the need for expanding, integrating, and curating protein databases, as well as the benefits of combining protein-level datasets with those from genetic analyses and other high-throughput large-scale approaches for a systems-level view of plant-microbe interactions.

 

Dhileepkumar Jayaraman, Kari L. Forshey, Paul A. Grimsrud and Jean-Michel Ané


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Plant-Microbe Symbiosis
Beneficial associations between plants and microbes
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Plant species, mycorrhiza, and aphid age influence the performance and behaviour of a generalist

1. Life-history traits of herbivores are shaped by the combination of various extrinsic and intrinsic variables. However, studies investigating the impact of both variables on insect behavioural phenotypes are rare, and research including the modulation of host plant quality by arbuscular mycorrhiza (AM) (extrinsic variable) and the herbivore developmental stage (intrinsic variable) on aphid behaviour is lacking.

2. To study the influences of extrinsic and intrinsic variables on aphid performance and behaviour, individuals of the generalist aphid pest Myzus persicae (Sulzer) were reared on Plantago lanceolata and Poa annua plants that were either non-mycorrhized (NM) or mycorrhized (AM). Aphid performance was monitored over 2 weeks. Behavioural traits of nymphs were recorded twice during development after removing individuals from their feeding sites and placing them in an unknown environment (‘open field’), causing disturbance. Plant quality was determined by measuring the water content and leaf mass per area (LMA).

3. Differences in body mass of nymphs at day 6 dependent on plant species and treatment were compensated by the individuals within 4 days. Behavioural traits, considered as activity and exploration, were affected by the interaction between extrinsic and intrinsic variables (activity and exploration) and changed over ontogeny (activity). Independent of AM, a lower water content and LMA were recorded in P. annua leaves.

4. Overall, this study demonstrates that extrinsic and intrinsic variables need to be considered in combination and behavioural traits should be studied repeatedly during insect ontogeny to understand the complexity of microbe-modulated plant–herbivore interactions.
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Cell autonomous sanctions in legumes target ineffective rhizobia in nodules with mixed infections

PREMISE OF THE STUDY: To maximize benefits from symbiosis, legumes must limit physiological inputs into ineffective rhizobia that nodulate hosts without fixing nitrogen. The capacity of legumes to decrease the relative fitness of ineffective rhizobia—known as sanctions—has been demonstrated in several legume species, but its mechanisms remain unclear. Sanctions are predicted to work at the whole-nodule level. However, whole-nodule sanctions would make the host vulnerable to mixed-nodule infections, which have been demonstrated in the laboratory and observed in natural settings. Here, we present and test a cell-autonomous model of legume sanctions that can resolve this dilemma.

METHODS: We analyzed histological and ultrastructural evidence of sanctions in two legume species, Acmispon strigosus and Lotus japonicus. For the former, we inoculated seedlings with rhizobia that naturally vary in their abilities to fix nitrogen. In the latter, we inoculated seedlings with near-isogenic strains that differ only in the ability to fix nitrogen.

KEY RESULTS: In both hosts, plants inoculated with ineffective rhizobia exhibited evidence for a cell autonomous and accelerated program of senescence within nodules. In plants that received mixed inoculations, only the plant cells harboring ineffective rhizobia exhibited features consistent with programmed cell death, including collapsed vacuoles, ruptured symbiosomes, and bacteroids that are released into the cytosol. These features were consistently linked with ultrastructural evidence of reduced survival of ineffective rhizobia in planta.

CONCLUSIONS: Our data suggest an elegant cell autonomous mechanism by which legumes can detect and defend against ineffective rhizobia even when nodules harbor a mix of effective and ineffective rhizobial genotypes.
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Rhizospheric fungi and their link with the nitrogen‐fixing Frankia harbored in host plant Hippophae rhamnoides L.

Sea buckthorn (Hippophae rhamnoides L.) is a pioneer plant used for land reclamation and an appropriate material for studying the interactions of symbiotic microorganisms because of its nitrogen-fixing root nodules and mycorrhiza. We used high-throughput sequencing to reveal the diversities and community structures of rhizospheric fungi and their link with nitrogen-fixing Frankia harbored in sea buckthorn collected along an altitude gradient from the Qinghai Tibet Plateau to interior areas. We found that the fungal diversities and compositions varied between different sites. Ascomycota, Basidiomycota, and Zygomycota were the dominant phyla. The distribution of sea buckthorn rhizospheric fungi was driven by both environmental factors and the geographic distance. Among all examined soil characteristics, altitude, AP, and pH were found to have significant (p < 0.05) effect on the rhizospheric fungal community. The rhizospheric fungal communities became more distinct as the distance increased. Moreover, co-inertia analysis identified significant co-structures between Frankia and AMF communities in the rhizosphere of sea buckthorn. We conclude that at the large scale, there are certain linkages between nitrogen-fixing bacteria and the AMF expressed in the distributional pattern.
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Feed in summer, rest in winter: microbial carbon utilization in forest topsoil

Feed in summer, rest in winter: microbial carbon utilization in forest topsoil | Plant-Microbe Symbiosis | Scoop.it
Evergreen coniferous forests contain high stocks of organic matter. Significant carbon transformations occur in litter and soil of these ecosystems, making them important for the global carbon cycle. Due to seasonal allocation of photosynthates to roots, carbon availability changes seasonally in the topsoil. The aim of this paper was to describe the seasonal differences in C source utilization and the involvement of various members of soil microbiome in this process. Here, we show that microorganisms in topsoil encode a diverse set of carbohydrate-active enzymes, including glycoside hydrolases and auxiliary enzymes. While the transcription of genes encoding enzymes degrading reserve compounds, such as starch or trehalose, was high in soil in winter, summer was characterized by high transcription of ligninolytic and cellulolytic enzymes produced mainly by fungi. Fungi strongly dominated the transcription in litter and an equal contribution of bacteria and fungi was found in soil. The turnover of fungal biomass appeared to be faster in summer than in winter, due to high activity of enzymes targeting its degradation, indicating fast growth in both litter and soil. In each enzyme family, hundreds to thousands of genes were typically transcribed simultaneously. Seasonal differences in the transcription of glycoside hydrolases and auxiliary enzyme genes are more pronounced in soil than in litter. Our results suggest that mainly fungi are involved in decomposition of recalcitrant biopolymers in summer, while bacteria replace them in this role in winter. Transcripts of genes encoding enzymes targeting plant biomass biopolymers, reserve compounds and fungal cell walls were especially abundant in the coniferous forest topsoil.

Via Petr Baldrian
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Multiple nodulation genes are up-regulated during establishment of reniform nematode feeding sites in soybean

The semi-endoparastic reniform nematode (Rotylenchulus reniformis) infects over 300 plant species. Females penetrate host roots and induce formation of complex, multinucleate feeding sites called syncytia. While anatomical changes associated with reniform nematode infection are well documented, little is known about their molecular basis. We grew soybean (Glycine max) in a split-root growth system, inoculated half of each root system with R. reniformis, and quantified gene expression in infected and control root tissue at four dates after inoculation. Over 6,000 genes were differentially expressed between inoculated and control roots on at least one date (FDR = 0.01, |log2FC| ≥ 1), and 507 gene sets were significantly enriched or depleted in inoculated roots (FDR = 0.05). Numerous genes up-regulated during syncytium formation had previously been associated with rhizobia nodulation. These included the nodule-initiating transcription factors CYCLOPS, NSP1, NSP2, and NIN, as well as multiple nodulins associated with the plant-derived peribacteroid membrane. Nodulation-related NIP aquaporins and SWEET sugar transporters were induced, as were plant CLAVATA3/ESR-related (CLE) signaling proteins and cell cycle regulators such as CCS52A and E2F. Nodulins and nodule-associated genes may have ancestral functions in normal root development and mycorrhization that have been co-opted by both parasitic nematodes and rhizobial bacteria to promote feeding site and nodule formation.

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Auxin transport, metabolism, and signalling during nodule initiation: indeterminate and determinate nodules 

Most legumes can form a unique type of lateral organ on their roots: root nodules. These structures host symbiotic nitrogen-fixing bacteria called rhizobia. Several different types of nodules can be found in nature, but the two best-studied types are called indeterminate and determinate nodules. These two types differ with respect to the presence or absence of a persistent nodule meristem, which consistently correlates with the cortical cell layers giving rise to the nodule primordia. Similar to other plant developmental processes, auxin signalling overlaps with the site of organ initiation and meristem activity. Here, we review how auxin contributes to early nodule development. We focus on changes in auxin transport, signalling, and metabolism during nodule initiation, describing both experimental evidence and computer modelling. We discuss how indeterminate and determinate nodules may differ in their mechanisms for generating localized auxin response maxima and highlight outstanding questions for future research.


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Understanding the Arbuscule at the Heart of Endomycorrhizal Symbioses in Plants

Understanding the Arbuscule at the Heart of Endomycorrhizal Symbioses in Plants | Plant-Microbe Symbiosis | Scoop.it
Arbuscular mycorrhizal fungi form associations with most land plants and facilitate nutrient uptake from the soil, with the plant receiving mineral nutrients from the fungus and in return providing the fungus with fixed carbon. This nutrient exchange takes place through highly branched fungal structures called arbuscules that are formed in cortical cells of the host root. Recent discoveries have highlighted the importance of fatty acids, in addition to sugars, acting as the form of fixed carbon transferred from the plant to the fungus and several studies have begun to elucidate the mechanisms that control the plant processes necessary for fungal colonisation and arbuscule development. In this review, we analyse the mechanisms that allow arbuscule development and the processes necessary for nutrient exchange between the plant and the fungus.

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Epichloë Fungal Endophytes and Plant Defenses: Not Just Alkaloids

Epichloë Fungal Endophytes and Plant Defenses: Not Just Alkaloids | Plant-Microbe Symbiosis | Scoop.it
Although the role of fungal alkaloids in protecting grasses associated with Epichloë fungal endophytes has been extensively documented, the effects of the symbiont on the host plant’s immune responses have received little attention. We propose that, in addition to producing protective alkaloids, endophytes enhance plant immunity against chewing insects by promoting endogenous defense responses mediated by the jasmonic acid (JA) pathway. We advance a model that integrates this dual effect of endophytes on plant defenses and test its predictions by means of a standard meta-analysis. This analysis supports a role of Epichloë endophytes in boosting JA-mediated plant defenses. We discuss the ecological scenarios where this effect of endophytes on plant defenses would be most beneficial for increasing plant fitness.

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Identifying the active microbiome associated with roots and rhizosphere soil of oilseed rape

RNA stable isotope probing and high throughput sequencing were used to characterize the active microbiomes of bacteria and fungi colonizing roots and rhizosphere soil of oilseed rape, to identify taxa assimilating plant-derived carbon following 13CO2 labeling. Root- and rhizosphere soil-associated communities of both bacteria and fungi differed from each other and there were highly significant differences between their DNA- and RNA-based community profiles. Verrucomicrobia, Proteobacteria, Planctomycetes, Acidobacteria, Gemmatimonadetes, Actinobacteria and Chloroflexi were the most active bacterial phyla in the rhizosphere soil. Bacteroidetes were more active in roots. The most abundant bacterial genera were well represented in both the 13C- and 12C-RNA fractions, while the fungal taxa were more differentiated. Streptomyces, Rhizobium and Flavobacterium were dominant in roots, whereas Rhodoplanes and Kaistobacter were dominant in rhizosphere soil. Candidatus Nitrososphaera was enriched in 13C in rhizosphere soil. Olpidium and Dendryphion were abundant in the 12C-RNA fraction of roots; Clonostachys was abundant in both roots and rhizosphere soil and heavily 13C enriched. Cryptococcus was dominant in rhizosphere soil and less abundant, but 13C enriched in roots.
The patterns of colonization and C-acquisition revealed in this study assist in identifying microbial taxa that may be superior competitors for plant-derived carbon in the rhizosphere of B. napus.
IMPORTANCE This microbiome study characterizes the active bacteria and fungi colonizing roots and rhizosphere soil of Brassica napus using high-throughput sequencing and RNA-stable isotope probing. It identifies taxa assimilating plant-derived carbon following 13CO2 labeling and compares these with other, less active groups not incorporating plant assimilate. Brassica napus is an economically and globally important oilseed crop, cultivated for edible oil, biofuel production and phytoextraction of heavy metals, however it is susceptible to several diseases. Identification of the fungal and bacterial species successfully competing for plant-derived carbon, enabling them to colonize the roots and rhizosphere soil of this plant, should enable identification of microorganisms that can be evaluated in more detailed functional studies and ultimately be used to improve plant health and productivity in sustainable agriculture.

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Silencing of putative cytokinin receptor Histidine Kinase1 inhibits both inception and differentiation of root nodules in Arachis hypogaea

Rhizobia-legume interaction activates SYM-pathway that recruits cytokinin signaling for induction of nodule primordia in the cortex. In Arachis hypogaea, bradyrhizobia invade through natural cracks developed in the lateral root base and are directly endocytosed in the cortical cells to generate the nodule primordia. To unravel the role of cytokinin signaling in Arachis hypogaea, RNA-interference (RNAi) of cytokinin receptor Histidine-Kinase1 (AhHK1) was done. AhHK1-RNAi downregulated the expression of Type-A Response Regulators like AhRR5 and AhRR3 along with several symbiotic genes indicating both cytokinin signaling and SYM-Pathway was affected. Accordingly, there was a drastic downregulation of nodulation in AhHK1-RNAi roots and the nodules that developed were ineffective. These nodules were densely packed with infected cells having higher nucleo-cytoplasmic ratio and distinctively high mitotic-index where the rod shaped rhizobia failed to differentiate into bacteroids within spherical symbiosomes. In accordance with the proliferating state, expression of a mitotic-cyclin AhCycB2.1 was higher in AhHK1-RNAi nodules, whereas expression of Retinoblastoma-related (AhRBR) that restrains proliferation was lower. Also higher expression of meristem maintenance factor WUSHEL-RELATED HOMEOBOX5 (AhWOX5) correlates with the undifferentiated state of AhHK1-RNAi nodules. Our results suggest AhHK1-mediated cytokinin signaling to be important for both inception and differentiation during nodule development in Arachis hypogaea.Silencing of putative cytokinin receptor Histidine Kinase1 inhibits both inception and differentiation of root nodules in Arachis hypogaea

Via Pierre-Marc Delaux
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Receptor-mediated chitin perception in legume roots is functionally separable from Nod factor perception

Receptor-mediated chitin perception in legume roots is functionally separable from Nod factor perception | Plant-Microbe Symbiosis | Scoop.it
The ability of root cells to distinguish mutualistic microbes from pathogens is crucial for plants that allow symbiotic microorganisms to infect and colonize their internal root tissues. Here we show that Lotus japonicus and Medicago truncatula possess very similar LysM pattern-recognition receptors, LjLYS6/MtLYK9 and MtLYR4, enabling root cells to separate the perception of chitin oligomeric microbe-associated molecular patterns from the perception of lipochitin oligosaccharide by the LjNFR1/MtLYK3 and LjNFR5/MtNFP receptors triggering symbiosis. Inactivation of chitin-receptor genes in Ljlys6, Mtlyk9, and Mtlyr4 mutants eliminates early reactive oxygen species responses and induction of defense-response genes in roots. Ljlys6, Mtlyk9, and Mtlyr4 mutants were also more susceptible to fungal and bacterial pathogens, while infection and colonization by rhizobia and arbuscular mycorrhizal fungi was maintained. Biochemical binding studies with purified LjLYS6 ectodomains further showed that at least six GlcNAc moieties (CO6) are required for optimal binding efficiency. The 2.3-Å crystal structure of the LjLYS6 ectodomain reveals three LysM βααβ motifs similar to other LysM proteins and a conserved chitin-binding site. These results show that distinct receptor sets in legume roots respond to chitin and lipochitin oligosaccharides found in the heterogeneous mixture of chitinaceous compounds originating from soil microbes. This establishes a foundation for genetic and biochemical dissection of the perception and the downstream responses separating defense from symbiosis in the roots of the 80–90% of land plants able to develop rhizobial and/or mycorrhizal endosymbiosis.

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Functional characterisation of brassinosteroid receptor MtBRI1 in Medicago truncatula

Functional characterisation of brassinosteroid receptor MtBRI1 in Medicago truncatula | Plant-Microbe Symbiosis | Scoop.it
Brassinosteroids are phytohormones involved in plant development and physiological processes. Brassinosteroids Insensitive 1 (BRI1) is required for BR perception and initiation of subsequent signal transduction in Arabidopsis. In this study, the orthologue of BRI1 in the model legume species Medicago truncatula, MtBRI1, was identified and characterised. Three allelic Tnt1 insertion mutants, mtbri1-1, mtbri1-2, and mtbri1-3, were obtained from the M. truncatula Tnt1 insertion population. mtbri1 mutants displayed characteristic bri1 mutant phenotypes: extreme dwarfness, dark green curled leaves, short primary roots, less lateral roots, and insensitive to exogenous brassinolide (BL). Moreover, mtbri1 mutants show decreased total nodule number and defects in nitrogen fixation. MtBRI1 is able to complement an Arabidopsis BRI1 mutant, bri1-5. Similar to the interaction of BRI1 and BAK1 in Arabidopsis, MtBRI1 interacts with MtSERK1 in vivo. Global gene expression profiling revealed that the expression of BR biosynthesis genes and SAUR genes are significantly altered in mtbri1 mutants. MapMan analysis indicated that genes involved in signaling, hormone, cell wall, and biotic stress responses are over-represented in differentially expressed genes. Taken together, the results indicate that MtBRI1 is the BR receptor in M. truncatula and that BR signaling may play a conserved role in balancing plant growth and defenses.

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Tree roots select specific bacterial communities in the subsurface critical zone

In soils characterized by nutrient-poor conditions trees have developed strategies to maximize the exploration of the environment through their root system. Notably, in shallow soils, trees adopt a deep-rooting strategy to access appropriate levels of water and nutrients from the bedrock. Despite the critical importance of microorganisms in nutrient access in topsoil, understanding their involvement in subsoil was rarely addressed. Our study provides the first comprehensive picture of the bacterial communities colonizing deep roots at the bedrock interface. Particularly, we aimed at deciphering if the subsoil edaphic conditions allowed the enrichment of specific bacterial communities in the rhizosphere. To answer such questioning, we focused on a shallow soil dominated by deep-rooting beech trees (Fagus sylvatica). The taxonomic and functional structures of bacterial communities were investigated through 16S rRNA-pyrosequencing analyses and in vitro bioassays on culturable representatives isolated from the saprolite, the limestone rocks and the roots penetrating those two compartments at the bedrock interface. Our taxonomic analyses revealed a rhizosphere effect, with no difference between the limestone- and saprolite-rhizosphere bacterial communities. Notably, our functional assays highlighted a significant enrichment of bacteria effective at mineral weathering in the limestone-rhizosphere compared to the surrounding environment, whereas organic matter decomposing bacteria were exclusively enriched in the saprolite-rhizosphere. Altogether our results suggest that tree roots select specific bacterial communities in subsoil as potential allies to improve nutrient availability and tree nutrition.

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Endophytic bacteria: a new source of bioactive compounds

Endophytic bacteria: a new source of bioactive compounds | Plant-Microbe Symbiosis | Scoop.it
In recent years, bioactive compounds are in high demand in the pharmaceuticals and naturopathy, due to their health benefits to human and plants. Microorganisms synthesize these compounds and some enzymes either alone or in association with plants. Microbes residing inside the plant tissues, known as endophytes, also produce an array of these compounds. Endophytic actinomycetes act as a promising resource of biotechnologically valuable bioactive compounds and secondary metabolites. Endophytic Streptomyces sp. produced some novel antibiotics which are effective against multi-drug-resistant bacteria Antimicrobial agents produced by endophytes are eco-friendly, toxic to pathogens and do not harm the human. Endophytic inoculation of the plants modulates the synthesis of bioactive compounds with high pharmaceutical properties besides promoting growth of the plants. Hydrolases, the extracellular enzymes, produced by endophytic bacteria, help the plants to establish systemic resistance against pathogens invasion. Phytohormones produced by endophytes play an essential role in plant development and drought resistance management. The high diversity of endophytes and their adaptation to various environmental stresses seem to be an untapped source of new secondary metabolites. The present review summarizes the role of endophytic bacteria in synthesis and modulation of bioactive compounds.

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Total synthesis and functional analysis of microbial signalling molecules - Chemical Society Reviews (RSC Publishing)

Total synthesis and functional analysis of microbial signalling molecules - Chemical Society Reviews (RSC Publishing) | Plant-Microbe Symbiosis | Scoop.it
Communication is essential for all domains of life. Bacteria use a plethora of small molecules to sense and orchestrate intra- and interspecies communication. Within this review, we will discuss different groups of signalling molecules, including autoinducers, virulence factors and morphogenic substances. On selected examples, we will shortly discuss their ecological roles and biosynthetic proposals. The major part of this review will focus on a systematic overview of the different synthetic methods applied towards the synthesis of signalling molecules and derivatives thereof. The described examples highlight the importance of organic synthetic method development and diversity-oriented total syntheses for structure verification, structure–function analysis and target identification.

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Arbuscular Mycorrhizal Association Contributes to Cr Accumulation and Tolerance in Plants Growing on Cr Contaminated Soils

Arbuscular mycorrhizal (AM) fungi are well known root symbionts in heavy metal polluted soils. To assess AM fungal association and their contribution to the host plants naturally growing on a highly chromium (Cr) contaminated soil, the present study has been undertaken. The soil of the study site was contaminated with 32,562 ppm Cr coming from tannery industry. The study site was dominated by Cynodon dactylon (L.) Pers., Parthenium hysterophorus L., Croton bonplandianum Baill and Prosopis juliflora (Sw.) DC. High mycorrhizal colonization (31–83%) and low spore population (5–11 spores/g) was recorded. The diversity of AM fungi was very low because of stress caused by Cr. Only seven AM fungal isolates have been recovered. Funneliformis mosseae, Rhizophagus intraradices, Funneliformis geosporus and Glomus sinuosum have been recovered from two hosts, while, Rhizophagus fasciculatus, Glomus aggregatum and Acaulospora scrobiculata from single host only. Cr accumulation in the roots were analyzed through AAS and correlated with various mycorrhization parameters. The results of correlation through PCA showed that, various mycorrhization parameters were under strong influence of Cr accumulation in the roots. Furthermore, all the AM fungi showed certain adaptive features like compact sporocarp, thick spore wall, sloughing outermost wall layer and formation of water stable aggregates. Low species diversity, high mycorrhizal colonization, presence of adaptive features and strong correlation of mycorrhizal parameters with the Cr accumulation in the roots clearly indicated that, these AM fungi have contributed to the Cr accumulation and tolerance to the host plants in Cr sludge deposit.

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Expression in rice of an autoactive variant of Medicago truncatula DMI3, the Ca+2/calmodulin-dependent protein kinase from the common symbiotic pathway modifies root transcriptome and improves myco...

Rice is the principle staple food for more than half of humankind. Frequently, productivity of rice is affected by low nitrogen in the soil and hence, for enhanced rice production it heavily relies on synthetic nitrogen fertilizers that beget economic and ecological costs. In this context, the interest in transferring legume-like biological nitrogen fixation capability to rice has increased lately. The rice-arbuscular mycorrhizal (AM) symbiosis is mediated by genes that are orthologous to legume-genes known to be essential constituents of the common symbiotic pathway (CSP) that facilitates the establishment of both rhizobial nitrogen fixation- and AM-symbioses in legumes. Particularly, DMI3 (Ca+2/calmodulin-dependent serine/threonine protein kinase, CCaMK), a component of the CSP, was found to play a paramount role in promoting the development of both types of symbioses. In fact, expression of autoactive version of DMI3 was shown to be sufficient to trigger downstream developmental processes leading to the induction of spontaneous nodulation in the absence of rhizobia. Hence, in the present investigation, we expressed in transgenic rice a gain-of-function Medicago truncatula DMI3T271D gene (gofMtDMI3) and assessed if legume-like symbiotic responses can be mimicked in rice roots. Ectopic expression of gofMtDMI3 in common bean induced spontaneous nodulation in the roots in the absence of rhizobia, but in rice plants it did not produce any such legume-like nodular manifestations. Conversely, the expression of gofMtDMI3 supported elevated AM colonization in rice roots that could improve plant nutrition/growth. In addition, gofMtDMI3 expression induced higher transcript levels of the CSP orthologues OsDMI3, OsIPD3 and OsNSP1, as well as triggered changes in the expression of several genes involved in biotic and abiotic stress responses. Our results with gofMtDMI3 lay the basis for the potential development of a biotechnological approach towards improvement of rice production.

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PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives

Second-generation, high-throughput sequencing methods have greatly improved our understanding of the ecology of soil microorganisms, yet the short barcodes (< 500 bp) provide limited taxonomic and phylogenetic information for species discrimination and taxonomic assignment.
Here, we utilized the third-generation Pacific Biosciences (PacBio) RSII and Sequel instruments to evaluate the suitability of full-length internal transcribed spacer (ITS) barcodes and longer rRNA gene amplicons for metabarcoding Fungi, Oomycetes and other eukaryotes in soil samples.
Metabarcoding revealed multiple errors and biases: Taq polymerase substitution errors and mis-incorporating indels in sequencing homopolymers constitute major errors; sequence length biases occur during PCR, library preparation, loading to the sequencing instrument and quality filtering; primer–template mismatches bias the taxonomic profile when using regular and highly degenerate primers.
The RSII and Sequel platforms enable the sequencing of amplicons up to 3000 bp, but the sequence quality remains slightly inferior to Illumina sequencing especially in longer amplicons. The full ITS barcode and flanking rRNA small subunit gene greatly improve taxonomic identification at the species and phylum levels, respectively. We conclude that PacBio sequencing provides a viable alternative for metabarcoding of organisms that are of relatively low diversity, require > 500-bp barcode for reliable identification or when phylogenetic approaches are intended.
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Is there genetic variation in mycorrhization of Medicago truncatula?

Is there genetic variation in mycorrhization of Medicago truncatula? | Plant-Microbe Symbiosis | Scoop.it
Differences in the plant’s response among ecotypes or accessions are often used to identify molecular markers for the respective process. In order to analyze genetic diversity of Medicago truncatula in respect to interaction with the arbuscular mycorrhizal (AM) fungus Rhizophagus irregularis, mycorrhizal colonization was evaluated in 32 lines of the nested core collection representing the genetic diversity of the SARDI collection. All studied lines and the reference line Jemalong A17 were inoculated with R. irregularis and the mycorrhization rate was determined at three time points after inoculation. There were, however, no reliable and consistent differences in mycorrhization rates among all lines. To circumvent possible overlay of potential differences by use of the highly effective inoculum, native sandy soil was used in an independent experiment. Here, significant differences in mycorrhization rates among few of the lines were detectable, but the overall high variability in the mycorrhization rate hindered clear conclusions. To narrow down the number of lines to be tested in more detail, root system architecture (RSA) of in vitro-grown seedlings of all lines under two different phosphate (Pi) supply condition was determined in terms of primary root length and number of lateral roots. Under high Pi supply (100 µM), only minor differences were observed, whereas in response to Pi-limitation (3 µM) several lines exhibited a drastically changed number of lateral roots. Five lines showing the highest alterations or deviations in RSA were selected and inoculated with R. irregularis using two different Pi-fertilization regimes with either 13 mM or 3 mM Pi. Mycorrhization rate of these lines was checked in detail by molecular markers, such as transcript levels of RiTubulin and MtPT4. Under high phosphate supply, the ecotypes L000368 and L000555 exhibited slightly increased fungal colonization and more functional arbuscules, respectively. To address the question, whether capability for mycorrhizal colonization might be correlated to general invasion by microorganisms, selected lines were checked for infection by the root rot causing pathogen, Aphanoymces euteiches. The mycorrhizal colonization phenotype, however, did not correlate with the resistance phenotype upon infection with two strains of A. euteiches as L000368 showed partial resistance and L000555 exhibited high susceptibility as determined by quantification of A. euteiches rRNA within infected roots. Although there is genetic diversity in respect to pathogen infection, genetic diversity in mycorrhizal colonization of M. truncatula is rather low and it will be rather difficult to use it as a trait to access genetic markers.

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Nature Communications: Preprints under peer review

We are now offering authors whose submitted manuscript has been deposited in a preprint server, and is selected for peer review, the option of including their paper on a public list of articles under review at Nature Communications. The list, which will appear on our dedicated website and will be freely accessible to all without registration, will provide a link to the preprint on the recognized preprint server. Only preprints that are currently under peer review at Nature Communications or are being revised for further consideration will be listed on the site, and, once a final decision has been made, papers will be removed from the list. Authors can opt to deposit their work on a preprint server and join the service at any time and we will update our site accordingly, and they can also ask to be removed at any time. This service will initially run as a trial during which we will assess the level of uptake and any feedback we receive from authors and readers.


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MAP Kinase-Mediated Negative Regulation of Symbiotic Nodule Formation in Medicago truncatula

MAP Kinase-Mediated Negative Regulation of Symbiotic Nodule Formation in Medicago truncatula | Plant-Microbe Symbiosis | Scoop.it
Mitogen-activated protein kinase (MAPK) signaling cascades play critical roles in various cellular events in plants, including stress responses, innate immunity, hormone signaling, and cell specificity. MAPK-mediated stress signaling is also known to negatively regulate nitrogen-fixing symbiotic interactions, but the molecular mechanism of the MAPK signaling cascades underlying the symbiotic nodule development remains largely unknown. We show that the MtMKK5-MtMPK3/6 signaling module negatively regulates the early symbiotic nodule formation, probably upstream of ERN1 (ERF Required for Nodulation 1) and NSP1 (Nod factor Signaling Pathway 1) in Medicago truncatula. The overexpression of MtMKK5 stimulated stress and defense signaling pathways but also reduced nodule formation in M. truncatula roots. Conversely, a MAPK specific inhibitor, U0126, enhanced nodule formation and the expression of an early nodulation marker gene, MtNIN. We found that MtMKK5 directly activates MtMPK3/6 by phosphorylating the TEY motif within the activation loop and that the MtMPK3/6 proteins physically interact with the early nodulation-related transcription factors ERN1 and NSP1. These data suggest that the stress signaling-mediated MtMKK5/MtMPK3/6 module suppresses symbiotic nodule development via the action of early nodulation transcription factors.

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The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae

The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae | Plant-Microbe Symbiosis | Scoop.it
A reference genome sequence for Pseudotsuga menziesii var. menziesii (Mirb.) Franco (Coastal Douglas-fir) is reported, thus providing a reference sequence for a third genus of the family Pinaceae. The contiguity and quality of the genome assembly far exceeds that of other conifer reference genome sequences (contig N50 = 44,136 bp and scaffold N50 = 340,704 bp). Incremental improvements in sequencing and assembly technologies are in part responsible for the higher quality reference genome, but it may also be due to a slightly lower exact repeat content in Douglas-fir vs. pine and spruce. Comparative genome annotation with angiosperm species reveals gene-family expansion and contraction in Douglas-fir and other conifers which may account for some of the major morphological and physiological differences between the two major plant groups. Notable differences in the size of the NDH-complex gene family and genes underlying the functional basis of shade tolerance/intolerance were observed. This reference genome sequence not only provides an important resource for Douglas-fir breeders and geneticists but also sheds additional light on the evolutionary processes that have led to the divergence of modern angiosperms from the more ancient gymnosperms.

Via Niklaus Grunwald
Jean-Michel Ané's insight:

One more genome of gymnosperm... cool!

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Crop Ecology, Management & Quality Phosphorus and Potassium Uptake, Partitioning, and Removal across a Wide Range of Soybean Seed Yield Levels

Maintenance of adequate soil phosphorus (P) and potassium (K) levels is critical for profitable soybean [Glycine max (L.) Merr.] production. To accomplish this, precise knowledge of soybean P and K uptake, utilization, and removal is critical, yet a comprehensive study characterizing these requirements across wide-ranging seed yield environments is nonexistent for modern soybean production systems. Using six site-years and eight soybean varieties, plants were sampled at six growth stages , partitioned into their respective plant parts, and analyzed. Distinctly different uptake patterns and rates were found between P and K, where soybean accumulated greater relative amounts of K by R1 and 91 to 100% of its season-long K total by R5.5, compared with only 68 to 77% of its season-long P total. Removal of P (0.0054 kg P kg−1 grain) and K (0.016 kg K kg−1 grain) with the seed was consistent across environments and varieties and displayed strong relations with yield (R2 = 0.89–0.92). For each kilogram increase in yield, total P and K uptake increased by 0.0054 kg and 0.017 to 0.030 kg, respectively. The difference between total uptake and removal for each nutrient resulted in average nutrient harvest indices of 81 and 49% for P and K, respectively. However, significant variation in total uptake and nutrient harvest indices existed due to the environment, not variety, and was more pronounced for K, resulting in significant variability in the amount of K removed in stover. These results can be incorporated into future fertility recommendations to improve P and K management for profitable and environmentally sound soybean production.

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Do Endophytes Promote Growth of Host Plants Under Stress? A Meta-Analysis on Plant Stress Mitigation by Endophytes

Endophytes are microbial symbionts living inside plants and have been extensively researched in recent decades for their functions associated with plant responses to environmental stress. We conducted a meta-analysis of endophyte effects on host plants’ growth and fitness in response to three abiotic stress factors: drought, nitrogen deficiency, and excessive salinity. Ninety-four endophyte strains and 42 host plant species from the literature were evaluated in the analysis. Endophytes increased biomass accumulation of host plants under all three stress conditions. The stress mitigation effects by endophytes were similar among different plant taxa or functional groups with few exceptions; eudicots and C4 species gained more biomass than monocots and C3 species with endophytes, respectively, under drought conditions. Our analysis supports the effectiveness of endophytes in mitigating drought, nitrogen deficiency, and salinity stress in a wide range of host species with little evidence of plant-endophyte specificity.

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WillistonPlantPath's curator insight, September 5, 4:47 PM
More evidence to promote the importance of the plant associated microbiome!