Plant-Microbe Symbiosis
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Conditional Requirement for Exopolysaccharide in the Mesorhizobium-Lotus Symbiosis

Conditional Requirement for Exopolysaccharide in the Mesorhizobium-Lotus Symbiosis | Plant-Microbe Symbiosis | Scoop.it

Rhizobial surface polysaccharides are required for nodule formation on the roots of at least some legumes but the mechanism(s) by which they act are yet to be determined. As a first step to investigate the function of exopolysaccharide (EPS) in the formation of determinate nodules, we isolated Mesorhizobium loti mutants affected in various steps of EPS biosynthesis and characterised their symbiotic phenotypes on two Lotus species. The wild-type M. loti strain R7A produced both high-molecular-weight EPS and lower-molecular-weight (LMW) polysaccharide fractions whilst most mutant strains produced only LMW fractions. Mutants affected in predicted early biosynthetic steps (e.g. exoB) formed nitrogen-fixing nodules on L. corniculatus and L. japonicus cv. Gifu, whereas mutants affected in mid/late biosynthetic steps (e.g. exoU) induced uninfected nodule primordia, and occasionally a few infected nodules following a lengthy delay. These mutants were disrupted at the stage of infection thread (IT) development. Symbiotically-defective EPS and Nod factor mutants functionally complemented each other in co-inoculation experiments. The majority of full-length ITs observed harbored only the EPS mutant strain and did not show bacterial release, whereas the nitrogen-fixing nodules contained both mutants. Examination of the symbiotic proficiency of the exoU mutant on various L. japonicus ecotypes revealed both host and environmental factors were linked to the requirement for EPS. These results reveal a complex function for M. loti EPS in determinate nodule formation and suggest that EPS plays a signalling role at both the stages of IT initiation and bacterial release.

 

Kelly S, Muszyński A, Kawaharada Y, Hubber AM, Sullivan J, Sandal N, Carlson R, Stougaard J, Ronson C. (2012). Mol Plant Microbe Interact. Nov 7. [Epub ahead of print]


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Plant-Microbe Symbiosis
Beneficial associations between plants and microbes
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Integrated proteomics and metabolomics suggests symbiotic metabolism and multimodal regulation in a fungal-endobacterial system

Integrated proteomics and metabolomics suggests symbiotic metabolism and multimodal regulation in a fungal-endobacterial system | Plant-Microbe Symbiosis | Scoop.it
Many plant-associated fungi host endosymbiotic endobacteria with reduced genomes. While endobacteria play important roles in these tri-partite plant–fungal–endobacterial systems, the active physiology of fungal endobacteria has not been characterized extensively by systems biology approaches. Here, we use integrated proteomics and metabolomics to characterize the relationship between the endobacterium Mycoavidus sp. and the root-associated fungus Mortierella elongata. In nitrogen-poor media, M. elongata had decreased growth but hosted a large and growing endobacterial population. The active endobacterium likely extracted malate from the fungal host as the primary carbon substrate for energy production and biosynthesis of phospho-sugars, nucleobases, peptidoglycan and some amino acids. The endobacterium obtained nitrogen by importing a variety of nitrogen-containing compounds. Further, nitrogen limitation significantly perturbed the carbon and nitrogen flows in the fungal metabolic network. M. elongata regulated many pathways by concordant changes on enzyme abundances, post-translational modifications, reactant concentrations and allosteric effectors. Such multimodal regulations may be a general mechanism for metabolic modulation.

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Diversity of arbuscular mycorrhizal fungi in Tectona grandis Linn.f. plantations and their effects on growth of micropropagated plantlets

Regeneration of stands of valuable tropical hardwood tree species for sustainable harvest requires production of seedlings with high probabilities of survival. One way to enhance the vigor of plants for outplanting is pre-colonization of roots by arbuscular mycorrhizal (AM) fungi. We pursued the strategy that the most promising AM fungus candidates for inoculation would be those associated with the tree of interest in the field. AM fungus communities were assessed in five plantations of Tectona grandis Linn.f. A total of 18 AM fungal morphotypes were found, representing four families: Glomeraceae (49.6%), Acaulosporaceae (24.9%), Claroideoglomeraceae (20.8%), and Gigasporaceae (4.8%). AM fungus spore density was negatively correlated with soil organic carbon. Some of these AM fungi, plus Rhizophagus irregularis, were established in pot culture and in vitro with transformed carrot roots, and subsequently used to inoculate micropropagated plantlets of T. grandis. Tectona grandis plantlets inoculated in vitro were successfully colonized by all AM fungi studied. Plants inoculated with Funneliformis mosseae were taller than uninoculated plants. Tectona grandis plantlets inoculated with the AM fungus Claroideoglomus etunicatum PBT03 were taller than uninoculated controls in ex vitro experiments. This study provides early insight for the targeted use of the AM symbiosis in production of important tree species in future greenhouse studies and reforestation.

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Persistence of endophytic fungi in cultivars of Lolium perenne grown from seeds stored for 22 years

PREMISE OF THE STUDY: Genetic resources for forage crops often consist of seeds of specific species and cultivars in cold storage for future use in breeding and selection programs. Temperate grasses such as Lolium perenne, used worldwide for forage and turf, produce seeds commonly infected by hyphae of an endophytic fungus (Epichloë festucae var. lolii). This research determined whether endophytes could persist and infect seedlings of L. perenne emerging from seeds stored for over two decades.

METHODS: Endophyte-infected seeds (>90% infected) of four cultivars were obtained in 1994 and stored dry in plastic bags at 4°C. Seed germination was tested after 12 yr (for two cultivars) and after 18 and 22 yr (for all cultivars). Seedling leaf sheaths were excised, stained, and examined at 400× for endophytic hyphae to quantify infection frequency (% plants infected) and intensity (mean number of endophytic hyphae per field of view).

KEY RESULTS: Seed germination after 22 yr depended on cultivar, ranging from 53 to 78%. Between 58 and 73% of plants grown from seeds stored for 22 yr still contained viable endophytic hyphae. Infection intensity remained at original levels for 18 yr in one cultivar; however, in all cultivars, infection intensity declined significantly between 18 and 22 yr.

CONCLUSIONS: Persistence of the grass seed–endophyte symbiosis for over 20 yr surpasses all prior records of endophyte longevity within stored seeds. Storage of germplasm of cool-season grass cultivars that contain potentially beneficial fungal endophytes should be possible for several decades under dry, cold conditions.
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Wow... 22 years!

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Predicted protein-protein interactions in the moss Physcomitrella patens : a new bioinformatic resource

Predicted protein-protein interactions in the moss Physcomitrella patens : a new bioinformatic resource | Plant-Microbe Symbiosis | Scoop.it
Background
Physcomitrella patens, a haploid dominant plant, is fast becoming a useful molecular genetics and bioinformatics tool due to its key phylogenetic position as a bryophyte in the post-genomic era. Genome sequences from select reference species were compared bioinformatically to Physcomitrella patens using reciprocal blasts with the InParanoid software package. A reference protein interaction database assembled using MySQL by compiling BioGrid, BIND, DIP, and Intact databases was queried for moss orthologs existing for both interacting partners. This method has been used to successfully predict interactions for a number of angiosperm plants.

Results
The first predicted protein-protein interactome for a bryophyte based on the interolog method contains 67,740 unique interactions from 5,695 different Physcomitrella patens proteins. Most conserved interactions among proteins were those associated with metabolic processes. Over-represented Gene Ontology categories are reported here.

Conclusion
Addition of moss, a plant representative 200 million years diverged from angiosperms to interactomic research greatly expands the possibility of conducting comparative analyses giving tremendous insight into network evolution of land plants. This work helps demonstrate the utility of “guilt-by-association” models for predicting protein interactions, providing provisional roadmaps that can be explored using experimental approaches. Included with this dataset is a method for characterizing subnetworks and investigating specific processes, such as the Calvin-Benson-Bassham cycle.
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Changes in richness and community composition of ectomycorrhizal fungi among altitudinal vegetation types on Mount Kinabalu in Borneo

Changes in richness and community composition of ectomycorrhizal fungi among altitudinal vegetation types on Mount Kinabalu in Borneo | Plant-Microbe Symbiosis | Scoop.it
The distribution patterns of tropical ectomycorrhizal (ECM) fungi along altitudinal gradients remain largely unknown. Furthermore, despite being an iconic site for biodiversity research, virtually nothing is known about the diversity and spatial patterns of fungi on Mt Kinabalu and neighbouring mountain ranges.
We carried out deep DNA sequencing of soil samples collected between 425 and 4000 m above sea level to compare richness and community composition of ECM fungi among altitudinal forest types in Borneo. In addition, we tested whether the observed patterns are driven by habitat or by geometric effect of overlapping ranges of species (mid-domain effect).
Community composition of ECM fungi was strongly correlated with elevation. In most genera, richness peaked in the mid-elevation montane forest zone, with the exception of tomentelloid fungi, which showed monotonal decrease in richness with increasing altitude. Richness in lower-mid- and mid-elevations was significantly greater than predicted under the mid-domain effect model.
We provide the first insight into the composition of ECM fungal communities and their strong altitudinal turnover in Borneo. The high richness and restricted distribution of many ECM fungi in the montane forests suggest that mid-elevation peak richness is primarily driven by environmental characteristics of this habitat and not by the mid-domain effect.
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Tuber indicum shapes the microbial communities of ectomycorhizosphere soil and ectomycorrhizae of an indigenous tree (Pinus armandii)

Tuber indicum shapes the microbial communities of ectomycorhizosphere soil and ectomycorrhizae of an indigenous tree (Pinus armandii) | Plant-Microbe Symbiosis | Scoop.it
The aim of this study was to investigate the effect of an ectomycorrhizal fungus (Tuber indicum) on the diversity of microbial communities associated with an indigenous tree, Pinus armandii, and the microbial communities in the surrounding ectomycorhizosphere soil. High-throughput sequencing was used to analyze the richness of microbial communities in the roots or rhizosphere of treatments with or without ectomycorrhizae. The results indicated that the bacterial diversity of ectomycorhizosphere soil was significantly lower compared with the control soil. Presumably, the dominance of truffle mycelia in ectomycorhizosphere soil (80.91%) and ectomycorrhizae (97.64%) was the main factor that resulted in lower diversity and abundance of endophytic pathogenic fungi, including Fusarium, Monographella, Ustilago and Rhizopus and other competitive mycorrhizal fungi, such as Amanita, Lactarius and Boletus. Bacterial genera Reyranena, Rhizomicrobium, Nordella, Pseudomonas and fungal genera, Cuphophyllus, Leucangium, Histoplasma were significantly more abundant in ectomycorrhizosphere soil and ectomycorrhizae. Hierarchical cluster analysis of the similarities between rhizosphere and ectomycorrhizosphere soil based on the soil properties differed significantly, indicating the mycorrhizal synthesis may have a feedback effect on soil properties. Meanwhile, some soil properties were significantly correlated with bacterial and fungal diversity in the rhizosphere or root tips. Overall, this work illustrates the interactive network that exists among ectomycorrhizal fungi, soil properties and microbial communities associated with the host plant and furthers our understanding of the ecology and cultivation of T. indicum.

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Inducing phenolic production and volatile organic compounds emission by inoculating Mentha piperita with plant growth-promoting rhizobacteria

Inducing phenolic production and volatile organic compounds emission by inoculating Mentha piperita with plant growth-promoting rhizobacteria | Plant-Microbe Symbiosis | Scoop.it
Plant growth-promoting rhizobacteria (PGPR) work primarily by improving the nutrient status of plants and increasing plants’ phytohormone production. Although this response has been demonstrated in many plant species, it is not well understood in aromatic plant species. To examine the effect of PGPR strains on the emission of volatile organic compounds (VOCs), total phenolic production and phenylalanine ammonia-lyase (PAL) activity, shoots of peppermint (Mentha piperita) plants were inoculated or co-inoculated with strains of beneficial rhizobacteria.VOC emissions for the inoculated groups were ∼3-fold higher than for controls. Co-inoculated plants produced the greatest increase in VOC emission in comparison to singly inoculated and control plants. The synthesis of phenolic compounds in leaves of all the treated plants was enhanced in comparison with controls; and higher activity of the PAL enzyme was observed in inoculated plants. In view of the economic importance of VOCs and phenolic compounds for a variety of applications in the food and cosmetic industries, P. fluorescens, B. subtilis and P. putida SJ04 have the potential to improve the productivity of cultivated aromatic plants. Better understanding of the processes that affect secondary metabolites accumulation will lead to increased yields of these commercially valuable natural products.

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SEED: The Untold Story | Documentary About Importance of Seed Keeping | Independent Lens | PBS

SEED: The Untold Story | Documentary About Importance of Seed Keeping | Independent Lens | PBS | Plant-Microbe Symbiosis | Scoop.it
SEED: The Untold Story follows passionate seed-keepers protecting our 12,000-year-old food legacy, seeds.
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Can Plant Microbiome Studies Lead to Effective Biocontrol of Plant Diseases?

In this review, the wisdom and efficacy of studies seeking disease attenuating microbes and microbiomes only in healthy plant communities is questioned and an alternative view is posited, namely that success in biocontrol of crop diseases may also come from studies of microbiota, or at least individual species isolates, associated with diseased plants. In support of this view, I summarize the current extensive knowledge of the biology behind what is probably the most successful biocontrol of a plant disease, namely the biocontrol of crown gall of stone fruit using non-pathogenic Rhizobium rhizogenes K84, in which the biocontrol agent itself came from a diseased plant.

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Gut Hack

Gut Hack | Plant-Microbe Symbiosis | Scoop.it
After a lifetime of stomach problems, Josiah Zayner declared war on his own body’s microbes.
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Crazy...

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Permanent Draft Genome Sequence of Ensifer sp. Strain LCM 4579, a Salt-Tolerant, Nitrogen-Fixing Bacterium Isolated from Senegalese Soil

The genus Ensifer (formerly Sinorhizobium) contains many species able to form nitrogen-fixing nodules on plants of the legume family. Here, we report the 6.1-Mb draft genome sequence of Ensifer sp. strain LCM 4579, with a G+C content of 62.4% and 5,613 candidate protein-encoding genes.

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Agrobacterium deltaense sp. nov., an endophytic bacteria isolated from nodule of Sesbania cannabina

A Gram-negative, non-spore-forming, aerobic rods, strain YIC4121T, was isolated from root nodule of Sesbania cannabina grown in Dongying (Yellow River Delta), Shandong Province, PR China. Based on phylogenetic analysis of 16 S rRNA gene sequences, strain YIC4121T was assigned to the genus Agrobacterium with 99.7, 99.3, 99.0, 98.8 and 98.7% sequence similarities to Agrobacterium radiobacter LMG140T, A. pusense NRCPB10T, A. arsenijevicii KFB 330T, A. nepotum 39/7T and A. larrymoorei ATCC51759T. Analysis of the concatenated housekeeping genes (recA-atpD-glnII), showed lower sequence similarities (≤94.6%) between strain YIC4121T and other recognized Agrobacterium species. Strain YIC4121T shared whole-genome average nucleotide identities (ANI) 87.94, 91.27 and 77.42%, with A. pusense NRCPB10T, A. radiobacter LMG140T and A. larrymoorei ATCC51759T. The predominant cellular fatty acids were C19:0 cyclo ω8c, summed feature 2 (C12:0 aldehyde/unknown 10.9525), summed feature 8 (C18:1ω7c/C18:1ω6c), C16:0 3 OH and C16:0. The G + C content of strain YIC4121T was 59.80 mol%. Tween 80, lactulose, citric acid, α-ketoglutaric acid, glycyl-l-glutamic acid and 2, 3-butanediol could not be utilized as carbon source, distinguishing strain YIC4121T from the other related species. Based on the distinctly genetic and phenotypic dissimilarity, a novel species Agrobacterium deltaense sp. nov. is proposed with YIC4121T (=HAMBI 3654T = LMG 29283T) as the type strain.

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Bound by Fate: Reactive Oxygen Species in Receptor-Like Kinase Signaling

In plants, receptor-like kinases (RLKs) and extracellular reactive oxygen species (ROS) contribute to the communication between the environment and the interior of the cell. Apoplastic ROS production is a frequent result of RLK signaling in a multitude of cellular processes. However, it is as yet unclear how ROS signaling downstream of receptor activation is executed. In this review, we provide a broad view of the intricate connections between RLKs and ROS signaling and describe the regulatory events that control and coordinate extracellular ROS production. We propose that concurrent initiation of ROS dependent and independent signaling might be a critical element in establishing cellular responses. Further, we discuss the possible ROS sensing mechanisms in the context of the biochemical environment in the apoplast. We suggest that RLK-dependent modulation of apoplastic and intracellular conditions facilitates ROS perception and signaling. Based on data from plant as well as animal models, we argue that specific RLKs could be components of the ROS sensing machinery or ROS sensors. The importance of the crosstalk between RLK and ROS signaling is discussed in the context of stomatal immunity. Finally, we highlight challenges in the understanding of these signaling processes and provide perspectives for future research.

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Roles of Nuclear Pores and Nucleo-cytoplasmic Trafficking in Plant Stress Responses 

Roles of Nuclear Pores and Nucleo-cytoplasmic Trafficking in Plant Stress Responses  | Plant-Microbe Symbiosis | Scoop.it
The nuclear pore complex (NPC) is a large protein complex that controls the exchange of components between the nucleus and the cytoplasm. In plants, the NPC family components play critical roles not only in essential growth and developmental processes, but also in plant responses to various environmental stress conditions. The involvement of NPC components in plant stress responses is mainly attributed to different mechanisms including control of mRNA/protein nucleo-cytoplasmic trafficking and transcriptional gene regulation. This mini review summarizes current knowledge of the NPC-mediated plant stress responses and provides an overview of the underlying molecular mechanisms.

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Managing and manipulating the rhizosphere microbiome for plant health: A systems approach

Managing and manipulating the rhizosphere microbiome for plant health: A systems approach | Plant-Microbe Symbiosis | Scoop.it
Plants co-evolved with microbes, and plant genotypes that supported microbiomes that increased their own health likely had a fitness advantage under natural selection. Plant domestication and crop breeding under fertilization have largely decoupled the rhizosphere microbiome from plant selection. If important interactions have been lost as a result, there is an exciting opportunity to re-engineer characteristics of beneficial rhizosphere microbiomes back into agricultural cropping systems. New tools will allow us to engineer the rhizosphere with increasing sophistication in the future, but must recognize that the rhizosphere is a highly connected and interactive system.

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Longterm effects of grazing on arbuscular mycorrhizal fungi

Longterm effects of grazing on arbuscular mycorrhizal fungi | Plant-Microbe Symbiosis | Scoop.it
Arbuscular mycorrhizal (AM) fungi are obligate root symbionts and are thought to help plants tolerate grazing. Evidence shows that grazing can stimulate, inhibit, or have no effect on AM fungi. This inconsistency may be due to empirical limitations, specifically: (i) choice of AM fungal response variable, (ii) confounding effects of soil and plant responses to grazing, and (iii) variation in the duration of studies. To test these hypotheses, we compared AM fungi between grazed and ungrazed grassland plots, with grazing exclosures varying in age from 17 to 85 years. Our findings clearly show that grazing does not universally inhibit AM fungi: grazing had no effect on root colonization plots but spore density was higher and soil hyphal length was lower in grazed plots. While soil and plant variables were unrelated to fungal responses, time since grazing cessation was an important factor explaining the difference between grazed and ungrazed AM fungal communities at a site, indicating possible time lags in responses. Understanding of grazing effects on AM fungi can be enhanced by considering multiple fungal responses and increasing the time scale under which they are studied.

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Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change

Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change | Plant-Microbe Symbiosis | Scoop.it

 The ecology of forest soils is an important field of research due to the role of forests as carbon sinks. Consequently, a significant amount of information has been accumulated concerning their ecology, especially for temperate and boreal forests. Although most studies have focused on fungi, forest soil bacteria also play important roles in this environment. In forest soils, bacteria inhabit multiple habitats with specific properties, including bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are shaped by nutrient availability and biotic interactions. Bacteria contribute to a range of essential soil processes involved in the cycling of carbon, nitrogen, and phosphorus. They take part in the decomposition of dead plant biomass and are highly important for the decomposition of dead fungal mycelia. In rhizospheres of forest trees, bacteria interact with plant roots and mycorrhizal fungi as commensalists or mycorrhiza helpers. Bacteria also mediate multiple critical steps in the nitrogen cycle, including N fixation. Bacterial communities in forest soils respond to the effects of global change, such as climate warming, increased levels of carbon dioxide, or anthropogenic nitrogen deposition. This response, however, often reflects the specificities of each studied forest ecosystem, and it is still impossible to fully incorporate bacteria into predictive models. The understanding of bacterial ecology in forest soils has advanced dramatically in recent years, but it is still incomplete. The exact extent of the contribution of bacteria to forest ecosystem processes will be recognized only in the future, when the activities of all soil community members are studied simultaneously.

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Bob Reeves's curator insight, April 19, 7:28 AM
Our understanding of the highly-integrated microbial communities that constitute the Microbiome in healthy, naturalized soils is increasing daily. When nurtured and allowed to run, this engine of nutrient cycling and capture supports all forests - and can be re-engaged to help urban and agricultural ecosystems as well.
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Two Pseudomonad strains facilitate AMF mycorrhization of litchi (Litchi chinensis Sonn.) and improving phosphorous uptake

Two Pseudomonad strains facilitate AMF mycorrhization of litchi (Litchi chinensis Sonn.) and improving phosphorous uptake | Plant-Microbe Symbiosis | Scoop.it
Litchi air-layers were inoculated with fluorescent pseudomonad R62 and R81 (PGPR), and Glomus intraradices (AM fungi) at the time of layering on tree and after detachment of layers from mother tree.

Addition of fluorescent pseudomonad R62 and R81 enhance P uptake in AM fungi inoculated litchi air-layers.

Fluorescent pseudomonad R62 and R81 also increase the colonization of AM fungi in litchi roots.

Litchi air-layers inoculated after detachment from mother tree performed better over tree inoculated air-layers.

For better P nutrition, inoculation of litchi air-layers with fluorescent pseudomonad R62 and R81, and Glomus intraradices is suggested.
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Note that "The leaves samples dried in herbarium sheets were exposed to the X-ray film in the cassettes for 45 days)"

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Arbuscular mycorrhiza formation and its function under elevated atmospheric O3: A meta-analysis

Arbuscular mycorrhiza formation and its function under elevated atmospheric O3: A meta-analysis | Plant-Microbe Symbiosis | Scoop.it
We quantitatively evaluated the effects of elevated O3 on arbuscular mycorrhiza (AM) formation and on AM role in promoting plant growth in regard to several moderating variables (O3 levels, O3 exposure duration, plant types, AM fungi family, and additional stress) by means of meta-analysis of published data. The analysis consisted of 117 trials representing 20 peer-reviewed articles and 16 unpublished trials. Relative to non-mycorrhizal controls, AM inoculation did not significantly alter plant growth (shoot biomass, root biomass, total biomass and plant height) when O3 concentration was less than 80 ppb, but at concentrations above 80 ppb symbiosis was associated with increases of 68% in shoot biomass and 131% in root biomass. AM effects on plant growth were affected by the duration of O3 exposure but did not differ much with AM fungi taxa or plant type. AM symbiosis has also led to higher yields under O3 stress, relative to the non-mycorrhizal plants, and the AM effects have been more pronounced as O3 concentration increases. As with biomass, AM effects on yield have been affected by the duration of O3 exposure, with the greatest increase (100%) occurring at 61–90 d. AM-induced promotion of yield differed with fungal species but not with plant type or other abiotic stress. Colonization of roots by AM fungi has been negatively affected by elevated O3 compared to ambient O3; total mycorrhizal colonization rate (MCR), arbuscular MCR, vesicular MCR and hyphal coil MCR declined as O3 levels rose. AM colonization rates were affected by duration of O3 exposure, plant type, AM fungal taxa and other concurrent stresses in most cases. The analysis showed that AM inoculation has the potential to ameliorate detrimental effects of elevated O3 on plant growth and productivity, despite colonization rates being negatively affected by elevated O3.

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Brachypodium: A Potential Model Host for Fungal Pathogens of Turfgrasses

Brachypodium: A Potential Model Host for Fungal Pathogens of Turfgrasses | Plant-Microbe Symbiosis | Scoop.it
Brachypodium distachyon is a C3 grass that is an attractive model host system for studying pathogenicity of major turfgrass pathogens due to its genetic similarity to many cool-season turfgrasses. Infection assays with two or more isolates of the casual agents of dollar spot, brown patch, and Microdochium patch resulted in compatible interactions with B. distachyon inbred line Bd21-3. The symptoms produced by these pathogens on Bd21-3 closely resembled those observed on the natural turfgrass host (creeping bentgrass), demonstrating that B. distachyon is susceptible to the fungal pathogens that cause dollar spot, brown patch, and Microdochium patch on turfgrasses. The interaction between Sclerotinia homoeocarpa isolates and Brachypodium ecotypes was also investigated. Interestingly, differential responses of these ecotypes to S. homoeocarpa isolates was found, particularly when comparing B. distachyon to B. hybridum ecotypes. Taken together, these findings demonstrate that B. distachyon can be used as a model host system for these turfgrass diseases and leveraged for studies of molecular mechanisms contributing to host resistance.

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A Global Co-expression Network Approach for Connecting Genes to Specialized Metabolic Pathways in Plants

Plants produce diverse specialized metabolites (SMs), but the genes responsible for their production and regulation remain largely unknown, hindering efforts to tap plant pharmacopeia. Given that genes comprising SM pathways exhibit environmentally dependent co-regulation, we hypothesized that genes within a SM pathway would form tight associations (modules) with each other in co-expression networks, facilitating their identification. To evaluate this hypothesis, we used 10 global co-expression datasets, each a meta-analysis of hundreds to thousands of experiments, across eight plant species to identify hundreds of co-expressed gene modules per dataset. In support of our hypothesis, 15.3-52.6% of modules contained two or more known SM biosynthetic genes, and module genes were enriched in SM functions. Moreover, modules recovered many experimentally validated SM pathways, including all six known to form biosynthetic gene clusters (BGCs). In contrast, bioinformatically predicted BGCs (i.e. those lacking an associated metabolite) were no more co-expressed than the null distribution for neighboring genes. These results suggest that most predicted plant BGCs are not genuine SM pathways and argue that BGCs are not a hallmark of plant specialized metabolism. We submit that global gene co-expression is a rich, largely untapped resource for discovering the genetic basis and architecture of plant natural products.

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Formation of Nitrogenase NifDK Tetramers in the Mitochondria of Saccharomyces cerevisiae

Formation of Nitrogenase NifDK Tetramers in the Mitochondria of Saccharomyces cerevisiae | Plant-Microbe Symbiosis | Scoop.it
Transferring the prokaryotic enzyme nitrogenase into a eukaryotic host with the final aim of developing N2 fixing cereal crops would revolutionize agricultural systems worldwide. Targeting it to mitochondria has potential advantages because of the organelle’s high O2 consumption and the presence of bacterial-type iron–sulfur cluster biosynthetic machinery. In this study, we constructed 96 strains of Saccharomyces cerevisiae in which transcriptional units comprising nine Azotobacter vinelandii nif genes (nifHDKUSMBEN) were integrated into the genome. Two combinatorial libraries of nif gene clusters were constructed: a library of mitochondrial leading sequences consisting of 24 clusters within four subsets of nif gene expression strength, and an expression library of 72 clusters with fixed mitochondrial leading sequences and nif expression levels assigned according to factorial design. In total, 29 promoters and 18 terminators were combined to adjust nif gene expression levels. Expression and mitochondrial targeting was confirmed at the protein level as immunoblot analysis showed that Nif proteins could be efficiently accumulated in mitochondria. NifDK tetramer formation, an essential step of nitrogenase assembly, was experimentally proven both in cell-free extracts and in purified NifDK preparations. This work represents a first step toward obtaining functional nitrogenase in the mitochondria of a eukaryotic cell.

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Fungal endophytes from seeds of invasive, non-native Phragmites australis and their potential role in germination and seedling growth

Background and aims

We characterized fungal endophytes of seeds of invasive, non-native Phragmites from three sites in the Great Lakes region to determine if fungal symbiosis could contribute to invasiveness through their effects on seed germination and seedling growth.

Methods

Field-collected seeds were surface sterilized and plated on agar to culture endophytes for ITS sequencing. Prevalence of specific endophytes from germinated and non-germinated seeds, and from seedlings, was compared.

Results

One-third of 740 seeds yielded endophyte isolates. Fifteen taxa were identified with Alternaria sp. representing 54% of all isolates followed by Phoma sp. (21%) and Penicillium corylophilum (12%). Overall germination of seeds producing an isolate (36%) was significantly higher than seeds not producing an isolate (20%). Penicillium in particular was strongly associated with increased germination of seeds from one site. Sixty-three isolates and 11 taxa were also obtained from 30 seedlings where Phoma, Penicillium and Alternaria respectively were most prevalent. There was a significant effect of isolating an endophyte from the seed on seedling growth.

Conclusions

These results suggest that many endophyte taxa are transmitted in seeds and can increase seed germination and seedling growth of invasive Phragmites. The role of fungal endophytes in host establishment, growth and invasiveness in nature requires further research.
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Pseudomonas fluorescens Transportome Is Linked to Strain-Specific Plant Growth Promotion in Aspen Seedlings under Nutrient Stress

Pseudomonas fluorescens Transportome Is Linked to Strain-Specific Plant Growth Promotion in Aspen Seedlings under Nutrient Stress | Plant-Microbe Symbiosis | Scoop.it
Diverse communities of bacteria colonize plant roots and the rhizosphere. Many of these rhizobacteria are symbionts and provide plant growth promotion (PGP) services, protecting the plant from biotic and abiotic stresses and increasing plant productivity by providing access to nutrients that would otherwise be unavailable to roots. In return, these symbiotic bacteria receive photosynthetically-derived carbon (C), in the form of sugars and organic acids, from plant root exudates. PGP activities have been characterized for a variety of forest tree species and are important in C cycling and sequestration in terrestrial ecosystems. The molecular mechanisms of these PGP activities, however, are less well-known. In a previous analysis of Pseudomonas genomes, we found that the bacterial transportome, the aggregate activity of a bacteria's transmembrane transporters, was most predictive for the ecological niche of Pseudomonads in the rhizosphere. Here, we used Populus tremuloides Michx. (trembling aspen) seedlings inoculated with one of three Pseudomonas fluorescens strains (Pf0-1, SBW25, and WH6) and one Pseudomonas protegens (Pf-5) as a laboratory model to further investigate the relationships between the predicted transportomic capacity of a bacterial strain and its observed PGP effects in laboratory cultures. Conditions of low nitrogen (N) or low phosphorus (P) availability and the corresponding replete media conditions were investigated. We measured phenotypic and biochemical parameters of P. tremuloides seedlings and correlated P. fluorescens strain-specific transportomic capacities with P. tremuloides seedling phenotype to predict the strain and nutrient environment-specific transporter functions that lead to experimentally observed, strain, and media-specific PGP activities and the capacity to protect plants against nutrient stress. These predicted transportomic functions fall in three groups: (i) transport of compounds that modulate aspen seedling root architecture, (ii) transport of compounds that help to mobilize nutrients for aspen roots, and (iii) transporters that enable bacterial acquisition of C sources from seedling root exudates. These predictions point to specific molecular mechanisms of PGP activities that can be directly tested through future, hypothesis-driven biological experiments.

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Scooped by Jean-Michel Ané
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Selection and characterization of coal mine autochthonous rhizobia for the inoculation of herbaceous legumes

Coal open pit mining in the South of Santa Catarina state (Brazil) was inappropriately developed, affecting approximately 6.700 ha. Re-vegetation is an alternative for the recovery of these areas. Furthermore, the use of herbaceous legumes inoculated with nitrogen fixing bacteria is motivated due to the difficulty implementing a vegetation cover in these areas, mainly due to low nutrient availability. Therefore, the aim of this work was to evaluate, among 16 autochthonous rhizobia isolated from the coal mining areas, those with the greatest potential to increase growth of the herbaceous legumes Vicia sativa and Calopogonium mucunoides. Tests were conducted in greenhouse containing 17 inoculation treatments (16 autochthonous rhizobia + Brazilian recommended strain for each plant species), plus two treatments without inoculation (with and without mineral nitrogen). After 60 days, nodulation, growth, N uptake, and symbiotic efficiency were evaluated. Isolates characterization was assessed by the production of indole acetic acid, ACC deaminase, siderophores, and inorganic phosphate solubilization. The classification of the isolates was performed by 16 S rDNA gene sequencing. Only isolates UFSC-M4 and UFSC-M8 were able to nodulate C. mucunoides. Among rhizobia capable of nodulating V. sativa, only UFSC-M8 was considered efficient. It was found the presence of more than one growth-promoting attributes in the same organism, and isolate UFSC-M8 presented all of them. Isolates were classified as belonging to Rhizobium, Burkholderia and Curtobacterium. The results suggest the inoculation of Vicia sativa with strain UFSC-M8, classified as Rhizobium sp., as a promising alternative for the revegetation of coal mining degraded areas.

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