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Expression dynamics of the Medicago truncatula transcriptome during the symbiotic interaction with Sinorhizobium meliloti: which role for nitric oxide ?

Medicago truncatula is one of the most studied model plants. Nevertheless, the genome of this legume remains incompletely determined. We used RNA-Seq to characterize the transcriptome during the early organogenesis of the nodule and during its functioning. We detected 37,333 expressed transcription units (TUs), 1,670 had never been described before and were functionally annotated. We identified 7,595 new transcribed regions, mostly corresponding to 5’ and 3’ UTR extensions and new exons associated with 5,264 previously annotated genes. We also inferred 23,165 putative transcript isoforms from 6,587 genes and measured the abundance of transcripts for each isoform, which suggests an important role for alternative splicing in the generation of proteome diversity in M. truncatula. Finally, we carried out a differential expression analysis, which provided a comprehensive view of transcriptional reprogramming during nodulation. In particular, depletion of nitric oxide in roots inoculated with Sinorhizobium meliloti greatly increased our understanding of the role of this reactive species in the optimal establishment of the symbiotic interaction, in revealing differential patterns of expression for 2,030 genes and, in pointing to the inhibition of the expression of defense genes.

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Plant-Microbe Symbioses
Symbiotic associations between plants and microbes
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Microbiology Today: Soil

Microbiology Today: Soil | Plant-Microbe Symbioses | Scoop.it
The United Nations General Assembly has designated 2015 International Year of Soils to raise awareness of the importance of soil to human existence and to widen the understanding and function of soil and soil ‘health’. To tie in with this initiative the May issue of Microbiology Today, the Society’s quarterly magazine, focuses on soil.

Leonardo Da Vinci’s words “we know more about the movement of celestial bodies than about the soil underfoot” echo through the magazine because there is so much still to learn about soil and the microbes within it. Soil is a source of life-saving therapeutics, from microbes such as Streptomyces spp but is also the home of hazardous microbes such as Clostridium tetani that can cause tetanus in humans, and many other as yet unknown organisms that could help or hinder humanity. 
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Pyridine-type alkaloid composition affects bacterial community composition of floral nectar

Pyridine-type alkaloid composition affects bacterial community composition of floral nectar | Plant-Microbe Symbioses | Scoop.it
Pyridine-type alkaloids are most common in Nicotiana species. To study the effect of alkaloid composition on bacterial community composition in floral nectar, we compared the nicotine-rich wild type (WT) N. attenuata, the nicotine biosynthesis-silenced N. attenuata that was rich in anatabine and the anabasine-rich WT N. glauca plants. We found that the composition of these secondary metabolites in the floral nectar drastically affected the bacterial community richness, diversity and composition. Significant differences were found between the bacterial community compositions in the nectar of the three plants with a much greater species richness and diversity in the nectar from the transgenic plant. The highest community composition similarity index was detected between the two wild type plants. The different microbiome composition and diversity, caused by the different pyridine-type alkaloid composition, could modify the nutritional content of the nectar and consequently, may contribute to the change in the nectar consumption and visitation. These may indirectly have an effect on plant fitness.
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Any change in metabolite composition will affect the bacterial community... The biological consequences of this remain to be demonstrated.

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Can the defensive mutualism between grasses and fungal endophytes protect non-symbiotic neighbours from soil pathogens?

Background and aims
It is proposed that Epichloë endophytes have a role protecting host grasses against pathogens. However, it is unclear whether this protection is extended to other non-symbiotic plants. Here we explored the effect of the asexual fungal symbiont, Epichloë occultans, on the interaction between Lolium multiflorum host plants and soil pathogens, and its potential positive side-effect on neighbouring plants.
Methods
We conducted two microcosm experiments to assess the endophyte effect on seedling establishment of the host grass and other non-symbiotic grasses in the presence of soil pathogens. With an in-vitro experiment, we tested whether the endophyte inhibits, during seed germination, the growth of these pathogens.
Results
Independently of pathogen identity, the endophyte improved host establishment (6 %). The endophyte also enhanced the establishment of the neighbouring grass Bromus catharticus (≈20 %) only in soil with Rhizoctonia solani. The endophyte in seed reduced the growth (≈20 %) of two out of four pathogens (Fusarium acuminatum and R. solani).
Conclusions
We conclude that asexual endophytes could protect host grasses against pathogens but most importantly, that they can have protective effects beyond their hosts. Since effects depended on pathogen and plant identity, more experiments are needed in order understand the ecological meaning of these positive side-effects.
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Study of nitrogen and carbon transfer from soil organic matter to Tuber melanosporum mycorrhizas and ascocarps using 15N and 13C soil labelling and whole-genome oligoarrays

Study of nitrogen and carbon transfer from soil organic matter to Tuber melanosporum mycorrhizas and ascocarps using 15N and 13C soil labelling and whole-genome oligoarrays | Plant-Microbe Symbioses | Scoop.it
Background and aims
We previously showed by 13CO2 host labelling that almost all of the constitutive carbon allocated to the truffles originated from the host. The objective of this present work was to determine the putative capacity of T. melanosporum ectomycorrhizas and ascocarps to use soil carbon and to uptake or assimilate soil nitrate.
Methods
The current investigation involved 13C and 15N soil labelling by incorporating labelled leaf litter and expression of genes involved in carbon and nitrogen metabolism in ascocarps and ectomycorrhizas.
Results
The ascocarps harvested in the labelled plots were highly enriched in 15N but were almost never enriched in 13C. The main source of soil mineral nitrogen was nitrate. A nitrate transporter, one nitrate reductase and a nitrite reductase were well expressed in ectomycorrhizas. Several genes involved in aminoacid synthesis or in transamination processes were also well expressed in ectomycorrhizas. No nitrate transporter was expressed in ascocarps where the CAZyme genes upregulated were mainly Glycosyltransferases involved in saccharide transfer.
Conclusion
Ascocarps did not exhibit saprotrophic capacity for C, supporting previous results from 13CO2 host labelling showing that C is provided by the host tree. The 15N present in the ascocarps after soil labelling is supplied as ammonium or aminoacids by the ectomycorrhizas, which are able to uptake, reduce and metabolize nitrate.
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Differences in Arbuscular Mycorrhizal Fungal Community Composition in Soils of Three Land Use Types in Subtropical Hilly Area of Southern China

Land use type is key factor in restoring the degraded soils due to its impact on soil chemical properties and microbial community. In this study, the influences of land use type on arbuscular mycorrhizal fungal (AMF) community and soil chemical properties were assessed in a long-run experimental station in subtropical hilly area of southern China. Soil samples were collected from forest land, orchard and vegetable field. Soil chemical properties were analyzed, and PCR-DGGE was performed to explore the AMF community structure. Cloning and sequencing of DGGE bands were conducted to monitor AMF community composition. Results indicate that the contents of total P, available P and available K were the highest while the contents of soil organic matter, total N, total K and available N were the lowest in vegetable field soils, with forest land soils vice versa. According to DGGE profiling, AMF community in forest soils was more closely related to that in orchard soils than that in vegetable field soils. Sequencing indicated that 45 out of 53 excised bands were AMF and 64.4% of AMF belonged to Glomeraceae, including some “generalists” present in all soils and some “specialists” present only in soils of particular land use. Category principle component analysis demonstrated that total N, soil organic matter and available P were the most important factors affecting AMF community, and some AMF phylotypes were closely associated with particular soil chemical properties. Our data suggest that AMF communities are different with different land use types.
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Elements and ectomycorrhizal symbiosis affecting the growth of Japanese larch seedlings regenerated on slopes of an active volcano in northern Japan

Elements and ectomycorrhizal symbiosis affecting the growth of Japanese larch seedlings regenerated on slopes of an active volcano in northern Japan | Plant-Microbe Symbioses | Scoop.it
The mountain slope of an active volcano is a severe environment for the regeneration of larch (Larix kaempferi Sarg. hereafter larch) seedlings. To determine parameters affecting the growth of larch seedlings, we analyzed stoichiometry of elements in the soils and plant organs, ectomycorrhizal (ECM) colonization, and photosynthetic abilities. These parameters were compared with two different elevations. From nutrient analysis of plant organs from larch seedlings grown on the slope of a volcano, potassium (K) was insufficient compared with the seedlings grown in other habitats. Symbiosis with ECM fungi enabled the uptake of nutrients, especially phosphorous (P) and nitrogen (N). The main factor affecting the differences in relative height growth rate (RHGr) of larch was attributed to ECM colonization. There was a positive relationship between ECM colonization and concentrations of P or N in needles. Larch seedlings with high rates of ECM colonization showed high concentrations of P and N, and had high photosynthetic rates. At lower elevation sites, concentrations of N and K in needles were low with high density of individuals. Moreover, larch showed a high accumulation of aluminum (Al) and iron (Fe) even though the amount of these elements in the soil was small. These seedlings exhibited a suppressed photosynthetic rate and RHGr. Symbiosis with ECM fungi could suppress the excessive uptake of Al and Fe.
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Mechanotransduction: use the force(s)

Mechanotransduction - how cells sense physical forces and translate them into biochemical and biological responses - is a vibrant and rapidly-progressing field, and is important for a broad range of biological phenomena. This forum explores the role of mechanotransduction in a variety of cellular activities and highlights intriguing questions that deserve further attention.
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Genome-wide association analysis of symbiotic nitrogen fixation in common bean

Genome-wide association analysis of symbiotic nitrogen fixation in common bean | Plant-Microbe Symbioses | Scoop.it
A genome-wide association study (GWAS) was conducted to explore the genetic basis of variation for symbiotic nitrogen fixation (SNF) and related traits in the Andean Diversity Panel (ADP) comprising 259 common bean (Phaseolus vulgaris) genotypes. The ADP was evaluated for SNF and related traits in both greenhouse and field experiments. After accounting for population structure and cryptic relatedness, significant SNPs were identified on chromosomes Pv03, Pv07 and Pv09 for nitrogen derived from atmosphere (Ndfa) in the shoot at flowering, and for Ndfa in seed. The SNPs for Ndfa in shoot and Ndfa in seed co-localized on Pv03 and Pv09. Two genes Phvul.007G050500 and Phvul.009G136200 that code for leucine-rich repeat receptor-like protein kinases (LRR-RLK) were identified as candidate genes for Ndfa. LRR-RLK genes play a key role in signal transduction required for nodule formation. Significant SNPs identified in this study could potentially be used in marker-assisted breeding to accelerate genetic improvement of common bean for SNF.

Via Christophe Jacquet
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Identification of an Endophytic Antifungal Bacterial Strain Isolated from the Rubber Tree and Its Application in the Biological Control of Banana Fusarium Wilt

Identification of an Endophytic Antifungal Bacterial Strain Isolated from the Rubber Tree and Its Application in the Biological Control of Banana Fusarium Wilt | Plant-Microbe Symbioses | Scoop.it
Banana Fusarium wilt (also known as Panama disease) is one of the most disastrous plant diseases. Effective control methods are still under exploring. The endophytic bacterial strain ITBB B5-1 was isolated from the rubber tree, and identified as Serratia marcescens by morphological, biochemical, and phylogenetic analyses. This strain exhibited a high potential for biological control against the banana Fusarium disease. Visual agar plate assay showed that ITBB B5-1 restricted the mycelial growth of the pathogenic fungus Fusarium oxysporum f. sp. cubense race 4 (FOC4). Microscopic observation revealed that the cell wall of the FOC4 mycelium close to the co-cultured bacterium was partially decomposed, and the conidial formation was prohibited. The inhibition ratio of the culture fluid of ITBB B5-1 against the pathogenic fungus was 95.4% as estimated by tip culture assay. Chitinase and glucanase activity was detected in the culture fluid, and the highest activity was obtained at Day 2 and Day 3 of incubation for chitinase and glucanase, respectively. The filtrated cell-free culture fluid degraded the cell wall of FOC4 mycelium. These results indicated that chitinase and glucanase were involved in the antifungal mechanism of ITBB B5-1. The potted banana plants that were inoculated with ITBB B5-1 before infection with FOC4 showed 78.7% reduction in the disease severity index in the green house experiments. In the field trials, ITBB B5-1 showed a control effect of approximately 70.0% against the disease. Therefore, the endophytic bacterial strain ITBB B5-1 could be applied in the biological control of banana Fusarium wilt.
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Autralian fungi: Mycorrhiza

Autralian fungi: Mycorrhiza | Plant-Microbe Symbioses | Scoop.it
he word mycorrhiza is derived from the Classical Greek words for 'mushroom' and 'root'. In a mycorrhizal association the fungal hyphae of an underground mycelium are in contact with plant roots, but without the fungus parasitizing the plant. In fact the association is commonly (but by no means always) mutually beneficial. Through photosynthesis a chlorophyll-containing plant makes simple carbohydrates (using carbon dioxide, water and sunlight). While it is clear that the majority of plants form mycorrhizas, the exact percentage is uncertain, but it is likely to lie somewhere between 80% and 90%. In many of these associations between 10% and 30% of the food produced by the plant moves through to the fungi.

A point about spelling - you’ll often see mycorrhizae as another older spelling of the plural of mycorrhiza.

While the classical Greek word for mushroom is part of the word mycorrhiza, there are many mycorrhizal fungi which have fruiting bodies other than mushrooms. An example is Hydnum repandum . It’s superficially mushroom-like (stem and cap), but below the cap there are spines rather than gills. There’s more about the fruiting bodies of mycorrhizal fungi later on.

This section gives some basic facts about mycorrhizas. As these associations are important for plant health, they have been extensively researched, both in Australia and overseas. Hence, there is a lot of information available, both on the internet and in printed form. An excellent mycorrhizal website, especially from an Australian perspective, has been created by Mark Brundrett of the University of Western Australia [http://mycorrhizas.info/].It deals mainly with ectomycorrhizas and VA mycorrhizas (both of which will be explained shortly) and gives much detailed information, numerous illustrations, many references and links to numerous other mycorrhizal sites. Further in this section there will be links to specific areas within that site.

Another very useful website, with links to numerous other sites and bibliographies of printed information, is the Mycorrhiza Literature Exchange. [http://mycorrhiza.ag.utk.edu/] The webpage of the new International Mycorrhizal Society (formed in 2002) [http://www.mycorrhizas.org/] may eventually replace the Mycorrhiza Information Exchange.

The printed references given in the button give useful overviews and are the source of much of the information presented here. I’ll make special mention of the first of these because it is very recent and with copious references. It also has further information on all the topics discussed below and contains some interesting hypotheses about the evolution of mycorrhizas.
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Methylobacterium aquaticum strain NO00 the guardian of rice

Methylobacterium aquaticum strain NO00 the guardian of rice | Plant-Microbe Symbioses | Scoop.it
MicrobeWorld explores the world of microbes with vivid images and descriptions. Learn about microbiology, what microbiologists do, how they do it, and current topics in the news.
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Science (perspective) : Ecological communities by design

In synthetic ecology, a nascent offshoot of synthetic biology, scientists aim to design and construct microbial communities with desirable properties. Such mixed populations of microorganisms can simultaneously perform otherwise incompatible functions (1). Compared with individual organisms, they can also better resist losses in function as a result of environmental perturbation or invasion by other species (2). Synthetic ecology may thus be a promising approach for developing robust, stable biotechnological processes, such as the conversion of cellulosic biomass to biofuels (3). However, achieving this will require detailed knowledge of the principles that guide the structure and function of microbial communities


Via Stéphane Hacquard, Francis Martin
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Hologenome theory supported by co-occurrence networks of species-specific bacterial communities in siphonous algae (Caulerpa)

Hologenome theory supported by co-occurrence networks of species-specific bacterial communities in siphonous algae (Caulerpa) | Plant-Microbe Symbioses | Scoop.it

The siphonous algae of the Caulerpa genus harbor internal microbial communities hypothesized to play important roles in development, defense and metabolic activities of the host. Here we characterize the endophytic bacterial community of four Caulerpa taxa in the Mediterranean Sea, through 16S rRNA amplicon sequencing. Results reveal a striking alpha diversity of the bacterial communities, similar to levels found in sponges and coral holobionts. These comprise 1) a very small core community shared across all hosts (<1% of the total community), 2) a variable portion (ca. 25%) shared by some Caulerpa taxa but not by all, that might represent environmentally acquired bacteria and 3) a large (>70%) species-specific fraction of the community, forming very specific clusters revealed by modularity in networks of co-occurrence, even in areas where distinct Caulerpa taxa occurred in sympatry. Indirect inferences based on sequence homology suggest that these communities may play an important role in the metabolism of their host, in particular on their ability to grow on anoxic sediment. These findings support the hologenome theory and the need for a holistic framework in ecological and evolutionary studies of these holobionts that frequently become invasive.


Via Stéphane Hacquard
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Healthy, Happy Soil with Mycorrhizal -

Healthy, Happy Soil with Mycorrhizal - | Plant-Microbe Symbioses | Scoop.it

While mycelium wears a lot of hats, it has one primary job – to turn everything into soil, and then to feed the plants and trees that surround it. With an amazing intelligence, it’s wraps its mycelium filaments – called hyphae – around the roots of plants and trees. Fungal hyphae and plant roots working together are called mycorrhizae and it’s truly a symbiotic, life-giving relationship that sustains entire ecosystems.

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The effect of lime on the rhizosphere processes and elemental uptake of white lupin

Acid soils cover 30–40% of the world’s arable land and represent one of the major constraints to agricultural production. Lime is routinely added to soil to improve fertility and to reduce the solubility of elements such as aluminum (Al) and cadmium (Cd). White lupin is cultivated globally, however, this is done mainly on acidic soils because of its calcifuge characteristics resulting from its limited ability to compartmentalize calcium (Ca). In abiotic stress conditions, lupins exude organic acids and flavonoids from cluster roots. This can increase the availability of essential soil nutrients to the plant but also exacerbate the uptake of contaminants. We aimed to determine the effect of liming on the rhizosphere processes of white lupin plants in two high-fertility soils, which were treated with seven levels of lime. Nutrient availability and plant uptake was assessed with a pot experiment. Three lime levels have been chosen for a further rhizotron study. Diffusive gradient in thin layers (DGT) gels were applied on selected root zones and then analyzed by laser ablation inductively-coupled plasma mass spectrometry (LA ICP-MS).

The results showed that lime affected the solubility of extractable elements and the plant uptake. In soils treated with different levels of lime, the uptake of nutrients was sufficient to avoid nutrient deficiency. However, analysis of the DGT gels only showed mobilization around the cluster root of the plant grown in the untreated soil. The results indicate that white lupin can be grown at pH as high as 7.50 with 10 wt% lime without suffering from nutrient deficiencies.
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Elevated CO2: Plant associated microorganisms and carbon sequestration

Alterations in plant rhizodeposition under elevated CO2 (eCO2) are likely to influence below-ground plant–microbe interactions and soil C dynamics. There are studies on influence of elevated CO2 on soil microorganisms and below-ground microbial processes. However there is general lack of information on how altered plant–microbe interactions under eCO2 will influence belowground C-sequestration. In the present review we focus on the greenhouse gas CO2 with relevance to its effect on plant associated beneficial and pathogenic microorganisms in terrestrial ecosystems. Role of these microorganisms in belowground nutrient cycling and soil aggregation is discussed with reference to soil C-sequestration. This review demonstrates that eCO2 influence the richness, composition and structure of soil microbial community and the influence is more on active microbial communities and in the vicinity of roots. High C:N ratio under eCO2 favors fungi with wider C:N ratio and nutrient acquisition ability and biological nitrogen fixers. The ecosystems with fungal-dominated soil communities may have higher C retention than bacterial dominated soil communities. However, soil C-sequestration through plant growth, is strongly controlled by availability of nitrogen and nutrients required for biological nitrogen fixation. Nitrogenous and other chemical fertilizers show positive effect on C-sequestration but carry a carbon cost. Promotion of biological nitrogen fixers, and nutrient solubilizers and mobilizers may help in maintaining soil nutrient balance for higher C-sequestration. However more data need to be generated on the response of various plant beneficial as well as pathogenic microbial communities to eCO2. We suggest that plant associated communities and related processes to be researched in long term studies for alteration under eCO2 so as to assess their C-sequestration potential and identify management strategies for enhanced sequestration.
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Some Morpho-Physiological Characteristics of Mung Bean Mycorrhizal Plants under Different Irrigation Regimes in Field Condition

In this study we determined some morpho-physiological characteristics of mung bean plants under various irrigation regimes (irrigation after 50, 100, 150 and 200 mm evaporation from pan class A) and mycorrhizal fungi inoculation (Glomus mosseae, Glomus intraradices). The highest and lowest seed yield was obtained from plants irrigated after 50 and 200 mm evaporation from pan, respectively. Root dry weight, root volume, leaf phosphorus and relative water content were decreased in plants under water deficit stress. Whereas, under various level of severe water deficit the proline content, total soluble carbohydrates and leaf nitrogen were increased. Mycorrhizal colonization was observed to be higher in well-watered plants rather than in stressed plants. Furthermore, the mycorrhizal plants produced a higher seed yield (161 g/m2), leaf phosphorus, leaf nitrogen, chlorophyll index, proline, total soluble carbohydrates content, relative water content, root length, root volume, root dry weight and root/shoot weight ratio as compared with non-mycorrhizal plants.
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Diversifying selection by Desmodiinae legume species on Bradyrhizobium symbionts

Diversifying selection by Desmodiinae legume species on Bradyrhizobium symbionts | Plant-Microbe Symbioses | Scoop.it
Desmodium and Hylodesmum (Papilionoideae Subtribe Desmodiinae) are among the most common herbaceous perennial legumes native to eastern North America. To analyze the population structure of their Bradyrhizobium sp. root-nodule bacteria, 159 isolates were sampled from ten host species across a 1000 km region. Phylogenetic analysis of four housekeeping loci (2164 bp) and two loci in the symbiosis island (SI) chromosomal region (1374 bp) indicated extensive overlap in symbiont utilization, with each common bacterial clade found on 2–7 species of these legume genera. However, host species differed considerably in the relative proportion of symbionts belonging to different Bradyrhizobium clades. High phylogenetic incongruence between trees for housekeeping loci and SI loci suggested that diversification of these Bradyrhizobium lineages involved substantial horizontal gene transfer. Plant inoculation with strains from six Bradyrhizobium clades revealed marked disparity in relative bacterial reproductive success across four Desmodium species. Estimated yield of Bradyrhizobium progeny cells per plant ranged from zero to >109, and strains with high fitness on one host sometimes reproduced poorly on other host species. Diversifying selection on bacteria, arising from differential success in habitats with different Desmodium and Hylodesmum taxa, is therefore likely to affect Bradyrhizobium diversity patterns at the landscape level.
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Some Morpho-Physiological Characteristics of Mung Bean Mycorrhizal Plants under Different Irrigation Regimes in Field Condition

In this study we determined some morpho-physiological characteristics of mung bean plants under various irrigation regimes (irrigation after 50, 100, 150 and 200 mm evaporation from pan class A) and mycorrhizal fungi inoculation (Glomus mosseae, Glomus intraradices). The highest and lowest seed yield was obtained from plants irrigated after 50 and 200 mm evaporation from pan, respectively. Root dry weight, root volume, leaf phosphorus and relative water content were decreased in plants under water deficit stress. Whereas, under various level of severe water deficit the proline content, total soluble carbohydrates and leaf nitrogen were increased. Mycorrhizal colonization was observed to be higher in well-watered plants rather than in stressed plants. Furthermore, the mycorrhizal plants produced a higher seed yield (161 g/m2), leaf phosphorus, leaf nitrogen, chlorophyll index, proline, total soluble carbohydrates content, relative water content, root length, root volume, root dry weight and root/shoot weight ratio as compared with non-mycorrhizal plants.
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Plant cutin genesis: unanswered questions

Plant cutin genesis: unanswered questions | Plant-Microbe Symbioses | Scoop.it
•Recent advances improved our understanding of how biopolyester cutin is constructed; two main approaches have been reported, as follows.
•Cutin is polymerized by specific extracellular acyltransferase enzymes.
•Cutin is the final result of a nonprotein extracellular self-assembly process of its monomers.
•Both models still need further development and improvement, as critically described in this review.
The genesis of cutin, the main lipid polymer present in the biosphere, has remained elusive for many years. Recently, two main approaches have attempted to explain the process of cutin polymerization. One describes the existence of an acyltransferase cutin synthase enzyme that links activated monomers of cutin in the outer cell wall, while the other shows that plant cutin is the final result of an extracellular nonenzymatic self-assembly and polymerizing process of cutin monomers. In this opinion article, we explain both models and suggest that they could be pieces of a more complex biological scenario. We also highlight their different characteristics and current limitations, and suggest a potential synergism of both hypotheses.
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Jason Downing - Mycorrhizal Associations of Two Native Florida Orchids

Mycorrhizal associations of two native Florida orchids: Cyrtopodium punctatum and Eulophia alta – Jason Downing, Florida International University – 1st Annua...
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Use of cover crops increases diversity in soil pore sizes, organic matter

As we walk along a forest path, the soil beneath our feet seems like a uniform substance. However, it is an intricate network of soil particles, pores, minerals, soil microbes, and more. It is awash in variety.

Soil is a living, dynamic substance, and the microbial life within it is crucial to providing plant life with the food they need to grow. The microbes can be bacteria or fungi, but both need space—the pores—for a good living environment.

Soil particles that clump together are aggregates. These are the architectural building blocks of soil.  Their presence has a major effect on the behavior of the soil as a community. Multiple processes form the aggregates:  cycles of wetting-drying, thawing-freezing, earthworm activity, actions by fungi, and interaction with plant roots.
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Diversifying selection by Desmodiinae legume species on Bradyrhizobium symbionts

Diversifying selection by Desmodiinae legume species on Bradyrhizobium symbionts | Plant-Microbe Symbioses | Scoop.it
Desmodium and Hylodesmum (Papilionoideae Subtribe Desmodiinae) are among the most common herbaceous perennial legumes native to eastern North America. To analyze the population structure of their Bradyrhizobium sp. root-nodule bacteria, 159 isolates were sampled from ten host species across a 1000 km region. Phylogenetic analysis of four housekeeping loci (2164 bp) and two loci in the symbiosis island (SI) chromosomal region (1374 bp) indicated extensive overlap in symbiont utilization, with each common bacterial clade found on 2–7 species of these legume genera. However, host species differed considerably in the relative proportion of symbionts belonging to different Bradyrhizobium clades. High phylogenetic incongruence between trees for housekeeping loci and SI loci suggested that diversification of these Bradyrhizobium lineages involved substantial horizontal gene transfer. Plant inoculation with strains from six Bradyrhizobium clades revealed marked disparity in relative bacterial reproductive success across four Desmodium species. Estimated yield of Bradyrhizobium progeny cells per plant ranged from zero to >109, and strains with high fitness on one host sometimes reproduced poorly on other host species. Diversifying selection on bacteria, arising from differential success in habitats with different Desmodium and Hylodesmum taxa, is therefore likely to affect Bradyrhizobium diversity patterns at the landscape level.
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Rhizosphere bacteria and fungi associated with plant growth in soils of three replanted apple orchards

Rhizosphere bacteria and fungi associated with plant growth in soils of three replanted apple orchards | Plant-Microbe Symbioses | Scoop.it
Background and aims
High-throughput 454 pyrosequencing was applied to investigate differences in bacterial and fungal communities between replant and closely situated control non-replant (fallow) soils.
Methods
The V1-V3 region of the bacterial 16S rRNA gene and the ITS1 region of fungi from the different soils were sequenced using 454 pyrosequencing (Titanium chemistry), and data were analysed using the MOTHUR pipeline.
Results
The bacterial phyla Proteobacteria, Actinobacteria and Acidobacteria dominated in both fallow and replant apple orchard soils, and community composition at both phylum and genus level did not significantly differ according to NP-MANOVA. The fungal phyla Ascomycota, Zygomycota and Basidiomycota were dominant, and communities also did not differ in composition at either phylum or genus level. High positive Pearson correlations with plant growth in a plant growth assay performed with apple rootstocks plantlets were detected for the bacterial genera Gp16 and Solirubrobacter (r: >0.82) and fungal genera Scutellinia, Penicillium, Lecythophora and Paecilomyces (r: >0.65). Strong negative correlations with plant growth were detected for the bacterial genera Chitinophaga and Hyphomicrobium (r: <−0.78) and the fungal genera Acremonium, Fusarium and Cylindrocarpon (r: <−0.81).
Conclusions
Study findings are in part consistent with those of previous research, but also highlight associations between apple plants and certain microbial genera. The functional role of these genera in affecting soil health and fertility should be further investigated.
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Rescooped by Jean-Michel Ané from Plant roots and rhizosphere
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Reconsidering mutualistic plant–fungal interactions through the lens of effector biology

Reconsidering mutualistic plant–fungal interactions through the lens of effector biology | Plant-Microbe Symbioses | Scoop.it

Highlights•

Mutualistic mycorrhizal plant–fungal interactions have shaped the evolution of plant life on land.

Effector-like small secreted proteins are used by beneficial fungi to alter the physiological status of the plant host such that symbiosis is favoured.

Known symbiotic effectors divert host cellular defense pathways.

Mutualistic mycorrhizal plant–fungal interactions have shaped the evolution of plant life on land. In these intimate associations, fungal hyphae grow invasively within plant tissues. Despite this invasion, these mycorrhizal fungi are not repulsed leading to a great deal of research focused on the signals exchanged between mutualistic fungi and their host plants in an effort to understand how these relationships are established. In this review, we focus on one type of signal used by mutualistic fungi during symbiosis: effector proteins. These small secreted proteins have recently been found to be used by a range of beneficial fungi to alter the physiological status of the plant host such that symbiosis is favoured. We discuss how the role of these novel proteins has altered our vision of how the ‘mutualistic’ lifestyle evolved in fungi: rather than being perceived as beneficial by their plant hosts, these microbes currently viewed as ‘beneficial’ may actually be overcoming the defences of their plant hosts in a mechanism originally thought to be unique to pathogenic microbes.


Via Christophe Jacquet
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