Plant-Microbe Symbiosis
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Rhizobia with 16S rRNA and nifH Similar to M. huakuii but Novel recA, glnII, nodA and nodC Genes Are Symbionts of New Zealand Carmichaelinae

Rhizobia with 16S rRNA and nifH Similar to M. huakuii but Novel recA, glnII, nodA and nodC Genes Are Symbionts of New Zealand Carmichaelinae | Plant-Microbe Symbiosis | Scoop.it

New Zealand became geographically isolated about 80 million years ago and this separation gave rise to a unique native flora including four genera of legume, Carmichaelia, Clianthus and Montigena in the Carmichaelinae clade, tribe Galegeae, and Sophora, tribe Sophoreae, sub-family Papilionoideae. Ten bacterial strains isolated from NZ Carmichaelinae growing in natural ecosystems grouped close to the Mesorhizobium huakuii type strain in relation to their 16S rRNA and nifH gene sequences. However, the ten strains separated into four groups on the basis of their recA and glnII sequences: all groups were clearly distinct from all Mesorhizobium type strains. The ten strains separated into two groups on the basis of their nodA sequences but grouped closely together in relation to nodC sequences; all nodA and nodC sequences were novel. Seven strains selected and the M. huakuii type strain (isolated from Astragalus sinicus) produced functional nodules on Carmichaelia spp., Clianthus puniceus and A. sinicus but did not nodulate two Sophora species. We conclude that rhizobia closely related to M. huakuii on the basis of 16S rRNA and nifH gene sequences, but with variable recA and glnII genes and novel nodA and nodC genes, are common symbionts of NZ Carmichaelinae.

 

Heng Wee Tan, Bevan S. Weir, Noel Carter, Peter B. Heenan, Hayley J. Ridgway, Euan K. James, Janet I. Sprent, J. Peter W. Young, Mitchell Andrews (2012).  PLoS ONE 7(10): e47677. 


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Plant-Microbe Symbiosis
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Do soybeans select specific species of Bradyrhizobium during growth?

Do soybeans select specific species of Bradyrhizobium during growth? | Plant-Microbe Symbiosis | Scoop.it
Soybean is an important crop, with processed soybeans being the second largest source of vegetable oil and the largest source of animal protein feed in the world. Nodules on soybean roots are responsible for symbiotic nitrogen fixation, enabling soybean plants to obtain sufficient nitrogen for growth and seed production. Because nitrogen is an essential, but often limiting, nutrient for plant growth, improvements in nitrogen fixation are highly required in agriculture. We recently reported a comprehensive analysis of rhizosphere bacterial communities during soybean growth in a field in Kyoto prefecture, Japan. The bacterial communities of the rhizosphere changed significantly during growth, with potential plant growth-promoting rhizobacteria, including Bacillus, Bradyrhizobium, and Rhizobium, increasing in a stage-specific manner. In this addendum, we focus on changes in Bradyrhizobium during soybean growth, suggesting that soybean plants select for symbiotic partners.
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YES

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Ray Collier's comment, February 13, 9:16 PM
Some of the older literature shows that nodule occupancy is often a mixture of strains. Very interesting research topic.
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USDA ARS Fixing Nitrogen for the World

USDA ARS Fixing Nitrogen for the World | Plant-Microbe Symbiosis | Scoop.it
One of the Agricultural Research Service’s more unusual germplasm collections is devoted to Rhizobium, bacteria that form symbiotic (mutually beneficial) relationships with soybeans, alfalfa, peanuts, beans, and other legumes to convert nitrogen gas from the air into fertilizer for the plants. This process is known as “nitrogen fixation.”

The oldest part of the Rhizobium collection dates back to samples taken more than 100 years ago at the U.S. Department of Agriculture’s Arlington Farm, now the site of the Pentagon. Although informally a collection since 1913, it was formally established as the ARS National Rhizobium Germplasm Resource Collection in 1975 and is currently part of the Soybean Genomics and Improvement Laboratory at the Beltsville [Maryland] Agricultural Research Center.

Driving the formalization of the collection was the 1973 oil embargo and the associated energy crisis, which highlighted the fact that petroleum-based nitrogen fertilizers were limited resources for food production. This emphasized the need to rely more on biological nitrogen fixation for global food security. As a result, the U.S. Agency for International Development provided the original funding to establish the national Rhizobium collection. While petroleum-based nitrogen has remained readily available and production costs have declined, reducing reliance on these fertilizers is still important. Biological nitrogen fixation is also key to growing organic crops.

Today, the National Rhizobium Germplasm Resource Collection has more than 5,000 curated specimens. An additional 5,000 strains have come from other collections around the world and will be incorporated into the national collection.
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Good news... I thought that this collection was not available anymore!

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Microcystin-tolerant Rhizobium protects plants and improves nitrogen assimilation in Vicia faba irrigated with microcystin-containing waters

Irrigation of crops with microcystins (MCs)-containing waters—due to cyanobacterial blooms—affects plant productivity and could be a way for these potent toxins entering the food chain. This study was performed to establish whether MC-tolerant rhizobia could benefit growth, nodulation, and nitrogen metabolism of faba bean plants irrigated with MC-containing waters. For that, three different rhizobial strains—with different sensitivity toward MCs—were used: RhOF96 (most MC-sensitive strain), RhOF125 (most MC-tolerant strain), or Vicz1.1 (reference strain). As a control, plants grown without rhizobia and fertilized by NH4NO3 were included in the study. MC exposure decreased roots (30–37 %) and shoots (up to 15 %) dry weights in un-inoculated plants, whereas inoculation with rhizobia protects plants toward the toxic effects of MCs. Nodulation and nitrogen content were significantly impaired by MCs, with the exception of plants inoculated with the most tolerant strain RhOF125. In order to deep into the effect of inoculation on nitrogen metabolism, the nitrogen assimilatory enzymes (glutamine synthetase (GS) and glutamate synthase (GOGAT)) were investigated: Fertilized plants showed decreased levels (15–30 %) of these enzymes, both in shoots and roots. By contrast, inoculated plants retained the levels of these enzymes in shoots and roots, as well as the levels of NADH-GOGAT activity in nodules. We conclude that the microcystin-tolerant Rhizobium protects faba bean plants and improves nitrogen assimilation when grown in the presence of MCs.
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Biochemical and ecophysiological responses to manganese stress by ectomycorrhizal fungus Pisolithus tinctorius and in association with Eucalyptus grandis

At relatively low concentrations, the element manganese (Mn) is essential for plant metabolism, especially for photosynthesis and as an enzyme antioxidant cofactor. However, industrial and agricultural activities have greatly increased Mn concentrations, and thereby contamination, in soils. We tested whether and how growth of Pisolithus tinctorius is influenced by Mn and glucose and compare the activities of oxidative stress enzymes as biochemical markers of Mn stress. We also compared nutrient accumulation, ecophysiology, and biochemical responses in Eucalyptus grandis which had been colonized by the ectomycorrhizal Pisolithus tinctorius with those which had not, when both were exposed to increasing Mn concentrations. In vitro experiments comprised six concentrations of Mn in three concentrations of glucose. In vivo experiments used plants colonized by Pisolithus tinctorius, or not colonized, grown with three concentrations of Mn (0, 200, and 1000 μM). We found that fungal growth and glucose concentration were correlated, but these were not influenced by Mn levels in the medium. The anti-oxidative enzymes catalase and glutathione S-transferase were both activated when the fungus was exposed to Mn. Also, mycorrhizal plants grew more and faster than non-mycorrhizal plants, whatever Mn exposure. Photosynthesis rate, intrinsic water use efficiency, and carboxylation efficiency were all inversely correlated with Mn concentration. Thus, we originally show that the ectomycorrhizal fungus provides protection for its host plants against varying and potentially toxic concentrations of Mn.
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Mitochondrial comparative genomics and phylogenetic signal assessment of mtDNA among arbuscular mycorrhizal fungi

Mitochondrial comparative genomics and phylogenetic signal assessment of mtDNA among arbuscular mycorrhizal fungi | Plant-Microbe Symbiosis | Scoop.it
Mitochondrial (mt) genes, such as cytochrome C oxidase genes (cox), have been widely used for barcoding in many groups of organisms, although this approach has been less powerful in the fungal kingdom due to the rapid evolution of their mt genomes. The use of mt genes in phylogenetic studies of Dikarya has been met with success, while early diverging fungal lineages remain less studied, particularly the arbuscular mycorrhizal fungi (AMF). Advances in next-generation sequencing have substantially increased the number of publically available mtDNA sequences for the Glomeromycota. As a result, comparison of mtDNA across key AMF taxa can now be applied to assess the phylogenetic signal of individual mt coding genes, as well as concatenated subsets of coding genes. Here we show comparative analyses of publically available mt genomes of Glomeromycota, augmented with two mtDNA genomes that were newly sequenced for this study (Rhizophagus irregularis DAOM240159 and Glomus aggregatum DAOM240163), resulting in 16 complete mtDNA datasets. R. irregularis isolate DAOM240159 and G. aggregatum isolate DAOM240163 showed mt genomes measuring 72,293 bp and 69,505 bp with G + C contents of 37.1% and 37.3%, respectively. We assessed the phylogenies inferred from single mt genes and complete sets of coding genes, which are referred to as “supergenes” (16 concatenated coding genes), using Shimodaira–Hasegawa tests, in order to identify genes that best described AMF phylogeny. We found that rnl, nad5, cox1, and nad2 genes, as well as concatenated subset of these genes, provided phylogenies that were similar to the supergene set. This mitochondrial genomic analysis was also combined with principal coordinate and partitioning analyses, which helped to unravel certain evolutionary relationships in the Rhizophagus genus and for G. aggregatum within the Glomeromycota. We showed evidence to support the position of G. aggregatum within the R. irregularis ‘species complex’.
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Molecular mechanisms of chitin recognition and immune signaling by LysM-receptors

Plants have the ability to recognize microbe-associated molecular patterns (MAMPs) and initiate various defense responses. Chitin is a representative fungal MAMP that triggers defense signaling in a wide range of plant species. In rice, OsCEBiP and OsCERK1 form a receptor complex and play critical roles in chitin-triggered defense signaling. Recently, we found the formation of a unique sandwich-type dimer of OsCEBiP plays an important role for activation of chitin signaling. We now understand why N-acetyl groups and the longer chitin-oligosaccharides are required for receptor binding. We also found OsCERK1 is a bifunctional molecule acting in defense and also in AM symbiosis.
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USDA Blog » USDA Scientists Take an Organic Approach to Improving Carrots

USDA Blog » USDA Scientists Take an Organic Approach to Improving Carrots | Plant-Microbe Symbiosis | Scoop.it
Organic carrots are coming into their own. About 14 percent of U.S.-produced carrots are now classified as organic, making carrots one of the highest ranked crops in terms of the total percentage produced organically. With production and demand increasing in recent years, organic-carrot growers need help deciding which varieties to grow. Some varieties perform well as a conventional crop, but not so well under organic conditions. While conventional growers also can fumigate to control nematodes, bacterial diseases and fungal pathogens, organic growers don’t have that option.

That’s why the work of Agricultural Research Service (ARS) plant geneticist Philipp W. Simon and his colleagues is so important. Simon, who is the research leader of ARS’s Vegetable Crops Research Laboratory in Madison, Wisconsin, is leading the five-year Carrot Improvement for Organic Agriculture (CIOA) project that is ultimately aimed at providing information and helping breeders develop carrots that are tastier, more nutritious and better equipped to combat weeds, diseases and pathogens. It is funded with a National Institute of Food and Agriculture, Organic Agriculture Research and Extension Initiative grant.
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What Plantae can do for you and what you can do for Plantae | Plant Science Today

What Plantae can do for you and what you can do for Plantae | Plant Science Today | Plant-Microbe Symbiosis | Scoop.it
The American Society of Plant Biologists (@ASPB) and Global Plant Council (@GlobalPlantGPC) have recently launched Plantae. It is designed to be the central hub of plant science…your plant science.

Plantae may seem like just another social network, but it is designed to be a much more complex community.
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Medicago truncatula Gaertn. as a model for understanding the mechanism of growth promotion by bacteria from rhizosphere and nodules of alfalfa

The present study showed all the 16 strains isolated and identified from the alfalfa rhizosphere and nodules, and registered in GenBank, to be good candidates for targeted use in studies addressing the rather weak known mechanism of plant growth promotion, including that of Medicago truncatula, a molecular crop model.
Based on physiological, biochemical and molecular analysis, the 16 isolates obtained were ascribed to the following five families: Bacillaceae, Rhizobiaceae, Xantomonadaceae, Enterobacteriaceae and Pseudomonadaceae, within which 9 genera and 16 species were identified. All these bacteria were found to significantly enhance fresh and dry weight of root, shoots and whole 5-week-old seedlings. The bacteria were capable of the in vitro use of tryptophan to produce indolic compounds at various concentrations. The ability of almost all the strains to enhance growth of seedlings and individual roots was positively correlated with the production of the indolic compounds (r = 0.69; P = 0.0001), but not with the 1-aminocyclopropane-1-carboxylate deaminase (ACCD) activity (no correlation). For some strains, it was difficult to conclude whether the growth promotion was related to the production of indolic compounds or to the ACCD activity. It is likely that promotion of M. truncatula root development involves also root interaction with pseudomonads, known to produce 2,4-diacetylphloroglucinol (DAPG), a secondary metabolite reported to alter the root architecture by interacting with an auxin-dependent signaling pathway. Inoculation of seedlings with Pseudomonas brassicacearum KK 5, a bacterium known for its lowest ability to produce indolic compounds, the highest ACCD activity and the presence of the phlD gene responsible for DAPG precursor synthesis, resulted in a substantial promotion of root development. Inoculation with the strain increased the endogenous IAA level in M. truncatula leaves after inoculation of 5-week-old seedlings. Three other strains examined in this study also increased the IAA level in the leaves upon inoculation. Moreover, several other factors such as mobilization of phosphorus and zinc to make them available to plants, iron sequestration by siderophore production and the ability to ammonia production also contributed substantially to the phytostimulatory biofertilizing potential of isolated strains. There is, thus, evidence that Medicago truncatula growth promotion by rhizobacteria involves more than one mechanism.
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A remorin gene is implicated in quantitative disease resistance in maize

A remorin gene is implicated in quantitative disease resistance in maize | Plant-Microbe Symbiosis | Scoop.it
Quantitative disease resistance (QDR) is important for the development of crop cultivars and is particularly useful when loci also confer multiple disease resistance. Despite its widespread use, the underlying mechanisms of QDR remain largely unknown. In this study, we fine-mapped a known quantitative trait locus (QTL) conditioning disease resistance on chromosome 1 of maize. This locus confers resistance to three foliar diseases: northern leaf blight (NLB), caused by the fungus Setosphaeria turcica; Stewart’s wilt, caused by the bacterium Pantoea stewartii; and common rust, caused by the fungus Puccinia sorghi. The Stewart’s wilt QTL was confined to a 5.26-Mb interval, while the rust QTL was reduced to an overlapping 2.56-Mb region. We show tight linkage between the NLB QTL locus and the loci conferring resistance to Stewart’s wilt and common rust. Pleiotropy cannot be excluded for the Stewart’s wilt and the common rust QTL, as they were fine-mapped to overlapping regions. Four positional candidate genes within the 243-kb NLB interval were examined with expression and mutant analysis: a gene with homology to an F-box gene, a remorin gene (ZmREM6.3), a chaperonin gene, and an uncharacterized gene. The F-box gene and ZmREM6.3 were more highly expressed in the resistant line. Transposon tagging mutants were tested for the chaperonin and ZmREM6.3, and the remorin mutant was found to be more susceptible to NLB. The putative F-box is a strong candidate, but mutants were not available to test this gene. Multiple lines of evidence strongly suggest a role for ZmREM6.3 in quantitative disease resistance.
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Inoculation of Brachiaria spp. with the plant growth-promoting bacterium Azospirillum brasilense: An environment-friendly component in the reclamation of degraded pastures in the tropics

Inoculation of Brachiaria spp. with the plant growth-promoting bacterium Azospirillum brasilense: An environment-friendly component in the reclamation of degraded pastures in the tropics | Plant-Microbe Symbiosis | Scoop.it
Estimates are that in Brazil there are about 180 million hectares of pasturelands, 70% with some degree of degradation. Reclamation of such areas demands re-establishment of soil fertility, plant growth and forage production, and microbial inoculants might help in these processes. We evaluated the ability of two strains of Azospirillum brasilense to promote the growth of two genotypes of Brachiaria spp. (=Urochloa spp.). The experiments were set up at three different sites in Brazil, and forage production estimated for 26 cuts in two years. On average, increases of 5.4% and 22.1% in response to N-fertilizer alone and to N-fertilizer in combination with Azospirillum, respectively, were observed over the non-inoculated and non-N-fertilized control treatment. Increase in N accumulation in the biomass in response to Azospirillum was equivalent to a second application of 40 kg of N-fertilizer ha−1. Estimates attributed to the inoculation were of gains of 0.103 Mg C ha−1, corresponding to 0.309 Mg CO2-eq ha−1. Inoculation with Azospirillum may represent a key component of programs to reclaim degraded pastures and help sequestration of CO2 from the atmosphere.
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Distribution of Petrosavia sakuraii (Petrosaviaceae), a rare mycoheterotrophic plant, may be determined by the abundance of its mycobionts

Distribution of Petrosavia sakuraii (Petrosaviaceae), a rare mycoheterotrophic plant, may be determined by the abundance of its mycobionts | Plant-Microbe Symbiosis | Scoop.it
Petrosavia sakuraii (Petrosaviaceae) is a rare, mycoheterotrophic plant species that has a specific symbiotic interaction with a narrow clade of arbuscular mycorrhizal (AM) fungi. In the present study, we tested the hypothesis that the distribution and abundance of mycobionts in two P. sakuraii habitats, Nagiso and Sengenyama (central Honshu, Japan), determine the distribution pattern of this rare plant. Nagiso is a thriving habitat with hundreds of P. sakuraii individuals per 100 m2, whereas Sengenyama is a sparsely populated habitat with fewer than 10 individuals per 100 m2. AM fungal communities associated with tree roots were compared at 20-cm distances from P. sakuraii shoots between the two habitats by molecular identification of AM fungal partial sequences of the small subunit ribosomal RNA gene. The percentage of AM fungal sequences showing over 99 % identity with those of the dominant P. sakuraii mycobionts was high (54.9 %) in Nagiso, but low (13.2 %) in Sengenyama. Accordingly, the abundance of P. sakuraii seems to reflect the proportion of potential mycobionts. It is likely that P. sakuraii mycobionts are not rare in Japanese warm temperate forests since 11.2 % of AM fungal sequences previously obtained from a deciduous broad-leaved forest devoid of P. sakuraii in Mizuho, central Honshu, Japan, were >99 % identical to those of the dominant P. sakuraii mycobionts. Thus, results suggest that the abundant mycobionts may be required for sufficient propagation of P. sakuraii, and this quantitative trait of AM fungal communities required for P. sakuraii may explain the rarity of this plant.
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Appraisal of diversity and functional attributes of thermotolerant wheat associated bacteria from peninsular zone of India

Appraisal of diversity and functional attributes of thermotolerant wheat associated bacteria from peninsular zone of India | Plant-Microbe Symbiosis | Scoop.it
The biodiversity of wheat associated bacteria were deciphered from peninsular zone of India. A total 264 isolated bacteria were analysed through amplified ribosomal DNA restriction analysis (ARDRA, using three restriction enzymes Alu I, Msp I and Hae III, which led to the clustering of these isolates into 12-16 groups for the different sites at >75% similarity index, adding up to 70 groups. 16S rRNA gene based phylogenetic analysis, revealed that all the bacteria were belonged to three phyla Proteobacteria, Firmicutes, and Actinobacteria of 32 disticnt specieces of 15 genera namely: Achromobacter, Alcaligenes, Arthrobacter, Bacillus, Delftia, Enterobacter, Exiguobacterium, Klebsiella, Methylobacterium, Micrococcus, Paenibacillus, Pseudomonas, Rhodobacter, Salmonella and Staphylococcus. Representative strains from each cluster were screened in vitro for plant growth promoting traits. Among plant growth promoting activities, siderophore producers were highest (15%), when compared to indole acetic acid producers (13%), Zn-solubilizers (11%), P- solubilizers (11%), ammonia (10%), hydrogen cyanide producers (9%), biocontrol (8%), N2-fixation (7%), 1-aminocyclopropane-1-carboxylate deaminase (6%), GA producers (6%) and K-solubilizers (5%). Among 32 represenatative strains, Alcaligenes faecalis, Arthrobacter sp., Bacillus siamensis, Bacillus subtilis, Delftia acidovorans, Methylobacterium mesophilicum, Methylobacterium sp., Pseudomonas poae, Pseudomonas putida, and Pseudomonas stutzeri exhibited more than six different plant growth promoting activities at high temperature. Thermotolerant bacterial isolates may have application as inoculants for plant growth promotion and biocontrol agents for crops growing at high temperature condition.
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The LPS O -Antigen in Photosynthetic Bradyrhizobium Strains Is Dispensable for the Establishment of a Successful Symbiosis with Aeschynomene Legumes

The LPS  O -Antigen in Photosynthetic  Bradyrhizobium  Strains Is Dispensable for the Establishment of a Successful Symbiosis with  Aeschynomene  Legumes | Plant-Microbe Symbiosis | Scoop.it
The photosynthetic bradyrhizobia are able to use a Nod-factor independent process to induce nitrogen-fixing nodules on some semi-aquatic Aeschynomene species. These bacteria display a unique LPS O-antigen composed of a new sugar, the bradyrhizose that is regarded as a key symbiotic factor due to its non-immunogenic character. In this study, to check this hypothesis, we isolated mutants affected in the O-antigen synthesis by screening a transposon mutant library of the ORS285 strain for clones altered in colony morphology. Over the 10,000 mutants screened, five were selected and found to be mutated in two genes, rfaL, encoding for a putative O-antigen ligase and gdh encoding for a putative dTDP-glucose 4,6-dehydratase. Biochemical analysis confirmed that the LPS of these mutants completely lack the O-antigen region. However, no effect of the mutations could be detected on the symbiotic properties of the mutants indicating that the O-antigen region of photosynthetic Bradyrhizobium strains is not required for the establishment of symbiosis with Aeschynomene.
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One more time... genetic evidence is the best!

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expVIP: a customisable RNA-seq data analysis and visualisation platform opens up gene expression analysis

The majority of RNA-seq expression studies in plants remain underutilised and inaccessible due to the use of disparate transcriptome references and the lack of skills and resources to analyse and visualise this data. We have developed expVIP, an expression Visualisation and Integration Platform, which allows easy analysis of RNA-seq data combined with an intuitive and interactive interface. Users can analyse public and user-specified datasets with minimal bioinformatics knowledge using the expVIP virtual machine. This generates a custom web browser to visualise, sort and filter the RNA-seq data and provides outputs for differential gene expression analysis. We demonstrate expVIP's suitability for polyploid crops and evaluate its performance across a range of biologically-relevant scenarios. To exemplify its use in crop research we developed a flexible wheat expression browser (www.wheat-expression.com) which can be expanded with user-generated data in a local virtual machine environment. The open-access expVIP platform will facilitate the analysis of gene expression data from a wide variety of species by enabling the easy integration, visualisation and comparison of RNA-seq data across experiments.
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Mycorrhization between Cistus ladanifer L. and Boletus edulis Bull is enhanced by the mycorrhiza helper bacteria Pseudomonas fluorescens Migula

Boletus edulis Bull. is one of the most economically and gastronomically valuable fungi worldwide. Sporocarp production normally occurs when symbiotically associated with a number of tree species in stands over 40 years old, but it has also been reported in 3-year-old Cistus ladanifer L. shrubs. Efforts toward the domestication of B. edulis have thus focused on successfully generating C. ladanifer seedlings associated with B. edulis under controlled conditions. Microorganisms have an important role mediating mycorrhizal symbiosis, such as some bacteria species which enhance mycorrhiza formation (mycorrhiza helper bacteria). Thus, in this study, we explored the effect that mycorrhiza helper bacteria have on the efficiency and intensity of the ectomycorrhizal symbiosis between C. ladanifer and B. edulis. The aim of this work was to optimize an in vitro protocol for the mycorrhizal synthesis of B. edulis with C. ladanifer by testing the effects of fungal culture time and coinoculation with the helper bacteria Pseudomonas fluorescens Migula. The results confirmed successful mycorrhizal synthesis between C. ladanifer and B. edulis. Coinoculation of B. edulis with P. fluorescens doubled within-plant mycorrhization levels although it did not result in an increased number of seedlings colonized with B. edulis mycorrhizae. B. edulis mycelium culture time also increased mycorrhization levels but not the presence of mycorrhizae. These findings bring us closer to controlled B. edulis sporocarp production in plantations.
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Ray Collier's comment, February 13, 9:23 PM
Yes, yes, yes to boletes!
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Micronutrient Enrichment Mediated by Plant-Microbe Interactions and Rice Cultivation Practices

A field experiment was conducted to evaluate the effect of different plant growth promoting microorganisms (PGPM) on micronutrient enrichment of rice crops grown under conventional (flooded) and SRI (System of Rice Intensification) practices. Significant differences were recorded among treatments and cultivation practices in terms of soil microbial activity reflected in enhanced nutrient uptake, enzyme activity, and yield. The Anabaena-based biofilm inoculants were particularly superior under both methods of cultivation, leading to 13-46% enhancement of iron and 15-41% enhancement of zinc in rice grains over uninoculated controls. SRI was found to be superior in terms of enhancing the concentration of zinc, copper, iron, and manganese (Zn, Cu, Fe and Mn), particularly in grains, and significant in increasing the activity of defense- and pathogenesis- related enzymes and yield parameters. This study illustrates the utility of cyanobacteria-based inoculants for both methods of rice cultivation and their significant interactions with the plant, leading to micronutrient enrichment of rice grains. Such formulations can complement the current biofortification strategies and help in combating the problems of malnutrition globally.
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Fungal endophytes in germinated seeds of the common bean, Phaseolus vulgaris

Fungal endophytes in germinated seeds of the common bean, Phaseolus vulgaris | Plant-Microbe Symbiosis | Scoop.it
We conducted a survey of fungal endophytes in 582 germinated seeds belonging to 11 Colombian cultivars of the common bean (Phaseolus vulgaris). The survey yielded 394 endophytic isolates belonging to 42 taxa, as identified by sequence analysis of the ribosomal DNA internal transcribed spacer (ITS) region. Aureobasidium pullulans was the dominant endophyte, isolated from 46.7% of the samples. Also common were Fusarium oxysporum, Xylaria sp. and Cladosporium cladosporioides, but found in only 13.4%, 11.7% and 7.6% of seedlings, respectively. Endophytic colonization differed significantly among common bean cultivars and seedling parts, with the highest colonization occurring in the first true leaves of the seedlings.
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Networking in the Plant Microbiome

Networking in the Plant Microbiome | Plant-Microbe Symbiosis | Scoop.it

Almost all higher organisms, including plants, insects, and mammals, are colonized by complex microbial communities and harbor a microbiome. Emerging studies with plants reveal that these microbiomes are structured and form complex, interconnected microbial networks. Within these networks, different taxa have different roles, and keystone species have been identified that could be crucial for plant health and ecosystem functioning. A new paper in this issue of PLOS Biology by Agler et al. highlights the presence of microbial hubs in these networks that may act as mediators between the plant and its microbiome. A next major frontier is now to link microbiome composition to function. In order to do this, we present a number of hypothetical examples of how microbiome diversity and function potentially influence host performance.


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Beneficial Microbes Affect Endogenous Mechanisms Controlling Root Development

Beneficial Microbes Affect Endogenous Mechanisms Controlling Root Development | Plant-Microbe Symbiosis | Scoop.it
Plants have incredible developmental plasticity, enabling them to respond to a wide range of environmental conditions. Among these conditions is the presence of plant growth-promoting rhizobacteria (PGPR) in the soil. Recent studies show that PGPR affect Arabidopsis thaliana root growth and development by modulating cell division and differentiation in the primary root and influencing lateral root development. These effects lead to dramatic changes in root system architecture that significantly impact aboveground plant growth. Thus, PGPR may promote shoot growth via their effect on root developmental programs. This review focuses on contextualizing root developmental changes elicited by PGPR in light of our understanding of plant–microbe interactions and root developmental biology.

Trends
Interaction between plant roots and the beneficial bacteria within their rhizosphere shapes the bacteria community composition, and enhances plant growth and plant pathogen defense.

Plant growth-promoting rhizobacteria (PGPR) affect cell division and differentiation leading to changes in root system architecture, which contributes to enhanced shoot growth. These modifications are established by changing plant endogenous signaling pathways.

While several PGPR can produce phytohormones, many effects on plant developmental pathways are exerted by other molecules.

Several fungi have the same effects on root system architecture as PGPR, indicating that growth-promoting mechanisms might be conserved across kingdoms.
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Great review. Too bad that it is so Arabidopsis-centric...

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Role of Legumes for and as Horticultural Crops in Sustainable Agriculture

Role of Legumes for and as Horticultural Crops in Sustainable Agriculture | Plant-Microbe Symbiosis | Scoop.it
Legumes are the second largest plant family on earth and arguably the second group of importance to current and past agricultural systems and human nutrition. Despite differences among legumes, their variability as early, medium, to late maturity annual crops that fix nitrogen and survive shading by larger adjacent plants, makes them very versatile in agronomics and horticultural cropping systems. In this chapter, we describe the importance of four vegetable legumes (garden peas, purple-hulled peas, snap beans, and yard-long beans) and a range of more minor legume crops as vegetables in today’s world. Each crop is highlighted for its value in the local diets of peoples of different regions and the cropping systems to which they belong. We follow this by providing a large number of examples where vegetable and non-vegetable legumes can be used as intercrops between cereal crops such as corn or sorghum, between vegetables from the tomato/pepper and eggplant or cabbage/broccoli and cauliflower family or fruit tree seedlings and saplings that are being established. All of this shows that legumes are an amazingly diverse group of vegetable species which are advantageous to intensive horticultural systems.
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The Metagenome of Utricularia gibba 's Traps: Into the Microbial Input to a Carnivorous Plant

The Metagenome of  Utricularia gibba 's Traps: Into the Microbial Input to a Carnivorous Plant | Plant-Microbe Symbiosis | Scoop.it
The genome and transcriptome sequences of the aquatic, rootless, and carnivorous plant Utricularia gibba L. (Lentibulariaceae), were recently determined. Traps are necessary for U. gibba because they help the plant to survive in nutrient-deprived environments. The U. gibba's traps (Ugt) are specialized structures that have been proposed to selectively filter microbial inhabitants. To determine whether the traps indeed have a microbiome that differs, in composition or abundance, from the microbiome in the surrounding environment, we used whole-genome shotgun (WGS) metagenomics to describe both the taxonomic and functional diversity of the Ugt microbiome. We collected U. gibba plants from their natural habitat and directly sequenced the metagenome of the Ugt microbiome and its surrounding water. The total predicted number of species in the Ugt was more than 1,100. Using pan-genome fragment recruitment analysis, we were able to identify to the species level of some key Ugt players, such as Pseudomonas monteilii. Functional analysis of the Ugt metagenome suggests that the trap microbiome plays an important role in nutrient scavenging and assimilation while complementing the hydrolytic functions of the plant.
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Identification of Unknown Carboxydovore Bacteria Dominant in Deciduous Forest Soil via Succession of Bacterial Communities, coxL Genotypes, and Carbon Monoxide Oxidation Activity in Soil Microcosms

Identification of Unknown Carboxydovore Bacteria Dominant in Deciduous Forest Soil via Succession of Bacterial Communities, coxL Genotypes, and Carbon Monoxide Oxidation Activity in Soil Microcosms | Plant-Microbe Symbiosis | Scoop.it
Surveys of the coxL gene, encoding the large subunit of the CO dehydrogenase, are used as a standard approach in ecological studies of carboxydovore bacteria scavenging atmospheric CO. Recent soil surveys unveiled that the distribution of coxL sequences encompassing the atypical genotype coxL type I group x was correlated to the CO oxidation activity. Based on phylogenetic analysis including the available coxL reference genome sequences, this unusual genotype was assigned to an unknown member of the Deltaproteobacteria, with the coxL sequence from Haliangium ochraceum being the sole and closest reference sequence. Here we seek to challenge the proposed taxonomic assignation of the coxL group x genotype through the monitoring of CO consumption activity and microbial community successions during the colonization of sterile soil microcosms inoculated with indigenous microorganisms. In our study, we established that the estimated population density of Deltaproteobacteria was too small to account for the abundance of the coxL group x genotype detected in soil. Furthermore, we computed a correlation network to relate 16S rRNA gene profiles with the succession of coxL genotypes and CO uptake activity in soil. We found that most of the coxL genotypes for which the colonization profile displayed covariance with CO uptake activity were related to potential carboxydovore bacteria belonging to Actinobacteria and Alphaproteobacteria. Our analysis did not provide any evidence that coxL group x genotypes belonged to Deltaproteobacteria. Considering the colonization profile of CO-oxidizing bacteria and the theoretical energy yield of measured CO oxidation rates in soil microcosms, we propose that unknown carboxydovore bacteria harboring the atypical coxL group x genotype are mixotrophic K-strategists.
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Ammonia-oxidizing bacteria are more responsive than archaea to nitrogen source in an agricultural soil

Ammonia-oxidizing bacteria are more responsive than archaea to nitrogen source in an agricultural soil | Plant-Microbe Symbiosis | Scoop.it
In the majority of agricultural soils, ammonium (NH4+) is rapidly converted to nitrate (NO3−) in the biological ammonia and nitrite oxidation processes known as nitrification. The often rate-limiting step of ammonia oxidation to nitrite is mediated by ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA). The response of AOA and AOB communities to organic and conventional nitrogen (N) fertilizers, and their relative contributions to the nitrification process were examined for an agricultural silage corn system using a randomized block design with 4 N treatments: control (no additional N), ammonium sulfate (AS) fertilizer at 100 and 200 kg N ha−1, and steer-waste compost (200 kg total N ha−1) over four seasons. DNA was extracted from the soil, and real-time PCR and 454-pyrosequencing were used to evaluate the quantity and diversity of the amoA gene which encodes subunit A of ammonia monooxygenase. Soil pH, nitrate pools, and nitrification potentials were influenced by ammonium and organic fertilizers after the first fertilization, while changes in AOB abundance and community structure were not apparent until after the second fertilization or later. The abundance of AOA was always greater than AOB but was unaffected by N treatments. In contrast, AOB abundance and community structure were changed significantly by ammonium fertilizers. Specific inhibitors of nitrification were used to evaluate the relative contribution of AOA and AOB to nitrification. We found that AOB dominantly contributed to potential nitrification activity determined at 1 mM ammonium in soil slurries and nitrification potential activity was higher in soils treated with ammonium fertilizers relative to control soils. However, AOA dominated gross nitrification activity in moist soils. Our result suggests that AOB activity and community are more responsive to ammonium fertilizers than AOA, but that in situ nitrification rate is controlled by ammonium availability in this agricultural soil. Understanding this response of AOA and AOB to N fertilizers may contribute to improving strategies for the management of nitrate production in agricultural soils.
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Soil phosphorus fractions and arbuscular mycorrhizal fungi diversity following long-term grazing exclusion on semi-arid steppes in Inner Mongolia

Soil phosphorus fractions and arbuscular mycorrhizal fungi diversity following long-term grazing exclusion on semi-arid steppes in Inner Mongolia | Plant-Microbe Symbiosis | Scoop.it
Grazing exclusion is one of the common grassland management strategies to restore degraded grasslands. The effectiveness of grazing exclusion on sequestering soil organic carbon, increasing total nitrogen and improving soil biological activity has been documented in literature. Few studies, however, have examined the responses of phosphorus (P) fractions and arbuscular mycorrhizal fungi (AMF) diversity to long-term grazing exclusion. In this study, the variations of soil chemical properties, the status of inorganic and organic P fractions in the rhizosphere soil, and the AMF diversity in roots of Leymus chinensis, Stipa krylovii and Cleistogenes squarrosa and in bulk soils were investigated in continuously grazed and ungrazed paddocks (exclusion from grazing for 10–12 years) on typical and meadow steppes in Inner Mongolia, aiming to evaluate the effectiveness of grazing exclusion in improving AMF diversity and soil P status. Grazing exclusion altered plant species compositions and increased aboveground biomass and ground cover, resulting in increased concentrations of soil organic carbon and total nitrogen. The concentration of total phosphorus increased in typical steppes but reduced in meadow steppes, while the concentrations of available P and most P fractions remained unchanged or reduced following 10–12 years of grazing exclusion. Grazing exclusion improved AMF colonization in meadow steppes, but not in typical steppes, attributing to the differences in soil quality, plant species, and AMF phylotypes between two types of steppes. AMF diversity was positively correlated with soil pH, concentrations of soil total nitrogen, total organic carbon, total P, Ca10–P, medium labile organic P, and the activity of alkaline phosphatase, indicating that, on semi-arid steppes in northern China, improved soil conditions would increase the AMF diversity, thus enhancing the productivity of the steppe ecosystem. However, changes of soil AMF phylotypes due to overgrazing would be detrimental to this fragile ecosystem.
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