Plant-Microbe Symbiosis
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Plant-Microbe Symbiosis
Beneficial associations between plants and microbes
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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 roles of arbuscular mycorrhizal fungi (AMF) in phytoremediation and tree-herb interactions in Pb contaminated soil

The roles of arbuscular mycorrhizal fungi (AMF) in phytoremediation and tree-herb interactions in Pb contaminated soil | Plant-Microbe Symbiosis | Scoop.it
Understanding the roles of arbuscular mycorrhizal fungi (AMF) in plant interaction is essential for optimizing plant distribution to restore degraded ecosystems. This study investigated the effects of AMF and the presence of legume or grass herbs on phytoremediation with a legume tree, Robinia pseudoacacia, in Pb polluted soil. In monoculture, mycorrhizal dependency of legumes was higher than that of grass, and AMF benefited the plant biomass of legumes but had no effect on grass. Mycorrhizal colonization of plant was enhanced by legume neighbors but inhibited by grass neighbor in co-culture system. N, P, S and Mg concentrations of mycorrhizal legumes were larger than these of non-mycorrhizal legumes. Legume herbs decreased soil pH and thereby increased the Pb concentrations of plants. The neighbor effects of legumes shifted from negative to positive with increasing Pb stress levels, whereas grass provided a negative effect on the growth of legume tree. AMF enhanced the competition but equalized growth of legume-legume under unpolluted and Pb stress conditions, respectively. In conclusion, (1) AMF mediate plant interaction through directly influencing plant biomass, and/or indirectly influencing plant photosynthesis, macronutrient acquisition, (2) legume tree inoculated with AMF and co-planted with legume herbs provides an effective way for Pb phytoremediation.
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The soil-borne supremacy

The soil-borne supremacy | Plant-Microbe Symbiosis | Scoop.it
Plants invest a significant proportion of their photosynthetically-fixed carbon sources in the maintenance of rhizosphere microbiota, for example, via exudation of sugars, amino acids, organic acids, mucilage, and dead border cells. In return, beneficial microbes in this so-called rhizosphere microbiome provide important services to the plant as they improve root architecture, enhance nutrient uptake, and provide protection against plant pathogens (Figure 1) [1]. In recent years, advances in next-generation sequencing technology greatly boosted the field of host microbiomics. Detailed analysis of microbial community assembly in the rhizosphere and phyllosphere revived the notion that the microbial composition of the soil is a major determinant of rhizosphere microbiome composition. It also showed in unprecedented detail that root interior, root surface, soil close to the root surface, and unplanted bulk soil have distinct microbiomes [2], and that soil serves as an important microbial reservoir for microbial community assembly in the phyllosphere [3]. Underlying principles of plant-microbiome interactions have been nicely described in the microbial market theory [4], in which economic market characteristics, such as exchange of commodities between trading partners (plant vs. microbe and microbe vs. microbe), ‘price wars’ (best return of investment), supply and demand dynamics, and elimination of the competition, drive community assembly of microbiota at the root-soil interface.
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Strong differences in Quercus robur-associated ectomycorrhizal fungal communities along a forest-city soil sealing gradient

Ectomycorrhizal fungi (EM) that associate with tree roots in a symbiotic relationship may be crucial in mediating tree health in urban environments, but research on the effects of urbanization on EM communities is very limited so far. Here, we compared EM communities of adult pedunculate oaks (Quercus robur) between urban and forest environments, and assessed the effect of soil sealing around the trees on their EM community composition and EM diversity. We sampled 32 oak individuals across 4 sampling classes (Street, Lane, Park and Forest), and we characterized their EM communities using 454 amplicon pyrosequencing. The EM communities were not nested but they were significantly different between all sampling classes, with a very strong community differentiation between forest and urban trees. There were indications that EM richness declined with increasing sealed soil surface, with a significant effect of sampling class on estimated EM richness and diversity. We also identified indicator EM of the different sampling classes. The most important soil factor affecting EM community composition was pH, followed by plant available phosphorus, total nitrogen content and organic matter. Our results may have important implications when developing EM inocula for managing tree health in urban environments.
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Molecular docking of Glycine max and Medicago truncatula ureases with urea; bioinformatics approaches.

Urease (EC 3.5.1.5) is a nickel-dependent metalloenzyme catalyzing the hydrolysis of urea into ammonia and carbon dioxide. It is present in many bacteria, fungi, yeasts and plants. Most species, with few exceptions, use nickel metalloenzyme urease to hydrolyze urea, which is one of the commonly used nitrogen fertilizer in plant growth thus its enzymatic hydrolysis possesses vital importance in agricultural practices. Considering the essentiality and importance of urea and urease activity in most plants, this study aimed to comparatively investigate the ureases of two important legume species such as Glycine max (soybean) and Medicago truncatula (barrel medic) from Fabaceae family. With additional plant species, primary and secondary structures of 37 plant ureases were comparatively analyzed using various bioinformatics tools. A structure based phylogeny was constructed using predicted 3D models of G. max and M. truncatula, whose crystallographic structures are not available, along with three additional solved urease structures from Canavalia ensiformis (PDB: 4GY7), Bacillus pasteurii (PDB: 4UBP) and Klebsiella aerogenes (PDB: 1FWJ). In addition, urease structures of these species were docked with urea to analyze the binding affinities, interacting amino acids and atom distances in urease-urea complexes. Furthermore, mutable amino acids which could potentially affect the protein active site, stability and flexibility as well as overall protein stability were analyzed in urease structures of G. max and M. truncatula. Plant ureases demonstrated similar physico-chemical properties with 833-878 amino acid residues and 89.39-90.91 kDa molecular weight with mainly acidic (5.15-6.10 pI) nature. Four protein domain structures such as urease gamma, urease beta, urease alpha and amidohydro 1 characterized the plant ureases. Secondary structure of plant ureases also demonstrated conserved protein architecture, with predominantly α-helix and random coil structures. In structure-based phylogeny, plant ureases from G. max, M. truncatula and C. ensiformis were clearly diverged from bacterial ureases of B. pasteurii and K. aerogenes. Glu, Thr, His and Gly were commonly found as interacting residues in most urease-urea docking complexes while Glu was available in all docked structures. Besides, Ala and Arg residues, which are reported in active-site architecture of plant and bacterial ureases were present in G. max urea-urease complex but not present in others. Moreover, Arg435 and Arg437 in M. truncatula and G. max, respectively were identified as highly mutable hotspot residues residing in amidohydro 1 domain of enzyme. In addition, a number of stabilizing residues were predicted upon mutation of these hotspot residues however Cys and Thr made strong implications since they were also found in codon-aligned sequences as substitutions of hotspot residues. Comparative analyses of primary sequence and secondary structure in 37 different plants demonstrated quite conserved natures of ureases in plant kingdom. Structure-based phylogeny indicated the presence of a possible prokaryote-eukaryote split and implicated the subjection of bacterial ureases to heavy selection in prokaryotic evolution compared to plants. Urea-urease docking complexes suggested that different species could share common interacting residues as well as may have some other uncommon residues at species-dependent way. In silico mutation analyses identified mutable amino acids, which were predicted to reside in catalytic site of enzyme therefore mutagenesis at these sites seemed to have adverse effects on enzyme efficiency or function. This study findings will become valuable preliminary resource for future studies to further understand the primary, secondary and tertiary structures of urease sequences in plants as well as it will provide insights about various binding features of urea-urease complexes.
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N2 fixation, carbon accumulation, and plant water relations in soybean (Glycine max L. Merrill) varieties sampled from farmers’ fields in South Africa, measured using 15N and 13C natural abundance

N2 fixation, carbon accumulation, and plant water relations in soybean (Glycine max L. Merrill) varieties sampled from farmers’ fields in South Africa, measured using 15N and 13C natural abundance | Plant-Microbe Symbiosis | Scoop.it
In this study, the natural isotopes of N (15N) and C (13C) were used to evaluate symbiotic N nutrition, C accumulation, and plant water-use efficiency in soybean varieties sampled from 37 farmers’ fields across the soybean-producing region of South Africa. The data revealed significant differences in all the parameters measured. Shoot dry matter ranged from 17 to 104 g plant−1, δ15N from −1.11 to +5.51‰, percent N derived from fixation from 21 to 96%, and N-fixed varied from 18 to 298 kg N ha−1. The high δ15N and low %Ndfa in some soybean genotypes were due to inhibition of N2 fixation by soil N uptake. Across the board, soybean variety PAN373 contributed the most symbiotic N (298, 242, and 217 kg N ha−1 in fields 3, 2 and 4, respectively, at Parys), followed by LS6164 (with 271 and 245 kg N ha−1 at Endcot field 1 and Devon field 2, respectively), and LS6150 (with 290 kg N ha−1 in field 1 at Parys). C concentration varied from 44 to 50% in soybean shoots, resulting in high shoot C ranging from 8 to 48 g C plant−1. The δ13C values of soybean shoots ranged from −27.3‰ to −21.1‰ in the 37 fields studied, with PAN1453 from Gransvlei field 1 and PAN737 from Parys field 4 exhibiting much greater δ13C values (−21.1‰ and −23.1‰, respectively), and hence increased water-use efficiency. The positive correlation found between N-fixed and dry matter yield (r = 0.70***), N-fixed and C content (r = 0.62***), and N-fixed and C concentration (r = 0.35*) indicates a functional relationship between N2 fixation and photosynthesis. Conventional tillage, as an agronomic tool, decreased water-use efficiency (or δ13C) in soybean plants possibly through alteration in soil structure and soil water retention. Due to a 2.6 °C higher daily maximum temperature in the North West Province than KwaZulu–Natal and Mpumalanga, soybean plants sampled from that province showed better growth, higher dry matter yield, and enhanced symbiotic performance. This argument was supported by a significantly positive correlation found between average daily maximum temperature and both dry matter yield (r = 0.39*), and N-fixed (r = 0.46**). Furthermore, the plants sampled from North West also showed much greater water-use efficiency due to a 127 and 67 mm less rainfall at that province than KwaZulu–Natal and Mpumalanga, respectively.
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Development of root system architecture of Arabidopsis thaliana in response to colonization by Martelella endophytica YC6887 depends on auxin signaling

Development of root system architecture of Arabidopsis thaliana in response to colonization by Martelella endophytica YC6887 depends on auxin signaling | Plant-Microbe Symbiosis | Scoop.it
Background and aims

Many rhizobacteria promote plant growth by producing hormones that stimulate the development of plant root system and increase plant biomass. The aim of this study was to investigate the growth promotion activity of the bacterial strain Martelella endophytica YC6887 and elucidate the signaling pathways potentially involved in Arabidopsis interaction with M. endophytica YC6887.
Methods

The growth regulation was evaluated by inoculation of strain YC6887 with wild-type Arabidopsis Col-0 seedlings and mutants defective in auxin aux1-7, axr4-2, eir1-1, ethylene ein2-1, etr1-3, jasmonic acid signaling jar1, and root hair deficient mutant rhd6. The auxin response was further determined by using transgenic line DR5::GUS and a polar auxin transport inhibitor, 1-N-naphthylphthalamic acid (NPA).
Results

M. endophytica YC6887 increased the number of lateral roots and plant biomass of Arabidopsis by producing phenylacetic acid. The growth promotion and improved lateral root development by the bacterium decreased in the auxin related mutants, whereas the ethylene and jasmonic acid mutants had a wild type response. The strain YC6887 increased root hair density in wild type Col-0 and recovered the root hair forming ability in root hair deficient mutant rhd6. Moreover, strain YC6887 treatment showed distinct response in DR5::GUS transgenic line compared to the control. Strain YC6887 lost its growth-promoting activity in the presence of NPA, an auxin transport inhibitor. This indicated that strain YC6887 activated the auxin signaling mechanism.
Conclusions

Our results showed that M. endophytica YC6887 promoted plant growth in terms of plant biomass and root system development. Arabidopsis root system development upon M. endophytica YC6887 colonization was dependent on auxin signaling, but independent of ethylene and jasmonic acid signaling.
Jean-Michel Ané's insight:

Martelella endophytica... never heard about this one before!

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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.
Jean-Michel Ané's insight:

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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How do fungal partners affect the evolution and habitat preferences of mycoheterotrophic plants? A case study in Gastrodia

PREMISE OF THE STUDY: Since mycoheterotrophic plants (MHPs) completely depend on their mycorrhizal fungi for carbon, selection of fungal partners has an important role in the speciation of MHPs. However, the causes and mechanisms of mycobiont changes during speciation are not clear. We tested fungal partner shifts and changes in mycorrhizal specificity during speciation of three closely related MHPs—Gastrodia confusa (Gc), G. pubilabiata (Gp), and G. nipponica (Gn) (Orchidaceae)—and correlations between these changes and the vegetation types where each species grows.

METHODS: We investigated the diversity of mycobionts of the three species by sequencing nrDNA ITS, and the sequence data were subjected to test changes in fungal specificity and fungal partner shifts among the three species. Furthermore, we conducted multivariate analysis to test for differences in mycobiont communities of vegetation types where each species grows.

KEY RESULTS: Two saprobic Basidiomycota, Marasmiaceae and Mycenaceae, were dominant fungal partners of the three species, and Gn was simultaneously associated with the ectomycorrhizal Russulaceae and Sebacinaceae. Although mycobiont composition differed among the three species, they also sometimes shared identical fungal species. Multivariate analysis revealed that mycobiont communities of the three species in bamboo thickets differed significantly from those in other vegetation types.

CONCLUSIONS: Fungal partner shifts are not necessarily associated with the evolution of MHPs, and fungal specificity of Gc and Gp was significantly higher than that of Gn, implying that the specificity fluctuates during speciation. Further, Gc exclusively inhabits bamboo thickets, which suggests that adaptation to particular fungi specific to bamboo thickets triggered speciation of this species.
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The arbuscular mycorrhizal fungi colonising roots and root nodules of New Zealand kauri Agathis australis

The arbuscular mycorrhizal fungi colonising roots and root nodules of New Zealand kauri Agathis australis | Plant-Microbe Symbiosis | Scoop.it
As the only endemic member in New Zealand of the ancient conifer family, Araucariaceae, Agathis australis is an ideal species to study putatively long-evolved mycorrhizal symbioses. However, little is known about A. australis root and nodular endophytes, and how mycorrhizal colonisation occurs. We used light, scanning and transmission electron microscopy to characterise colonisation, and 454-sequencing to identify the arbuscular mycorrhizal fungal (AMF) endophyte(s) associated with A. australis roots and nodules. We interpreted the results in terms of the edaphic characteristics of the A. australis-influenced ecosystem. Representatives of five families of Glomeromycota were identified via high-throughput pyrosequencing. Imaging studies showed that there is abundant, but not ubiquitous, colonisation of nodules, which suggests that nodules are mostly colonised by horizontal transmission. Roots were also found to harbour AMF. This study is the first to demonstrate the multiple Glomeromycota lineages associated with A. australis including some that may not have been previously detected.
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Mycorrhizal "nodules"

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Mycorrhizal Fungal Communities Respond to Experimental Elevation of Soil pH and P Availability in Temperate Hardwood Forests

Many forests are affected by chronic acid deposition, which can lower soil pH and limit the availability of nutrients such as phosphorus (P), but the response of mycorrhizal fungi to changes in soil pH and P availability and how this affects tree acquisition of nutrients is not well understood. Here we describe an ecosystem-level manipulation in 72 plots, which increased pH and/or P availability across six forests in Ohio, USA. Two years after treatment initiation, mycorrhizal fungi on roots were examined with molecular techniques, including 454 pyrosequencing. Elevating pH significantly increased arbuscular mycorrhizal (AM) fungal colonization and total fungal biomass, and affected community structure of AM and ectomycorrhizal (EcM) fungi, suggesting that raising soil pH altered both mycorrhizal fungal communities and fungal growth. AM fungal taxa were generally negatively correlated with recalcitrant P pools and soil enzyme activity, whereas EcM fungal taxa displayed variable responses, suggesting that these groups respond differently to P availability. Additionally, the production of extracellular phosphatase enzymes in soil decreased under elevated pH, suggesting a shift in functional activity of soil microbes with pH alteration. Thus, our findings suggest that elevating pH increased soil P availability, which may partly underlie the mycorrhizal fungal responses we observed.
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Plant evolution and terrestrialization during palaeozoic times - the phylogenetic context

Plant evolution and terrestrialization during palaeozoic times - the phylogenetic context | Plant-Microbe Symbiosis | Scoop.it
Terrestrialization probably began more than one billion years ago and irreversibly altered biogeochemical processes at planetary scale. In this paper, we focus on the terrestrialization process of the Streptophyta, the division that includes charophytes and land plants (embryophytes) and whose members are today ecologically dominant in all terrestrial environments. The timing and the phylogenetic context of the early evolution of land plants are reviewed. The available information on the relationships within embryophytes and related organisms is compiled in two informal consensus trees based either on morphological/anatomical or on molecular data. We also consider the algal/embryophyte transition through the analysis of the evidence provided by microfossils (cryptospores and spores). The ongoing debate about the definition of the term cryptospores, but more importantly about the biological affinities of these microfossils that are possibly derived from early land plants, is discussed. All important clades of embryophytes, with a focus on their Palaeozoic representatives, are described; the significance of several embryophyte key characters is evaluated. The terrestrialization of land plants evolved in different steps. The new term “proembryophytic phase” is introduced to define the very long period of time during which the green algae ancestor of land plants acquired all the evolutionary characters that ultimately allowed their terrestrialization since the late Precambrian. Since the Middle Ordovician, an “eoembryophytic phase” characterized the earliest evidence of liverwort-like plants, before the first fossil record of trilete miospores in the Late Ordovician and of first macrofossils of vascular land plants in the Silurian, marking the “eo −/eutracheophytic phase.”
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Endophytic colonization of sugarcane ( Saccharum officinarum ) by the novel diazotrophs Shinella sp. UYSO24 and Enterobacter sp. UYSO10

Endophytic colonization of sugarcane ( Saccharum officinarum ) by the novel diazotrophs Shinella sp. UYSO24 and Enterobacter sp. UYSO10 | Plant-Microbe Symbiosis | Scoop.it
Aims

Sugarcane is a multipurpose crop mostly used in Uruguay for bioethanol production. It requires high amounts of N fertilization for optimal growth, which causes environmental degradation and high production costs. Previously, a bacterial collection associated with surface-sterilized stems of sugarcane was characterized for in vitro plant growth-promoting (PGP) traits. The aims of this study were (1) to determine if selected isolates from the collection are sugarcane growth promoters and (2) to determine if they are true endophytes of sugarcane.
Methods

Plant growth promotion assays were used to study the effects of selected isolates on sugarcane plantlets. Light microscopy, transmission electron, and scanning electron microscopy (TEM, SEM) were employed to describe the structure of the interaction between the plant growth-promoting bacteria and the plants. qPCR was used to quantify the bacteria residing in the inner plant tissues.
Results

Enterobacter sp. UYSO10 and Shinella sp. UYSO24 were confirmed to have a PGP effect on the commercial sugarcane cv. LCP 85384. Both strains were defined as true endophytes of sugarcane plants with this being the first case for a strain in the genus Shinella in grasses.
Conclusions

These data will contribute to the final development of a sugarcane PGP inoculant based on endophytic plant growth-promoting bacteria.
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Medium optimization of β-glucanase production by Bacillus subtilis SAHA 32.6 used as biological control of oil palm pathogen

Beta-glucanase enzyme can degrade β-glucan polysaccharide to saccharide oligomers and glucose monomers. The enzyme can be used as biological control to degrade β-glucan in cell wall of fungal pathogens The objective of this study was to determine the optimum medium for bacterial β-glucanase production and to use the enzyme as biological control of oil palm pathogenic fungi. Medium optimization were carried out using Response Surface Methodology (RSM) with 18 experimental run of Central Composite Design (CCD) on three variables (oat β-glucan, yeast extract, and bacterial inoculum). The results showed that β-glucanase produced by Bacillus subtilis SAHA 32.6 was strongly influenced by bacterial inoculum size than oat β-glucan and yeast extract concentration. Beta-glucanase of optimized medium could inhibit the growth of oil palm pathogenic fungi, i.e Curvularia affinis and Colletotrichum gloeosporioides. The ammonium sulphate fractionation of the β-glucanase could inhibit the fungi better than crude enzyme. The bacterial β-glucanase of B. subtilis SAHA 32.6 can be used as bio-fungicide to attack of pathogenic fungi in the oil palm nursery.
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