Arbuscular mycorrhizal (AM) fungi associate with the vast majority of land plants, providing mutual nutritional benefits and protecting hosts against biotic and abiotic stresses. Significant progress was made recently in our understanding of the genomic organization, the obligate requirements, and the sexual nature of these fungi through the release and subsequent mining of genome sequences. Genomic and genetic approaches also improved our understanding of the signal repertoire used by AM fungi and their plant hosts to recognize each other for the initiation and maintenance of this association. Evolutionary and bioinformatic analyses of host and nonhost plant genomes represent novel ways with which to decipher host mechanisms controlling these associations and shed light on the stepwise acquisition of this genetic toolkit during plant evolution. Mining fungal and plant genomes along with evolutionary and genetic approaches will improve understanding of these symbiotic associations and, in the long term, their usefulness in agricultural settings.
In an approaching scenario of soil nutrient depletion, root association with soil microorganisms can be key for plant health and sustainability [ 1–3 ]. Symbiotic arbuscular mycorrhizal (AM) fungi are major players in helping plants growing under nutrient starvation conditions. They provide plants with minerals like phosphate and, furthermore, act as modulators of plant growth altering the root developmental program [ 4, 5 ]. However, the precise mechanisms involved in this latter process are not well understood. Here, we show that AM fungi are able to modulate root cortex development in Medicago truncatula by activating a novel GRAS-domain transcription factor, MIG1, that determines the size of cortical root cells. MIG1 expression peaks in arbuscule-containing cells, suggesting a role in cell remodeling during fungal accommodation. Roots ectopically expressing MIG1 become thicker due to an increase in the number and width of cortical cells. This phenotype is fully counteracted by gibberellin (GA) and phenocopied with a GA biosynthesis inhibitor or by expression of a dominant DELLA (Δ18DELLA1) protein. MIG1 downregulation leads to malformed arbuscules, a phenotype rescued by Δ18DELLA1, suggesting that MIG1 intersects with the GA signaling to control cell morphogenesis through DELLA1. DELLA1 was shown to be a central node controlling arbuscule branching [ 6–8 ]. Now we provide evidence that, together with MIG1, DELLA1 is responsible for radial cortical cell expansion during arbuscule development. Our data point toward DELLA proteins being not only longitudinal root growth repressors [ 9 ] but also positive regulators of cortical radial cell expansion, extending the knowledge of how DELLAs control root growth.
One of the most detailed genomic studies of any ecosystem to date has revealed an underground world of stunning microbial diversity, and added dozens of new branches to the tree of life.
The bacterial bonanza comes from scientists who reconstructed the genomes of more than 2,500 microbes from sediment and groundwater samples collected at an aquifer in Colorado. The effort was led by researchers from the Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) and UC Berkeley. DNA sequencing was performed at the Joint Genome Institute, a DOE Office of Science User Facility.
As reported online October 24 in the journal Nature Communications, the scientists netted genomes from 80 percent of all known bacterial phyla, a remarkable degree of biological diversity at one location. They also discovered 47 new phylum-level bacterial groups, naming many of them after influential microbiologists and other scientists. And they learned new insights about how microbial communities work together to drive processes that are critical to the planet's climate and life everywhere, such as the carbon and nitrogen cycles.
These findings shed light on one of Earth's most important and least understood realms of life. The subterranean world hosts up to one-fifth of all biomass, but it remains a mystery.
"We didn't expect to find this incredible microbial diversity. But then again, we know little about the roles of subsurface microbes in biogeochemical processes, and more broadly, we don't really know what's down there," says Jill Banfield, a Senior Faculty Scientist in Berkeley Lab's Climate & Ecosystem Sciences Division and a UC Berkeley professor in the departments of Earth and Planetary Science, and Environmental Science, Policy, and Management.
The objective of this symposium is to create a scientific event that is at the forefront of fundamental research in beneficial plant-microbe interactions.
The symposium will bring together about 150 participants in a rather informal atmosphere, facilitating exchanges. We also aim at proposing a highly attractive program at a moderate inscription fee to give the opportunity to researchers - in particular those at the early stage of their career – to participate to an exciting top-level scientific event. Young researchers will have the opportunity to present their work with a poster.
Legumes are essential components of agricultural systems because they enrich the soil in nitrogen and require little environmentally deleterious fertilizers. A complex symbiotic association between legumes and nitrogen-fixing soil bacteria called rhizobia culminates in the development of root nodules, where rhizobia fix atmospheric nitrogen and transfer it to their plant host. Here we describe a quantitative proteomic atlas of the model legume Medicago truncatula and its rhizobial symbiont Sinorhizobium meliloti, which includes more than 23,000 proteins, 20,000 phosphorylation sites, and 700 lysine acetylation sites. Our analysis provides insight into mechanisms regulating symbiosis. We identify a calmodulin-binding protein as a key regulator in the host and assign putative roles and targets to host factors (bioactive peptides) that control gene expression in the symbiont. Further mining of this proteomic resource may enable engineering of crops and their microbial partners to increase agricultural productivity and sustainability.
Rhizobium sp. IRBG74 develops a classical nitrogen-fixing symbiosis with the aquatic legume Sesbania cannabina (Retz.). It also promotes the growth of wetland rice (Oryza sativa L.), but little is known about the rhizobial determinants important for these interactions. In this study, we analyzed the colonization of S. cannabina and rice using a strain of Rhizobium sp. IRBG74 dually marked with β-glucuronidase and the green fluorescent protein. This bacterium colonized S. cannabina by crack entry and through root hair infection under flooded and non-flooded conditions, respectively. Rhizobium sp. IRBG74 colonized the surfaces of wetland rice roots, but also entered them at the base of lateral roots. It became endophytically established within intercellular spaces in the rice cortex, and intracellularly within epidermal and hypodermal cells. A mutant of Rhizobium sp. IRBG74 altered in the synthesis of the rhamnose-containing O-antigen exhibited significant defects, not only in nodulation and symbiotic nitrogen fixation with S. cannabina, but also in rice colonization and plant growth promotion. Supplementation with purified lipopolysaccharides from the wild-type strain, but not from the mutant, restored the beneficial colonization of rice roots, but not fully effective nodulation of S. cannabina. Commonalities and differences in the rhizobial colonization of the roots of wetland legume and rice hosts are discussed.
Ectomycorrhizal fungi (EMF) represent one of the major guilds of symbiotic fungi associated with roots of forest trees, where they function to improve plant nutrition and fitness in exchange for plant carbon. Many groups of EMF exhibit preference or specificity for different plant host genera; a good example is the genus Suillus, which grows in association with the conifer family Pinaceae. We investigated genetics of EMF host-specificity by cross-inoculating basidiospores of five species of Suillus onto ten species of Pinus, and screened them for their ability to form ectomycorrhizae. Several Suillus spp. including S. granulatus, S. spraguei, and S. americanus readily formed ectomycorrhizae (compatible reaction) with white pine hosts (subgenus Strobus), but were incompatible with other pine hosts (subgenus Pinus). Metatranscriptomic analysis of inoculated roots reveals that plant and fungus each express unique gene sets during incompatible vs. compatible pairings. The Suillus-Pinus metatranscriptomes utilize highly conserved gene regulatory pathways, including fungal G-protein signaling, secretory pathways, leucine-rich repeat and pathogen resistance proteins that are similar to those associated with host-pathogen interactions in other plant-fungal systems. Metatranscriptomic study of the combined Suillus-Pinus transcriptome has provided new insight into mechanisms of adaptation and coevolution of forest trees with their microbial community, and revealed that genetic regulation of ectomycorrhizal symbiosis utilizes universal gene regulatory pathways used by other types of fungal-plant interactions including pathogenic fungal-host interactions.
Soil management is fundamental to all agricultural systems and fertilization practices have contributed substantially to the impressive increases in food production. Despite the pivotal role of soil microorganisms in agro-ecosystems, we still have a limited understanding of the complex response of the soil microbiota to organic and mineral fertilization in the very long-term. Here, we report the effects of different fertilization regimes (mineral, organic and combined mineral and organic fertilization), carried out for more than a century, on the structure and activity of the soil microbiome. Organic matter content, nutrient concentrations, and microbial biomass carbon were significantly increased by mineral, and even more strongly by organic fertilization. Pyrosequencing revealed significant differences between the structures of bacterial and fungal soil communities associated to each fertilization regime. Organic fertilization increased bacterial diversity, and stimulated microbial groups (Firmicutes, Proteobacteria, and Zygomycota) that are known to prefer nutrient-rich environments, and that are involved in the degradation of complex organic compounds. In contrast, soils not receiving manure harbored distinct microbial communities enriched in oligotrophic organisms adapted to nutrient-limited environments, as Acidobacteria. The fertilization regime also affected the relative abundances of plant beneficial and detrimental microbial taxa, which may influence productivity and stability of the agroecosystem. As expected, the activity of microbial exoenzymes involved in carbon, nitrogen, and phosphorous mineralization were enhanced by both types of fertilization. However, in contrast to comparable studies, the highest chitinase and phosphatase activities were observed in the solely mineral fertilized soil. Interestingly, these two enzymes showed also a particular high biomass-specific activities and a strong negative relation with soil pH. As many soil parameters are known to change slowly, the particularity of unchanged fertilization treatments since 1902 allows a profound assessment of linkages between management and abiotic as well as biotic soil parameters. Our study revealed that pH and TOC were the majors, while nitrogen and phosphorous pools were minors, drivers for structure and activity of the soil microbial community. Due to the long-term treatments studied, our findings likely represent permanent and stable, rather than transient, responses of soil microbial communities to fertilization.
Endophytes are an endosymbiotic group of microorganisms that colonize in plants and microbes that can be readily isolated from any microbial or plant growth medium. They act as reservoirs of novel bioactive secondary metabolites, such as alkaloids, phenolic acids, quinones, steroids, saponins, tannins, and terpenoids that serve as a potential candidate for antimicrobial, anti-insect, anticancer and many more properties. While plant sources are being extensively explored for new chemical entities for therapeutic purposes, endophytic microbes also constitute an important source for drug discovery. This review aims to comprehend the contribution and uses of endophytes as an impending source of drugs against various forms of diseases and other possible medicinal use.
The other day I was talking to a friend about the need to demystify plants, so that teachers feel as confident in their teaching of plant biology as they do about animal biology. I wonder if sometimes we teach plants too much in isolation, so it’s not always clear how plants relate to other organisms (other than as food).
For me, comparing the evolutionary trajectory of plants as compared to that of other organisms builds a more intuitive understanding of plants. Here are 12 perspectives that highlight how plants are similar to and different from other organisms. The figures are from the Teaching Tools in Plant Biology article “How to be a plant“, where you can also find references to articles that discuss these statements in more depth.
Rising atmospheric carbon dioxide concentration ([CO2]) may modulate the functioning of mycorrhizal associations by altering the relative degree of nutrient and carbohydrate limitations in plants. To test this, we grew Taraxacum ceratophorum and Taraxacum officinale (native and exotic dandelions) with and without mycorrhizal fungi across a broad [CO2] gradient (180–1,000 µL L−1). Differential plant growth rates and vegetative plasticity were hypothesized to drive species-specific responses to [CO2] and arbuscular mycorrhizal fungi. To evaluate [CO2] effects on mycorrhizal functioning, we calculated response ratios based on the relative biomass of mycorrhizal (MBio) and nonmycorrhizal (NMBio) plants (RBio = [MBio − NMBio]/NMBio). We then assessed linkages between RBio and host physiology, fungal growth, and biomass allocation using structural equation modeling. For T. officinale, RBio increased with rising [CO2], shifting from negative to positive values at 700 µL L−1. [CO2] and mycorrhizal effects on photosynthesis and leaf growth rates drove shifts in RBio in this species. For T. ceratophorum, RBio increased from 180 to 390 µL L−1 and further increases in [CO2] caused RBio to shift from positive to negative values. [CO2] and fungal effects on plant growth and carbon sink strength were correlated with shifts in RBio in this species. Overall, we show that rising [CO2] significantly altered the functioning of mycorrhizal associations. These symbioses became more beneficial with rising [CO2], but nonlinear effects may limit plant responses to mycorrhizal fungi under future [CO2]. The magnitude and mechanisms driving mycorrhizal-CO2 responses reflected species-specific differences in growth rate and vegetative plasticity, indicating that these traits may provide a framework for predicting mycorrhizal responses to global change.
Bottom-up evolutionary approaches, including geographically-explicit population genomic analyses, have the power to reveal the mechanistic basis of adaptation. Here we conduct a population genomic analysis in the model legume, Medicago truncatula, in order to characterize population genetic structure and identify symbiosis-related genes showing evidence of spatially-variable selection. Using RAD-seq, we generated over 26,000 SNPs from 191 accessions from within three regions of the native range in Europe. Results from STRUCTURE analysis identify 5 distinct genetic clusters with divisions that separate east and west regions in the Mediterranean basin. Much of the genetic variation is maintained within sampling sites, and there is evidence for isolation by distance. Extensive linkage disequilibrium was identified, particularly within populations. We conducted genetic outlier analysis with FST-based genome scans and a bayesian modeling approach (PCAdapt). There were 70 core outlier loci shared between these distinct methods with one clear candidate symbiosis related gene, DMI1. This work sets that stage for functional experiments to determine the important phenotypes that selection has acted upon and complementary efforts in rhizobium populations.
Experimental evolution is a powerful approach to study the process of adaptation to new environments, including the colonization of eukaryotic hosts. Facultative endosymbionts, including pathogens and mutualists, face changing and spatially structured environments during the symbiotic process, which impose diverse selection pressures. Here we provide evidence that different selection regimes, involving different times spent in the plant environment, can result in either intra- or extracellular symbiotic adaptations.
In previous work, we introduced the symbiotic plasmid of Cupriavidus taiwanensis, the rhizobial symbiont of Mimosa pudica, into the phytopathogen Ralstonia solanacearum and selected three variants able to form root nodules on M. pudica, two (CBM212 and CBM349) being able to rudimentarily infect nodule cells and the third one (CBM356) only capable of extracellular infection of nodules. Each nodulating ancestor was further challenged to evolve using serial ex planta-in planta cycles of either 21 (3 short cycle lineages) or 42 days (3 long cycle lineages). In this study we compared the phenotype of the 18 final evolved clones. Evolution through short and long cycles resulted in similar adaptive paths on lineages deriving from the two intracellularly infectious ancestors, CBM212 and CBM349. In contrast, only short cycles allowed a stable acquisition of intracellular infection in lineages deriving from the extracellularly infecting ancestor, CBM356. Long cycles, instead, favoured improvement of extracellular infection. Our work highlights the importance of the selection regime in shaping desired traits during host-mediated selection experiments.
To profitably produce corn in on Midwestern farms, nitrogen must be added to the soil. But the practice has an unwanted environmental impact: water contamination. A University of Nebraska professor thinks he may have a solution. Special correspondent Ariana Brocious of Harvest Public Media in Nebraska reports.
Legumes are able to access atmospheric di-nitrogen (N2) through a symbiotic relationship with rhizobia that reside within root nodules. In soybean, following N2 fixation by the bacteroids, ammonia is finally reduced in uninfected cells to allantoin and allantoic acid . These ureides present the primary long-distance transport forms of nitrogen (N), and are exported from nodules via the xylem for shoot N supply. Transport of allantoin and allantoic acid out of nodules requires the function of ureide permeases (UPS1) located in cells adjacent to the vasculature [2, 3]. We expressed a common bean UPS1 transporter in cortex and endodermis cells of soybean nodules and found that delivery of N from nodules to shoot, as well as seed set, was significantly increased. In addition, the number of transgenic nodules was increased and symbiotic N2 fixation per nodule was elevated, indicating that transporter function in nodule N export is a limiting step in bacterial N acquisition. Further, the transgenic nodules showed considerable increases in nodule N assimilation, ureide synthesis, and metabolite levels. This suggests complex adjustments of nodule N metabolism and partitioning processes in support of symbiotic N2 fixation. We propose that the transgenic UPS1 plants display metabolic and allocation plasticity to overcome N2 fixation and seed yield limitations. Overall, it is demonstrated that transporter function in N export from nodules is a key step for enhancing atmospheric N2 fixation and nodule function and for improving shoot N nutrition and seed development in legumes.
Soil microorganisms can be used to decrease the input of fertilizers, pesticides and other chemicals. Among soil microorganisms, arbuscular mycorrhizal fungi (AMF) and Rhizobium spp. can promote plant growth. Integration of arbuscular mycorrhizal fungus with Rhizobium spp. thus appears to be a promising approach for sustainable agriculture. The study evaluated the response of pea (Pisum sativum) to AMF species Glomus fasciculatum and Glomus intraradix and Rhizobium leguminosarum bv. viceae, regarding the growth, nodulation and yield. Pea plants were grown in pots until the flowering stage (35 days). Five replicates of control, with Rhizobium and mycorrhiza alone and the dual inoculation of Rhizobium and AMF were maintained during present studies. The obtained results demonstrated that the dual inoculation of pea plants significantly increased the plant growth, nodule biomass and nodule number in comparison with single inoculation with AMF and Rhizobium leguminosarum bv. viceae.
Inorganic phosphate is one of key macronutrients essential for plant growth. The acquisition and distribution of phosphate are mediated by phosphate transporters functioning in various physiological and biochemical processes. In the present study, we comprehensively evaluated the phosphate transporter (PHT) gene family in the latest release of the Populus trichocarpa genome (version 3.0; Phytozome 11.0) and a total of 42 PHT genes were identified which formed five clusters: PHT1, PHT2, PHT3, PHT4, and PHO. Among the 42 PHT genes, 41 were localized to 15 Populus chromosomes. Analysis of these genes led to identification of 5–14 transmembrane segments, most of which were conserved within the same cluster. We identified 234 putative cis elements in the 2-kb upstream regions of the 42 PHT genes, many of which are related to development, stress, or hormone. Tissue-specific expression analysis of the 42 PtPHT genes revealed that 25 were highly expressed in the roots of P. tremula, suggesting that most of them might be involved in Pi uptake. Some PtPHT genes were highly expressed in more than six of the twelve investigated tissues of P. tremula, while the expression of a few of them was very low in all investigated tissues. In addition, the expression of the PtPHT genes was verified by quantitative real-time PCR in four tissues of P. simonii. Transcripts of 7 PtPHT genes were detected in all four tested tissues of P. simonii. Most PtPHT genes were expressed in the roots of P. simonii at high levels. Further, PtPHT1.2 and PtPHO9 expression was increased under drought conditions, irrespective of the phosphate levels. In particular, PtPHT1.2 expression was significantly induced by approximately 90-fold. However, the transcriptional changes of some PtPHT genes under drought stress were highly dependent on the phosphate levels. These results will aid in elucidation of the functions of PtPHT in the growth, development, and stress response of the poplar plant.
In this study four Mesorhizobium strains isolated from Lotus corniculatus nodules in Granada (Spain) were characterized. Their 16S rRNA gene sequences were closely related to those of M. albiziae LMG 23507T and M. chacoense Pr5T showing 99.4 and 99.2% similarity values, respectively. The analysis of concatenated rpoB, recA, atpD and glnII genes showed they formed a cluster with internal similarities higher than 97%. The closest species also were M. albiziae LMG 23507T and M. chacoense Pr5T showing similarity values lower than 92% in rpoB, recA and glnII genes and lower than 96.5% in the atpD gene. These results indicated that the L. corniculatus strains belong to a new species of genus Mesorhizobium which was confirmed by DNA–DNA hybridization and phenotypic characterization. Therefore a new species with the name Mesorhizobium olivaresii sp. nov. is proposed, and the type strain is CPS13T (LMG 29295T = CECT 9099T).
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