No organism is an island - a fact that also applies to plants. Healthy plants host complex microbial communities comprising over 100 bacterial species which presumably play important roles in plant growth and health. Plants allow access only to a select community of bacteria, designated the plant microbiota, that originate mainly from a vast diversity of microorganisms present in natural soil. Researchers from the Max Planck Institute for Plant Breeding Research in Cologne together with scientists in Switzerland cultivated over half of the bacteria found on and in the leaves and roots of the model plant Arabidopsis thaliana (thale cress). Using this representative collection of over 400 bacterial strains in pure culture, the researchers can now reconstitute any microbial community in the leaves and roots of Arabidopsis under laboratory settings. This development marks the beginning of a new era in plant-microbe ecology using defined microbiota. One aim of the relatively young field of plant microbiota research has been to generate an inventory of plant-associated microbial communities. Paul Schulze-Lefert from the Max Planck Institute for Plant Breeding Research in Cologne and Julia Vorholt from the ETH Zurich and their colleagues have now taken another important step towards this goal. The team cultivated far in excess of half of the bacterial species colonizing leaves and roots of Arabidopsis plants grown in nature and established a collection of bacterial strains with which the leaf and root microbiota can be reconstituted on germ-free plants. The astonishing similarity between the bacterial communities produced in the laboratory and those found in nature opens the door to microbiota reconstitution biology. The use of such defined communities enables for the first time controlled perturbation of the microbiota under controlled environmental conditions without the vagaries that are inevitable in nature due to environmental fluctuations. The two scientists cultivated up to 65 percent of the bacterial species found in the root microbiota and up to 54 percent of the species of the leaf microbiota as pure cultures. Yet according to the received wisdom in microbial ecology states, it is not possible to cultivate more than one percent of the bacteria from natural environmental samples. "This is simply incorrect," says Schulze-Lefert. "We know from our bacterial cultivation efforts that our core culture collection contains the majority of the bacterial species that is present in the communities and provides a very good representation of the taxonomic diversity of the natural leaf and root microbiota. The collection may not be perfect but it provides a very good starting point for microbiota reconstruction experiments," he adds. Upon closer inspection of bacterial species profiles, Schulze-Lefert and Vorholt observed a considerable similarity between the microbial communities found in the Arabidopsis leaf and root. "Almost half of the species are identical," explains Schulze-Lefert. "Despite the fact that the samples for the root microbiota were collected in Cologne and those for the leaf microbiota in Zurich and Tübingen, if you consider the root and leaf microbiota from a higher taxonomic perspective, that is from the level of the bacterial families and classes present, there are no differences at all. So the microbiota are highly robust in different natural environments," he adds. The Research Groups determined the genomes of 432 bacterial isolates from their collection by DNA sequencing and compared them. "Not only do we have pure cultures for the reconstitution experiments, we also know the complete genome of each community member in our core collection," says Schulze-Lefert. The scientists were then able to compare the biochemical capabilities of the leaf and root microbiota. To do this they combined the genes from the genomes with a computer into functional networks. The similarity of the profiles of bacterial species present in the leaf and root communities corresponds to an extensive overlap in functional capabilities encoded by the corresponding genomes. Such experiments are possible today because the biochemical functions of many genes are known, as are the cellular networks and metabolic reactions in which they are involved. Due to the extensive overlap of genome-encoded functional capabilities and the similarities of the species profiles, Vorholt and Schulze-Lefert concluded that the majority of the leaf- and root-associated bacteria originate from the extraordinarily diverse soil microbiota. This suggests that a plant's leaves are colonized mainly by soil-derived bacteria via the root as stopover site. Nevertheless, it is also possible to observe functional differences encoded by the genomes of leaf- and root-associated bacteria. These relate to apparent differences in the ecological niches of the leaf and root. This can be construed, for example, from the bacterial genes needed to feed on complex carbohydrates that are present on leaves and roots; the root microbiota needs fewer of these, as only roots exude large amounts of simple sugars. The scientists also carried out microbiota reconstitution experiments. To do this, they used a closed artificial environment with sterile clay as a soil substitute, a sterile liquid nutrient medium without organic carbon, and germ-free Arabidopsis seeds. Cultivation was carried out in transparent sterile chambers which were inoculated with defined bacterial communities at different time points. "Although the system is highly artificial, the communities that populate the leaves and roots are remarkably similar to the communities on plants grown in nature," says Schulze-Lefert. Even if the defined microbiota inoculum was added to the clay or on leaves alone, the leaf or root microbiota were able to populate not only their corresponding plant organ but, to a considerable extent, also the remotely located leaf and root organ. If the leaf and root microbiota were mixed and then applied to the clay, the root microbiota outcompeted the leaf-derived bacterial community in the root. A corresponding competitive advantage exists for the leaf microbiota in leaves. This points to a specialization of bacterial communities to leaf and root ecological niches despite the extensive functional overlap between the leaf and root microbiota. The scientists are at an early stage in these microbiota reconstitution experiments. They can now leave out individual bacterial species or entire families from the defined microbiota and test these under different environmental stress conditions. They expect that such controlled perturbation experiments will provide molecular insights into how the bacterial communities mobilize and supply soil nutrients for plant growth and how the microbiota protects its host against microbial pathogens. More information: Yang Bai et al. Functional overlap of the Arabidopsis leaf and root microbiota, Nature (2015). DOI: 10.1038/nature16192
Fluorescent microscopy image of a root of Arabidopsis thaliana (violet) surrounded by a fungal mesh of Colletotrichum tofieldiae (green). The mesh also grows within the root cells (not shown). Credit: MPI f. Plant Breeding Research For a long time, it was thought that the sole role of the immune system was to distinguish between friend and foe and to fend off pathogens. In fact, it is more like a microbial management system that is also involved in accommodating beneficial microorganisms in the plant when required. Researchers from the Max Planck Institute for Plant Breeding Research in Cologne in collaboration with an international consortium of other laboratories discovered this relationship between the model plant Arabidopsis thaliana, or thale cress, and the fungus Colletotrichum tofieldiae. The plant tolerates the fungus when it needs help in obtaining soluble phosphate from the soil and rejects the microbe if it can accomplish this task on its own. Plants grow and thrive only if they have access to soluble phosphate in the soil. They are unable to utilize bound phosphate without help from other organisms. Most plants therefore maintain a mycorrhiza - a fungal mesh around their roots - that supplies them with vital soil-derived nutrients in exchange for carbohydrates, which they produce by photosynthesis. Arabidopsis is one of the few plants that do not have a mycorrhiza. Instead, this species engages in a beneficial relationship with the soil fungus Colletotrichum tofieldiae. This fungus colonizes thale cress through its roots and then lives within and between the root cells. It converts insoluble phosphate in the soil into soluble phosphate and releases the nutrient via the fungal mesh to its plant host, which needs it for growth. "The beneficial interaction between thale cress and Colletotrichum came as a surprise to us, because this fungal family occurs almost everywhere as a pathogen," says Paul Schulze-Lefert, Director of the Max Planck Institute in Cologne. "In maize alone, a relative of this fungus causes crop losses that run into billions of dollars. We therefore wanted to know why Colletotrichum tofieldiae doesn't harm the thale cress plant." Because Schulze-Lefert and colleagues isolated the fungus from a thale cress plant in the Central Plateau of Spain and the fungus does not occur in thale cress plants growing in other regions, they suspected from the outset that the symbiotic relationship has something to do with the local environment. They noted that very little soluble phosphate is present in the soil in the Central Plateau. The Cologne-based scientists demonstrated that an intact innate immune system is needed for the symbiosis and allows the fungus to take up residence in the plant's roots only if the plant is not able to obtain enough soil phosphate on its own. However, if phosphate is plentiful, the plant launches a massive immune response. "It's a fantastically well-regulated system," Schulze-Lefert says. "A foe is therefore recognized as such only in specific circumstances. That's an entirely new take on the immune system." The scientists were also able to show which processes are involved. One process is known as the "phosphate starvation response", by means of which the plant senses the availability of phosphate in the soil and relays this information to a circuit that accelerates or slows plant growth. If soluble phosphate becomes scarce, the nutrient sensing system communicates with one branch of the plant immune system to accommodate the fungal tenant inside roots. This branch of the immune system directs the synthesis of mustard oil glycosides. These compounds are responsible for the sharp and bitter taste of brassicas, which include thale cress, rapeseed, mustard and horseradish. Schulze-Lefert and his colleagues showed that in the absence of this synthesis pathway, C. tofieldiae becomes a life-threatening pathogen for thale cress. "The thale cress plant controls its interaction with its tenant by linking its immune system to a sensor for phosphate availability," says Schulze-Lefert. "It's an elegant solution that extends the role of the immune system to ensure an external supply of nutrients under malnutrition conditions. This has not been previously observed in the plant kingdom." Helper to one, pathogen to others As a next step, the Max Planck researchers want to clarify which molecules mediate communication between the nutrient sensing and the immune systems and how this decision-making process is organized. The only species among the brassicas that do not synthesize mustard oil glycosides, namely the shepherd's purse, does not tolerate the fungus. For the shepherd's purse, C. tofieldiae is a deadly pathogen. Evidently, absence of the synthesis pathway for mustard oil glycosides means that the molecular basis for a beneficial coexistence is missing. The findings are also remarkable in another sense. Whereas healthy plants are colonized by bacterial communities with a reproducible composition, there appears to be less selectivity in the choice of fungal tenants. It is almost as if the individual fungal species are present in the plants purely by accident, because there is no obvious pattern. "We've now shown that a Colletotrichum fungus which we discovered by accident does not take up residence in the plant by accident," says Schulze-Lefert. It serves the thale cress as a substitute for the missing mycorrhiza fungus. Without Colletotrichum, the plant would have a very poor chance of survival in low phosphate soils. The mutual coexistence is beneficial to both partners, but only as long as the right conditions prevail." More information: Hiruma, K., Gerlach, N., Sacristán, S., Nakano, R. T., Hacquard, S., Kracher, B., Neumann, U., Ramírez, D., Bucher, M., O'Connell, R. and P. Schulze-Lefert. Root endophyte Colletotrichum tofieldiae confers plant fitness benefits that are phosphate status-dependent. Cell, 2016.
Srinivasa Rao N.,Computer Application |
Geetha K.A.,Plant Breeding |
Computers and Electronics in Agriculture | Year: 2014
van Dijk J.P.,RIKILT |
de Mello C.S.,RIKILT |
de Mello C.S.,Federal University of Santa Catarina |
Voorhuijzen M.M.,RIKILT |
And 6 more authors.
Regulatory Toxicology and Pharmacology | Year: 2014
An important part of the current hazard identification of novel plant varieties is comparative targeted analysis of the novel and reference varieties. Comparative analysis will become much more informative with unbiased analytical approaches, e.g. omics profiling. Data analysis estimating the similarity of new varieties to a reference baseline class of known safe varieties would subsequently greatly facilitate hazard identification. Further biological and eventually toxicological analysis would then only be necessary for varieties that fall outside this reference class. For this purpose, a one-class classifier tool was explored to assess and classify transcriptome profiles of potato ( Solanum tuberosum) varieties in a model study. Profiles of six different varieties, two locations of growth, two year of harvest and including biological and technical replication were used to build the model. Two scenarios were applied representing evaluation of a 'different' variety and a 'similar' variety. Within the model higher class distances resulted for the 'different' test set compared with the 'similar' test set. The present study may contribute to a more global hazard identification of novel plant varieties. © 2014 Elsevier Inc. Source
Costa F.,University of Bologna |
Costa F.,Research and Innovation Center |
Peace C.P.,Washington State University |
Stella S.,University of Bologna |
And 5 more authors.
Journal of Experimental Botany | Year: 2010
Apple fruit are well known for their storage life, although a wide range of flesh softening occurs among cultivars. Loss of firmness is genetically coordinated by the action of several cell wall enzymes, including polygalacturonase (PG) which depolymerizes cell wall pectin. By the analysis of 'Fuji' (Fj) and 'Mondial Gala' (MG), two apple cultivars characterized by a distinctive ripening behaviour, the involvement of Md-PG1 in the fruit softening process was confirmed to be ethylene dependent by its transcript being down-regulated by 1-methylcyclopropene treatment in MG and in the low ethylene-producing cultivar Fj. Comparing the PG sequence of MG and Fj, a single nucleotide polymorphism (SNP) was discovered. Segregation of the Md-PG1 SNP marker within a full-sib population, obtained by crossing Fj and MG, positioned Md-PG1 in the linkage group 10 of MG, co-located with a quantitative trait locus (QTL) identified for fruit firmness in post-harvest ripening. Fruit firmness and softening analysed in different stages, from harvest to post-storage, determined a shift of the QTL from the top of this linkage group to the bottom, where Md-ACO1, a gene involved in ethylene biosynthesis in apple, is mapped. This PG-ethylene-related gene has beeen positioned in the apple genome on chromosome 10, which contains several QTLs controlling fruit firmness and softening, and the interplay among the allelotypes of the linked loci should be considered in the design of a markerassisted selection breeding scheme for apple texture. © 2010 The Author(s). Source