BackgroundTomato (Solanum lycopersicum) establishes a beneficial symbiosis with arbuscular mycorrhizal (AM) fungi. The formation of the mycorrhizal association in the roots leads to plant-wide modulation of gene expression. To understand the systemic effect of the fungal symbiosis on the tomato fruit, we used RNA-Seq to perform global transcriptome profiling on Moneymaker tomato fruits at the turning ripening stage.ResultsFruits were collected at 55 days after flowering, from plants colonized with Funneliformis mosseae and from control plants, which were fertilized to avoid responses related to nutrient deficiency. Transcriptome analysis identified 712 genes that are differentially expressed in fruits from mycorrhizal and control plants. Gene Ontology (GO) enrichment analysis of these genes showed 81 overrepresented functional GO classes. Up-regulated GO classes include photosynthesis, stress response, transport, amino acid synthesis and carbohydrate metabolism functions, suggesting a general impact of fungal symbiosis on primary metabolisms and, particularly, on mineral nutrition. Down-regulated GO classes include cell wall, metabolism and ethylene response pathways. Quantitative RT-PCR validated the RNA-Seq results for 12 genes out of 14 when tested at three fruit ripening stages, mature green, breaker and turning. Quantification of fruit nutraceutical and mineral contents produced values consistent with the expression changes observed by RNA-Seq analysis.ConclusionsThis RNA-Seq profiling produced a novel data set that explores the intersection of mycorrhization and fruit development. We found that the fruits of mycorrhizal plants show two transcriptomic “signatures”: genes characteristic of a climacteric fleshy fruit, and genes characteristic of mycorrhizal status, like phosphate and sulphate transporters. Moreover, mycorrhizal plants under low nutrient conditions produce fruits with a nutrient content similar to those from non-mycorrhizal plants under high nutrient conditions, indicating that AM fungi can help replace exogenous fertilizer for fruit crops.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-221) contains supplementary material, which is available to authorized users.

Several studies have investigated soil microbial biodiversity, but understanding of the mechanisms underlying plant responses to soil microbiota remains in its infancy. Here, we focused on tomato (Solanum lycopersicum), testing the hypothesis that plants grown on native soils display different responses to soil microbiotas. Using transcriptomics, proteomics, and biochemistry, we describe the responses of two tomato genotypes (susceptible or resistant to Fusarium oxysporum f. sp. lycopersici) grown on an artificial growth substrate and two native soils (conducive and suppressive to Fusarium). Native soils affected tomato responses by modulating pathways involved in responses to oxidative stress, phenol biosynthesis, lignin deposition, and innate immunity, particularly in the suppressive soil. In tomato plants grown on steam-disinfected soils, total phenols and lignin decreased significantly. The inoculation of a mycorrhizal fungus partly rescued this response locally and systemically. Plants inoculated with the fungal pathogen showed reduced disease symptoms in the resistant genotype in both soils, but the susceptible genotype was partially protected from the pathogen only when grown on the suppressive soil. The 'state of alert' detected in tomatoes reveals novel mechanisms operating in plants in native soils and the soil microbiota appears to be one of the drivers of these plant responses.

Plants growing in nature live in association with beneficial, commensal, and pathogenic microbes, which make up the plant microbiota. The close interaction between plants and their microbiotas has raised fundamental questions about plant responses to these microbes and the identity of the main factors driving microbiota structure, diversity, and function in bulk soil, in the rhizosphere, and in the plant organs. Beneficial microorganisms have long been used as inoculants for crops; the current development of synthetic microbial communities and the identification of plant traits that respond to the microbiota form the basis for rational engineering of the plant microbiota to improve sustainable agriculture.

Scientists' research interests are often skewed toward charismatic organisms, but quantifying research biases is challenging. By combining bibliometric data with trait-based approaches and using a well-studied alpine flora as a case study, we demonstrate that morphological and colour traits, as well as range size, have significantly more impact on species choice for wild flowering plants than traits related to ecology and rarity. These biases should be taken into account to inform more objective plant conservation efforts.Throughout human history, plants have played the role of silent partners in the growth of virtually every civilization 1 . Humans have exploited wild plants and crops as sources of food 2 , used trees as combustible material and to craft manufactured goods 1,3 and taken inspiration from the beauty of flowers for poetic and artistic endeavours 4,5 . Since the birth of modern science, plants have also become the subjects of intense investigation. As scientists systematically studied the natural history of plants 6 , they soon realized that many of these species could function as model organisms to address fundamental scientific questions 7 . Edward O. Wilson famously stated that '[…] for every scientific question, there is the ideal study system to test it' and thus, the choice of a researcher to study one species or another is often driven by functional criteria (for example, ploidy level for genetics studies and ease of growth under controlled conditions). Still, outside of the laboratory or the greenhouse, field scientists may be challenged in their choice of focus organisms by concerns that exceed strictly scientific research interests. As a result, when plant scientists select to study a specific wild plant among the pool of species available in a given study region, it may be that factors unrelated to the biological question end up influencing species choice and introducing biases in the research outcome. Whereas this is not a problem per se, a disparity in scientific attention towards certain species may become a concern in conservation biology, where it is paramount to ensure a 'level playing field' in selecting conservation priorities 8,9 .Given their global diversity 10 and ecological importance 11,12 , plants should be prominent in conservation biology's effort to curb species loss under mounting anthropogenic pressures [13][14][15] . Yet, it is well documented that plants receive less attention and consequently less funding in conservation than do animals 16,17 . This particular case of taxonomic bias has been connected to 'plant blindness' 18 or 'plant awareness disparity' 19 , two terms proposed to indicate the lack of awareness for plants. Associated with both the evolutionary

Microbial communities associated to plants are greatly influenced by water availability in soil. In flooded crops, such as rice, the impact of water management on microbial dynamics is not fully understood. Here, we present a comprehensive study of the rice microbiota investigated in an experimental field located in one of the most productive area of North Italy. The microbiota associated to paddy soil and root was investigated using 454 pyrosequencing of 16S, ITS and 18S rRNA gene amplicons under two different water managements, upland (non-flooded, aerobic) and lowland (traditional flooding, anaerobic) at three plant development stages. Results highlighted a major role of the soil water status in shaping microbial communities, while phenological stage had low impacts. Compositional shifts in prokaryotic and fungal communities upon water management consisted in significant abundances changes of Firmicutes, Methanobacteria, Chloroflexi, Sordaryomycetes, Dothideomycetes and Glomeromycotina. A vicariance in plant beneficial microbes and between saprotrophs/pathotrophs was observed between lowland and upland. Moreover, through network analysis we demonstrated different co-abundances dynamics between lowland and upland conditions with a major impact on microbial HUBs (strongly interconnected microbes) which fully shifted to aerobic microbes in the absence of flooding.