Felipe H. Barrios-Masias

Transcriptomic and metabolic responses of mycorrhizal roots to nitrogen patches under field conditions

BackgroundArbuscular mycorrhizal (AM) fungi contribute to plant nutrient uptake in systems managed with reduced fertilizer and pesticide inputs such as organic agriculture by extending the effective size of the rhizosphere and delivering minerals to the root. Connecting the molecular study of the AM symbiosis with agriculturally- and ecologically-relevant field environments remains a challenge and is a largely unexplored research topic.MethodsThis study utilized a cross-disciplinary approach to examine the transcriptional, metabolic, and physiological responses of tomato (Solanum lycopersicum) AM roots to a localized patch of nitrogen (N). A wild-type mycorrhizal tomato and a closely-related non-mycorrhizal mutant were grown at an organic farm in soil that contained an active AM extraradical hyphal network and soil microbe community.ResultsThe majority of genes regulated by upon enrichment of nitrogen were similarly expressed in mycorrhizal and non-mycorrhizal roots, suggesting that the primary response to an enriched N patch is mediated by mycorrhiza-independent root processes. However where inorganic N concentrations in the soil were low, differential regulation of key tomato N transport and assimilation genes indicate a transcriptome shift towards mycorrhiza-mediated N uptake over direct root supplied N. Furthermore, two novel mycorrhizal-specific tomato ammonium transporters were also found to be regulated under low N conditions. A conceptual model is presented integrating the transcriptome response to low N and highlighting the mycorrhizal-specific ammonium transporters.ConclusionsThese results enhance our understanding of the role of the AM symbiosis in sensing and response to an enriched N patch, and demonstrate that transcriptome analyses of complex plant-microbe-soil interactions provide a global snapshot of biological processes relevant to soil processes in organic agriculture.

Effects of arbuscular mycorrhizae on tomato yield, nutrient uptake, water relations, and soil carbon dynamics under deficit irrigation in field conditions.

Plant strategies to cope with future droughts may be enhanced by associations between roots and soil microorganisms, including arbuscular mycorrhizal (AM) fungi. But how AM fungi affect crop growth and yield, together with plant physiology and soil carbon (C) dynamics, under water stress in actual field conditions is not well understood. The well-characterized mycorrhizal tomato (Solanum lycopersicum L.) genotype 76R (referred to as MYC+) and the mutant nonmycorrhizal tomato genotype rmc were grown in an organic farm with a deficit irrigation regime and control regime that replaced evapotranspiration. AM increased marketable tomato yields by ~25% in both irrigation regimes but did not affect shoot biomass. In both irrigation regimes, MYC+ plants had higher plant nitrogen (N) and phosphorus (P) concentrations (e.g. 5 and 24% higher N and P concentrations in leaves at fruit set, respectively), 8% higher stomatal conductance (gs), 7% higher photosynthetic rates (Pn), and greater fruit set. Stem water potential and leaf relative water content were similar in both genotypes within each irrigation regime. Three-fold higher rates of root sap exudation in detopped MYC+ plants suggest greater capacity for water uptake through osmotic driven flow, especially in the deficit irrigation regime in which root sap exudation in rmc was nearly absent. Soil with MYC+ plants also had slightly higher soil extractable organic C and microbial biomass C at anthesis but no changes in soil CO2 emissions, although the latter were 23% lower under deficit irrigation. This study provides novel, field-based evidence for how indigenous AM fungi increase crop yield and crop water use efficiency during a season-long deficit irrigation and thus play an important role in coping with increasingly limited water availability in the future.

Inside Arbuscular Mycorrhizal Roots - Molecular Probes to Understand the Symbiosis

Associations between arbuscular mycorrhizal (AM) fungi and plants are an ancient and widespread plant microbe symbioses. Most land plants can associate with this specialized group of soil fungi (in the Glomeromycota), which enhance plant nutrient uptake in return for C derived from plant photosynthesis. Elucidating the mechanisms involved in the symbiosis between obligate symbionts such as AM fungi and plant roots is challenging because AM fungal transcripts in roots are in low abundance and reference genomes for the fungi have not been available. A deep sequencing metatranscriptomics approach was applied to a wild‐type tomato and a tomato mutant (Solanum lycopersicum L. cultivar RioGrande 76R) incapable of supporting a functional AM symbiosis, revealing novel AM fungal and microbial transcripts expressed in colonized roots. We confirm transcripts known to be mycorrhiza associated and report the discovery of more than 500 AM fungal and novel plant transcripts associated with mycorrhizal tomato roots including putative Zn, Fe, aquaporin, and carbohydrate transporters as well as mycorrhizal‐associated alternative gene splicing. This analysis provides a fundamental step toward identifying the molecular mechanisms of mineral and carbohydrate exchange during the symbiosis. The utility of this metatranscriptomic approach to explore an obligate biotrophic interaction is illustrated, especially as it relates to agriculturally relevant biological processes.

Useofintrogressionlinestodeterminetheecophysiological basis for changes in water use efficiency and yield in California processing tomatoes

Field and greenhouse studies examined the effects of growth habit and chloroplast presence in leaf veins for their role in increasing agronomic water use efficiency and yields of California modern processing tomato (Solanum lycopersicum L.) cultivars. Five introgression lines (ILs), made with Solanum pennellii Cor. in the genetic background of cultivar M82, differ in genes that map to a region on Chromosome 5, including the SP5G gene (determinate vs. semideterminate (Det vs. SemiDet)) and the obv gene (presence (obscure) vs. absence (clear) of leaf vein chloroplasts (Obs vs. Clr)). The five ILs and M82 represented three of the four gene combinations (Det-Clr was unavailable). Det-Obs ILs had less leaf, stem and total aboveground biomass with earlier fruit set and ripening than SemiDet-Clr ILs. By harvest, total fruit biomass was not different among ILs. Photosynthetic rates and stomatal conductance were 4-7% and 13-26% higher, respectively, in Det-Obs ILs than SemiDet-Clr ILs. SemiDet-Obs ILs were intermediate for growth and gas exchange variables. The Det-Obs ILs had lower leaf N concentration and similar chlorophyll content per leaf area (but slightly higher per leaf mass) than SemiDet-Clr ILs. The Obs trait was associated with gains in leaf gas exchange-related traits. This study suggests that a more compact growth habit, less leaf biomass and higher C assimilation capacity per leaf area were relevant traits for the increased yields in cultivars with determinate growth. Developing new introgression libraries would contribute to understanding the multiple trait effects of desirable phenotypes.

Development and application of a digestion-Raman analysis approach for studying multiwall carbon nanotube uptake in lettuce

With increasing production and use of carbon nanotubes (CNTs) and their inevitable release during the life cycle of CNT-based products, these engineered nanomaterials are likely to accumulate in environmental compartments such as wastewater and biosolids, sediments, and biosolids-amended soils. Subsequent uptake of CNTs by agricultural crops could increase the risk of human exposure through the food chain. Unambiguous detection of CNTs in crop plants is essential for food safety assessment. In this study, we developed a method for the detection of multiwall CNTs (MWCNTs) in tissues of lettuce (Lactuca sativa L.), coupling digestion and Raman analysis. Five digestion reagents, including sulfuric acid, hydrochloric acid, nitric acid, ammonium hydroxide, and hydrogen peroxide, were examined. Nitric acid showed the best performance, removing 98–99% leaf/stem/root biomass (dry weight) and minimizing matrix background signals that can interfere with MWCNT Raman signals. Application of nitric acid digestion-Raman analysis to spiked lettuce tissues suggested a detection limit of 25 mg kg−1 dry weight or lower. We then applied this method to lettuce plants grown hydroponically with 0, 5, 10, and 20 mg L−1 pristine (p-) or carboxyl-functionalized (c-) MWCNT. Both p-MWCNT and c-MWCNT were detected in the root, stem, and leaf tissues of most exposed lettuce plants, indicating uptake and translocation of both MWCNTs in this edible plant. Comparisons of the plants grown with 20 mg L−1 p-MWCNT or c-MWCNT suggested that carboxylation facilitated uptake and translocation of MWCNT in lettuce. Our results demonstrated that nitric acid digestion in conjunction with Raman analysis is an effective approach for detecting MWCNTs in food crops, contributing to the potential development of new analytical platforms for studying the environmental fate of CNTs in the soil–plant system and human exposure through the food chain.

Variations in xylem embolism susceptibility under drought between intact saplings of three walnut species

A germplasm collection containing varied Juglans genotypes holds potential to improve drought resistance of plant materials for commercial production. We used X-ray computed microtomography to evaluate stem xylem embolism susceptibility/repair in relation to vessel anatomical features (size, arrangement, connectivity and pit characteristics) in 2-year-old saplings of three Juglans species. In vivo analysis revealed interspecific variations in embolism susceptibility among Juglans microcarpa, J. hindsii (both native to arid habitats) and J. ailantifolia (native to mesic habitats). Stem xylem of J. microcarpa was more resistant to drought-induced embolism as compared with J. hindsii and J. ailantifolia (differences in embolism susceptibility among older and current year xylem were not detected in any species). Variations in most vessel anatomical traits were negligible among the three species; however, we detected substantial interspecific differences in intervessel pit characteristics. As compared with J. hindsii and J. ailantifolia, low embolism susceptibility in J. microcarpa was associated with smaller pit size in larger diameter vessels, a smaller area of the shared vessel wall occupied by pits, lower pit frequency and no changes in pit characteristics as vessel diameters increased. Changes in amount of embolized vessels following 40 days of re-watering were minor in intact saplings of all three species highlighting that an embolism repair mechanism did not contribute to drought recovery. In conclusion, our data indicate that interspecific variations in drought-induced embolism susceptibility are associated with species-specific pit characteristics, and these traits may provide a future target for breeding efforts aimed at selecting walnut germplasm with improved drought resistance.