Plant roots have the best-understood mutualisms with microbes, but leaf and bract cell endosymbiosis have not been previously reported. Leaf and bract cells of more than 30 species in 18 families of seed plants were surveyed for the presence of intracellular bacteria and several experiments were designed to find and analyze nutrient exchanges between bacteria and plant cells. This dataset contains the results of 1) histochemical analyses to detect hormones, superoxide, and nitrogenous chemicals around bacteria within plant leaf and bract cells, 2) experiments to assess the differential absorption of isotopic nitrogen into plants, and 3) genetic analysis of bacteria isolated from plant material.

,This Ag Data Commons submission includes the 94 sunflower paired-end sequencing FASTQ files, the corresponding 16S bacterial FASTQ files, and other relevant data to the study described below:,Host-microbe interactions are increasingly recognized as important drivers of organismal health, growth, longevity, and community-scale ecological processes. However, less is known about how genetic variation affects hosts' associated microbiomes and downstream phenotypes. We demonstrate that sunflower Helianthus annuus harbors substantial, heritable variation in microbial communities under field conditions. We show that microbial communities co-vary with heritable variation in resistance to root infection caused by the necrotrophic pathogen Sclerotinia sclerotiorum, and that plants grown in autoclaved soil showed almost complete elimination of pathogen resistance. Association mapping suggests at least 59 genetic locations with effects on both microbial relative abundance and Sclerotinia resistance. Although the genetic architecture appears quantitative, we have elucidated previously unexplained genetic variation for resistance to this pathogen. We identify new targets for plant breeding and demonstrate the potential for heritable microbial associations to play important roles in defense in natural and human-altered environments.,See README for details of each table in the spreadsheet and related information.,

This dataset includes field measurements of biological nitrogen fixation (BNF) in all major N-fixing niches across natural terrestrial biomes globally. The dataset comprises 32 variables including site location, biome type, N-fixing niche, sampling year, quantification method, BNF rate (in kgN/(ha*y)), the percentage of nitrogen derived from the atmosphere, N-fixer or N-fixing substrate abundance, BNF rate per unit of N-fixer abundance, and species identity.

Background: In nitrate-poor soils, many leguminous plants form nitrogen-fixing symbioses with members of the bacterial family Rhizobiaceae. We selected Rhizobium sp. NGR234 for its exceptionally broad host range, which includes more than I 12 genera of legumes. Unlike the genome of Bradyrhizobium japonicum, which is composed of a single 8.7 Mb chromosome, that of NGR234 is partitioned into three replicons: a chromosome of about 3.5 Mb, a megaplasmid of more than 2 Mb (pNGR234b) and pNGR234a, a 536,165 bp plasmid that carries most of the genes required for symbioses with legumes. Symbiotic loci represent only a small portion of all the genes coded by rhizobial genomes, however. To rapidly characterize the two largest replicons of NGR234, the genome of strain ANU265 (a derivative strain cured of pNGR234a) was analyzed by shotgun sequencing. Results: Homology searches of public databases with 2,275 random sequences of strain ANU265 resulted in the identification of 1,130 putative protein-coding sequences, of which 922 (41%) could be classified into functional groups. In contrast to the 18% of insertion-like sequences (ISs) found on the symbiotic plasmid pNGR234a, only 2.2% of the shotgun sequences represent known ISs, suggesting that pNGR234a is enriched in such elements. Hybridization data also indicate that the density of known transposable elements is higher in pNGR234b (the megaplasmid) than on the chromosome. Rhizobium-specific intergenic mosaic elements (RIMEs) were found in 35 shotgun sequences, 6 of which carry RIME2 repeats previously thought to be present only in Rhizobium meliloti. As non-overlapping shotgun sequences together represent approximately 10% of ANU265 genome, the chromosome and megaplasmid may carry a total of over 200 RIMEs. Conclusions: 'Skimming' the genome of Rhizobium sp. NGR234 sheds new light on the fine structure and evolution of its replicons, as well as on the integration of symbiotic functions in the genome of a soil bacterium. Although most putative coding sequences could be distributed into functional classes similar to those in Bacillus subtilis, functions related to transposable elements were more abundant in NGR234. In contrast to ISs that accumulated in pNGR234a and pNGR234b, the hundreds of RIME elements seem mostly attributes of the chromosome.

These data show grass crop and model species response to toxic chemicals (Arsenic (As)) and humic acids. Experiments were performed by collaboration between the U.S. Geological Survey, Rutgers University, and Rey Juan Carlos University. A series of individual experiments investigated beneficial effects of endophytic bacteria on grass crop growth and resilience to known plant toxicity.

These data show grass crop and model species response to toxic chemicals (Arsenic (As)) and humic acids. Experiments were performed by collaboration between the U.S. Geological Survey, Rutgers University, and Rey Juan Carlos University. A series of individual experiments investigated beneficial effects of endophytic bacteria on grass crop growth and resilience to known plant toxicity.

,Phenotypic evaluation of 37 crimson clover (Trifolium incarnatum L.) accessions from the US National Plant Germplasm System. Focus of the trial was on traits important for cover crop performance, including fall emergence, winter survival, flowering time, biomass, nitrogen (N) content in aboveground biomass, and proportion of plant N from biological nitrogen fixation (BNF). Experiments were conducted at the Beltsville Agricultural Research Center (Maryland, USA) across three growing seasons (2012-2013, 2013-2014, 2014-2015).,The field design was a randomized complete block design (RCBD) with four replications in each year, except for five accessions planted in 2015, which only had three replications due to limited seed availability. Each plot was a single row 0.6 m in length and 1.5 m between plots. Between 37 and 45 seeds were planted per plot, depending on seed availability in each year.,Fall emergence was evaluated in late October of each year by counting the total number of plants in each plot. Winter survival was determined by counting total number of plants per plot in late April divided by the total number of plants counted in the fall.,Flowering time was evaluated by recording percent flowering on a per-plot basis on a scale from 0% (no flower buds present) to 100% (all flowers dried up entire length of head). Flowering evaluations took place periodically between late April and early June. In 2013, evaluation took place on six dates: 23 Apr., 9 May, 15 May, 24 May, 30 May, and 4 June. In 2014, evaluation took place on five dates: 28 Apr., 6 May, 13 May, 19 May, and 27 May. In 2015, evaluation took place on eight dates: 25 Apr., 29 Apr., 4 May, 7 May, 11 May, 14 May, 18 May, and 21 May. Frequency of evaluations and total duration of evaluation period varied from year-to-year primarily due to the effects of year-to-year weather variation on the rate of growth and development.,Once an accession was rated at 50% or greater for flowering, biomass was collected. All plants in the plot were pulled up with roots attached. Plants were counted and the roots were clipped. All plants within a plot were placed in the same brown paper bag and dried. Dry weight was recorded and plants were ground for laboratory evaluation of nitrogen content, proportion of nitrogen from BNF, and metagenomic analysis.,The crimson clover biomass samples were separated into shoots and roots. Shoots were oven dried (60 °C) for approximately 72 h, weighed, and ground to pass a 1.0-mm screen. Tissue C and N concentrations and 15N natural abundance were determined for the shoot material of each accession using a Thermo Delta V Isotope Ratio Mass Spectrometer (Thermo Scientific, Waltham, MA) and Carlo Erba NC2500 Elemental Analyzer (Carlo Erba, Milan, Italy). Isotopic abundance data were expressed as δ15N in parts per thousand (‰), representing the abundance of plant tissue 15N relative to that of atmospheric N2.,,

Background The legume Medicago truncatula has emerged as a model plant for the molecular and genetic dissection of various plant processes involved in rhizobial, mycorrhizal and pathogenic plant-microbe interactions. Aiming to develop essential tools for such genetic approaches, we have established the first genetic map of this species. Two parental homozygous lines were selected from the cultivar Jemalong and from the Algerian natural population (DZA315) on the basis of their molecular and phenotypic polymorphism. Results An F2 segregating population of 124 individuals between these two lines was obtained using an efficient manual crossing technique established for M. truncatula and was used to construct a genetic map. This map spans 1225 cM (average 470 kb/cM) and comprises 289 markers including RAPD, AFLP, known genes and isoenzymes arranged in 8 linkage groups (2n = 16). Markers are uniformly distributed throughout the map and segregation distortion is limited to only 3 linkage groups. By mapping a number of common markers, the eight linkage groups are shown to be homologous to those of diploid alfalfa (M. sativa), implying a good level of macrosynteny between the two genomes. Using this M. truncatula map and the derived F3 populations, we were able to map the Mtsym6 symbiotic gene on linkage group 8 and the SPC gene, responsible for the direction of pod coiling, on linkage group 7. Conclusions These results demonstrate that Medicago truncatula is amenable to diploid genetic analysis and they open the way to map-based cloning of symbiotic or other agronomically-important genes using this model plant.