Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria.

Although microorganisms are known to dominate Earth's biospheres and drive biogeochemical cycling, little is known about the geographic distributions of microbial populations or the environmental factors that pattern those distributions. We used a global-level hierarchical sampling scheme to comprehensively characterize the evolutionary relationships and distributional limitations of the nitrogen-fixing bacterial symbionts of the crop chickpea, generating 1,027 draft whole-genome sequences at the level of bacterial populations, including 14 high-quality PacBio genomes from a phylogenetically representative subset. We find that diverse Mesorhizobium taxa perform symbiosis with chickpea and have largely overlapping global distributions. However, sampled locations cluster based on the phylogenetic diversity of Mesorhizobium populations, and diversity clusters correspond to edaphic and environmental factors, primarily soil type and latitude. Despite long-standing evolutionary divergence and geographic isolation, the diverse taxa observed to nodulate chickpea share a set of integrative conjugative elements (ICEs) that encode the major functions of the symbiosis. This symbiosis ICE takes 2 forms in the bacterial chromosome-tripartite and monopartite-with tripartite ICEs confined to a broadly distributed superspecies clade. The pairwise evolutionary relatedness of these elements is controlled as much by geographic distance as by the evolutionary relatedness of the background genome. In contrast, diversity in the broader gene content of Mesorhizobium genomes follows a tight linear relationship with core genome phylogenetic distance, with little detectable effect of geography. These results illustrate how geography and demography can operate differentially on the evolution of bacterial genomes and offer useful insights for the development of improved technologies for sustainable agriculture.

Gene amplification confers glyphosate resistance in Amaranthus palmeri.

The herbicide glyphosate became widely used in the United States and other parts of the world after the commercialization of glyphosate-resistant crops. These crops have constitutive overexpression of a glyphosate-insensitive form of the herbicide target site gene, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). Increased use of glyphosate over multiple years imposes selective genetic pressure on weed populations. We investigated recently discovered glyphosate-resistant Amaranthus palmeri populations from Georgia, in comparison with normally sensitive populations. EPSPS enzyme activity from resistant and susceptible plants was equally inhibited by glyphosate, which led us to use quantitative PCR to measure relative copy numbers of the EPSPS gene. Genomes of resistant plants contained from 5-fold to more than 160-fold more copies of the EPSPS gene than did genomes of susceptible plants. Quantitative RT-PCR on cDNA revealed that EPSPS expression was positively correlated with genomic EPSPS relative copy number. Immunoblot analyses showed that increased EPSPS protein level also correlated with EPSPS genomic copy number. EPSPS gene amplification was heritable, correlated with resistance in pseudo-F(2) populations, and is proposed to be the molecular basis of glyphosate resistance. FISH revealed that EPSPS genes were present on every chromosome and, therefore, gene amplification was likely not caused by unequal chromosome crossing over. This occurrence of gene amplification as an herbicide resistance mechanism in a naturally occurring weed population is particularly significant because it could threaten the sustainable use of glyphosate-resistant crop technology.

Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation.

Domesticated species are impacted in unintended ways during domestication and breeding. Changes in the nature and intensity of selection impart genetic drift, reduce diversity, and increase the frequency of deleterious alleles. Such outcomes constrain our ability to expand the cultivation of crops into environments that differ from those under which domestication occurred. We address this need in chickpea, an important pulse legume, by harnessing the diversity of wild crop relatives. We document an extreme domestication-related genetic bottleneck and decipher the genetic history of wild populations. We provide evidence of ancestral adaptations for seed coat color crypsis, estimate the impact of environment on genetic structure and trait values, and demonstrate variation between wild and cultivated accessions for agronomic properties. A resource of genotyped, association mapping progeny functionally links the wild and cultivated gene pools and is an essential resource chickpea for improvement, while our methods inform collection of other wild crop progenitor species.

Germination Biology of Two Invasive Physalis Species and Implications for Their Management in Arid and Semi-arid Regions.

Two Solanaceae invasive plant species (Physalis angulata L. and P. philadelphica Lam. var. immaculata Waterfall) infest several arable crops and natural habitats in Southeastern Anatolia region, Turkey. However, almost no information is available regarding germination biology of both species. We performed several experiments to infer the effects of environmental factors on seed germination and seedling emergence of different populations of both species collected from various locations with different elevations and habitat characteristics. Seed dormancy level of all populations was decreased with increasing age of the seeds. Seed dormancy of freshly harvested and aged seeds of all populations was effectively released by running tap water. Germination was slightly affected by photoperiods, which suggests that seeds are slightly photoblastic. All seeds germinated under wide range of temperature (15-40 °C), pH (4-10), osmotic potential (0 to -1.2 MPa) and salinity (0-400 mM sodium chloride) levels. The germination ability of both plant species under wide range of environmental conditions suggests further invasion potential towards non-infested areas in the country. Increasing seed burial depth significantly reduced the seedling emergence, and seeds buried below 4 cm of soil surface were unable to emerge. In arable lands, soil inversion to maximum depth of emergence (i.e., 6 cm) followed by conservational tillage could be utilized as a viable management option.

Invasion Potential of Two Tropical Physalis Species in Arid and Semi-Arid Climates: Effect of Water-Salinity Stress and Soil Types on Growth and Fecundity.

Invasive plants are recognized for their impressive abilities to withstand adverse environmental conditions however, all invaders do not express the similar abilities. Therefore, survival, growth, nutrient uptake and fecundity of two co-occurring, invasive Physalis species were tested under water and salinity stresses, and different soil textures in the current study. Five different water stress levels (100, 75, 50, 25, and 12.5% pot water contents), four different soil salinity levels (0, 3, 6, and 12 dSm-1) and four different soil textures (67% clay, 50% clay, silt clay loam and sandy loam) were included in three different pot experiments. Both weeds survived under all levels of water stress except 12.5% water contents and on all soil types however, behaved differently under increasing salinity. The weeds responded similarly to salinity up till 3 dSm-1 whereas, P. philadelphica survived for longer time than P. angulata under remaining salinity regimes. Water and salinity stress hampered the growth and fecundity of both weeds while, soil textures had slight effect. Both weeds preferred clay textured soils for better growth and nutrient uptake however, interactive effect of weeds and soil textures was non-significant. P. angulata accumulated higher K and Na while P. philadelphica accrued more Ca and Mg as well as maintained better K/Na ratio. P. angulata accumulated more Na and P under salinity stress while, P. philadelphica accrued higher K and Mg, and maintained higher K/Na ratio. Collectively, highest nutrient accumulation was observed under stress free conditions and on clay textured soils. P. philadelphica exhibited higher reproductive output under all experimental conditions than P. angulata. It is predicted that P. philadelphica will be more problematic under optimal water supply and high salinity while P. angulata can better adapt water limited environments. The results indicate that both weeds have considerable potential to further expand their ranges in semi-arid regions of Turkey.

Interspecific hybridization transfers a previously unknown glyphosate resistance mechanism in Amaranthus species.

A previously unknown glyphosate resistance mechanism, amplification of the 5-enolpyruvyl shikimate-3-phosphate synthase gene, was recently reported in Amaranthus palmeri. This evolved mechanism could introgress to other weedy Amaranthus species through interspecific hybridization, representing an avenue for acquisition of a novel adaptive trait. The objective of this study was to evaluate the potential for this glyphosate resistance trait to transfer via pollen from A. palmeri to five other weedy Amaranthus species (Amaranthus hybridus, Amaranthus powellii, Amaranthus retroflexus, Amaranthus spinosus, and Amaranthus tuberculatus). Field and greenhouse crosses were conducted using glyphosate-resistant male A. palmeri as pollen donors and the other Amaranthus species as pollen recipients. Hybridization between A. palmeri and A. spinosus occurred with frequencies in the field studies ranging from <0.01% to 0.4%, and 1.4% in greenhouse crosses. A majority of the A. spinosus × A. palmeri hybrids grown to flowering were monoecious and produced viable seed. Hybridization occurred in the field study between A. palmeri and A. tuberculatus (<0.2%), and between A. palmeri and A. hybridus (<0.01%). This is the first documentation of hybridization between A. palmeri and both A. spinosus and A. hybridus.