Phylogeography of a widely distributed plant species reveals cryptic genetic lineages with parallel phenotypic responses to warming and drought conditions

To predict how widely distributed species will perform under future climate change, it is crucial to understand and reveal their underlying phylogenetics. However, detailed information about plant adaptation and its genetic basis and history remains scarce and especially widely distributed species receive little attention despite their putatively high adaptability. To examine the adaptation potential of a widely distributed species, we sampled the model plant Silene vulgaris across Europe. In a greenhouse experiment, we exposed the offspring of these populations to a climate change scenario for central Europe and revealed the population structure through whole-genome sequencing. Plants were grown under two temperatures (18°C and 21°C) and three precipitation regimes (65, 75, and 90 mm) to measure their response in biomass and fecundity-related traits. To reveal the population genetic structure, ddRAD sequencing was employed for a whole-genome approach. We found three major genetic clusters in S. vulgaris from Europe: one cluster comprising Southern European populations, one cluster of Western European populations, and another cluster containing central European populations. Population genetic diversity decreased with increasing latitude, and a Mantel test revealed significant correlations between F ST and geographic distances as well as between genetic and environmental distances. Our trait analysis showed that the genetic clusters significantly differed in biomass-related traits and in the days to flowering. However, half of the traits showed parallel response patterns to the experimental climate change scenario. Due to the differentiated but parallel response patterns, we assume that phenotypic plasticity plays an important role for the adaptation of the widely distributed species S. vulgaris and its intraspecific genetic lineages.

Differentially Expressed Genes Shared by Two Distinct Cytoplasmic Male Sterility (CMS) Types of Silene vulgaris Suggest the Importance of Oxidative Stress in Pollen Abortion

Cytoplasmic male sterility (CMS), encoded by the interacting mitochondrial and nuclear genes, causes pollen abortion or non-viability. CMS is widely used in agriculture and extensively studied in crops. Much less is known about CMS in wild species. We performed a comparative transcriptomic analysis of male sterile and fertile individuals of Silene vulgaris, a model plant for the study of gynodioecy, to reveal the genes responsible for pollen abortion in this species. We used RNA-seq datasets previously employed for the analysis of mitochondrial and plastid transcriptomes of female and hermaphrodite flower buds, making it possible to compare the transcriptomes derived from three genomes in the same RNA specimen. We assembled de novo transcriptomes for two haplotypes of S. vulgaris and identified differentially expressed genes between the females and hermaphrodites, associated with stress response or pollen development. The gene for alternative oxidase was downregulated in females. The genetic pathways controlling CMS in S. vulgaris are similar to those in crops. The high number of the differentially expressed nuclear genes contrasts with the uniformity of organellar transcriptomes across genders, which suggests these pathways are evolutionarily conserved and that selective mechanisms may shield organellar transcription against changes in the cytoplasmic transcriptome.

Evaluating Cr behaviour in two different polluted soils: Mechanisms and implications for soil functionality

This work investigates the mechanisms determining Cr speciation and availability in two different soils polluted with two chromium sources (an industrial sludge, highly polluted with Cr, and Cr(VI) solution) and the influence of these parameters on the recovery of the soil functions related with biological quality and plant growth. The experiment was carried out in greenhouse conditions using 36 pots of 17 kg for the growth of Silene vulgaris for 21 months. Logistic Regression Model using Lasso estimator shows that soil organic matter (SOM) and pH control Cr availability in studied soils. In soils treated with the sludge, X ray Absorption spectroscopy showed that Cr was present as Cr(III), biological quality indicators increased and plants were able to grow. However, in soils polluted with Cr(VI), Cr availability was significantly different in the two soils. In the alkaline and poor in organic matter soil, 12% of Cr(VI) remained in the soil leading to the decrease of soil quality indicators and the total inhibition of plant growth. In the neutral soil, Cr(VI) was totally reduced to Cr(III) by soil organic matter (SOM), quality indicators were not affected and plants grown properly. Infrared Spectroscopy showed that different functional groups reacted with Cr in the two soils. This study highlights the importance to understand the mechanisms underlaying Cr redox and adsorption reactions in Cr polluted soils as they determine the potential recovery of the functions related with biological quality indicators and plant growth. The methodology proposed allows this study in complex soil samples at realistic concentrations and may be useful for risk assessment and for the planning of managing strategies in Cr polluted soils.

Restoration of Vegetation in Relation to Soil Properties of Spoil Heap Heavily Contaminated with Heavy Metals

The main objectives of our study were to evaluate soil contamination on a zinc-lead spoil heap in the Upper Silesian Industrial Region in southern Poland using pollution indices, and to investigate the relation between soil properties and the natural succession of vegetation. Organic carbon and nitrogen, pH, soil texture, base cations, and heavy metal content were analyzed in soil samples at depths of 0-15 cm below the organic horizon over a regular grid of 14 sampling plots. The contents of Zn, Pb, and Cd exceeded by several times the acceptable thresholds. Measurements of soil enzyme activity were used to evaluate the progress of vegetation development in relation to soil chemical properties. The results indicate that heavy metals had a significant impact on soil enzyme activity and the development of vegetation cover. High contents of Pb and Cd reduced enzyme activity, while this activity increased with increasing amounts of soil organic matter. Further, the accumulative capacities of heavy metals in needles of Scots pine (Pinus sylvestris L.) and aboveground biomass of bladder campion (Silene vulgaris (Moench) Garcke) were examined. A high accumulation of Zn, Pb, and Cd in the aboveground tissues of S. vulgaris indicated an unusual tolerance of this species to heavy metals and the possibility of using this species in phytoremediation of post-industrial sites.

Effect of Silene vulgaris and Heavy Metal Pollution on Soil Microbial Diversity in Long-Term Contaminated Soil

In this study, we analysed the impact of heavy metals and plant rhizodeposition on the structure of indigenous microbial communities in rhizosphere and bulk soil that had been exposed to heavy metals for more than 150 years. Samples of the rhizosphere of Silene vulgaris and non-rhizosphere soils 250 and 450 m from the source of emission that had different metal concentrations were collected for analyses. The results showed that soils were collected 250 m from the smelter had a higher number of Cd-resistant CFU compared with the samples that were collected from 450 m, but no significant differences were observed in the number of total and oligotrophic CFU or the equivalent cell numbers between rhizosphere and non-rhizosphere soils that were taken 250 and 450 m from the emitter. Unweighted pair group method with arithmetic mean (UPGMA) cluster analysis of the denaturing gradient gel electrophoresis (DGGE) profiles, as well as a cluster analysis that was generated on the phospholipid fatty acid (PLFA) profiles, showed that the bacterial community structure of rhizosphere soils depended more on the plant than on the distance and metal concentrations. The sequencing of the 16S rDNA fragments that were excised from the DGGE gel revealed representatives of the phyla Bacteroidetes, Acidobacteria, Gemmatimonadetes, Actinobacteria and Betaproteobacteria in the analysed soil with a predominance of the first three groups. The obtained results demonstrated that the presence of S. vulgaris did not affect the number of CFUs, except for those of Cd-resistant bacteria. However, the presence of S. vulgaris altered the soil bacterial community structure, regardless of the sampling site, which supported the thesis that plants have a higher impact on soil microbial community than metal contamination.

Sex-biased oviposition by a nursery pollinator on a gynodioecious host plant: Implications for breeding system evolution and evolution of mutualism

Dioecy, a breeding system where individual plants are exclusively male or female, has evolved repeatedly. Extensive theory describes when dioecy should arise from hermaphroditism, frequently through gynodioecy, where females and hermaphrodites coexist, and when gynodioecy should be stable. Both pollinators and herbivores often prefer the pollen‐bearing sex, with sex‐specific fitness effects that can affect breeding system evolution. Nursery pollination, where adult insects pollinate flowers but their larvae feed on plant reproductive tissues, is a model for understanding mutualism evolution but could also yield insights into plant breeding system evolution. We studied a recently established nursery pollination interaction between native Hadena ectypa moths and introduced gynodioecious Silene vulgaris plants in North America to assess whether oviposition was biased toward females or hermaphrodites, which traits were associated with oviposition, and the effect of oviposition on host plant fitness. Oviposition was hermaphrodite‐biased and associated with deeper flowers and more stems. Sexual dimorphism in flower depth, a trait also associated with oviposition on the native host plant (Silene stellata), explained the hermaphrodite bias. Egg‐receiving plants experienced more fruit predation than plants that received no eggs, but relatively few fruits were lost, and egg receipt did not significantly alter total fruit production at the plant level. Oviposition did not enhance pollination; egg‐receiving flowers usually failed to expand and produce seeds. Together, our results suggest that H. ectypa oviposition does not exert a large fitness cost on host plants, sex‐biased interactions can emerge from preferences developed on a hermaphroditic host species, and new nursery pollination interactions can arise as negative or neutral rather than as mutualistic for the plant.

Non-coding RNA may be associated with cytoplasmic male sterility in Silene vulgaris

Cytoplasmic male sterility (CMS) is a widespread phenomenon in flowering plants caused by mitochondrial (mt) genes. CMS genes typically encode novel proteins that interfere with mt functions and can be silenced by nuclear fertility-restorer genes. Although the molecular basis of CMS is well established in a number of crop systems, our understanding of it in natural populations is far more limited. To identify CMS genes in a gynodioecious plant, Silene vulgaris, we constructed mt transcriptomes and compared transcript levels and RNA editing patterns in floral bud tissue from female and hermaphrodite full siblings. The transcriptomes from female and hermaphrodite individuals were very similar overall with respect to variation in levels of transcript abundance across the genome, the extent of RNA editing, and the order in which RNA editing and intron splicing events occurred. We found only a single genomic region that was highly overexpressed and differentially edited in females relative to hermaphrodites. This region is not located near any other transcribed elements and lacks an open-reading frame (ORF) of even moderate size. To our knowledge, this transcript would represent the first non-coding mt RNA associated with CMS in plants and is, therefore, an important target for future functional validation studies.

Role of the polycarboxylic compounds in the response of Silene vulgaris to chromium

This work aims to investigate the nature and the specific mechanisms by which polycarboxylic compounds participate in the tolerance of Silene vulgaris to Cr with special attention given to the rhizosphere system. This knowledge is important to use this species in the implementation of phytoremediation technologies in Cr-polluted soils. According to the results, chromium is chelated and mobilized by the citric and malic acids in plant tissues, while oxalic acid might participate in the reduction and chelation of Cr in the rhizosphere. At the applied doses, the response of both exudation rate and root exudate composition (total polyphenols and quercitin) seems to involve a rearrangement in the lignification of the plant cell wall to immobilize Cr. Quercetin-3-dirhamnosyl-galactoside and apiin (apigenin-7-O-apiosyl-glucoside) have been identified as the major polyphenols in the root exudates of S. vulgaris. The increments found in the apiin concentration in root exudates seem to be related to the protection against Cr toxicity by chelation of Cr or by free radical scavenging. Though earlier response is detected in plant tissues, results from this work together with previous studies in S. vulgaris indicate that exudation might be a regulated mechanism of protection under Cr exposition in S. vulgaris that may involve mainly Cr reduction and chelation.

Investigating past range dynamics for a weed of cultivation, Silene vulgaris

Since the last glacial maximum (LGM), many plant and animal taxa have expanded their ranges by migration from glacial refugia. Weeds of cultivation may have followed this trend or spread globally following the expansion of agriculture or ruderal habitats associated with human‐mediated disturbance. We tested whether the range expansion of the weed Silene vulgaris across Europe fit the classical model of postglacial expansion from southern refugia, or followed known routes of the expansion of human agricultural practices. We used species distribution modeling to predict spatial patterns of postglacial expansion and contrasted these with the patterns of human agricultural expansion. A population genetic analysis using microsatellite loci was then used to test which scenario was better supported by spatial patterns of genetic diversity and structure. Genetic diversity was highest in southern Europe and declined with increasing latitude. Locations of ancestral demes from genetic cluster analysis were consistent with areas of predicted refugia. Species distribution models showed the most suitable habitat in the LGM on the southern coasts of Europe. These results support the typical postglacial northward colonization from southern refugia while refuting the east‐to‐west agricultural spread as the main mode of expansion for S. vulgaris. We know that S. vulgaris has recently colonized many regions (including North America and other continents) through human‐mediated dispersal, but there is no evidence for a direct link between the Neolithic expansion of agriculture and current patterns of genetic diversity of S. vulgaris in Europe. Therefore, the history of range expansion of S. vulgaris likely began with postglacial expansion after the LGM, followed by more recent global dispersal by humans.

Scale dependence of sex ratio in wild plant populations: implications for social selection

Social context refers to the composition of an individual's social interactants, including potential mates. In spatially structured populations, social context can vary among individuals within populations, generating the opportunity for social selection to drive differences in fitness functions among individuals at a fine spatial scale. In sexually polymorphic plants, the local sex ratio varies at a fine scale and thus has the potential to generate this opportunity. We measured the spatial distribution of two wild populations of the gynodioecious plant Silene vulgaris and show that there is fine‐scale heterogeneity in the local distribution of the sexes within these populations. We demonstrate that the largest variance in sex ratio is among nearest neighbors. This variance is greatly reduced as the spatial scale of social interactions increases. These patterns suggest the sex of neighbors has the potential to generate fine‐scale differences in selection differentials among individuals. One of the most important determinants of social interactions in plants is the behavior of pollinators. These results suggest that the potential for selection arising from sex ratio will be greatest when pollen is shared among nearest neighbors. Future studies incorporating the movement of pollinators may reveal whether and how this fine‐scale variance in sex ratio affects the fitness of individuals in these populations.

Multiple tolerance and co-tolerance to heavy metals in Silene vulgaris: a co-segregation analysis

Plants from metalliferous soils often exhibit combined tolerance to different heavy metals. Such tolerance could rely either on the possession of a combination of different metal-specific tolerance mechanisms ('multiple tolerance'), or on less specific mechanisms that pleiotropically confer tolerance to different metals ('co-tolerance'). In this study, we examined the co-segregation of tolerances to Cu, Zn, Ni, Co and Cd in crosses between distinctly tolerant ecotypes of Silene vulgaris (Moench) Garcke. The results demonstrate non-pleiotropic genetic control of tolerance to Cu, Zn and Cd. Tolerance to Ni and Co, on the other hand, seems to represent the pleiotropic byproduct of the tolerance allele of one particular locus for zinc tolerance.

Arsenic, cobalt and nickel tolerances in two populations of Silene vulgaris (Moench) Garcke from Ontario, Canada

A population of Silene vulgaris (Moench) Garcke collected from mine tailings near the town of Cobalt, Ontario was compared in its metal tolerance with a population collected at an uncontaminated site (Baymouth, Ontario). Seedlings of the Cobalt population were tolerant to elevated levels of arsenic, cobalt and nickel, both compared with the Baymouth population and with other literature reports for this species. However, the tolerance indices in the Cobalt plants for these toxic elements did not correlate well with their concentration in water extractions in the mine soils. Indices of arsenic tolerance, based on the inhibition of root growth in 12 d experiments, showed a similar response to that in a 28 d experiment for both populations. The latter however, appeared to be a more accurate indicator of As tolerance in S. vulgaris, because the longer-term tolerance indices had lower standard deviations and higher probabilities for tolerance than the short-term tolerance indices. Reduced uptake of As occurred in the roots of tolerant individuals compared with non-tolerant individuals at a low As treatment. At a higher arsenic exposure, however, arsenic entered the roots of tolerant individuals. A partial exclusion or reduced translocation of arsenic to the shoots then appeared to operate in the shoots of tolerant individuals, i.e. arsenic levels were higher in shoots of non-tolerant plants. At the highest arsenic exposure, where the individuals from the Cobalt population were no longer tolerant, this exclusion pattern broke down. From a preliminary selection experiment, some arsenic tolerant individuals occurred in the Baymouth population. This suggests that under circumstances of arsenic contamination this population also has the potential to develop a tolerance to high arsenic exposure.

Cadmium tolerance and co-tolerance in Silene vulgaris (Moench.) Garcke [=S. cucubalus (L.) Wib.]

This paper is the first to report cadmium tolerance in a dicotyledonous species, Silene vulgaris (Moench.) Garcke. The response to cadmium of five populations originating from one uncontaminated and various heavy-metal contaminated sites was examined under standardized conditions for three weeks. The tolerance index (TI), based on the mean relative growth rate (R), was determined. Populations originating from cadmium-contaminated sites showed a distinct tolerance to cadmium. A population from a site enriched only with copper also exhibited a marked co-tolerance to cadmium. A clear difference in biomass production between the sensitive and tolerant populations was attained at 1 μM cadmium. An optimum biomass production in tolerant populations at a metal concentration higher than in the control, as demonstrated for zinc and copper, could not be established for cadmium. The pattern of cadmium uptake and translocation differed between tolerant and sensitive populations. All tolerant populations accumulated cadmium in the roots and showed some degree of restricted transport to the shoots. The effect of cadmium on the elemental distribution in roots and shoots was population-independent for some elements (copper, zinc, potassium) and population-specific for others (phosphorus, magnesium and sodium). The phenomenon of co-tolerance to cadmium is discussed in relation to possible tolerance mechanisms, especially with regard to metal-binding compounds (metallothioneins, phytochelatins).