Plant community data from a statewide survey of paired serpentine and non-serpentine soils in California, USA

Soils derived from ultramafic parent materials (hereafter serpentine) provide habitat for unique plant communities containing species with adaptations to the low nutrient levels, high magnesium: calcium ratios, and high metal content (Ni, Zn) that characterize serpentine. Plants on serpentine have long been studied in evolution and ecology, and plants adapted to serpentine contribute disproportionately to plant diversity in many parts of the world. In 2000-2003, serpentine plant communities were sampled at 107 locations representing the full range of occurrence of serpentine in California, USA, spanning large gradients in climate. In 2009-2010, plant communities were similarly sampled at 97 locations on nonserpentine soil, near to and paired with 97 of the serpentine sampling locations. (Some serpentine locations were revisited in 2009-2010 to assess the degree of change since 2000-2003, which was minimal.) At each serpentine or nonserpentine location, a north- and a south-facing 50 m x10 m plot were sampled. This design produced 97 “sites” each consisting of four “plots” (north-south exposure, serpentine-nonserpentine soil). All plots were initially visited >3 times over 2 years to record plant diversity and cover, and a subset were revisited in 2014 to examine community change after a drought. The original question guiding the study was how plant diversity is shaped by the spatially patchy nature of the serpentine habitat. Subsequently, we investigated how climate drives plant diversity at multiple scales (within locations, between locations on the same and different soil types, and across entire regions) and at different levels of organization (taxonomic, functional, and phylogenetic).

Parallel adaptation in autopolyploid Arabidopsis arenosa is dominated by repeated recruitment of shared alleles

Relative contributions of pre-existing vs de novo genomic variation to adaptation are poorly understood, especially in polyploid organisms. We assess this in high resolution using autotetraploid Arabidopsis arenosa, which repeatedly adapted to toxic serpentine soils that exhibit skewed elemental profiles. Leveraging a fivefold replicated serpentine invasion, we assess selection on SNPs and structural variants (TEs) in 78 resequenced individuals and discover significant parallelism in candidate genes involved in ion homeostasis. We further model parallel selection and infer repeated sweeps on a shared pool of variants in nearly all these loci, supporting theoretical expectations. A single striking exception is represented by TWO PORE CHANNEL 1, which exhibits convergent evolution from independent de novo mutations at an identical, otherwise conserved site at the calcium channel selectivity gate. Taken together, this suggests that polyploid populations can rapidly adapt to environmental extremes, calling on both pre-existing variation and novel polymorphisms.

A Test of the Inadvertent Uptake Hypothesis Using Plant Species Adapted to Serpentine Soil

Serpentine soils are a stressful growing environment for plants, largely due to nutrient deficiencies and high concentrations of toxic heavy metals (e.g., Ni). Plants have evolved various adaptations for tolerating these extreme environments, including metal hyperaccumulation into above-ground tissues. However, the adaptive significance of metal hyperaccumulation is a topic of debate, with several non-mutually-exclusive hypotheses under study. For example, the inadvertent uptake hypothesis (IUH) states that heavy metal accumulation is a consequence of an efficient nutrient-scavenging mechanism for plants growing in nutrient-deficient soils. Thus, it is possible that metal hyperaccumulation is simply a byproduct of non-specific ion transport mechanisms allowing plants to grow in nutrient-deficient soils, such as serpentine soils, while simultaneously tolerating other potentially toxic heavy metals. Furthermore, some nutrient needs are tissue-specific, and heavy metal toxicity can be more pronounced in reproductive tissues; thus, studies are needed that document nutrient and metal uptake into vegetative and reproductive plant tissues across species of plants that vary in the degree to which they accumulate soil metals. To test these ideas, we grew nine plant species that are variously adapted to serpentine soils (i.e., Ni-hyperaccumulating endemic, non-hyperaccumulating endemic, indicator, or indifferent) in a common garden greenhouse experiment. All species were grown in control soils, as well as those that were amended with the heavy metal Ni, and then analyzed for macronutrient (Ca, Mg, K, and P), micronutrient (Cu, Fe, Zn, Mn, and Mo), and heavy metal (Cr and Co) concentrations in their vegetative and reproductive organs (leaves, anthers, and pistils). In accordance with the IUH, we found that hyperaccumulators often accumulated higher concentrations of nutrients and metals compared to non-hyperaccumulating species, although these differences were often organ-specific. Specifically, while hyperaccumulators accumulated significantly more K and Co across all organs, Cu was higher in leaves only, while Mn and Zn were higher in anthers only. Furthermore, hyperaccumulators accumulated significantly more Co and Mo across all organs when Ni was added to the soil environment. Our work provides additional evidence in support of the IUH, and contributes to our understanding of serpentine adaptation in plants.

Broomrape Species Parasitizing Odontarrhena lesbiaca (Brassicaceae) Individuals Act as Nickel Hyperaccumulators

The elemental defense hypothesis supports that metal hyperaccumulation in plant tissues serves as a mechanism underpinning plant resistance to herbivores and pathogens. In this study, we investigate the interaction between Odontarrhena lesbiaca and broomrape parasitic species, in the light of the defense hypothesis of metal hyperaccumulation. Plant and soil samples collected from three serpentine sites in Lesbos, Greece were analyzed for Ni concentrations. Phelipanche nowackiana and Phelipanche nana were found to infect O. lesbiaca. In both species, Ni concentration decreased gradually from tubercles to shoots and flowers. Specimens of both species with shoot nickel concentrations above 1000 mg.kg−1 were found, showing that they act as nickel hyperaccumulators. Low values of parasite to O. lesbiaca leaf or soil nickel quotients were observed. Orobanche pubescens growing on a serpentine habitat but not in association with O. lesbiaca had very low Ni concentrations in its tissues analogous to excluder plants growing on serpentine soils. Infected O. lesbiaca individuals showed lower leaf nickel concentrations relative to the non-infected ones. Elevated leaf nickel concentration of O. lesbiaca individuals did not prevent parasitic plants to attack them and to hyperaccumulate metals to their tissues, contrary to predictions of the elemental defense hypothesis.

Parallel evolution of phenological isolation across the speciation continuum in serpentine-adapted annual wildflowers

Understanding the relative importance of reproductive isolating mechanisms across the speciation continuum remains an outstanding challenge in evolutionary biology. Here, we examine a common isolating mechanism, reproductive phenology, between plant sister taxa at different stages of adaptive divergence to gain insight into its relative importance during speciation. We study 17 plant taxa that have independently adapted to inhospitable serpentine soils, and contrast each with a nonserpentine sister taxon to form pairs at either ecotypic or species-level divergence. We use greenhouse-based reciprocal transplants in field soils to quantify how often flowering time (FT) shifts accompany serpentine adaptation, when FT shifts evolve during speciation, and the genetic versus plastic basis of these shifts. We find that genetically based shifts in FT in serpentine-adapted taxa are pervasive regardless of the stage of divergence. Although plasticity increases FT shifts in five of the pairs, the degree of plasticity does not differ when comparing ecotypic versus species-level divergence. FT shifts generally led to significant, but incomplete, reproductive isolation that did not vary in strength by stage of divergence. Our work shows that adaptation to a novel habitat may predictably drive phenological isolation early in the speciation process.

Plant phenology influences rhizosphere microbial community and is accelerated by serpentine microorganisms in Plantago erecta

ABSTRACTSerpentine soils are drought-prone and rich in heavy metals, and plants growing on serpentine soils host distinct microbial communities that may affect plant survival and phenotype. However, whether the rhizosphere communities of plants from different soil chemistries are initially distinct or diverge over time may help us understand drivers of microbial community structure and function in stressful soils. Here, we test the hypothesis that rhizosphere microbial communities will converge over time (plant development), independent of soil chemistry and microbial source. We grew Plantago erecta in serpentine or nonserpentine soil, with serpentine or nonserpentine microbes and tracked plant growth and root phenotypes. We used 16S rRNA barcoding to compare bacterial species composition at seedling, vegetative, early-, and late-flowering phases. Plant phenotype and rhizosphere bacterial communities were mainly structured by soil type, with minor contributions by plant development, microbe source and their interactions. Serpentine microorganisms promoted early flowering in plants on non-serpentine soils. Despite strong effects of soil chemistry, the convergence in bacterial community composition across development demonstrates the importance of the plant-microbe interactions in shaping microbial assembly processes across soil types.

Use of machine learning to establish limits in the classification of hyperaccumulator plants growing on serpentine, gypsum and dolomite soils

The so-called hyperaccumulator plants are capable of storing hundred or thousand times bigger quantities of heavy metals than normal plants, which makes hyperaccumulators very useful in fields such as phytoremediation and phytomining. Among these plants there are many serpentinophytes, i.e., plants that grow exclusively on ultramafic rocks which produce soils with a great proportion of heavy metals. Even though there are multiple classifications, the lack of consensus regarding which parameters to use to determine whether a plant is a hyperaccumulator, as well as the arbitrariness of stablished thresholds, bring about the need to propose more objective criteria. To this end, plant mineral composition data from different vegetal species were analysed using machine learning techniques. Three complementary case studies were established. Firstly, plants were classified in three types of soils: dolomite, gypsum and serpentine. Secondly, data about normal and hyperaccumulator plant Ni composition were analysed with machine learning to find differentiated subgroups. Lastly, association studies were carried out using data about mineral composition and soil type. Results in the classification task reach a success rate over 75%. Clustering of plants by Ni concentration in parts per million (ppm) resulted in four groups with cut-off points in 2.25, 100 (accumulators) and 3000 ppm (hyperaccumulators). Associations with a confidence level above 90% were found between high Ni levels and serpentine soils, as well as between high Ni and Zn levels and the same type of soil. Overall, this work demonstrates the potential of machine learning to analyse data about plant mineral composition. Finally, after consulting the red list of the IUCN and those of countries with high richness in hyperaccumulator species, it is evident that a greater effort should be made to establish the conservation status of this type of flora.