Czech Academy of Sciences, Institute of Botany

A rare and threatened pleurocarpous amblystegiaceaen dendrothelmatic moss, Anacamptodon splachnoides, was the subject of in vitro establishment and propagation. Tests on growth and rapid propagation were applied with the aim of preparing plant material for outdoor ex situ conservation and reintroduction into nature. This integrative conservation approach provides novel methodologies applicable to conservation programmes and management strategies, while also providing fundamental insights into the species’ biology. It further enables research on the species without harming its native populations, allowing for the exploration of questions raised during this investigation, such as spore biology and sex expression. A. splachnoides acts as both a shelter and signal species for a special microhabitat type, which also supports other rare organisms, and prolonged drought seems to affect reproduction, spore dispersal, and germinability more strongly than gametophore survival.

"Cytosine methylation plays an important role in the regulation of gene expression in plants." Some iteration of this statement can be found in most papers centered on plant epigenetics and has become a widely accepted textbook claim. However, our generalized understanding of how DNA methylation exerts control over transcription is now challenged by observations demonstrating that transcriptional levels of most genes are unresponsive to DNA methylation changes. On a genome-wide scale, associations between DNA methylation and transcription are usually statistically weak. Even when correlations are found, the cause and effect can be difficult to identify, as methylation changes sometimes follow rather than precede transcriptional changes. While a growing number of studies explore a possible connection between differentially expressed genes (DEGs) and differentially methylated genes (DMGs), we demonstrate here that DEG-DMG overlaps are often significantly smaller than what could be expected by chance. This indicates that, contrary to expectations, changes in DNA methylation and changes in transcription sometimes avoid one another. Here, we discuss such observations and their implications for the hypothesis of a widespread control of gene expression directly by DNA methylation. While there are well-documented examples where DNA methylation regulates transcription, we argue that such cases represent a minority of genes, and we opine that approaches of reverse epigenetics are therefore unlikely to find broad application in breeding.

Abstract The long‐standing debate around the processes involved in species assembly has generated a conceptual gradient from deterministic to stochastic postulates. Environment selects traits to determine the species that ultimately participate in realised assemblages. However, neutral ecological processes (e.g. random seed dispersal, demographic stochasticity) can also lead to species co‐occurrence in the community. Despite the current consensus that both filtering and unpredictable events drive the organisation of communities, little information is available regarding the actual contribution of each. We experimentally analysed the contributions of both functional filtering and stochasticity (i.e. lack of trait selection) to assembly processes at a fine spatial scale in a dryland gypsum annual plant‐dominated community by evaluating the effects of seed availability (natural soil seed banks vs. seed‐free soil) and main biotic filters (biocrusts vs. perennial tussocks) on realised assemblages. Species richness, cover, diversity and functional properties were measured based on major plant traits defining fundamental life strategies in assemblages during four consecutive years. Biotic scenarios decisively affected community features. Biocrusts substantially promoted richness and productivity, whereas perennial tussocks restrained assemblage complexity in their vicinity. However, other than some weak filtering effects on maximum plant height and leaf dry matter content, the experimental treatments did not clearly select for either functional or compositional patterns in the community during four consecutive annual assembly events, which matched an unusual spring rainy period. Synthesis . Stochastic processes linked to active secondary, horizontal seed movements may play a prominent role in driving local species assembly at a fine spatial scale. Dryland gypsum soil systems have been described as harsh environments that impose strong deterministic filtering effects during plant assembly. However, even in restrictive, environmentally unpredictable habitats, the weightings of deterministic versus stochastic processes can shift, making stochasticity an eventual force of species coexistence contributing to the maintenance of diversity in the regional pool. Importantly, our results suggest that environmental filters would operate not only through a spatial but also through an intensity hierarchy, in which the intensity of the local biotic filtering depends on that of the regional abiotic one.

Abstract The amount and frequency of atmospheric nitrogen (N) deposition have dramatically increased, profoundly influencing population regeneration, community composition and productivity in grasslands. Perennial species in grasslands primarily grow and expand clonally, yet it remains unclear how their below‐ground buds and above‐ground shoots respond to the amount and frequency of N deposition. We conducted a long‐term (2008–2022) N addition experiment in a semiarid grassland. The experiment included nine addition amounts (0, 1, 2, 3, 5, 10, 15, 20 and 50 g N m −2 year −1 ) and two addition frequencies: low frequency (twice per year) and high frequency (once per month). This allowed us to assess the interactive effects of N addition amount and frequency on bud density, shoot density and the ratio of bud to shoot density (meristem limitation index, MLI) in semiarid grasslands. We found a significant interaction between N addition amount and frequency on community bud and shoot densities. Community bud and shoot densities declined with increasing N amount under low addition frequency but remained stable under high addition frequency. However, community MLI was unchanged under low addition frequency but increased with increasing N amount under high addition frequency. Both N addition amount and frequency significantly altered the composition of community buds and shoots, with more pronounced effects under low versus high addition frequency. Bud and shoot densities and MLI declined with N amount under both addition frequencies for bunchgrasses. In contrast, rhizomatous grasses exhibited increased bud density and MLI under high N addition frequency, while shoot density remained unchanged regardless of addition frequency. These demographic responses did not alter above‐ground net primary productivity (ANPP) but shifted community composition toward greater dominance of rhizomatous grasses under N addition. Synthesis. These results suggest that grassland bud and shoot responses to N deposition depend on both the deposition amount and frequency. Commonly used low frequency N addition experiments may lead to inaccurate plant demographic and community responses to chronic N deposition.

Across the planet, angiosperm diversification has been shaped by palaeoclimates and biotic interactions, particularly with pollinators, leaving signatures in the angiosperm age structure. Regional floras represent biased samples of this global diversification shaped by dispersal, extinction and environmental filtering, yet it remains unclear whether floristic age structure reflects pollination strategies or their interaction with palaeoclimates. We constructed a 97% resolved phylogeny of all 1,178 angiosperms in the Netherlands and characterized age structure of eight pollination syndromes by standardized epoch-specific lineage diversities (stELDs) quantifying the proportional increase in lineages per 10-Myr interval. Overall, stELDs peaked under the coldest intervals and were lowest for intermediate-temperature intervals (geological age alone had no effect). This age structure was strongest in wind-pollinated species. Resolving insect pollination into six syndromes revealed strong heterogeneity: lepidoptera-pollination was most strongly associated with warmest palaeotemperatures, bumblebee and wasp-pollination under intermediate temperatures, and fly, lepidoptera and beetle-pollination under coldest temperatures. Paleotemperature signatures correlated positively with contemporary seasonal flowering temperatures, indicating conserved thermal niches across ecological and macroevolutionary timescales. We suggest that temperate floras reflect both recent cold-house diversification of wind- and certain insect-pollinated lineages and earlier warm-house radiations of lineages pollinated by older insect clades. Phylogenetic age structures permit detecting such patterns.

Polyploidy, particularly allopolyploidy resulting from interspecific hybridization followed by chromosome duplication, plays a key role in plant diversification and ecological success. Chenopodium album s. str. is one of the world's most widespread and morphologically variable weeds, yet the timing and mechanism of its origin as an allohexaploid (2n=6x=54) remained unresolved. Using RADseq data, this study investigated the origin of 'BBCCDD' allohexaploid C. album s. str. and closely related hexaploid taxa by analyzing their relationship to putative diploid progenitors with the 'BB' genome (C. ficifolium, C. suecicum, C. ucrainicum) and tetraploid species with the 'CCDD' subgenomic combination (C. betaceum, C. glaucophyllum, C. novopokrovskyanum, C. striatiforme). The genomic sequences were mapped to the chromosome-scale reference genome of C. formosanum, a closely related allohexaploid. Results reveal that C. album s. str. does not genetically align with contemporary diploid or tetraploid taxa, suggesting its origin from extinct ancestors rather than ongoing hybridization. Both its 'BB' and 'CCDD' subgenomes show higher or comparable number of genetic lineages, respectively, than its extant di- and tetraploid relatives, implying conservation of ancestral variation in the allohexaploid. Furthermore, 16 distinct subgenomic combinations were identified within C. album s. str., confirming its polytopic and repeated origin across geographic regions. This explains the remarkable morphological and ecological plasticity observed across its range. This research underscores C. album s. str. as an ancient, stabilized, and globally invasive polyploid, shaped by multiple hybridization events and fixed heterozygosity, offering parallels with other polyploid species such as Triticum/Aegilops complex.

Abstract Soil–plant–microbe interactions are integral throughout most terrestrial ecosystems, yet the importance of plant phenology and seasonal dynamism upon these relationships remains unknown. Given the pronounced seasonality of alpine environments, we sampled eight plant species occurring in two habitats (alpine meadow and subnival zone) across four seasons (including the snow‐covered winter) in the Central Eastern Alps to determine the plant growth strategies and plant nutrient parameters which closely couple with rhizosphere microbial parameters. In subnival locations, plants exhibited stronger seasonal changes among leaf and root tissue nutrient concentrations and non‐structural carbohydrates (NSCs) compared to those in lower elevation alpine meadows. However, rhizosphere microbial parameters (microbial biomass carbon (MBC), extracellular enzymes, and community composition) demonstrated more seasonal changes in the alpine meadow locations. Notably, a phenological delay was observed in bacterial and fungal communities of the subnival zone, with peak plant rhizosphere differentiation occurring later in the season than in alpine meadows. Therefore, the prolonged cold conditions and shorter growing season in higher elevations likely add a temporal aspect to the commonly used elevational gradient approach, which is not often considered. MBC and enzymatic potential within the rhizosphere were high across all plant species in the alpine meadow during the winter sampling, despite notable differences in microbial community composition. In contrast, winter rhizosphere communities did not differ between plant species in subnival locations, although one species, Oxyria digyna , demonstrated much higher microbial activity along with higher NSCs and root nitrogen, suggesting some alpine plant species may acquire nutrients through microbial interactions during snow‐covered winter periods. This study provides the first look at the annual phenology of multiple alpine plant species and their associated rhizosphere microbiome. Our results demonstrate that seasonal microbial dynamics are highly influenced by abiotic factors (soil and microclimatic conditions), but plants are able to modulate these conditions through growth and nutrient acquisition strategies. Taken together, seasonality and independent plant species effects cannot be overlooked when assessing habitat nutrient cycling and ecosystem stability.

It is broadly assumed that polyploidy success results from increased fitness associated with whole genome duplication due to higher tolerance to stressful conditions. In agreement, several theoretical models found that, among other factors, a better tolerance to new environmental conditions can promote polyploidy establishment. Here, we investigated the effect of the genetic and environmental factors affecting the architecture of unreduced gamete production, to see how it affects the origin and persistence of autopolyploids in both stable and disturbed environments. We developed a theoretical model in which we modeled the joint evolution of a quantitative trait under selection and the production of unreduced gametes; both traits were pleiotropically linked. We followed the adaptation of initially diploid populations to a new environment to which tetraploid individuals were directly adapted. The generation of these autotetraploid individuals was enabled by the genetic production of unreduced gametes and by the environmental change modifying the average production of these gametes. We found that for realistic values of unreduced gamete production adaptation to new environmental conditions was mainly achieved through adaptation of diploids to the new optimum rather than the persistence of newly adapted tetraploid individuals. In broader parameter sets, we found that the adaptation process led to mixed-ploidy populations, except when the populations were swamped with unreduced gametes, and that pleiotropy and environmental effects favored the co-existence of both cytotypes.