Ancient large-scale gene duplications and diversification in bryophytes illuminate the plant terrestrialization.

Large-scale gene duplications (LSGDs) are crucial for evolutionary adaptation and recurrent in vascular plants. However, the role of ancient LSGDs in the terrestrialization and diversification of bryophytes, the second most species-rich group of land plants, remains largely elusive due to limited sampling in bryophytes. Employing the most extensive nuclear gene dataset in bryophytes to date, we reconstructed a time-calibrated phylogenetic tree from 209 species, covering virtually all key bryophyte lineages, for phylogenomic analyses of LSGDs and diversification. We newly identified two ancient LSGDs: one in the most recent common ancestor (MRCA) of extant bryophytes and another in the MRCA of the majority of Jungermanniales s. lato. Duplicated genes from these two LSGDs show significant enrichment in photosynthesis-related processes and structures. Rhizoid-responsive ROOTHAIR DEFECTIVE SIX-LIKE (RSL) genes from ancient LSGDs are present in rhizoidless bryophytes, challenging assumptions about rhizoid absence mechanisms. We highlighted four major diversification rate upshifts, two of which slightly postdated LSGDs, potentially linked to the flourishing of gymnosperms and angiosperms and explaining over 80% of bryophyte diversity. Our findings, supported by extensive bryophyte sampling, highlight the significance of LSGDs in the early terrestrialization and diversification of bryophytes, offering new insights into land plant evolution.

A step forward in botanical exploration with three new Polytrichaceae records from Tibet, China.

Background: According to the Species Catalogue of China, Tibet, China, has more than 1,000 species of bryophytes, showing its remarkably high biodiversity. Amongst them, the Polytrichaceae is one of the largest family, with six genera and 25 species, one subspecies and two varieties reported previously. New information: Based on a field survey and specimen identification, the following species have been newly recorded in the bryoflora of Tibet, namely Oligotrichumobtusatum Broth., Pogonatumcontortum (Menzies ex Brid.) Lesq. and Polytrichumsphaerothecium (Besch.) Müll. Hal.

Landscape Heterogeneity Drives Genetic Diversity in the Highly Dispersive Moss Funaria hygrometrica Hedw.

Funaria hygrometrica, a cosmopolitan moss species known for its remarkable dispersal capacity, was selected as the focal organism to investigate the relationship between landscape features and genetic diversity. Our study encompassed samples collected from two distinct regions: the Spanish Sierra Nevada Mountains (SN), characterized by a diverse landscape with an altitudinal difference of nearly 3500 m within a short distance, and the Murcia Region (MU) in Southeast Spain, characterized by a uniform landscape akin to the lowlands of Sierra Nevada. Genotyping analysis targeted three genetic regions: the nuclear ribosomal internal transcribed spacer (nrITS), the chloroplast rps3-rpl16 region, and the mitochondrial rpl5-rpl16 spacer. Through this analysis, we aimed to assess genetic variability and population structure across these environmentally contrasting regions. The Sierra Nevada populations exhibited significantly higher haplotype diversity (Hd = 0.78 in the highlands and 0.67 overall) and nucleotide diversity (π% = 0.51 for ITS1) compared to the Murcia populations (Hd = 0.35, π% = 0.14). Further investigation unveiled that samples from the lowlands of Sierra Nevada showed a closer genetic affinity to Murcia than to the highlands of Sierra Nevada. Furthermore, the genetic differentiation between highland and lowland populations was significant (ΦST = 0.55), with partial Mantel tests and ResistanceGA analysis revealing a strong correlation between ITS1-based genetic diversity and landscape features, including altitude and bioclimatic variables. Our study elucidated potential explanations for the observed genetic structuring within F. hygrometrica samples' populations. These included factors such as a high selfing rate within restricted habitats, a limited average dispersal distance of spores, hybrid depression affecting partially incompatible genetic lineages, and recent migration facilitated via human activities into formerly unoccupied areas of the dry zones of Southeast Spain.

The MOVECLIM - AZORES project: Bryophytes from Terceira Island along an elevation gradient.

Background: Systematic studies on the biodiversity of bryophytes along elevational gradients have been conductuted within the native vegetation of the Azores, using the MOVECLIM framework. The primary objective of this study was to inventory the bryophytes present within preserved areas of native vegetation in Terceira Island (Azores). From 25 to 28 September 2012, an inventory of the bryoflora was carried out along an elevational gradient, starting near Serreta lighthouse (38.76658 Latitude; -27.37539 Longitude; 40 m a.s.l.) and culminating on the top of Santa Bárbara Mountain (38.73064 Latitude; -27.32164 Longitude; 1000 m a.s.l.). The study followed the adapted MOVECLIM standardised protocol, as follows: i) six sites were selected along an elevational transect, each site spaced at 200 m elevation intervals; ii) within each site, two 10 m x 10 m plots were established in close proximity from each other (10-15 m); iii) within these plots, three 2 m x 2 m quadrats were randomly selected and sampled for bryophytes. The following substrates were surveyed in each quadrat: rock, soil, humus, organic matter, tree bark at three different heights and leaves/fronds. For each available and bryophyte-colonised substrate, three replicate microplots of 10 cm x 5 cm were collected, resulting in a maximum of 24 microplots per quadrat. New information: Nearly three-quarters of the maximum expected number of microplots (636 out of 864; eventID) were found across the six sites on Terceira Island, resulting in a total of 3677 records (occurrenceID). A high proportion of the specimens could be identified to the species rank (n = 3661; 99.6%), representing 38 families, 60 genera and 92 species, including 58 species of liverworts (Marchantiophyta) and 34 species of mosses (Bryophyta). The inventory included several endemic species: two liverwort species endemic to the Azores, five species endemic to Macaronesia (three mosses and two liverworts) and 11 European endemic species (three mosses and eight liverworts). The elevations with the highest species richness, the highest number of endemic species and the highest number of conservation concern species, spanned between 600 and 1000 m a.s.l. above sea level, coinciding with the best preserved forest vegetation. Overall, tree-dwelling and ground-dwelling substrates showed similar levels of bryophyte occupation (75% vs. 72%). However, the 636 events were unevenly distributed across substrates: leaves and rocks had the fewest replicates (n = 54; 50.0%), while humus and the lowest tree height had the highest values (n = 106; 98.1% and n = 98; 90.7%, respectively).The study contributed to expanding knowledge about the diversity and distribution of the Azorean Bryoflora, both on a local and a regional scale.

Microplastic contamination of bryophytes: A review on mechanisms and impacts.

This systematic review investigates the interactions of microplastics (MPs) and nanoplastics (NPs) with bryophytes, incorporating findings from 11 articles identified through a comprehensive database search using a combination of keywords. The review explores mechanisms such as adsorption and internalization by which MPs and NPs are present in bryophytes and examines the ecological ramifications, including changes in bryophyte community structure and impacts on ecosystem functions such as nutrient cycling, soil formation, habitat provision, water balance, and erosion control. Despite providing valuable insights, this review highlights several critical knowledge gaps that warrant further investigation. Future research should address the following areas: the long-term effects of MPs and NPs on bryophyte health and survival, the mechanisms of MP and NP uptake and translocation within bryophytes, and the broader ecological consequences of plastic pollution on bryophyte-dominated ecosystems. Additionally, studies should explore the effectiveness of various mitigation and management strategies, including advanced waste management techniques and innovative technologies, in reducing plastic pollution and protecting these vital ecosystems.

Presence of vitamin B12 metabolism in the last common ancestor of land plants.

Vitamin B12, also known as cobalamin, is an essential organic cofactor for methionine synthase (METH), and is only synthesized by a subset of bacteria. Plants and fungi have an alternative methionine synthase (METE) that does not need B12 and are typically considered not to utilize it. Some algae facultatively utilize B12 because they encode both METE and METH, while other algae are dependent on B12 as they encode METH only. We performed phylogenomic analyses of METE, METH and 11 further proteins involved in B12 metabolism across more than 1600 plant and algal genomes and transcriptomes (e.g. from OneKp), demonstrating the presence of B12-associated metabolism deep into the streptophytes. METH and five further accessory proteins (MTRR, CblB, CblC, CblD and CblJ) were detected in the hornworts (Anthocerotophyta), and two (CblB and CblJ) were identified in liverworts (Marchantiophyta) in the bryophytes, suggesting a retention of B12-metabolism in the last common land plant ancestor. Our data further show more limited distributions for other B12-related proteins (MCM and RNR-II) and B12 dependency in several algal orders. Finally, considering the collection sites of algae that have lost B12 metabolism, we propose freshwater-to-land transitions and symbiotic associations to have been constraining factors for B12 availability in early plant evolution. This article is part of the theme issue 'The evolution of plant metabolism'.

Regulation of ROP GTPase cycling between active and inactive states is essential for vegetative organogenesis in Marchantia polymorpha.

Rho/Rac of plant (ROP) GTPases are plant-specific proteins that function as molecular switches, activated by guanine nucleotide exchange factors (GEFs) and inactivated by GTPase-activating proteins (GAPs). The bryophyte Marchantia polymorpha contains single copies of ROP (MpROP), GEFs [ROPGEF and SPIKE (SPK)] and GAPs [ROPGAP and ROP ENHANCER (REN)]. MpROP regulates the development of various tissues and organs, such as rhizoids, gemmae and air chambers. The ROPGEF KARAPPO (MpKAR) is essential for gemma initiation, but the functions of other ROP regulatory factors are less understood. This study focused on two GAPs: MpROPGAP and MpREN. Mpren single mutants showed defects in thallus growth, rhizoid tip growth, gemma development, and air-chamber formation, whereas Mpropgap mutants showed no visible abnormalities. However, Mpropgap Mpren double mutants had more severe phenotypes than the Mpren single mutants, suggesting backup roles of MpROPGAP in processes involving MpREN. Overexpression of MpROPGAP and MpREN resulted in similar gametophyte defects, highlighting the importance of MpROP activation/inactivation cycling (or balancing). Thus, MpREN predominantly, and MpROPGAP as a backup, regulate gametophyte development, likely by controlling MpROP activation in M. polymorpha.

Host tree availability shapes potential distribution of a target epiphytic moss species more than direct climate effects.

Climate change significantly impacts the distribution of woody plants, indirectly influencing the dynamics of entire ecosystems. Understanding species' varied responses to the environment and their reliance on biotic interactions is crucial for predicting the global changes' impact on woodland biodiversity. Our study focusses on Dicranum viride, a moss of conservation priority, and its dependence on specific phorophytes (host trees). Using species distribution modelling (SDM) techniques, we initially modelled its distribution using climate-only variables. As a novel approach, we also modelled the distribution of the main phorophyte species and incorporated them into D. viride SDM alongside climate data. Finally, we analysed the overlap of climatic and geographic niches between the epiphyte and the phorophytes. Inclusion of biotic interactions significantly improved model performance, with phorophyte availability emerging as the primary predictor. This underscores the significance of epiphyte-phorophyte interactions, supported by substantial niche overlap. Predictions indicate a potential decline in the suitability of most of the current areas for D. viride, with noticeable shifts towards the northern regions of Europe. Our study underscores the importance of incorporating biotic interactions into SDMs, especially for dependent organisms. Understanding such connections is essential to implement successful conservation strategies and adapt forest management practices to environmental changes.

Predicting the Threat Status of Mosses Using Functional Traits.

Mosses are an early lineage of the plant kingdom, with around 13,000 species. Although an important part of biodiversity, providing crucial ecosystem services, many species are threatened with extinction. However, only circa 300 species have so far had their extinction risk evaluated globally for the IUCN Red List. Functional traits are known to help predict the extinction risk of species in other plant groups. In this study, a matrix of 15 functional traits was produced for 723 moss species from around the world to evaluate the potential of such predictability. Binary generalized linear models showed that monoicous species were more likely to be threatened than dioicous species, and the presence of a sporophyte (sexual reproduction), vegetative reproduction and an erect (straight) capsule instead of a pendent (immersed) one lowers the risk of species extinction. A longer capsule, seta and stem length, as well as broader substrate breadth, are indicative of species with a lower risk of extinction. The best-performing models fitted with few traits were able to predict extinction risks of species with good accuracy. These models applied to Data Deficient (DD) species proved how useful they may be to speed up the IUCN Red List assessment process while reducing the number of listed DD species, by selecting species most in need of a full, detailed assessment. Some traits tested in this study are a novelty in conservation research on mosses, opening new possibilities for future studies. The traits studied and the models presented here are a significant contribution to the knowledge of mosses at risk of extinction and will help to improve conservation efforts.

Anthracene-Induced Alterations in Liverwort Architecture In Vitro: Potential for Bioindication of Environmental Pollution.

Polycyclic aromatic hydrocarbons (PAHs) are widespread globally, primarily due to long-term anthropogenic pollution sources. Since PAHs tend to accumulate in soil sediments, liverwort plants, such as Lunularia cruciata, are susceptible to their adverse effects, making them good models for bioindicators. The aim of this study was to probe the impact of anthracene, a three-ring linear PAH, on the growth parameters of L. cruciata and the relationship established with the internalization of the pollutant throughout the phenology of the plant. Intrinsic plant responses, isolated from external factors, were assessed in vitro. L. cruciata absorbed anthracene from the culture medium, and its bioaccumulation was monitored throughout the entire process, from the gemma germination stage to the development of the adult plant, over a total period of 60 days. Consequently, plants exposed to concentrations higher than 50 µM anthracene, decreased the growth area of the thallus, the biomass and number of tips. Moreover, anthracene also impinged on plant symmetry. This concentration represented the maximum limit of bioaccumulation in the tissues. This study provides the first evidence that architectural variables in liverwort plants are suitable parameters for their use as bioindicators of PAHs.

A Comparative Bryo-Ecological Study of Habitat 3170*: Sites of Particular Phytogeographic Interest in the Mediterranean Area.

In accordance with the 92/43/EEC "Habitats" Directive, Mediterranean temporary ponds are identified as a priority natural habitat within the European context. They are a very interesting and unique habitat type, as ecological conditions can vary greatly in a short period of time. Due to their small size, many Mediterranean hydrophytic bryophytes typical of this habitat are often overlooked or misinterpreted. Their distribution, habitats, ecology, and strategies are generally poorly understood. Several of them are currently considered rare or endangered in the Mediterranean. As these ponds are particularly sensitive to human activities and natural changes, such bryophytes and associated vegetation communities may be at risk. This study is focused on their floristic variability in different environmental conditions in two sites of particular phytogeographic interest in the Mediterranean area. In the Sardinian Pauli of Giara, 56 taxa (50 Bryophyta and 6 Marchantiophyta) were found, and in the Umbria Piana di Ferretto, 54 taxa (34 Bryophyta and 20 Marchantiophyta) were documented. The taxa from the two areas were analysed and compared. Life strategies, life macroforms, light and moisture preferences, chorological elements, and moisture belts were considered. The data are presented here together with information on the phytogeography and ecology of the species recorded. The findings indicate that a bespoke monitoring strategy and dedicated conservation measures are essential for the effective protection of bryophytes, ensuring the achievement of meaningful and sustainable conservation outcomes.

Centromere drive may propel the evolution of chromosome and genome size in plants.

BACKGROUND: Genome size is influenced by natural selection and genetic drift acting on variations from polyploidy and repetitive DNA sequences. We hypothesized that centromere drive, where centromeres compete for inclusion in the functional gamete during meiosis, may also affect genome and chromosome size. This competition occurs in asymmetric meiosis, where only one of the four meiotic products becomes a gamete. If centromere drive influences chromosome size evolution, it may also impact post-polyploid diploidization, where a polyploid genome is restructured to function more like a diploid through chromosomal rearrangements, including fusions. We tested if plant lineages with asymmetric meiosis exhibit faster chromosome size evolution compared to those with only symmetric meiosis, which lack centromere drive as all four meiotic products become gametes. We also examined if positive selection on centromeric histone H3 (CENH3), a protein that can suppress centromere drive, is more frequent in these asymmetric lineages. METHODS: We analyzed plant groups with different meiotic modes: asymmetric in gymnosperms and angiosperms, and symmetric in bryophytes, lycophytes, and ferns. We selected species based on available CENH3 gene sequences and chromosome size data. Using Ornstein-Uhlenbeck evolutionary models and phylogenetic regressions, we assessed the rates of chromosome size evolution and the frequency of positive selection on CENH3 in these clades. RESULTS: Our analyses showed that clades with asymmetric meiosis have a higher frequency of positive selection on CENH3 and increased rates of chromosome size evolution compared to symmetric clades. CONCLUSIONS: Our findings support the hypothesis that centromere drive accelerates chromosome and genome size evolution, potenatially also influencing the process of post-polyploid diploidization. We propose a model which in a single famework helps explain the stability of chromosome size in symmetric lineages (bryophytes, lycophytes, and ferns) and its variability in asymmetric lineages (gymnosperms and angiosperms), providing a foundation for future research in plant genome evolution.

State Of The Art Of Sex Determination In Bryophytes.

With the advent of genomic and other omics technologies the last decades have witnessed a series of steady and important breakthroughs in the understanding of the genetic determinants of the different reproductive systems of vascular plants and especially on how sexual reproduction shaped their evolution. In contrast, the molecular mechanisms of these fundamental aspects of the biology of bryophytes, a group of non-vascular embryophyte plants sister to all tracheophytes, are still largely obscure. The recent characterization of the sex chromosomes and genetic switches determining sex in bryophytes as well as emerging approaches for molecular sexing of gametophytes hold great promise for elucidation of the evolutionary history as well as the conservation of this species-rich but understudied group of land plants.

An ancient role for CYP73 monooxygenases in phenylpropanoid biosynthesis and embryophyte development.

The phenylpropanoid pathway is one of the plant metabolic pathways most prominently linked to the transition to terrestrial life, but its evolution and early functions remain elusive. Here, we show that activity of the t-cinnamic acid 4-hydroxylase (C4H), the first plant-specific step in the pathway, emerged concomitantly with the CYP73 gene family in a common ancestor of embryophytes. Through structural studies, we identify conserved CYP73 residues, including a crucial arginine, that have supported C4H activity since the early stages of its evolution. We further demonstrate that impairing C4H function via CYP73 gene inactivation or inhibitor treatment in three bryophyte species-the moss Physcomitrium patens, the liverwort Marchantia polymorpha and the hornwort Anthoceros agrestis-consistently resulted in a shortage of phenylpropanoids and abnormal plant development. The latter could be rescued in the moss by exogenous supply of p-coumaric acid, the product of C4H. Our findings establish the emergence of the CYP73 gene family as a foundational event in the development of the plant phenylpropanoid pathway, and underscore the deep-rooted function of the C4H enzyme in embryophyte biology.

Surviving adversity: Exploring the presence of Lunularia cruciata (L.) Dum. on metal-polluted mining waste.

The tailings dump of Barraxiutta (Sardinia, Italy) contains considerable concentrations of heavy metals and, consequently, is scarcely colonized by plants. However, wild populations of the liverwort Lunularia cruciata (L.) Dum. form dense and healthy-looking carpets on this tailing dump. L. cruciata colonizing the tailing dump was compared with a control population growing in a pristine environment in terms of: (i) pollutant content, (ii) photochemical efficiency, and (iii) volatile secondary metabolites in thalli extracts. L. cruciata maintained optimal photosynthesis despite containing considerable amounts of soil pollutants in its thalli and had higher sesquiterpene content compared to control plants. Sesquiterpenes have a role in plant stress resistance and adaptation to adverse environments. In the present study, we propose enhanced sesquiterpenes featuring Contaminated L. cruciata as a defence strategy implemented in the post-mining environment.

Canopy cover and soil moisture influence forest understory plant responses to experimental summer drought.

Extreme droughts are globally increasing in frequency and severity. Most research on drought in forests focuses on the response of trees, while less is known about the impacts of drought on forest understory species and how these effects are moderated by the local environment. We assessed the impacts of a 45-day experimental summer drought on the performance of six boreal forest understory plants, using a transplant experiment with rainout shelters replicated across 25 sites. We recorded growth, vitality and reproduction immediately, 2 months, and 1 year after the simulated drought, and examined how differences in ambient soil moisture and canopy cover among sites influenced the effects of drought on the performance of each species. Drought negatively affected the growth and/or vitality of all species, but the effects were stronger and more persistent in the bryophytes than in the vascular plants. The two species associated with older forests, the moss Hylocomiastrum umbratum and the orchid Goodyera repens, suffered larger effects than the more generalist species included in the experiment. The drought reduced reproductive output in the moss Hylocomium splendens in the next growing season, but increased reproduction in the graminoid Luzula pilosa. Higher ambient soil moisture reduced some negative effects of drought on vascular plants. Both denser canopy cover and higher soil moisture alleviated drought effects on bryophytes, likely through alleviating cellular damage. Our experiment shows that boreal understory species can be adversely affected by drought and that effects might be stronger for bryophytes and species associated with older forests. Our results indicate that the effects of drought can vary over small spatial scales and that forest landscapes can be actively managed to alleviate drought effects on boreal forest biodiversity. For example, by managing the tree canopy and protecting hydrological networks.

Moss species and precipitation mediate experimental warming stimulation of growing season N2 fixation in subarctic tundra.

Climate change in high latitude regions leads to both higher temperatures and more precipitation but their combined effects on terrestrial ecosystem processes are poorly understood. In nitrogen (N) limited and often moss-dominated tundra and boreal ecosystems, moss-associated N2 fixation is an important process that provides new N. We tested whether high mean annual precipitation enhanced experimental warming effects on growing season N2 fixation in three common arctic-boreal moss species adapted to different moisture conditions and evaluated their N contribution to the landscape level. We measured in situ N2 fixation rates in Hylocomium splendens, Pleurozium schreberi and Sphagnum spp. from June to September in subarctic tundra in Sweden. We exposed mosses occurring along a natural precipitation gradient (mean annual precipitation: 571-1155 mm) to 8 years of experimental summer warming using open-top chambers before our measurements. We modelled species-specific seasonal N input to the ecosystem at the colony and landscape level. Higher mean annual precipitation clearly increased N2 fixation, especially during peak growing season and in feather mosses. For Sphagnum-associated N2 fixation, high mean annual precipitation reversed a small negative warming response. By contrast, in the dry-adapted feather moss species higher mean annual precipitation led to negative warming effects. Modelled total growing season N inputs for Sphagnum spp. colonies were two to three times that of feather mosses at an area basis. However, at the landscape level where feather mosses were more abundant, they contributed 50% more N than Sphagnum. The discrepancy between modelled estimates of species-specific N input via N2 fixation at the moss core versus ecosystem scale, exemplify how moss cover is essential for evaluating impact of altered N2 fixation. Importantly, combined effects of warming and higher mean annual precipitation may not lead to similar responses across moss species, which could affect moss fitness and their abilities to buffer environmental changes.

Cell death in bryophytes: emerging models to study core regulatory modules and conserved pathways.

This review summarizes recent progress in our current understanding of the mechanisms underlying the cell death pathways in bryophytes, focusing on conserved pathways and particularities in comparison to angiosperms. Regulated cell death (RCD) plays key roles during essential processes along the plant life cycle. It is part of specific developmental programmes and maintains homeostasis of the organism in response to unfavourable environments. Bryophytes could provide valuable models to study developmental RCD processes as well as those triggered by biotic and abiotic stresses. Some pathways analogous to those present in angiosperms occur in the gametophytic haploid generation of bryophytes, allowing direct genetic studies. In this review, we focus on such RCD programmes, identifying core conserved mechanisms and raising new key questions to analyse RCD from an evolutionary perspective.

Illuminating the role of the calyptra in sporophyte development.

The study of moss calyptra form and function began almost 250 years ago, but calyptra research has remained a niche endeavor focusing on only a small number of species. Recent advances have focused on calyptra cuticular waxes, which function in dehydration protection of the immature sporophyte apex. The physical presence of the calyptra also plays a role in sporophyte development, potentially via its influence on auxin transport. Progress developing genomic resources for mosses beyond the model Physcomitrium patens, specifically for species with larger calyptrae and taller sporophytes, in combination with advances in CRISPR-Cas9 genome editing will enable the influence of the calyptra on gene expression and the production of RNAs and proteins that coordinate sporophyte development to be explored.