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S National Science Foundation DEB-1240045 DEB-1239992 DEB-1239980 Fundacao para a Ciencia e a Technologia (FCT), Portugal PTDC/BIA-EVF/1499/2014 National Natural Science Foundation of China 31470314 Scottish Government's Rural and Environment Science and Analytical Services Division DEB-1146168

In karst rocky desertification areas, bryophytes coexist with algae, bacteria, and fungi on exposed calcareous rocks to form a bryophyte crust, which plays an irreplaceable role in the restoration of karst degraded ecosystems. We investigated the biodiversity of crust bryophytes in karst rocky desertification areas from Guizhou Province, China. A total of 145 species in 22 families and 56 genera were identified. According to frequency and coverage, seven candidate dominant mosses were screened out, and five drought-resistant indexes of them were measured. Hypnum leptothallum, Racopilum cuspidigerum, and Hyophila involuta have high drought adaptability. We explored the interactions between two dominant mosses (H. leptothallum, H. involuta) and the structure of microbial communities in three karst rocky desertification types. Microbial diversity and function analysis showed that both moss species and karst rocky desertification types affect microbial communities. Moss species much more strongly affected the diversity and changed the community composition of these microbial groups. Bacteria were more sensitive in the microbiome as their communities changed strongly between mosses and drought resistance factors. Moreover, several species of fungi and bacteria could be significantly associated with three drought-resistant indexes: Pro (free proline content), SOD (superoxide dismutase activity), and POD (peroxidase activity), which were closely related to the drought adaptability of mosses. Our results enforced the potential role of moss-associated microbes that are important components involved in the related biological processes when bryophytes adapted to arid habitats, or as one kind of promoters in the distribution pattern of early mosses succession in karst rocky desertification areas.

Fil: Sanchez Puerta, Maria Virginia. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Mendoza. Instituto de Biologia Agricola de Mendoza; Argentina. Universidad Nacional de Cuyo. Facultad de Ciencias Exactas y Naturales. Departamento de Biologia; Argentina

Among land plants, angiosperms have the structurally most labile mitochondrial (mt) genomes. In contrast, the so-called early land plants (e.g., mosses) seem to have completely static mt chromosomes. We assembled the complete mt genomes from 12 mosses spanning the moss tree of life, to assess 1) the phylogenetic depth of the conserved mt gene content and order and 2) the correlation between scattered sequence repeats and gene order lability in land plants. The mt genome of most mosses is approximately 100 kb in size, and thereby the smallest among land plants. Based on divergence time estimates, moss mt genome structure has remained virtually frozen for 350 My, with only two independent gene losses and a single gene relocation detected across the macroevolutionary tree. This is the longest period of mt genome stasis demonstrated to date in a plant lineage. The complete lack of intergenic repeat sequences, considered to be essential for intragenomic recombinations, likely accounts for the evolutionary stability of moss mt genomes.

Fourier-transform infrared spectroscopy (FTIR) with the attenuated total reflectance technique was used to identify Rhodobryum roseum from its four adulterants. The FTIR spectra of six samples in the range from 4000 cm-1 to 600 cm-1 were obtained. The second-derivative transformation test was used to identify the small and nearby absorption peaks. A cluster analysis was performed to classify the spectra in a dendrogram based on the spectral similarity. Principal component analysis (PCA) was used to classify the species of six moss samples. A cluster analysis with PCA was used to identify different genera. However, some species of the same genus exhibited highly similar chemical components and FTIR spectra. Fourier self-deconvolution and discrete wavelet transform (DWT) were used to enhance the differences among the species with similar chemical components and FTIR spectra. Three scales were selected as the feature-extracting space in the DWT domain. The results show that FTIR spectroscopy with chemometrics is suitable for identifying Rhodobryum roseum and its adulterants.

Background Andreaeopsida represents a distinct group of nonperistomate mosses, characterized by its phylogenetic position as a sister to peristomate species. However, plastome data for this lineage remains scarce, limiting our understanding of its genomic features and the evolution of plastome within Bryophyta. To bridge this gap, we sequenced the plastome of Andreaea regularis , a prominent species within the Andreaeopsida, found in Antarctica. This study aims to characterize the plastome of A. regularis and compare its features across nonperistomate and peristomate moss lineages, focusing on phylogenetic placement, plastome characteristics variations, and potential selection pressures. Results The assembled plastome of A. regularis spans 135,217 bp with 30.3% GC content and 122 annotated genes. Phylogenetic analysis confirms the position of A . regularis among the nonperistomate mosses, forming a sister group to the peristomate lineage. Comparative analysis reveals a reduction pattern in plastome size, GC content, and protein-coding gene (PCG) content along the evolutionary trajectory from nonperistomate mosses to peristomate mosses, with A. regularis exhibiting intermediate characteristics. This pattern is mirrored by structural variation in the large single-copy (LSC) region, where A. regularis retains more PCGs and exhibits lower deletion rates than peristomate species but shows signs of genome contraction relative to nonperistomate mosses. Correlation analysis further indicates that total plastome size and GC content are most strongly associated with LSC length ( r  = 0.994) and GC content ( r  = 0.999), respectively, suggesting that LSC variation is closely linked to plastome structural differences among mosses. Purifying selection is prevalent across genic regions in mosses, while codon usage patterns remain minimally affected by mutational pressure. The genes rpoC2 and ndhF exhibit dynamic evolution, marked by elevated nonsynonymous substitution rates, high nucleotide diversity, and numerous diagnostic sites. Additionally, positively selected residues in these genes, alongside those in rbcL , indicate potential evolutionary pressures in A. regularis . Conclusions Altogether, this study establishes a critical genomic reference for Andreaeopsida, advances our understanding of nonperistomate-peristomate plastome evolution, and highlights the intricate nucleotide variation underlying plastome diversity and evolutionary differentiation in mosses.

Across the Canadian Arctic Archipelago, widespread ice retreat during the 20th century has sharply accelerated since 2004. In Sverdrup Pass, central Ellesmere Island, rapid glacier retreat is exposing intact plant communities whose radiocarbon dates demonstrate entombment during the Little Ice Age (1550–1850 AD). The exhumed bryophyte assemblages have exceptional structural integrity (i.e., setae, stem structures, leaf hair points) and have remarkable species richness (60 of 144 extant taxa in Sverdrup Pass). Although the populations are often discolored (blackened), some have developed green stem apices or lateral branches suggesting in vivo regrowth. To test their biological viability, Little Ice Age populations emerging from the ice margin were collected for in vitro growth experiments. Our results include a unique successful regeneration of subglacial bryophytes following 400 y of ice entombment. This finding demonstrates the totipotent capacity of bryophytes, the ability of a cell to dedifferentiate into a meristematic state (analogous to stem cells) and develop a new plant. In polar ecosystems, regrowth of bryophyte tissue buried by ice for 400 y significantly expands our understanding of their role in recolonization of polar landscapes (past or present). Regeneration of subglacial bryophytes broadens the concept of Ice Age refugia, traditionally confined to survival of land plants to sites above and beyond glacier margins. Our results emphasize the unrecognized resilience of bryophytes, which are commonly overlooked vis-a-vis their contribution to the establishment, colonization, and maintenance of polar terrestrial ecosystems.

In plant ecology, biochemical analyses of bryophytes and vascular plants are often conducted on dried herbarium specimen as species typically grow in distant and inaccessible locations. Here, we present an automated in silico compound classification framework to annotate metabolites using an untargeted data independent acquisition (DIA)–LC/MS–QToF-sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH) ecometabolomics analytical method. We perform a comparative investigation of the chemical diversity at the global level and the composition of metabolite families in ten different species of bryophytes using fresh samples collected on-site and dried specimen stored in a herbarium for half a year. Shannon and Pielou’s diversity indices, hierarchical clustering analysis (HCA), sparse partial least squares discriminant analysis (sPLS-DA), distance-based redundancy analysis (dbRDA), ANOVA with post-hoc Tukey honestly significant difference (HSD) test, and the Fisher’s exact test were used to determine differences in the richness and composition of metabolite families, with regard to herbarium conditions, ecological characteristics, and species. We functionally annotated metabolite families to biochemical processes related to the structural integrity of membranes and cell walls (proto-lignin, glycerophospholipids, carbohydrates), chemical defense (polyphenols, steroids), reactive oxygen species (ROS) protection (alkaloids, amino acids, flavonoids), nutrition (nitrogen- and phosphate-containing glycerophospholipids), and photosynthesis. Changes in the composition of metabolite families also explained variance related to ecological functioning like physiological adaptations of bryophytes to dry environments (proteins, peptides, flavonoids, terpenes), light availability (flavonoids, terpenes, carbohydrates), temperature (flavonoids), and biotic interactions (steroids, terpenes). The results from this study allow to construct chemical traits that can be attributed to biogeochemistry, habitat conditions, environmental changes and biotic interactions. Our classification framework accelerates the complex annotation process in metabolomics and can be used to simplify biochemical patterns. We show that compound classification is a powerful tool that allows to explore relationships in both molecular biology by “zooming in” and in ecology by “zooming out”. The insights revealed by our framework allow to construct new research hypotheses and to enable detailed follow-up studies.

Background Plant polyphenol oxidases (PPOs) are enzymes that typically use molecular oxygen to oxidize ortho -diphenols to ortho -quinones. These commonly cause browning reactions following tissue damage, and may be important in plant defense. Some PPOs function as hydroxylases or in cross-linking reactions, but in most plants their physiological roles are not known. To better understand the importance of PPOs in the plant kingdom, we surveyed PPO gene families in 25 sequenced genomes from chlorophytes, bryophytes, lycophytes, and flowering plants. The PPO genes were then analyzed in silico for gene structure, phylogenetic relationships, and targeting signals. Results Many previously uncharacterized PPO genes were uncovered. The moss, Physcomitrella patens , contained 13 PPO genes and Selaginella moellendorffii (spike moss) and Glycine max (soybean) each had 11 genes. Populus trichocarpa (poplar) contained a highly diversified gene family with 11 PPO genes, but several flowering plants had only a single PPO gene. By contrast, no PPO - like sequences were identified in several chlorophyte (green algae) genomes or Arabidopsis ( A. lyrata and A. thaliana ). We found that many PPOs contained one or two introns often near the 3’ terminus. Furthermore, N-terminal amino acid sequence analysis using ChloroP and TargetP 1.1 predicted that several putative PPOs are synthesized via the secretory pathway, a unique finding as most PPOs are predicted to be chloroplast proteins. Phylogenetic reconstruction of these sequences revealed that large PPO gene repertoires in some species are mostly a consequence of independent bursts of gene duplication, while the lineage leading to Arabidopsis must have lost all PPO genes. Conclusion Our survey identified PPOs in gene families of varying sizes in all land plants except in the genus Arabidopsis. While we found variation in intron numbers and positions, overall PPO gene structure is congruent with the phylogenetic relationships based on primary sequence data. The dynamic nature of this gene family differentiates PPO from other oxidative enzymes, and is consistent with a protein important for a diversity of functions relating to environmental adaptation.

Early-diverging land plants such as mosses are known for their outstanding abilities to grow in various terrestrial habitats, incorporating tremendous structural and physiological innovations, as well as many lineage-specific genes. How these genes and functional innovations evolved remains unclear. In this study, we show that a dual-coding gene YAN/AltYAN in the moss Physcomitrella patens evolved from a pre-existing hemerythrin gene. Experimental evidence indicates that YAN/AltYAN is involved in fatty acid and lipid metabolism, as well as oil body and wax formation. Strikingly, both the recently evolved dual-coding YAN/AltYAN and the pre-existing hemerythrin gene might have similar physiological effects on oil body biogenesis and dehydration resistance. These findings bear important implications in understanding the mechanisms of gene origination and the strategies of plants to fine-tune their adaptation to various habitats. Extant representatives of the earliest land plant lineages adapt to various terrestrial habitats with structural and physiological innovations. Here the authors show a dual-coding gene in the moss Physcomitrella patens evolved from a hemerythrin gene, with effects on oil body biogenesis and dehydration resistance.