How plants conquered land: evolution of terrestrial adaptation

Alpine Adaptive Mechanism on Rhizosphere Microbes Recruitment of Crepis napifera (Franch.) Babc. by Multi-Omics Analysis

Background: The accumulation of secondary metabolites in medicinal plants is often influenced by a variety of factors, and rhizosphere microorganisms typically engage in complex interactions with their host plants. Crepis napifera (Franch.) Babc., a regionally significant medicinal plant, contains a diverse array of terpenoids and demonstrates substantial potential for resource development and utilization. Methods: Transcriptome sequencing, metabolomic profiling, and 16S rRNA gene amplicon sequencing were employed to assess the transcriptional expression patterns, metabolic variations, and rhizosphere microbial community composition of C. napifera (Franch.) Babc. roots distributed across various regions. Results: A total of 3679, 8615, and 11,333 differentially expressed genes (DEGs) were identified in the pairwise comparisons between H1 vs. H2, H2 vs. H3, and H1 vs. H3, respectively. Notably, 497 DEGs were consistently detected across all three comparisons. Additionally, Weighted Gene Co-expression Network Analysis (WGCNA) revealed that the expression levels of genes within the turquoise and yellow modules exhibited a significant positive correlation with elevation. In total, 462 differentially expressed metabolites (DEMs) were identified across the same comparisons. Among these compounds, terpenoids, phenolic acids, amino acids and their derivatives, lipids, and alkaloids accounted for 62.98% of the total differential metabolite content. The accumulation patterns of DEMs varied significantly across different regions in the roots of C. napifera (Franch.) Babc. under the three altitude conditions. In response to environmental conditions and the survival strategy of C. napifera (Franch.) Babc. in alpine areas, an investigation into the rhizosphere microbial community was conducted. Four key microbial genera were identified as being correlated with terpenoid biosynthesis and plant nutritional metabolism. Specifically, Pedosphaera, Acidothermus, and Nevskia exhibited terpene biosynthesis capabilities. Additionally, Herbaspirillum, a common microorganism involved in plant nitrogen fixation, respiration, carbon metabolism, and cell wall metabolism, was also enriched in the rhizosphere of C. napifera (Franch.) Babc. These findings suggested that C. napifera (Franch.) Babc. might recruit these microorganisms to enhance its resistance to environmental stress in alpine areas. Conclusions: The accumulation of terpene in C. napifera (Franch.) Babc. across different regions was influenced by transcriptional changes. The rhizosphere microbial communities also changed during this process, showing a recruitment effect that enhances plant growth and offers potential value.

Deciphering Molecular Mechanisms and Diversity of Plant Holobiont Bacteria: Microhabitats, Community Ecology, and Nutrient Acquisition

While gaining increasing attention, plant-microbiome-environment interactions remain insufficiently understood, with many aspects still underexplored. This article explores bacterial biodiversity across plant compartments, including underexplored niches such as seeds and flowers. Furthermore, this study provides a systematic dataset on the taxonomic structure of the anthosphere microbiome, one of the most underexplored plant niches. This review examines ecological processes driving microbial community assembly and interactions, along with the discussion on mechanisms and diversity aspects of processes concerning the acquisition of nitrogen, phosphorus, potassium, and iron-elements essential in both molecular and ecological contexts. These insights are crucial for advancing molecular biology, microbial ecology, environmental studies, biogeochemistry, and applied studies. Moreover, the authors present the compilation of molecular markers for discussed processes, which will find application in (phylo)genetics, various (meta)omic approaches, strain screening, and monitoring. Such a review can be a valuable source of information for specialists in the fields concerned and for applied researchers, contributing to developments in sustainable agriculture, environmental protection, and conservation biology.

MpPUB9, a U-box E3 ubiquitin ligase, acts as a positive regulator by promoting the turnover of MpEXO70.1 under high salinity in Marchantia polymorpha

Marchantia polymorpha, occupying a basal position in the monophyletic assemblage of land plants, displays a notable expansion of plant U-box (PUB) proteins compared with those in animals. We elucidated the roles of MpPUB9 in regulating salt stress tolerance in M. polymorpha. MpPUB9 expression was rapidly induced by high salinity and dehydration. MpPUB9 possessed an intact U-box domain in the N-terminus. MpPUB9-Citrine localized to punctate structures and was peripherally associated with microsomal membranes. Phenotypic analyses demonstrate that the hyponastic and epinastic thallus growth phenotypes, which were induced by the overexpression and suppression of MpPUB9, may provoke salt stress-resistant and -susceptible phenotypes, respectively. MpPUB9 was also found to directly interact with the exocyst protein MpEXO70.1, leading to its ubiquitination. Under high-salinity conditions, though the stability of MpPUB9 was dramatically increased, MpEXO70.1 showed slightly faster turnover rates. Transcriptome analyses showed that salt treatment and the overexpression of MpPUB9 co-upregulated the genes related to the modulation of H2O2 and cell wall organization. Overall, our results suggest that MpPUB9 plays a crucial role in the positive regulation of salt stress tolerance, resulting from its interaction with MpEXO70.1 and modulating turnover of the protein under high-salt conditions via the coordination of UPS with autophagy.

Zygospore formation in Zygnematophyceae predates several land plant traits

Recent research on a special type of sexual reproduction and zygospore formation in Zygnematophyceae, the sister group of land plants, is summarized. Within this group, gamete fusion occurs by conjugation. Zygospore development in Mougeotia, Spirogyra and Zygnema is highlighted, which has recently been studied using Raman spectroscopy, allowing chemical imaging and detection of changes in starch and lipid accumulation. Three-dimensional reconstructions after serial block-face scanning electron microscopy (SBF-SEM) or focused ion beam SEM (FIB-SEM) made it possible to visualize and quantify cell wall and organelle changes during zygospore development. The zygospore walls undergo strong modifications starting from uniform thin cell walls to a multilayered structure. The mature cell wall is composed of a cellulosic endospore and exospore and a central mesospore built up by aromatic compounds. In Spirogyra, the exospore and endospore consist of thick layers of helicoidally arranged cellulose fibrils, which are otherwise only known from stone cells of land plants. While starch is degraded during maturation, providing building blocks for cell wall formation, lipid droplets accumulate and fill large parts of the ripe zygospores, similar to spores and seeds of land plants. Overall, data show similarities between streptophyte algae and embryophytes, suggesting that the genetic toolkit for many land plant traits already existed in their shared algal ancestor. This article is part of the theme issue 'The evolution of plant metabolism'.

Exploring agro-ecological significance, knowledge gaps, and research priorities in arbuscular mycorrhizal fungi

This systematic review examines the global agricultural relevance and practical environmental implications of arbuscular mycorrhizal fungi (AMF) within the phylum Glomeromycota. Following PRISMA guidelines, ensuring a comprehensive and unbiased literature review, a literature search was conducted, focusing on the functional roles of AMF in enhancing crop productivity, nutrient uptake, and soil health. Key findings reveal that AMF contribute significantly to sustainable agriculture by reducing the need for chemical fertilizers and increasing plant resilience to environmental stressors like drought, salinity, or pest resistance. The review highlights the importance of AMF in forming symbiotic relationships with plants, which enhance nutrient absorption and improve soil structure, showcasing long-term benefits such as reduced erosion or improved water retention. However, the current literature lacks in-depth exploration of the taxonomy and evolutionary aspects of AMF, as well as the specific functional roles they play in different agricultural contexts, e.g., understanding evolution could enhance strain selection for specific crops. This review identifies several urgent research gaps, including a need for a more refined understanding of AMF community dynamics under varying land management practices. For example, there are gaps in and a critical evaluation of advanced molecular techniques. Such techniques are essential for studying these interactions. Addressing these gaps will enhance the integration of AMF into sustainable agricultural systems and improve ecosystem management practices across different geographical regions. Future research should prioritize developing precise molecular imaging techniques and optimizing AMF applications for different crops and soil types to maximize their ecological and agricultural benefits. This could be practical through interdisciplinary collaboration (e.g., involving molecular biologists, agronomists, etc.). In conclusion, this review advances the practical application of AMF in agriculture and its contribution to biodiversity conservation in agroecosystems. Integrating these findings into policy frameworks could encourage sustainable farming practices, promote the adoption of AMF inoculants, and foster incentives for environmentally friendly land management strategies.

Systematic review registration

https://www.bmj.com/content/372/bmj.n71.

UDP-glycosyltransferase UGT96C10 functions as a novel detoxification factor for conjugating the activated dinitrotoluene sulfonate in switchgrass

Dinitrotoluene sulfonates (DNTSes) are highly toxic hazards regulated by the Resource Conservation and Recovery Act (RCRA) in the United States. The trinitrotoluene (TNT) red water formed during the TNT purification process consists mainly of DNTSes. Certain plants, including switchgrass, reed and alfalfa, can detoxify low concentrations of DNTS in TNT red water-contaminated soils. However, the precise mechanism by which these plants detoxify DNTS remains unknown. In order to aid in the development of phytoremediation resources with high DNTS removal rates, we identified and characterized 1-hydroxymethyl-2,4-dinitrobenzene sulfonic acid (HMDNBS) and its glycosylated product HMDNBS O-glucoside as the degradation products of 2,4-DNT-3-SO3Na, the major isoform of DNTS in TNT red water-contaminated soils, in switchgrass via LC-MS/MS- and NMR-based metabolite analyses. Transcriptomic analysis revealed that 15 UDP-glycosyltransferase genes were dramatically upregulated in switchgrass plants following 2,4-DNT-3-SO3Na treatment. We expressed, purified and assayed the activity of recombinant UGT proteins in vitro and identified PvUGT96C10 as the enzyme responsible for the glycosylation of HMDNBS in switchgrass. Overexpression of PvUGT96C10 in switchgrass significantly alleviated 2,4-DNT-3-SO3Na-induced plant growth inhibition. Notably, PvUGT96C10-overexpressing transgenic switchgrass plants removed 83.1% of 2,4-DNT-3-SO3Na in liquid medium after 28 days, representing a 3.2-fold higher removal rate than that of control plants. This work clarifies the DNTS detoxification mechanism in plants for the first time, suggesting that PvUGT96C10 is crucial for DNTS degradation. Our results indicate that PvUGT96C10-overexpressing plants may hold great potential for the phytoremediation of TNT red water-contaminated soils.

Functional characterization of plant specific Indeterminate Domain (IDD) transcription factors in tomato (Solanum lycopersicum L.)

Plant-specific transcription factors (TFs) are responsible for regulating the genes involved in the development of plant-specific organs and response systems for adaptation to terrestrial environments. This includes the development of efficient water transport systems, efficient reproductive organs, and the ability to withstand the effects of terrestrial factors, such as UV radiation, temperature fluctuations, and soil-related stress factors, and evolutionary advantages over land predators. In rice and Arabidopsis, INDETERMINATE DOMAIN (IDD) TFs are plant-specific TFs with crucial functions, such as development, reproduction, and stress response. However, in tomatoes, IDD TFs remain uncharacterized. Here, we examined the presence, distribution, structure, characteristics, and expression patterns of SlIDDs. Database searches, multiple alignments, and motif alignments suggested that 24 TFs were related to Arabidopsis IDDs. 18 IDDs had two characteristic C2H2 domains and two C2HC domains in their coding regions. Expression analyses suggest that some IDDs exhibit multi-stress responsive properties and can respond to specific stress conditions, while others can respond to multiple stress conditions in shoots and roots, either in a tissue-specific or universal manner. Moreover, co-expression database analyses suggested potential interaction partners within IDD family and other proteins. This study functionally characterized SlIDDs, which can be studied using molecular and bioinformatics methods for crop improvement.

Adaptive evolution and co-evolution of chloroplast genomes in Pteridaceae species occupying different habitats: overlapping residues are always highly mutated

BACKGROUND

The evolution of protein residues depends on the mutation rates of their encoding nucleotides, but it may also be affected by co-evolution with other residues. Chloroplasts function as environmental sensors, transforming fluctuating environmental signals into different physiological responses. We reasoned that habitat diversity may affect their rate and mode of evolution, which might be evidenced in the chloroplast genome. The Pteridaceae family of ferns occupy an unusually broad range of ecological niches, which provides an ideal system for analysis.

RESULTS

We conducted adaptive evolution and intra-molecular co-evolution analyses of Pteridaceae chloroplast DNAs (cpDNAs). The results indicate that the residues undergoing adaptive evolution and co-evolution were mostly independent, with only a few residues being simultaneously involved in both processes, and these overlapping residues tend to exhibit high mutations. Additionally, our data showed that Pteridaceae chloroplast genes are under purifying selection. Regardless of whether we grouped species by lineage (which corresponded with ecological niches), we determined that positively selected residues mainly target photosynthetic genes.

CONCLUSIONS

Our work provides evidence for the adaptive evolution of Pteridaceae cpDNAs, especially photosynthetic genes, to different habitats and sheds light on the adaptive evolution and co-evolution of proteins.

Structural insights into the assembly and energy transfer of the Lhcb9-dependent photosystem I from moss Physcomitrium patens

In plants and green algae, light-harvesting complexes I and II (LHCI and LHCII) constitute the antennae of photosystem I (PSI), thus effectively increasing the cross-section of the PSI core. The moss Physcomitrium patens (P. patens) represents a well-studied primary land-dwelling photosynthetic autotroph branching from the common ancestor of green algae and land plants at the early stage of evolution. P. patens possesses at least three types of PSI with different antenna sizes. The largest PSI form (PpPSI-L) exhibits a unique organization found neither in flowering plants nor in algae. Its formation is mediated by the P. patens-specific LHC protein, Lhcb9. While previous studies have revealed the overall architecture of PpPSI-L, its assembly details and the relationship between different PpPSI types remain unclear. Here we report the high-resolution structure of PpPSI-L. We identified 14 PSI core subunits, one Lhcb9, one phosphorylated LHCII trimer and eight LHCI monomers arranged as two belts. Our structural analysis established the essential role of Lhcb9 and the phosphorylated LHCII in stabilizing the complex. In addition, our results suggest that PpPSI switches between different types, which share identical modules. This feature may contribute to the dynamic adjustment of the light-harvesting capability of PSI under different light conditions.

Dynamic Regulation of the Light-Harvesting System through State Transitions in Land Plants and Green Algae

Photosynthesis constitutes the only known natural process that captures the solar energy to convert carbon dioxide and water into biomass. The primary reactions of photosynthesis are catalyzed by the photosystem II (PSII) and photosystem I (PSI) complexes. Both photosystems associate with antennae complexes whose main function is to increase the light-harvesting capability of the core. In order to maintain optimal photosynthetic activity under a constantly changing natural light environment, plants and green algae regulate the absorbed photo-excitation energy between PSI and PSII through processes known as state transitions. State transitions represent a short-term light adaptation mechanism for balancing the energy distribution between the two photosystems by relocating light-harvesting complex II (LHCII) proteins. The preferential excitation of PSII (state 2) results in the activation of a chloroplast kinase which in turn phosphorylates LHCII, a process followed by the release of phosphorylated LHCII from PSII and its migration to PSI, thus forming the PSI-LHCI-LHCII supercomplex. The process is reversible, as LHCII is dephosphorylated and returns to PSII under the preferential excitation of PSI. In recent years, high-resolution structures of the PSI-LHCI-LHCII supercomplex from plants and green algae were reported. These structural data provide detailed information on the interacting patterns of phosphorylated LHCII with PSI and on the pigment arrangement in the supercomplex, which is critical for constructing the excitation energy transfer pathways and for a deeper understanding of the molecular mechanism of state transitions progress. In this review, we focus on the structural data of the state 2 supercomplex from plants and green algae and discuss the current state of knowledge concerning the interactions between antenna and the PSI core and the potential energy transfer pathways in these supercomplexes.